# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 15:17:05 2020
#   Inital geometry file: a 162 line input string
#   Ligand name: N-{(3S,4S)-4-[(E)-2-{4-[(2-fluoro-6-hydroxy-3-methoxyphenyl)carbonyl]phenyl}ethenyl]azepan-3-yl}pyridine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(O)c(c1F)C(=O)c2ccc(\C=C\[C@@H]3CCCNC[C@H]3NC(=O)c4ccncc4)cc2
#
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
 I08  I08  N-{(3S,4S)-4-[(E)-2-{4-[(2-fluoro-6-hydroxy-3-methoxyphenyl)carbonyl]phenyl}ethenyl]azepan-3-yl}pyridine-4-carboxamide  ligand  64  36  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_I08
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
 I08  F96   F  F     0  -0.298   4.7244  -1.4792  -1.1008
 I08  C76   C  CR6   0   0.502   4.9850  -0.6419  -0.0882
 I08  C75   C  CR6   0   0.220   5.7410  -1.1129   0.9842
 I08  O95   O  O2    0  -0.469   6.1666  -2.3873   0.9102
 I08  C98   C  CH3   0  -0.439   6.8854  -2.9056   2.0122
 I08  C74   C  CR16  0  -0.366   5.9832  -0.2268   2.0243
 I08  C73   C  CR16  0  -0.381   5.4869   1.0727   1.9923
 I08  C72   C  CR6   0   0.369   4.7314   1.5109   0.9176
 I08  O92   O  OH1   0  -0.622   4.2200   2.7528   0.8127
 I08  C71   C  CR6   0  -0.392   4.4727   0.6347  -0.1401
 I08  C61   C  C     0   0.386   3.7011   1.0951  -1.3424
 I08  O62   O  O     0  -0.371   4.2816   1.3085  -2.3848
 I08  C54   C  CR6   0  -0.042   2.2438   1.2639  -1.1974
 I08  C55   C  CR16  0  -0.245   1.5077   1.8505  -2.2281
 I08  C56   C  CR16  0  -0.310   0.1408   2.0054  -2.1085
 I08  C53   C  CR16  0  -0.236   1.5699   0.8256  -0.0560
 I08  C52   C  CR16  0  -0.307   0.2012   0.9694   0.0543
 I08  C51   C  CR6   0   0.152  -0.5406   1.5771  -0.9636
 I08  C42   C  C1    0  -0.310  -1.9906   1.7585  -0.8916
 I08  C41   C  C1    0  -0.158  -2.7528   1.5624   0.1854
 I08  C37   C  CH1   0  -0.317  -4.2407   1.7186   0.2088
 I08  C36   C  CH2   0  -0.427  -4.6104   2.7298   1.3075
 I08  C35   C  CH2   0  -0.407  -6.0570   3.2089   1.3379
 I08  C34   C  CH2   0  -0.311  -7.1095   2.1095   1.2969
 I08  N33   N  NH1   0  -0.607  -7.0936   1.4338   0.0089
 I08  C32   C  CH2   0  -0.266  -6.3283   0.2118  -0.0659
 I08  C31   C  CH1   0  -0.077  -4.9043   0.3420   0.4857
 I08  N23   N  NH1   0  -0.642  -4.1226  -0.7538  -0.0533
 I08  C21   C  C     0   0.522  -3.3206  -1.5455   0.6748
 I08  O22   O  O     0  -0.472  -3.2910  -1.5655   1.8960
 I08  C14   C  CR6   0   0.052  -2.4232  -2.4476  -0.1175
 I08  C13   C  CR16  0  -0.342  -2.1414  -3.7208   0.3620
 I08  C12   C  CR16  0  -0.057  -1.2775  -4.5263  -0.3620
 I08  N11   N  N     0  -0.399  -0.6781  -4.1376  -1.4826
 I08  C16   C  CR16  0  -0.054  -0.9327  -2.9131  -1.9237
 I08  C15   C  CR16  0  -0.353  -1.7974  -2.0342  -1.2868
 I08  H981  H  HCH3  0   0.230   7.8179  -2.3624   2.1863
 I08  H982  H  HCH3  0   0.231   6.2907  -2.8880   2.9295
 I08  H983  H  HCH3  0   0.263   7.1232  -3.9374   1.7669
 I08  H74   H  HCR6  0   0.298   6.5638  -0.5320   2.8840
 I08  H73   H  HCR6  0   0.282   5.6999   1.7402   2.8186
 I08  H92   H  HOH1  0   0.481   4.4654   3.2853   1.5776
 I08  H55   H  HCR6  0   0.266   2.0077   2.1952  -3.1234
 I08  H56   H  HCR6  0   0.260  -0.4147   2.4684  -2.9149
 I08  H53   H  HCR6  0   0.260   2.1104   0.3462   0.7497
 I08  H52   H  HCR6  0   0.253  -0.2921   0.5896   0.9389
 I08  H42   H  H     0   0.251  -2.4669   2.0814  -1.8135
 I08  H41   H  H     0   0.259  -2.2962   1.2690   1.1289
 I08  H37   H  HCH1  0   0.247  -4.5714   2.0902  -0.7673
 I08  H361  H  HCH2  0   0.220  -4.3533   2.2844   2.2751
 I08  H362  H  HCH2  0   0.241  -3.9654   3.6062   1.2030
 I08  H351  H  HCH2  0   0.222  -6.1946   3.8131   2.2393
 I08  H352  H  HCH2  0   0.213  -6.2375   3.8723   0.4878
 I08  H341  H  HCH2  0   0.202  -6.9810   1.4175   2.1424
 I08  H342  H  HCH2  0   0.239  -8.0917   2.5665   1.4290
 I08  H33   H  HNH1  0   0.359  -8.0357   1.2426  -0.2991
 I08  H321  H  HCH2  0   0.213  -6.7979  -0.6337   0.4593
 I08  H322  H  HCH2  0   0.224  -6.2683  -0.0731  -1.1212
 I08  H31   H  HCH1  0   0.256  -4.9233   0.1970   1.5672
 I08  H23   H  HNH1  0   0.405  -4.0847  -0.8332  -1.0585
 I08  H13   H  HCR6  0   0.277  -2.5907  -4.0874   1.2746
 I08  H12   H  HCR6  0   0.271  -1.0571  -5.5299  -0.0171
 I08  H16   H  HCR6  0   0.272  -0.4242  -2.6064  -2.8306
 I08  H15   H  HCR6  0   0.279  -1.9412  -1.0417  -1.6943

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
 I08  F96  C76   single    1.340  0.020  1.340
 I08  C76  C75   aromatic  1.394  0.020  1.394
 I08  C76  C71   aromatic  1.377  0.020  1.377
 I08  C75  O95   single    1.346  0.020  1.346
 I08  C75  C74   aromatic  1.388  0.020  1.388
 I08  O95  C98   single    1.414  0.020  1.414
 I08  C98  H981  single    0.970  0.020  1.090
 I08  C98  H982  single    0.970  0.020  1.090
 I08  C98  H983  single    0.970  0.020  1.090
 I08  C74  C73   aromatic  1.391  0.020  1.391
 I08  C74  H74   single    0.930  0.020  1.080
 I08  C73  C72   aromatic  1.385  0.020  1.385
 I08  C73  H73   single    0.930  0.020  1.080
 I08  C72  O92   single    1.347  0.020  1.347
 I08  C72  C71   aromatic  1.398  0.020  1.398
 I08  O92  H92   single    0.850  0.020  0.980
 I08  C71  C61   single    1.501  0.020  1.501
 I08  C61  O62   double    1.212  0.020  1.212
 I08  C61  C54   single    1.474  0.020  1.474
 I08  C54  C55   aromatic  1.396  0.020  1.396
 I08  C54  C53   aromatic  1.396  0.020  1.396
 I08  C55  C56   aromatic  1.381  0.020  1.381
 I08  C55  H55   single    0.930  0.020  1.080
 I08  C56  C51   aromatic  1.400  0.020  1.400
 I08  C56  H56   single    0.930  0.020  1.080
 I08  C53  C52   aromatic  1.381  0.020  1.381
 I08  C53  H53   single    0.930  0.020  1.080
 I08  C52  C51   aromatic  1.398  0.020  1.398
 I08  C52  H52   single    0.930  0.020  1.080
 I08  C51  C42   single    1.463  0.020  1.463
 I08  C42  C41   double    1.334  0.020  1.334
 I08  C42  H42   single    0.930  0.020  1.080
 I08  C41  C37   single    1.496  0.020  1.496
 I08  C41  H41   single    0.930  0.020  1.080
 I08  C37  C36   single    1.538  0.020  1.538
 I08  C37  C31   single    1.553  0.020  1.553
 I08  C37  H37   single    0.970  0.020  1.090
 I08  C36  C35   single    1.524  0.020  1.524
 I08  C36  H361  single    0.970  0.020  1.090
 I08  C36  H362  single    0.970  0.020  1.090
 I08  C35  C34   single    1.522  0.020  1.522
 I08  C35  H351  single    0.970  0.020  1.090
 I08  C35  H352  single    0.970  0.020  1.090
 I08  C34  N33   single    1.455  0.020  1.455
 I08  C34  H341  single    0.970  0.020  1.090
 I08  C34  H342  single    0.970  0.020  1.090
 I08  N33  C32   single    1.444  0.020  1.444
 I08  N33  H33   single    0.890  0.020  1.040
 I08  C32  C31   single    1.533  0.020  1.533
 I08  C32  H321  single    0.970  0.020  1.090
 I08  C32  H322  single    0.970  0.020  1.090
 I08  C31  N23   single    1.450  0.020  1.450
 I08  C31  H31   single    0.970  0.020  1.090
 I08  N23  C21   single    1.342  0.020  1.342
 I08  N23  H23   single    0.860  0.020  1.020
 I08  C21  O22   double    1.222  0.020  1.222
 I08  C21  C14   single    1.499  0.020  1.499
 I08  C14  C13   aromatic  1.389  0.020  1.389
 I08  C14  C15   aromatic  1.389  0.020  1.389
 I08  C13  C12   aromatic  1.385  0.020  1.385
 I08  C13  H13   single    0.930  0.020  1.080
 I08  C12  N11   aromatic  1.329  0.020  1.329
 I08  C12  H12   single    0.930  0.020  1.080
 I08  N11  C16   aromatic  1.326  0.020  1.326
 I08  C16  C15   aromatic  1.388  0.020  1.388
 I08  C16  H16   single    0.930  0.020  1.080
 I08  C15  H15   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
 I08  C71   C76  C75   122.97  3.000
 I08  C71   C76  F96   118.60  3.000
 I08  C75   C76  F96   118.41  3.000
 I08  C74   C75  O95   126.21  3.000
 I08  C74   C75  C76   117.09  3.000
 I08  O95   C75  C76   116.70  3.000
 I08  C98   O95  C75   117.71  3.000
 I08  H983  C98  H982  108.88  3.000
 I08  H983  C98  H981  108.72  3.000
 I08  H982  C98  H981  108.81  3.000
 I08  H983  C98  O95   106.46  3.000
 I08  H982  C98  O95   111.81  3.000
 I08  H981  C98  O95   112.06  3.000
 I08  H74   C74  C73   118.26  3.000
 I08  H74   C74  C75   120.62  3.000
 I08  C73   C74  C75   121.12  3.000
 I08  H73   C73  C72   120.28  3.000
 I08  H73   C73  C74   119.19  3.000
 I08  C72   C73  C74   120.53  3.000
 I08  C71   C72  O92   116.66  3.000
 I08  C71   C72  C73   119.34  3.000
 I08  O92   C72  C73   124.00  3.000
 I08  H92   O92  C72   110.54  3.000
 I08  C61   C71  C72   120.60  3.000
 I08  C61   C71  C76   120.40  3.000
 I08  C72   C71  C76   118.94  3.000
 I08  C54   C61  O62   122.54  3.000
 I08  C54   C61  C71   117.68  3.000
 I08  O62   C61  C71   119.79  3.000
 I08  C53   C54  C55   118.75  3.000
 I08  C53   C54  C61   121.44  3.000
 I08  C55   C54  C61   119.79  3.000
 I08  H55   C55  C56   119.57  3.000
 I08  H55   C55  C54   120.08  3.000
 I08  C56   C55  C54   120.35  3.000
 I08  H56   C56  C51   119.35  3.000
 I08  H56   C56  C55   119.42  3.000
 I08  C51   C56  C55   121.23  3.000
 I08  H53   C53  C52   118.81  3.000
 I08  H53   C53  C54   120.44  3.000
 I08  C52   C53  C54   120.74  3.000
 I08  H52   C52  C51   120.39  3.000
 I08  H52   C52  C53   118.74  3.000
 I08  C51   C52  C53   120.86  3.000
 I08  C42   C51  C52   122.94  3.000
 I08  C42   C51  C56   119.00  3.000
 I08  C52   C51  C56   118.05  3.000
 I08  H42   C42  C41   118.56  3.000
 I08  H42   C42  C51   115.44  3.000
 I08  C41   C42  C51   126.00  3.000
 I08  H41   C41  C37   115.58  3.000
 I08  H41   C41  C42   119.99  3.000
 I08  C37   C41  C42   124.43  3.000
 I08  H37   C37  C31   109.30  3.000
 I08  H37   C37  C36   109.93  3.000
 I08  C31   C37  C36   110.64  3.000
 I08  H37   C37  C41   108.77  3.000
 I08  C31   C37  C41   109.58  3.000
 I08  C36   C37  C41   108.59  3.000
 I08  H362  C36  H361  105.77  3.000
 I08  H362  C36  C35   108.06  3.000
 I08  H361  C36  C35   109.44  3.000
 I08  H362  C36  C37   108.47  3.000
 I08  H361  C36  C37   107.89  3.000
 I08  C35   C36  C37   116.68  3.000
 I08  H352  C35  H351  106.54  3.000
 I08  H352  C35  C34   107.64  3.000
 I08  H351  C35  C34   109.52  3.000
 I08  H352  C35  C36   109.38  3.000
 I08  H351  C35  C36   108.02  3.000
 I08  C34   C35  C36   115.38  3.000
 I08  H342  C34  H341  105.99  3.000
 I08  H342  C34  N33   108.15  3.000
 I08  H341  C34  N33   112.77  3.000
 I08  H342  C34  C35   108.45  3.000
 I08  H341  C34  C35   110.66  3.000
 I08  N33   C34  C35   110.59  3.000
 I08  H33   N33  C32   108.58  3.000
 I08  H33   N33  C34   110.36  3.000
 I08  C32   N33  C34   116.41  3.000
 I08  H322  C32  H321  106.47  3.000
 I08  H322  C32  C31   108.55  3.000
 I08  H321  C32  C31   106.86  3.000
 I08  H322  C32  N33   107.41  3.000
 I08  H321  C32  N33   113.54  3.000
 I08  C31   C32  N33   113.70  3.000
 I08  H31   C31  N23   106.11  3.000
 I08  H31   C31  C32   109.22  3.000
 I08  N23   C31  C32   107.63  3.000
 I08  H31   C31  C37   107.57  3.000
 I08  N23   C31  C37   111.92  3.000
 I08  C32   C31  C37   114.09  3.000
 I08  H23   N23  C21   118.14  3.000
 I08  H23   N23  C31   116.75  3.000
 I08  C21   N23  C31   124.50  3.000
 I08  C14   C21  O22   120.27  3.000
 I08  C14   C21  N23   115.22  3.000
 I08  O22   C21  N23   124.51  3.000
 I08  C15   C14  C13   118.15  3.000
 I08  C15   C14  C21   122.38  3.000
 I08  C13   C14  C21   119.37  3.000
 I08  H13   C13  C12   120.21  3.000
 I08  H13   C13  C14   121.18  3.000
 I08  C12   C13  C14   118.62  3.000
 I08  H12   C12  N11   116.58  3.000
 I08  H12   C12  C13   119.93  3.000
 I08  N11   C12  C13   123.49  3.000
 I08  C16   N11  C12   117.64  3.000
 I08  H16   C16  C15   119.80  3.000
 I08  H16   C16  N11   116.71  3.000
 I08  C15   C16  N11   123.49  3.000
 I08  H15   C15  C16   119.39  3.000
 I08  H15   C15  C14   121.99  3.000
 I08  C16   C15  C14   118.59  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
 I08  CONST_01  C73   C74  C75  C76     0.00   0.0  0
 I08  CONST_02  C73   C72  C71  C76     0.00   0.0  0
 I08  CONST_03  C72   C71  C76  C75     0.00   0.0  0
 I08  CONST_04  C72   C73  C74  C75     0.00   0.0  0
 I08  CONST_05  C71   C76  C75  C74     0.00   0.0  0
 I08  CONST_06  C71   C72  C73  C74     0.00   0.0  0
 I08  CONST_07  C51   C56  C55  C54     0.00   0.0  0
 I08  CONST_08  C51   C52  C53  C54     0.00   0.0  0
 I08  CONST_09  C52   C53  C54  C55     0.00   0.0  0
 I08  CONST_10  C52   C51  C56  C55     0.00   0.0  0
 I08  CONST_11  C53   C54  C55  C56     0.00   0.0  0
 I08  CONST_12  C53   C52  C51  C56     0.00   0.0  0
 I08  CONST_13  N11   C12  C13  C14     0.00   0.0  0
 I08  CONST_14  N11   C16  C15  C14     0.00   0.0  0
 I08  CONST_15  C16   C15  C14  C13     0.00   0.0  0
 I08  CONST_16  C16   N11  C12  C13     0.00   0.0  0
 I08  CONST_17  C15   C14  C13  C12     0.00   0.0  0
 I08  CONST_18  C15   C16  N11  C12     0.00   0.0  0
 I08  CONST_19  C74   C75  C76  F96   180.00   0.0  0
 I08  CONST_20  C72   C71  C76  F96   180.00   0.0  0
 I08  CONST_21  O92   C72  C71  C76   180.00   0.0  0
 I08  CONST_22  C61   C71  C76  C75   180.00   0.0  0
 I08  CONST_23  C71   C76  C75  O95   180.00   0.0  0
 I08  CONST_24  C73   C74  C75  O95   180.00   0.0  0
 I08  CONST_25  O92   C72  C73  C74   180.00   0.0  0
 I08  CONST_26  C61   C71  C72  C73   180.00   0.0  0
 I08  CONST_27  C56   C55  C54  C61   180.00   0.0  0
 I08  CONST_28  C52   C53  C54  C61   180.00   0.0  0
 I08  CONST_29  C42   C51  C56  C55   180.00   0.0  0
 I08  CONST_30  C42   C51  C52  C53   180.00   0.0  0
 I08  CONST_31  C12   C13  C14  C21   180.00   0.0  0
 I08  CONST_32  C16   C15  C14  C21   180.00   0.0  0
 I08  CONST_33  H74   C74  C75  C76   180.00   0.0  0
 I08  CONST_34  H73   C73  C74  C75   180.00   0.0  0
 I08  CONST_35  H56   C56  C55  C54   180.00   0.0  0
 I08  CONST_36  H52   C52  C53  C54   180.00   0.0  0
 I08  CONST_37  H53   C53  C54  C55   180.00   0.0  0
 I08  CONST_38  H55   C55  C54  C53   180.00   0.0  0
 I08  CONST_39  H12   C12  C13  C14   180.00   0.0  0
 I08  CONST_40  H16   C16  C15  C14   180.00   0.0  0
 I08  CONST_41  H15   C15  C14  C13   180.00   0.0  0
 I08  CONST_42  H13   C13  C12  N11   180.00   0.0  0
 I08  CONST_43  C14   C21  N23  C31   180.00   0.0  0
 I08  CONST_44  O22   C21  N23  C31     0.00   0.0  0
 I08  CONST_45  H23   N23  C21  C14     0.00   0.0  0
 I08  Var_01    C54   C61  C71  C76   107.95  30.0  2
 I08  Var_02    C55   C54  C61  C71   171.82  30.0  2
 I08  Var_03    C37   C41  C42  C51  -178.05   0.0  2
 I08  Var_04    C74   C75  O95  C98     2.70  30.0  2
 I08  Var_05    C41   C42  C51  C56  -170.94  30.0  2
 I08  Var_06    C13   C14  C21  N23  -144.31  30.0  2
 I08  Var_07    H981  C98  O95  C75   -62.08  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
 I08  chir_01  C37  C41  C36  C31  positiv
 I08  chir_02  C31  N23  C37  C32  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
 I08  plan-1  F96  0.020
 I08  plan-1  C76  0.020
 I08  plan-1  C75  0.020
 I08  plan-1  O95  0.020
 I08  plan-1  C74  0.020
 I08  plan-1  C73  0.020
 I08  plan-1  C72  0.020
 I08  plan-1  O92  0.020
 I08  plan-1  C71  0.020
 I08  plan-1  C61  0.020
 I08  plan-1  H74  0.020
 I08  plan-1  H73  0.020
 I08  plan-2  C61  0.020
 I08  plan-2  C54  0.020
 I08  plan-2  C55  0.020
 I08  plan-2  C56  0.020
 I08  plan-2  C53  0.020
 I08  plan-2  C52  0.020
 I08  plan-2  C51  0.020
 I08  plan-2  C42  0.020
 I08  plan-2  H55  0.020
 I08  plan-2  H56  0.020
 I08  plan-2  H53  0.020
 I08  plan-2  H52  0.020
 I08  plan-3  C21  0.020
 I08  plan-3  C14  0.020
 I08  plan-3  C13  0.020
 I08  plan-3  C12  0.020
 I08  plan-3  N11  0.020
 I08  plan-3  C16  0.020
 I08  plan-3  C15  0.020
 I08  plan-3  H13  0.020
 I08  plan-3  H12  0.020
 I08  plan-3  H16  0.020
 I08  plan-3  H15  0.020
 I08  plan-4  C31  0.020
 I08  plan-4  N23  0.020
 I08  plan-4  C21  0.020
 I08  plan-4  O22  0.020
 I08  plan-4  C14  0.020
 I08  plan-4  H23  0.020
 I08  plan-5  C71  0.020
 I08  plan-5  C61  0.020
 I08  plan-5  O62  0.020
 I08  plan-5  C54  0.020
 I08  plan-6  C51  0.020
 I08  plan-6  C42  0.020
 I08  plan-6  C41  0.020
 I08  plan-6  C37  0.020
 I08  plan-6  H42  0.020
 I08  plan-6  H41  0.020

