# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 20:22:01 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: ~{N}-[(1~{R})-1-(4-methoxyphenyl)-2-oxidanylidene-2-[(4-propan-2-ylphenyl)amino]ethyl]-2-oxidanylidene-3~{H}-pyridine-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)[C@@H](NC(=O)C2=CCC(=O)N=C2)C(=O)Nc3ccc(cc3)C(C)C
#
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
 JUE  JUE  ~{N}-[(1~{R})-1-(4-methoxyphenyl)-2-oxidanylidene-2-[(4-propan-2-ylphenyl)amino]ethyl]-2-oxidanylidene-3~{H}-pyridine-5-carboxamide  ligand  56  31  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JUE
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
 JUE  C1   C  CH3   0  -0.437  -0.5872   6.3991  -0.8006
 JUE  O2   O  O2    0  -0.468  -0.7237   5.2148  -1.5614
 JUE  C3   C  CR6   0   0.377  -0.7227   4.0344  -0.9174
 JUE  C4   C  CR16  0  -0.374  -0.6280   3.8905   0.4633
 JUE  C5   C  CR16  0  -0.292  -0.6417   2.6175   1.0238
 JUE  C6   C  CR6   0   0.108  -0.7359   1.4829   0.2366
 JUE  C7   C  CR16  0  -0.267  -0.8335   1.6376  -1.1463
 JUE  C8   C  CR16  0  -0.329  -0.8281   2.8927  -1.7195
 JUE  C9   C  CH1   0  -0.280  -0.7217   0.1047   0.8582
 JUE  N10  N  NH1   0  -0.675  -1.8762  -0.6770   0.5023
 JUE  C11  C  C     0   0.573  -3.0900  -0.3995   1.0069
 JUE  O12  O  O     0  -0.469  -3.2840   0.5130   1.7939
 JUE  C13  C  CR6   0  -0.113  -4.2033  -1.2870   0.5602
 JUE  C14  C  CR16  0  -0.024  -4.1436  -2.0725  -0.6632
 JUE  N15  N  N     0  -0.421  -5.0214  -2.9131  -1.0714
 JUE  C16  C  CR6   0   0.479  -6.1431  -3.1535  -0.2774
 JUE  O17  O  O     0  -0.408  -6.8519  -4.1014  -0.5219
 JUE  C18  C  C     0  -0.654  -6.4604  -2.1986   0.8437
 JUE  C19  C  CR16  0  -0.140  -5.3430  -1.3300   1.2636
 JUE  C20  C  C     0   0.551   0.5235  -0.6734   0.4106
 JUE  O21  O  O     0  -0.456   0.4327  -1.7158  -0.2120
 JUE  N22  N  NH1   0  -0.736   1.6769  -0.0801   0.7714
 JUE  C23  C  CR6   0   0.359   2.9986  -0.4655   0.5068
 JUE  C24  C  CR16  0  -0.335   4.0005   0.4108   0.9211
 JUE  C25  C  CR16  0  -0.320   5.3348   0.1129   0.7010
 JUE  C26  C  CR6   0   0.163   5.7193  -1.0626   0.0635
 JUE  C27  C  CR16  0  -0.303   4.7075  -1.9293  -0.3405
 JUE  C28  C  CR16  0  -0.296   3.3648  -1.6521  -0.1290
 JUE  C29  C  CH1   0  -0.326   7.1755  -1.3762  -0.1870
 JUE  C30  C  CH3   0  -0.646   7.5934  -2.6928   0.4670
 JUE  C31  C  CH3   0  -0.642   7.4901  -1.3883  -1.6837
 JUE  H1   H  HCH3  0   0.229  -1.4140   6.5310  -0.0981
 JUE  H2   H  HCH3  0   0.230   0.3540   6.4196  -0.2454
 JUE  H3   H  HCH3  0   0.261  -0.5951   7.2243  -1.5079
 JUE  H4   H  HCR6  0   0.282  -0.5541   4.7465   1.1197
 JUE  H5   H  HCR6  0   0.263  -0.5824   2.5197   2.1013
 JUE  H6   H  HCR6  0   0.258  -0.9143   0.7691  -1.7897
 JUE  H7   H  HCR6  0   0.266  -0.9022   3.0021  -2.7943
 JUE  H8   H  HCH1  0   0.312  -0.6709   0.2157   1.9475
 JUE  H9   H  HNH1  0   0.412  -1.7024  -1.5151  -0.0338
 JUE  H10  H  HCR6  0   0.276  -3.2963  -1.9234  -1.3292
 JUE  H11  H  H     0   0.333  -7.2935  -1.5557   0.5255
 JUE  H12  H  H     0   0.322  -6.8578  -2.7515   1.6987
 JUE  H13  H  HCR6  0   0.300  -5.4766  -0.7191   2.1476
 JUE  H14  H  HNH1  0   0.417   1.5884   0.7954   1.2677
 JUE  H15  H  HCR6  0   0.268   3.7351   1.3362   1.4195
 JUE  H16  H  HCR6  0   0.251   6.0899   0.8156   1.0333
 JUE  H17  H  HCR6  0   0.249   4.9627  -2.8579  -0.8376
 JUE  H18  H  HCR6  0   0.277   2.6230  -2.3611  -0.4579
 JUE  H19  H  HCH1  0   0.239   7.7635  -0.5742   0.2703
 JUE  H20  H  HCH3  0   0.219   7.0663  -3.5415   0.0266
 JUE  H21  H  HCH3  0   0.230   8.6624  -2.8651   0.3309
 JUE  H22  H  HCH3  0   0.231   7.3884  -2.6907   1.5381
 JUE  H23  H  HCH3  0   0.230   7.2279  -0.4391  -2.1522
 JUE  H24  H  HCH3  0   0.229   8.5537  -1.5647  -1.8517
 JUE  H25  H  HCH3  0   0.220   6.9398  -2.1791  -2.1977

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
 JUE  C31  C29  single    1.529  0.020  1.529
 JUE  O2   C1   single    1.414  0.020  1.414
 JUE  O2   C3   single    1.345  0.020  1.345
 JUE  C29  C26  single    1.510  0.020  1.510
 JUE  C29  C30  single    1.528  0.020  1.528
 JUE  C25  C26  aromatic  1.391  0.020  1.391
 JUE  C25  C24  aromatic  1.385  0.020  1.385
 JUE  C4   C3   aromatic  1.391  0.020  1.391
 JUE  C4   C5   aromatic  1.391  0.020  1.391
 JUE  C26  C27  aromatic  1.392  0.020  1.392
 JUE  C3   C8   aromatic  1.399  0.020  1.399
 JUE  C24  C23  aromatic  1.394  0.020  1.394
 JUE  C5   C6   aromatic  1.384  0.020  1.384
 JUE  C27  C28  aromatic  1.387  0.020  1.387
 JUE  C8   C7   aromatic  1.380  0.020  1.380
 JUE  C23  C28  aromatic  1.395  0.020  1.395
 JUE  C23  N22  single    1.402  0.020  1.402
 JUE  C6   C7   aromatic  1.395  0.020  1.395
 JUE  C6   C9   single    1.512  0.020  1.512
 JUE  N22  C20  single    1.346  0.020  1.346
 JUE  C20  C9   single    1.535  0.020  1.535
 JUE  C20  O21  double    1.218  0.020  1.218
 JUE  C9   N10  single    1.439  0.020  1.439
 JUE  N10  C11  single    1.343  0.020  1.343
 JUE  O12  C11  double    1.220  0.020  1.220
 JUE  C11  C13  single    1.492  0.020  1.492
 JUE  C14  C13  single    1.455  0.020  1.455
 JUE  C14  N15  double    1.282  0.020  1.282
 JUE  C13  C19  double    1.340  0.020  1.340
 JUE  N15  C16  single    1.395  0.020  1.395
 JUE  C19  C18  single    1.476  0.020  1.476
 JUE  C16  C18  single    1.506  0.020  1.506
 JUE  C16  O17  double    1.209  0.020  1.209
 JUE  C1   H1   single    0.970  0.020  1.090
 JUE  C1   H2   single    0.970  0.020  1.090
 JUE  C1   H3   single    0.970  0.020  1.090
 JUE  C4   H4   single    0.930  0.020  1.080
 JUE  C5   H5   single    0.930  0.020  1.080
 JUE  C7   H6   single    0.930  0.020  1.080
 JUE  C8   H7   single    0.930  0.020  1.080
 JUE  C9   H8   single    0.970  0.020  1.090
 JUE  N10  H9   single    0.860  0.020  1.020
 JUE  C14  H10  single    0.930  0.020  1.080
 JUE  C18  H11  single    0.970  0.020  1.090
 JUE  C18  H12  single    0.970  0.020  1.090
 JUE  C19  H13  single    0.930  0.020  1.080
 JUE  N22  H14  single    0.860  0.020  1.020
 JUE  C24  H15  single    0.930  0.020  1.080
 JUE  C25  H16  single    0.930  0.020  1.080
 JUE  C27  H17  single    0.930  0.020  1.080
 JUE  C28  H18  single    0.930  0.020  1.080
 JUE  C29  H19  single    0.970  0.020  1.090
 JUE  C30  H20  single    0.970  0.020  1.090
 JUE  C30  H21  single    0.970  0.020  1.090
 JUE  C30  H22  single    0.970  0.020  1.090
 JUE  C31  H23  single    0.970  0.020  1.090
 JUE  C31  H24  single    0.970  0.020  1.090
 JUE  C31  H25  single    0.970  0.020  1.090

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
 JUE  H3   C1   H2   108.82  3.000
 JUE  H3   C1   H1   108.74  3.000
 JUE  H2   C1   H1   108.83  3.000
 JUE  H3   C1   O2   106.56  3.000
 JUE  H2   C1   O2   111.85  3.000
 JUE  H1   C1   O2   111.95  3.000
 JUE  C3   O2   C1   118.52  3.000
 JUE  C8   C3   C4   119.31  3.000
 JUE  C8   C3   O2   116.21  3.000
 JUE  C4   C3   O2   124.47  3.000
 JUE  H4   C4   C5   118.73  3.000
 JUE  H4   C4   C3   121.68  3.000
 JUE  C5   C4   C3   119.59  3.000
 JUE  H5   C5   C6   119.69  3.000
 JUE  H5   C5   C4   118.87  3.000
 JUE  C6   C5   C4   121.44  3.000
 JUE  C9   C6   C7   120.62  3.000
 JUE  C9   C6   C5   120.85  3.000
 JUE  C7   C6   C5   118.54  3.000
 JUE  H6   C7   C8   118.85  3.000
 JUE  H6   C7   C6   120.33  3.000
 JUE  C8   C7   C6   120.83  3.000
 JUE  H7   C8   C7   120.26  3.000
 JUE  H7   C8   C3   119.45  3.000
 JUE  C7   C8   C3   120.29  3.000
 JUE  H8   C9   C20  107.67  3.000
 JUE  H8   C9   N10  109.75  3.000
 JUE  C20  C9   N10  107.66  3.000
 JUE  H8   C9   C6   108.46  3.000
 JUE  N10  C9   C6   112.71  3.000
 JUE  C20  C9   C6   110.47  3.000
 JUE  H9   N10  C11  121.76  3.000
 JUE  H9   N10  C9   116.36  3.000
 JUE  C11  N10  C9   121.31  3.000
 JUE  C13  C11  O12  121.27  3.000
 JUE  C13  C11  N10  116.03  3.000
 JUE  O12  C11  N10  122.70  3.000
 JUE  C19  C13  C14  117.32  3.000
 JUE  C19  C13  C11  119.77  3.000
 JUE  C14  C13  C11  122.83  3.000
 JUE  H10  C14  N15  115.35  3.000
 JUE  H10  C14  C13  118.21  3.000
 JUE  N15  C14  C13  126.41  3.000
 JUE  C16  N15  C14  118.83  3.000
 JUE  C18  C16  O17  121.61  3.000
 JUE  O17  C16  N15  119.44  3.000
 JUE  C18  C16  N15  118.93  3.000
 JUE  H12  C18  H11  104.29  3.000
 JUE  H12  C18  C19  110.50  3.000
 JUE  H11  C18  C19  108.17  3.000
 JUE  H12  C18  C16  109.76  3.000
 JUE  H11  C18  C16  108.36  3.000
 JUE  C19  C18  C16  115.16  3.000
 JUE  H13  C19  C18  118.08  3.000
 JUE  H13  C19  C13  121.03  3.000
 JUE  C18  C19  C13  120.88  3.000
 JUE  N22  C20  O21  125.33  3.000
 JUE  O21  C20  C9   121.51  3.000
 JUE  N22  C20  C9   113.17  3.000
 JUE  H14  N22  C23  114.43  3.000
 JUE  H14  N22  C20  116.01  3.000
 JUE  C23  N22  C20  129.49  3.000
 JUE  C28  C23  C24  118.78  3.000
 JUE  C28  C23  N22  124.56  3.000
 JUE  C24  C23  N22  116.66  3.000
 JUE  H15  C24  C25  119.52  3.000
 JUE  H15  C24  C23  119.82  3.000
 JUE  C25  C24  C23  120.66  3.000
 JUE  H16  C25  C26  119.72  3.000
 JUE  H16  C25  C24  118.89  3.000
 JUE  C26  C25  C24  121.39  3.000
 JUE  C29  C26  C27  121.55  3.000
 JUE  C27  C26  C25  117.26  3.000
 JUE  C29  C26  C25  121.19  3.000
 JUE  H17  C27  C28  117.97  3.000
 JUE  H17  C27  C26  119.70  3.000
 JUE  C28  C27  C26  122.33  3.000
 JUE  H18  C28  C27  119.23  3.000
 JUE  H18  C28  C23  121.20  3.000
 JUE  C27  C28  C23  119.57  3.000
 JUE  H19  C29  C31  107.70  3.000
 JUE  H19  C29  C30  107.79  3.000
 JUE  C31  C29  C30  110.84  3.000
 JUE  H19  C29  C26  107.24  3.000
 JUE  C30  C29  C26  111.81  3.000
 JUE  C31  C29  C26  111.24  3.000
 JUE  H22  C30  H21  107.88  3.000
 JUE  H22  C30  H20  107.88  3.000
 JUE  H21  C30  H20  107.45  3.000
 JUE  H22  C30  C29  111.55  3.000
 JUE  H21  C30  C29  110.51  3.000
 JUE  H20  C30  C29  111.41  3.000
 JUE  H25  C31  H24  107.56  3.000
 JUE  H25  C31  H23  107.87  3.000
 JUE  H24  C31  H23  108.00  3.000
 JUE  H25  C31  C29  111.26  3.000
 JUE  H24  C31  C29  110.64  3.000
 JUE  H23  C31  C29  111.35  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
 JUE  CONST_01  C6   C5   C4   C3      0.00   0.0  0
 JUE  CONST_02  C6   C7   C8   C3      0.00   0.0  0
 JUE  CONST_03  C7   C8   C3   C4      0.00   0.0  0
 JUE  CONST_04  C7   C6   C5   C4      0.00   0.0  0
 JUE  CONST_05  C8   C3   C4   C5      0.00   0.0  0
 JUE  CONST_06  C8   C7   C6   C5      0.00   0.0  0
 JUE  CONST_07  C26  C25  C24  C23     0.00   0.0  0
 JUE  CONST_08  C26  C27  C28  C23     0.00   0.0  0
 JUE  CONST_09  C27  C26  C25  C24     0.00   0.0  0
 JUE  CONST_10  C27  C28  C23  C24     0.00   0.0  0
 JUE  CONST_11  C28  C27  C26  C25     0.00   0.0  0
 JUE  CONST_12  C28  C23  C24  C25     0.00   0.0  0
 JUE  CONST_13  C5   C4   C3   O2    180.00   0.0  0
 JUE  CONST_14  C7   C8   C3   O2    180.00   0.0  0
 JUE  CONST_15  C9   C6   C5   C4    180.00   0.0  0
 JUE  CONST_16  C9   C6   C7   C8    180.00   0.0  0
 JUE  CONST_17  C25  C24  C23  N22   180.00   0.0  0
 JUE  CONST_18  C27  C28  C23  N22   180.00   0.0  0
 JUE  CONST_19  C29  C26  C25  C24   180.00   0.0  0
 JUE  CONST_20  C29  C26  C27  C28   180.00   0.0  0
 JUE  CONST_21  H5   C5   C4   C3    180.00   0.0  0
 JUE  CONST_22  H6   C7   C8   C3    180.00   0.0  0
 JUE  CONST_23  H7   C8   C3   C4    180.00   0.0  0
 JUE  CONST_24  H4   C4   C5   C6    180.00   0.0  0
 JUE  CONST_25  H16  C25  C24  C23   180.00   0.0  0
 JUE  CONST_26  H17  C27  C28  C23   180.00   0.0  0
 JUE  CONST_27  H18  C28  C23  C24   180.00   0.0  0
 JUE  CONST_28  H15  C24  C25  C26   180.00   0.0  0
 JUE  CONST_29  C24  C23  N22  C20   180.00   0.0  0
 JUE  CONST_30  C28  C23  N22  C20     0.00   0.0  0
 JUE  CONST_31  H14  N22  C23  C24     0.00   0.0  0
 JUE  CONST_32  C23  N22  C20  C9    180.00   0.0  0
 JUE  CONST_33  C13  C11  N10  C9    180.00   0.0  0
 JUE  CONST_34  C23  N22  C20  O21     0.00   0.0  0
 JUE  CONST_35  H9   N10  C11  C13     0.00   0.0  0
 JUE  CONST_36  O12  C11  N10  C9      0.00   0.0  0
 JUE  Var_01    C16  C18  C19  C13     8.73  30.0  1
 JUE  Var_02    C18  C19  C13  C14     3.17  30.0  1
 JUE  Var_03    C18  C16  N15  C14    14.72  30.0  1
 JUE  Var_04    C19  C13  C14  N15    -7.69  30.0  1
 JUE  Var_05    C19  C18  C16  N15   -17.93  30.0  1
 JUE  Var_06    H10  C14  N15  C16  -179.59  30.0  1
 JUE  Var_07    C4   C3   O2   C1      1.62  30.0  2
 JUE  Var_08    C14  C13  C11  N10   -21.56  30.0  2
 JUE  Var_09    C31  C29  C26  C25  -113.99  30.0  2
 JUE  Var_10    H1   C1   O2   C3    -62.22  30.0  3
 JUE  Var_11    H23  C31  C29  C26    56.97  30.0  3
 JUE  Var_12    H20  C30  C29  C26    64.46  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
 JUE  chir_01  C9  C6  C20  N10  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
 JUE  plan-1  O2   0.020
 JUE  plan-1  C3   0.020
 JUE  plan-1  C4   0.020
 JUE  plan-1  C5   0.020
 JUE  plan-1  C6   0.020
 JUE  plan-1  C7   0.020
 JUE  plan-1  C8   0.020
 JUE  plan-1  C9   0.020
 JUE  plan-1  H4   0.020
 JUE  plan-1  H5   0.020
 JUE  plan-1  H6   0.020
 JUE  plan-1  H7   0.020
 JUE  plan-2  N22  0.020
 JUE  plan-2  C23  0.020
 JUE  plan-2  C24  0.020
 JUE  plan-2  C25  0.020
 JUE  plan-2  C26  0.020
 JUE  plan-2  C27  0.020
 JUE  plan-2  C28  0.020
 JUE  plan-2  C29  0.020
 JUE  plan-2  H15  0.020
 JUE  plan-2  H16  0.020
 JUE  plan-2  H17  0.020
 JUE  plan-2  H18  0.020
 JUE  plan-3  C9   0.020
 JUE  plan-3  C20  0.020
 JUE  plan-3  O21  0.020
 JUE  plan-3  N22  0.020
 JUE  plan-3  C23  0.020
 JUE  plan-3  H14  0.020
 JUE  plan-4  C9   0.020
 JUE  plan-4  N10  0.020
 JUE  plan-4  C11  0.020
 JUE  plan-4  O12  0.020
 JUE  plan-4  C13  0.020
 JUE  plan-4  H9   0.020
 JUE  plan-5  N15  0.020
 JUE  plan-5  C16  0.020
 JUE  plan-5  O17  0.020
 JUE  plan-5  C18  0.020

