# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 18:27:22 2020
#   Inital geometry file: a 159 line input string
#   Ligand name: (3R,4R)-3-[(pyridin-4-ylcarbonyl)amino]azepan-4-yl 4-[(2-fluoro-6-hydroxy-3-methoxyphenyl)carbonyl]benzoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(O)c(c1F)C(=O)c2ccc(cc2)C(=O)O[C@@H]3CCCNC[C@H]3NC(=O)c4ccncc4
#
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
 I01  I01  '(3R,4R)-3-[(pyridin-4-ylcarbonyl)amino]azepan-4-yl 4-[(2-fluoro-6-hydroxy-3-methoxyphenyl)carbonyl]benzoate'  ligand  63  37  .  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_I01
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
 I01  F96   F  F     0  -0.295   3.7952  -1.9822  -0.8565
 I01  C76   C  CR6   0   0.510   4.2426  -1.2764   0.1897
 I01  C75   C  CR6   0   0.221   4.8704  -1.9545   1.2334
 I01  O95   O  O2    0  -0.468   4.9919  -3.2879   1.1015
 I01  C98   C  CH3   0  -0.438   5.6395  -3.9938   2.1418
 I01  C74   C  CR16  0  -0.366   5.3095  -1.1932   2.3077
 I01  C73   C  CR16  0  -0.380   5.1238   0.1856   2.3379
 I01  C72   C  CR6   0   0.369   4.4902   0.8321   1.2900
 I01  O92   O  OH1   0  -0.622   4.2721   2.1604   1.2397
 I01  C71   C  CR6   0  -0.396   4.0410   0.0850   0.1991
 I01  C61   C  C     0   0.393   3.3927   0.7615  -0.9714
 I01  O62   O  O     0  -0.355   4.0148   0.9381  -1.9930
 I01  C54   C  CR6   0  -0.012   1.9763   1.1769  -0.8315
 I01  C55   C  CR16  0  -0.241   1.3576   1.8618  -1.8785
 I01  C56   C  CR16  0  -0.241   0.0204   2.1908  -1.7962
 I01  C53   C  CR16  0  -0.242   1.2437   0.8642   0.3094
 I01  C52   C  CR16  0  -0.248  -0.0972   1.1992   0.3966
 I01  C51   C  CR6   0  -0.098  -0.7198   1.8466  -0.6654
 I01  C42   C  C     0   0.599  -2.1898   2.0734  -0.6969
 I01  O43   O  O     0  -0.432  -2.7723   2.4577  -1.6821
 I01  O41   O  O2    0  -0.472  -2.7767   1.7686   0.4497
 I01  C37   C  CH1   0   0.051  -4.1960   1.5614   0.4695
 I01  C36   C  CH2   0  -0.472  -4.6690   1.9606   1.8610
 I01  C35   C  CH2   0  -0.417  -6.1851   2.0294   2.0216
 I01  C34   C  CH2   0  -0.316  -6.9612   0.8249   1.5022
 I01  N33   N  NH1   0  -0.612  -6.8476   0.7238   0.0542
 I01  C32   C  CH2   0  -0.275  -5.8390  -0.1803  -0.4487
 I01  C31   C  CH1   0  -0.110  -4.4677   0.0568   0.1879
 I01  N23   N  NH1   0  -0.672  -3.4567  -0.5507  -0.6455
 I01  C21   C  C     0   0.543  -2.3969  -1.2179  -0.1478
 I01  O22   O  O     0  -0.460  -2.2552  -1.4675   1.0377
 I01  C14   C  CR6   0   0.069  -1.3485  -1.6362  -1.1366
 I01  C13   C  CR16  0  -0.339  -0.4562  -2.6372  -0.7720
 I01  C12   C  CR16  0  -0.048   0.5608  -2.9783  -1.6477
 I01  N11   N  N     0  -0.398   0.7413  -2.3906  -2.8248
 I01  C16   C  CR16  0  -0.049  -0.1057  -1.4299  -3.1664
 I01  C15   C  CR16  0  -0.362  -1.1634  -1.0202  -2.3676
 I01  H981  H  HCH3  0   0.231   6.6700  -3.6568   2.2823
 I01  H982  H  HCH3  0   0.230   5.1047  -3.9027   3.0912
 I01  H983  H  HCH3  0   0.263   5.6498  -5.0393   1.8447
 I01  H74   H  HCR6  0   0.299   5.8045  -1.6600   3.1479
 I01  H73   H  HCR6  0   0.283   5.4850   0.7479   3.1905
 I01  H92   H  HOH1  0   0.482   4.5954   2.5882   2.0408
 I01  H55   H  HCR6  0   0.272   1.9178   2.1213  -2.7665
 I01  H56   H  HCR6  0   0.272  -0.4596   2.6924  -2.6249
 I01  H53   H  HCR6  0   0.266   1.7030   0.3319   1.1314
 I01  H52   H  HCR6  0   0.275  -0.6510   0.9235   1.2819
 I01  H37   H  HCH1  0   0.255  -4.6675   2.1853  -0.2921
 I01  H361  H  HCH2  0   0.233  -4.2484   1.2574   2.5869
 I01  H362  H  HCH2  0   0.252  -4.2549   2.9429   2.0999
 I01  H351  H  HCH2  0   0.231  -6.4054   2.1739   3.0822
 I01  H352  H  HCH2  0   0.221  -6.5630   2.9125   1.5003
 I01  H341  H  HCH2  0   0.208  -6.6487  -0.0939   2.0197
 I01  H342  H  HCH2  0   0.245  -8.0138   0.9668   1.7516
 I01  H33   H  HNH1  0   0.363  -7.7370   0.4727  -0.3518
 I01  H321  H  HCH2  0   0.222  -6.0851  -1.2422  -0.3025
 I01  H322  H  HCH2  0   0.231  -5.7621  -0.0207  -1.5291
 I01  H31   H  HCH1  0   0.265  -4.4299  -0.4674   1.1444
 I01  H23   H  HNH1  0   0.409  -3.5635  -0.4738  -1.6451
 I01  H13   H  HCR6  0   0.272  -0.5414  -3.1424   0.1796
 I01  H12   H  HCR6  0   0.265   1.2623  -3.7608  -1.3827
 I01  H16   H  HCR6  0   0.270   0.0619  -0.9488  -4.1233
 I01  H15   H  HCR6  0   0.265  -1.7882  -0.2086  -2.7164

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
 I01  F96  C76   single    1.339  0.020  1.339
 I01  C76  C75   aromatic  1.394  0.020  1.394
 I01  C76  C71   aromatic  1.376  0.020  1.376
 I01  C75  O95   single    1.345  0.020  1.345
 I01  C75  C74   aromatic  1.388  0.020  1.388
 I01  O95  C98   single    1.414  0.020  1.414
 I01  C98  H981  single    0.970  0.020  1.090
 I01  C98  H982  single    0.970  0.020  1.090
 I01  C98  H983  single    0.970  0.020  1.090
 I01  C74  C73   aromatic  1.392  0.020  1.392
 I01  C74  H74   single    0.930  0.020  1.080
 I01  C73  C72   aromatic  1.385  0.020  1.385
 I01  C73  H73   single    0.930  0.020  1.080
 I01  C72  O92   single    1.347  0.020  1.347
 I01  C72  C71   aromatic  1.396  0.020  1.396
 I01  O92  H92   single    0.850  0.020  0.980
 I01  C71  C61   single    1.499  0.020  1.499
 I01  C61  O62   double    1.209  0.020  1.209
 I01  C61  C54   single    1.483  0.020  1.483
 I01  C54  C55   aromatic  1.396  0.020  1.396
 I01  C54  C53   aromatic  1.391  0.020  1.391
 I01  C55  C56   aromatic  1.380  0.020  1.380
 I01  C55  H55   single    0.930  0.020  1.080
 I01  C56  C51   aromatic  1.395  0.020  1.395
 I01  C56  H56   single    0.930  0.020  1.080
 I01  C53  C52   aromatic  1.385  0.020  1.385
 I01  C53  H53   single    0.930  0.020  1.080
 I01  C52  C51   aromatic  1.391  0.020  1.391
 I01  C52  H52   single    0.930  0.020  1.080
 I01  C51  C42   single    1.488  0.020  1.488
 I01  C42  O43   double    1.207  0.020  1.207
 I01  C42  O41   single    1.324  0.020  1.324
 I01  O41  C37   single    1.435  0.020  1.435
 I01  C37  C36   single    1.523  0.020  1.523
 I01  C37  C31   single    1.555  0.020  1.555
 I01  C37  H37   single    0.970  0.020  1.090
 I01  C36  C35   single    1.526  0.020  1.526
 I01  C36  H361  single    0.970  0.020  1.090
 I01  C36  H362  single    0.970  0.020  1.090
 I01  C35  C34   single    1.524  0.020  1.524
 I01  C35  H351  single    0.970  0.020  1.090
 I01  C35  H352  single    0.970  0.020  1.090
 I01  C34  N33   single    1.456  0.020  1.456
 I01  C34  H341  single    0.970  0.020  1.090
 I01  C34  H342  single    0.970  0.020  1.090
 I01  N33  C32   single    1.445  0.020  1.445
 I01  N33  H33   single    0.890  0.020  1.040
 I01  C32  C31   single    1.530  0.020  1.530
 I01  C32  H321  single    0.970  0.020  1.090
 I01  C32  H322  single    0.970  0.020  1.090
 I01  C31  N23   single    1.444  0.020  1.444
 I01  C31  H31   single    0.970  0.020  1.090
 I01  N23  C21   single    1.348  0.020  1.348
 I01  N23  H23   single    0.860  0.020  1.020
 I01  C21  O22   double    1.220  0.020  1.220
 I01  C21  C14   single    1.501  0.020  1.501
 I01  C14  C13   aromatic  1.390  0.020  1.390
 I01  C14  C15   aromatic  1.389  0.020  1.389
 I01  C13  C12   aromatic  1.385  0.020  1.385
 I01  C13  H13   single    0.930  0.020  1.080
 I01  C12  N11   aromatic  1.328  0.020  1.328
 I01  C12  H12   single    0.930  0.020  1.080
 I01  N11  C16   aromatic  1.325  0.020  1.325
 I01  C16  C15   aromatic  1.387  0.020  1.387
 I01  C16  H16   single    0.930  0.020  1.080
 I01  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
 I01  C71   C76  C75   122.82  3.000
 I01  C71   C76  F96   118.54  3.000
 I01  C75   C76  F96   118.63  3.000
 I01  C74   C75  O95   126.22  3.000
 I01  C74   C75  C76   117.08  3.000
 I01  O95   C75  C76   116.70  3.000
 I01  C98   O95  C75   117.64  3.000
 I01  H983  C98  H982  108.79  3.000
 I01  H983  C98  H981  108.83  3.000
 I01  H982  C98  H981  108.89  3.000
 I01  H983  C98  O95   106.46  3.000
 I01  H982  C98  O95   111.91  3.000
 I01  H981  C98  O95   111.86  3.000
 I01  H74   C74  C73   118.17  3.000
 I01  H74   C74  C75   120.63  3.000
 I01  C73   C74  C75   121.20  3.000
 I01  H73   C73  C72   120.39  3.000
 I01  H73   C73  C74   119.14  3.000
 I01  C72   C73  C74   120.48  3.000
 I01  C71   C72  O92   116.50  3.000
 I01  C71   C72  C73   119.25  3.000
 I01  O92   C72  C73   124.24  3.000
 I01  H92   O92  C72   110.63  3.000
 I01  C61   C71  C72   120.51  3.000
 I01  C61   C71  C76   120.28  3.000
 I01  C72   C71  C76   119.17  3.000
 I01  C54   C61  O62   122.02  3.000
 I01  C54   C61  C71   117.76  3.000
 I01  O62   C61  C71   120.21  3.000
 I01  C53   C54  C55   119.47  3.000
 I01  C53   C54  C61   121.15  3.000
 I01  C55   C54  C61   119.35  3.000
 I01  H55   C55  C56   119.60  3.000
 I01  H55   C55  C54   120.27  3.000
 I01  C56   C55  C54   120.13  3.000
 I01  H56   C56  C51   120.03  3.000
 I01  H56   C56  C55   119.68  3.000
 I01  C51   C56  C55   120.26  3.000
 I01  H53   C53  C52   118.84  3.000
 I01  H53   C53  C54   120.67  3.000
 I01  C52   C53  C54   120.47  3.000
 I01  H52   C52  C51   121.01  3.000
 I01  H52   C52  C53   119.10  3.000
 I01  C51   C52  C53   119.86  3.000
 I01  C42   C51  C52   121.96  3.000
 I01  C42   C51  C56   118.01  3.000
 I01  C52   C51  C56   119.76  3.000
 I01  O41   C42  O43   124.49  3.000
 I01  O41   C42  C51   112.62  3.000
 I01  O43   C42  C51   122.85  3.000
 I01  C37   O41  C42   118.94  3.000
 I01  H37   C37  C31   110.56  3.000
 I01  H37   C37  C36   110.71  3.000
 I01  C31   C37  C36   111.40  3.000
 I01  H37   C37  O41   109.58  3.000
 I01  C31   C37  O41   108.07  3.000
 I01  C36   C37  O41   106.38  3.000
 I01  H362  C36  H361  106.67  3.000
 I01  H362  C36  C35   108.24  3.000
 I01  H361  C36  C35   109.93  3.000
 I01  H362  C36  C37   108.53  3.000
 I01  H361  C36  C37   108.55  3.000
 I01  C35   C36  C37   114.62  3.000
 I01  H352  C35  H351  106.64  3.000
 I01  H352  C35  C34   107.46  3.000
 I01  H351  C35  C34   109.43  3.000
 I01  H352  C35  C36   109.26  3.000
 I01  H351  C35  C36   107.96  3.000
 I01  C34   C35  C36   115.74  3.000
 I01  H342  C34  H341  105.98  3.000
 I01  H342  C34  N33   108.15  3.000
 I01  H341  C34  N33   112.82  3.000
 I01  H342  C34  C35   108.10  3.000
 I01  H341  C34  C35   110.81  3.000
 I01  N33   C34  C35   110.74  3.000
 I01  H33   N33  C32   108.63  3.000
 I01  H33   N33  C34   110.40  3.000
 I01  C32   N33  C34   116.36  3.000
 I01  H322  C32  H321  106.72  3.000
 I01  H322  C32  C31   108.97  3.000
 I01  H321  C32  C31   107.15  3.000
 I01  H322  C32  N33   107.53  3.000
 I01  H321  C32  N33   113.68  3.000
 I01  C31   C32  N33   112.57  3.000
 I01  H31   C31  N23   106.23  3.000
 I01  H31   C31  C32   108.73  3.000
 I01  N23   C31  C32   108.79  3.000
 I01  H31   C31  C37   107.46  3.000
 I01  N23   C31  C37   112.91  3.000
 I01  C32   C31  C37   112.45  3.000
 I01  H23   N23  C21   119.15  3.000
 I01  H23   N23  C31   117.77  3.000
 I01  C21   N23  C31   123.07  3.000
 I01  C14   C21  O22   120.15  3.000
 I01  C14   C21  N23   116.37  3.000
 I01  O22   C21  N23   123.47  3.000
 I01  C15   C14  C13   117.80  3.000
 I01  C15   C14  C21   123.61  3.000
 I01  C13   C14  C21   118.46  3.000
 I01  H13   C13  C12   119.97  3.000
 I01  H13   C13  C14   121.14  3.000
 I01  C12   C13  C14   118.89  3.000
 I01  H12   C12  N11   116.63  3.000
 I01  H12   C12  C13   119.91  3.000
 I01  N11   C12  C13   123.46  3.000
 I01  C16   N11  C12   117.54  3.000
 I01  H16   C16  C15   119.67  3.000
 I01  H16   C16  N11   116.77  3.000
 I01  C15   C16  N11   123.56  3.000
 I01  H15   C15  C16   118.44  3.000
 I01  H15   C15  C14   122.78  3.000
 I01  C16   C15  C14   118.75  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
 I01  CONST_01  C73   C74  C75  C76     0.00   0.0  0
 I01  CONST_02  C73   C72  C71  C76     0.00   0.0  0
 I01  CONST_03  C72   C71  C76  C75     0.00   0.0  0
 I01  CONST_04  C72   C73  C74  C75     0.00   0.0  0
 I01  CONST_05  C71   C76  C75  C74     0.00   0.0  0
 I01  CONST_06  C71   C72  C73  C74     0.00   0.0  0
 I01  CONST_07  C51   C56  C55  C54     0.00   0.0  0
 I01  CONST_08  C51   C52  C53  C54     0.00   0.0  0
 I01  CONST_09  C52   C53  C54  C55     0.00   0.0  0
 I01  CONST_10  C52   C51  C56  C55     0.00   0.0  0
 I01  CONST_11  C53   C54  C55  C56     0.00   0.0  0
 I01  CONST_12  C53   C52  C51  C56     0.00   0.0  0
 I01  CONST_13  N11   C12  C13  C14     0.00   0.0  0
 I01  CONST_14  N11   C16  C15  C14     0.00   0.0  0
 I01  CONST_15  C16   C15  C14  C13     0.00   0.0  0
 I01  CONST_16  C16   N11  C12  C13     0.00   0.0  0
 I01  CONST_17  C15   C14  C13  C12     0.00   0.0  0
 I01  CONST_18  C15   C16  N11  C12     0.00   0.0  0
 I01  CONST_19  C74   C75  C76  F96   180.00   0.0  0
 I01  CONST_20  C72   C71  C76  F96   180.00   0.0  0
 I01  CONST_21  O92   C72  C71  C76   180.00   0.0  0
 I01  CONST_22  C61   C71  C76  C75   180.00   0.0  0
 I01  CONST_23  C71   C76  C75  O95   180.00   0.0  0
 I01  CONST_24  C73   C74  C75  O95   180.00   0.0  0
 I01  CONST_25  O92   C72  C73  C74   180.00   0.0  0
 I01  CONST_26  C61   C71  C72  C73   180.00   0.0  0
 I01  CONST_27  C56   C55  C54  C61   180.00   0.0  0
 I01  CONST_28  C52   C53  C54  C61   180.00   0.0  0
 I01  CONST_29  C42   C51  C56  C55   180.00   0.0  0
 I01  CONST_30  C42   C51  C52  C53   180.00   0.0  0
 I01  CONST_31  C12   C13  C14  C21   180.00   0.0  0
 I01  CONST_32  C16   C15  C14  C21   180.00   0.0  0
 I01  CONST_33  H74   C74  C75  C76   180.00   0.0  0
 I01  CONST_34  H73   C73  C74  C75   180.00   0.0  0
 I01  CONST_35  H56   C56  C55  C54   180.00   0.0  0
 I01  CONST_36  H52   C52  C53  C54   180.00   0.0  0
 I01  CONST_37  H53   C53  C54  C55   180.00   0.0  0
 I01  CONST_38  H55   C55  C54  C53   180.00   0.0  0
 I01  CONST_39  H12   C12  C13  C14   180.00   0.0  0
 I01  CONST_40  H16   C16  C15  C14   180.00   0.0  0
 I01  CONST_41  H15   C15  C14  C13   180.00   0.0  0
 I01  CONST_42  H13   C13  C12  N11   180.00   0.0  0
 I01  CONST_43  C14   C21  N23  C31   180.00   0.0  0
 I01  CONST_44  O22   C21  N23  C31     0.00   0.0  0
 I01  CONST_45  H23   N23  C21  C14     0.00   0.0  0
 I01  Var_01    C54   C61  C71  C76   103.84  30.0  2
 I01  Var_02    C55   C54  C61  C71   177.20  30.0  2
 I01  Var_03    C74   C75  O95  C98    -0.74  30.0  2
 I01  Var_04    O43   C42  C51  C56     4.91  30.0  2
 I01  Var_05    C13   C14  C21  N23  -161.47  30.0  2
 I01  Var_06    H981  C98  O95  C75   -60.43  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
 I01  chir_01  C37  O41  C36  C31  positiv
 I01  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
 I01  plan-1  F96  0.020
 I01  plan-1  C76  0.020
 I01  plan-1  C75  0.020
 I01  plan-1  O95  0.020
 I01  plan-1  C74  0.020
 I01  plan-1  C73  0.020
 I01  plan-1  C72  0.020
 I01  plan-1  O92  0.020
 I01  plan-1  C71  0.020
 I01  plan-1  C61  0.020
 I01  plan-1  H74  0.020
 I01  plan-1  H73  0.020
 I01  plan-2  C61  0.020
 I01  plan-2  C54  0.020
 I01  plan-2  C55  0.020
 I01  plan-2  C56  0.020
 I01  plan-2  C53  0.020
 I01  plan-2  C52  0.020
 I01  plan-2  C51  0.020
 I01  plan-2  C42  0.020
 I01  plan-2  H55  0.020
 I01  plan-2  H56  0.020
 I01  plan-2  H53  0.020
 I01  plan-2  H52  0.020
 I01  plan-3  C21  0.020
 I01  plan-3  C14  0.020
 I01  plan-3  C13  0.020
 I01  plan-3  C12  0.020
 I01  plan-3  N11  0.020
 I01  plan-3  C16  0.020
 I01  plan-3  C15  0.020
 I01  plan-3  H13  0.020
 I01  plan-3  H12  0.020
 I01  plan-3  H16  0.020
 I01  plan-3  H15  0.020
 I01  plan-4  C31  0.020
 I01  plan-4  N23  0.020
 I01  plan-4  C21  0.020
 I01  plan-4  O22  0.020
 I01  plan-4  C14  0.020
 I01  plan-4  H23  0.020
 I01  plan-5  C71  0.020
 I01  plan-5  C61  0.020
 I01  plan-5  O62  0.020
 I01  plan-5  C54  0.020
 I01  plan-6  C51  0.020
 I01  plan-6  C42  0.020
 I01  plan-6  O43  0.020
 I01  plan-6  O41  0.020

