# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 14:43:17 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: 4-{6-(3,5-dimethyl-1,2-oxazol-4-yl)-1-[(1S)-1-(pyridin-2-yl)ethyl]-1H-pyrrolo[3,2-b]pyridin-3-yl}benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](n1cc(c2ccc(cc2)C(O)=O)c3ncc(cc13)c4c(C)onc4C)c5ccccn5
#
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
 6JF  6JF  '4-{6-(3,5-dimethyl-1,2-oxazol-4-yl)-1-[(1S)-1-(pyridin-2-yl)ethyl]-1H-pyrrolo[3,2-b]pyridin-3-yl}benzoic acid'  ligand  54  33  .  2021-08-05  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_6JF
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
 6JF  C26   C  CR5    0   0.423   4.6683   0.5901  -1.0229
 6JF  C11   C  CR16   0  -0.314   0.4357  -3.6283  -0.6117
 6JF  C14   C  CH1    0  -0.189   0.7052  -2.6003   1.6865
 6JF  C20   C  CR16   0  -0.147   1.2974   1.9982  -0.4941
 6JF  C16   C  CR15   0  -0.066  -1.3133  -1.1201   1.2766
 6JF  C22   C  CH3    0  -0.774   4.6454  -0.8293  -1.4445
 6JF  O1    O  OC    -1  -0.596  -7.8368   1.6896   0.2924
 6JF  O2    O  O      0  -0.595  -6.9212   3.7063   0.0463
 6JF  N4    N  N      0  -0.420   2.5322  -3.6712   0.5238
 6JF  C5    C  CR16   0  -0.077   3.0532  -4.3231  -0.5111
 6JF  C7    C  CR16   0  -0.321   2.3262  -4.6613  -1.6405
 6JF  C9    C  CR16   0  -0.150   0.9853  -4.3058  -1.6868
 6JF  C13   C  CR6    0   0.261   1.2511  -3.3300   0.4751
 6JF  N18   N  NR5    0  -0.544   0.0259  -1.3807   1.2747
 6JF  N19   N  N      0  -0.416   0.0198   1.7920  -0.2453
 6JF  O27   O  O      0  -0.343   5.8158   1.2574  -1.1485
 6JF  N28   N  N      0  -0.180   5.6604   2.5411  -0.7114
 6JF  C29   C  CH3    0  -0.754   3.9064   3.9350   0.2216
 6JF  C33   C  CR5    0   0.248   4.4227   2.6531  -0.3286
 6JF  C34   C  CR5    0  -0.181   3.7234   1.4201  -0.5016
 6JF  C35   C  CR6    0  -0.036   2.3362   1.1031  -0.1701
 6JF  C36   C  CR16   0  -0.277   2.0092  -0.0936   0.4540
 6JF  C38   C  CR56   0   0.372   0.6663  -0.3207   0.7003
 6JF  C39   C  CR56   0   0.083  -0.3044   0.6407   0.3468
 6JF  C40   C  CR5    0  -0.014  -1.5832   0.1101   0.7249
 6JF  C41   C  C1     0  -0.272  -5.3200   0.4839   0.5084
 6JF  C43   C  C1     0  -0.330  -4.0612  -0.0797   0.6216
 6JF  C45   C  C      0   0.089  -2.9071   0.7106   0.5736
 6JF  C46   C  C1     0  -0.331  -3.0715   2.0865   0.3887
 6JF  C48   C  C1     0  -0.272  -4.3365   2.6422   0.2712
 6JF  C50   C  C      0  -0.118  -5.4837   1.8566   0.3325
 6JF  C51   C  C      0   0.392  -6.8694   2.4719   0.2125
 6JF  C52   C  CH3    0  -0.697  -0.1898  -3.5019   2.5224
 6JF  H14   H  HCH1   0   0.291   1.5614  -2.3049   2.2980
 6JF  H20   H  HCR6   0   0.249   1.5419   2.9265  -0.9995
 6JF  H16   H  HCR5   0   0.302  -2.0059  -1.8315   1.6969
 6JF  H223  H  HCH3   0   0.278   5.2800  -0.9918  -2.3149
 6JF  H221  H  HCH3   0   0.272   5.0016  -1.4830  -0.6459
 6JF  H222  H  HCH3   0   0.264   3.6314  -1.1349  -1.6956
 6JF  H5    H  HCR6   0   0.266   4.1032  -4.5825  -0.4365
 6JF  H7    H  HCR6   0   0.273   2.7991  -5.1861  -2.4587
 6JF  H9    H  HCR6   0   0.277   0.3775  -4.5530  -2.5472
 6JF  H292  H  HCH3   0   0.263   3.2857   4.4555  -0.5084
 6JF  H291  H  HCH3   0   0.259   3.2933   3.7557   1.1043
 6JF  H293  H  HCH3   0   0.267   4.7263   4.5959   0.4962
 6JF  H36   H  HCR6   0   0.277   2.7758  -0.8039   0.7377
 6JF  H41   H  H      0   0.241  -6.1927  -0.1543   0.5497
 6JF  H43   H  H      0   0.238  -3.9758  -1.1537   0.7362
 6JF  H46   H  H      0   0.246  -2.2031   2.7286   0.3372
 6JF  H48   H  H      0   0.239  -4.4334   3.7115   0.1349
 6JF  H523  H  HCH3   0   0.260  -0.5532  -2.9824   3.4088
 6JF  H521  H  HCH3   0   0.243  -1.0436  -3.8735   1.9558
 6JF  H522  H  HCH3   0   0.272   0.3889  -4.3636   2.8508
 6JF  H11   H  HCR6   0   0.272  -0.6073  -3.3373  -0.6193

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
 6JF  C5   C7    aromatic  1.385  0.020  1.385
 6JF  C5   N4    aromatic  1.329  0.020  1.329
 6JF  C7   C9    aromatic  1.388  0.020  1.388
 6JF  N4   C13   aromatic  1.327  0.020  1.327
 6JF  C9   C11   aromatic  1.385  0.020  1.385
 6JF  C52  C14   single    1.521  0.020  1.521
 6JF  C13  C11   aromatic  1.391  0.020  1.391
 6JF  C13  C14   single    1.516  0.020  1.516
 6JF  C14  N18   single    1.455  0.020  1.455
 6JF  C29  C33   single    1.487  0.020  1.487
 6JF  N18  C16   aromatic  1.364  0.020  1.364
 6JF  N18  C38   aromatic  1.365  0.020  1.365
 6JF  C36  C38   aromatic  1.384  0.020  1.384
 6JF  C36  C35   aromatic  1.389  0.020  1.389
 6JF  C33  N28   aromatic  1.300  0.020  1.300
 6JF  C33  C34   aromatic  1.428  0.020  1.428
 6JF  N28  O27   aromatic  1.365  0.020  1.365
 6JF  C16  C40   aromatic  1.375  0.020  1.375
 6JF  C38  C39   aromatic  1.411  0.020  1.411
 6JF  C34  C35   single    1.461  0.020  1.461
 6JF  C34  C26   aromatic  1.361  0.020  1.361
 6JF  O27  C26   aromatic  1.333  0.020  1.333
 6JF  C35  C20   aromatic  1.409  0.020  1.409
 6JF  C26  C22   single    1.481  0.020  1.481
 6JF  C40  C39   aromatic  1.435  0.020  1.435
 6JF  C40  C45   single    1.462  0.020  1.462
 6JF  C39  N19   aromatic  1.335  0.020  1.335
 6JF  C46  C45   aromatic  1.398  0.020  1.398
 6JF  C46  C48   aromatic  1.387  0.020  1.387
 6JF  C20  N19   aromatic  1.318  0.020  1.318
 6JF  C45  C43   aromatic  1.400  0.020  1.400
 6JF  C48  C50   aromatic  1.392  0.020  1.392
 6JF  C43  C41   aromatic  1.384  0.020  1.384
 6JF  C50  C41   aromatic  1.394  0.020  1.394
 6JF  C50  C51   single    1.521  0.020  1.521
 6JF  O2   C51   deloc     1.247  0.020  1.247
 6JF  C51  O1    deloc     1.247  0.020  1.247
 6JF  C11  H11   single    0.930  0.020  1.080
 6JF  C14  H14   single    0.970  0.020  1.090
 6JF  C20  H20   single    0.930  0.020  1.080
 6JF  C16  H16   single    0.930  0.020  1.080
 6JF  C22  H223  single    0.970  0.020  1.090
 6JF  C22  H221  single    0.970  0.020  1.090
 6JF  C22  H222  single    0.970  0.020  1.090
 6JF  C5   H5    single    0.930  0.020  1.080
 6JF  C7   H7    single    0.930  0.020  1.080
 6JF  C9   H9    single    0.930  0.020  1.080
 6JF  C29  H292  single    0.970  0.020  1.090
 6JF  C29  H291  single    0.970  0.020  1.090
 6JF  C29  H293  single    0.970  0.020  1.090
 6JF  C36  H36   single    0.930  0.020  1.080
 6JF  C41  H41   single    0.930  0.020  1.080
 6JF  C43  H43   single    0.930  0.020  1.080
 6JF  C46  H46   single    0.930  0.020  1.080
 6JF  C48  H48   single    0.930  0.020  1.080
 6JF  C52  H523  single    0.970  0.020  1.090
 6JF  C52  H521  single    0.970  0.020  1.090
 6JF  C52  H522  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
 6JF  C34   C26  O27   109.17  3.000
 6JF  O27   C26  C22   117.78  3.000
 6JF  C34   C26  C22   133.05  3.000
 6JF  H11   C11  C13   120.83  3.000
 6JF  H11   C11  C9    120.56  3.000
 6JF  C13   C11  C9    118.61  3.000
 6JF  H14   C14  C52   108.28  3.000
 6JF  H14   C14  N18   107.31  3.000
 6JF  C52   C14  N18   112.19  3.000
 6JF  H14   C14  C13   107.17  3.000
 6JF  N18   C14  C13   110.20  3.000
 6JF  C52   C14  C13   111.46  3.000
 6JF  H20   C20  C35   118.99  3.000
 6JF  H20   C20  N19   116.13  3.000
 6JF  C35   C20  N19   124.88  3.000
 6JF  H16   C16  C40   128.36  3.000
 6JF  H16   C16  N18   120.33  3.000
 6JF  C40   C16  N18   111.29  3.000
 6JF  H222  C22  H221  107.74  3.000
 6JF  H222  C22  H223  108.45  3.000
 6JF  H221  C22  H223  107.77  3.000
 6JF  H222  C22  C26   110.44  3.000
 6JF  H221  C22  C26   111.14  3.000
 6JF  H223  C22  C26   111.19  3.000
 6JF  C13   N4   C5    118.42  3.000
 6JF  H5    C5   C7    120.40  3.000
 6JF  H5    C5   N4    116.31  3.000
 6JF  C7    C5   N4    123.29  3.000
 6JF  H7    C7   C9    121.44  3.000
 6JF  H7    C7   C5    120.41  3.000
 6JF  C9    C7   C5    118.15  3.000
 6JF  H9    C9   C7    120.70  3.000
 6JF  H9    C9   C11   120.42  3.000
 6JF  C7    C9   C11   118.87  3.000
 6JF  N4    C13  C14   116.25  3.000
 6JF  C14   C13  C11   121.09  3.000
 6JF  N4    C13  C11   122.66  3.000
 6JF  C38   N18  C16   108.22  3.000
 6JF  C38   N18  C14   123.42  3.000
 6JF  C16   N18  C14   128.16  3.000
 6JF  C39   N19  C20   117.01  3.000
 6JF  N28   O27  C26   110.03  3.000
 6JF  C33   N28  O27   106.48  3.000
 6JF  H293  C29  H291  108.62  3.000
 6JF  H293  C29  H292  107.93  3.000
 6JF  H291  C29  H292  107.50  3.000
 6JF  H293  C29  C33   110.80  3.000
 6JF  H291  C29  C33   110.68  3.000
 6JF  H292  C29  C33   111.18  3.000
 6JF  C34   C33  C29   128.24  3.000
 6JF  C34   C33  N28   110.86  3.000
 6JF  C29   C33  N28   120.90  3.000
 6JF  C35   C34  C33   128.67  3.000
 6JF  C35   C34  C26   127.85  3.000
 6JF  C33   C34  C26   103.47  3.000
 6JF  C36   C35  C34   120.83  3.000
 6JF  C34   C35  C20   120.66  3.000
 6JF  C36   C35  C20   118.50  3.000
 6JF  H36   C36  C38   122.18  3.000
 6JF  H36   C36  C35   121.08  3.000
 6JF  C38   C36  C35   116.74  3.000
 6JF  C39   C38  C36   120.73  3.000
 6JF  C39   C38  N18   108.16  3.000
 6JF  C36   C38  N18   131.10  3.000
 6JF  C40   C39  C38   107.16  3.000
 6JF  C40   C39  N19   130.71  3.000
 6JF  C38   C39  N19   122.13  3.000
 6JF  C45   C40  C39   128.90  3.000
 6JF  C45   C40  C16   125.94  3.000
 6JF  C39   C40  C16   105.16  3.000
 6JF  H41   C41  C50   119.41  3.000
 6JF  H41   C41  C43   119.36  3.000
 6JF  C50   C41  C43   121.22  3.000
 6JF  H43   C43  C45   119.90  3.000
 6JF  H43   C43  C41   118.95  3.000
 6JF  C45   C43  C41   121.15  3.000
 6JF  C46   C45  C43   117.60  3.000
 6JF  C43   C45  C40   120.76  3.000
 6JF  C46   C45  C40   121.64  3.000
 6JF  H46   C46  C48   119.39  3.000
 6JF  H46   C46  C45   119.76  3.000
 6JF  C48   C46  C45   120.85  3.000
 6JF  H48   C48  C50   119.31  3.000
 6JF  H48   C48  C46   119.22  3.000
 6JF  C50   C48  C46   121.47  3.000
 6JF  C51   C50  C48   121.27  3.000
 6JF  C51   C50  C41   121.03  3.000
 6JF  C48   C50  C41   117.70  3.000
 6JF  C50   C51  O2    116.68  3.000
 6JF  O2    C51  O1    126.70  3.000
 6JF  C50   C51  O1    116.62  3.000
 6JF  H522  C52  H521  107.65  3.000
 6JF  H522  C52  H523  108.01  3.000
 6JF  H521  C52  H523  108.91  3.000
 6JF  H522  C52  C14   108.80  3.000
 6JF  H521  C52  C14   112.17  3.000
 6JF  H523  C52  C14   111.15  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
 6JF  CONST_01  N28   C33  C34  C26     0.00   0.0  0
 6JF  CONST_04  C33   N28  O27  C26     0.00   0.0  0
 6JF  CONST_05  C5    C7   C9   C11     0.00   0.0  0
 6JF  CONST_06  C5    N4   C13  C11     0.00   0.0  0
 6JF  CONST_07  C38   C36  C35  C20     0.00   0.0  0
 6JF  CONST_09  C38   C39  N19  C20     0.00   0.0  0
 6JF  CONST_10  C40   C39  N19  C20   180.00   0.0  0
 6JF  CONST_11  C36   C38  N18  C16   180.00   0.0  0
 6JF  CONST_12  C39   C38  N18  C16     0.00   0.0  0
 6JF  CONST_13  C38   C39  C40  C16     0.00   0.0  0
 6JF  CONST_14  N19   C39  C40  C16   180.00   0.0  0
 6JF  CONST_17  C9    C7   C5   N4      0.00   0.0  0
 6JF  CONST_18  C9    C11  C13  N4      0.00   0.0  0
 6JF  CONST_19  C13   N4   C5   C7      0.00   0.0  0
 6JF  CONST_20  C13   C11  C9   C7      0.00   0.0  0
 6JF  CONST_21  C39   C40  C16  N18     0.00   0.0  0
 6JF  CONST_22  C45   C40  C16  N18   180.00   0.0  0
 6JF  CONST_23  C35   C36  C38  N18   180.00   0.0  0
 6JF  CONST_24  C40   C39  C38  N18     0.00   0.0  0
 6JF  CONST_25  N19   C39  C38  N18   180.00   0.0  0
 6JF  CONST_26  C36   C38  C39  N19     0.00   0.0  0
 6JF  CONST_27  C45   C40  C39  N19     0.00   0.0  0
 6JF  CONST_28  C36   C35  C20  N19     0.00   0.0  0
 6JF  CONST_29  C34   C35  C20  N19   180.00   0.0  0
 6JF  CONST_30  C34   C33  N28  O27     0.00   0.0  0
 6JF  CONST_31  C33   C34  C26  O27     0.00   0.0  0
 6JF  CONST_32  C35   C34  C26  O27   180.00   0.0  0
 6JF  CONST_33  C35   C34  C33  N28   180.00   0.0  0
 6JF  CONST_34  C34   C26  O27  N28     0.00   0.0  0
 6JF  CONST_36  C38   C36  C35  C34   180.00   0.0  0
 6JF  CONST_37  C39   C38  C36  C35     0.00   0.0  0
 6JF  CONST_38  C39   N19  C20  C35     0.00   0.0  0
 6JF  CONST_39  C40   C39  C38  C36   180.00   0.0  0
 6JF  CONST_40  C40   C16  N18  C38     0.00   0.0  0
 6JF  CONST_41  C45   C40  C39  C38   180.00   0.0  0
 6JF  CONST_44  C48   C46  C45  C40   180.00   0.0  0
 6JF  CONST_45  C41   C43  C45  C40   180.00   0.0  0
 6JF  CONST_46  C46   C45  C43  C41     0.00   0.0  0
 6JF  CONST_47  C46   C48  C50  C41     0.00   0.0  0
 6JF  CONST_48  C48   C46  C45  C43     0.00   0.0  0
 6JF  CONST_49  C48   C50  C41  C43     0.00   0.0  0
 6JF  CONST_50  C50   C48  C46  C45     0.00   0.0  0
 6JF  CONST_51  C50   C41  C43  C45     0.00   0.0  0
 6JF  CONST_52  C29   C33  C34  C26   180.00   0.0  0
 6JF  CONST_53  C5    N4   C13  C14   180.00   0.0  0
 6JF  CONST_54  C9    C11  C13  C14   180.00   0.0  0
 6JF  CONST_55  C40   C16  N18  C14   180.00   0.0  0
 6JF  CONST_56  C36   C38  N18  C14     0.00   0.0  0
 6JF  CONST_57  C39   C38  N18  C14   180.00   0.0  0
 6JF  CONST_58  C33   C34  C26  C22   180.00   0.0  0
 6JF  CONST_59  C35   C34  C26  C22     0.00   0.0  0
 6JF  CONST_60  N28   O27  C26  C22   180.00   0.0  0
 6JF  CONST_61  C29   C33  N28  O27   180.00   0.0  0
 6JF  CONST_62  C35   C34  C33  C29     0.00   0.0  0
 6JF  CONST_63  C51   C50  C41  C43   180.00   0.0  0
 6JF  CONST_64  C51   C50  C48  C46   180.00   0.0  0
 6JF  CONST_65  H7    C7   C9   C11   180.00   0.0  0
 6JF  CONST_66  H36   C36  C35  C20   180.00   0.0  0
 6JF  CONST_67  H11   C11  C13  N4    180.00   0.0  0
 6JF  CONST_68  H9    C9   C7   C5    180.00   0.0  0
 6JF  CONST_69  H5    C5   C7   C9    180.00   0.0  0
 6JF  CONST_70  H20   C20  C35  C34     0.00   0.0  0
 6JF  CONST_71  H16   C16  N18  C38   180.00   0.0  0
 6JF  CONST_72  H46   C46  C45  C40     0.00   0.0  0
 6JF  CONST_73  H43   C43  C45  C40     0.00   0.0  0
 6JF  CONST_74  H48   C48  C50  C41   180.00   0.0  0
 6JF  CONST_75  H41   C41  C43  C45   180.00   0.0  0
 6JF  Var_01    C48   C50  C51  O1   -179.32  30.0  2
 6JF  Var_02    H223  C22  C26  O27   -35.63  30.0  2
 6JF  Var_03    H292  C29  C33  N28   104.49  30.0  2

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
 6JF  chir_01  C14  C52  C13  N18  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
 6JF  plan-1  C26  0.020
 6JF  plan-1  C22  0.020
 6JF  plan-1  O27  0.020
 6JF  plan-1  N28  0.020
 6JF  plan-1  C29  0.020
 6JF  plan-1  C33  0.020
 6JF  plan-1  C34  0.020
 6JF  plan-1  C35  0.020
 6JF  plan-2  C11  0.020
 6JF  plan-2  C14  0.020
 6JF  plan-2  N4   0.020
 6JF  plan-2  C5   0.020
 6JF  plan-2  C7   0.020
 6JF  plan-2  C9   0.020
 6JF  plan-2  C13  0.020
 6JF  plan-2  H5   0.020
 6JF  plan-2  H7   0.020
 6JF  plan-2  H9   0.020
 6JF  plan-2  H11  0.020
 6JF  plan-3  C40  0.020
 6JF  plan-3  C41  0.020
 6JF  plan-3  C43  0.020
 6JF  plan-3  C45  0.020
 6JF  plan-3  C46  0.020
 6JF  plan-3  C48  0.020
 6JF  plan-3  C50  0.020
 6JF  plan-3  C51  0.020
 6JF  plan-3  H41  0.020
 6JF  plan-3  H43  0.020
 6JF  plan-3  H46  0.020
 6JF  plan-3  H48  0.020
 6JF  plan-4  C14  0.020
 6JF  plan-4  C20  0.020
 6JF  plan-4  C16  0.020
 6JF  plan-4  N18  0.020
 6JF  plan-4  N19  0.020
 6JF  plan-4  C34  0.020
 6JF  plan-4  C35  0.020
 6JF  plan-4  C36  0.020
 6JF  plan-4  C38  0.020
 6JF  plan-4  C39  0.020
 6JF  plan-4  C40  0.020
 6JF  plan-4  C45  0.020
 6JF  plan-4  H20  0.020
 6JF  plan-4  H16  0.020
 6JF  plan-4  H36  0.020
 6JF  plan-5  O1   0.020
 6JF  plan-5  O2   0.020
 6JF  plan-5  C50  0.020
 6JF  plan-5  C51  0.020

