# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Mon Jun  1 14:29:27 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: L-gamma-glutamyl-S-hexyl-L-cysteinylglycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCSC[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
 LEE  LEE  L-gamma-glutamyl-S-hexyl-L-cysteinylglycine  peptide  53  26  .  2022-07-25  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_LEE
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
 LEE  N     N  NH2    0  -0.787  -5.4043   2.4390   1.6311
 LEE  CA    C  CH1    0  -0.215  -4.7791   2.8436   0.3814
 LEE  C     C  C      0   0.386  -5.7501   3.3642  -0.7084
 LEE  O     O  O      0  -0.607  -6.9664   3.1371  -0.5542
 LEE  CB    C  CH2    0  -0.418  -3.9685   1.6799  -0.1963
 LEE  CG    C  CH2    0  -0.570  -2.8791   1.1922   0.7488
 LEE  CD    C  C      0   0.572  -2.1274   0.0011   0.2070
 LEE  OE1   O  O      0  -0.501  -2.6643  -0.8908  -0.4368
 LEE  OXT   O  OC    -1  -0.623  -5.2212   3.9529  -1.6746
 LEE  N1    N  NH1    0  -0.642  -0.8102  -0.0322   0.4828
 LEE  CA1   C  CH1    0  -0.182   0.0082  -1.1450   0.0824
 LEE  CB1   C  CH2    0  -0.573   1.4604  -0.8997   0.4730
 LEE  SG    S  S2     0  -0.028   2.0687   0.6320  -0.2913
 LEE  C1    C  CH2    0  -0.544   3.8057   0.5547   0.2318
 LEE  C2    C  CH2    0  -0.422   4.5236   1.8370  -0.1591
 LEE  C3    C  CH2    0  -0.410   6.0031   1.7923   0.2070
 LEE  C4    C  CH2    0  -0.408   6.7351   3.0846  -0.1306
 LEE  C5    C  CH2    0  -0.419   8.2194   3.0388   0.2109
 LEE  C6    C  CH3    0  -0.662   8.9415   4.3377  -0.1187
 LEE  C7    C  C      0   0.554  -0.4617  -2.4415   0.7555
 LEE  O1    O  O      0  -0.502  -0.8723  -2.4481   1.9074
 LEE  N2    N  NH1    0  -0.627  -0.3206  -3.5310   0.0047
 LEE  CA2   C  CH2    0  -0.410  -0.6403  -4.8648   0.4426
 LEE  C8    C  C      0   0.399  -0.3919  -5.8876  -0.6850
 LEE  O2    O  O      0  -0.599   0.0110  -5.4425  -1.7768
 LEE  OXT1  O  OC    -1  -0.609  -0.6247  -7.0714  -0.3865
 LEE  H     H  HNH2   0   0.336  -5.8087   3.2556   2.0734
 LEE  H2    H  HNH2   0   0.324  -6.2028   1.8581   1.4004
 LEE  HA    H  HCH1   0   0.210  -4.0771   3.6543   0.6089
 LEE  HB2   H  HCH2   0   0.218  -4.6458   0.8528  -0.4303
 LEE  HB3   H  HCH2   0   0.229  -3.5223   1.9956  -1.1415
 LEE  HG2   H  HCH2   0   0.242  -2.1861   2.0070   0.9756
 LEE  HG3   H  HCH2   0   0.269  -3.3305   0.9012   1.7015
 LEE  H1    H  HNH1   0   0.401  -0.4076   0.6885   1.0606
 LEE  HA1   H  HCH1   0   0.276  -0.0454  -1.2631  -1.0048
 LEE  HB21  H  HCH2   0   0.279   1.5592  -0.8314   1.5588
 LEE  HB31  H  HCH2   0   0.290   2.0675  -1.7383   0.1295
 LEE  H11   H  HCH2   0   0.261   3.8442   0.4126   1.3142
 LEE  H12   H  HCH2   0   0.260   4.2801  -0.3103  -0.2366
 LEE  H21   H  HCH2   0   0.228   4.4208   2.0061  -1.2352
 LEE  H22   H  HCH2   0   0.228   4.0469   2.6871   0.3375
 LEE  H31   H  HCH2   0   0.214   6.1070   1.5844   1.2774
 LEE  H32   H  HCH2   0   0.215   6.4807   0.9556  -0.3136
 LEE  H41   H  HCH2   0   0.209   6.6164   3.3033  -1.1976
 LEE  H42   H  HCH2   0   0.209   6.2651   3.9183   0.4027
 LEE  H51   H  HCH2   0   0.211   8.3383   2.8121   1.2749
 LEE  H52   H  HCH2   0   0.211   8.6879   2.2100  -0.3287
 LEE  H61   H  HCH3   0   0.216   8.8727   4.5678  -1.1837
 LEE  H62   H  HCH3   0   0.216   8.5083   5.1783   0.4268
 LEE  H63   H  HCH3   0   0.226   9.9997   4.2858   0.1397
 LEE  H3    H  HNH1   0   0.388  -0.0228  -3.4632  -0.9586
 LEE  HA2   H  HCH2   0   0.242  -0.0407  -5.1438   1.3143
 LEE  HA3   H  HCH2   0   0.242  -1.6875  -4.9300   0.7541

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
 LEE  N    CA    single  1.458  0.019  1.458
 LEE  N    H     single  0.860  0.020  0.860
 LEE  N    H2    single  0.890  0.020  1.040
 LEE  CA   C     single  1.525  0.021  1.525
 LEE  CA   CB    single  1.521  0.033  1.521
 LEE  CA   HA    single  0.970  0.020  0.970
 LEE  C    O     deloc   1.231  0.020  1.231
 LEE  C    OXT   deloc   1.249  0.020  1.249
 LEE  CB   CG    single  1.522  0.020  1.522
 LEE  CB   HB2   single  0.970  0.020  1.090
 LEE  CB   HB3   single  0.970  0.020  1.090
 LEE  CG   CD    single  1.509  0.020  1.509
 LEE  CG   HG2   single  0.970  0.020  1.090
 LEE  CG   HG3   single  0.970  0.020  1.090
 LEE  CD   OE1   double  1.224  0.020  1.224
 LEE  N1   CA1   single  1.438  0.020  1.438
 LEE  N1   H1    single  0.860  0.020  1.020
 LEE  CA1  CB1   single  1.524  0.020  1.524
 LEE  CA1  C7    single  1.535  0.020  1.535
 LEE  CA1  HA1   single  0.970  0.020  1.090
 LEE  CB1  SG    single  1.817  0.020  1.817
 LEE  CB1  HB21  single  0.970  0.020  1.090
 LEE  CB1  HB31  single  0.970  0.020  1.090
 LEE  SG   C1    single  1.816  0.020  1.816
 LEE  C1   C2    single  1.521  0.020  1.521
 LEE  C1   H11   single  0.970  0.020  1.090
 LEE  C1   H12   single  0.970  0.020  1.090
 LEE  C2   C3    single  1.525  0.020  1.525
 LEE  C2   H21   single  0.970  0.020  1.090
 LEE  C2   H22   single  0.970  0.020  1.090
 LEE  C3   C4    single  1.523  0.020  1.523
 LEE  C3   H31   single  0.970  0.020  1.090
 LEE  C3   H32   single  0.970  0.020  1.090
 LEE  C4   C5    single  1.524  0.020  1.524
 LEE  C4   H41   single  0.970  0.020  1.090
 LEE  C4   H42   single  0.970  0.020  1.090
 LEE  C5   C6    single  1.522  0.020  1.522
 LEE  C5   H51   single  0.970  0.020  1.090
 LEE  C5   H52   single  0.970  0.020  1.090
 LEE  C6   H61   single  0.970  0.020  1.090
 LEE  C6   H62   single  0.970  0.020  1.090
 LEE  C6   H63   single  0.970  0.020  1.090
 LEE  C7   O1    double  1.223  0.020  1.223
 LEE  N2   CA2   single  1.440  0.020  1.440
 LEE  N2   H3    single  0.860  0.020  1.020
 LEE  CA2  C8    single  1.543  0.020  1.543
 LEE  CA2  HA2   single  0.970  0.020  1.090
 LEE  CA2  HA3   single  0.970  0.020  1.090
 LEE  C8   O2    deloc   1.246  0.020  1.246
 LEE  C8   OXT1  deloc   1.243  0.020  1.243
 LEE  CD   N1    single  1.346  0.020  1.346
 LEE  C7   N2    single  1.331  0.020  1.331

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
 LEE  H2    N    H     104.29  3.000
 LEE  H2    N    CA    107.59  3.000
 LEE  H     N    CA    114.00  3.000
 LEE  HA    CA   CB    109.00  3.000
 LEE  HA    CA   C     110.00  3.000
 LEE  CB    CA   C     110.50  1.500
 LEE  HA    CA   N     110.00  3.000
 LEE  CB    CA   N     110.40  1.500
 LEE  C     CA   N     111.00  2.800
 LEE  OXT   C    O     126.48  3.000
 LEE  OXT   C    CA    120.80  1.700
 LEE  O     C    CA    120.80  1.700
 LEE  HB3   CB   HB2   106.64  3.000
 LEE  HB3   CB   CG    109.73  3.000
 LEE  HB2   CB   CG    109.48  3.000
 LEE  HB3   CB   CA    108.86  3.000
 LEE  HB2   CB   CA    109.11  3.000
 LEE  CG    CB   CA    112.83  3.000
 LEE  HG3   CG   HG2   106.21  3.000
 LEE  HG3   CG   CD    107.96  3.000
 LEE  HG2   CG   CD    110.30  3.000
 LEE  HG3   CG   CB    109.31  3.000
 LEE  HG2   CG   CB    110.09  3.000
 LEE  CD    CG   CB    112.73  3.000
 LEE  N1    CD   OE1   121.26  3.000
 LEE  N1    CD   CG    115.68  3.000
 LEE  OE1   CD   CG    123.05  3.000
 LEE  H1    N1   CA1   119.05  3.000
 LEE  H1    N1   CD    119.39  3.000
 LEE  CA1   N1   CD    121.26  3.000
 LEE  HA1   CA1  C7    109.23  3.000
 LEE  HA1   CA1  CB1   108.57  3.000
 LEE  C7    CA1  CB1   108.39  3.000
 LEE  HA1   CA1  N1    109.39  3.000
 LEE  C7    CA1  N1    110.94  3.000
 LEE  CB1   CA1  N1    110.27  3.000
 LEE  HB31  CB1  HB21  108.10  3.000
 LEE  HB31  CB1  SG    109.23  3.000
 LEE  HB21  CB1  SG    109.58  3.000
 LEE  HB31  CB1  CA1   109.03  3.000
 LEE  HB21  CB1  CA1   110.55  3.000
 LEE  SG    CB1  CA1   110.31  3.000
 LEE  C1    SG   CB1    99.40  3.000
 LEE  H12   C1   H11   107.86  3.000
 LEE  H12   C1   C2    110.64  3.000
 LEE  H11   C1   C2    110.35  3.000
 LEE  H12   C1   SG    109.01  3.000
 LEE  H11   C1   SG    108.95  3.000
 LEE  C2    C1   SG    109.98  3.000
 LEE  H22   C2   H21   106.59  3.000
 LEE  H22   C2   C3    109.67  3.000
 LEE  H21   C2   C3    109.38  3.000
 LEE  H22   C2   C1    109.45  3.000
 LEE  H21   C2   C1    109.80  3.000
 LEE  C3    C2   C1    111.81  3.000
 LEE  H32   C3   H31   106.15  3.000
 LEE  H32   C3   C4    109.47  3.000
 LEE  H31   C3   C4    109.39  3.000
 LEE  H32   C3   C2    109.36  3.000
 LEE  H31   C3   C2    109.41  3.000
 LEE  C4    C3   C2    112.84  3.000
 LEE  H42   C4   H41   106.00  3.000
 LEE  H42   C4   C5    109.37  3.000
 LEE  H41   C4   C5    109.26  3.000
 LEE  H42   C4   C3    109.36  3.000
 LEE  H41   C4   C3    109.46  3.000
 LEE  C5    C4   C3    113.14  3.000
 LEE  H52   C5   H51   106.02  3.000
 LEE  H52   C5   C6    109.65  3.000
 LEE  H51   C5   C6    109.62  3.000
 LEE  H52   C5   C4    109.22  3.000
 LEE  H51   C5   C4    109.27  3.000
 LEE  C6    C5   C4    112.83  3.000
 LEE  H63   C6   H62   107.66  3.000
 LEE  H63   C6   H61   107.60  3.000
 LEE  H62   C6   H61   107.46  3.000
 LEE  H63   C6   C5    111.62  3.000
 LEE  H62   C6   C5    111.13  3.000
 LEE  H61   C6   C5    111.17  3.000
 LEE  N2    C7   O1    124.24  3.000
 LEE  N2    C7   CA1   114.32  3.000
 LEE  O1    C7   CA1   121.37  3.000
 LEE  H3    N2   CA2   114.68  3.000
 LEE  H3    N2   C7    120.94  3.000
 LEE  CA2   N2   C7    124.29  3.000
 LEE  HA3   CA2  HA2   106.40  3.000
 LEE  HA3   CA2  C8    108.82  3.000
 LEE  HA2   CA2  C8    108.97  3.000
 LEE  HA3   CA2  N2    110.75  3.000
 LEE  HA2   CA2  N2    110.90  3.000
 LEE  C8    CA2  N2    110.87  3.000
 LEE  OXT1  C8   O2    127.69  3.000
 LEE  OXT1  C8   CA2   115.20  3.000
 LEE  O2    C8   CA2   117.11  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
 LEE  CONST_01  CA1   N1   CD   CG    180.00   0.0  0
 LEE  CONST_02  CA1   N1   CD   OE1     0.00   0.0  0
 LEE  CONST_03  CA2   N2   C7   CA1   180.00   0.0  0
 LEE  CONST_04  CA2   N2   C7   O1      0.00   0.0  0
 LEE  CONST_05  H1    N1   CD   CG      0.00   0.0  0
 LEE  CONST_06  H3    N2   C7   CA1     0.00   0.0  0
 LEE  Var_01    CD    CG   CB   CA    177.11  30.0  3
 LEE  Var_02    OE1   CD   CG   CB    -36.95  30.0  3
 LEE  Var_03    C2    C1   SG   CB1  -173.59  30.0  3
 LEE  Var_04    C3    C2   C1   SG   -177.52  30.0  3
 LEE  Var_05    C4    C3   C2   C1   -178.01  30.0  3
 LEE  Var_06    C5    C4   C3   C2   -179.03  30.0  3
 LEE  Var_07    C6    C5   C4   C3   -179.53  30.0  3
 LEE  Var_08    C8    CA2  N2   C7    178.61  30.0  3
 LEE  Var_09    O2    C8   CA2  N2     -1.10  30.0  3
 LEE  Var_10    HB21  CB1  SG   C1     62.80  30.0  1
 LEE  Var_11    H61   C6   C5   C4    -60.25  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
 LEE  chir_01  CA   N   C    CB  positiv
 LEE  chir_02  CA1  N1  CB1  C7  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
 LEE  plan-1  CG    0.020
 LEE  plan-1  CD    0.020
 LEE  plan-1  OE1   0.020
 LEE  plan-1  N1    0.020
 LEE  plan-1  CA1   0.020
 LEE  plan-1  H1    0.020
 LEE  plan-2  CA1   0.020
 LEE  plan-2  C7    0.020
 LEE  plan-2  O1    0.020
 LEE  plan-2  N2    0.020
 LEE  plan-2  CA2   0.020
 LEE  plan-2  H3    0.020
 LEE  plan-3  CA    0.020
 LEE  plan-3  C     0.020
 LEE  plan-3  O     0.020
 LEE  plan-3  OXT   0.020
 LEE  plan-4  CA2   0.020
 LEE  plan-4  C8    0.020
 LEE  plan-4  O2    0.020
 LEE  plan-4  OXT1  0.020

