# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jun  4 17:58:50 2020
#   Inital geometry file: a 60 line input string
#   Ligand name: 5-iodanyl-~{N}-methyl-1~{H}-indazole-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)c1n[nH]c2ccc(I)cc12
#
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
 M6Z  M6Z  5-iodanyl-~{N}-methyl-1~{H}-indazole-3-carboxamide  ligand  22  14  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M6Z
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
 M6Z  N12  N  NR15  0  -0.527   2.5327   2.4075   0.0290
 M6Z  C01  C  CH3   0  -0.513   5.4247  -2.2780   0.0453
 M6Z  C03  C  C     0   0.515   3.3258  -1.0433   0.0192
 M6Z  C04  C  CR5   0   0.090   2.6885   0.2914   0.0224
 M6Z  C05  C  CR56  0  -0.061   1.2952   0.5843   0.0153
 M6Z  C06  C  CR16  0  -0.300   0.1062  -0.1591   0.0072
 M6Z  C07  C  CR6   0  -0.228  -1.0741   0.5454   0.0042
 M6Z  C08  C  CR16  0  -0.236  -1.1189   1.9554   0.0073
 M6Z  C09  C  CR16  0  -0.276   0.0395   2.6950   0.0149
 M6Z  C11  C  CR56  0   0.423   1.2445   1.9876   0.0200
 M6Z  I10  I  I     0   0.054  -2.8975  -0.5074  -0.0049
 M6Z  N02  N  NH1   0  -0.636   4.6623  -1.0532   0.0454
 M6Z  N13  N  N     0  -0.236   3.3894   1.4026   0.0306
 M6Z  O14  O  O     0  -0.490   2.6402  -2.0588  -0.0082
 M6Z  H1   H  HNR5  0   0.429   2.8737   3.3563   0.0347
 M6Z  H2   H  HCH3  0   0.253   6.4801  -2.0227   0.0354
 M6Z  H3   H  HCH3  0   0.239   5.2257  -2.8802   0.9328
 M6Z  H4   H  HCH3  0   0.240   5.2111  -2.8856  -0.8344
 M6Z  H5   H  HCR6  0   0.279   0.1323  -1.2386   0.0041
 M6Z  H6   H  HCR6  0   0.285  -2.0703   2.4693   0.0029
 M6Z  H7   H  HCR6  0   0.287   0.0097   3.7760   0.0175
 M6Z  H8   H  HNH1  0   0.410   5.1547  -0.1755   0.0805

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
 M6Z  C01  N02  single    1.443  0.020  1.443
 M6Z  O14  C03  double    1.226  0.020  1.226
 M6Z  N02  C03  single    1.337  0.020  1.337
 M6Z  C03  C04  single    1.479  0.020  1.479
 M6Z  N13  C04  aromatic  1.314  0.020  1.314
 M6Z  N13  N12  aromatic  1.321  0.020  1.321
 M6Z  C04  C05  aromatic  1.424  0.020  1.424
 M6Z  N12  C11  aromatic  1.355  0.020  1.355
 M6Z  C05  C11  aromatic  1.404  0.020  1.404
 M6Z  C05  C06  aromatic  1.402  0.020  1.402
 M6Z  C11  C09  aromatic  1.397  0.020  1.397
 M6Z  C06  C07  aromatic  1.375  0.020  1.375
 M6Z  C09  C08  aromatic  1.374  0.020  1.374
 M6Z  C07  C08  aromatic  1.411  0.020  1.411
 M6Z  C07  I10  single    2.105  0.020  2.105
 M6Z  N12  H1   single    0.860  0.020  1.020
 M6Z  C01  H2   single    0.970  0.020  1.090
 M6Z  C01  H3   single    0.970  0.020  1.090
 M6Z  C01  H4   single    0.970  0.020  1.090
 M6Z  C06  H5   single    0.930  0.020  1.080
 M6Z  C08  H6   single    0.930  0.020  1.080
 M6Z  C09  H7   single    0.930  0.020  1.080
 M6Z  N02  H8   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
 M6Z  H1   N12  N13  119.78  3.000
 M6Z  H1   N12  C11  127.82  3.000
 M6Z  N13  N12  C11  112.39  3.000
 M6Z  H4   C01  H3   108.25  3.000
 M6Z  H4   C01  H2   108.31  3.000
 M6Z  H3   C01  H2   108.34  3.000
 M6Z  H4   C01  N02  111.69  3.000
 M6Z  H3   C01  N02  111.85  3.000
 M6Z  H2   C01  N02  108.30  3.000
 M6Z  O14  C03  N02  123.61  3.000
 M6Z  N02  C03  C04  115.94  3.000
 M6Z  O14  C03  C04  120.45  3.000
 M6Z  N13  C04  C05  110.37  3.000
 M6Z  C05  C04  C03  127.39  3.000
 M6Z  N13  C04  C03  122.24  3.000
 M6Z  C11  C05  C06  119.95  3.000
 M6Z  C06  C05  C04  136.11  3.000
 M6Z  C11  C05  C04  103.94  3.000
 M6Z  H5   C06  C07  122.22  3.000
 M6Z  H5   C06  C05  120.63  3.000
 M6Z  C07  C06  C05  117.15  3.000
 M6Z  I10  C07  C08  118.18  3.000
 M6Z  I10  C07  C06  119.17  3.000
 M6Z  C08  C07  C06  122.65  3.000
 M6Z  H6   C08  C09  119.07  3.000
 M6Z  H6   C08  C07  120.19  3.000
 M6Z  C09  C08  C07  120.74  3.000
 M6Z  H7   C09  C11  121.99  3.000
 M6Z  H7   C09  C08  120.98  3.000
 M6Z  C11  C09  C08  117.03  3.000
 M6Z  C09  C11  C05  122.48  3.000
 M6Z  C09  C11  N12  131.53  3.000
 M6Z  C05  C11  N12  105.99  3.000
 M6Z  H8   N02  C03  118.89  3.000
 M6Z  H8   N02  C01  118.79  3.000
 M6Z  C03  N02  C01  122.32  3.000
 M6Z  C04  N13  N12  107.31  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
 M6Z  CONST_01  C05  C04  N13  N12    0.00   0.0  0
 M6Z  CONST_02  C04  C05  C11  N12    0.00   0.0  0
 M6Z  CONST_03  C06  C05  C11  N12  180.00   0.0  0
 M6Z  CONST_04  C08  C09  C11  N12  180.00   0.0  0
 M6Z  CONST_05  C11  N12  N13  C04    0.00   0.0  0
 M6Z  CONST_06  C09  C11  C05  C04  180.00   0.0  0
 M6Z  CONST_07  C07  C06  C05  C04  180.00   0.0  0
 M6Z  CONST_08  N13  N12  C11  C05    0.00   0.0  0
 M6Z  CONST_09  C08  C09  C11  C05    0.00   0.0  0
 M6Z  CONST_10  C08  C07  C06  C05    0.00   0.0  0
 M6Z  CONST_11  N13  C04  C05  C06  180.00   0.0  0
 M6Z  CONST_12  C09  C11  C05  C06    0.00   0.0  0
 M6Z  CONST_13  C09  C08  C07  C06    0.00   0.0  0
 M6Z  CONST_14  C11  C05  C06  C07    0.00   0.0  0
 M6Z  CONST_15  C11  C09  C08  C07    0.00   0.0  0
 M6Z  CONST_16  N13  N12  C11  C09  180.00   0.0  0
 M6Z  CONST_17  N13  C04  C05  C11    0.00   0.0  0
 M6Z  CONST_18  C03  C04  N13  N12  180.00   0.0  0
 M6Z  CONST_19  C11  C05  C04  C03  180.00   0.0  0
 M6Z  CONST_20  C06  C05  C04  C03    0.00   0.0  0
 M6Z  CONST_21  I10  C07  C06  C05  180.00   0.0  0
 M6Z  CONST_22  I10  C07  C08  C09  180.00   0.0  0
 M6Z  CONST_23  H7   C09  C11  N12    0.00   0.0  0
 M6Z  CONST_24  H1   N12  N13  C04  180.00   0.0  0
 M6Z  CONST_25  H5   C06  C05  C04    0.00   0.0  0
 M6Z  CONST_26  H6   C08  C07  C06  180.00   0.0  0
 M6Z  CONST_27  C04  C03  N02  C01  180.00   0.0  0
 M6Z  CONST_28  H8   N02  C03  C04    0.00   0.0  0
 M6Z  CONST_29  O14  C03  N02  C01    0.00   0.0  0
 M6Z  Var_01    O14  C03  C04  C05    0.96  30.0  2
 M6Z  Var_02    H2   C01  N02  C03  178.12  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
 M6Z  plan-1  N12  0.020
 M6Z  plan-1  C03  0.020
 M6Z  plan-1  C04  0.020
 M6Z  plan-1  C05  0.020
 M6Z  plan-1  C06  0.020
 M6Z  plan-1  C07  0.020
 M6Z  plan-1  C08  0.020
 M6Z  plan-1  C09  0.020
 M6Z  plan-1  C11  0.020
 M6Z  plan-1  I10  0.020
 M6Z  plan-1  N13  0.020
 M6Z  plan-1  H1   0.020
 M6Z  plan-1  H5   0.020
 M6Z  plan-1  H6   0.020
 M6Z  plan-1  H7   0.020
 M6Z  plan-2  C01  0.020
 M6Z  plan-2  C03  0.020
 M6Z  plan-2  C04  0.020
 M6Z  plan-2  N02  0.020
 M6Z  plan-2  O14  0.020
 M6Z  plan-2  H8   0.020

