# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 21:38:19 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: N~3~-[5-(1H-indol-6-yl)-2-(pyridin-2-ylmethoxy)benzyl]pyridine-2,3-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncccc1NCc2cc(ccc2OCc3ccccn3)c4ccc5cc[nH]c5c4
#
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
 IP7  IP7  N~3~-[5-(1H-indol-6-yl)-2-(pyridin-2-ylmethoxy)benzyl]pyridine-2,3-diamine  ligand  55  32  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_IP7
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
 IP7  N1    N  NH2   0  -0.832   0.5776  -4.8505  -4.9197
 IP7  C2    C  CR6   0   0.362   0.2891  -3.9446  -5.9138
 IP7  N3    N  N     0  -0.441   0.1456  -4.3936  -7.1453
 IP7  C4    C  CR16  0  -0.101  -0.1575  -3.5315  -8.1205
 IP7  C5    C  CR16  0  -0.341  -0.3172  -2.1831  -7.9025
 IP7  C6    C  CR16  0  -0.249  -0.1830  -1.7013  -6.5976
 IP7  C7    C  CR6   0   0.226   0.1120  -2.5759  -5.5685
 IP7  N8    N  NH1   0  -0.683   0.3110  -2.2061  -4.2466
 IP7  C9    C  CH2   0  -0.347   0.2342  -0.8090  -3.8767
 IP7  C10   C  CR6   0   0.009   0.6667  -0.6197  -2.4494
 IP7  C11   C  CR16  0  -0.360  -0.2523  -0.2723  -1.4741
 IP7  C12   C  CR6   0   0.089   0.1045  -0.0970  -0.1335
 IP7  C13   C  CR16  0  -0.316   1.4426  -0.2795   0.2007
 IP7  C14   C  CR16  0  -0.360   2.3894  -0.6223  -0.7554
 IP7  C15   C  CR6   0   0.371   2.0081  -0.7982  -2.0800
 IP7  O16   O  O2    0  -0.469   2.8600  -1.1159  -3.0714
 IP7  C17   C  CH2   0  -0.217   4.1416  -1.6111  -2.7653
 IP7  C18   C  CR6   0   0.195   4.6920  -2.3049  -3.9819
 IP7  C19   C  CR16  0  -0.346   3.8710  -2.7728  -5.0021
 IP7  C20   C  CR16  0  -0.147   4.4563  -3.4441  -6.0644
 IP7  C21   C  CR16  0  -0.326   5.8305  -3.6263  -6.0725
 IP7  C22   C  CR16  0  -0.077   6.5597  -3.1233  -5.0057
 IP7  N23   N  N     0  -0.429   6.0097  -2.4759  -3.9861
 IP7  C24   C  CR6   0   0.064  -0.9015   0.2635   0.8852
 IP7  C25   C  CR16  0  -0.328  -0.5618   1.1468   1.9344
 IP7  C26   C  CR16  0  -0.329  -1.4683   1.5052   2.9089
 IP7  C27   C  CR56  0   0.046  -2.7659   0.9827   2.8607
 IP7  C28   C  CR15  0  -0.417  -3.9347   1.1185   3.6710
 IP7  C29   C  CR15  0  -0.030  -4.8991   0.3406   3.0972
 IP7  N30   N  NR15  0  -0.685  -4.3994  -0.2680   1.9813
 IP7  C31   C  CR56  0   0.376  -3.0983   0.1034   1.8060
 IP7  C32   C  CR16  0  -0.375  -2.1842  -0.2632   0.8222
 IP7  HN11  H  HNH2  0   0.379   1.1554  -4.5069  -4.1667
 IP7  HN12  H  HNH2  0   0.379   0.8892  -5.7471  -5.2600
 IP7  H4    H  HCR6  0   0.247  -0.2620  -3.9505  -9.1151
 IP7  H5    H  HCR6  0   0.254  -0.5491  -1.5131  -8.7189
 IP7  H6    H  HCR6  0   0.273  -0.3243  -0.6465  -6.4018
 IP7  HN8   H  HNH1  0   0.375  -0.1533  -2.8121  -3.5827
 IP7  H91   H  HCH2  0   0.240  -0.7758  -0.3987  -4.0064
 IP7  H92   H  HCH2  0   0.251   0.8866  -0.2420  -4.5452
 IP7  H11   H  HCR6  0   0.250  -1.2822  -0.1173  -1.7758
 IP7  H13   H  HCR6  0   0.256   1.7662  -0.1699   1.2284
 IP7  H14   H  HCR6  0   0.283   3.4195  -0.7461  -0.4476
 IP7  H171  H  HCH2  0   0.253   4.0932  -2.3300  -1.9380
 IP7  H172  H  HCH2  0   0.249   4.8200  -0.8079  -2.4586
 IP7  H19   H  HCR6  0   0.295   2.8023  -2.6183  -4.9629
 IP7  H20   H  HCR6  0   0.267   3.8460  -3.8212  -6.8752
 IP7  H21   H  HCR6  0   0.271   6.3281  -4.1425  -6.8816
 IP7  H22   H  HCR6  0   0.264   7.6369  -3.2446  -4.9744
 IP7  H25   H  HCR6  0   0.243   0.4337   1.5720   1.9620
 IP7  H26   H  HCR6  0   0.246  -1.1777   2.1885   3.6974
 IP7  H28   H  HCR5  0   0.248  -4.0446   1.7134   4.5635
 IP7  H29   H  HCR5  0   0.281  -5.9195   0.1705   3.4008
 IP7  HN30  H  HNR5  0   0.410  -4.9140  -0.8987   1.3899
 IP7  H32   H  HCR6  0   0.257  -2.4629  -0.9609   0.0419

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
 IP7  N1   C2    single    1.376  0.020  1.376
 IP7  N1   HN11  single    0.890  0.020  1.040
 IP7  N1   HN12  single    0.890  0.020  1.040
 IP7  C2   N3    aromatic  1.319  0.020  1.319
 IP7  C2   C7    aromatic  1.423  0.020  1.423
 IP7  N3   C4    aromatic  1.336  0.020  1.336
 IP7  C4   C5    aromatic  1.375  0.020  1.375
 IP7  C4   H4    single    0.930  0.020  1.080
 IP7  C5   C6    aromatic  1.397  0.020  1.397
 IP7  C5   H5    single    0.930  0.020  1.080
 IP7  C6   C7    aromatic  1.382  0.020  1.382
 IP7  C6   H6    single    0.930  0.020  1.080
 IP7  C7   N8    single    1.387  0.020  1.387
 IP7  N8   C9    single    1.447  0.020  1.447
 IP7  N8   HN8   single    0.890  0.020  1.040
 IP7  C9   C10   single    1.503  0.020  1.503
 IP7  C9   H91   single    0.970  0.020  1.090
 IP7  C9   H92   single    0.970  0.020  1.090
 IP7  C10  C11   aromatic  1.384  0.020  1.384
 IP7  C10  C15   aromatic  1.403  0.020  1.403
 IP7  C11  C12   aromatic  1.398  0.020  1.398
 IP7  C11  H11   single    0.930  0.020  1.080
 IP7  C12  C24   single    1.476  0.020  1.476
 IP7  C12  C13   aromatic  1.391  0.020  1.391
 IP7  C13  C14   aromatic  1.389  0.020  1.389
 IP7  C13  H13   single    0.930  0.020  1.080
 IP7  C14  C15   aromatic  1.390  0.020  1.390
 IP7  C14  H14   single    0.930  0.020  1.080
 IP7  C15  O16   single    1.345  0.020  1.345
 IP7  O16  C17   single    1.408  0.020  1.408
 IP7  C17  C18   single    1.505  0.020  1.505
 IP7  C17  H171  single    0.970  0.020  1.090
 IP7  C17  H172  single    0.970  0.020  1.090
 IP7  C18  N23   aromatic  1.329  0.020  1.329
 IP7  C18  C19   aromatic  1.391  0.020  1.391
 IP7  C19  C20   aromatic  1.386  0.020  1.386
 IP7  C19  H19   single    0.930  0.020  1.080
 IP7  C20  C21   aromatic  1.386  0.020  1.386
 IP7  C20  H20   single    0.930  0.020  1.080
 IP7  C21  C22   aromatic  1.387  0.020  1.387
 IP7  C21  H21   single    0.930  0.020  1.080
 IP7  C22  N23   aromatic  1.327  0.020  1.327
 IP7  C22  H22   single    0.930  0.020  1.080
 IP7  C24  C32   aromatic  1.388  0.020  1.388
 IP7  C24  C25   aromatic  1.413  0.020  1.413
 IP7  C25  C26   aromatic  1.378  0.020  1.378
 IP7  C25  H25   single    0.930  0.020  1.080
 IP7  C26  C27   aromatic  1.400  0.020  1.400
 IP7  C26  H26   single    0.930  0.020  1.080
 IP7  C27  C28   aromatic  1.429  0.020  1.429
 IP7  C27  C31   aromatic  1.413  0.020  1.413
 IP7  C28  C29   aromatic  1.365  0.020  1.365
 IP7  C28  H28   single    0.930  0.020  1.080
 IP7  C29  N30   aromatic  1.366  0.020  1.366
 IP7  C29  H29   single    0.930  0.020  1.080
 IP7  N30  C31   aromatic  1.364  0.020  1.364
 IP7  N30  HN30  single    0.860  0.020  1.020
 IP7  C31  C32   aromatic  1.392  0.020  1.392
 IP7  C32  H32   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
 IP7  HN12  N1   HN11  112.18  3.000
 IP7  HN12  N1   C2    113.99  3.000
 IP7  HN11  N1   C2    115.78  3.000
 IP7  C7    C2   N3    122.73  3.000
 IP7  C7    C2   N1    118.97  3.000
 IP7  N3    C2   N1    118.27  3.000
 IP7  C4    N3   C2    119.12  3.000
 IP7  H4    C4   C5    120.87  3.000
 IP7  H4    C4   N3    116.23  3.000
 IP7  C5    C4   N3    122.89  3.000
 IP7  H5    C5   C6    120.80  3.000
 IP7  H5    C5   C4    120.84  3.000
 IP7  C6    C5   C4    118.35  3.000
 IP7  H6    C6   C7    120.66  3.000
 IP7  H6    C6   C5    119.50  3.000
 IP7  C7    C6   C5    119.84  3.000
 IP7  N8    C7   C6    124.85  3.000
 IP7  N8    C7   C2    118.04  3.000
 IP7  C6    C7   C2    117.03  3.000
 IP7  HN8   N8   C9    112.71  3.000
 IP7  HN8   N8   C7    113.57  3.000
 IP7  C9    N8   C7    119.57  3.000
 IP7  H92   C9   H91   106.44  3.000
 IP7  H92   C9   C10   110.11  3.000
 IP7  H91   C9   C10   109.25  3.000
 IP7  H92   C9   N8    108.23  3.000
 IP7  H91   C9   N8    112.29  3.000
 IP7  C10   C9   N8    110.43  3.000
 IP7  C15   C10  C11   118.77  3.000
 IP7  C15   C10  C9    120.60  3.000
 IP7  C11   C10  C9    120.63  3.000
 IP7  H11   C11  C12   119.42  3.000
 IP7  H11   C11  C10   118.06  3.000
 IP7  C12   C11  C10   122.51  3.000
 IP7  C24   C12  C13   121.44  3.000
 IP7  C13   C12  C11   117.34  3.000
 IP7  C24   C12  C11   121.21  3.000
 IP7  H13   C13  C14   118.34  3.000
 IP7  H13   C13  C12   120.14  3.000
 IP7  C14   C13  C12   121.52  3.000
 IP7  H14   C14  C15   121.19  3.000
 IP7  H14   C14  C13   118.78  3.000
 IP7  C15   C14  C13   120.03  3.000
 IP7  O16   C15  C14   123.96  3.000
 IP7  O16   C15  C10   116.21  3.000
 IP7  C14   C15  C10   119.82  3.000
 IP7  C17   O16  C15   119.96  3.000
 IP7  H172  C17  H171  107.26  3.000
 IP7  H172  C17  C18   109.75  3.000
 IP7  H171  C17  C18   108.88  3.000
 IP7  H172  C17  O16   111.53  3.000
 IP7  H171  C17  O16   110.76  3.000
 IP7  C18   C17  O16   108.63  3.000
 IP7  N23   C18  C19   122.67  3.000
 IP7  C19   C18  C17   122.16  3.000
 IP7  N23   C18  C17   115.13  3.000
 IP7  H19   C19  C20   120.97  3.000
 IP7  H19   C19  C18   120.61  3.000
 IP7  C20   C19  C18   118.41  3.000
 IP7  H20   C20  C21   120.57  3.000
 IP7  H20   C20  C19   120.31  3.000
 IP7  C21   C20  C19   119.12  3.000
 IP7  H21   C21  C22   120.46  3.000
 IP7  H21   C21  C20   121.56  3.000
 IP7  C22   C21  C20   117.97  3.000
 IP7  H22   C22  N23   116.36  3.000
 IP7  H22   C22  C21   120.26  3.000
 IP7  N23   C22  C21   123.37  3.000
 IP7  C22   N23  C18   118.44  3.000
 IP7  C32   C24  C25   119.54  3.000
 IP7  C25   C24  C12   120.08  3.000
 IP7  C32   C24  C12   120.38  3.000
 IP7  H25   C25  C26   118.98  3.000
 IP7  H25   C25  C24   119.05  3.000
 IP7  C26   C25  C24   121.96  3.000
 IP7  H26   C26  C27   120.62  3.000
 IP7  H26   C26  C25   120.15  3.000
 IP7  C27   C26  C25   119.23  3.000
 IP7  C31   C27  C28   106.86  3.000
 IP7  C31   C27  C26   118.44  3.000
 IP7  C28   C27  C26   134.70  3.000
 IP7  H28   C28  C29   126.17  3.000
 IP7  H28   C28  C27   127.25  3.000
 IP7  C29   C28  C27   106.58  3.000
 IP7  H29   C29  N30   120.40  3.000
 IP7  H29   C29  C28   129.80  3.000
 IP7  N30   C29  C28   109.80  3.000
 IP7  HN30  N30  C31   125.66  3.000
 IP7  HN30  N30  C29   124.92  3.000
 IP7  C31   N30  C29   109.43  3.000
 IP7  C32   C31  N30   130.19  3.000
 IP7  C32   C31  C27   122.48  3.000
 IP7  N30   C31  C27   107.33  3.000
 IP7  H32   C32  C31   120.65  3.000
 IP7  H32   C32  C24   120.99  3.000
 IP7  C31   C32  C24   118.35  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
 IP7  CONST_01  C5    C4   N3   C2      0.00   0.0  0
 IP7  CONST_02  C5    C6   C7   C2      0.00   0.0  0
 IP7  CONST_03  C6    C7   C2   N3      0.00   0.0  0
 IP7  CONST_04  C6    C5   C4   N3      0.00   0.0  0
 IP7  CONST_05  C7    C2   N3   C4      0.00   0.0  0
 IP7  CONST_06  C7    C6   C5   C4      0.00   0.0  0
 IP7  CONST_07  C24   C12  C11  C10   180.00   0.0  0
 IP7  CONST_08  C13   C12  C11  C10     0.00   0.0  0
 IP7  CONST_09  C13   C14  C15  C10     0.00   0.0  0
 IP7  CONST_10  C14   C15  C10  C11     0.00   0.0  0
 IP7  CONST_13  C14   C13  C12  C11     0.00   0.0  0
 IP7  CONST_14  C15   C10  C11  C12     0.00   0.0  0
 IP7  CONST_15  C31   C32  C24  C12   180.00   0.0  0
 IP7  CONST_16  C26   C25  C24  C12   180.00   0.0  0
 IP7  CONST_17  C15   C14  C13  C12     0.00   0.0  0
 IP7  CONST_20  C24   C12  C13  C14   180.00   0.0  0
 IP7  CONST_21  C21   C22  N23  C18     0.00   0.0  0
 IP7  CONST_22  C21   C20  C19  C18     0.00   0.0  0
 IP7  CONST_23  C22   N23  C18  C19     0.00   0.0  0
 IP7  CONST_24  C22   C21  C20  C19     0.00   0.0  0
 IP7  CONST_25  N23   C18  C19  C20     0.00   0.0  0
 IP7  CONST_26  N23   C22  C21  C20     0.00   0.0  0
 IP7  CONST_27  C27   C31  C32  C24     0.00   0.0  0
 IP7  CONST_28  N30   C31  C32  C24   180.00   0.0  0
 IP7  CONST_29  C27   C26  C25  C24     0.00   0.0  0
 IP7  CONST_30  C31   C32  C24  C25     0.00   0.0  0
 IP7  CONST_31  C28   C27  C26  C25   180.00   0.0  0
 IP7  CONST_32  C31   C27  C26  C25     0.00   0.0  0
 IP7  CONST_33  C32   C24  C25  C26     0.00   0.0  0
 IP7  CONST_34  C29   C28  C27  C26   180.00   0.0  0
 IP7  CONST_35  N30   C31  C27  C26   180.00   0.0  0
 IP7  CONST_36  C32   C31  C27  C26     0.00   0.0  0
 IP7  CONST_37  N30   C29  C28  C27     0.00   0.0  0
 IP7  CONST_38  C29   N30  C31  C27     0.00   0.0  0
 IP7  CONST_39  N30   C31  C27  C28     0.00   0.0  0
 IP7  CONST_40  C32   C31  C27  C28   180.00   0.0  0
 IP7  CONST_41  C31   N30  C29  C28     0.00   0.0  0
 IP7  CONST_42  C31   C27  C28  C29     0.00   0.0  0
 IP7  CONST_43  C32   C31  N30  C29   180.00   0.0  0
 IP7  CONST_44  C4    N3   C2   N1    180.00   0.0  0
 IP7  CONST_45  C6    C7   C2   N1    180.00   0.0  0
 IP7  CONST_46  N8    C7   C2   N3    180.00   0.0  0
 IP7  CONST_47  N8    C7   C6   C5    180.00   0.0  0
 IP7  CONST_48  C12   C11  C10  C9    180.00   0.0  0
 IP7  CONST_49  C14   C15  C10  C9    180.00   0.0  0
 IP7  CONST_50  O16   C15  C10  C11   180.00   0.0  0
 IP7  CONST_51  O16   C15  C14  C13   180.00   0.0  0
 IP7  CONST_52  C22   N23  C18  C17   180.00   0.0  0
 IP7  CONST_53  C20   C19  C18  C17   180.00   0.0  0
 IP7  CONST_54  H4    C4   N3   C2    180.00   0.0  0
 IP7  CONST_55  H6    C6   C7   C2    180.00   0.0  0
 IP7  CONST_56  H5    C5   C4   N3    180.00   0.0  0
 IP7  CONST_57  H14   C14  C15  C10   180.00   0.0  0
 IP7  CONST_58  H13   C13  C12  C11   180.00   0.0  0
 IP7  CONST_59  H32   C32  C24  C12     0.00   0.0  0
 IP7  CONST_60  H25   C25  C24  C12     0.00   0.0  0
 IP7  CONST_61  H11   C11  C12  C13   180.00   0.0  0
 IP7  CONST_62  H22   C22  N23  C18   180.00   0.0  0
 IP7  CONST_63  H20   C20  C19  C18   180.00   0.0  0
 IP7  CONST_64  H21   C21  C20  C19   180.00   0.0  0
 IP7  CONST_65  H19   C19  C20  C21   180.00   0.0  0
 IP7  CONST_66  H26   C26  C25  C24   180.00   0.0  0
 IP7  CONST_67  H28   C28  C27  C26     0.00   0.0  0
 IP7  CONST_68  H29   C29  C28  C27   180.00   0.0  0
 IP7  CONST_69  HN30  N30  C31  C27   180.00   0.0  0
 IP7  CONST_70  C9    N8   C7   C2    180.00   0.0  0
 IP7  CONST_71  C9    N8   C7   C6      0.00   0.0  0
 IP7  Var_01    C10   C9   N8   C7   -172.16  30.0  3
 IP7  Var_02    C11   C10  C9   N8   -110.30  30.0  2
 IP7  Var_03    C18   C17  O16  C15   161.13  30.0  3
 IP7  Var_04    N23   C18  C17  O16   161.13  30.0  2

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
 IP7  plan-1  N1    0.020
 IP7  plan-1  C2    0.020
 IP7  plan-1  N3    0.020
 IP7  plan-1  C4    0.020
 IP7  plan-1  C5    0.020
 IP7  plan-1  C6    0.020
 IP7  plan-1  C7    0.020
 IP7  plan-1  N8    0.020
 IP7  plan-1  H4    0.020
 IP7  plan-1  H5    0.020
 IP7  plan-1  H6    0.020
 IP7  plan-2  C9    0.020
 IP7  plan-2  C10   0.020
 IP7  plan-2  C11   0.020
 IP7  plan-2  C12   0.020
 IP7  plan-2  C13   0.020
 IP7  plan-2  C14   0.020
 IP7  plan-2  C15   0.020
 IP7  plan-2  O16   0.020
 IP7  plan-2  C24   0.020
 IP7  plan-2  H11   0.020
 IP7  plan-2  H13   0.020
 IP7  plan-2  H14   0.020
 IP7  plan-3  C17   0.020
 IP7  plan-3  C18   0.020
 IP7  plan-3  C19   0.020
 IP7  plan-3  C20   0.020
 IP7  plan-3  C21   0.020
 IP7  plan-3  C22   0.020
 IP7  plan-3  N23   0.020
 IP7  plan-3  H19   0.020
 IP7  plan-3  H20   0.020
 IP7  plan-3  H21   0.020
 IP7  plan-3  H22   0.020
 IP7  plan-4  C12   0.020
 IP7  plan-4  C24   0.020
 IP7  plan-4  C25   0.020
 IP7  plan-4  C26   0.020
 IP7  plan-4  C27   0.020
 IP7  plan-4  C28   0.020
 IP7  plan-4  C29   0.020
 IP7  plan-4  N30   0.020
 IP7  plan-4  C31   0.020
 IP7  plan-4  C32   0.020
 IP7  plan-4  H25   0.020
 IP7  plan-4  H26   0.020
 IP7  plan-4  H28   0.020
 IP7  plan-4  H29   0.020
 IP7  plan-4  HN30  0.020
 IP7  plan-4  H32   0.020
 IP7  plan-5  N1    0.020
 IP7  plan-5  C2    0.020
 IP7  plan-5  HN11  0.020
 IP7  plan-5  HN12  0.020
 IP7  plan-6  C7    0.020
 IP7  plan-6  N8    0.020
 IP7  plan-6  C9    0.020
 IP7  plan-6  HN8   0.020

