# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jun  4 14:54:56 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: 3-imidazolidin-2-yl-2~{H}-indazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CNC(N1)c2[nH]nc3ccccc23
#
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
 M5H  M5H  3-imidazolidin-2-yl-2~{H}-indazole  ligand  26  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_M5H
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
 M5H  CAA  C  CR16  0  -0.266   3.6573   0.8073  -0.1201
 M5H  CAB  C  CR16  0  -0.275   2.6865   1.8380   0.0303
 M5H  CAC  C  CR16  0  -0.298   3.3098  -0.5138  -0.1489
 M5H  CAD  C  CR16  0  -0.328   1.3554   1.5509   0.1497
 M5H  CAE  C  CH2   0  -0.348  -3.8471  -0.1542  -0.1508
 M5H  CAF  C  CH2   0  -0.337  -3.3642   1.3265  -0.2338
 M5H  CAK  C  CH1   0  -0.041  -1.6445  -0.0309   0.4192
 M5H  CAL  C  CR5   0   0.397  -0.2456  -0.4929   0.2165
 M5H  CAM  C  CR56  0   0.237   1.9383  -0.8377  -0.0218
 M5H  CAN  C  CR56  0  -0.153   0.9656   0.1929   0.1229
 M5H  NAG  N  NH1   0  -0.594  -2.6300  -0.9660  -0.1094
 M5H  NAH  N  NR15  0  -0.472   0.0789  -1.7874   0.1327
 M5H  NAI  N  NH1   0  -0.586  -1.9015   1.2721  -0.1765
 M5H  NAJ  N  N     0  -0.309   1.3704  -2.0463  -0.0131
 M5H  H1   H  HCR6  0   0.255   4.6994   1.0852  -0.2134
 M5H  H2   H  HCR6  0   0.253   3.0184   2.8680   0.0481
 M5H  H3   H  HCR6  0   0.257   4.0534  -1.2919  -0.2623
 M5H  H4   H  HCR6  0   0.249   0.6180   2.3346   0.2619
 M5H  H6   H  HCH2  0   0.250  -4.4663  -0.4491  -0.9965
 M5H  H7   H  HCH2  0   0.247  -3.6847   1.8243  -1.1477
 M5H  H8   H  HCH2  0   0.235  -3.7553   1.8999   0.6085
 M5H  H9   H  HCH1  0   0.267  -1.8353   0.0623   1.4968
 M5H  H10  H  HNH1  0   0.348  -2.3682  -1.1852  -1.0661
 M5H  H12  H  HNR5  0   0.424  -0.5761  -2.5554   0.1799
 M5H  H13  H  HNH1  0   0.349  -1.5393   1.2617  -1.1242
 M5H  H5   H  HCH2  0   0.238  -4.4322  -0.3106   0.7572

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
 M5H  NAJ  NAH  aromatic  1.325  0.020  1.325
 M5H  NAJ  CAM  aromatic  1.335  0.020  1.335
 M5H  NAH  CAL  aromatic  1.337  0.020  1.337
 M5H  NAI  CAF  single    1.465  0.020  1.465
 M5H  NAI  CAK  single    1.456  0.020  1.456
 M5H  CAL  CAK  single    1.487  0.020  1.487
 M5H  CAL  CAN  aromatic  1.395  0.020  1.395
 M5H  CAM  CAC  aromatic  1.415  0.020  1.415
 M5H  CAM  CAN  aromatic  1.425  0.020  1.425
 M5H  CAF  CAE  single    1.560  0.020  1.560
 M5H  CAK  NAG  single    1.458  0.020  1.458
 M5H  CAC  CAA  aromatic  1.366  0.020  1.366
 M5H  CAN  CAD  aromatic  1.413  0.020  1.413
 M5H  NAG  CAE  single    1.464  0.020  1.464
 M5H  CAA  CAB  aromatic  1.424  0.020  1.424
 M5H  CAD  CAB  aromatic  1.367  0.020  1.367
 M5H  CAA  H1   single    0.930  0.020  1.080
 M5H  CAB  H2   single    0.930  0.020  1.080
 M5H  CAC  H3   single    0.930  0.020  1.080
 M5H  CAD  H4   single    0.930  0.020  1.080
 M5H  CAE  H5   single    0.970  0.020  1.090
 M5H  CAE  H6   single    0.970  0.020  1.090
 M5H  CAF  H7   single    0.970  0.020  1.090
 M5H  CAF  H8   single    0.970  0.020  1.090
 M5H  CAK  H9   single    0.970  0.020  1.090
 M5H  NAG  H10  single    0.890  0.020  1.040
 M5H  NAH  H12  single    0.860  0.020  1.020
 M5H  NAI  H13  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
 M5H  H1   CAA  CAC  119.42  3.000
 M5H  H1   CAA  CAB  118.66  3.000
 M5H  CAC  CAA  CAB  121.92  3.000
 M5H  H2   CAB  CAD  119.80  3.000
 M5H  H2   CAB  CAA  118.79  3.000
 M5H  CAD  CAB  CAA  121.41  3.000
 M5H  H3   CAC  CAM  120.72  3.000
 M5H  H3   CAC  CAA  121.51  3.000
 M5H  CAM  CAC  CAA  117.77  3.000
 M5H  H4   CAD  CAN  120.66  3.000
 M5H  H4   CAD  CAB  121.38  3.000
 M5H  CAN  CAD  CAB  117.96  3.000
 M5H  H6   CAE  H5   107.61  3.000
 M5H  H6   CAE  NAG  110.16  3.000
 M5H  H5   CAE  NAG  110.05  3.000
 M5H  H6   CAE  CAF  113.07  3.000
 M5H  H5   CAE  CAF  110.26  3.000
 M5H  NAG  CAE  CAF  105.70  3.000
 M5H  H8   CAF  H7   107.59  3.000
 M5H  H8   CAF  NAI  110.32  3.000
 M5H  H7   CAF  NAI  110.10  3.000
 M5H  H8   CAF  CAE  110.29  3.000
 M5H  H7   CAF  CAE  112.80  3.000
 M5H  NAI  CAF  CAE  105.77  3.000
 M5H  H9   CAK  NAI  107.15  3.000
 M5H  H9   CAK  NAG  107.02  3.000
 M5H  NAI  CAK  NAG  107.84  3.000
 M5H  H9   CAK  CAL  108.88  3.000
 M5H  NAG  CAK  CAL  112.78  3.000
 M5H  NAI  CAK  CAL  112.85  3.000
 M5H  NAH  CAL  CAN  105.14  3.000
 M5H  CAN  CAL  CAK  132.31  3.000
 M5H  NAH  CAL  CAK  122.52  3.000
 M5H  NAJ  CAM  CAN  111.33  3.000
 M5H  CAN  CAM  CAC  120.36  3.000
 M5H  NAJ  CAM  CAC  128.31  3.000
 M5H  CAM  CAN  CAL  104.12  3.000
 M5H  CAM  CAN  CAD  120.58  3.000
 M5H  CAL  CAN  CAD  135.30  3.000
 M5H  H10  NAG  CAK  107.80  3.000
 M5H  H10  NAG  CAE  107.91  3.000
 M5H  CAK  NAG  CAE  102.52  3.000
 M5H  H12  NAH  NAJ  119.23  3.000
 M5H  H12  NAH  CAL  125.14  3.000
 M5H  NAJ  NAH  CAL  115.63  3.000
 M5H  H13  NAI  CAK  108.07  3.000
 M5H  H13  NAI  CAF  108.68  3.000
 M5H  CAK  NAI  CAF  103.04  3.000
 M5H  NAH  NAJ  CAM  103.79  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
 M5H  CONST_01  NAJ  CAM  CAC  CAA  180.00   0.0  0
 M5H  CONST_02  CAN  CAM  CAC  CAA    0.00   0.0  0
 M5H  CONST_03  CAN  CAD  CAB  CAA    0.00   0.0  0
 M5H  CONST_04  CAM  CAC  CAA  CAB    0.00   0.0  0
 M5H  CONST_05  CAL  CAN  CAD  CAB  180.00   0.0  0
 M5H  CONST_06  CAM  CAN  CAD  CAB    0.00   0.0  0
 M5H  CONST_07  NAH  NAJ  CAM  CAC  180.00   0.0  0
 M5H  CONST_08  CAL  CAN  CAM  CAC  180.00   0.0  0
 M5H  CONST_09  CAD  CAN  CAM  CAC    0.00   0.0  0
 M5H  CONST_10  CAD  CAB  CAA  CAC    0.00   0.0  0
 M5H  CONST_11  NAH  CAL  CAN  CAD  180.00   0.0  0
 M5H  CONST_12  NAJ  CAM  CAN  CAD  180.00   0.0  0
 M5H  CONST_13  CAM  NAJ  NAH  CAL    0.00   0.0  0
 M5H  CONST_14  NAJ  CAM  CAN  CAL    0.00   0.0  0
 M5H  CONST_15  NAH  CAL  CAN  CAM    0.00   0.0  0
 M5H  CONST_16  NAJ  NAH  CAL  CAN    0.00   0.0  0
 M5H  CONST_17  NAH  NAJ  CAM  CAN    0.00   0.0  0
 M5H  CONST_18  CAK  CAL  CAN  CAD    0.00   0.0  0
 M5H  CONST_19  NAJ  NAH  CAL  CAK  180.00   0.0  0
 M5H  CONST_20  CAM  CAN  CAL  CAK  180.00   0.0  0
 M5H  CONST_21  H4   CAD  CAB  CAA  180.00   0.0  0
 M5H  CONST_22  H3   CAC  CAA  CAB  180.00   0.0  0
 M5H  CONST_23  H2   CAB  CAA  CAC  180.00   0.0  0
 M5H  CONST_24  H1   CAA  CAB  CAD  180.00   0.0  0
 M5H  CONST_25  H12  NAH  CAL  CAK    0.00   0.0  0
 M5H  Var_01    CAK  NAI  CAF  CAE  -20.48  30.0  1
 M5H  Var_02    CAK  NAG  CAE  CAF   24.14  30.0  1
 M5H  Var_03    NAI  CAF  CAE  NAG   -2.37  30.0  1

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
 M5H  chir_01  CAK  NAI  CAL  NAG  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
 M5H  plan-1  CAA  0.020
 M5H  plan-1  CAB  0.020
 M5H  plan-1  CAC  0.020
 M5H  plan-1  CAD  0.020
 M5H  plan-1  CAK  0.020
 M5H  plan-1  CAL  0.020
 M5H  plan-1  CAM  0.020
 M5H  plan-1  CAN  0.020
 M5H  plan-1  NAH  0.020
 M5H  plan-1  NAJ  0.020
 M5H  plan-1  H1   0.020
 M5H  plan-1  H2   0.020
 M5H  plan-1  H3   0.020
 M5H  plan-1  H4   0.020
 M5H  plan-1  H12  0.020

