# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 14 16:01:32 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  55  26  .  2022-07-25  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.777  -5.2338   2.5743   1.7432
 LEE  CA    C  CH1   0  -0.209  -4.8562   2.7674   0.3654
 LEE  C     C  C     0   0.522  -6.0369   3.0566  -0.5541
 LEE  O     O  O     0  -0.439  -7.1933   2.8976  -0.2531
 LEE  CB    C  CH2   0  -0.432  -4.0949   1.5449  -0.1653
 LEE  CG    C  CH2   0  -0.577  -2.8442   1.2593   0.6517
 LEE  CD    C  C     0   0.580  -2.0848   0.0587   0.1386
 LEE  OE1   O  O     0  -0.495  -2.6127  -0.8505  -0.4861
 LEE  OXT   O  OH1   0  -0.594  -5.6482   3.4992  -1.7445
 LEE  N1    N  NH1   0  -0.644  -0.7695   0.0378   0.4245
 LEE  CA1   C  CH1   0  -0.185   0.0512  -1.0766   0.0346
 LEE  CB1   C  CH2   0  -0.574   1.5003  -0.8408   0.4427
 LEE  SG    S  S2    0  -0.026   2.1297   0.6800  -0.3245
 LEE  C1    C  CH2   0  -0.544   3.8566   0.5944   0.2308
 LEE  C2    C  CH2   0  -0.422   4.5903   1.8722  -0.1462
 LEE  C3    C  CH2   0  -0.411   6.0660   1.8078   0.2320
 LEE  C4    C  CH2   0  -0.408   6.8180   3.0913  -0.0954
 LEE  C5    C  CH2   0  -0.419   8.2991   3.0225   0.2553
 LEE  C6    C  CH3   0  -0.662   9.0436   4.3104  -0.0676
 LEE  C7    C  C     0   0.568  -0.4327  -2.3661   0.7054
 LEE  O1    O  O     0  -0.484  -0.8372  -2.3836   1.8551
 LEE  N2    N  NH1   0  -0.644  -0.3098  -3.4629  -0.0514
 LEE  CA2   C  CH2   0  -0.370  -0.6660  -4.7650   0.4374
 LEE  C8    C  C     0   0.521  -0.4057  -5.8068  -0.6200
 LEE  O2    O  O     0  -0.434   0.0351  -5.5720  -1.7159
 LEE  OXT1  O  OH1   0  -0.584  -0.7283  -7.0124  -0.1863
 LEE  H     H  HNH2  0   0.356  -5.6733   3.4070   2.1127
 LEE  H2    H  HNH2  0   0.345  -5.9163   1.8301   1.8217
 LEE  HA    H  HCH1  0   0.270  -4.1881   3.6340   0.3125
 LEE  HB2   H  HCH2  0   0.242  -4.7577   0.6759  -0.1497
 LEE  HB3   H  HCH2  0   0.253  -3.8187   1.7121  -1.2075
 LEE  HG2   H  HCH2  0   0.257  -2.1918   2.1365   0.6618
 LEE  HG3   H  HCH2  0   0.283  -3.1135   1.0691   1.6939
 LEE  HXT   H  HOH1  0   0.481  -6.4183   3.6507  -2.3131
 LEE  H1    H  HNH1  0   0.404  -0.3655   0.7756   0.9800
 LEE  HA1   H  HCH1  0   0.283   0.0095  -1.1976  -1.0529
 LEE  HB21  H  HCH2  0   0.282   1.5854  -0.7656   1.5291
 LEE  HB31  H  HCH2  0   0.293   2.1041  -1.6871   0.1124
 LEE  H11   H  HCH2  0   0.262   3.8740   0.4514   1.3135
 LEE  H12   H  HCH2  0   0.261   4.3342  -0.2730  -0.2296
 LEE  H21   H  HCH2  0   0.229   4.4991   2.0488  -1.2222
 LEE  H22   H  HCH2  0   0.229   4.1183   2.7244   0.3511
 LEE  H31   H  HCH2  0   0.215   6.1592   1.5951   1.3024
 LEE  H32   H  HCH2  0   0.215   6.5368   0.9666  -0.2876
 LEE  H41   H  HCH2  0   0.209   6.7091   3.3156  -1.1624
 LEE  H42   H  HCH2  0   0.209   6.3563   3.9293   0.4382
 LEE  H51   H  HCH2  0   0.211   8.4082   2.7924   1.3197
 LEE  H52   H  HCH2  0   0.211   8.7585   2.1874  -0.2827
 LEE  H61   H  HCH3  0   0.216   8.9861   4.5423  -1.1329
 LEE  H62   H  HCH3  0   0.216   8.6198   5.1571   0.4757
 LEE  H63   H  HCH3  0   0.226  10.0989   4.2415   0.1986
 LEE  H3    H  HNH1  0   0.407  -0.0301  -3.3800  -1.0167
 LEE  HA2   H  HCH2  0   0.293  -0.0919  -5.0258   1.3313
 LEE  HA3   H  HCH2  0   0.292  -1.7218  -4.8132   0.7222
 LEE  HXT1  H  HOH1  0   0.490  -0.5547  -7.6766  -0.8707

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     double  1.231  0.020  1.231
 LEE  C     OXT   single  1.328  0.020  1.328
 LEE  CB    CG    single  1.521  0.020  1.521
 LEE  CB    HB2   single  0.970  0.020  1.090
 LEE  CB    HB3   single  0.970  0.020  1.090
 LEE  CG    CD    single  1.510  0.020  1.510
 LEE  CG    HG2   single  0.970  0.020  1.090
 LEE  CG    HG3   single  0.970  0.020  1.090
 LEE  CD    OE1   double  1.223  0.020  1.223
 LEE  OXT   HXT   single  0.850  0.020  0.980
 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  1.532  0.020  1.532
 LEE  CA1   HA1   single  0.970  0.020  1.090
 LEE  CB1   SG    single  1.816  0.020  1.816
 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  1.219  0.020  1.219
 LEE  N2    CA2   single  1.436  0.020  1.436
 LEE  N2    H3    single  0.860  0.020  1.020
 LEE  CA2   C8    single  1.507  0.020  1.507
 LEE  CA2   HA2   single  0.970  0.020  1.090
 LEE  CA2   HA3   single  0.970  0.020  1.090
 LEE  C8    O2    double  1.204  0.020  1.204
 LEE  C8    OXT1  single  1.321  0.020  1.321
 LEE  OXT1  HXT1  single  0.850  0.020  0.980
 LEE  CD    N1    single  1.346  0.020  1.346
 LEE  C7    N2    single  1.338  0.020  1.338

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     106.48  3.000
 LEE  H2    N     CA    110.43  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     123.27  3.000
 LEE  OXT   C     CA    120.80  1.700
 LEE  O     C     CA    120.80  1.700
 LEE  HB3   CB    HB2   106.79  3.000
 LEE  HB3   CB    CG    109.50  3.000
 LEE  HB2   CB    CG    109.98  3.000
 LEE  HB3   CB    CA    109.50  3.000
 LEE  HB2   CB    CA    109.12  3.000
 LEE  CG    CB    CA    111.82  3.000
 LEE  HG3   CG    HG2   106.14  3.000
 LEE  HG3   CG    CD    108.03  3.000
 LEE  HG2   CG    CD    109.93  3.000
 LEE  HG3   CG    CB    110.01  3.000
 LEE  HG2   CG    CB    110.18  3.000
 LEE  CD    CG    CB    112.34  3.000
 LEE  N1    CD    OE1   121.25  3.000
 LEE  N1    CD    CG    115.55  3.000
 LEE  OE1   CD    CG    123.20  3.000
 LEE  HXT   OXT   C     110.20  3.000
 LEE  H1    N1    CA1   119.20  3.000
 LEE  H1    N1    CD    119.83  3.000
 LEE  CA1   N1    CD    120.80  3.000
 LEE  HA1   CA1   C7    109.25  3.000
 LEE  HA1   CA1   CB1   108.61  3.000
 LEE  C7    CA1   CB1   108.26  3.000
 LEE  HA1   CA1   N1    109.47  3.000
 LEE  C7    CA1   N1    110.70  3.000
 LEE  CB1   CA1   N1    110.51  3.000
 LEE  HB31  CB1   HB21  108.14  3.000
 LEE  HB31  CB1   SG    109.27  3.000
 LEE  HB21  CB1   SG    109.60  3.000
 LEE  HB31  CB1   CA1   108.98  3.000
 LEE  HB21  CB1   CA1   110.55  3.000
 LEE  SG    CB1   CA1   110.25  3.000
 LEE  C1    SG    CB1    99.26  3.000
 LEE  H12   C1    H11   107.87  3.000
 LEE  H12   C1    C2    110.61  3.000
 LEE  H11   C1    C2    110.37  3.000
 LEE  H12   C1    SG    108.93  3.000
 LEE  H11   C1    SG    108.93  3.000
 LEE  C2    C1    SG    110.08  3.000
 LEE  H22   C2    H21   106.59  3.000
 LEE  H22   C2    C3    109.74  3.000
 LEE  H21   C2    C3    109.35  3.000
 LEE  H22   C2    C1    109.49  3.000
 LEE  H21   C2    C1    109.83  3.000
 LEE  C3    C2    C1    111.71  3.000
 LEE  H32   C3    H31   106.14  3.000
 LEE  H32   C3    C4    109.45  3.000
 LEE  H31   C3    C4    109.38  3.000
 LEE  H32   C3    C2    109.32  3.000
 LEE  H31   C3    C2    109.44  3.000
 LEE  C4    C3    C2    112.89  3.000
 LEE  H42   C4    H41   106.01  3.000
 LEE  H42   C4    C5    109.39  3.000
 LEE  H41   C4    C5    109.27  3.000
 LEE  H42   C4    C3    109.38  3.000
 LEE  H41   C4    C3    109.44  3.000
 LEE  C5    C4    C3    113.11  3.000
 LEE  H52   C5    H51   106.01  3.000
 LEE  H52   C5    C6    109.64  3.000
 LEE  H51   C5    C6    109.60  3.000
 LEE  H52   C5    C4    109.23  3.000
 LEE  H51   C5    C4    109.28  3.000
 LEE  C6    C5    C4    112.86  3.000
 LEE  H63   C6    H62   107.65  3.000
 LEE  H63   C6    H61   107.61  3.000
 LEE  H62   C6    H61   107.48  3.000
 LEE  H63   C6    C5    111.60  3.000
 LEE  H62   C6    C5    111.15  3.000
 LEE  H61   C6    C5    111.16  3.000
 LEE  N2    C7    O1    123.51  3.000
 LEE  N2    C7    CA1   114.42  3.000
 LEE  O1    C7    CA1   122.00  3.000
 LEE  H3    N2    CA2   117.98  3.000
 LEE  H3    N2    C7    119.96  3.000
 LEE  CA2   N2    C7    121.88  3.000
 LEE  HA3   CA2   HA2   106.45  3.000
 LEE  HA3   CA2   C8    108.59  3.000
 LEE  HA2   CA2   C8    108.53  3.000
 LEE  HA3   CA2   N2    111.58  3.000
 LEE  HA2   CA2   N2    111.35  3.000
 LEE  C8    CA2   N2    110.20  3.000
 LEE  OXT1  C8    O2    124.47  3.000
 LEE  OXT1  C8    CA2   110.99  3.000
 LEE  O2    C8    CA2   124.53  3.000
 LEE  HXT1  OXT1  C8    110.47  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  CONST_07  HXT   OXT   C    CA    180.00   0.0  0
 LEE  CONST_08  HXT1  OXT1  C8   CA2   180.00   0.0  0
 LEE  Var_01    CD    CG    CB   CA   -179.94  30.0  3
 LEE  Var_02    OE1   CD    CG   CB    -25.62  30.0  3
 LEE  Var_03    C2    C1    SG   CB1  -173.11  30.0  3
 LEE  Var_04    C3    C2    C1   SG   -176.73  30.0  3
 LEE  Var_05    C4    C3    C2   C1   -178.25  30.0  3
 LEE  Var_06    C5    C4    C3   C2   -178.87  30.0  3
 LEE  Var_07    C6    C5    C4   C3   -179.70  30.0  3
 LEE  Var_08    C8    CA2   N2   C7   -179.20  30.0  3
 LEE  Var_09    O2    C8    CA2  N2     -0.16  30.0  3
 LEE  Var_10    HB21  CB1   SG   C1     62.52  30.0  1
 LEE  Var_11    H61   C6    C5   C4    -60.31  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-3  HXT   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
 LEE  plan-4  HXT1  0.020

