# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 00:49:17 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: N~3~-[3-(5-methoxypyridin-3-yl)benzyl]pyridine-2,3-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cncc(c1)c2cccc(CNc3cccnc3N)c2
#
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
 9IP  9IP  N~3~-[3-(5-methoxypyridin-3-yl)benzyl]pyridine-2,3-diamine  ligand  41  23  .  2022-07-24  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_9IP
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
 9IP  C1    C  CH3   0  -0.440  8.5910  -3.8711  -0.8732
 9IP  O2    O  O2    0  -0.466  7.6381  -3.1514  -0.1120
 9IP  C3    C  CR6   0   0.340  6.3808  -3.0723  -0.5724
 9IP  C4    C  CR16  0  -0.196  5.9357  -3.6231  -1.7733
 9IP  N5    N  N     0  -0.381  4.6758  -3.5115  -2.1799
 9IP  C6    C  CR16  0  -0.124  3.8089  -2.8563  -1.4302
 9IP  C7    C  CR6   0   0.018  4.1485  -2.2603  -0.2117
 9IP  C8    C  CR16  0  -0.310  5.4632  -2.3788   0.2126
 9IP  C9    C  CR6   0   0.105  3.1385  -1.5473   0.5917
 9IP  C10   C  CR16  0  -0.321  2.1601  -0.7668  -0.0199
 9IP  C11   C  CR16  0  -0.226  1.2124  -0.1030   0.7478
 9IP  C12   C  CR16  0  -0.294  1.2286  -0.2102   2.1292
 9IP  C13   C  CR6   0   0.117  2.1977  -0.9887   2.7593
 9IP  C14   C  CH2   0  -0.351  2.2130  -1.1242   4.2574
 9IP  N15   N  NH1   0  -0.684  2.3641   0.1745   4.8760
 9IP  C16   C  CR6   0   0.222  2.3467   0.2700   6.2603
 9IP  C17   C  CR16  0  -0.249  2.1057  -0.7846   7.1212
 9IP  C18   C  CR16  0  -0.341  2.0935  -0.5649   8.5015
 9IP  C19   C  CR16  0  -0.102  2.3425   0.7060   8.9636
 9IP  N20   N  N     0  -0.441  2.5628   1.7433   8.1495
 9IP  C21   C  CR6   0   0.360  2.5558   1.5490   6.8459
 9IP  N22   N  NH2   0  -0.833  2.8122   2.6228   6.0228
 9IP  C23   C  CR16  0  -0.376  3.1443  -1.6438   1.9848
 9IP  H11A  H  HCH3  0   0.262  9.5249  -3.8260  -0.3191
 9IP  H12A  H  HCH3  0   0.233  8.7445  -3.4271  -1.8600
 9IP  H13   H  HCH3  0   0.233  8.3041  -4.9184  -0.9957
 9IP  H4    H  HCR6  0   0.279  6.6029  -4.1715  -2.4279
 9IP  H6    H  HCR6  0   0.258  2.7879  -2.8120  -1.7939
 9IP  H8    H  HCR6  0   0.276  5.7925  -1.9258   1.1403
 9IP  H10   H  HCR6  0   0.257  2.1461  -0.6570  -1.0970
 9IP  H11   H  HCR6  0   0.260  0.4594   0.5032   0.2612
 9IP  H12   H  HCR6  0   0.254  0.4849   0.3082   2.7217
 9IP  H141  H  HCH2  0   0.255  1.2659  -1.5577   4.5917
 9IP  H142  H  HCH2  0   0.238  3.0012  -1.8288   4.5546
 9IP  HN15  H  HNH1  0   0.375  3.1110   0.7131   4.4560
 9IP  H17   H  HCR6  0   0.277  1.9358  -1.7824   6.7384
 9IP  H18   H  HCR6  0   0.255  1.9065  -1.3783   9.1888
 9IP  H19   H  HCR6  0   0.247  2.3572   0.9195  10.0264
 9IP  H221  H  HNH2  0   0.379  2.7728   3.5133   6.4951
 9IP  H222  H  HNH2  0   0.379  2.2938   2.6360   5.1563
 9IP  H23   H  HCR6  0   0.255  3.8919  -2.2567   2.4759

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
 9IP  C1   O2    single    1.416  0.020  1.416
 9IP  C1   H11A  single    0.970  0.020  1.090
 9IP  C1   H12A  single    0.970  0.020  1.090
 9IP  C1   H13   single    0.970  0.020  1.090
 9IP  O2   C3    single    1.341  0.020  1.341
 9IP  C3   C4    aromatic  1.394  0.020  1.394
 9IP  C3   C8    aromatic  1.392  0.020  1.392
 9IP  C4   N5    aromatic  1.329  0.020  1.329
 9IP  C4   H4    single    0.930  0.020  1.080
 9IP  N5   C6    aromatic  1.320  0.020  1.320
 9IP  C6   C7    aromatic  1.398  0.020  1.398
 9IP  C6   H6    single    0.930  0.020  1.080
 9IP  C7   C8    aromatic  1.387  0.020  1.387
 9IP  C7   C9    single    1.474  0.020  1.474
 9IP  C8   H8    single    0.930  0.020  1.080
 9IP  C9   C23   aromatic  1.397  0.020  1.397
 9IP  C9   C10   aromatic  1.393  0.020  1.393
 9IP  C10  C11   aromatic  1.389  0.020  1.389
 9IP  C10  H10   single    0.930  0.020  1.080
 9IP  C11  C12   aromatic  1.386  0.020  1.386
 9IP  C11  H11   single    0.930  0.020  1.080
 9IP  C12  C13   aromatic  1.394  0.020  1.394
 9IP  C12  H12   single    0.930  0.020  1.080
 9IP  C13  C23   aromatic  1.387  0.020  1.387
 9IP  C13  C14   single    1.504  0.020  1.504
 9IP  C14  N15   single    1.446  0.020  1.446
 9IP  C14  H141  single    0.970  0.020  1.090
 9IP  C14  H142  single    0.970  0.020  1.090
 9IP  N15  C16   single    1.388  0.020  1.388
 9IP  N15  HN15  single    0.890  0.020  1.040
 9IP  C16  C21   aromatic  1.422  0.020  1.422
 9IP  C16  C17   aromatic  1.382  0.020  1.382
 9IP  C17  C18   aromatic  1.398  0.020  1.398
 9IP  C17  H17   single    0.930  0.020  1.080
 9IP  C18  C19   aromatic  1.375  0.020  1.375
 9IP  C18  H18   single    0.930  0.020  1.080
 9IP  C19  N20   aromatic  1.337  0.020  1.337
 9IP  C19  H19   single    0.930  0.020  1.080
 9IP  N20  C21   aromatic  1.318  0.020  1.318
 9IP  C21  N22   single    1.377  0.020  1.377
 9IP  N22  H221  single    0.890  0.020  1.040
 9IP  N22  H222  single    0.890  0.020  1.040
 9IP  C23  H23   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
 9IP  H13   C1   H12A  108.97  3.000
 9IP  H13   C1   H11A  108.82  3.000
 9IP  H12A  C1   H11A  108.83  3.000
 9IP  H13   C1   O2    111.75  3.000
 9IP  H12A  C1   O2    111.92  3.000
 9IP  H11A  C1   O2    106.44  3.000
 9IP  C3    O2   C1    118.44  3.000
 9IP  C8    C3   C4    118.16  3.000
 9IP  C8    C3   O2    116.97  3.000
 9IP  C4    C3   O2    124.86  3.000
 9IP  H4    C4   N5    116.20  3.000
 9IP  H4    C4   C3    121.58  3.000
 9IP  N5    C4   C3    122.22  3.000
 9IP  C6    N5   C4    119.38  3.000
 9IP  H6    C6   C7    120.23  3.000
 9IP  H6    C6   N5    116.61  3.000
 9IP  C7    C6   N5    123.15  3.000
 9IP  C9    C7   C8    121.61  3.000
 9IP  C9    C7   C6    120.97  3.000
 9IP  C8    C7   C6    117.42  3.000
 9IP  H8    C8   C7    120.95  3.000
 9IP  H8    C8   C3    119.38  3.000
 9IP  C7    C8   C3    119.66  3.000
 9IP  C23   C9   C10   118.66  3.000
 9IP  C10   C9   C7    120.86  3.000
 9IP  C23   C9   C7    120.49  3.000
 9IP  H10   C10  C11   119.52  3.000
 9IP  H10   C10  C9    120.17  3.000
 9IP  C11   C10  C9    120.30  3.000
 9IP  H11   C11  C12   119.98  3.000
 9IP  H11   C11  C10   119.61  3.000
 9IP  C12   C11  C10   120.41  3.000
 9IP  H12   C12  C13   119.84  3.000
 9IP  H12   C12  C11   120.02  3.000
 9IP  C13   C12  C11   120.14  3.000
 9IP  C23   C13  C14   120.43  3.000
 9IP  C14   C13  C12   120.50  3.000
 9IP  C23   C13  C12   119.06  3.000
 9IP  H142  C14  H141  106.52  3.000
 9IP  H142  C14  N15   112.66  3.000
 9IP  H141  C14  N15   108.40  3.000
 9IP  H142  C14  C13   109.54  3.000
 9IP  H141  C14  C13   109.34  3.000
 9IP  N15   C14  C13   110.25  3.000
 9IP  HN15  N15  C16   112.74  3.000
 9IP  HN15  N15  C14   112.18  3.000
 9IP  C16   N15  C14   119.15  3.000
 9IP  C21   C16  C17   117.08  3.000
 9IP  C17   C16  N15   124.81  3.000
 9IP  C21   C16  N15   118.09  3.000
 9IP  H17   C17  C18   119.53  3.000
 9IP  H17   C17  C16   120.69  3.000
 9IP  C18   C17  C16   119.78  3.000
 9IP  H18   C18  C19   120.87  3.000
 9IP  H18   C18  C17   120.73  3.000
 9IP  C19   C18  C17   118.40  3.000
 9IP  H19   C19  N20   116.23  3.000
 9IP  H19   C19  C18   120.92  3.000
 9IP  N20   C19  C18   122.84  3.000
 9IP  C21   N20  C19   119.14  3.000
 9IP  N22   C21  N20   118.37  3.000
 9IP  N22   C21  C16   118.85  3.000
 9IP  N20   C21  C16   122.73  3.000
 9IP  H222  N22  H221  111.72  3.000
 9IP  H222  N22  C21   115.31  3.000
 9IP  H221  N22  C21   113.66  3.000
 9IP  H23   C23  C13   118.98  3.000
 9IP  H23   C23  C9    119.58  3.000
 9IP  C13   C23  C9    121.43  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
 9IP  CONST_01  C6    N5   C4   C3      0.00   0.0  0
 9IP  CONST_02  C6    C7   C8   C3      0.00   0.0  0
 9IP  CONST_03  C9    C7   C8   C3    180.00   0.0  0
 9IP  CONST_04  C7    C8   C3   C4      0.00   0.0  0
 9IP  CONST_05  C7    C6   N5   C4      0.00   0.0  0
 9IP  CONST_06  C8    C3   C4   N5      0.00   0.0  0
 9IP  CONST_07  C8    C7   C6   N5      0.00   0.0  0
 9IP  CONST_08  C9    C7   C6   N5    180.00   0.0  0
 9IP  CONST_11  C13   C23  C9   C7    180.00   0.0  0
 9IP  CONST_12  C11   C10  C9   C7    180.00   0.0  0
 9IP  CONST_15  C12   C13  C23  C9      0.00   0.0  0
 9IP  CONST_16  C12   C11  C10  C9      0.00   0.0  0
 9IP  CONST_17  C13   C23  C9   C10     0.00   0.0  0
 9IP  CONST_18  C13   C12  C11  C10     0.00   0.0  0
 9IP  CONST_19  C23   C9   C10  C11     0.00   0.0  0
 9IP  CONST_20  C23   C13  C12  C11     0.00   0.0  0
 9IP  CONST_21  C19   N20  C21  C16     0.00   0.0  0
 9IP  CONST_22  C19   C18  C17  C16     0.00   0.0  0
 9IP  CONST_23  N20   C21  C16  C17     0.00   0.0  0
 9IP  CONST_24  N20   C19  C18  C17     0.00   0.0  0
 9IP  CONST_25  C21   C16  C17  C18     0.00   0.0  0
 9IP  CONST_26  C21   N20  C19  C18     0.00   0.0  0
 9IP  CONST_27  N5    C4   C3   O2    180.00   0.0  0
 9IP  CONST_28  C7    C8   C3   O2    180.00   0.0  0
 9IP  CONST_29  C14   C13  C23  C9    180.00   0.0  0
 9IP  CONST_30  C14   C13  C12  C11   180.00   0.0  0
 9IP  CONST_31  N20   C21  C16  N15   180.00   0.0  0
 9IP  CONST_32  C18   C17  C16  N15   180.00   0.0  0
 9IP  CONST_33  N22   C21  C16  C17   180.00   0.0  0
 9IP  CONST_34  N22   C21  N20  C19   180.00   0.0  0
 9IP  CONST_35  H8    C8   C3   C4    180.00   0.0  0
 9IP  CONST_36  H6    C6   N5   C4    180.00   0.0  0
 9IP  CONST_37  H4    C4   N5   C6    180.00   0.0  0
 9IP  CONST_38  H23   C23  C9   C7      0.00   0.0  0
 9IP  CONST_39  H10   C10  C9   C7      0.00   0.0  0
 9IP  CONST_40  H11   C11  C10  C9    180.00   0.0  0
 9IP  CONST_41  H12   C12  C11  C10   180.00   0.0  0
 9IP  CONST_42  H18   C18  C17  C16   180.00   0.0  0
 9IP  CONST_43  H19   C19  C18  C17   180.00   0.0  0
 9IP  CONST_44  H17   C17  C18  C19   180.00   0.0  0
 9IP  CONST_45  C21   C16  N15  C14   180.00   0.0  0
 9IP  CONST_46  C17   C16  N15  C14     0.00   0.0  0
 9IP  CONST_47  H221  N22  C21  C16   180.00   0.0  0
 9IP  Var_01    C4    C3   O2   C1     -1.59  30.0  2
 9IP  Var_02    N15   C14  C13  C12   -59.42  30.0  2
 9IP  Var_03    C16   N15  C14  C13   177.41  30.0  3
 9IP  Var_04    H11A  C1   O2   C3   -178.98  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
 9IP  plan-1  O2    0.020
 9IP  plan-1  C3    0.020
 9IP  plan-1  C4    0.020
 9IP  plan-1  N5    0.020
 9IP  plan-1  C6    0.020
 9IP  plan-1  C7    0.020
 9IP  plan-1  C8    0.020
 9IP  plan-1  C9    0.020
 9IP  plan-1  H4    0.020
 9IP  plan-1  H6    0.020
 9IP  plan-1  H8    0.020
 9IP  plan-2  C7    0.020
 9IP  plan-2  C9    0.020
 9IP  plan-2  C10   0.020
 9IP  plan-2  C11   0.020
 9IP  plan-2  C12   0.020
 9IP  plan-2  C13   0.020
 9IP  plan-2  C14   0.020
 9IP  plan-2  C23   0.020
 9IP  plan-2  H10   0.020
 9IP  plan-2  H11   0.020
 9IP  plan-2  H12   0.020
 9IP  plan-2  H23   0.020
 9IP  plan-3  N15   0.020
 9IP  plan-3  C16   0.020
 9IP  plan-3  C17   0.020
 9IP  plan-3  C18   0.020
 9IP  plan-3  C19   0.020
 9IP  plan-3  N20   0.020
 9IP  plan-3  C21   0.020
 9IP  plan-3  N22   0.020
 9IP  plan-3  H17   0.020
 9IP  plan-3  H18   0.020
 9IP  plan-3  H19   0.020
 9IP  plan-4  C14   0.020
 9IP  plan-4  N15   0.020
 9IP  plan-4  C16   0.020
 9IP  plan-4  HN15  0.020
 9IP  plan-5  C21   0.020
 9IP  plan-5  N22   0.020
 9IP  plan-5  H221  0.020
 9IP  plan-5  H222  0.020

