# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 04:47:03 2022
#   Inital geometry file: a 147 line input string
#   Ligand name: L-gamma-glutamyl-S-nonyl-L-cysteinylglycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCSC[C@H](NC(=O)CC[C@H](N)C(O)=O)C(=O)NCC(O)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 0HH  0HH  L-gamma-glutamyl-S-nonyl-L-cysteinylglycine  peptide  62  29  .  2016-04-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_0HH
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 0HH  N     N  NH2    0  -0.804  14.8354  11.0640  24.3615
 0HH  CA    C  CH1    0  -0.162  14.6102   9.9347  25.2565
 0HH  C     C  C      0   0.386  15.6642   8.8213  25.0455
 0HH  O     O  O      0  -0.613  15.9285   8.1277  26.0505
 0HH  CB    C  CH2    0  -0.422  13.2003   9.3994  24.9841
 0HH  CG    C  CH2    0  -0.586  12.7488   8.3181  25.9538
 0HH  CD    C  C      0   0.568  11.2978   7.9221  25.7792
 0HH  OE1   O  O      0  -0.495  10.6616   8.1399  24.7573
 0HH  OXT   O  OC    -1  -0.601  16.1390   8.6887  23.9016
 0HH  N1    N  NH1    0  -0.648  10.7624   7.2835  26.8376
 0HH  CA1   C  CH1    0  -0.201   9.4013   6.8218  26.8786
 0HH  CB1   C  CH2    0  -0.545   9.1945   5.5426  26.0641
 0HH  SG    S  S2     0  -0.040  10.2256   4.1910  26.7111
 0HH  C1    C  C      0   0.552   9.0149   6.6097  28.3459
 0HH  O1    O  O      0  -0.488   9.8532   6.6411  29.2356
 0HH  C11   C  CH2    0  -0.570   9.1344   2.7640  26.4252
 0HH  C2    C  CH2    0  -0.411   7.9203   2.6849  27.3381
 0HH  C3    C  CH2    0  -0.412   8.2484   2.5171  28.8144
 0HH  C4    C  CH2    0  -0.433   6.9950   2.3818  29.6716
 0HH  C5    C  CH2    0  -0.443   7.2697   2.3207  31.1713
 0HH  C6    C  CH2    0  -0.432   8.1493   1.1544  31.6206
 0HH  C7    C  CH2    0  -0.422   7.6530  -0.2266  31.2002
 0HH  C8    C  CH2    0  -0.421   6.2583  -0.5723  31.7093
 0HH  C9    C  CH3    0  -0.657   5.8328  -1.9851  31.3369
 0HH  N2    N  NH1    0  -0.611   7.7214   6.3489  28.5529
 0HH  CA2   C  CH2    0  -0.452   7.1627   6.2438  29.8776
 0HH  CC    C  C      0   0.407   6.9737   7.5915  30.6190
 0HH  O2    O  O      0  -0.613   6.5537   7.4750  31.7863
 0HH  OXT1  O  OC    -1  -0.593   7.2343   8.6335  29.9967
 0HH  H     H  HNH2   0   0.328  14.2401  11.8320  24.6490
 0HH  H2    H  HNH2   0   0.332  15.7840  11.4007  24.4684
 0HH  HA    H  HCH1   0   0.174  14.6536  10.2270  26.3173
 0HH  HB2   H  HCH2   0   0.219  12.5018  10.2412  25.0379
 0HH  HB3   H  HCH2   0   0.216  13.1596   9.0317  23.9560
 0HH  HG2   H  HCH2   0   0.271  13.3523   7.4147  25.8301
 0HH  HG3   H  HCH2   0   0.246  12.9159   8.6395  26.9859
 0HH  H1    H  HNH1   0   0.398  11.3011   7.1744  27.6846
 0HH  HA1   H  HCH1   0   0.289   8.7437   7.5888  26.4543
 0HH  HB21  H  HCH2   0   0.277   8.1472   5.2423  26.1004
 0HH  HB31  H  HCH2   0   0.285   9.4400   5.7329  25.0200
 0HH  H11   H  HCH2   0   0.273   8.8315   2.7660  25.3767
 0HH  H12   H  HCH2   0   0.270   9.7746   1.8906  26.5682
 0HH  H21   H  HCH2   0   0.222   7.2870   3.5670  27.2016
 0HH  H22   H  HCH2   0   0.229   7.3183   1.8337  27.0024
 0HH  H31   H  HCH2   0   0.214   8.8897   1.6384  28.9385
 0HH  H32   H  HCH2   0   0.214   8.8335   3.3733  29.1632
 0HH  H41   H  HCH2   0   0.222   6.3388   3.2364  29.4755
 0HH  H42   H  HCH2   0   0.214   6.4317   1.4978  29.3546
 0HH  H51   H  HCH2   0   0.222   7.7452   3.2573  31.4810
 0HH  H52   H  HCH2   0   0.218   6.3151   2.2838  31.7041
 0HH  H61   H  HCH2   0   0.218   9.1657   1.2946  31.2415
 0HH  H62   H  HCH2   0   0.216   8.2345   1.1841  32.7116
 0HH  H71   H  HCH2   0   0.209   7.6708  -0.3149  30.1084
 0HH  H72   H  HCH2   0   0.215   8.3601  -0.9776  31.5670
 0HH  H81   H  HCH2   0   0.208   6.2305  -0.4540  32.7974
 0HH  H82   H  HCH2   0   0.215   5.5301   0.1394  31.3102
 0HH  H91   H  HCH3   0   0.224   4.8332  -2.2145  31.7078
 0HH  H92   H  HCH3   0   0.214   5.8216  -2.1190  30.2535
 0HH  H93   H  HCH3   0   0.214   6.5180  -2.7267  31.7519
 0HH  H3    H  HNH1   0   0.398   7.0782   6.4822  27.7892
 0HH  HA2   H  HCH2   0   0.252   6.1926   5.7510  29.7879
 0HH  HA3   H  HCH2   0   0.245   7.7830   5.5813  30.4842

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 0HH  N    CA    single  1.458  0.019  1.458
 0HH  N    H     single  0.860  0.020  0.860
 0HH  N    H2    single  0.890  0.020  1.040
 0HH  CA   C     single  1.525  0.021  1.525
 0HH  CA   CB    single  1.521  0.033  1.521
 0HH  CA   HA    single  0.970  0.020  0.970
 0HH  C    O     deloc   1.231  0.020  1.231
 0HH  C    OXT   deloc   1.246  0.020  1.246
 0HH  CB   CG    single  1.521  0.020  1.521
 0HH  CB   HB2   single  0.970  0.020  1.090
 0HH  CB   HB3   single  0.970  0.020  1.090
 0HH  CG   CD    single  1.514  0.020  1.514
 0HH  CG   HG2   single  0.970  0.020  1.090
 0HH  CG   HG3   single  0.970  0.020  1.090
 0HH  CD   OE1   double  1.223  0.020  1.223
 0HH  N1   CA1   single  1.438  0.020  1.438
 0HH  N1   H1    single  0.860  0.020  1.020
 0HH  CA1  CB1   single  1.531  0.020  1.531
 0HH  CA1  C1    single  1.532  0.020  1.532
 0HH  CA1  HA1   single  0.970  0.020  1.090
 0HH  CB1  SG    single  1.819  0.020  1.819
 0HH  CB1  HB21  single  0.970  0.020  1.090
 0HH  CB1  HB31  single  0.970  0.020  1.090
 0HH  SG   C11   single  1.819  0.020  1.819
 0HH  C1   O1    double  1.223  0.020  1.223
 0HH  C11  C2    single  1.521  0.020  1.521
 0HH  C11  H11   single  0.970  0.020  1.090
 0HH  C11  H12   single  0.970  0.020  1.090
 0HH  C2   C3    single  1.522  0.020  1.522
 0HH  C2   H21   single  0.970  0.020  1.090
 0HH  C2   H22   single  0.970  0.020  1.090
 0HH  C3   C4    single  1.524  0.020  1.524
 0HH  C3   H31   single  0.970  0.020  1.090
 0HH  C3   H32   single  0.970  0.020  1.090
 0HH  C4   C5    single  1.526  0.020  1.526
 0HH  C4   H41   single  0.970  0.020  1.090
 0HH  C4   H42   single  0.970  0.020  1.090
 0HH  C5   C6    single  1.528  0.020  1.528
 0HH  C5   H51   single  0.970  0.020  1.090
 0HH  C5   H52   single  0.970  0.020  1.090
 0HH  C6   C7    single  1.527  0.020  1.527
 0HH  C6   H61   single  0.970  0.020  1.090
 0HH  C6   H62   single  0.970  0.020  1.090
 0HH  C7   C8    single  1.524  0.020  1.524
 0HH  C7   H71   single  0.970  0.020  1.090
 0HH  C7   H72   single  0.970  0.020  1.090
 0HH  C8   C9    single  1.522  0.020  1.522
 0HH  C8   H81   single  0.970  0.020  1.090
 0HH  C8   H82   single  0.970  0.020  1.090
 0HH  C9   H91   single  0.970  0.020  1.090
 0HH  C9   H92   single  0.970  0.020  1.090
 0HH  C9   H93   single  0.970  0.020  1.090
 0HH  N2   CA2   single  1.442  0.020  1.442
 0HH  N2   H3    single  0.890  0.020  1.040
 0HH  CA2  CC    single  1.550  0.020  1.550
 0HH  CA2  HA2   single  0.970  0.020  1.090
 0HH  CA2  HA3   single  0.970  0.020  1.090
 0HH  CC   O2    deloc   1.246  0.020  1.246
 0HH  CC   OXT1  deloc   1.241  0.020  1.241
 0HH  CD   N1    single  1.347  0.020  1.347
 0HH  C1   N2    single  1.336  0.020  1.336

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 0HH  H2    N    H     105.58  3.000
 0HH  H2    N    CA    109.72  3.000
 0HH  H     N    CA    114.00  3.000
 0HH  HA    CA   CB    109.00  3.000
 0HH  HA    CA   C     110.00  3.000
 0HH  CB    CA   C     110.50  1.500
 0HH  HA    CA   N     110.00  3.000
 0HH  CB    CA   N     110.40  1.500
 0HH  C     CA   N     111.00  2.800
 0HH  OXT   C    O     126.80  3.000
 0HH  OXT   C    CA    120.80  1.700
 0HH  O     C    CA    120.80  1.700
 0HH  HB3   CB   HB2   106.32  3.000
 0HH  HB3   CB   CG    110.46  3.000
 0HH  HB2   CB   CG    109.01  3.000
 0HH  HB3   CB   CA    108.61  3.000
 0HH  HB2   CB   CA    108.03  3.000
 0HH  CG    CB   CA    114.09  3.000
 0HH  HG3   CG   HG2   105.38  3.000
 0HH  HG3   CG   CD    109.39  3.000
 0HH  HG2   CG   CD    107.45  3.000
 0HH  HG3   CG   CB    110.32  3.000
 0HH  HG2   CG   CB    110.57  3.000
 0HH  CD    CG   CB    113.38  3.000
 0HH  N1    CD   OE1   122.28  3.000
 0HH  N1    CD   CG    114.47  3.000
 0HH  OE1   CD   CG    123.24  3.000
 0HH  H1    N1   CA1   116.51  3.000
 0HH  H1    N1   CD    119.89  3.000
 0HH  CA1   N1   CD    123.42  3.000
 0HH  HA1   CA1  C1    108.44  3.000
 0HH  HA1   CA1  CB1   107.33  3.000
 0HH  C1    CA1  CB1   111.09  3.000
 0HH  HA1   CA1  N1    109.41  3.000
 0HH  C1    CA1  N1    108.09  3.000
 0HH  CB1   CA1  N1    112.41  3.000
 0HH  HB31  CB1  HB21  107.26  3.000
 0HH  HB31  CB1  SG    110.06  3.000
 0HH  HB21  CB1  SG    109.15  3.000
 0HH  HB31  CB1  CA1   109.49  3.000
 0HH  HB21  CB1  CA1   110.02  3.000
 0HH  SG    CB1  CA1   110.80  3.000
 0HH  C11   SG   CB1   100.77  3.000
 0HH  N2    C1   O1    123.79  3.000
 0HH  N2    C1   CA1   114.82  3.000
 0HH  O1    C1   CA1   121.35  3.000
 0HH  H12   C11  H11   106.86  3.000
 0HH  H12   C11  C2    110.34  3.000
 0HH  H11   C11  C2    110.80  3.000
 0HH  H12   C11  SG    104.78  3.000
 0HH  H11   C11  SG    108.43  3.000
 0HH  C2    C11  SG    115.17  3.000
 0HH  H22   C2   H21   105.67  3.000
 0HH  H22   C2   C3    109.28  3.000
 0HH  H21   C2   C3    109.55  3.000
 0HH  H22   C2   C11   107.17  3.000
 0HH  H21   C2   C11   110.18  3.000
 0HH  C3    C2   C11   114.58  3.000
 0HH  H32   C3   H31   106.18  3.000
 0HH  H32   C3   C4    109.26  3.000
 0HH  H31   C3   C4    110.28  3.000
 0HH  H32   C3   C2    109.77  3.000
 0HH  H31   C3   C2    108.95  3.000
 0HH  C4    C3   C2    112.21  3.000
 0HH  H42   C4   H41   105.66  3.000
 0HH  H42   C4   C5    110.16  3.000
 0HH  H41   C4   C5    108.37  3.000
 0HH  H42   C4   C3    109.38  3.000
 0HH  H41   C4   C3    108.83  3.000
 0HH  C5    C4   C3    114.09  3.000
 0HH  H52   C5   H51   105.66  3.000
 0HH  H52   C5   C6    109.47  3.000
 0HH  H51   C5   C6    108.63  3.000
 0HH  H52   C5   C4    108.85  3.000
 0HH  H51   C5   C4    108.78  3.000
 0HH  C6    C5   C4    115.03  3.000
 0HH  H62   C6   H61   105.64  3.000
 0HH  H62   C6   C7    108.92  3.000
 0HH  H61   C6   C7    108.82  3.000
 0HH  H62   C6   C5    108.49  3.000
 0HH  H61   C6   C5    109.58  3.000
 0HH  C7    C6   C5    114.98  3.000
 0HH  H72   C7   H71   105.56  3.000
 0HH  H72   C7   C8    108.87  3.000
 0HH  H71   C7   C8    109.23  3.000
 0HH  H72   C7   C6    108.56  3.000
 0HH  H71   C7   C6    110.00  3.000
 0HH  C8    C7   C6    114.24  3.000
 0HH  H82   C8   H81   105.99  3.000
 0HH  H82   C8   C9    109.19  3.000
 0HH  H81   C8   C9    109.66  3.000
 0HH  H82   C8   C7    109.87  3.000
 0HH  H81   C8   C7    109.30  3.000
 0HH  C9    C8   C7    112.62  3.000
 0HH  H93   C9   H92   107.48  3.000
 0HH  H93   C9   H91   107.65  3.000
 0HH  H92   C9   H91   107.60  3.000
 0HH  H93   C9   C8    111.24  3.000
 0HH  H92   C9   C8    111.07  3.000
 0HH  H91   C9   C8    111.61  3.000
 0HH  H3    N2   CA2   117.31  3.000
 0HH  H3    N2   C1    118.36  3.000
 0HH  CA2   N2   C1    122.14  3.000
 0HH  HA3   CA2  HA2   106.06  3.000
 0HH  HA3   CA2  CC    109.34  3.000
 0HH  HA2   CA2  CC    108.87  3.000
 0HH  HA3   CA2  N2    109.55  3.000
 0HH  HA2   CA2  N2    107.56  3.000
 0HH  CC    CA2  N2    115.05  3.000
 0HH  OXT1  CC   O2    128.24  3.000
 0HH  OXT1  CC   CA2   117.68  3.000
 0HH  O2    CC   CA2   114.08  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 0HH  CONST_01  CA1   N1   CD   CG    180.00   0.0  0
 0HH  CONST_02  CA1   N1   CD   OE1     0.00   0.0  0
 0HH  CONST_03  CA2   N2   C1   CA1   180.00   0.0  0
 0HH  CONST_04  CA2   N2   C1   O1      0.00   0.0  0
 0HH  CONST_05  H1    N1   CD   CG      0.00   0.0  0
 0HH  CONST_06  H3    N2   C1   CA1     0.00   0.0  0
 0HH  Var_01    CD    CG   CB   CA    172.88  30.0  3
 0HH  Var_02    OE1   CD   CG   CB     19.80  30.0  3
 0HH  Var_03    C2    C11  SG   CB1   -71.66  30.0  3
 0HH  Var_04    C3    C2   C11  SG    -63.11  30.0  3
 0HH  Var_05    CC    CA2  N2   C1     74.66  30.0  3
 0HH  Var_06    C4    C3   C2   C11  -177.46  30.0  3
 0HH  Var_07    C5    C4   C3   C2   -175.47  30.0  3
 0HH  Var_08    C6    C5   C4   C3    -60.05  30.0  3
 0HH  Var_09    C7    C6   C5   C4    -54.96  30.0  3
 0HH  Var_10    C8    C7   C6   C5    -58.75  30.0  3
 0HH  Var_11    C9    C8   C7   C6   -176.71  30.0  3
 0HH  Var_12    O2    CC   CA2  N2   -176.55  30.0  3
 0HH  Var_13    HB21  CB1  SG   C11    23.88  30.0  2
 0HH  Var_14    H91   C9   C8   C7   -179.93  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 0HH  chir_01  CA   N   C    CB  positiv
 0HH  chir_02  CA1  N1  CB1  C1  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 0HH  plan-1  CG    0.020
 0HH  plan-1  CD    0.020
 0HH  plan-1  OE1   0.020
 0HH  plan-1  N1    0.020
 0HH  plan-1  CA1   0.020
 0HH  plan-1  H1    0.020
 0HH  plan-2  CA1   0.020
 0HH  plan-2  C1    0.020
 0HH  plan-2  O1    0.020
 0HH  plan-2  N2    0.020
 0HH  plan-2  CA2   0.020
 0HH  plan-2  H3    0.020
 0HH  plan-3  CA    0.020
 0HH  plan-3  C     0.020
 0HH  plan-3  O     0.020
 0HH  plan-3  OXT   0.020
 0HH  plan-4  CA2   0.020
 0HH  plan-4  CC    0.020
 0HH  plan-4  O2    0.020
 0HH  plan-4  OXT1  0.020

