# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 19:39:31 2020
#   Inital geometry file: a 158 line input string
#   Ligand name: N-[(3R,4R)-4-({4-[(2-fluoro-6-hydroxy-3-methoxyphenyl)carbonyl]benzyl}oxy)azepan-3-yl]pyridine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(O)c(c1F)C(=O)c2ccc(CO[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
 I05  I05  N-[(3R,4R)-4-({4-[(2-fluoro-6-hydroxy-3-methoxyphenyl)carbonyl]benzyl}oxy)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_I05
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
 I05  F96   F  F     0  -0.299   3.2254  -2.5977  -1.2747
 I05  C76   C  CR6   0   0.521   3.8940  -1.7511  -0.4838
 I05  C75   C  CR6   0   0.234   4.5055  -2.2515   0.6645
 I05  O95   O  O2    0  -0.467   4.3782  -3.5703   0.8926
 I05  C97   C  CH3   0  -0.437   4.8948  -4.0780   2.1049
 I05  C74   C  CR16  0  -0.371   5.1943  -1.3461   1.4585
 I05  C73   C  CR16  0  -0.382   5.2688   0.0016   1.1161
 I05  C72   C  CR6   0   0.358   4.6461   0.4712  -0.0272
 I05  O92   O  OH1   0  -0.624   4.6771   1.7582  -0.4297
 I05  C71   C  CR6   0  -0.385   3.9352  -0.4208  -0.8337
 I05  C61   C  C     0   0.379   3.2518   0.0397  -2.0883
 I05  O62   O  O     0  -0.371   3.7480  -0.1950  -3.1684
 I05  C54   C  CR6   0  -0.036   1.9600   0.7404  -1.9465
 I05  C55   C  CR16  0  -0.247   1.2361   1.0896  -3.0902
 I05  C56   C  CR16  0  -0.286  -0.0003   1.6941  -2.9758
 I05  C53   C  CR16  0  -0.232   1.4261   1.0455  -0.6973
 I05  C52   C  CR16  0  -0.278   0.1978   1.6751  -0.5869
 I05  C51   C  CR6   0   0.049  -0.5420   1.9833  -1.7225
 I05  C42   C  CH2   0  -0.167  -1.9097   2.6027  -1.6303
 I05  O41   O  O2    0  -0.500  -2.4702   2.3178  -0.3793
 I05  C37   C  CH1   0   0.103  -3.8786   2.2578  -0.3148
 I05  C36   C  CH2   0  -0.478  -4.4345   3.6406   0.0351
 I05  C35   C  CH2   0  -0.411  -5.9459   3.8099  -0.0763
 I05  C34   C  CH2   0  -0.310  -6.7729   2.7382   0.6218
 I05  N33   N  NH1   0  -0.611  -6.5903   1.4508  -0.0300
 I05  C32   C  CH2   0  -0.275  -5.6124   0.5638   0.5565
 I05  C31   C  CH1   0  -0.129  -4.2431   1.2172   0.7755
 I05  N23   N  NH1   0  -0.650  -3.2620   0.1594   0.8639
 I05  C21   C  C     0   0.565  -2.1698   0.2367   1.6409
 I05  O22   O  O     0  -0.479  -2.0335   1.0535   2.5390
 I05  C14   C  CR6   0   0.043  -1.0847  -0.7669   1.3732
 I05  C13   C  CR16  0  -0.338  -0.1302  -0.9856   2.3598
 I05  C12   C  CR16  0  -0.055   0.9158  -1.8566   2.0994
 I05  N11   N  N     0  -0.379   1.0679  -2.4947   0.9459
 I05  C16   C  CR16  0  -0.052   0.1643  -2.2744   0.0016
 I05  C15   C  CR16  0  -0.348  -0.9239  -1.4294   0.1628
 I05  H971  H  HCH3  0   0.228   5.9810  -3.9686   2.1668
 I05  H972  H  HCH3  0   0.226   4.4426  -3.5930   2.9745
 I05  H973  H  HCH3  0   0.261   4.6502  -5.1369   2.1269
 I05  H74   H  HCR6  0   0.294   5.6918  -1.6698   2.3624
 I05  H73   H  HCR6  0   0.279   5.8255   0.6781   1.7533
 I05  H92   H  HOH1  0   0.480   5.1788   2.2949   0.1943
 I05  H55   H  HCR6  0   0.264   1.6320   0.8647  -4.0716
 I05  H56   H  HCR6  0   0.257  -0.5625   1.9273  -3.8724
 I05  H53   H  HCR6  0   0.255   1.9533   0.7784   0.2090
 I05  H52   H  HCR6  0   0.262  -0.1871   1.9023   0.3966
 I05  H421  H  HCH2  0   0.233  -1.8346   3.6860  -1.8024
 I05  H422  H  HCH2  0   0.224  -2.5302   2.2054  -2.4439
 I05  H37   H  HCH1  0   0.213  -4.2777   1.9197  -1.2821
 I05  H361  H  HCH2  0   0.222  -4.1108   3.8841   1.0528
 I05  H362  H  HCH2  0   0.243  -3.9633   4.3786  -0.6206
 I05  H351  H  HCH2  0   0.224  -6.2109   4.7924   0.3231
 I05  H352  H  HCH2  0   0.215  -6.2351   3.8132  -1.1308
 I05  H341  H  HCH2  0   0.204  -6.5454   2.7086   1.6978
 I05  H342  H  HCH2  0   0.239  -7.8267   3.0121   0.5462
 I05  H33   H  HNH1  0   0.360  -7.4701   0.9605  -0.0960
 I05  H321  H  HCH2  0   0.216  -5.9280   0.1380   1.5206
 I05  H322  H  HCH2  0   0.226  -5.4888  -0.2786  -0.1319
 I05  H31   H  HCH1  0   0.257  -4.2405   1.7295   1.7394
 I05  H23   H  HNH1  0   0.401  -3.2841  -0.5300   0.1296
 I05  H13   H  HCR6  0   0.271  -0.1920  -0.4869   3.3168
 I05  H12   H  HCR6  0   0.260   1.6668  -2.0433   2.8590
 I05  H16   H  HCR6  0   0.265   0.3087  -2.7890  -0.9411
 I05  H15   H  HCR6  0   0.264  -1.5931  -1.2875  -0.6747

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
 I05  F96  C76   single    1.338  0.020  1.338
 I05  C76  C75   aromatic  1.394  0.020  1.394
 I05  C76  C71   aromatic  1.376  0.020  1.376
 I05  C75  O95   single    1.344  0.020  1.344
 I05  C75  C74   aromatic  1.387  0.020  1.387
 I05  O95  C97   single    1.412  0.020  1.412
 I05  C97  H971  single    0.970  0.020  1.090
 I05  C97  H972  single    0.970  0.020  1.090
 I05  C97  H973  single    0.970  0.020  1.090
 I05  C74  C73   aromatic  1.392  0.020  1.392
 I05  C74  H74   single    0.930  0.020  1.080
 I05  C73  C72   aromatic  1.384  0.020  1.384
 I05  C73  H73   single    0.930  0.020  1.080
 I05  C72  O92   single    1.349  0.020  1.349
 I05  C72  C71   aromatic  1.397  0.020  1.397
 I05  O92  H92   single    0.850  0.020  0.980
 I05  C71  C61   single    1.501  0.020  1.501
 I05  C61  O62   double    1.212  0.020  1.212
 I05  C61  C54   single    1.476  0.020  1.476
 I05  C54  C55   aromatic  1.398  0.020  1.398
 I05  C54  C53   aromatic  1.392  0.020  1.392
 I05  C55  C56   aromatic  1.381  0.020  1.381
 I05  C55  H55   single    0.930  0.020  1.080
 I05  C56  C51   aromatic  1.396  0.020  1.396
 I05  C56  H56   single    0.930  0.020  1.080
 I05  C53  C52   aromatic  1.385  0.020  1.385
 I05  C53  H53   single    0.930  0.020  1.080
 I05  C52  C51   aromatic  1.390  0.020  1.390
 I05  C52  H52   single    0.930  0.020  1.080
 I05  C51  C42   single    1.504  0.020  1.504
 I05  C42  O41   single    1.400  0.020  1.400
 I05  C42  H421  single    0.970  0.020  1.090
 I05  C42  H422  single    0.970  0.020  1.090
 I05  O41  C37   single    1.411  0.020  1.411
 I05  C37  C36   single    1.531  0.020  1.531
 I05  C37  C31   single    1.551  0.020  1.551
 I05  C37  H37   single    0.970  0.020  1.090
 I05  C36  C35   single    1.525  0.020  1.525
 I05  C36  H361  single    0.970  0.020  1.090
 I05  C36  H362  single    0.970  0.020  1.090
 I05  C35  C34   single    1.523  0.020  1.523
 I05  C35  H351  single    0.970  0.020  1.090
 I05  C35  H352  single    0.970  0.020  1.090
 I05  C34  N33   single    1.454  0.020  1.454
 I05  C34  H341  single    0.970  0.020  1.090
 I05  C34  H342  single    0.970  0.020  1.090
 I05  N33  C32   single    1.445  0.020  1.445
 I05  N33  H33   single    0.890  0.020  1.040
 I05  C32  C31   single    1.533  0.020  1.533
 I05  C32  H321  single    0.970  0.020  1.090
 I05  C32  H322  single    0.970  0.020  1.090
 I05  C31  N23   single    1.445  0.020  1.445
 I05  C31  H31   single    0.970  0.020  1.090
 I05  N23  C21   single    1.343  0.020  1.343
 I05  N23  H23   single    0.860  0.020  1.020
 I05  C21  O22   double    1.222  0.020  1.222
 I05  C21  C14   single    1.502  0.020  1.502
 I05  C14  C13   aromatic  1.390  0.020  1.390
 I05  C14  C15   aromatic  1.389  0.020  1.389
 I05  C13  C12   aromatic  1.386  0.020  1.386
 I05  C13  H13   single    0.930  0.020  1.080
 I05  C12  N11   aromatic  1.327  0.020  1.327
 I05  C12  H12   single    0.930  0.020  1.080
 I05  N11  C16   aromatic  1.325  0.020  1.325
 I05  C16  C15   aromatic  1.387  0.020  1.387
 I05  C16  H16   single    0.930  0.020  1.080
 I05  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
 I05  C71   C76  C75   122.92  3.000
 I05  C71   C76  F96   118.45  3.000
 I05  C75   C76  F96   118.63  3.000
 I05  C74   C75  O95   126.17  3.000
 I05  C74   C75  C76   117.06  3.000
 I05  O95   C75  C76   116.77  3.000
 I05  C97   O95  C75   117.62  3.000
 I05  H973  C97  H972  108.83  3.000
 I05  H973  C97  H971  108.65  3.000
 I05  H972  C97  H971  108.75  3.000
 I05  H973  C97  O95   106.57  3.000
 I05  H972  C97  O95   111.83  3.000
 I05  H971  C97  O95   112.09  3.000
 I05  H74   C74  C73   118.08  3.000
 I05  H74   C74  C75   120.76  3.000
 I05  C73   C74  C75   121.17  3.000
 I05  H73   C73  C72   120.34  3.000
 I05  H73   C73  C74   119.16  3.000
 I05  C72   C73  C74   120.50  3.000
 I05  C71   C72  O92   116.66  3.000
 I05  C71   C72  C73   119.29  3.000
 I05  O92   C72  C73   124.05  3.000
 I05  H92   O92  C72   110.49  3.000
 I05  C61   C71  C72   121.22  3.000
 I05  C61   C71  C76   119.70  3.000
 I05  C72   C71  C76   119.06  3.000
 I05  C54   C61  O62   122.40  3.000
 I05  C54   C61  C71   117.63  3.000
 I05  O62   C61  C71   119.95  3.000
 I05  C53   C54  C55   118.74  3.000
 I05  C53   C54  C61   121.71  3.000
 I05  C55   C54  C61   119.54  3.000
 I05  H55   C55  C56   119.59  3.000
 I05  H55   C55  C54   120.05  3.000
 I05  C56   C55  C54   120.35  3.000
 I05  H56   C56  C51   119.80  3.000
 I05  H56   C56  C55   119.36  3.000
 I05  C51   C56  C55   120.84  3.000
 I05  H53   C53  C52   118.54  3.000
 I05  H53   C53  C54   120.70  3.000
 I05  C52   C53  C54   120.75  3.000
 I05  H52   C52  C51   120.50  3.000
 I05  H52   C52  C53   118.96  3.000
 I05  C51   C52  C53   120.52  3.000
 I05  C42   C51  C52   121.68  3.000
 I05  C42   C51  C56   119.56  3.000
 I05  C52   C51  C56   118.76  3.000
 I05  H422  C42  H421  106.22  3.000
 I05  H422  C42  O41   111.24  3.000
 I05  H421  C42  O41   111.57  3.000
 I05  H422  C42  C51   108.63  3.000
 I05  H421  C42  C51   109.51  3.000
 I05  O41   C42  C51   109.57  3.000
 I05  C37   O41  C42   116.69  3.000
 I05  H37   C37  C31   109.08  3.000
 I05  H37   C37  C36   110.30  3.000
 I05  C31   C37  C36   111.11  3.000
 I05  H37   C37  O41   109.57  3.000
 I05  C31   C37  O41   107.17  3.000
 I05  C36   C37  O41   109.54  3.000
 I05  H362  C36  H361  106.24  3.000
 I05  H362  C36  C35   107.96  3.000
 I05  H361  C36  C35   109.63  3.000
 I05  H362  C36  C37   108.42  3.000
 I05  H361  C36  C37   107.81  3.000
 I05  C35   C36  C37   116.33  3.000
 I05  H352  C35  H351  106.58  3.000
 I05  H352  C35  C34   107.49  3.000
 I05  H351  C35  C34   109.47  3.000
 I05  H352  C35  C36   109.45  3.000
 I05  H351  C35  C36   108.26  3.000
 I05  C34   C35  C36   115.25  3.000
 I05  H342  C34  H341  105.91  3.000
 I05  H342  C34  N33   108.20  3.000
 I05  H341  C34  N33   112.86  3.000
 I05  H342  C34  C35   108.42  3.000
 I05  H341  C34  C35   110.78  3.000
 I05  N33   C34  C35   110.44  3.000
 I05  H33   N33  C32   108.56  3.000
 I05  H33   N33  C34   110.47  3.000
 I05  C32   N33  C34   116.52  3.000
 I05  H322  C32  H321  106.60  3.000
 I05  H322  C32  C31   108.47  3.000
 I05  H321  C32  C31   107.22  3.000
 I05  H322  C32  N33   107.07  3.000
 I05  H321  C32  N33   113.53  3.000
 I05  C31   C32  N33   113.64  3.000
 I05  H31   C31  N23   106.72  3.000
 I05  H31   C31  C32   109.16  3.000
 I05  N23   C31  C32   107.64  3.000
 I05  H31   C31  C37   107.78  3.000
 I05  N23   C31  C37   112.00  3.000
 I05  C32   C31  C37   113.30  3.000
 I05  H23   N23  C21   118.62  3.000
 I05  H23   N23  C31   116.19  3.000
 I05  C21   N23  C31   123.06  3.000
 I05  C14   C21  O22   119.81  3.000
 I05  C14   C21  N23   116.50  3.000
 I05  O22   C21  N23   123.69  3.000
 I05  C15   C14  C13   117.64  3.000
 I05  C15   C14  C21   123.88  3.000
 I05  C13   C14  C21   118.34  3.000
 I05  H13   C13  C12   119.97  3.000
 I05  H13   C13  C14   121.09  3.000
 I05  C12   C13  C14   118.94  3.000
 I05  H12   C12  N11   116.54  3.000
 I05  H12   C12  C13   119.96  3.000
 I05  N11   C12  C13   123.51  3.000
 I05  C16   N11  C12   117.47  3.000
 I05  H16   C16  C15   119.66  3.000
 I05  H16   C16  N11   116.74  3.000
 I05  C15   C16  N11   123.59  3.000
 I05  H15   C15  C16   118.38  3.000
 I05  H15   C15  C14   122.73  3.000
 I05  C16   C15  C14   118.85  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
 I05  CONST_01  C73   C74  C75  C76     0.00   0.0  0
 I05  CONST_02  C73   C72  C71  C76     0.00   0.0  0
 I05  CONST_03  C72   C71  C76  C75     0.00   0.0  0
 I05  CONST_04  C72   C73  C74  C75     0.00   0.0  0
 I05  CONST_05  C71   C76  C75  C74     0.00   0.0  0
 I05  CONST_06  C71   C72  C73  C74     0.00   0.0  0
 I05  CONST_07  C51   C56  C55  C54     0.00   0.0  0
 I05  CONST_08  C51   C52  C53  C54     0.00   0.0  0
 I05  CONST_09  C52   C53  C54  C55     0.00   0.0  0
 I05  CONST_10  C52   C51  C56  C55     0.00   0.0  0
 I05  CONST_11  C53   C54  C55  C56     0.00   0.0  0
 I05  CONST_12  C53   C52  C51  C56     0.00   0.0  0
 I05  CONST_13  N11   C12  C13  C14     0.00   0.0  0
 I05  CONST_14  N11   C16  C15  C14     0.00   0.0  0
 I05  CONST_15  C16   C15  C14  C13     0.00   0.0  0
 I05  CONST_16  C16   N11  C12  C13     0.00   0.0  0
 I05  CONST_17  C15   C14  C13  C12     0.00   0.0  0
 I05  CONST_18  C15   C16  N11  C12     0.00   0.0  0
 I05  CONST_19  C74   C75  C76  F96   180.00   0.0  0
 I05  CONST_20  C72   C71  C76  F96   180.00   0.0  0
 I05  CONST_21  O92   C72  C71  C76   180.00   0.0  0
 I05  CONST_22  C61   C71  C76  C75   180.00   0.0  0
 I05  CONST_23  C71   C76  C75  O95   180.00   0.0  0
 I05  CONST_24  C73   C74  C75  O95   180.00   0.0  0
 I05  CONST_25  O92   C72  C73  C74   180.00   0.0  0
 I05  CONST_26  C61   C71  C72  C73   180.00   0.0  0
 I05  CONST_27  C56   C55  C54  C61   180.00   0.0  0
 I05  CONST_28  C52   C53  C54  C61   180.00   0.0  0
 I05  CONST_29  C42   C51  C56  C55   180.00   0.0  0
 I05  CONST_30  C42   C51  C52  C53   180.00   0.0  0
 I05  CONST_31  C12   C13  C14  C21   180.00   0.0  0
 I05  CONST_32  C16   C15  C14  C21   180.00   0.0  0
 I05  CONST_33  H74   C74  C75  C76   180.00   0.0  0
 I05  CONST_34  H73   C73  C74  C75   180.00   0.0  0
 I05  CONST_35  H56   C56  C55  C54   180.00   0.0  0
 I05  CONST_36  H52   C52  C53  C54   180.00   0.0  0
 I05  CONST_37  H53   C53  C54  C55   180.00   0.0  0
 I05  CONST_38  H55   C55  C54  C53   180.00   0.0  0
 I05  CONST_39  H12   C12  C13  C14   180.00   0.0  0
 I05  CONST_40  H16   C16  C15  C14   180.00   0.0  0
 I05  CONST_41  H15   C15  C14  C13   180.00   0.0  0
 I05  CONST_42  H13   C13  C12  N11   180.00   0.0  0
 I05  CONST_43  C14   C21  N23  C31   180.00   0.0  0
 I05  CONST_45  H23   N23  C21  C14     0.00   0.0  0
 I05  Var_01    C54   C61  C71  C76   103.40  30.0  2
 I05  Var_02    C55   C54  C61  C71  -174.79  30.0  2
 I05  Var_03    C74   C75  O95  C97     5.57  30.0  2
 I05  Var_04    O41   C42  C51  C56   156.28  30.0  2
 I05  Var_05    C13   C14  C21  N23  -161.85  30.0  2
 I05  Var_06    H971  C97  O95  C75   -64.23  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
 I05  chir_01  C37  O41  C36  C31  positiv
 I05  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
 I05  plan-1  F96  0.020
 I05  plan-1  C76  0.020
 I05  plan-1  C75  0.020
 I05  plan-1  O95  0.020
 I05  plan-1  C74  0.020
 I05  plan-1  C73  0.020
 I05  plan-1  C72  0.020
 I05  plan-1  O92  0.020
 I05  plan-1  C71  0.020
 I05  plan-1  C61  0.020
 I05  plan-1  H74  0.020
 I05  plan-1  H73  0.020
 I05  plan-2  C61  0.020
 I05  plan-2  C54  0.020
 I05  plan-2  C55  0.020
 I05  plan-2  C56  0.020
 I05  plan-2  C53  0.020
 I05  plan-2  C52  0.020
 I05  plan-2  C51  0.020
 I05  plan-2  C42  0.020
 I05  plan-2  H55  0.020
 I05  plan-2  H56  0.020
 I05  plan-2  H53  0.020
 I05  plan-2  H52  0.020
 I05  plan-3  C21  0.020
 I05  plan-3  C14  0.020
 I05  plan-3  C13  0.020
 I05  plan-3  C12  0.020
 I05  plan-3  N11  0.020
 I05  plan-3  C16  0.020
 I05  plan-3  C15  0.020
 I05  plan-3  H13  0.020
 I05  plan-3  H12  0.020
 I05  plan-3  H16  0.020
 I05  plan-3  H15  0.020
 I05  plan-4  C31  0.020
 I05  plan-4  N23  0.020
 I05  plan-4  C21  0.020
 I05  plan-4  O22  0.020
 I05  plan-4  C14  0.020
 I05  plan-4  H23  0.020
 I05  plan-5  C71  0.020
 I05  plan-5  C61  0.020
 I05  plan-5  O62  0.020
 I05  plan-5  C54  0.020

