# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 22:58:18 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: (2~{S})-4-methyl-~{N}-[(1~{R})-2-(oxidanylamino)-2-oxidanylidene-1-phenyl-ethyl]-2-[(phenylmethyl)carbamoylamino]pentanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](NC(=O)NCc1ccccc1)C(=O)N[C@@H](C(=O)NO)c2ccccc2
#
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
 89X  89X  (2~{S})-4-methyl-~{N}-[(1~{R})-2-(oxidanylamino)-2-oxidanylidene-1-phenyl-ethyl]-2-[(phenylmethyl)carbamoylamino]pentanamide  ligand  58  30  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_89X
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
 89X  O1   O  OH1   0  -0.541  -3.6337   4.0235   0.4620
 89X  N    N  NH1   0  -0.369  -3.5918   2.7039   0.7866
 89X  CA   C  C     0   0.538  -2.9388   1.8324   0.0064
 89X  O2   O  O     0  -0.462  -2.2411   2.1428  -0.9375
 89X  CB   C  CH1   0  -0.249  -3.2106   0.3717   0.3896
 89X  N2   N  NH1   0  -0.646  -2.0215  -0.4185   0.2078
 89X  C3   C  C     0   0.587  -0.9099  -0.1795   0.9229
 89X  O    O  O     0  -0.486  -0.8450   0.7222   1.7413
 89X  C4   C  CH1   0  -0.216   0.2379  -1.1596   0.6762
 89X  C5   C  CH2   0  -0.438  -0.0453  -2.4711   1.4156
 89X  C6   C  CH1   0  -0.230   1.0434  -3.5382   1.2803
 89X  C7   C  CH3   0  -0.653   0.6128  -4.7958   2.0294
 89X  C8   C  CH3   0  -0.665   1.3581  -3.8606  -0.1758
 89X  N3   N  NH1   0  -0.674   1.4922  -0.6094   1.1024
 89X  C9   C  C     0   0.757   2.0094   0.4789   0.4612
 89X  O4   O  O     0  -0.539   1.5393   0.8922  -0.5929
 89X  N4   N  NH1   0  -0.670   3.0782   1.0462   1.0775
 89X  C10  C  CH2   0  -0.388   3.8652   2.0940   0.4686
 89X  C11  C  CR6   0   0.124   5.0661   1.5793  -0.2884
 89X  C12  C  CR16  0  -0.308   6.3507   1.7858   0.2033
 89X  C13  C  CR16  0  -0.242   7.4614   1.3014  -0.4784
 89X  C14  C  CR16  0  -0.267   7.2966   0.6016  -1.6648
 89X  C15  C  CR16  0  -0.241   6.0163   0.3887  -2.1643
 89X  C16  C  CR16  0  -0.297   4.9106   0.8735  -1.4815
 89X  CG   C  CR6   0   0.102  -4.3368  -0.1501  -0.4721
 89X  CD1  C  CR16  0  -0.315  -5.5572  -0.4813   0.1062
 89X  CE1  C  CR16  0  -0.238  -6.6042  -0.9489  -0.6775
 89X  CZ   C  CR16  0  -0.260  -6.4371  -1.0916  -2.0477
 89X  CE2  C  CR16  0  -0.238  -5.2195  -0.7633  -2.6310
 89X  CD2  C  CR16  0  -0.287  -4.1751  -0.2915  -1.8494
 89X  H1   H  HOH1  0   0.479  -2.8896   4.4413   0.9160
 89X  H2   H  HNH1  0   0.417  -4.1781   2.4300   1.5617
 89X  H3   H  HCH1  0   0.295  -3.5244   0.3208   1.4376
 89X  H4   H  HNH1  0   0.410  -2.0301  -1.1572  -0.4772
 89X  H5   H  HCH1  0   0.272   0.2874  -1.3613  -0.3970
 89X  H6   H  HCH2  0   0.244  -0.2077  -2.2541   2.4770
 89X  H7   H  HCH2  0   0.242  -0.9889  -2.8806   1.0416
 89X  H8   H  HCH1  0   0.223   1.9591  -3.1673   1.7522
 89X  H9   H  HCH3  0   0.215  -0.2911  -5.2233   1.5881
 89X  H10  H  HCH3  0   0.229   1.3912  -5.5592   1.9949
 89X  H11  H  HCH3  0   0.226   0.4014  -4.5858   3.0794
 89X  H12  H  HCH3  0   0.231   1.7554  -2.9983  -0.7126
 89X  H13  H  HCH3  0   0.232   2.1046  -4.6535  -0.2438
 89X  H14  H  HCH3  0   0.216   0.4646  -4.2024  -0.7048
 89X  H15  H  HNH1  0   0.390   1.7483  -0.7602   2.0660
 89X  H16  H  HNH1  0   0.392   3.4961   0.5644   1.8578
 89X  H17  H  HCH2  0   0.263   3.2168   2.6689  -0.1911
 89X  H18  H  HCH2  0   0.263   4.1948   2.7724   1.2570
 89X  H19  H  HCR6  0   0.251   6.4870   2.3333   1.1290
 89X  H20  H  HCR6  0   0.254   8.4536   1.4708  -0.0805
 89X  H21  H  HCR6  0   0.255   8.1592   0.2256  -2.1998
 89X  H22  H  HCR6  0   0.254   5.8796  -0.1545  -3.0908
 89X  H23  H  HCR6  0   0.251   3.9181   0.7060  -1.8817
 89X  H24  H  HCR6  0   0.259  -5.6916  -0.3791   1.1763
 89X  H25  H  HCR6  0   0.262  -7.5479  -1.2067  -0.2149
 89X  H26  H  HCR6  0   0.261  -7.2518  -1.4576  -2.6588
 89X  H27  H  HCR6  0   0.261  -5.0829  -0.8708  -3.6991
 89X  H28  H  HCR6  0   0.263  -3.2352  -0.0286  -2.3191

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
 89X  CZ   CE1  aromatic  1.388  0.020  1.388
 89X  CZ   CE2  aromatic  1.389  0.020  1.389
 89X  CE1  CD1  aromatic  1.389  0.020  1.389
 89X  C13  C12  aromatic  1.390  0.020  1.390
 89X  C13  C14  aromatic  1.387  0.020  1.387
 89X  CE2  CD2  aromatic  1.387  0.020  1.387
 89X  C12  C11  aromatic  1.391  0.020  1.391
 89X  CD1  CG   aromatic  1.390  0.020  1.390
 89X  C14  C15  aromatic  1.391  0.020  1.391
 89X  CD2  CG   aromatic  1.394  0.020  1.394
 89X  O4   C9   double    1.226  0.020  1.226
 89X  C11  C10  single    1.510  0.020  1.510
 89X  C11  C16  aromatic  1.395  0.020  1.395
 89X  CG   CB   single    1.511  0.020  1.511
 89X  C10  N4   single    1.445  0.020  1.445
 89X  C15  C16  aromatic  1.387  0.020  1.387
 89X  C9   N4   single    1.358  0.020  1.358
 89X  C9   N3   single    1.365  0.020  1.365
 89X  CB   N2   single    1.439  0.020  1.439
 89X  CB   CA   single    1.534  0.020  1.534
 89X  N2   C3   single    1.343  0.020  1.343
 89X  O    C3   double    1.220  0.020  1.220
 89X  C3   C4   single    1.529  0.020  1.529
 89X  C4   N3   single    1.434  0.020  1.434
 89X  C4   C5   single    1.532  0.020  1.532
 89X  CA   O2   double    1.214  0.020  1.214
 89X  CA   N    single    1.340  0.020  1.340
 89X  N    O1   single    1.360  0.020  1.360
 89X  C5   C6   single    1.531  0.020  1.531
 89X  C6   C7   single    1.526  0.020  1.526
 89X  C6   C8   single    1.524  0.020  1.524
 89X  O1   H1   single    0.850  0.020  0.980
 89X  N    H2   single    0.860  0.020  1.020
 89X  CB   H3   single    0.970  0.020  1.090
 89X  N2   H4   single    0.860  0.020  1.020
 89X  C4   H5   single    0.970  0.020  1.090
 89X  C5   H6   single    0.970  0.020  1.090
 89X  C5   H7   single    0.970  0.020  1.090
 89X  C6   H8   single    0.970  0.020  1.090
 89X  C7   H9   single    0.970  0.020  1.090
 89X  C7   H10  single    0.970  0.020  1.090
 89X  C7   H11  single    0.970  0.020  1.090
 89X  C8   H12  single    0.970  0.020  1.090
 89X  C8   H13  single    0.970  0.020  1.090
 89X  C8   H14  single    0.970  0.020  1.090
 89X  N3   H15  single    0.890  0.020  1.040
 89X  N4   H16  single    0.860  0.020  1.020
 89X  C10  H17  single    0.970  0.020  1.090
 89X  C10  H18  single    0.970  0.020  1.090
 89X  C12  H19  single    0.930  0.020  1.080
 89X  C13  H20  single    0.930  0.020  1.080
 89X  C14  H21  single    0.930  0.020  1.080
 89X  C15  H22  single    0.930  0.020  1.080
 89X  C16  H23  single    0.930  0.020  1.080
 89X  CD1  H24  single    0.930  0.020  1.080
 89X  CE1  H25  single    0.930  0.020  1.080
 89X  CZ   H26  single    0.930  0.020  1.080
 89X  CE2  H27  single    0.930  0.020  1.080
 89X  CD2  H28  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
 89X  H1   O1   N    106.48  3.000
 89X  H2   N    CA   123.62  3.000
 89X  H2   N    O1   115.39  3.000
 89X  CA   N    O1   120.48  3.000
 89X  CB   CA   O2   122.64  3.000
 89X  O2   CA   N    124.52  3.000
 89X  CB   CA   N    112.80  3.000
 89X  H3   CB   CG   108.43  3.000
 89X  H3   CB   N2   109.39  3.000
 89X  CG   CB   N2   110.74  3.000
 89X  H3   CB   CA   109.51  3.000
 89X  N2   CB   CA   110.17  3.000
 89X  CG   CB   CA   108.56  3.000
 89X  H4   N2   C3   119.96  3.000
 89X  H4   N2   CB   118.78  3.000
 89X  C3   N2   CB   121.26  3.000
 89X  C4   C3   O    122.83  3.000
 89X  C4   C3   N2   114.92  3.000
 89X  O    C3   N2   122.20  3.000
 89X  H5   C4   N3   108.83  3.000
 89X  H5   C4   C5   108.93  3.000
 89X  N3   C4   C5   110.28  3.000
 89X  H5   C4   C3   108.09  3.000
 89X  C5   C4   C3   109.39  3.000
 89X  N3   C4   C3   111.26  3.000
 89X  H7   C5   H6   106.11  3.000
 89X  H7   C5   C6   108.80  3.000
 89X  H6   C5   C6   109.22  3.000
 89X  H7   C5   C4   108.35  3.000
 89X  H6   C5   C4   108.99  3.000
 89X  C6   C5   C4   115.00  3.000
 89X  H8   C6   C8   108.11  3.000
 89X  H8   C6   C7   107.68  3.000
 89X  C8   C6   C7   110.67  3.000
 89X  H8   C6   C5   108.70  3.000
 89X  C8   C6   C5   112.26  3.000
 89X  C7   C6   C5   109.30  3.000
 89X  H11  C7   H10  107.65  3.000
 89X  H11  C7   H9   107.67  3.000
 89X  H10  C7   H9   107.68  3.000
 89X  H11  C7   C6   111.62  3.000
 89X  H10  C7   C6   111.09  3.000
 89X  H9   C7   C6   110.95  3.000
 89X  H14  C8   H13  107.57  3.000
 89X  H14  C8   H12  107.86  3.000
 89X  H13  C8   H12  107.13  3.000
 89X  H14  C8   C6   111.08  3.000
 89X  H13  C8   C6   110.76  3.000
 89X  H12  C8   C6   112.22  3.000
 89X  H15  N3   C9   118.16  3.000
 89X  H15  N3   C4   116.65  3.000
 89X  C9   N3   C4   119.84  3.000
 89X  N4   C9   O4   123.45  3.000
 89X  N4   C9   N3   114.71  3.000
 89X  O4   C9   N3   121.83  3.000
 89X  H16  N4   C10  116.56  3.000
 89X  H16  N4   C9   118.56  3.000
 89X  C10  N4   C9   122.70  3.000
 89X  H18  C10  H17  106.82  3.000
 89X  H18  C10  C11  109.51  3.000
 89X  H17  C10  C11  110.47  3.000
 89X  H18  C10  N4   108.11  3.000
 89X  H17  C10  N4   108.29  3.000
 89X  C11  C10  N4   113.41  3.000
 89X  C16  C11  C12  118.71  3.000
 89X  C16  C11  C10  120.83  3.000
 89X  C12  C11  C10  120.45  3.000
 89X  H19  C12  C13  119.61  3.000
 89X  H19  C12  C11  119.54  3.000
 89X  C13  C12  C11  120.85  3.000
 89X  H20  C13  C14  120.15  3.000
 89X  H20  C13  C12  119.84  3.000
 89X  C14  C13  C12  120.01  3.000
 89X  H21  C14  C15  120.20  3.000
 89X  H21  C14  C13  120.21  3.000
 89X  C15  C14  C13  119.59  3.000
 89X  H22  C15  C16  119.74  3.000
 89X  H22  C15  C14  120.02  3.000
 89X  C16  C15  C14  120.24  3.000
 89X  H23  C16  C15  119.64  3.000
 89X  H23  C16  C11  119.76  3.000
 89X  C15  C16  C11  120.60  3.000
 89X  CD2  CG   CD1  119.25  3.000
 89X  CD2  CG   CB   120.80  3.000
 89X  CD1  CG   CB   119.95  3.000
 89X  H24  CD1  CE1  119.71  3.000
 89X  H24  CD1  CG   119.81  3.000
 89X  CE1  CD1  CG   120.47  3.000
 89X  H25  CE1  CZ   120.17  3.000
 89X  H25  CE1  CD1  119.76  3.000
 89X  CZ   CE1  CD1  120.06  3.000
 89X  H26  CZ   CE2  120.17  3.000
 89X  H26  CZ   CE1  120.11  3.000
 89X  CE2  CZ   CE1  119.72  3.000
 89X  H27  CE2  CD2  119.66  3.000
 89X  H27  CE2  CZ   120.10  3.000
 89X  CD2  CE2  CZ   120.24  3.000
 89X  H28  CD2  CE2  119.45  3.000
 89X  H28  CD2  CG   120.30  3.000
 89X  CE2  CD2  CG   120.25  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
 89X  CONST_01  C14  C13  C12  C11     0.00   0.0  0
 89X  CONST_02  C14  C15  C16  C11     0.00   0.0  0
 89X  CONST_03  C15  C14  C13  C12     0.00   0.0  0
 89X  CONST_04  C15  C16  C11  C12     0.00   0.0  0
 89X  CONST_05  C16  C11  C12  C13     0.00   0.0  0
 89X  CONST_06  C16  C15  C14  C13     0.00   0.0  0
 89X  CONST_07  CZ   CE1  CD1  CG      0.00   0.0  0
 89X  CONST_08  CZ   CE2  CD2  CG      0.00   0.0  0
 89X  CONST_09  CE2  CZ   CE1  CD1     0.00   0.0  0
 89X  CONST_10  CE2  CD2  CG   CD1     0.00   0.0  0
 89X  CONST_11  CD2  CE2  CZ   CE1     0.00   0.0  0
 89X  CONST_12  CD2  CG   CD1  CE1     0.00   0.0  0
 89X  CONST_13  CE1  CD1  CG   CB    180.00   0.0  0
 89X  CONST_14  CE2  CD2  CG   CB    180.00   0.0  0
 89X  CONST_15  C13  C12  C11  C10   180.00   0.0  0
 89X  CONST_16  C15  C16  C11  C10   180.00   0.0  0
 89X  CONST_17  H20  C13  C12  C11   180.00   0.0  0
 89X  CONST_18  H22  C15  C16  C11   180.00   0.0  0
 89X  CONST_19  H21  C14  C13  C12   180.00   0.0  0
 89X  CONST_20  H23  C16  C11  C12   180.00   0.0  0
 89X  CONST_21  H19  C12  C13  C14   180.00   0.0  0
 89X  CONST_22  H25  CE1  CD1  CG    180.00   0.0  0
 89X  CONST_23  H27  CE2  CD2  CG    180.00   0.0  0
 89X  CONST_24  H26  CZ   CE1  CD1   180.00   0.0  0
 89X  CONST_25  H28  CD2  CG   CD1   180.00   0.0  0
 89X  CONST_26  H24  CD1  CE1  CZ    180.00   0.0  0
 89X  CONST_27  CB   CA   N    O1    180.00   0.0  0
 89X  CONST_28  O2   CA   N    O1      0.00   0.0  0
 89X  CONST_29  O    C3   N2   CB      0.00   0.0  0
 89X  CONST_30  C4   C3   N2   CB    180.00   0.0  0
 89X  CONST_31  O4   C9   N3   C4      0.00   0.0  0
 89X  CONST_32  C10  N4   C9   O4      0.00   0.0  0
 89X  CONST_33  N4   C9   N3   C4    180.00   0.0  0
 89X  CONST_34  C10  N4   C9   N3    180.00   0.0  0
 89X  CONST_35  H2   N    CA   O2    180.00   0.0  0
 89X  CONST_36  H4   N2   C3   O     180.00   0.0  0
 89X  CONST_37  H16  N4   C9   O4    180.00   0.0  0
 89X  Var_01    C12  C11  C10  N4   -109.21  30.0  2
 89X  Var_02    C11  C10  N4   C9    -93.08  30.0  1
 89X  Var_03    C7   C6   C5   C4   -178.42  30.0  3
 89X  Var_04    H9   C7   C6   C5     63.15  30.0  3
 89X  Var_05    H12  C8   C6   C5     62.79  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
 89X  chir_01  CB  CG  N2  CA  negativ
 89X  chir_02  C4  N3  C3  C5  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
 89X  plan-1  C10  0.020
 89X  plan-1  C11  0.020
 89X  plan-1  C12  0.020
 89X  plan-1  C13  0.020
 89X  plan-1  C14  0.020
 89X  plan-1  C15  0.020
 89X  plan-1  C16  0.020
 89X  plan-1  H19  0.020
 89X  plan-1  H20  0.020
 89X  plan-1  H21  0.020
 89X  plan-1  H22  0.020
 89X  plan-1  H23  0.020
 89X  plan-2  CB   0.020
 89X  plan-2  CG   0.020
 89X  plan-2  CD1  0.020
 89X  plan-2  CE1  0.020
 89X  plan-2  CZ   0.020
 89X  plan-2  CE2  0.020
 89X  plan-2  CD2  0.020
 89X  plan-2  H24  0.020
 89X  plan-2  H25  0.020
 89X  plan-2  H26  0.020
 89X  plan-2  H27  0.020
 89X  plan-2  H28  0.020
 89X  plan-3  O1   0.020
 89X  plan-3  N    0.020
 89X  plan-3  CA   0.020
 89X  plan-3  O2   0.020
 89X  plan-3  CB   0.020
 89X  plan-3  H2   0.020
 89X  plan-4  CB   0.020
 89X  plan-4  N2   0.020
 89X  plan-4  C3   0.020
 89X  plan-4  O    0.020
 89X  plan-4  C4   0.020
 89X  plan-4  H4   0.020
 89X  plan-5  C4   0.020
 89X  plan-5  N3   0.020
 89X  plan-5  C9   0.020
 89X  plan-5  O4   0.020
 89X  plan-5  N4   0.020
 89X  plan-5  C10  0.020
 89X  plan-5  H15  0.020
 89X  plan-5  H16  0.020

