# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 17:38:32 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: N-[4-(4-methylpiperazin-1-yl)phenyl]-1H-indazole-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1)c2ccc(NC(=O)c3n[nH]c4ccccc34)cc2
#
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
 JVT  JVT  N-[4-(4-methylpiperazin-1-yl)phenyl]-1H-indazole-3-carboxamide  ligand  46  25  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JVT
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
 JVT  O     O  O     0  -0.468   2.1635  -1.5535  -0.2961
 JVT  C11   C  C     0   0.514   2.3038  -0.3581  -0.0853
 JVT  C12   C  CR5   0   0.081   3.6529   0.2280   0.0402
 JVT  N4    N  N     0  -0.249   3.8371   1.5167   0.2251
 JVT  N3    N  NR15  0  -0.525   5.1390   1.7192   0.2932
 JVT  C18   C  CR56  0   0.418   5.8500   0.5713   0.1544
 JVT  C17   C  CR16  0  -0.290   7.2276   0.3310   0.1635
 JVT  C16   C  CR16  0  -0.265   7.6248  -0.9750  -0.0043
 JVT  C15   C  CR16  0  -0.261   6.6906  -2.0185  -0.1765
 JVT  C14   C  CR16  0  -0.331   5.3365  -1.7755  -0.1855
 JVT  C13   C  CR56  0  -0.065   4.9024  -0.4524  -0.0169
 JVT  N2    N  NH1   0  -0.758   1.2959   0.5305   0.0508
 JVT  C8    C  CR6   0   0.354  -0.0861   0.3108   0.0072
 JVT  C7    C  CR16  0  -0.341  -0.9103   1.3878   0.3434
 JVT  C6    C  CR16  0  -0.314  -2.2846   1.2780   0.3192
 JVT  C9    C  CR16  0  -0.307  -0.6961  -0.8858  -0.3544
 JVT  C10   C  CR16  0  -0.348  -2.0819  -0.9960  -0.3610
 JVT  C5    C  CR6   0   0.353  -2.9156   0.0749  -0.0309
 JVT  N1    N  NT    0  -0.516  -4.3079  -0.0039  -0.0763
 JVT  C2    C  CH2   0  -0.314  -4.9065  -1.2156  -0.5972
 JVT  C1    C  CH2   0  -0.278  -6.3706  -0.9806  -0.9221
 JVT  C3    C  CH2   0  -0.308  -5.0430   0.5071   1.0721
 JVT  C4    C  CH2   0  -0.282  -6.5011   0.7219   0.7204
 JVT  N     N  NT    0  -0.412  -7.0969  -0.5056   0.2364
 JVT  C     C  CH3   0  -0.520  -8.5033  -0.3385  -0.0482
 JVT  H2    H  HNH1  0   0.419   1.5757   1.4817   0.2478
 JVT  H3    H  HNR5  0   0.427   5.4925   2.6541   0.4245
 JVT  H17   H  HCR6  0   0.276   7.9438   1.1307   0.2950
 JVT  H16   H  HCR6  0   0.265   8.6811  -1.2100  -0.0045
 JVT  H15   H  HCR6  0   0.260   7.0532  -3.0298  -0.3048
 JVT  H14   H  HCR6  0   0.259   4.6273  -2.5796  -0.3177
 JVT  H7    H  HCR6  0   0.267  -0.4677   2.3375   0.6218
 JVT  H9    H  HCR6  0   0.275  -0.1118  -1.7505  -0.6236
 JVT  H6    H  HCR6  0   0.263  -2.8683   2.1560   0.5623
 JVT  H10   H  HCR6  0   0.267  -2.4964  -1.9575  -0.6297
 JVT  H21C  H  HCH2  0   0.251  -4.4002  -1.5071  -1.5180
 JVT  H22C  H  HCH2  0   0.211  -4.8149  -2.0540   0.1108
 JVT  H31C  H  HCH2  0   0.215  -4.9724  -0.1910   1.9198
 JVT  H32C  H  HCH2  0   0.254  -4.6238   1.4567   1.3972
 JVT  H11C  H  HCH2  0   0.192  -6.4379  -0.2692  -1.7643
 JVT  H12C  H  HCH2  0   0.240  -6.8089  -1.9227  -1.2596
 JVT  H41C  H  HCH2  0   0.240  -7.0338   1.0508   1.6158
 JVT  H42C  H  HCH2  0   0.193  -6.5794   1.5340  -0.0240
 JVT  HC1   H  HCH3  0   0.234  -8.9372  -1.2863  -0.3705
 JVT  HC2   H  HCH3  0   0.234  -9.0317  -0.0184   0.8512
 JVT  HC3   H  HCH3  0   0.192  -8.6997   0.4067  -0.8351

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
 JVT  O    C11   double    1.222  0.020  1.222
 JVT  C11  C12   single    1.476  0.020  1.476
 JVT  C11  N2    single    1.351  0.020  1.351
 JVT  C12  N4    aromatic  1.315  0.020  1.315
 JVT  C12  C13   aromatic  1.424  0.020  1.424
 JVT  N4   N3    aromatic  1.319  0.020  1.319
 JVT  N3   C18   aromatic  1.357  0.020  1.357
 JVT  C18  C17   aromatic  1.398  0.020  1.398
 JVT  C18  C13   aromatic  1.405  0.020  1.405
 JVT  C17  C16   aromatic  1.375  0.020  1.375
 JVT  C16  C15   aromatic  1.411  0.020  1.411
 JVT  C15  C14   aromatic  1.376  0.020  1.376
 JVT  C14  C13   aromatic  1.403  0.020  1.403
 JVT  N2   C8    single    1.400  0.020  1.400
 JVT  C8   C7    aromatic  1.397  0.020  1.397
 JVT  C8   C9    aromatic  1.391  0.020  1.391
 JVT  C7   C6    aromatic  1.379  0.020  1.379
 JVT  C6   C5    aromatic  1.403  0.020  1.403
 JVT  C9   C10   aromatic  1.390  0.020  1.390
 JVT  C10  C5    aromatic  1.397  0.020  1.397
 JVT  C5   N1    single    1.395  0.020  1.395
 JVT  N1   C2    single    1.448  0.020  1.448
 JVT  N1   C3    single    1.456  0.020  1.456
 JVT  C2   C1    single    1.518  0.020  1.518
 JVT  C1   N     single    1.447  0.020  1.447
 JVT  C3   C4    single    1.515  0.020  1.515
 JVT  C4   N     single    1.448  0.020  1.448
 JVT  N    C     single    1.445  0.020  1.445
 JVT  N2   H2    single    0.860  0.020  1.020
 JVT  N3   H3    single    0.860  0.020  1.020
 JVT  C17  H17   single    0.930  0.020  1.080
 JVT  C16  H16   single    0.930  0.020  1.080
 JVT  C15  H15   single    0.930  0.020  1.080
 JVT  C14  H14   single    0.930  0.020  1.080
 JVT  C7   H7    single    0.930  0.020  1.080
 JVT  C9   H9    single    0.930  0.020  1.080
 JVT  C6   H6    single    0.930  0.020  1.080
 JVT  C10  H10   single    0.930  0.020  1.080
 JVT  C2   H21C  single    0.970  0.020  1.090
 JVT  C2   H22C  single    0.970  0.020  1.090
 JVT  C3   H31C  single    0.970  0.020  1.090
 JVT  C3   H32C  single    0.970  0.020  1.090
 JVT  C1   H11C  single    0.970  0.020  1.090
 JVT  C1   H12C  single    0.970  0.020  1.090
 JVT  C4   H41C  single    0.970  0.020  1.090
 JVT  C4   H42C  single    0.970  0.020  1.090
 JVT  C    HC1   single    0.970  0.020  1.090
 JVT  C    HC2   single    0.970  0.020  1.090
 JVT  C    HC3   single    0.970  0.020  1.090

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
 JVT  N2    C11  C12   114.35  3.000
 JVT  N2    C11  O     125.13  3.000
 JVT  C12   C11  O     120.53  3.000
 JVT  C13   C12  N4    110.55  3.000
 JVT  C13   C12  C11   127.51  3.000
 JVT  N4    C12  C11   121.94  3.000
 JVT  N3    N4   C12   107.21  3.000
 JVT  H3    N3   C18   127.87  3.000
 JVT  H3    N3   N4    119.68  3.000
 JVT  C18   N3   N4    112.45  3.000
 JVT  C13   C18  C17   122.67  3.000
 JVT  C13   C18  N3    105.98  3.000
 JVT  C17   C18  N3    131.35  3.000
 JVT  H17   C17  C16   121.72  3.000
 JVT  H17   C17  C18   121.74  3.000
 JVT  C16   C17  C18   116.54  3.000
 JVT  H16   C16  C15   119.06  3.000
 JVT  H16   C16  C17   119.22  3.000
 JVT  C15   C16  C17   121.73  3.000
 JVT  H15   C15  C14   119.61  3.000
 JVT  H15   C15  C16   118.94  3.000
 JVT  C14   C15  C16   121.46  3.000
 JVT  H14   C14  C13   120.90  3.000
 JVT  H14   C14  C15   121.04  3.000
 JVT  C13   C14  C15   118.06  3.000
 JVT  C14   C13  C18   119.54  3.000
 JVT  C14   C13  C12   136.65  3.000
 JVT  C18   C13  C12   103.81  3.000
 JVT  H2    N2   C8    115.28  3.000
 JVT  H2    N2   C11   115.60  3.000
 JVT  C8    N2   C11   129.07  3.000
 JVT  C9    C8   C7    117.84  3.000
 JVT  C9    C8   N2    125.17  3.000
 JVT  C7    C8   N2    116.99  3.000
 JVT  H7    C7   C6    118.77  3.000
 JVT  H7    C7   C8    119.74  3.000
 JVT  C6    C7   C8    121.49  3.000
 JVT  H6    C6   C5    120.61  3.000
 JVT  H6    C6   C7    117.98  3.000
 JVT  C5    C6   C7    121.40  3.000
 JVT  H9    C9   C10   118.40  3.000
 JVT  H9    C9   C8    121.16  3.000
 JVT  C10   C9   C8    120.44  3.000
 JVT  H10   C10  C5    120.79  3.000
 JVT  H10   C10  C9    117.00  3.000
 JVT  C5    C10  C9    122.21  3.000
 JVT  N1    C5   C10   123.00  3.000
 JVT  N1    C5   C6    120.36  3.000
 JVT  C10   C5   C6    116.62  3.000
 JVT  C3    N1   C2    111.63  3.000
 JVT  C3    N1   C5    117.28  3.000
 JVT  C2    N1   C5    118.12  3.000
 JVT  H22C  C2   H21C  107.50  3.000
 JVT  H22C  C2   C1    109.62  3.000
 JVT  H21C  C2   C1    107.96  3.000
 JVT  H22C  C2   N1    111.80  3.000
 JVT  H21C  C2   N1    109.60  3.000
 JVT  C1    C2   N1    110.25  3.000
 JVT  H12C  C1   H11C  107.18  3.000
 JVT  H12C  C1   N     109.20  3.000
 JVT  H11C  C1   N     111.62  3.000
 JVT  H12C  C1   C2    108.64  3.000
 JVT  H11C  C1   C2    108.76  3.000
 JVT  N     C1   C2    111.31  3.000
 JVT  H32C  C3   H31C  107.39  3.000
 JVT  H32C  C3   C4    108.45  3.000
 JVT  H31C  C3   C4    109.30  3.000
 JVT  H32C  C3   N1    110.33  3.000
 JVT  H31C  C3   N1    110.64  3.000
 JVT  C4    C3   N1    110.64  3.000
 JVT  H42C  C4   H41C  107.24  3.000
 JVT  H42C  C4   N     111.65  3.000
 JVT  H41C  C4   N     109.19  3.000
 JVT  H42C  C4   C3    109.20  3.000
 JVT  H41C  C4   C3    108.76  3.000
 JVT  N     C4   C3    110.70  3.000
 JVT  C     N    C4    111.62  3.000
 JVT  C     N    C1    111.64  3.000
 JVT  C4    N    C1    109.84  3.000
 JVT  HC3   C    HC2   107.70  3.000
 JVT  HC3   C    HC1   107.80  3.000
 JVT  HC2   C    HC1   107.80  3.000
 JVT  HC3   C    N     113.12  3.000
 JVT  HC2   C    N     110.06  3.000
 JVT  HC1   C    N     110.17  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
 JVT  CONST_01  C18  N3   N4   C12     0.00   0.0  0
 JVT  CONST_02  N3   C18  C13  C12     0.00   0.0  0
 JVT  CONST_03  C17  C18  C13  C12   180.00   0.0  0
 JVT  CONST_04  C15  C14  C13  C12   180.00   0.0  0
 JVT  CONST_05  C18  C13  C12  N4      0.00   0.0  0
 JVT  CONST_06  C14  C13  C12  N4    180.00   0.0  0
 JVT  CONST_07  C17  C18  N3   N4    180.00   0.0  0
 JVT  CONST_08  C13  C18  N3   N4      0.00   0.0  0
 JVT  CONST_09  C13  C12  N4   N3      0.00   0.0  0
 JVT  CONST_10  C16  C17  C18  N3    180.00   0.0  0
 JVT  CONST_11  C14  C13  C18  N3    180.00   0.0  0
 JVT  CONST_12  C15  C16  C17  C18     0.00   0.0  0
 JVT  CONST_13  C15  C14  C13  C18     0.00   0.0  0
 JVT  CONST_14  C14  C13  C18  C17     0.00   0.0  0
 JVT  CONST_15  C14  C15  C16  C17     0.00   0.0  0
 JVT  CONST_16  C13  C18  C17  C16     0.00   0.0  0
 JVT  CONST_17  C13  C14  C15  C16     0.00   0.0  0
 JVT  CONST_18  C5   C6   C7   C8      0.00   0.0  0
 JVT  CONST_19  C5   C10  C9   C8      0.00   0.0  0
 JVT  CONST_20  C10  C9   C8   C7      0.00   0.0  0
 JVT  CONST_21  C10  C5   C6   C7      0.00   0.0  0
 JVT  CONST_22  C9   C8   C7   C6      0.00   0.0  0
 JVT  CONST_23  C9   C10  C5   C6      0.00   0.0  0
 JVT  CONST_24  N1   C5   C6   C7    180.00   0.0  0
 JVT  CONST_25  N1   C5   C10  C9    180.00   0.0  0
 JVT  CONST_26  N3   N4   C12  C11   180.00   0.0  0
 JVT  CONST_27  C18  C13  C12  C11   180.00   0.0  0
 JVT  CONST_28  C14  C13  C12  C11     0.00   0.0  0
 JVT  CONST_29  C6   C7   C8   N2    180.00   0.0  0
 JVT  CONST_30  C10  C9   C8   N2    180.00   0.0  0
 JVT  CONST_31  H3   N3   N4   C12   180.00   0.0  0
 JVT  CONST_32  H14  C14  C13  C12     0.00   0.0  0
 JVT  CONST_33  H17  C17  C18  N3      0.00   0.0  0
 JVT  CONST_34  H16  C16  C17  C18   180.00   0.0  0
 JVT  CONST_35  H15  C15  C16  C17   180.00   0.0  0
 JVT  CONST_36  H6   C6   C7   C8    180.00   0.0  0
 JVT  CONST_37  H10  C10  C9   C8    180.00   0.0  0
 JVT  CONST_38  H9   C9   C8   C7    180.00   0.0  0
 JVT  CONST_39  H7   C7   C8   C9    180.00   0.0  0
 JVT  CONST_40  C8   N2   C11  C12   180.00   0.0  0
 JVT  CONST_41  C7   C8   N2   C11   180.00   0.0  0
 JVT  CONST_42  C9   C8   N2   C11     0.00   0.0  0
 JVT  CONST_43  H2   N2   C8   C7      0.00   0.0  0
 JVT  CONST_44  C8   N2   C11  O       0.00   0.0  0
 JVT  Var_01    C2   N1   C5   C6    172.69  30.0  2
 JVT  Var_02    C1   C2   N1   C5   -164.54  30.0  1
 JVT  Var_03    C4   C3   N1   C5    163.69  30.0  1
 JVT  Var_04    N    C1   C2   N1    -56.63  30.0  1
 JVT  Var_05    N    C4   C3   N1     56.90  30.0  1
 JVT  Var_06    C4   N    C1   C2     58.30  30.0  1
 JVT  Var_07    C3   C4   N    C1    -58.22  30.0  1
 JVT  Var_08    N4   C12  C11  O     177.83  30.0  2
 JVT  Var_09    HC1  C    N    C1     59.02  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
 JVT  plan-1  N2   0.020
 JVT  plan-1  C8   0.020
 JVT  plan-1  C7   0.020
 JVT  plan-1  C6   0.020
 JVT  plan-1  C9   0.020
 JVT  plan-1  C10  0.020
 JVT  plan-1  C5   0.020
 JVT  plan-1  N1   0.020
 JVT  plan-1  H7   0.020
 JVT  plan-1  H9   0.020
 JVT  plan-1  H6   0.020
 JVT  plan-1  H10  0.020
 JVT  plan-2  C11  0.020
 JVT  plan-2  C12  0.020
 JVT  plan-2  N4   0.020
 JVT  plan-2  N3   0.020
 JVT  plan-2  C18  0.020
 JVT  plan-2  C17  0.020
 JVT  plan-2  C16  0.020
 JVT  plan-2  C15  0.020
 JVT  plan-2  C14  0.020
 JVT  plan-2  C13  0.020
 JVT  plan-2  H3   0.020
 JVT  plan-2  H17  0.020
 JVT  plan-2  H16  0.020
 JVT  plan-2  H15  0.020
 JVT  plan-2  H14  0.020
 JVT  plan-3  O    0.020
 JVT  plan-3  C11  0.020
 JVT  plan-3  C12  0.020
 JVT  plan-3  N2   0.020
 JVT  plan-3  C8   0.020
 JVT  plan-3  H2   0.020

