# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 12:22:01 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: 3-amino-1H-indazole-4-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1n[nH]c2cccc(C#N)c12
#
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
 YSO  YSO  3-amino-1H-indazole-4-carbonitrile  ligand  18  12  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_YSO
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
 YSO  CAK   C  CSP   0   0.003  -2.3344   0.2693  -0.0326
 YSO  NAA   N  NS    0  -0.244  -3.4215  -0.1138  -0.0359
 YSO  CAC   C  CR6   0   0.006  -0.9893   0.7404  -0.0221
 YSO  CAB   C  CR16  0  -0.276  -0.7336   2.0997  -0.0065
 YSO  CAD   C  CR16  0  -0.265   0.5889   2.5749  -0.0004
 YSO  CAL   C  CR16  0  -0.275   1.6682   1.7213  -0.0157
 YSO  CAH   C  CR56  0   0.438   1.4017   0.3469  -0.0340
 YSO  NAM   N  NR15  0  -0.562   2.2145  -0.7238  -0.0648
 YSO  NAJ   N  N     0  -0.267   1.5293  -1.8826  -0.0654
 YSO  CAE   C  CR5   0   0.341   0.2561  -1.5769  -0.0513
 YSO  C5    C  CR56  0  -0.078   0.0909  -0.1586  -0.0324
 YSO  NAI   N  NH2   0  -0.852  -0.7413  -2.5243  -0.1241
 YSO  HAB   H  HCR6  0   0.283  -1.5545   2.8027  -0.0011
 YSO  HAD   H  HCR6  0   0.277   0.7555   3.6432   0.0145
 YSO  HAL   H  HCR6  0   0.286   2.6823   2.0978  -0.0137
 YSO  HAM   H  HNR5  0   0.419   3.2200  -0.7393  -0.0827
 YSO  HAI1  H  HNH2  0   0.381  -0.4017  -3.4667   0.0024
 YSO  HAI2  H  HNH2  0   0.385  -1.5230  -2.3524   0.4901

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
 YSO  CAK  NAA   triple    1.153  0.020  1.153
 YSO  CAK  CAC   single    1.425  0.020  1.425
 YSO  CAC  CAB   aromatic  1.383  0.020  1.383
 YSO  CAC  C5    aromatic  1.405  0.020  1.405
 YSO  CAB  CAD   aromatic  1.405  0.020  1.405
 YSO  CAD  CAL   aromatic  1.376  0.020  1.376
 YSO  CAL  CAH   aromatic  1.400  0.020  1.400
 YSO  CAH  NAM   aromatic  1.345  0.020  1.345
 YSO  CAH  C5    aromatic  1.405  0.020  1.405
 YSO  NAM  NAJ   aromatic  1.346  0.020  1.346
 YSO  NAJ  CAE   aromatic  1.309  0.020  1.309
 YSO  CAE  NAI   single    1.378  0.020  1.378
 YSO  CAE  C5    aromatic  1.428  0.020  1.428
 YSO  CAB  HAB   single    0.930  0.020  1.080
 YSO  CAD  HAD   single    0.930  0.020  1.080
 YSO  CAL  HAL   single    0.930  0.020  1.080
 YSO  NAM  HAM   single    0.860  0.020  1.020
 YSO  NAI  HAI1  single    0.890  0.020  1.040
 YSO  NAI  HAI2  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
 YSO  CAC   CAK  NAA   180.00  3.000
 YSO  C5    CAC  CAB   119.12  3.000
 YSO  C5    CAC  CAK   120.92  3.000
 YSO  CAB   CAC  CAK   119.96  3.000
 YSO  HAB   CAB  CAD   119.66  3.000
 YSO  HAB   CAB  CAC   119.92  3.000
 YSO  CAD   CAB  CAC   120.42  3.000
 YSO  HAD   CAD  CAL   119.48  3.000
 YSO  HAD   CAD  CAB   118.63  3.000
 YSO  CAL   CAD  CAB   121.89  3.000
 YSO  HAL   CAL  CAH   121.34  3.000
 YSO  HAL   CAL  CAD   121.29  3.000
 YSO  CAH   CAL  CAD   117.37  3.000
 YSO  C5    CAH  NAM   106.11  3.000
 YSO  C5    CAH  CAL   122.06  3.000
 YSO  NAM   CAH  CAL   131.83  3.000
 YSO  HAM   NAM  NAJ   119.70  3.000
 YSO  HAM   NAM  CAH   128.10  3.000
 YSO  NAJ   NAM  CAH   112.20  3.000
 YSO  CAE   NAJ  NAM   107.09  3.000
 YSO  NAI   CAE  C5    126.86  3.000
 YSO  C5    CAE  NAJ   110.16  3.000
 YSO  NAI   CAE  NAJ   122.88  3.000
 YSO  CAE   C5   CAH   104.44  3.000
 YSO  CAE   C5   CAC   136.42  3.000
 YSO  CAH   C5   CAC   119.14  3.000
 YSO  HAI2  NAI  HAI1  110.08  3.000
 YSO  HAI2  NAI  CAE   114.31  3.000
 YSO  HAI1  NAI  CAE   113.06  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
 YSO  CONST_01  CAL   CAD  CAB  CAC    0.00  0.0  0
 YSO  CONST_02  CAL   CAH  C5   CAC    0.00  0.0  0
 YSO  CONST_03  NAM   CAH  C5   CAC  180.00  0.0  0
 YSO  CONST_04  NAJ   CAE  C5   CAC  180.00  0.0  0
 YSO  CONST_05  CAH   C5   CAC  CAB    0.00  0.0  0
 YSO  CONST_06  CAE   C5   CAC  CAB  180.00  0.0  0
 YSO  CONST_07  CAH   CAL  CAD  CAB    0.00  0.0  0
 YSO  CONST_08  C5    CAC  CAB  CAD    0.00  0.0  0
 YSO  CONST_09  NAM   CAH  CAL  CAD  180.00  0.0  0
 YSO  CONST_10  C5    CAH  CAL  CAD    0.00  0.0  0
 YSO  CONST_11  NAJ   NAM  CAH  CAL  180.00  0.0  0
 YSO  CONST_12  CAE   C5   CAH  CAL  180.00  0.0  0
 YSO  CONST_13  CAE   NAJ  NAM  CAH    0.00  0.0  0
 YSO  CONST_14  NAJ   CAE  C5   CAH    0.00  0.0  0
 YSO  CONST_15  CAE   C5   CAH  NAM    0.00  0.0  0
 YSO  CONST_16  C5    CAE  NAJ  NAM    0.00  0.0  0
 YSO  CONST_17  C5    CAH  NAM  NAJ    0.00  0.0  0
 YSO  CONST_18  CAD   CAB  CAC  CAK  180.00  0.0  0
 YSO  CONST_19  CAH   C5   CAC  CAK  180.00  0.0  0
 YSO  CONST_20  CAE   C5   CAC  CAK    0.00  0.0  0
 YSO  CONST_21  NAI   CAE  C5   CAC    0.00  0.0  0
 YSO  CONST_22  NAI   CAE  C5   CAH  180.00  0.0  0
 YSO  CONST_23  NAI   CAE  NAJ  NAM  180.00  0.0  0
 YSO  CONST_24  HAD   CAD  CAB  CAC  180.00  0.0  0
 YSO  CONST_25  HAL   CAL  CAD  CAB  180.00  0.0  0
 YSO  CONST_26  HAB   CAB  CAD  CAL  180.00  0.0  0
 YSO  CONST_27  HAM   NAM  CAH  CAL    0.00  0.0  0
 YSO  CONST_28  HAI1  NAI  CAE  NAJ    0.00  0.0  0

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
 YSO  plan-1  CAK   0.020
 YSO  plan-1  NAA   0.020
 YSO  plan-1  CAC   0.020
 YSO  plan-1  CAB   0.020
 YSO  plan-1  CAD   0.020
 YSO  plan-1  CAL   0.020
 YSO  plan-1  CAH   0.020
 YSO  plan-1  NAM   0.020
 YSO  plan-1  NAJ   0.020
 YSO  plan-1  CAE   0.020
 YSO  plan-1  C5    0.020
 YSO  plan-1  NAI   0.020
 YSO  plan-1  HAB   0.020
 YSO  plan-1  HAD   0.020
 YSO  plan-1  HAL   0.020
 YSO  plan-1  HAM   0.020
 YSO  plan-2  CAE   0.020
 YSO  plan-2  NAI   0.020
 YSO  plan-2  HAI1  0.020
 YSO  plan-2  HAI2  0.020

