# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 03:04:15 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: N~3~-[3-(1H-indol-6-yl)benzyl]pyridine-2,3-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncccc1NCc2cccc(c2)c3ccc4cc[nH]c4c3
#
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
 IP6  IP6  N~3~-[3-(1H-indol-6-yl)benzyl]pyridine-2,3-diamine  ligand  42  24  .  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_IP6
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
 IP6  N1    N  NH2   0  -0.816   0.7237   2.2001  -6.6936
 IP6  C2    C  CR6   0   0.369   1.6994   3.0995  -6.3237
 IP6  N3    N  N     0  -0.438   2.1012   3.9882  -7.2100
 IP6  C4    C  CR16  0  -0.083   3.0269   4.8865  -6.8584
 IP6  C5    C  CR16  0  -0.318   3.5947   4.9206  -5.6067
 IP6  C6    C  CR16  0  -0.229   3.1590   3.9958  -4.6534
 IP6  C7    C  CR6   0   0.231   2.1918   3.0668  -4.9896
 IP6  N8    N  NH1   0  -0.677   1.6985   2.0927  -4.1349
 IP6  C9    C  CH2   0  -0.336   2.1194   2.0836  -2.7499
 IP6  C10   C  CR6   0   0.119   1.5132   0.9071  -2.0350
 IP6  C11   C  CR16  0  -0.282   1.8410  -0.3908  -2.4223
 IP6  C12   C  CR16  0  -0.204   1.2926  -1.4726  -1.7527
 IP6  C13   C  CR16  0  -0.310   0.4100  -1.2733  -0.6994
 IP6  C14   C  CR6   0   0.117   0.0605   0.0161  -0.3003
 IP6  C15   C  CR16  0  -0.363   0.6269   1.0959  -0.9841
 IP6  C16   C  CR6   0   0.057  -0.8857   0.2372   0.8121
 IP6  C17   C  CR16  0  -0.311  -0.8450  -0.5975   1.9509
 IP6  C18   C  CR16  0  -0.313  -1.7085  -0.4255   3.0115
 IP6  C19   C  CR56  0   0.048  -2.6577   0.6021   2.9599
 IP6  C20   C  CR15  0  -0.405  -3.6868   1.0649   3.8359
 IP6  C21   C  CR15  0   0.019  -4.2875   2.1191   3.2093
 IP6  N22   N  NR15  0  -0.668  -3.6931   2.3386   1.9999
 IP6  C23   C  CR56  0   0.409  -2.6912   1.4310   1.8160
 IP6  C24   C  CR16  0  -0.340  -1.8188   1.2624   0.7450
 IP6  HN11  H  HNH2  0   0.365   0.8262   1.2697  -6.3145
 IP6  HN12  H  HNH2  0   0.360   0.5491   2.1804  -7.6869
 IP6  H4    H  HCR6  0   0.231   3.3235   5.5936  -7.6249
 IP6  H5    H  HCR6  0   0.236   4.3505   5.6536  -5.3610
 IP6  H6    H  HCR6  0   0.255   3.5749   4.0238  -3.6549
 IP6  HN8   H  HNH1  0   0.356   0.7005   1.9549  -4.2310
 IP6  H91   H  HCH2  0   0.223   1.8595   3.0134  -2.2263
 IP6  H92   H  HCH2  0   0.243   3.2094   2.0023  -2.7182
 IP6  H11   H  HCR6  0   0.231   2.5290  -0.5501  -3.2437
 IP6  H12   H  HCR6  0   0.236   1.5467  -2.4806  -2.0542
 IP6  H13   H  HCR6  0   0.232  -0.0228  -2.1306  -0.1992
 IP6  H15   H  HCR6  0   0.225   0.3870   2.1068  -0.6736
 IP6  H17   H  HCR6  0   0.225  -0.0993  -1.3807   2.0031
 IP6  H18   H  HCR6  0   0.222  -1.6459  -1.0753   3.8756
 IP6  H20   H  HCR5  0   0.223  -3.9486   0.6681   4.8036
 IP6  H21   H  HCR5  0   0.253  -5.1057   2.7402   3.5368
 IP6  HN22  H  HNR5  0   0.383  -3.9625   3.0558   1.3476
 IP6  H24   H  HCR6  0   0.224  -1.8840   1.9020  -0.1270

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
 IP6  N1   C2    single    1.378  0.020  1.378
 IP6  N1   HN11  single    0.890  0.020  1.040
 IP6  N1   HN12  single    0.890  0.020  1.040
 IP6  C2   N3    aromatic  1.318  0.020  1.318
 IP6  C2   C7    aromatic  1.422  0.020  1.422
 IP6  N3   C4    aromatic  1.337  0.020  1.337
 IP6  C4   C5    aromatic  1.375  0.020  1.375
 IP6  C4   H4    single    0.930  0.020  1.080
 IP6  C5   C6    aromatic  1.398  0.020  1.398
 IP6  C5   H5    single    0.930  0.020  1.080
 IP6  C6   C7    aromatic  1.383  0.020  1.383
 IP6  C6   H6    single    0.930  0.020  1.080
 IP6  C7   N8    single    1.387  0.020  1.387
 IP6  N8   C9    single    1.448  0.020  1.448
 IP6  N8   HN8   single    0.890  0.020  1.040
 IP6  C9   C10   single    1.504  0.020  1.504
 IP6  C9   H91   single    0.970  0.020  1.090
 IP6  C9   H92   single    0.970  0.020  1.090
 IP6  C10  C15   aromatic  1.388  0.020  1.388
 IP6  C10  C11   aromatic  1.394  0.020  1.394
 IP6  C11  C12   aromatic  1.385  0.020  1.385
 IP6  C11  H11   single    0.930  0.020  1.080
 IP6  C12  C13   aromatic  1.389  0.020  1.389
 IP6  C12  H12   single    0.930  0.020  1.080
 IP6  C13  C14   aromatic  1.394  0.020  1.394
 IP6  C13  H13   single    0.930  0.020  1.080
 IP6  C14  C16   single    1.477  0.020  1.477
 IP6  C14  C15   aromatic  1.398  0.020  1.398
 IP6  C15  H15   single    0.930  0.020  1.080
 IP6  C16  C24   aromatic  1.388  0.020  1.388
 IP6  C16  C17   aromatic  1.413  0.020  1.413
 IP6  C17  C18   aromatic  1.378  0.020  1.378
 IP6  C17  H17   single    0.930  0.020  1.080
 IP6  C18  C19   aromatic  1.400  0.020  1.400
 IP6  C18  H18   single    0.930  0.020  1.080
 IP6  C19  C20   aromatic  1.428  0.020  1.428
 IP6  C19  C23   aromatic  1.413  0.020  1.413
 IP6  C20  C21   aromatic  1.366  0.020  1.366
 IP6  C20  H20   single    0.930  0.020  1.080
 IP6  C21  N22   aromatic  1.365  0.020  1.365
 IP6  C21  H21   single    0.930  0.020  1.080
 IP6  N22  C23   aromatic  1.364  0.020  1.364
 IP6  N22  HN22  single    0.860  0.020  1.020
 IP6  C23  C24   aromatic  1.392  0.020  1.392
 IP6  C24  H24   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
 IP6  HN12  N1   HN11  111.67  3.000
 IP6  HN12  N1   C2    113.56  3.000
 IP6  HN11  N1   C2    115.39  3.000
 IP6  C7    C2   N3    122.74  3.000
 IP6  C7    C2   N1    118.81  3.000
 IP6  N3    C2   N1    118.40  3.000
 IP6  C4    N3   C2    119.16  3.000
 IP6  H4    C4   C5    120.97  3.000
 IP6  H4    C4   N3    116.21  3.000
 IP6  C5    C4   N3    122.82  3.000
 IP6  H5    C5   C6    120.76  3.000
 IP6  H5    C5   C4    120.82  3.000
 IP6  C6    C5   C4    118.41  3.000
 IP6  H6    C6   C7    120.71  3.000
 IP6  H6    C6   C5    119.50  3.000
 IP6  C7    C6   C5    119.79  3.000
 IP6  N8    C7   C6    124.82  3.000
 IP6  N8    C7   C2    118.11  3.000
 IP6  C6    C7   C2    117.05  3.000
 IP6  HN8   N8   C9    112.13  3.000
 IP6  HN8   N8   C7    112.82  3.000
 IP6  C9    N8   C7    119.39  3.000
 IP6  H92   C9   H91   106.57  3.000
 IP6  H92   C9   C10   109.25  3.000
 IP6  H91   C9   C10   109.89  3.000
 IP6  H92   C9   N8    108.54  3.000
 IP6  H91   C9   N8    112.45  3.000
 IP6  C10   C9   N8    110.03  3.000
 IP6  C15   C10  C11   119.18  3.000
 IP6  C11   C10  C9    120.10  3.000
 IP6  C15   C10  C9    120.72  3.000
 IP6  H11   C11  C12   120.21  3.000
 IP6  H11   C11  C10   119.81  3.000
 IP6  C12   C11  C10   119.98  3.000
 IP6  H12   C12  C13   119.62  3.000
 IP6  H12   C12  C11   119.97  3.000
 IP6  C13   C12  C11   120.41  3.000
 IP6  H13   C13  C14   119.98  3.000
 IP6  H13   C13  C12   119.39  3.000
 IP6  C14   C13  C12   120.61  3.000
 IP6  C16   C14  C15   120.82  3.000
 IP6  C15   C14  C13   118.21  3.000
 IP6  C16   C14  C13   120.97  3.000
 IP6  H15   C15  C14   119.37  3.000
 IP6  H15   C15  C10   119.01  3.000
 IP6  C14   C15  C10   121.60  3.000
 IP6  C24   C16  C17   119.66  3.000
 IP6  C17   C16  C14   120.02  3.000
 IP6  C24   C16  C14   120.32  3.000
 IP6  H17   C17  C18   118.99  3.000
 IP6  H17   C17  C16   119.09  3.000
 IP6  C18   C17  C16   121.91  3.000
 IP6  H18   C18  C19   120.60  3.000
 IP6  H18   C18  C17   120.18  3.000
 IP6  C19   C18  C17   119.21  3.000
 IP6  C23   C19  C20   106.82  3.000
 IP6  C23   C19  C18   118.46  3.000
 IP6  C20   C19  C18   134.72  3.000
 IP6  H20   C20  C21   126.09  3.000
 IP6  H20   C20  C19   127.31  3.000
 IP6  C21   C20  C19   106.59  3.000
 IP6  H21   C21  N22   120.45  3.000
 IP6  H21   C21  C20   129.73  3.000
 IP6  N22   C21  C20   109.82  3.000
 IP6  HN22  N22  C23   125.69  3.000
 IP6  HN22  N22  C21   124.91  3.000
 IP6  C23   N22  C21   109.40  3.000
 IP6  C24   C23  N22   130.14  3.000
 IP6  C24   C23  C19   122.49  3.000
 IP6  N22   C23  C19   107.37  3.000
 IP6  H24   C24  C23   120.68  3.000
 IP6  H24   C24  C16   121.03  3.000
 IP6  C23   C24  C16   118.28  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
 IP6  CONST_01  C5    C4   N3   C2      0.00   0.0  0
 IP6  CONST_02  C5    C6   C7   C2      0.00   0.0  0
 IP6  CONST_03  C6    C7   C2   N3      0.00   0.0  0
 IP6  CONST_04  C6    C5   C4   N3      0.00   0.0  0
 IP6  CONST_05  C7    C2   N3   C4      0.00   0.0  0
 IP6  CONST_06  C7    C6   C5   C4      0.00   0.0  0
 IP6  CONST_07  C13   C14  C15  C10     0.00   0.0  0
 IP6  CONST_08  C16   C14  C15  C10   180.00   0.0  0
 IP6  CONST_09  C13   C12  C11  C10     0.00   0.0  0
 IP6  CONST_10  C14   C15  C10  C11     0.00   0.0  0
 IP6  CONST_11  C14   C13  C12  C11     0.00   0.0  0
 IP6  CONST_12  C15   C10  C11  C12     0.00   0.0  0
 IP6  CONST_13  C16   C14  C13  C12   180.00   0.0  0
 IP6  CONST_14  C15   C14  C13  C12     0.00   0.0  0
 IP6  CONST_17  C23   C24  C16  C14   180.00   0.0  0
 IP6  CONST_18  C18   C17  C16  C14   180.00   0.0  0
 IP6  CONST_21  C19   C23  C24  C16     0.00   0.0  0
 IP6  CONST_22  N22   C23  C24  C16   180.00   0.0  0
 IP6  CONST_23  C19   C18  C17  C16     0.00   0.0  0
 IP6  CONST_24  C23   C24  C16  C17     0.00   0.0  0
 IP6  CONST_25  C20   C19  C18  C17   180.00   0.0  0
 IP6  CONST_26  C23   C19  C18  C17     0.00   0.0  0
 IP6  CONST_27  C24   C16  C17  C18     0.00   0.0  0
 IP6  CONST_28  C21   C20  C19  C18   180.00   0.0  0
 IP6  CONST_29  N22   C23  C19  C18   180.00   0.0  0
 IP6  CONST_30  C24   C23  C19  C18     0.00   0.0  0
 IP6  CONST_31  N22   C21  C20  C19     0.00   0.0  0
 IP6  CONST_32  C21   N22  C23  C19     0.00   0.0  0
 IP6  CONST_33  N22   C23  C19  C20     0.00   0.0  0
 IP6  CONST_34  C24   C23  C19  C20   180.00   0.0  0
 IP6  CONST_35  C23   N22  C21  C20     0.00   0.0  0
 IP6  CONST_36  C23   C19  C20  C21     0.00   0.0  0
 IP6  CONST_37  C24   C23  N22  C21   180.00   0.0  0
 IP6  CONST_38  C4    N3   C2   N1    180.00   0.0  0
 IP6  CONST_39  C6    C7   C2   N1    180.00   0.0  0
 IP6  CONST_40  N8    C7   C2   N3    180.00   0.0  0
 IP6  CONST_41  N8    C7   C6   C5    180.00   0.0  0
 IP6  CONST_42  C14   C15  C10  C9    180.00   0.0  0
 IP6  CONST_43  C12   C11  C10  C9    180.00   0.0  0
 IP6  CONST_44  H4    C4   N3   C2    180.00   0.0  0
 IP6  CONST_45  H6    C6   C7   C2    180.00   0.0  0
 IP6  CONST_46  H5    C5   C4   N3    180.00   0.0  0
 IP6  CONST_47  H12   C12  C11  C10   180.00   0.0  0
 IP6  CONST_48  H15   C15  C10  C11   180.00   0.0  0
 IP6  CONST_49  H13   C13  C12  C11   180.00   0.0  0
 IP6  CONST_50  H11   C11  C12  C13   180.00   0.0  0
 IP6  CONST_51  H24   C24  C16  C14     0.00   0.0  0
 IP6  CONST_52  H17   C17  C16  C14     0.00   0.0  0
 IP6  CONST_53  H18   C18  C17  C16   180.00   0.0  0
 IP6  CONST_54  H20   C20  C19  C18     0.00   0.0  0
 IP6  CONST_55  H21   C21  C20  C19   180.00   0.0  0
 IP6  CONST_56  HN22  N22  C23  C19   180.00   0.0  0
 IP6  CONST_57  C9    N8   C7   C2    180.00   0.0  0
 IP6  CONST_58  C9    N8   C7   C6      0.00   0.0  0
 IP6  CONST_61  HN12  N1   C2   N3      0.00   0.0  0
 IP6  Var_01    C10   C9   N8   C7   -177.27  30.0  3
 IP6  Var_02    C15   C10  C9   N8   -116.71  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
 IP6  plan-1  N1    0.020
 IP6  plan-1  C2    0.020
 IP6  plan-1  N3    0.020
 IP6  plan-1  C4    0.020
 IP6  plan-1  C5    0.020
 IP6  plan-1  C6    0.020
 IP6  plan-1  C7    0.020
 IP6  plan-1  N8    0.020
 IP6  plan-1  H4    0.020
 IP6  plan-1  H5    0.020
 IP6  plan-1  H6    0.020
 IP6  plan-2  C9    0.020
 IP6  plan-2  C10   0.020
 IP6  plan-2  C11   0.020
 IP6  plan-2  C12   0.020
 IP6  plan-2  C13   0.020
 IP6  plan-2  C14   0.020
 IP6  plan-2  C15   0.020
 IP6  plan-2  C16   0.020
 IP6  plan-2  H11   0.020
 IP6  plan-2  H12   0.020
 IP6  plan-2  H13   0.020
 IP6  plan-2  H15   0.020
 IP6  plan-3  C14   0.020
 IP6  plan-3  C16   0.020
 IP6  plan-3  C17   0.020
 IP6  plan-3  C18   0.020
 IP6  plan-3  C19   0.020
 IP6  plan-3  C20   0.020
 IP6  plan-3  C21   0.020
 IP6  plan-3  N22   0.020
 IP6  plan-3  C23   0.020
 IP6  plan-3  C24   0.020
 IP6  plan-3  H17   0.020
 IP6  plan-3  H18   0.020
 IP6  plan-3  H20   0.020
 IP6  plan-3  H21   0.020
 IP6  plan-3  HN22  0.020
 IP6  plan-3  H24   0.020
 IP6  plan-4  N1    0.020
 IP6  plan-4  C2    0.020
 IP6  plan-4  HN11  0.020
 IP6  plan-4  HN12  0.020
 IP6  plan-5  C7    0.020
 IP6  plan-5  N8    0.020
 IP6  plan-5  C9    0.020
 IP6  plan-5  HN8   0.020

