# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 03:47:23 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: N-[(2R)-3-phenyl-2-sulfanylpropanoyl]-L-phenylalanyl-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@H](S)Cc2ccccc2)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
 OIR  OIR  N-[(2R)-3-phenyl-2-sulfanylpropanoyl]-L-phenylalanyl-L-alanine  ligand  51  28  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OIR
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
 OIR  O19   O  O      0  -0.485   0.0894  -1.2332   1.2670
 OIR  C18   C  C      0   0.615   0.5653  -0.6202   0.3242
 OIR  C20   C  CH1    0  -0.528   2.0073  -0.8153  -0.1091
 OIR  C21   C  CH2    0  -0.500   2.9528  -0.6719   1.0861
 OIR  C23   C  C      0   0.147   4.4025  -0.7337   0.7002
 OIR  C24   C  C1     0  -0.308   5.0388   0.3890   0.1750
 OIR  C25   C  C1     0  -0.241   6.3750   0.3413  -0.1981
 OIR  C26   C  C1     0  -0.271   7.0973  -0.8358  -0.0478
 OIR  C27   C  C1     0  -0.244   6.4738  -1.9606   0.4761
 OIR  C28   C  C1     0  -0.300   5.1358  -1.9081   0.8444
 OIR  S26   S  S2     0  -0.183   2.1542  -2.4196  -0.9589
 OIR  N9    N  NH1    0  -0.635  -0.1301   0.2851  -0.3777
 OIR  C2    C  CH1    0  -0.180  -1.5182   0.5432  -0.1024
 OIR  C11   C  C      0   0.555  -2.3834  -0.6702  -0.4583
 OIR  O12   O  O      0  -0.500  -2.1272  -1.3662  -1.4302
 OIR  N13   N  NH1    0  -0.630  -3.4404  -0.8326   0.3363
 OIR  C14   C  CH1    0  -0.205  -4.4987  -1.7957   0.1309
 OIR  C15   C  C      0   0.419  -5.7386  -1.3670   0.9540
 OIR  O16   O  OC    -1  -0.604  -6.7615  -2.0495   0.7745
 OIR  O17   O  O      0  -0.598  -5.6028  -0.3979   1.7274
 OIR  C19   C  CH3    0  -0.655  -4.0668  -3.2091   0.5153
 OIR  C1    C  CH2    0  -0.560  -1.9975   1.7583  -0.9082
 OIR  C3    C  CR6    0   0.149  -1.2117   2.9991  -0.5864
 OIR  C4    C  CR16   0  -0.329  -0.2441   3.4806  -1.4630
 OIR  C5    C  CR16   0  -0.239   0.5044   4.6083  -1.1476
 OIR  C6    C  CR16   0  -0.270   0.2920   5.2702   0.0532
 OIR  C7    C  CR16   0  -0.239  -0.6738   4.7992   0.9352
 OIR  C8    C  CR16   0  -0.303  -1.4183   3.6733   0.6161
 OIR  H20   H  HCH1   0   0.312   2.2750  -0.0829  -0.8753
 OIR  H211  H  HCH2   0   0.270   2.7438   0.2913   1.5612
 OIR  H212  H  HCH2   0   0.264   2.7215  -1.4435   1.8222
 OIR  H24   H  H      0   0.247   4.4839   1.3139   0.0622
 OIR  H25   H  H      0   0.254   6.8535   1.2253  -0.5996
 OIR  H1    H  H      0   0.254   8.1409  -0.8753  -0.3324
 OIR  H27   H  H      0   0.253   7.0304  -2.8809   0.5998
 OIR  H28   H  H      0   0.244   4.6574  -2.7893   1.2540
 OIR  H26   H  HSH1   0   0.225   1.8499  -3.1861   0.0961
 OIR  HN9   H  HNH1   0   0.404   0.2920   0.7047  -1.1906
 OIR  H2    H  HCH1   0   0.276  -1.6297   0.7682   0.9630
 OIR  H13   H  HNH1   0   0.383  -3.6054  -0.1908   1.0997
 OIR  H14   H  HCH1   0   0.237  -4.7780  -1.7942  -0.9277
 OIR  H191  H  HCH3   0   0.217  -3.7964  -3.2602   1.5715
 OIR  H192  H  HCH3   0   0.227  -4.8768  -3.9141   0.3354
 OIR  H193  H  HCH3   0   0.232  -3.2056  -3.5277  -0.0704
 OIR  H11   H  HCH2   0   0.272  -1.9310   1.5352  -1.9762
 OIR  H12   H  HCH2   0   0.280  -3.0552   1.9133  -0.6849
 OIR  H4    H  HCR6   0   0.253  -0.0762   2.9744  -2.4072
 OIR  H5    H  HCR6   0   0.256   1.2508   4.9706  -1.8426
 OIR  H6    H  HCR6   0   0.256   0.8714   6.1503   0.3006
 OIR  H7    H  HCR6   0   0.256  -0.8488   5.3115   1.8726
 OIR  H8    H  HCR6   0   0.249  -2.1699   3.3135   1.3097

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
 OIR  O19  C18   double    1.221  0.020  1.221
 OIR  C18  C20   single    1.518  0.020  1.518
 OIR  C18  N9    single    1.340  0.020  1.340
 OIR  C20  C21   single    1.531  0.020  1.531
 OIR  C20  S26   single    1.821  0.020  1.821
 OIR  C20  H20   single    0.970  0.020  1.090
 OIR  C21  C23   single    1.501  0.020  1.501
 OIR  C21  H211  single    0.970  0.020  1.090
 OIR  C21  H212  single    0.970  0.020  1.090
 OIR  C23  C24   aromatic  1.393  0.020  1.393
 OIR  C23  C28   aromatic  1.392  0.020  1.392
 OIR  C24  C25   aromatic  1.388  0.020  1.388
 OIR  C24  H24   single    0.930  0.020  1.080
 OIR  C25  C26   aromatic  1.389  0.020  1.389
 OIR  C25  H25   single    0.930  0.020  1.080
 OIR  C26  C27   aromatic  1.389  0.020  1.389
 OIR  C26  H1    single    0.930  0.020  1.080
 OIR  C27  C28   aromatic  1.389  0.020  1.389
 OIR  C27  H27   single    0.930  0.020  1.080
 OIR  C28  H28   single    0.930  0.020  1.080
 OIR  S26  H26   single    1.200  0.020  1.300
 OIR  N9   C2    single    1.438  0.020  1.438
 OIR  N9   HN9   single    0.860  0.020  1.020
 OIR  C2   C11   single    1.532  0.020  1.532
 OIR  C2   C1    single    1.535  0.020  1.535
 OIR  C2   H2    single    0.970  0.020  1.090
 OIR  C11  O12   double    1.223  0.020  1.223
 OIR  C11  N13   single    1.332  0.020  1.332
 OIR  N13  C14   single    1.446  0.020  1.446
 OIR  N13  H13   single    0.860  0.020  1.020
 OIR  C14  C15   single    1.549  0.020  1.549
 OIR  C14  C19   single    1.527  0.020  1.527
 OIR  C14  H14   single    0.970  0.020  1.090
 OIR  C15  O16   deloc     1.243  0.020  1.243
 OIR  C15  O17   deloc     1.247  0.020  1.247
 OIR  C19  H191  single    0.970  0.020  1.090
 OIR  C19  H192  single    0.970  0.020  1.090
 OIR  C19  H193  single    0.970  0.020  1.090
 OIR  C1   C3    single    1.504  0.020  1.504
 OIR  C1   H11   single    0.970  0.020  1.090
 OIR  C1   H12   single    0.970  0.020  1.090
 OIR  C3   C4    aromatic  1.392  0.020  1.392
 OIR  C3   C8    aromatic  1.394  0.020  1.394
 OIR  C4   C5    aromatic  1.390  0.020  1.390
 OIR  C4   H4    single    0.930  0.020  1.080
 OIR  C5   C6    aromatic  1.387  0.020  1.387
 OIR  C5   H5    single    0.930  0.020  1.080
 OIR  C6   C7    aromatic  1.390  0.020  1.390
 OIR  C6   H6    single    0.930  0.020  1.080
 OIR  C7   C8    aromatic  1.387  0.020  1.387
 OIR  C7   H7    single    0.930  0.020  1.080
 OIR  C8   H8    single    0.930  0.020  1.080

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
 OIR  N9    C18  C20   115.48  3.000
 OIR  N9    C18  O19   122.78  3.000
 OIR  C20   C18  O19   121.73  3.000
 OIR  H20   C20  S26   104.09  3.000
 OIR  H20   C20  C21   109.47  3.000
 OIR  S26   C20  C21   113.39  3.000
 OIR  H20   C20  C18   110.27  3.000
 OIR  S26   C20  C18   108.84  3.000
 OIR  C21   C20  C18   110.59  3.000
 OIR  H212  C21  H211  106.81  3.000
 OIR  H212  C21  C23   110.42  3.000
 OIR  H211  C21  C23   109.41  3.000
 OIR  H212  C21  C20   109.24  3.000
 OIR  H211  C21  C20   107.67  3.000
 OIR  C23   C21  C20   113.07  3.000
 OIR  C28   C23  C24   118.57  3.000
 OIR  C28   C23  C21   121.11  3.000
 OIR  C24   C23  C21   120.31  3.000
 OIR  H24   C24  C25   119.60  3.000
 OIR  H24   C24  C23   119.52  3.000
 OIR  C25   C24  C23   120.88  3.000
 OIR  H25   C25  C26   120.15  3.000
 OIR  H25   C25  C24   119.81  3.000
 OIR  C26   C25  C24   120.04  3.000
 OIR  H1    C26  C27   120.17  3.000
 OIR  H1    C26  C25   120.25  3.000
 OIR  C27   C26  C25   119.58  3.000
 OIR  H27   C27  C28   119.81  3.000
 OIR  H27   C27  C26   120.05  3.000
 OIR  C28   C27  C26   120.14  3.000
 OIR  H28   C28  C27   119.68  3.000
 OIR  H28   C28  C23   119.53  3.000
 OIR  C27   C28  C23   120.79  3.000
 OIR  H26   S26  C20    96.79  3.000
 OIR  HN9   N9   C2    118.95  3.000
 OIR  HN9   N9   C18   119.12  3.000
 OIR  C2    N9   C18   121.45  3.000
 OIR  H2    C2   C1    108.45  3.000
 OIR  H2    C2   C11   109.35  3.000
 OIR  C1    C2   C11   109.19  3.000
 OIR  H2    C2   N9    108.75  3.000
 OIR  C1    C2   N9    110.06  3.000
 OIR  C11   C2   N9    111.00  3.000
 OIR  N13   C11  O12   124.82  3.000
 OIR  N13   C11  C2    113.96  3.000
 OIR  O12   C11  C2    121.14  3.000
 OIR  H13   N13  C14   114.25  3.000
 OIR  H13   N13  C11   120.16  3.000
 OIR  C14   N13  C11   125.26  3.000
 OIR  H14   C14  C19   108.47  3.000
 OIR  H14   C14  C15   108.01  3.000
 OIR  C19   C14  C15   110.42  3.000
 OIR  H14   C14  N13   108.86  3.000
 OIR  C19   C14  N13   111.95  3.000
 OIR  C15   C14  N13   109.04  3.000
 OIR  O17   C15  O16   127.29  3.000
 OIR  O17   C15  C14   117.22  3.000
 OIR  O16   C15  C14   115.48  3.000
 OIR  H193  C19  H192  108.06  3.000
 OIR  H193  C19  H191  108.11  3.000
 OIR  H192  C19  H191  108.30  3.000
 OIR  H193  C19  C14   111.04  3.000
 OIR  H192  C19  C14   110.32  3.000
 OIR  H191  C19  C14   110.92  3.000
 OIR  H12   C1   H11   106.72  3.000
 OIR  H12   C1   C3    110.20  3.000
 OIR  H11   C1   C3    110.23  3.000
 OIR  H12   C1   C2    107.91  3.000
 OIR  H11   C1   C2    109.41  3.000
 OIR  C3    C1   C2    112.19  3.000
 OIR  C8    C3   C4    118.62  3.000
 OIR  C8    C3   C1    120.42  3.000
 OIR  C4    C3   C1    120.94  3.000
 OIR  H4    C4   C5    119.54  3.000
 OIR  H4    C4   C3    119.64  3.000
 OIR  C5    C4   C3    120.82  3.000
 OIR  H5    C5   C6    120.11  3.000
 OIR  H5    C5   C4    119.82  3.000
 OIR  C6    C5   C4    120.07  3.000
 OIR  H6    C6   C7    120.16  3.000
 OIR  H6    C6   C5    120.25  3.000
 OIR  C7    C6   C5    119.59  3.000
 OIR  H7    C7   C8    119.78  3.000
 OIR  H7    C7   C6    120.09  3.000
 OIR  C8    C7   C6    120.13  3.000
 OIR  H8    C8   C7    119.62  3.000
 OIR  H8    C8   C3    119.61  3.000
 OIR  C7    C8   C3    120.77  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
 OIR  CONST_01  C26  C25  C24  C23    0.00   0.0  0
 OIR  CONST_02  C26  C27  C28  C23    0.00   0.0  0
 OIR  CONST_03  C27  C28  C23  C24    0.00   0.0  0
 OIR  CONST_04  C27  C26  C25  C24    0.00   0.0  0
 OIR  CONST_05  C28  C23  C24  C25    0.00   0.0  0
 OIR  CONST_06  C28  C27  C26  C25    0.00   0.0  0
 OIR  CONST_07  C6   C5   C4   C3     0.00   0.0  0
 OIR  CONST_08  C6   C7   C8   C3     0.00   0.0  0
 OIR  CONST_09  C7   C8   C3   C4     0.00   0.0  0
 OIR  CONST_10  C7   C6   C5   C4     0.00   0.0  0
 OIR  CONST_11  C8   C3   C4   C5     0.00   0.0  0
 OIR  CONST_12  C8   C7   C6   C5     0.00   0.0  0
 OIR  CONST_13  C25  C24  C23  C21  180.00   0.0  0
 OIR  CONST_14  C27  C28  C23  C21  180.00   0.0  0
 OIR  CONST_15  C5   C4   C3   C1   180.00   0.0  0
 OIR  CONST_16  C7   C8   C3   C1   180.00   0.0  0
 OIR  CONST_17  H25  C25  C24  C23  180.00   0.0  0
 OIR  CONST_18  H27  C27  C28  C23  180.00   0.0  0
 OIR  CONST_19  H28  C28  C23  C24  180.00   0.0  0
 OIR  CONST_20  H1   C26  C25  C24  180.00   0.0  0
 OIR  CONST_21  H24  C24  C25  C26  180.00   0.0  0
 OIR  CONST_22  H5   C5   C4   C3   180.00   0.0  0
 OIR  CONST_23  H7   C7   C8   C3   180.00   0.0  0
 OIR  CONST_24  H8   C8   C3   C4   180.00   0.0  0
 OIR  CONST_25  H6   C6   C5   C4   180.00   0.0  0
 OIR  CONST_26  H4   C4   C5   C6   180.00   0.0  0
 OIR  CONST_27  C2   N9   C18  O19    0.00   0.0  0
 OIR  CONST_28  C2   N9   C18  C20  180.00   0.0  0
 OIR  CONST_29  C14  N13  C11  C2   180.00   0.0  0
 OIR  CONST_30  C14  N13  C11  O12    0.00   0.0  0
 OIR  CONST_31  HN9  N9   C18  O19  180.00   0.0  0
 OIR  CONST_32  H13  N13  C11  C2     0.00   0.0  0
 OIR  Var_01    C24  C23  C21  C20   80.25  30.0  2
 OIR  Var_02    C4   C3   C1   C2   104.09  30.0  2

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
 OIR  chir_01  C20  C18  C21  S26  negativ
 OIR  chir_02  C2   N9   C11  C1   positiv
 OIR  chir_03  C14  N13  C15  C19  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
 OIR  plan-1  C21  0.020
 OIR  plan-1  C23  0.020
 OIR  plan-1  C24  0.020
 OIR  plan-1  C25  0.020
 OIR  plan-1  C26  0.020
 OIR  plan-1  C27  0.020
 OIR  plan-1  C28  0.020
 OIR  plan-1  H24  0.020
 OIR  plan-1  H25  0.020
 OIR  plan-1  H1   0.020
 OIR  plan-1  H27  0.020
 OIR  plan-1  H28  0.020
 OIR  plan-2  C1   0.020
 OIR  plan-2  C3   0.020
 OIR  plan-2  C4   0.020
 OIR  plan-2  C5   0.020
 OIR  plan-2  C6   0.020
 OIR  plan-2  C7   0.020
 OIR  plan-2  C8   0.020
 OIR  plan-2  H4   0.020
 OIR  plan-2  H5   0.020
 OIR  plan-2  H6   0.020
 OIR  plan-2  H7   0.020
 OIR  plan-2  H8   0.020
 OIR  plan-3  O19  0.020
 OIR  plan-3  C18  0.020
 OIR  plan-3  C20  0.020
 OIR  plan-3  N9   0.020
 OIR  plan-3  C2   0.020
 OIR  plan-3  HN9  0.020
 OIR  plan-4  C2   0.020
 OIR  plan-4  C11  0.020
 OIR  plan-4  O12  0.020
 OIR  plan-4  N13  0.020
 OIR  plan-4  C14  0.020
 OIR  plan-4  H13  0.020
 OIR  plan-5  C14  0.020
 OIR  plan-5  C15  0.020
 OIR  plan-5  O16  0.020
 OIR  plan-5  O17  0.020

