/usr/share/gromacs/top/gmx2.ff/aminoacids.rtp is in gromacs-data 4.5.5-2.
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1422 1423 1424 1425 1426 1427 1428 1429 1430 1431 1432 1433 1434 1435 1436 1437 1438 1439 1440 1441 1442 1443 1444 1445 1446 1447 1448 1449 1450 1451 1452 1453 1454 1455 1456 1457 1458 1459 1460 1461 1462 1463 1464 1465 1466 1467 1468 1469 1470 1471 1472 1473 1474 1475 1476 1477 1478 1479 1480 1481 1482 1483 1484 1485 1486 1487 1488 1489 1490 1491 1492 1493 1494 1495 1496 1497 1498 1499 1500 1501 1502 1503 1504 1505 1506 1507 1508 1509 1510 1511 1512 1513 1514 1515 1516 1517 1518 1519 1520 1521 1522 1523 1524 1525 1526 1527 1528 1529 1530 1531 1532 1533 1534 1535 1536 1537 1538 1539 1540 1541 1542 1543 1544 1545 1546 1547 1548 1549 1550 1551 1552 1553 1554 1555 1556 1557 1558 1559 1560 1561 1562 1563 1564 1565 1566 1567 1568 1569 1570 1571 1572 1573 1574 1575 1576 1577 1578 1579 1580 1581 1582 1583 1584 1585 1586 1587 1588 1589 1590 1591 1592 1593 1594 1595 1596 1597 1598 1599 1600 1601 1602 1603 1604 1605 1606 1607 1608 1609 | ;
;
; This source code is part of
;
; G R O M A C S
;
; GROningen MAchine for Chemical Simulations
;
; VERSION 3.0b
;
; Copyright (c) 1991-2001
; BIOSON Research Institute, Dept. of Biophysical Chemistry
; University of Groningen, The Netherlands
;
; Please use these references in all publications using GROMACS:
; GROMACS: A message-passing parallel molecular dynamics implementation
; H.J.C. Berendsen, D. van der Spoel and R. van Drunen
; Comp. Phys. Comm. 91, 43-56 (1995)
;
; GROMACS 3.0: A package for molecular simulation and trajectory analysis
; Erik Lindahl, Berk Hess and David van der Spoel
; J. Mol. Mod. 7 pp. 306-317 (2001)
;
; Also check out our WWW page:
; http://www.gromacs.org
; or e-mail to:
; gromacs@gromacs.org
;
; And Hey:
; Gyas ROwers Mature At Cryogenic Speed
;
[ bondedtypes ]
; Col 1: Type of bond
; Col 2: Type of angles
; Col 3: Type of proper dihedrals
; Col 4: Type of improper dihedrals
; Col 5: Generate all dihedrals if 1, only heavy atoms of 0.
; Col 6: Number of excluded neighbors for nonbonded interactions
; Col 7: Generate 1,4 interactions between pairs of hydrogens if 1
; Col 8: Remove propers over the same bond as an improper if it is 1
; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih
1 1 1 2 0 3 0 1
[ ACE ]
[ atoms ]
CA C3 0.000 1
HA1 HC 0.000 1
HA2 HC 0.000 1
HA3 HC 0.000 1
C C 0.380 2
O O -0.380 2
[ bonds ]
CA HA1
CA HA2
CA HA3
CA C
C O
[ ALA ]
[ atoms ]
N N -0.280 0
H H 0.280 0
CA C1 0.000 1
HA HC 0.000 1
CB C3 0.000 2
HB1 HC 0.000 2
HB2 HC 0.000 2
HB3 HC 0.000 2
C C 0.380 3
O O -0.380 3
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB HB3
C O
-C N
[ impropers ]
N -C CA H
-C -CA N -O
CA N C CB
[ ARG ]
[ atoms ]
N N -0.280 0
H H 0.280 0
CA C1 0.000 1
HA HC 0.000 1
CB C2 0.000 2
HB1 HC 0.000 2
HB2 HC 0.000 2
CG C2 0.000 3
HG1 HC 0.000 3
HG2 HC 0.000 3
CD C2 0.090 4
HD1 HC 0.000 4
HD2 HC 0.000 4
NE NE -0.110 4
HE H 0.240 4
CZ C 0.340 4
NH1 NZ -0.260 4
HH11 H 0.240 4
HH12 H 0.240 4
NH2 NZ -0.260 4
HH21 H 0.240 4
HH22 H 0.240 4
C C 0.380 5
O O -0.380 5
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD HD1
CD HD2
CD NE
NE HE
NE CZ
CZ NH1
CZ NH2
NH1 HH11
NH1 HH12
NH2 HH21
NH2 HH22
C O
-C N
[ impropers ]
N -C CA H
-C -CA N -O
CA N C CB
NE CD CZ HE
CZ NH1 NH2 NE
NH1 HH11 HH12 CZ
NH2 HH21 HH22 CZ
[ ASN ]
[ atoms ]
N N -0.280 0
H H 0.280 0
CA C1 0.000 1
HA HC 0.000 1
CB C2 0.000 2
HB1 HC 0.000 2
HB2 HC 0.000 2
CG C 0.380 3
OD1 O -0.380 3
ND2 NT -0.830 4
HD21 H 0.415 4
HD22 H 0.415 4
C C 0.380 5
O O -0.380 5
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG OD1
CG ND2
ND2 HD21
ND2 HD22
C O
-C N
[ impropers ]
N -C CA H
-C -CA N -O
CA N C CB
CG OD1 ND2 CB
ND2 HD21 HD22 CG
[ ASP ]
[ atoms ]
N N -0.280 0
H H 0.280 0
CA C1 0.000 1
HA HC 0.000 1
CB C2 0.000 2
HB1 HC 0.000 2
HB2 HC 0.000 2
CG C 0.270 3
OD1 OM -0.635 3
OD2 OM -0.635 3
C C 0.380 4
O O -0.380 4
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG OD1
CG OD2
C O
-C N
[ impropers ]
N -C CA H
-C -CA N -O
CA N C CB
CG OD1 OD2 CB
[ ASPH ]
[ atoms ]
N N -0.280 0
H H 0.280 0
CA C1 0.000 1
HA HC 0.000 1
CB C2 0.000 2
HB1 HC 0.000 2
HB2 HC 0.000 2
CG C 0.530 3
OD1 O -0.380 3
OD2 OA -0.548 3
HD2 HO 0.398 3
C C 0.380 4
O O -0.380 4
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG OD1
CG OD2
OD2 HD2
C O
-C N
[ impropers ]
N -C CA H
-C -CA N -O
CA N C CB
CG OD1 OD2 CB
[ CYS2 ]
[ atoms ]
N N -0.280 0
H H 0.280 0
CA C1 0.000 1
HA HC 0.000 1
CB C2 0.000 2
HB1 HC 0.000 2
HB2 HC 0.000 2
SG S 0.000 3
C C 0.380 4
O O -0.380 4
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB SG
C O
-C N
[ impropers ]
N -C CA H
-C -CA N -O
CA N C CB
[ CYSH ]
[ atoms ]
N N -0.280 0
H H 0.280 0
CA C1 0.000 1
HA HC 0.000 1
CB C2 0.000 2
HB1 HC 0.000 2
HB2 HC 0.000 2
SG S -0.064 3
HG HS 0.064 3
C C 0.380 4
O O -0.380 4
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB SG
SG HG
C O
-C N
[ impropers ]
N -C CA H
-C -CA N -O
CA N C CB
[ GLN ]
[ atoms ]
N N -0.280 0
H H 0.280 0
CA C1 0.000 1
HA HC 0.000 1
CB C2 0.000 2
HB1 HC 0.000 2
HB2 HC 0.000 2
CG C2 0.000 3
HG1 HC 0.000 3
HG2 HC 0.000 3
CD C 0.380 4
OE1 O -0.380 4
NE2 NT -0.830 5
HE21 H 0.415 5
HE22 H 0.415 5
C C 0.380 6
O O -0.380 6
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD OE1
CD NE2
NE2 HE21
NE2 HE22
C O
-C N
[ impropers ]
N -C CA H
CA N C CB
CD OE1 NE2 CG
NE2 HE21 HE22 CD
-C -CA N -O
[ GLU ]
[ atoms ]
N N -0.280 0
H H 0.280 0
CA C1 0.000 1
HA HC 0.000 1
CB C2 0.000 2
HB1 HC 0.000 2
HB2 HC 0.000 2
CG C2 0.000 3
HG1 HC 0.000 3
HG2 HC 0.000 3
CD C 0.270 4
OE1 OM -0.635 4
OE2 OM -0.635 4
C C 0.380 5
O O -0.380 5
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD OE1
CD OE2
C O
-C N
[ impropers ]
N -C CA H
CA N C CB
CD OE1 OE2 CG
-C -CA N -O
[ GLUH ]
[ atoms ]
N N -0.280 0
H H 0.280 0
CA C1 0.000 1
HA HC 0.000 1
CB C2 0.000 2
HB1 HC 0.000 2
HB2 HC 0.000 2
CG C2 0.000 3
HG1 HC 0.000 3
HG2 HC 0.000 3
CD C 0.530 4
OE1 O -0.380 4
OE2 OA -0.548 4
HE2 HO 0.398 4
C C 0.380 5
O O -0.380 5
[ bonds ]
N H
N CA
CA HA
CA CB
CB CA
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD OE1
CD OE2
OE2 HE2
C O
-C N
[ impropers ]
N -C CA H
CA N C CB
CD OE1 OE2 CG
-C -CA N -O
[ GLY ]
[ atoms ]
N N -0.280 0
H H 0.280 0
CA C2 0.000 1
HA1 HC 0.000 1
HA2 HC 0.000 1
C C 0.380 2
O O -0.380 2
[ bonds ]
N H
N CA
CA HA1
CA HA2
CA C
C O
-C N
[ impropers ]
N -C CA H
-C -CA N -O
[ HIS1 ]
[ atoms ]
N N -0.280 0
H H 0.280 0
CA C1 0.000 1
HA HC 0.000 1
CB C2 0.000 2
HB1 HC 0.000 2
HB2 HC 0.000 2
CG CB 0.000 3
ND1 NR5* 0.000 3
HD1 H 0.190 3
CD2 CR5 0.130 3
HD2 HC 0.000 3
CE1 CR5 0.260 3
HE1 HC 0.000 3
NE2 NR5* -0.580 3
C C 0.380 4
O O -0.380 4
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG ND1
CG CD2
ND1 HD1
ND1 CE1
CD2 HD2
CD2 NE2
CE1 HE1
CE1 NE2
C O
-C N
[ impropers ]
N -C CA H
CA N C CB
CG ND1 CD2 CB
CD2 CG ND1 CE1
ND1 CG CD2 NE2
CG ND1 CE1 NE2
CG CD2 NE2 CE1
CD2 NE2 CE1 ND1
ND1 CG CE1 HD1
CE1 ND1 NE2 HE1
CD2 CG NE2 HD2
-C -CA N -O
[ HISA ]
[ atoms ]
N N -0.280 0
H H 0.280 0
CA C1 0.000 1
HA HC 0.000 1
CB C2 0.000 2
HB1 HC 0.000 2
HB2 HC 0.000 2
CG CB 0.000 3
ND1 NR5* 0.000 3
HD1 H 0.190 3
CD2 CR5 0.130 3
HD2 HC 0.000 3
CE1 CR5 0.260 3
HE1 HC 0.000 3
NE2 NR5 -0.580 3
C C 0.380 4
O O -0.380 4
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG ND1
CG CD2
ND1 HD1
ND1 CE1
CD2 HD2
CD2 NE2
CE1 HE1
CE1 NE2
C O
-C N
[ impropers ]
N -C CA H
CA N C CB
CG ND1 CD2 CB
CD2 CG ND1 CE1
ND1 CG CD2 NE2
CG ND1 CE1 NE2
CG CD2 NE2 CE1
CD2 NE2 CE1 ND1
ND1 CG CE1 HD1
CD2 CG NE2 HD2
CE1 ND1 NE2 HE1
-C -CA N -O
[ HISB ]
[ atoms ]
N N -0.280 0
H H 0.280 0
CA C1 0.000 1
HA HC 0.000 1
CB C2 0.000 2
HB1 HC 0.000 2
HB2 HC 0.000 2
CG CB 0.130 3
ND1 NR5 -0.580 3
CD2 CR5 0.000 3
HD2 HC 0.000 3
CE1 CR5 0.260 3
HE1 HC 0.000 3
NE2 NR5* 0.000 3
HE2 H 0.190 3
C C 0.380 4
O O -0.380 4
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG ND1
CG CD2
ND1 CE1
CD2 HD2
CD2 NE2
CE1 HE1
CE1 NE2
NE2 HE2
C O
-C N
[ impropers ]
N -C CA H
CA N C CB
CG ND1 CD2 CB
CD2 CG ND1 CE1
ND1 CG CD2 NE2
CG ND1 CE1 NE2
CG CD2 NE2 CE1
CD2 NE2 CE1 ND1
CE1 ND1 NE2 HE1
NE2 CD2 CE1 HE2
CD2 CG NE2 HD2
-C -CA N -O
[ HISH ]
[ atoms ]
N N -0.280 0
H H 0.280 0
CA C1 0.000 1
HA HC 0.000 1
CB C2 0.000 2
HB1 HC 0.000 2
HB2 HC 0.000 2
CG CB -0.050 3
ND1 NR5* 0.380 3
HD1 H 0.300 3
CD2 CR5 0.000 3
HD2 HC 0.000 3
CE1 CR5 -0.240 3
HE1 HC 0.000 3
NE2 NR5* 0.310 3
HE2 H 0.300 3
C C 0.380 4
O O -0.380 4
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG ND1
CG CD2
ND1 HD1
ND1 CE1
CD2 HD2
CD2 NE2
CE1 HE1
CE1 NE2
NE2 HE2
C O
-C N
[ impropers ]
N -C CA H
CA N C CB
CG ND1 CD2 CB
CD2 CG ND1 CE1
ND1 CG CD2 NE2
CG ND1 CE1 NE2
CG CD2 NE2 CE1
CD2 NE2 CE1 ND1
ND1 CG CE1 HD1
CE1 ND1 NE2 HE1
NE2 CE1 CD2 HE2
CD2 CG NE2 HD2
-C -CA N -O
[ HOH ]
[ atoms ]
OW OW -0.820 0
HW1 HW 0.410 0
HW2 HW 0.410 0
[ bonds ]
OW HW1
OW HW2
[ HO4 ]
[ atoms ]
OW OWT4 0.0 0
HW1 H 0.52 0
HW2 H 0.52 0
MW IW -1.04 0
[ bonds ]
OW HW1
OW HW2
[ HYP ]
[ atoms ]
N N 0.000 0
CA C1 0.000 1
HA HC 0.000 1
CB C2 0.000 2
HB1 HC 0.000 2
HB2 HC 0.000 2
CG C1 0.150 3
HG HC 0.000 3
OD1 OA -0.548 3
HD1 HO 0.398 3
CD2 C2 0.000 4
HD1 HC 0.000 4
HD2 HC 0.000 4
C C 0.380 5
O O -0.380 5
[ bonds ]
N CA
CA C
C O
-C N
CA HA
CA CB
CB HB1
CB HB2
CB CG
CG HG
CG OD1
OD1 HD1
CG CD2
CD2 HD1
CD2 HD2
CD2 N
[ impropers ]
N -C CA CD2
-C -CA N -O
CA N C CB
CG CD2 CB OD1
[ ILE ]
[ atoms ]
N N -0.280 0
H H 0.280 0
CA C1 0.000 1
HA HC 0.000 1
CB C1 0.000 2
HB HC 0.000 2
CG1 C2 0.000 3
HG11 HC 0.000 3
HG12 HC 0.000 3
CG2 C3 0.000 4
HG21 HC 0.000 4
HG22 HC 0.000 4
HG23 HC 0.000 4
CD C3 0.000 5
HD1 HC 0.000 5
HD2 HC 0.000 5
HD3 HC 0.000 5
C C 0.380 6
O O -0.380 6
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB
CB CG1
CB CG2
CG1 HG11
CG1 HG12
CG1 CD
CG2 HG21
CG2 HG22
CG2 HG23
CD HD1
CD HD2
CD HD3
C O
-C N
[ impropers ]
N -C CA H
-C -CA N -O
CA N C CB
CB CG1 CG2 CA
[ LEU ]
[ atoms ]
N N -0.280 0
H H 0.280 0
CA C1 0.000 1
HA HC 0.000 1
CB C2 0.000 2
HB1 HC 0.000 2
HB2 HC 0.000 2
CG C1 0.000 3
HG HC 0.000 3
CD1 C3 0.000 4
HD11 HC 0.000 4
HD12 HC 0.000 4
HD13 HC 0.000 4
CD2 C3 0.000 5
HD21 HC 0.000 5
HD22 HC 0.000 5
HD23 HC 0.000 5
C C 0.380 6
O O -0.380 6
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG
CG CD1
CG CD2
CD1 HD11
CD1 HD12
CD1 HD13
CD2 HD21
CD2 HD22
CD2 HD23
C O
-C N
[ impropers ]
N -C CA H
-C -CA N -O
CA N C CB
CG CD2 CD1 CB
[ LYS ]
[ atoms ]
N N -0.280 0
H H 0.280 0
CA C1 0.000 1
HA HC 0.000 1
CB C2 0.000 2
HB1 HC 0.000 2
HB2 HC 0.000 2
CG C2 0.000 3
HG1 HC 0.000 3
HG2 HC 0.000 3
CD C2 0.000 4
HD1 HC 0.000 4
HD2 HC 0.000 4
CE C2 0.000 5
HE1 HC 0.000 5
HE2 HC 0.000 5
NZ NL -0.830 5
HZ1 H 0.415 5
HZ2 H 0.415 5
C C 0.380 6
O O -0.380 6
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD HD1
CD HD2
CD CE
CE HE1
CE HE2
CE NZ
NZ HZ1
NZ HZ2
C O
-C N
[ impropers ]
N -C CA H
NZ CE HZ2 NZ
-C -CA N -O
CA N C CB
NZ CE HZ2 HZ1
[ LYSH ]
[ atoms ]
N N -0.280 0
H H 0.280 0
CA C1 0.000 1
HA HC 0.000 1
CB C2 0.000 2
HB1 HC 0.000 2
HB2 HC 0.000 2
CG C2 0.000 3
HG1 HC 0.000 3
HG2 HC 0.000 3
CD C2 0.000 4
HD1 HC 0.000 4
HD2 HC 0.000 4
CE C2 0.127 5
HE1 HC 0.000 5
HE2 HC 0.000 5
NZ NL 0.129 5
HZ1 H 0.248 5
HZ2 H 0.248 5
HZ3 H 0.248 5
C C 0.380 6
O O -0.380 6
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD HD1
CD HD2
CD CE
CE HE1
CE HE2
CE NZ
NZ HZ1
NZ HZ2
NZ HZ3
C O
-C N
[ impropers ]
N -C CA H
-C -CA N -O
CA N C CB
[ MET ]
[ atoms ]
N N -0.280 0
H H 0.280 0
CA C1 0.000 1
HA HC 0.000 1
CB C2 0.000 2
HB1 HC 0.000 2
HB2 HC 0.000 2
CG C2 0.000 3
HG1 HC 0.000 3
HG2 HC 0.000 3
SD S 0.000 4
CE C3 0.000 5
HE1 HC 0.000 5
HE2 HC 0.000 5
HE3 HC 0.000 5
C C 0.380 6
O O -0.380 6
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG SD
SD CE
CE HE1
CE HE2
CE HE3
C O
-C N
[ impropers ]
N -C CA H
-C -CA N -O
CA N C CB
[ NAC ]
[ atoms ]
N N -0.280 0
H H 0.280 0
CA C3 0.000 1
HA1 HC 0.000 1
HA2 HC 0.000 1
HA3 HC 0.000 1
[ bonds ]
N H
N CA
CA HA1
CA HA2
CA HA3
-C N
[ impropers ]
N -C CA H
[ NH2 ]
[ atoms ]
N NT -0.830 0
H1 H 0.415 0
H2 H 0.415 0
[ bonds ]
-C N
N H1
N H2
[ impropers ]
-C H1 H2 N
-C -O N -CA
[ PHE ]
[ atoms ]
N N -0.280 0
H H 0.280 0
CA C1 0.000 1
HA HC 0.000 1
CB C2 0.000 2
HB1 HC 0.000 2
HB2 HC 0.000 2
CG CB 0.000 3
CD1 CR6 -0.140 4
HD1 HCR 0.140 4
CD2 CR6 -0.140 5
HD2 HCR 0.140 5
CE1 CR6 -0.140 6
HE1 HCR 0.140 6
CE2 CR6 -0.140 7
HE2 HCR 0.140 7
CZ CR6 -0.140 8
HZ HCR 0.140 8
C C 0.380 9
O O -0.380 9
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG CD1
CG CD2
CD1 HD1
CD1 CE1
CD2 HD2
CD2 CE2
CE1 HE1
CE1 CZ
CE2 HE2
CE2 CZ
CZ HZ
C O
-C N
[ impropers ]
N -C CA H
CA N C CB
CG CD1 CD2 CB
CD2 CG CD1 CE1
CD1 CG CD2 CE2
CG CD1 CE1 CZ
CG CD2 CE2 CZ
CD1 CE1 CZ CE2
CD2 CE2 CZ CE1
CD1 CE1 CG HD1
CE1 CZ CD1 HE1
CZ CE2 CE1 HZ
CE2 CD2 CZ HE2
CD2 CG CE2 HD2
-C -CA N -O
[ PRO ]
[ atoms ]
N N 0.000 0
CA C1 0.000 1
HA HC 0.000 1
CB C2 0.000 2
HB1 HC 0.000 2
HB2 HC 0.000 2
CG C2 0.000 3
HG1 HC 0.000 3
HG2 HC 0.000 3
CD C2 0.000 4
HD1 HC 0.000 4
HD2 HC 0.000 4
C C 0.380 5
O O -0.380 5
[ bonds ]
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD HD1
CD HD2
CD N
C O
-C N
[ impropers ]
N -C CA CD
-C -CA N -O
CA N C CB
[ SER ]
[ atoms ]
N N -0.280 0
H H 0.280 0
CA C1 0.000 1
HA HC 0.000 1
CB C2 0.150 2
HB1 HC 0.000 2
HB2 HC 0.000 2
OG OA -0.548 2
HG HO 0.398 2
C C 0.380 3
O O -0.380 3
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB OG
OG HG
C O
-C N
[ impropers ]
N -C CA H
-C -CA N -O
CA N C CB
[ THR ]
[ atoms ]
N N -0.280 0
H H 0.280 0
CA C1 0.000 1
HA HC 0.000 1
CB C1 0.150 2
HB HC 0.000 2
OG1 OA -0.548 2
HG1 HO 0.398 2
CG2 C3 0.000 3
HG21 HC 0.000 3
HG22 HC 0.000 3
HG23 HC 0.000 3
C C 0.380 4
O O -0.380 4
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB
CB OG1
CB CG2
OG1 HG1
CG2 HG21
CG2 HG22
CG2 HG23
C O
-C N
[ impropers ]
N -C CA H
-C -CA N -O
CA N C CB
CB OG1 CG2 CA
[ TRP ]
[ atoms ]
N N -0.280 0
H H 0.280 0
CA C1 0.000 1
HA HC 0.000 1
CB C2 0.000 2
HB1 HC 0.000 2
HB2 HC 0.000 2
CG CB -0.140 3
CD1 CR5 -0.140 3
HD1 HCR 0.140 3
CD2 CB 0.000 3
NE1 NR5* -0.050 3
HE1 H 0.190 3
CE2 CB 0.000 4
CE3 CR6 -0.140 5
HE3 HCR 0.140 5
CZ2 CR6 -0.140 6
HZ2 HCR 0.140 6
CZ3 CR6 -0.140 7
HZ3 HCR 0.140 7
CH2 CR6 -0.140 8
HH2 HCR 0.140 8
C C 0.380 9
O O -0.380 9
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG CD1
CG CD2
CD1 HD1
CD1 NE1
CD2 CE2
CD2 CE3
NE1 HE1
NE1 CE2
CE2 CZ2
CE3 HE3
CE3 CZ3
CZ2 HZ2
CZ2 CH2
CZ3 HZ3
CZ3 CH2
CH2 HH2
C O
-C N
[ impropers ]
N -C CA H
CA N C CB
CG CD1 CD2 CB
CD2 CG CD1 NE1
CD1 CG CD2 CE2
CG CD1 NE1 CE2
CG CD2 CE2 NE1
CD1 NE1 CE2 CD2
NE1 CD1 CE2 HE1
CD1 CG NE1 HD1
CD2 CE2 CE3 CG
CE2 CD2 CZ2 NE1
CE3 CD2 CE2 CZ2
CD2 CE2 CZ2 CH2
CE2 CD2 CE3 CZ3
CE2 CZ2 CH2 CZ3
CD2 CE3 CZ3 CH2
CE3 CZ3 CH2 CZ2
CE3 CD2 CZ3 HE3
CZ3 CE3 CH2 HZ3
CH2 CZ3 CZ2 HH2
CZ2 CH2 CE2 HZ2
-C -CA N -O
[ TYR ]
[ atoms ]
N N -0.280 0
H H 0.280 0
CA C1 0.000 1
HA HC 0.000 1
CB C2 0.000 2
HB1 HC 0.000 2
HB2 HC 0.000 2
CG CB 0.000 3
CD1 CR6 -0.140 4
HD1 HCR 0.140 4
CD2 CR6 -0.140 5
HD2 HCR 0.140 5
CE1 CR6 -0.140 6
HE1 HCR 0.140 6
CE2 CR6 -0.140 7
HE2 HCR 0.140 7
CZ CB 0.150 8
OH OA -0.548 8
HH HO 0.398 8
C C 0.380 9
O O -0.380 9
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG CD1
CG CD2
CD1 HD1
CD1 CE1
CD2 HD2
CD2 CE2
CE1 HE1
CE1 CZ
CE2 HE2
CE2 CZ
CZ OH
OH HH
C O
-C N
[ impropers ]
N -C CA H
CA N C CB
CG CD1 CD2 CB
CD2 CG CD1 CE1
CD1 CG CD2 CE2
CG CD1 CE1 CZ
CG CD2 CE2 CZ
CD1 CE1 CZ CE2
CD2 CE2 CZ CE1
CD1 CE1 CG HD1
CE1 CD1 CZ HE1
CZ CE1 CE2 OH
CE2 CZ CD2 HE2
CD2 CE2 CG HD2
-C -CA N -O
[ VAL ]
[ atoms ]
N N -0.280 0
H H 0.280 0
CA C1 0.000 1
HA HC 0.000 1
CB C1 0.000 2
HB HC 0.000 2
CG1 C3 0.000 3
HG11 HC 0.000 3
HG12 HC 0.000 3
HG13 HC 0.000 3
CG2 C3 0.000 4
HG21 HC 0.000 4
HG22 HC 0.000 4
HG23 HC 0.000 4
C C 0.380 5
O O -0.380 5
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB
CB CG1
CB CG2
CG1 HG11
CG1 HG12
CG1 HG13
CG2 HG21
CG2 HG22
CG2 HG23
C O
-C N
[ impropers ]
N -C CA H
-C -CA N -O
CA N C CB
CB CG2 CG1 CA
[ HEME ]
[ atoms ]
FE FE 0.400 0
NA NP -0.100 0
NB NP -0.100 0
NC NP -0.100 0
ND NP -0.100 0
CHA CR61 0.000 1
HHA HC 0.000 1
C1A CHE 0.000 2
C2A CHE 0.000 3
C3A CHE 0.000 4
C4A CHE 0.000 5
CMA C3 0.000 6
HMA1 HC 0 6
HMA2 HC 0 6
HMA3 HC 0 6
CAA C2 0.000 7
HAA1 HC 0 7
HAA2 HC 0 7
CBA C2 0.000 8
HBA1 HC 0 8
HBA2 HC 0 8
CGA C 0.270 9
O1A OM -0.635 9
O2A OM -0.635 9
H2A H 0 9
CHB CR61 0.000 10
HHB HC 0.000 10
C1B CHE 0.000 11
C2B CHE 0.000 12
H2B HC 0 12
C3B CHE 0.000 13
C4B CHE 0.000 14
CMB C3 0.000 15
HMB1 HC 0 15
HMB2 HC 0 15
HMB3 HC 0 15
CAB CR61 0.000 16
HAB1 HC 0.000 16
HAB2 HC 0.000 16
CBB C2 0.000 17
HBB1 HC 0.000 17
HBB2 HC 0.000 17
HBB3 HC 0.000 17
CHC CR61 0.000 18
HHC HC 0.000 18
C1C CHE 0.000 19
C2C CHE 0.000 20
H2C HC 0 20
C3C CHE 0.000 21
C4C CHE 0.000 22
CMC C3 0.000 23
HMC1 HC 0 23
HMC2 HC 0 23
HMC3 HC 0 23
CAC CR61 0.000 24
HAC1 HC 0 24
HAC2 HC 0 24
CBC C3 0.000 25
HBC1 HC 0 25
HBC2 HC 0 25
HBC3 HC 0 25
CHD CR61 0.000 26
HHD HC 0.000 26
C1D CHE 0.000 27
C2D CHE 0.000 28
C3D CHE 0.000 29
C4D CHE 0.000 30
CMD C3 0.000 31
HMD1 HC 0 31
HMD2 HC 0 31
HMD3 HC 0 31
CAD C2 0.000 32
HAD1 HC 0 32
HAD2 HC 0 32
CBD C2 0.000 33
HBD1 HC 0 33
HBD2 HC 0 33
CGD C 0.270 34
O1D OM -0.635 34
O2D OM -0.635 34
H2D H 0 34
[ bonds ]
FE NA
FE NB
FE NC
FE ND
NA C1A
C1A C2A
C2A C3A
C3A C4A
NA C4A
C2A CAA
CAA CBA
CBA CGA
CGA O1A
CGA O2A
C3A CMA
CMA HMA1
CMA HMA2
CMA HMA3
C4A CHB
CHB C1B
NB C1B
C1B C2B
C2B C3B
C3B C4B
NB C4B
C2B CMB
CMB HMB1
CMB HMB2
CMB HMB3
C3B CAB
CAB CBB
C4B CHC
CHC C1C
NC C1C
C1C C2C
C2C C3C
C3C C4C
NC C4C
C2C CMC
CMC HMC1
CMC HMC2
CMC HMC3
C3C CAC
CAC CBC
C4C CHD
CHD C1D
ND C1D
C1D C2D
C2D C3D
C3D C4D
ND C4D
C2D CMD
CMD HMD1
CMD HMD2
CMD HMD3
C3D CAD
CAD CBD
CBD CGD
CGD O1D
CGD O2D
CHA C4D
CHA C1A
[ angles ]
; ai aj ak
NA FE NC ANG_180_0
NB FE ND ANG_180_0
[ dihedrals ]
; ai aj ak al
ND FE NA C1A DIH_0_0_2
NA FE NB C1B DIH_0_0_2
NB FE NC C1C DIH_0_0_2
NC FE ND C1D DIH_0_0_2
FE NA C1A CHA DIH_0_0_2
FE NA C4A C3A DIH_0_0_2
FE NB C1B CHB DIH_0_0_2
FE NB C4B C3B DIH_0_0_2
FE NC C1C CHC DIH_0_0_2
FE NC C4C C3C DIH_0_0_2
FE ND C1D CHD DIH_0_0_2
FE ND C4D CHA DIH_0_0_2
NA C1A C2A C3A DIH_0_0_2
C1A C2A C3A C4A DIH_0_0_2
C2A C3A C4A NA DIH_0_0_2
NB C1B C2B C3B DIH_0_0_2
C1B C2B C3B C4B DIH_0_0_2
C2B C3B C4B NB DIH_0_0_2
NC C1C C2C C3C DIH_0_0_2
C1C C2C C3C C4C DIH_0_0_2
C2C C3C C4C NC DIH_0_0_2
ND C1D C2D C3D DIH_0_0_2
C1D C2D C3D C4D DIH_0_0_2
C2D C3D C4D ND DIH_0_0_2
[ impropers ]
FE C1A C4A NA
FE C1B C4B NB
FE C1C C4C NC
FE C1D C4D ND
CHA NA C2A C1A
CHB NA C3A C4A
CHB NB C2B C1B
CHC NB C3B C4B
CHC NC C2C C1C
CHD NC C3C C4C
CHD ND C2D C1D
CHA ND C3D C4D
C2A C1A C3A CAA
C3A C2A C4A CMA
C2B C1B C3B CMB
C3B C2B C4B CAB
C2C C1C C3C CMC
C3C C2C C4C CAC
C2D C1D C3D CMD
C3D C2D C4D CAD
CBA O1A O2A CGA
CBD O1D O2D CGD
[ OCT ]
[ atoms ]
C1 C3 0.0 0
H11 HC 0.0 0
H12 HC 0.0 0
H13 HC 0.0 0
C2 C2 0.0 1
H21 HC 0.0 1
H22 HC 0.0 1
C3 C2 0.0 2
H31 HC 0.0 2
H32 HC 0.0 2
C4 C2 0.0 3
H41 HC 0.0 3
H42 HC 0.0 3
C5 C2 0.0 4
H51 HC 0.0 4
H52 HC 0.0 4
C6 C2 0.0 5
H61 HC 0.0 5
H62 HC 0.0 5
C7 C2 0.0 6
H71 HC 0.0 6
H72 HC 0.0 6
C8 C2 0.15 7
H81 HC 0.0 7
H82 HC 0.0 7
O9 OA -0.548 7
H10 HO 0.398 7
[ bonds ]
C1 H11
C1 H12
C1 H13
C1 C2
C2 H21
C2 H22
C2 C3
C3 H31
C3 H32
C3 C4
C4 H41
C4 H42
C4 C5
C5 H51
C5 H52
C5 C6
C6 H61
C6 H62
C6 C7
C7 H71
C7 H72
C7 C8
C8 H81
C8 H82
C8 O9
O9 H10
[ ZN ]
[ atoms ]
ZN ZN 2.000 0
[ CA ]
[ atoms ]
CA CA 2.000 0
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