# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 11:56:59 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: 3-(5-{[4-(aminomethyl)piperidin-1-yl]methyl}-1H-indol-2-yl)-1H-indazole-6-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC1CCN(CC1)Cc2ccc3[nH]c(cc3c2)c4n[nH]c5cc(ccc45)C#N
#
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
 422  422  3-(5-{[4-(aminomethyl)piperidin-1-yl]methyl}-1H-indol-2-yl)-1H-indazole-6-carbonitrile  ligand  53  29  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_422
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
 422  C1    C  CR6   0   0.061   -1.7443  -1.3034  4.2702
 422  C2    C  CR16  0  -0.382   -2.5857  -0.6942  5.1836
 422  C3    C  CR56  0   0.101   -3.7595  -1.3447  5.5790
 422  C4    C  CR56  0   0.340   -4.0652  -2.6096  5.0323
 422  C5    C  CR16  0  -0.280   -3.2253  -3.2377  4.1194
 422  C6    C  CR16  0  -0.313   -2.0758  -2.5676  3.7503
 422  C11   C  CR15  0  -0.411   -4.8230  -1.0155  6.4726
 422  C12   C  CR5   0   0.343   -5.7121  -2.0554  6.4389
 422  N13   N  NR15  0  -0.747   -5.2630  -3.0070  5.5559
 422  C14   C  CR5   0   0.156   -6.9675  -2.2282  7.1407
 422  C15   C  CR56  0  -0.075   -8.1400  -2.9141  6.7020
 422  C16   C  CR56  0   0.451   -9.0491  -2.7522  7.7613
 422  N17   N  NR15  0  -0.536   -8.4018  -2.0166  8.6944
 422  N18   N  N     0  -0.232   -7.1629  -1.7080  8.3320
 422  C19   C  CR16  0  -0.310   -8.5362  -3.5987  5.5454
 422  C20   C  CR16  0  -0.225   -9.8037  -4.1213  5.4950
 422  C21   C  CR6   0   0.006  -10.6924  -3.9662  6.5846
 422  C22   C  CR16  0  -0.265  -10.3386  -3.2787  7.7296
 422  C23   C  CSP   0   0.040  -12.0018  -4.5300  6.4910
 422  C7    C  CH2   0  -0.291   -0.4535  -0.6449  3.8491
 422  N2    N  NT    0  -0.404   -0.5628   0.7888  3.6987
 422  C8    C  CH2   0  -0.258    0.7407   1.4082  3.5601
 422  C9    C  CH2   0  -0.265   -1.4395   1.1635  2.6053
 422  C10   C  CH2   0  -0.414   -1.6352   2.6701  2.5505
 422  C13   C  CH2   0  -0.415    0.6329   2.9239  3.5200
 422  C17   C  CH1   0  -0.260   -0.3034   3.3991  2.4134
 422  C18   C  CH2   0  -0.261   -0.4498   4.9223  2.4391
 422  N3    N  NH2   0  -0.745   -1.2853   5.5238  1.4195
 422  N1    N  NS    0  -0.194  -13.0555  -4.9872  6.4117
 422  H2    H  HCR6  0   0.234   -2.3372   0.2850  5.5752
 422  H5    H  HCR6  0   0.231   -3.4624  -4.2077  3.7021
 422  H6    H  HCR6  0   0.221   -1.4109  -3.0317  3.0319
 422  H11   H  HCR5  0   0.230   -4.9370  -0.1097  7.0456
 422  HN13  H  HNR5  0   0.383   -5.6369  -3.9375  5.4799
 422  HN17  H  HNR5  0   0.396   -8.7394  -1.7190  9.5929
 422  H19   H  HCR6  0   0.233   -7.8799  -3.7048  4.6926
 422  H20   H  HCR6  0   0.262  -10.1376  -4.6503  4.6143
 422  H22   H  HCR6  0   0.267  -11.0325  -3.1587  8.5492
 422  H71   H  HCH2  0   0.232    0.3082  -0.8398  4.6120
 422  H72   H  HCH2  0   0.190   -0.0853  -1.1307  2.9276
 422  H81   H  HCH2  0   0.174    1.2596   1.0546  2.6497
 422  H82   H  HCH2  0   0.220    1.3618   1.1066  4.4075
 422  H91   H  HCH2  0   0.238   -2.4049   0.6739  2.7415
 422  H92   H  HCH2  0   0.177   -1.0410   0.8112  1.6354
 422  H101  H  HCH2  0   0.206   -2.3001   2.9068  1.7157
 422  H102  H  HCH2  0   0.211   -2.1393   2.9982  3.4664
 422  H131  H  HCH2  0   0.213    0.2619   3.2802  4.4870
 422  H132  H  HCH2  0   0.218    1.6308   3.3507  3.3863
 422  H17   H  HCH1  0   0.194    0.1388   3.1145  1.4470
 422  H181  H  HCH2  0   0.214    0.5462   5.3704  2.3677
 422  H182  H  HCH2  0   0.204   -0.8426   5.2218  3.4161
 422  HN31  H  HNH2  0   0.323   -2.2497   5.2435  1.5309
 422  HN32  H  HNH2  0   0.315   -0.9970   5.2204  0.4986

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
 422  C1   C6    aromatic  1.407  0.020  1.407
 422  C1   C7    single    1.509  0.020  1.509
 422  C1   C2    aromatic  1.383  0.020  1.383
 422  C2   C3    aromatic  1.399  0.020  1.399
 422  C2   H2    single    0.930  0.020  1.080
 422  C3   C4    aromatic  1.411  0.020  1.411
 422  C3   C11   aromatic  1.428  0.020  1.428
 422  C4   C5    aromatic  1.390  0.020  1.390
 422  C4   N13   aromatic  1.366  0.020  1.366
 422  C5   C6    aromatic  1.381  0.020  1.381
 422  C5   H5    single    0.930  0.020  1.080
 422  C6   H6    single    0.930  0.020  1.080
 422  C11  C12   aromatic  1.369  0.020  1.369
 422  C11  H11   single    0.930  0.020  1.080
 422  C12  N13   aromatic  1.374  0.020  1.374
 422  C12  C14   single    1.449  0.020  1.449
 422  N13  HN13  single    0.860  0.020  1.020
 422  C14  N18   aromatic  1.315  0.020  1.315
 422  C14  C15   aromatic  1.427  0.020  1.427
 422  C15  C16   aromatic  1.405  0.020  1.405
 422  C15  C19   aromatic  1.401  0.020  1.401
 422  C16  N17   aromatic  1.353  0.020  1.353
 422  C16  C22   aromatic  1.393  0.020  1.393
 422  N17  N18   aromatic  1.327  0.020  1.327
 422  N17  HN17  single    0.860  0.020  1.020
 422  C19  C20   aromatic  1.372  0.020  1.372
 422  C19  H19   single    0.930  0.020  1.080
 422  C20  C21   aromatic  1.415  0.020  1.415
 422  C20  H20   single    0.930  0.020  1.080
 422  C21  C22   aromatic  1.382  0.020  1.382
 422  C21  C23   single    1.429  0.020  1.429
 422  C22  H22   single    0.930  0.020  1.080
 422  C23  N1    triple    1.151  0.020  1.151
 422  C7   N2    single    1.446  0.020  1.446
 422  C7   H71   single    0.970  0.020  1.090
 422  C7   H72   single    0.970  0.020  1.090
 422  N2   C8    single    1.450  0.020  1.450
 422  N2   C9    single    1.451  0.020  1.451
 422  C8   C13   single    1.520  0.020  1.520
 422  C8   H81   single    0.970  0.020  1.090
 422  C8   H82   single    0.970  0.020  1.090
 422  C9   C10   single    1.520  0.020  1.520
 422  C9   H91   single    0.970  0.020  1.090
 422  C9   H92   single    0.970  0.020  1.090
 422  C10  C17   single    1.524  0.020  1.524
 422  C10  H101  single    0.970  0.020  1.090
 422  C10  H102  single    0.970  0.020  1.090
 422  C13  C17   single    1.525  0.020  1.525
 422  C13  H131  single    0.970  0.020  1.090
 422  C13  H132  single    0.970  0.020  1.090
 422  C17  C18   single    1.530  0.020  1.530
 422  C17  H17   single    0.970  0.020  1.090
 422  C18  N3    single    1.449  0.020  1.449
 422  C18  H181  single    0.970  0.020  1.090
 422  C18  H182  single    0.970  0.020  1.090
 422  N3   HN31  single    0.890  0.020  1.040
 422  N3   HN32  single    0.890  0.020  1.040

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
 422  C7    C1   C6    119.39  3.000
 422  C7    C1   C2    120.82  3.000
 422  C6    C1   C2    119.77  3.000
 422  H2    C2   C3    120.70  3.000
 422  H2    C2   C1    119.82  3.000
 422  C3    C2   C1    119.48  3.000
 422  C11   C3   C4    106.73  3.000
 422  C11   C3   C2    134.00  3.000
 422  C4    C3   C2    119.27  3.000
 422  N13   C4   C5    130.52  3.000
 422  N13   C4   C3    107.58  3.000
 422  C5    C4   C3    121.89  3.000
 422  H5    C5   C6    120.95  3.000
 422  H5    C5   C4    121.71  3.000
 422  C6    C5   C4    117.33  3.000
 422  H6    C6   C5    118.71  3.000
 422  H6    C6   C1    119.04  3.000
 422  C5    C6   C1    122.25  3.000
 422  H11   C11  C12   125.66  3.000
 422  H11   C11  C3    127.25  3.000
 422  C12   C11  C3    107.06  3.000
 422  C14   C12  N13   120.81  3.000
 422  C14   C12  C11   129.92  3.000
 422  N13   C12  C11   109.26  3.000
 422  HN13  N13  C12   124.60  3.000
 422  HN13  N13  C4    124.48  3.000
 422  C12   N13  C4    109.36  3.000
 422  N18   C14  C15   110.28  3.000
 422  C15   C14  C12   128.34  3.000
 422  N18   C14  C12   121.37  3.000
 422  C19   C15  C16   119.71  3.000
 422  C19   C15  C14   136.12  3.000
 422  C16   C15  C14   104.14  3.000
 422  C22   C16  N17   131.60  3.000
 422  C22   C16  C15   122.55  3.000
 422  N17   C16  C15   105.84  3.000
 422  HN17  N17  N18   119.27  3.000
 422  HN17  N17  C16   128.08  3.000
 422  N18   N17  C16   112.63  3.000
 422  N17   N18  C14   107.11  3.000
 422  H19   C19  C20   119.63  3.000
 422  H19   C19  C15   121.82  3.000
 422  C20   C19  C15   118.54  3.000
 422  H20   C20  C21   119.17  3.000
 422  H20   C20  C19   120.14  3.000
 422  C21   C20  C19   120.69  3.000
 422  C23   C21  C22   119.03  3.000
 422  C23   C21  C20   118.82  3.000
 422  C22   C21  C20   122.14  3.000
 422  H22   C22  C21   121.29  3.000
 422  H22   C22  C16   122.36  3.000
 422  C21   C22  C16   116.35  3.000
 422  N1    C23  C21   180.00  3.000
 422  H72   C7   H71   105.72  3.000
 422  H72   C7   N2    111.99  3.000
 422  H71   C7   N2    107.55  3.000
 422  H72   C7   C1    109.02  3.000
 422  H71   C7   C1    108.83  3.000
 422  N2    C7   C1    113.40  3.000
 422  C9    N2   C8    111.16  3.000
 422  C9    N2   C7    112.35  3.000
 422  C8    N2   C7    111.44  3.000
 422  H82   C8   H81   106.46  3.000
 422  H82   C8   C13   109.62  3.000
 422  H81   C8   C13   109.30  3.000
 422  H82   C8   N2    108.59  3.000
 422  H81   C8   N2    111.34  3.000
 422  C13   C8   N2    111.39  3.000
 422  H92   C9   H91   106.58  3.000
 422  H92   C9   C10   109.29  3.000
 422  H91   C9   C10   109.59  3.000
 422  H92   C9   N2    111.16  3.000
 422  H91   C9   N2    108.95  3.000
 422  C10   C9   N2    111.16  3.000
 422  H102  C10  H101  107.08  3.000
 422  H102  C10  C17   109.50  3.000
 422  H101  C10  C17   111.05  3.000
 422  H102  C10  C9    109.01  3.000
 422  H101  C10  C9    108.69  3.000
 422  C17   C10  C9    111.39  3.000
 422  H132  C13  H131  106.86  3.000
 422  H132  C13  C17   110.48  3.000
 422  H131  C13  C17   109.34  3.000
 422  H132  C13  C8    109.13  3.000
 422  H131  C13  C8    108.98  3.000
 422  C17   C13  C8    111.92  3.000
 422  H17   C17  C18   108.10  3.000
 422  H17   C17  C13   108.05  3.000
 422  C18   C17  C13   110.89  3.000
 422  H17   C17  C10   107.85  3.000
 422  C18   C17  C10   113.01  3.000
 422  C13   C17  C10   108.79  3.000
 422  H182  C18  H181  105.83  3.000
 422  H182  C18  N3    107.91  3.000
 422  H181  C18  N3    107.99  3.000
 422  H182  C18  C17   108.76  3.000
 422  H181  C18  C17   108.62  3.000
 422  N3    C18  C17   117.16  3.000
 422  HN32  N3   HN31  106.81  3.000
 422  HN32  N3   C18   110.60  3.000
 422  HN31  N3   C18   110.95  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
 422  CONST_01  C4    C5   C6   C1     0.00   0.0  0
 422  CONST_02  C4    C3   C2   C1     0.00   0.0  0
 422  CONST_03  C11   C3   C2   C1   180.00   0.0  0
 422  CONST_04  C5    C6   C1   C2     0.00   0.0  0
 422  CONST_05  C5    C4   C3   C2     0.00   0.0  0
 422  CONST_06  N13   C4   C3   C2   180.00   0.0  0
 422  CONST_07  C12   C11  C3   C2   180.00   0.0  0
 422  CONST_08  C6    C1   C2   C3     0.00   0.0  0
 422  CONST_09  C6    C5   C4   C3     0.00   0.0  0
 422  CONST_10  C12   N13  C4   C3     0.00   0.0  0
 422  CONST_11  N13   C12  C11  C3     0.00   0.0  0
 422  CONST_12  C14   C12  C11  C3   180.00   0.0  0
 422  CONST_13  C12   C11  C3   C4     0.00   0.0  0
 422  CONST_14  C11   C12  N13  C4     0.00   0.0  0
 422  CONST_15  C14   C12  N13  C4   180.00   0.0  0
 422  CONST_16  C11   C3   C4   C5   180.00   0.0  0
 422  CONST_17  C12   N13  C4   C5   180.00   0.0  0
 422  CONST_18  N13   C4   C5   C6   180.00   0.0  0
 422  CONST_19  N13   C4   C3   C11    0.00   0.0  0
 422  CONST_22  N17   N18  C14  C12  180.00   0.0  0
 422  CONST_23  C16   C15  C14  C12  180.00   0.0  0
 422  CONST_24  C19   C15  C14  C12    0.00   0.0  0
 422  CONST_27  C16   N17  N18  C14    0.00   0.0  0
 422  CONST_28  N17   C16  C15  C14    0.00   0.0  0
 422  CONST_29  C22   C16  C15  C14  180.00   0.0  0
 422  CONST_30  C20   C19  C15  C14  180.00   0.0  0
 422  CONST_31  N17   N18  C14  C15    0.00   0.0  0
 422  CONST_32  N18   N17  C16  C15    0.00   0.0  0
 422  CONST_33  C21   C22  C16  C15    0.00   0.0  0
 422  CONST_34  C21   C20  C19  C15    0.00   0.0  0
 422  CONST_35  N18   C14  C15  C16    0.00   0.0  0
 422  CONST_36  C20   C19  C15  C16    0.00   0.0  0
 422  CONST_37  C20   C21  C22  C16    0.00   0.0  0
 422  CONST_38  C19   C15  C16  N17  180.00   0.0  0
 422  CONST_39  C21   C22  C16  N17  180.00   0.0  0
 422  CONST_40  C19   C15  C14  N18  180.00   0.0  0
 422  CONST_41  C22   C16  N17  N18  180.00   0.0  0
 422  CONST_42  C22   C16  C15  C19    0.00   0.0  0
 422  CONST_43  C22   C21  C20  C19    0.00   0.0  0
 422  CONST_44  C7    C1   C2   C3   180.00   0.0  0
 422  CONST_45  C7    C1   C6   C5   180.00   0.0  0
 422  CONST_46  C23   C21  C22  C16  180.00   0.0  0
 422  CONST_47  C23   C21  C20  C19  180.00   0.0  0
 422  CONST_48  H5    C5   C6   C1   180.00   0.0  0
 422  CONST_49  H6    C6   C1   C2   180.00   0.0  0
 422  CONST_50  H11   C11  C3   C2     0.00   0.0  0
 422  CONST_51  HN13  N13  C4   C3   180.00   0.0  0
 422  CONST_52  H2    C2   C3   C4   180.00   0.0  0
 422  CONST_53  HN17  N17  N18  C14  180.00   0.0  0
 422  CONST_54  H19   C19  C15  C14    0.00   0.0  0
 422  CONST_55  H22   C22  C16  C15  180.00   0.0  0
 422  CONST_56  H20   C20  C19  C15  180.00   0.0  0
 422  Var_01    C17   C13  C8   N2   -55.80  30.0  1
 422  Var_02    C17   C10  C9   N2    57.36  30.0  1
 422  Var_03    C10   C9   N2   C8   -59.51  30.0  1
 422  Var_04    C13   C8   N2   C9    58.64  30.0  1
 422  Var_05    C8    N2   C7   C1   168.47  30.0  3
 422  Var_06    N2    C7   C1   C2   -38.42  30.0  2
 422  Var_07    HN31  N3   C18  C17   65.38  30.0  3

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
 422  chir_01  C17  C10  C13  C18  positiv

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
 422  plan-1  C1    0.020
 422  plan-1  C2    0.020
 422  plan-1  C3    0.020
 422  plan-1  C4    0.020
 422  plan-1  C5    0.020
 422  plan-1  C6    0.020
 422  plan-1  C11   0.020
 422  plan-1  C12   0.020
 422  plan-1  N13   0.020
 422  plan-1  C14   0.020
 422  plan-1  C7    0.020
 422  plan-1  H2    0.020
 422  plan-1  H5    0.020
 422  plan-1  H6    0.020
 422  plan-1  H11   0.020
 422  plan-1  HN13  0.020
 422  plan-2  C12   0.020
 422  plan-2  C14   0.020
 422  plan-2  C15   0.020
 422  plan-2  C16   0.020
 422  plan-2  N17   0.020
 422  plan-2  N18   0.020
 422  plan-2  C19   0.020
 422  plan-2  C20   0.020
 422  plan-2  C21   0.020
 422  plan-2  C22   0.020
 422  plan-2  C23   0.020
 422  plan-2  N1    0.020
 422  plan-2  HN17  0.020
 422  plan-2  H19   0.020
 422  plan-2  H20   0.020
 422  plan-2  H22   0.020

