# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:08:15 2022
#   Inital geometry file: a 139 line input string
#   Ligand name: L-gamma-glutamyl-S-[2-(4-nitrophenyl)-2-oxoethyl]-L-cysteinylglycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCC(=O)N[C@@H](CSCC(=O)c1ccc(cc1)[N+]([O-])=O)C(=O)NCC(O)=O)C(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
 1R4  1R4  L-gamma-glutamyl-S-[2-(4-nitrophenyl)-2-oxoethyl]-L-cysteinylglycine  ligand  52  32  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_1R4
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
 1R4  O01   O  O      0  -0.499  -2.5169  -2.3652   1.8279
 1R4  C02   C  C      0   0.554  -2.1299  -2.4125   0.6695
 1R4  C03   C  CH1    0  -0.189  -1.5496  -1.1758  -0.0309
 1R4  N04   N  NH1    0  -0.642  -2.2124   0.0241   0.4013
 1R4  C05   C  C      0   0.574  -3.5276   0.2145   0.1779
 1R4  C06   C  CH2    0  -0.574  -4.1132   1.4674   0.7820
 1R4  C07   C  CH2    0  -0.417  -5.2231   2.0748  -0.0645
 1R4  C08   C  CH1    0  -0.215  -5.8452   3.3173   0.5780
 1R4  C09   C  C      0   0.385  -6.8404   3.9516  -0.4267
 1R4  O10   O  O      0  -0.607  -8.0576   3.8487  -0.1763
 1R4  O11   O  OC    -1  -0.623  -6.3314   4.4971  -1.4282
 1R4  O13   O  O      0  -0.499  -4.1846  -0.5889  -0.4696
 1R4  C14   C  CH2    0  -0.578  -0.0618  -1.1003   0.2910
 1R4  S15   S  S2     0   0.022   0.6768   0.3345  -0.5458
 1R4  C16   C  CH2    0  -0.704   2.3853   0.0497  -0.0344
 1R4  C17   C  C      0   0.404   3.2683   1.1271  -0.6030
 1R4  C18   C  C      0   0.011   4.7311   1.0625  -0.3110
 1R4  C19   C  C1     0  -0.252   5.5598   2.0569  -0.8292
 1R4  C20   C  C1     0  -0.255   6.9204   2.0356  -0.5894
 1R4  C21   C  C      0   0.261   7.4451   1.0045   0.1759
 1R4  N22   N  N      1   0.332   8.8820   0.9719   0.4314
 1R4  O23   O  O     -1  -0.369   9.3187   0.0567   1.0861
 1R4  O24   O  O      0  -0.369   9.5565   1.8622  -0.0259
 1R4  C25   C  C1     0  -0.247   6.6464   0.0044   0.7049
 1R4  C26   C  C1     0  -0.282   5.2850   0.0412   0.4570
 1R4  O27   O  O      0  -0.365   2.8088   2.0189  -1.2771
 1R4  N28   N  NH1    0  -0.627  -2.1096  -3.5187  -0.0704
 1R4  C29   C  CH2    0  -0.411  -2.5301  -4.8152   0.3938
 1R4  C30   C  C      0   0.400  -2.3813  -5.8707  -0.7213
 1R4  O31   O  OC    -1  -0.608  -2.7023  -7.0278  -0.4022
 1R4  O32   O  O      0  -0.599  -1.9607  -5.4733  -1.8250
 1R4  N01   N  NH2    0  -0.787  -6.4048   2.9764   1.8771
 1R4  H031  H  HCH1   0   0.279  -1.6685  -1.2872  -1.1136
 1R4  H041  H  HNH1   0   0.401  -1.7195   0.6626   1.0053
 1R4  H062  H  HCH2   0   0.271  -4.5088   1.2128   1.7696
 1R4  H061  H  HCH2   0   0.243  -3.3243   2.2054   0.9524
 1R4  H072  H  HCH2   0   0.229  -4.8311   2.3443  -1.0472
 1R4  H071  H  HCH2   0   0.218  -6.0063   1.3289  -0.2313
 1R4  H081  H  HCH1   0   0.210  -5.0414   4.0439   0.7445
 1R4  H141  H  HCH2   0   0.285   0.0922  -1.0196   1.3697
 1R4  H142  H  HCH2   0   0.297   0.4262  -2.0122  -0.0549
 1R4  H161  H  HCH2   0   0.314   2.4616   0.0504   1.0568
 1R4  H162  H  HCH2   0   0.313   2.7284  -0.9302  -0.3782
 1R4  H191  H  H      0   0.285   5.1421   2.8569  -1.4241
 1R4  H201  H  H      0   0.306   7.5499   2.8124  -0.9974
 1R4  H251  H  H      0   0.308   7.0626  -0.7954   1.2989
 1R4  H261  H  H      0   0.286   4.6710  -0.7433   0.8768
 1R4  H281  H  HNH1   0   0.388  -1.8170  -3.4922  -1.0376
 1R4  H292  H  HCH2   0   0.243  -1.9416  -5.1277   1.2617
 1R4  H291  H  HCH2   0   0.243  -3.5740  -4.7897   0.7212
 1R4  H01   H  HNH2   0   0.336  -6.6675   3.8311   2.3530
 1R4  H011  H  HNH2   0   0.324  -7.2847   2.4987   1.7160

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
 1R4  N01  C08   single    1.455  0.020  1.455
 1R4  C08  C09   single    1.550  0.020  1.550
 1R4  C08  C07   single    1.531  0.020  1.531
 1R4  S15  C16   single    1.806  0.020  1.806
 1R4  S15  C14   single    1.818  0.020  1.818
 1R4  C06  C07   single    1.522  0.020  1.522
 1R4  C06  C05   single    1.509  0.020  1.509
 1R4  O27  C17   double    1.209  0.020  1.209
 1R4  O10  C09   deloc     1.247  0.020  1.247
 1R4  N04  C05   single    1.348  0.020  1.348
 1R4  N04  C03   single    1.437  0.020  1.437
 1R4  C09  O11   deloc     1.249  0.020  1.249
 1R4  C05  O13   double    1.223  0.020  1.223
 1R4  C17  C16   single    1.505  0.020  1.505
 1R4  C17  C18   single    1.493  0.020  1.493
 1R4  C26  C25   aromatic  1.384  0.020  1.384
 1R4  C26  C18   aromatic  1.393  0.020  1.393
 1R4  C14  C03   single    1.524  0.020  1.524
 1R4  O32  C30   deloc     1.246  0.020  1.246
 1R4  C25  C21   aromatic  1.385  0.020  1.385
 1R4  C18  C19   aromatic  1.394  0.020  1.394
 1R4  C03  C02   single    1.535  0.020  1.535
 1R4  N28  C02   single    1.331  0.020  1.331
 1R4  N28  C29   single    1.440  0.020  1.440
 1R4  C30  O31   deloc     1.242  0.020  1.242
 1R4  C30  C29   single    1.543  0.020  1.543
 1R4  C02  O01   double    1.222  0.020  1.222
 1R4  O23  N22   single    1.207  0.020  1.207
 1R4  C19  C20   aromatic  1.382  0.020  1.382
 1R4  C21  N22   single    1.460  0.020  1.460
 1R4  C21  C20   aromatic  1.387  0.020  1.387
 1R4  N22  O24   double    1.207  0.020  1.207
 1R4  C03  H031  single    0.970  0.020  1.090
 1R4  N04  H041  single    0.860  0.020  1.020
 1R4  C06  H062  single    0.970  0.020  1.090
 1R4  C06  H061  single    0.970  0.020  1.090
 1R4  C07  H072  single    0.970  0.020  1.090
 1R4  C07  H071  single    0.970  0.020  1.090
 1R4  C08  H081  single    0.970  0.020  1.090
 1R4  C14  H141  single    0.970  0.020  1.090
 1R4  C14  H142  single    0.970  0.020  1.090
 1R4  C16  H161  single    0.970  0.020  1.090
 1R4  C16  H162  single    0.970  0.020  1.090
 1R4  C19  H191  single    0.930  0.020  1.080
 1R4  C20  H201  single    0.930  0.020  1.080
 1R4  C25  H251  single    0.930  0.020  1.080
 1R4  C26  H261  single    0.930  0.020  1.080
 1R4  N28  H281  single    0.860  0.020  1.020
 1R4  C29  H292  single    0.970  0.020  1.090
 1R4  C29  H291  single    0.970  0.020  1.090
 1R4  N01  H01   single    0.890  0.020  1.040
 1R4  N01  H011  single    0.890  0.020  1.040

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
 1R4  N28   C02  C03   114.21  3.000
 1R4  N28   C02  O01   124.32  3.000
 1R4  C03   C02  O01   121.40  3.000
 1R4  H031  C03  C14   108.65  3.000
 1R4  H031  C03  N04   109.40  3.000
 1R4  C14   C03  N04   110.20  3.000
 1R4  H031  C03  C02   109.16  3.000
 1R4  C14   C03  C02   108.22  3.000
 1R4  N04   C03  C02   111.16  3.000
 1R4  H041  N04  C05   119.15  3.000
 1R4  H041  N04  C03   118.92  3.000
 1R4  C05   N04  C03   121.22  3.000
 1R4  O13   C05  C06   123.28  3.000
 1R4  O13   C05  N04   121.27  3.000
 1R4  C06   C05  N04   115.45  3.000
 1R4  H061  C06  H062  106.10  3.000
 1R4  H061  C06  C07   110.08  3.000
 1R4  H062  C06  C07   109.35  3.000
 1R4  H061  C06  C05   110.04  3.000
 1R4  H062  C06  C05   107.96  3.000
 1R4  C07   C06  C05   113.05  3.000
 1R4  H071  C07  H072  106.74  3.000
 1R4  H071  C07  C08   109.04  3.000
 1R4  H072  C07  C08   108.87  3.000
 1R4  H071  C07  C06   109.55  3.000
 1R4  H072  C07  C06   109.71  3.000
 1R4  C08   C07  C06   112.75  3.000
 1R4  H081  C08  N01   107.56  3.000
 1R4  H081  C08  C09   107.33  3.000
 1R4  N01   C08  C09   115.32  3.000
 1R4  H081  C08  C07   107.68  3.000
 1R4  C09   C08  C07   108.72  3.000
 1R4  N01   C08  C07   109.93  3.000
 1R4  O11   C09  O10   126.50  3.000
 1R4  O11   C09  C08   115.91  3.000
 1R4  O10   C09  C08   117.57  3.000
 1R4  H142  C14  H141  108.17  3.000
 1R4  H142  C14  S15   109.40  3.000
 1R4  H141  C14  S15   109.81  3.000
 1R4  H142  C14  C03   109.17  3.000
 1R4  H141  C14  C03   110.47  3.000
 1R4  S15   C14  C03   109.79  3.000
 1R4  C16   S15  C14    97.45  3.000
 1R4  H162  C16  H161  107.00  3.000
 1R4  H162  C16  C17   109.80  3.000
 1R4  H161  C16  C17   109.61  3.000
 1R4  H162  C16  S15   110.42  3.000
 1R4  H161  C16  S15   110.39  3.000
 1R4  C17   C16  S15   109.59  3.000
 1R4  O27   C17  C18   120.89  3.000
 1R4  C18   C17  C16   118.04  3.000
 1R4  O27   C17  C16   121.07  3.000
 1R4  C26   C18  C19   119.44  3.000
 1R4  C19   C18  C17   118.61  3.000
 1R4  C26   C18  C17   121.95  3.000
 1R4  H191  C19  C20   119.17  3.000
 1R4  H191  C19  C18   120.18  3.000
 1R4  C20   C19  C18   120.65  3.000
 1R4  H201  C20  C21   121.51  3.000
 1R4  H201  C20  C19   119.83  3.000
 1R4  C21   C20  C19   118.66  3.000
 1R4  C25   C21  N22   119.00  3.000
 1R4  N22   C21  C20   119.04  3.000
 1R4  C25   C21  C20   121.96  3.000
 1R4  O24   N22  O23   124.24  3.000
 1R4  O24   N22  C21   117.86  3.000
 1R4  O23   N22  C21   117.90  3.000
 1R4  H251  C25  C26   119.82  3.000
 1R4  H251  C25  C21   121.52  3.000
 1R4  C26   C25  C21   118.66  3.000
 1R4  H261  C26  C25   118.02  3.000
 1R4  H261  C26  C18   121.36  3.000
 1R4  C25   C26  C18   120.62  3.000
 1R4  H281  N28  C29   114.62  3.000
 1R4  H281  N28  C02   120.97  3.000
 1R4  C29   N28  C02   124.38  3.000
 1R4  H291  C29  H292  106.41  3.000
 1R4  H291  C29  C30   108.91  3.000
 1R4  H292  C29  C30   109.03  3.000
 1R4  H291  C29  N28   110.73  3.000
 1R4  H292  C29  N28   110.85  3.000
 1R4  C30   C29  N28   110.79  3.000
 1R4  O32   C30  O31   127.71  3.000
 1R4  O31   C30  C29   115.26  3.000
 1R4  O32   C30  C29   117.03  3.000
 1R4  H011  N01  H01   104.31  3.000
 1R4  H011  N01  C08   107.59  3.000
 1R4  H01   N01  C08   108.76  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
 1R4  CONST_01  C21   C25  C26  C18     0.00   0.0  0
 1R4  CONST_02  C21   C20  C19  C18     0.00   0.0  0
 1R4  CONST_03  C25   C26  C18  C19     0.00   0.0  0
 1R4  CONST_04  C25   C21  C20  C19     0.00   0.0  0
 1R4  CONST_05  C26   C18  C19  C20     0.00   0.0  0
 1R4  CONST_06  C26   C25  C21  C20     0.00   0.0  0
 1R4  CONST_07  C25   C26  C18  C17   180.00   0.0  0
 1R4  CONST_08  C20   C19  C18  C17   180.00   0.0  0
 1R4  CONST_09  N22   C21  C20  C19   180.00   0.0  0
 1R4  CONST_10  C26   C25  C21  N22   180.00   0.0  0
 1R4  CONST_11  H251  C25  C26  C18   180.00   0.0  0
 1R4  CONST_12  H201  C20  C19  C18   180.00   0.0  0
 1R4  CONST_13  H261  C26  C18  C19   180.00   0.0  0
 1R4  CONST_14  H191  C19  C20  C21   180.00   0.0  0
 1R4  CONST_15  O23   N22  C21  C20   180.00   0.0  0
 1R4  CONST_16  O24   N22  C21  C20     0.00   0.0  0
 1R4  CONST_17  C25   C21  N22  O23     0.00   0.0  0
 1R4  CONST_18  C25   C21  N22  O24   180.00   0.0  0
 1R4  CONST_19  C29   N28  C02  O01     0.00   0.0  0
 1R4  CONST_20  C06   C05  N04  C03   180.00   0.0  0
 1R4  CONST_21  O13   C05  N04  C03     0.00   0.0  0
 1R4  CONST_22  C29   N28  C02  C03   180.00   0.0  0
 1R4  CONST_23  H281  N28  C02  O01   180.00   0.0  0
 1R4  CONST_24  H041  N04  C05  C06     0.00   0.0  0
 1R4  Var_01    C26   C18  C17  C16     0.31  30.0  2
 1R4  Var_02    C18   C17  C16  S15  -179.15  30.0  2
 1R4  Var_03    C30   C29  N28  C02   179.74  30.0  3
 1R4  Var_04    C07   C06  C05  N04   146.38  30.0  1
 1R4  Var_05    C08   C07  C06  C05   178.00  30.0  3
 1R4  Var_06    C17   C16  S15  C14   179.96  30.0  3
 1R4  Var_07    O32   C30  C29  N28    -1.18  30.0  2
 1R4  Var_08    H141  C14  S15  C16    61.50  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
 1R4  chir_01  C03  N04  C14  C02  negativ
 1R4  chir_02  C08  N01  C09  C07  positiv

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
 1R4  plan-1  C17   0.020
 1R4  plan-1  C18   0.020
 1R4  plan-1  C19   0.020
 1R4  plan-1  C20   0.020
 1R4  plan-1  C21   0.020
 1R4  plan-1  N22   0.020
 1R4  plan-1  C25   0.020
 1R4  plan-1  C26   0.020
 1R4  plan-1  H191  0.020
 1R4  plan-1  H201  0.020
 1R4  plan-1  H251  0.020
 1R4  plan-1  H261  0.020
 1R4  plan-2  O01   0.020
 1R4  plan-2  C02   0.020
 1R4  plan-2  C03   0.020
 1R4  plan-2  N28   0.020
 1R4  plan-2  C29   0.020
 1R4  plan-2  H281  0.020
 1R4  plan-3  C03   0.020
 1R4  plan-3  N04   0.020
 1R4  plan-3  C05   0.020
 1R4  plan-3  C06   0.020
 1R4  plan-3  O13   0.020
 1R4  plan-3  H041  0.020
 1R4  plan-4  C21   0.020
 1R4  plan-4  N22   0.020
 1R4  plan-4  O23   0.020
 1R4  plan-4  O24   0.020
 1R4  plan-5  C16   0.020
 1R4  plan-5  C17   0.020
 1R4  plan-5  C18   0.020
 1R4  plan-5  O27   0.020
 1R4  plan-6  C08   0.020
 1R4  plan-6  C09   0.020
 1R4  plan-6  O10   0.020
 1R4  plan-6  O11   0.020
 1R4  plan-7  C29   0.020
 1R4  plan-7  C30   0.020
 1R4  plan-7  O31   0.020
 1R4  plan-7  O32   0.020

