# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 13:42:07 2022
#   Inital geometry file: a 66 line input string
#   Ligand name: ~{N}-methyl-4,5,6,7-tetrahydro-1~{H}-indazole-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)c1n[nH]c2CCCCc12
#
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
 ID0  ID0  "N-methyl-4,5,6,7-tetrahydro-1H-indazole-3-carboxamide"
  ligand  26  13  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_ID0
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
 ID0  C10  C  CH2   0  -0.452  -25.1588  30.1366  -25.6493
 ID0  C01  C  CH3   0  -0.511  -21.9560  23.7073  -25.5877
 ID0  C03  C  C     0   0.499  -22.7782  25.9997  -25.7286
 ID0  C04  C  CR5   0   0.082  -22.4072  27.4313  -25.7130
 ID0  C07  C  CR5   0   0.393  -22.4203  29.6272  -25.7504
 ID0  C08  C  CR5   0  -0.116  -23.2683  28.5442  -25.8069
 ID0  C09  C  CH2   0  -0.496  -24.7489  28.6906  -25.9422
 ID0  C11  C  CH2   0  -0.447  -24.2461  31.1495  -26.3382
 ID0  C12  C  CH2   0  -0.503  -22.8120  31.0611  -25.8112
 ID0  N02  N  NH1   0  -0.637  -21.7628  25.1362  -25.5868
 ID0  N05  N  N     0  -0.288  -21.1412  27.8109  -25.6020
 ID0  N06  N  NR15  0  -0.490  -21.1738  29.1302  -25.6271
 ID0  O13  O  O     0  -0.488  -23.9441  25.6458  -25.8644
 ID0  H1   H  HCH2  0   0.224  -25.1308  30.3095  -24.5689
 ID0  H2   H  HCH2  0   0.237  -26.1925  30.2933  -25.9627
 ID0  H3   H  HCH3  0   0.249  -20.9868  23.2294  -25.4775
 ID0  H4   H  HCH3  0   0.235  -22.5920  23.3833  -24.7626
 ID0  H5   H  HCH3  0   0.236  -22.4047  23.3600  -26.5192
 ID0  H6   H  HCH2  0   0.241  -25.2713  28.0094  -25.2696
 ID0  H7   H  HCH2  0   0.232  -25.0614  28.4138  -26.9538
 ID0  H8   H  HCH2  0   0.241  -24.6248  32.1616  -26.1882
 ID0  H9   H  HCH2  0   0.228  -24.2496  30.9697  -27.4173
 ID0  H10  H  HCH2  0   0.260  -22.1284  31.6291  -26.4463
 ID0  H11  H  HCH2  0   0.253  -22.7531  31.5062  -24.8133
 ID0  H12  H  HNH1  0   0.403  -20.8311  25.5027  -25.4819
 ID0  H13  H  HNR5  0   0.416  -20.3129  29.6519  -25.5602

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
 ID0  C11  C12  single    1.530  0.020  1.530
 ID0  C11  C10  single    1.528  0.020  1.528
 ID0  C09  C10  single    1.531  0.020  1.531
 ID0  C09  C08  single    1.494  0.020  1.494
 ID0  C12  C07  single    1.488  0.020  1.488
 ID0  N02  C01  single    1.442  0.020  1.442
 ID0  N02  C03  single    1.340  0.020  1.340
 ID0  C08  C07  aromatic  1.377  0.020  1.377
 ID0  C08  C04  aromatic  1.410  0.020  1.410
 ID0  C07  N06  aromatic  1.348  0.020  1.348
 ID0  C04  C03  single    1.479  0.020  1.479
 ID0  C04  N05  aromatic  1.326  0.020  1.326
 ID0  C03  O13  double    1.226  0.020  1.226
 ID0  N06  N05  aromatic  1.320  0.020  1.320
 ID0  C10  H1   single    0.970  0.020  1.090
 ID0  C10  H2   single    0.970  0.020  1.090
 ID0  C01  H3   single    0.970  0.020  1.090
 ID0  C01  H4   single    0.970  0.020  1.090
 ID0  C01  H5   single    0.970  0.020  1.090
 ID0  C09  H6   single    0.970  0.020  1.090
 ID0  C09  H7   single    0.970  0.020  1.090
 ID0  C11  H8   single    0.970  0.020  1.090
 ID0  C11  H9   single    0.970  0.020  1.090
 ID0  C12  H10  single    0.970  0.020  1.090
 ID0  C12  H11  single    0.970  0.020  1.090
 ID0  N02  H12  single    0.860  0.020  1.020
 ID0  N06  H13  single    0.860  0.020  1.020

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
 ID0  H2   C10  H1   106.55  3.000
 ID0  H2   C10  C11  109.95  3.000
 ID0  H1   C10  C11  108.97  3.000
 ID0  H2   C10  C09  109.52  3.000
 ID0  H1   C10  C09  109.34  3.000
 ID0  C11  C10  C09  112.33  3.000
 ID0  H5   C01  H4   108.16  3.000
 ID0  H5   C01  H3   108.28  3.000
 ID0  H4   C01  H3   108.22  3.000
 ID0  H5   C01  N02  111.79  3.000
 ID0  H4   C01  N02  111.84  3.000
 ID0  H3   C01  N02  108.44  3.000
 ID0  O13  C03  N02  123.10  3.000
 ID0  O13  C03  C04  121.28  3.000
 ID0  N02  C03  C04  115.63  3.000
 ID0  N05  C04  C08  111.26  3.000
 ID0  N05  C04  C03  121.15  3.000
 ID0  C08  C04  C03  127.59  3.000
 ID0  N06  C07  C12  127.07  3.000
 ID0  N06  C07  C08  106.46  3.000
 ID0  C12  C07  C08  126.47  3.000
 ID0  C09  C08  C07  122.49  3.000
 ID0  C07  C08  C04  104.00  3.000
 ID0  C09  C08  C04  133.51  3.000
 ID0  H7   C09  H6   105.99  3.000
 ID0  H7   C09  C08  109.99  3.000
 ID0  H6   C09  C08  110.96  3.000
 ID0  H7   C09  C10  109.83  3.000
 ID0  H6   C09  C10  110.10  3.000
 ID0  C08  C09  C10  109.91  3.000
 ID0  H9   C11  H8   106.68  3.000
 ID0  H9   C11  C12  109.46  3.000
 ID0  H8   C11  C12  109.36  3.000
 ID0  H9   C11  C10  109.51  3.000
 ID0  H8   C11  C10  110.22  3.000
 ID0  C12  C11  C10  111.49  3.000
 ID0  H11  C12  H10  106.56  3.000
 ID0  H11  C12  C11  109.93  3.000
 ID0  H10  C12  C11  110.86  3.000
 ID0  H11  C12  C07  109.91  3.000
 ID0  H10  C12  C07  111.12  3.000
 ID0  C11  C12  C07  108.45  3.000
 ID0  H12  N02  C03  118.52  3.000
 ID0  H12  N02  C01  119.01  3.000
 ID0  C03  N02  C01  122.47  3.000
 ID0  N06  N05  C04  105.12  3.000
 ID0  H13  N06  N05  119.63  3.000
 ID0  H13  N06  C07  127.21  3.000
 ID0  N05  N06  C07  113.16  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
 ID0  CONST_01  N06  C07  C08  C04     0.00   0.0  0
 ID0  CONST_02  C07  N06  N05  C04     0.00   0.0  0
 ID0  CONST_03  N05  C04  C08  C07     0.00   0.0  0
 ID0  CONST_04  N05  N06  C07  C08     0.00   0.0  0
 ID0  CONST_05  N06  N05  C04  C08     0.00   0.0  0
 ID0  CONST_06  C09  C08  C04  C03     0.00   0.0  0
 ID0  CONST_07  C07  C08  C04  C03   180.00   0.0  0
 ID0  CONST_08  N06  N05  C04  C03   180.00   0.0  0
 ID0  CONST_09  H13  N06  N05  C04   180.00   0.0  0
 ID0  CONST_10  H13  N06  C07  C08   180.00   0.0  0
 ID0  CONST_11  H13  N06  C07  C12     0.00   0.0  0
 ID0  CONST_12  C04  C03  N02  C01   180.00   0.0  0
 ID0  CONST_13  H12  N02  C03  C04     0.00   0.0  0
 ID0  CONST_14  O13  C03  N02  C01     0.00   0.0  0
 ID0  CONST_15  H12  N02  C03  O13   180.00   0.0  0
 ID0  Var_01    C07  C12  C11  C10    45.73  30.0  1
 ID0  Var_02    C07  C08  C09  C10   -14.23  30.0  1
 ID0  Var_03    C04  C08  C09  C10   165.94  30.0  1
 ID0  Var_04    C11  C10  C09  C08    44.93  30.0  1
 ID0  Var_05    C11  C12  C07  C08   -15.80  30.0  1
 ID0  Var_06    C12  C11  C10  C09   -63.90  30.0  1
 ID0  Var_07    N06  C07  C12  C11   164.34  30.0  1
 ID0  Var_08    H10  C12  C11  C10   167.98  30.0  1
 ID0  Var_09    H11  C12  C11  C10   -74.47  30.0  1
 ID0  Var_10    H6   C09  C08  C04    43.92  30.0  1
 ID0  Var_11    H7   C09  C08  C04   -73.02  30.0  1
 ID0  Var_12    H8   C11  C12  C07   167.87  30.0  1
 ID0  Var_13    H9   C11  C12  C07   -75.59  30.0  1
 ID0  Var_14    H6   C09  C08  C07  -136.25  30.0  1
 ID0  Var_15    H7   C09  C08  C07   106.81  30.0  1
 ID0  Var_16    H1   C10  C09  C08   -76.18  30.0  1
 ID0  Var_17    H2   C10  C09  C08   167.41  30.0  1
 ID0  Var_18    H10  C12  C07  C08  -137.89  30.0  1
 ID0  Var_19    H11  C12  C07  C08   104.41  30.0  1
 ID0  Var_20    H8   C11  C10  C09   174.46  30.0  1
 ID0  Var_21    H9   C11  C10  C09    57.39  30.0  1
 ID0  Var_22    H6   C09  C10  C11   167.45  30.0  1
 ID0  Var_23    H7   C09  C10  C11   -76.20  30.0  1
 ID0  Var_24    H1   C10  C11  C12    57.42  30.0  1
 ID0  Var_25    H2   C10  C11  C12   173.86  30.0  1
 ID0  Var_26    H10  C12  C07  N06    42.25  30.0  1
 ID0  Var_27    H11  C12  C07  N06   -75.45  30.0  1
 ID0  Var_28    N02  C03  C04  C08  -178.26  30.0  2
 ID0  Var_29    O13  C03  C04  C08     1.79  30.0  2
 ID0  Var_30    N05  C04  C03  N02     1.78  30.0  2
 ID0  Var_31    O13  C03  C04  N05  -178.16  30.0  2
 ID0  Var_32    H3   C01  N02  C03   178.93  30.0  3
 ID0  Var_33    H4   C01  N02  C03   -61.81  30.0  3
 ID0  Var_34    H5   C01  N02  C03    59.64  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
 ID0  plan-1  C01  0.020
 ID0  plan-1  C03  0.020
 ID0  plan-1  C04  0.020
 ID0  plan-1  N02  0.020
 ID0  plan-1  O13  0.020
 ID0  plan-1  H12  0.020
 ID0  plan-2  C03  0.020
 ID0  plan-2  C04  0.020
 ID0  plan-2  C07  0.020
 ID0  plan-2  C08  0.020
 ID0  plan-2  C09  0.020
 ID0  plan-2  C12  0.020
 ID0  plan-2  N05  0.020
 ID0  plan-2  N06  0.020
 ID0  plan-2  H13  0.020

