# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 05:30:57 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 4-[2-amino-4-ethyl-5-(1H-indazol-5-yl)pyridin-3-yl]phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1c(cnc(N)c1c2ccc(O)cc2)c3ccc4[nH]ncc4c3
#
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
 8JM  8JM  4-[2-amino-4-ethyl-5-(1H-indazol-5-yl)pyridin-3-yl]phenol  ligand  43  25  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_8JM
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
 8JM  C7   C  CR6   0   0.414   1.6275  -2.1633   0.4026
 8JM  C9   C  CR6   0  -0.038   2.8988  -0.0471   0.0416
 8JM  C2   C  CH2   0  -0.534   0.3133   1.3678  -0.0993
 8JM  C10  C  CR16  0  -0.257   3.4389   0.1763  -1.2237
 8JM  C4   C  CR6   0  -0.087  -0.7884  -0.8672   0.3503
 8JM  C1   C  CH3   0  -0.657   0.0151   1.6421  -1.5738
 8JM  C3   C  CR6   0   0.195   0.3863  -0.1077   0.1830
 8JM  C5   C  CR16  0  -0.091  -0.6444  -2.2339   0.5149
 8JM  N6   N  N     0  -0.459   0.5154  -2.8767   0.5400
 8JM  C8   C  CR6   0  -0.117   1.6104  -0.7637   0.2116
 8JM  C11  C  CR16  0  -0.326   4.6509   0.8281  -1.3869
 8JM  C12  C  CR6   0   0.347   5.3563   1.2708  -0.2705
 8JM  C13  C  CR16  0  -0.372   4.8328   1.0509   1.0014
 8JM  C14  C  CR16  0  -0.255   3.6198   0.3958   1.1474
 8JM  O15  O  OH1   0  -0.631   6.5312   1.8985  -0.4742
 8JM  N16  N  NH2   0  -0.830   2.8085  -2.8423   0.4954
 8JM  C17  C  CR6   0   0.021  -2.1480  -0.2782   0.3543
 8JM  C18  C  CR16  0  -0.303  -2.5427   0.5822   1.4104
 8JM  C19  C  CR16  0  -0.279  -3.8006   1.1296   1.4905
 8JM  C20  C  CR56  0   0.406  -4.7009   0.7957   0.4720
 8JM  C21  C  CR56  0  -0.070  -4.3438  -0.0621  -0.5815
 8JM  C22  C  CR16  0  -0.363  -3.0514  -0.6014  -0.6375
 8JM  C23  C  CR15  0  -0.135  -5.5187  -0.1404  -1.3770
 8JM  N24  N  N     0  -0.228  -6.4783   0.5875  -0.8627
 8JM  N25  N  NR15  0  -0.545  -5.9878   1.1462   0.2455
 8JM  H1   H  HCH2  0   0.252   1.2513   1.8492   0.1776
 8JM  H2   H  HCH2  0   0.252  -0.4635   1.8298   0.5109
 8JM  H3   H  HCR6  0   0.250   2.9067  -0.1693  -2.1014
 8JM  H4   H  HCH3  0   0.226   0.8027   1.2477  -2.2164
 8JM  H5   H  HCH3  0   0.232  -0.9260   1.1834  -1.8779
 8JM  H6   H  HCH3  0   0.235  -0.0598   2.7143  -1.7557
 8JM  H7   H  HCR6  0   0.250  -1.5301  -2.8496   0.6414
 8JM  H8   H  HCR6  0   0.264   5.0532   0.9922  -2.3787
 8JM  H9   H  HCR6  0   0.271   5.3712   1.3870   1.8802
 8JM  H10  H  HCR6  0   0.255   3.2280   0.2300   2.1435
 8JM  H11  H  HOH1  0   0.474   6.9347   2.1374   0.3677
 8JM  H12  H  HNH2  0   0.381   2.7495  -3.8398   0.3717
 8JM  H13  H  HNH2  0   0.390   3.6275  -2.4235   0.0879
 8JM  H14  H  HCR6  0   0.259  -1.8247   0.8036   2.1904
 8JM  H15  H  HCR6  0   0.270  -4.0790   1.7790   2.3099
 8JM  H16  H  HCR6  0   0.252  -2.7616  -1.2550  -1.4514
 8JM  H17  H  HCR5  0   0.267  -5.6777  -0.6970  -2.2881
 8JM  H26  H  HNR5  0   0.416  -6.5665   1.7620   0.7924

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
 8JM  C13  C14  aromatic  1.386  0.020  1.386
 8JM  C13  C12  aromatic  1.393  0.020  1.393
 8JM  C14  C9   aromatic  1.392  0.020  1.392
 8JM  O15  C12  single    1.348  0.020  1.348
 8JM  N16  C7   single    1.365  0.020  1.365
 8JM  C12  C11  aromatic  1.393  0.020  1.393
 8JM  C7   N6   aromatic  1.328  0.020  1.328
 8JM  C7   C8   aromatic  1.413  0.020  1.413
 8JM  C9   C8   single    1.484  0.020  1.484
 8JM  C9   C10  aromatic  1.394  0.020  1.394
 8JM  N6   C5   aromatic  1.326  0.020  1.326
 8JM  C8   C3   aromatic  1.389  0.020  1.389
 8JM  C11  C10  aromatic  1.386  0.020  1.386
 8JM  C5   C4   aromatic  1.384  0.020  1.384
 8JM  C3   C4   aromatic  1.409  0.020  1.409
 8JM  C3   C2   single    1.504  0.020  1.504
 8JM  C4   C17  single    1.482  0.020  1.482
 8JM  C18  C17  aromatic  1.418  0.020  1.418
 8JM  C18  C19  aromatic  1.374  0.020  1.374
 8JM  C2   C1   single    1.529  0.020  1.529
 8JM  C17  C22  aromatic  1.380  0.020  1.380
 8JM  C19  C20  aromatic  1.400  0.020  1.400
 8JM  C22  C21  aromatic  1.401  0.020  1.401
 8JM  C20  C21  aromatic  1.405  0.020  1.405
 8JM  C20  N25  aromatic  1.353  0.020  1.353
 8JM  C21  C23  aromatic  1.421  0.020  1.421
 8JM  N25  N24  aromatic  1.335  0.020  1.335
 8JM  C23  N24  aromatic  1.310  0.020  1.310
 8JM  C2   H1   single    0.970  0.020  1.090
 8JM  C2   H2   single    0.970  0.020  1.090
 8JM  C10  H3   single    0.930  0.020  1.080
 8JM  C1   H4   single    0.970  0.020  1.090
 8JM  C1   H5   single    0.970  0.020  1.090
 8JM  C1   H6   single    0.970  0.020  1.090
 8JM  C5   H7   single    0.930  0.020  1.080
 8JM  C11  H8   single    0.930  0.020  1.080
 8JM  C13  H9   single    0.930  0.020  1.080
 8JM  C14  H10  single    0.930  0.020  1.080
 8JM  O15  H11  single    0.850  0.020  0.980
 8JM  N16  H12  single    0.890  0.020  1.040
 8JM  N16  H13  single    0.890  0.020  1.040
 8JM  C18  H14  single    0.930  0.020  1.080
 8JM  C19  H15  single    0.930  0.020  1.080
 8JM  C22  H16  single    0.930  0.020  1.080
 8JM  C23  H17  single    0.930  0.020  1.080
 8JM  N25  H26  single    0.860  0.020  1.020

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
 8JM  N16  C7   C8   120.82  3.000
 8JM  C8   C7   N6   122.40  3.000
 8JM  N16  C7   N6   116.75  3.000
 8JM  C14  C9   C8   120.81  3.000
 8JM  C8   C9   C10  121.19  3.000
 8JM  C14  C9   C10  117.99  3.000
 8JM  H2   C2   H1   106.48  3.000
 8JM  H2   C2   C3   110.19  3.000
 8JM  H1   C2   C3   110.10  3.000
 8JM  H2   C2   C1   108.95  3.000
 8JM  H1   C2   C1   109.48  3.000
 8JM  C3   C2   C1   111.50  3.000
 8JM  H3   C10  C11  118.98  3.000
 8JM  H3   C10  C9   119.61  3.000
 8JM  C11  C10  C9   121.42  3.000
 8JM  C17  C4   C5   119.19  3.000
 8JM  C17  C4   C3   123.44  3.000
 8JM  C5   C4   C3   117.37  3.000
 8JM  H6   C1   H5   107.93  3.000
 8JM  H6   C1   H4   107.89  3.000
 8JM  H5   C1   H4   107.87  3.000
 8JM  H6   C1   C2   110.54  3.000
 8JM  H5   C1   C2   111.21  3.000
 8JM  H4   C1   C2   111.26  3.000
 8JM  C8   C3   C4   118.54  3.000
 8JM  C4   C3   C2   120.71  3.000
 8JM  C8   C3   C2   120.66  3.000
 8JM  H7   C5   N6   115.86  3.000
 8JM  H7   C5   C4   119.26  3.000
 8JM  N6   C5   C4   124.87  3.000
 8JM  C5   N6   C7   118.03  3.000
 8JM  C3   C8   C9   122.32  3.000
 8JM  C3   C8   C7   118.77  3.000
 8JM  C9   C8   C7   118.91  3.000
 8JM  H8   C11  C12  119.86  3.000
 8JM  H8   C11  C10  120.27  3.000
 8JM  C12  C11  C10  119.87  3.000
 8JM  O15  C12  C13  122.63  3.000
 8JM  O15  C12  C11  117.94  3.000
 8JM  C13  C12  C11  119.43  3.000
 8JM  H9   C13  C14  119.71  3.000
 8JM  H9   C13  C12  120.31  3.000
 8JM  C14  C13  C12  119.98  3.000
 8JM  H10  C14  C13  119.06  3.000
 8JM  H10  C14  C9   119.63  3.000
 8JM  C13  C14  C9   121.31  3.000
 8JM  H11  O15  C12  110.40  3.000
 8JM  H13  N16  H12  114.23  3.000
 8JM  H13  N16  C7   118.01  3.000
 8JM  H12  N16  C7   115.70  3.000
 8JM  C22  C17  C18  119.67  3.000
 8JM  C22  C17  C4   120.38  3.000
 8JM  C18  C17  C4   119.90  3.000
 8JM  H14  C18  C19  118.91  3.000
 8JM  H14  C18  C17  118.41  3.000
 8JM  C19  C18  C17  122.67  3.000
 8JM  H15  C19  C20  121.92  3.000
 8JM  H15  C19  C18  121.25  3.000
 8JM  C20  C19  C18  116.83  3.000
 8JM  N25  C20  C21  105.93  3.000
 8JM  N25  C20  C19  132.21  3.000
 8JM  C21  C20  C19  121.86  3.000
 8JM  C23  C21  C22  135.96  3.000
 8JM  C23  C21  C20  104.08  3.000
 8JM  C22  C21  C20  119.96  3.000
 8JM  H16  C22  C21  120.59  3.000
 8JM  H16  C22  C17  120.40  3.000
 8JM  C21  C22  C17  119.00  3.000
 8JM  H17  C23  N24  120.67  3.000
 8JM  H17  C23  C21  128.51  3.000
 8JM  N24  C23  C21  110.82  3.000
 8JM  N25  N24  C23  106.82  3.000
 8JM  H26  N25  N24  119.73  3.000
 8JM  H26  N25  C20  127.91  3.000
 8JM  N24  N25  C20  112.35  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
 8JM  CONST_01  C4   C5   N6   C7     0.00   0.0  0
 8JM  CONST_04  C4   C3   C8   C7     0.00   0.0  0
 8JM  CONST_05  C12  C13  C14  C9     0.00   0.0  0
 8JM  CONST_06  N6   C7   C8   C9   180.00   0.0  0
 8JM  CONST_07  C4   C3   C8   C9   180.00   0.0  0
 8JM  CONST_08  C12  C11  C10  C9     0.00   0.0  0
 8JM  CONST_09  C13  C14  C9   C10    0.00   0.0  0
 8JM  CONST_11  C13  C12  C11  C10    0.00   0.0  0
 8JM  CONST_12  C19  C18  C17  C4   180.00   0.0  0
 8JM  CONST_13  C21  C22  C17  C4   180.00   0.0  0
 8JM  CONST_14  N6   C7   C8   C3     0.00   0.0  0
 8JM  CONST_16  N6   C5   C4   C3     0.00   0.0  0
 8JM  CONST_19  C8   C7   N6   C5     0.00   0.0  0
 8JM  CONST_20  C8   C3   C4   C5     0.00   0.0  0
 8JM  CONST_23  C17  C4   C5   N6   180.00   0.0  0
 8JM  CONST_24  C13  C14  C9   C8   180.00   0.0  0
 8JM  CONST_25  C11  C10  C9   C8   180.00   0.0  0
 8JM  CONST_26  C17  C4   C3   C8   180.00   0.0  0
 8JM  CONST_27  C14  C13  C12  C11    0.00   0.0  0
 8JM  CONST_28  C14  C9   C10  C11    0.00   0.0  0
 8JM  CONST_29  C20  C19  C18  C17    0.00   0.0  0
 8JM  CONST_30  C20  C21  C22  C17    0.00   0.0  0
 8JM  CONST_31  C23  C21  C22  C17  180.00   0.0  0
 8JM  CONST_32  C21  C22  C17  C18    0.00   0.0  0
 8JM  CONST_33  C21  C20  C19  C18    0.00   0.0  0
 8JM  CONST_34  N25  C20  C19  C18  180.00   0.0  0
 8JM  CONST_35  C22  C17  C18  C19    0.00   0.0  0
 8JM  CONST_36  C22  C21  C20  C19    0.00   0.0  0
 8JM  CONST_37  C23  C21  C20  C19  180.00   0.0  0
 8JM  CONST_38  N24  N25  C20  C19  180.00   0.0  0
 8JM  CONST_39  N24  C23  C21  C20    0.00   0.0  0
 8JM  CONST_40  C23  N24  N25  C20    0.00   0.0  0
 8JM  CONST_41  N24  N25  C20  C21    0.00   0.0  0
 8JM  CONST_42  N25  N24  C23  C21    0.00   0.0  0
 8JM  CONST_43  N25  C20  C21  C22  180.00   0.0  0
 8JM  CONST_44  N24  C23  C21  C22  180.00   0.0  0
 8JM  CONST_45  N25  C20  C21  C23    0.00   0.0  0
 8JM  CONST_46  C2   C3   C8   C7   180.00   0.0  0
 8JM  CONST_47  N16  C7   C8   C9     0.00   0.0  0
 8JM  CONST_48  C2   C3   C8   C9     0.00   0.0  0
 8JM  CONST_49  C5   C4   C3   C2   180.00   0.0  0
 8JM  CONST_50  C17  C4   C3   C2     0.00   0.0  0
 8JM  CONST_51  O15  C12  C11  C10  180.00   0.0  0
 8JM  CONST_52  N16  C7   C8   C3   180.00   0.0  0
 8JM  CONST_53  N16  C7   N6   C5   180.00   0.0  0
 8JM  CONST_54  O15  C12  C13  C14  180.00   0.0  0
 8JM  CONST_55  H7   C5   N6   C7   180.00   0.0  0
 8JM  CONST_56  H9   C13  C14  C9   180.00   0.0  0
 8JM  CONST_57  H8   C11  C10  C9   180.00   0.0  0
 8JM  CONST_58  H10  C14  C9   C10  180.00   0.0  0
 8JM  CONST_59  H14  C18  C17  C4     0.00   0.0  0
 8JM  CONST_60  H16  C22  C17  C4     0.00   0.0  0
 8JM  CONST_61  H3   C10  C9   C8     0.00   0.0  0
 8JM  CONST_62  H15  C19  C18  C17  180.00   0.0  0
 8JM  CONST_63  H26  N25  C20  C19    0.00   0.0  0
 8JM  CONST_64  H17  C23  C21  C20  180.00   0.0  0
 8JM  Var_01    C1   C2   C3   C4   -80.03  30.0  2
 8JM  Var_02    H4   C1   C2   C3   -61.62  30.0  3

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
 8JM  plan-1  C7   0.020
 8JM  plan-1  C9   0.020
 8JM  plan-1  C2   0.020
 8JM  plan-1  C4   0.020
 8JM  plan-1  C3   0.020
 8JM  plan-1  C5   0.020
 8JM  plan-1  N6   0.020
 8JM  plan-1  C8   0.020
 8JM  plan-1  N16  0.020
 8JM  plan-1  C17  0.020
 8JM  plan-1  H7   0.020
 8JM  plan-2  C9   0.020
 8JM  plan-2  C10  0.020
 8JM  plan-2  C8   0.020
 8JM  plan-2  C11  0.020
 8JM  plan-2  C12  0.020
 8JM  plan-2  C13  0.020
 8JM  plan-2  C14  0.020
 8JM  plan-2  O15  0.020
 8JM  plan-2  H3   0.020
 8JM  plan-2  H8   0.020
 8JM  plan-2  H9   0.020
 8JM  plan-2  H10  0.020
 8JM  plan-3  C4   0.020
 8JM  plan-3  C17  0.020
 8JM  plan-3  C18  0.020
 8JM  plan-3  C19  0.020
 8JM  plan-3  C20  0.020
 8JM  plan-3  C21  0.020
 8JM  plan-3  C22  0.020
 8JM  plan-3  C23  0.020
 8JM  plan-3  N24  0.020
 8JM  plan-3  N25  0.020
 8JM  plan-3  H14  0.020
 8JM  plan-3  H15  0.020
 8JM  plan-3  H16  0.020
 8JM  plan-3  H17  0.020
 8JM  plan-3  H26  0.020
 8JM  plan-4  C7   0.020
 8JM  plan-4  N16  0.020
 8JM  plan-4  H12  0.020
 8JM  plan-4  H13  0.020

