# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 21:54:41 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: ~{N}-[2,4-bis(fluoranyl)phenyl]-2-methyl-pyrazole-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1nccc1C(=O)Nc2ccc(F)cc2F
#
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
 5S9  5S9  ~{N}-[2,4-bis(fluoranyl)phenyl]-2-methyl-pyrazole-3-carboxamide  ligand  26  17  .  2022-07-23  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_5S9
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
 5S9  FAD  F  F     0  -0.296   1.1069  -1.3808   1.5417
 5S9  CAN  C  CR6   0   0.550   1.8034  -0.5866   0.7274
 5S9  CAI  C  CR16  0  -0.568   3.1740  -0.5241   0.8721
 5S9  CAM  C  CR6   0   0.544   3.8749   0.2756  -0.0111
 5S9  FAC  F  F     0  -0.307   5.2055   0.3450   0.1128
 5S9  CAG  C  CR16  0  -0.424   3.2525   0.9976  -1.0100
 5S9  CAH  C  CR16  0  -0.268   1.8712   0.9287  -1.1094
 5S9  CAO  C  CR6   0   0.157   1.1255   0.1382  -0.2449
 5S9  NAK  N  NH1   0  -0.742  -0.2722   0.0467  -0.3630
 5S9  CAL  C  C     0   0.517  -1.1052   0.4440   0.6320
 5S9  OAB  O  O     0  -0.447  -0.7094   0.9329   1.6723
 5S9  CAP  C  CR5   0   0.289  -2.5518   0.2806   0.3769
 5S9  CAF  C  CR15  0  -0.477  -3.5545   1.1270   0.8023
 5S9  CAE  C  CR15  0  -0.078  -4.7269   0.5499   0.3088
 5S9  NAJ  N  N     0  -0.257  -4.4681  -0.5694  -0.3468
 5S9  NAQ  N  NR5   0  -0.323  -3.1541  -0.7236  -0.3057
 5S9  CAA  C  CH3   0  -0.549  -2.5665  -1.9053  -0.9037
 5S9  H1   H  HCR6  0   0.309   3.6783  -1.0914   1.6432
 5S9  H2   H  HCR6  0   0.291   3.8279   1.6115  -1.6889
 5S9  H3   H  HCR6  0   0.291   1.3606   1.4970  -1.8756
 5S9  H4   H  HNH1  0   0.423  -0.6449  -0.1133  -1.2867
 5S9  H5   H  HCR5  0   0.277  -3.4421   2.0332   1.3733
 5S9  H6   H  HCR5  0   0.270  -5.7428   0.8986   0.4114
 5S9  H7   H  HCH3  0   0.265  -2.2265  -1.7098  -1.9201
 5S9  H8   H  HCH3  0   0.268  -1.7313  -2.2577  -0.3053
 5S9  H9   H  HCH3  0   0.283  -3.3265  -2.6795  -0.9328

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
 5S9  NAJ  CAE  aromatic  1.323  0.020  1.323
 5S9  NAJ  NAQ  aromatic  1.324  0.020  1.324
 5S9  CAA  NAQ  single    1.449  0.020  1.449
 5S9  CAE  CAF  aromatic  1.397  0.020  1.397
 5S9  NAQ  CAP  aromatic  1.356  0.020  1.356
 5S9  CAF  CAP  aromatic  1.379  0.020  1.379
 5S9  CAP  CAL  single    1.478  0.020  1.478
 5S9  OAB  CAL  double    1.216  0.020  1.216
 5S9  CAL  NAK  single    1.357  0.020  1.357
 5S9  NAK  CAO  single    1.406  0.020  1.406
 5S9  CAH  CAO  aromatic  1.389  0.020  1.389
 5S9  CAH  CAG  aromatic  1.387  0.020  1.387
 5S9  CAO  CAN  aromatic  1.389  0.020  1.389
 5S9  CAG  CAM  aromatic  1.381  0.020  1.381
 5S9  CAN  FAD  single    1.334  0.020  1.334
 5S9  CAN  CAI  aromatic  1.380  0.020  1.380
 5S9  CAM  CAI  aromatic  1.382  0.020  1.382
 5S9  CAM  FAC  single    1.338  0.020  1.338
 5S9  CAI  H1   single    0.930  0.020  1.080
 5S9  CAG  H2   single    0.930  0.020  1.080
 5S9  CAH  H3   single    0.930  0.020  1.080
 5S9  NAK  H4   single    0.860  0.020  1.020
 5S9  CAF  H5   single    0.930  0.020  1.080
 5S9  CAE  H6   single    0.930  0.020  1.080
 5S9  CAA  H7   single    0.970  0.020  1.090
 5S9  CAA  H8   single    0.970  0.020  1.090
 5S9  CAA  H9   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
 5S9  CAO  CAN  CAI  122.31  3.000
 5S9  CAI  CAN  FAD  118.80  3.000
 5S9  CAO  CAN  FAD  118.89  3.000
 5S9  H1   CAI  CAM  121.49  3.000
 5S9  H1   CAI  CAN  120.93  3.000
 5S9  CAM  CAI  CAN  117.58  3.000
 5S9  CAG  CAM  FAC  119.21  3.000
 5S9  FAC  CAM  CAI  118.36  3.000
 5S9  CAG  CAM  CAI  122.42  3.000
 5S9  H2   CAG  CAH  120.89  3.000
 5S9  H2   CAG  CAM  120.75  3.000
 5S9  CAH  CAG  CAM  118.35  3.000
 5S9  H3   CAH  CAO  119.10  3.000
 5S9  H3   CAH  CAG  119.65  3.000
 5S9  CAO  CAH  CAG  121.25  3.000
 5S9  NAK  CAO  CAH  121.25  3.000
 5S9  CAH  CAO  CAN  118.07  3.000
 5S9  NAK  CAO  CAN  120.67  3.000
 5S9  H4   NAK  CAL  119.41  3.000
 5S9  H4   NAK  CAO  117.03  3.000
 5S9  CAL  NAK  CAO  121.98  3.000
 5S9  CAP  CAL  OAB  120.72  3.000
 5S9  OAB  CAL  NAK  123.05  3.000
 5S9  CAP  CAL  NAK  116.22  3.000
 5S9  NAQ  CAP  CAF  106.67  3.000
 5S9  CAF  CAP  CAL  126.19  3.000
 5S9  NAQ  CAP  CAL  127.14  3.000
 5S9  H5   CAF  CAE  128.51  3.000
 5S9  H5   CAF  CAP  127.15  3.000
 5S9  CAE  CAF  CAP  104.34  3.000
 5S9  H6   CAE  NAJ  120.32  3.000
 5S9  H6   CAE  CAF  128.55  3.000
 5S9  NAJ  CAE  CAF  111.13  3.000
 5S9  NAQ  NAJ  CAE  106.11  3.000
 5S9  CAA  NAQ  NAJ  119.00  3.000
 5S9  CAA  NAQ  CAP  129.19  3.000
 5S9  NAJ  NAQ  CAP  111.74  3.000
 5S9  H9   CAA  H8   108.77  3.000
 5S9  H9   CAA  H7   108.76  3.000
 5S9  H8   CAA  H7   109.40  3.000
 5S9  H9   CAA  NAQ  107.99  3.000
 5S9  H8   CAA  NAQ  110.43  3.000
 5S9  H7   CAA  NAQ  111.42  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
 5S9  CONST_01  CAG  CAH  CAO  CAN    0.00   0.0  0
 5S9  CONST_02  CAG  CAM  CAI  CAN    0.00   0.0  0
 5S9  CONST_03  CAH  CAO  CAN  CAI    0.00   0.0  0
 5S9  CONST_04  CAH  CAG  CAM  CAI    0.00   0.0  0
 5S9  CONST_05  CAO  CAH  CAG  CAM    0.00   0.0  0
 5S9  CONST_06  CAO  CAN  CAI  CAM    0.00   0.0  0
 5S9  CONST_07  CAE  NAJ  NAQ  CAP    0.00   0.0  0
 5S9  CONST_08  NAJ  CAE  CAF  CAP    0.00   0.0  0
 5S9  CONST_09  NAQ  NAJ  CAE  CAF    0.00   0.0  0
 5S9  CONST_10  NAJ  NAQ  CAP  CAF    0.00   0.0  0
 5S9  CONST_11  NAQ  CAP  CAF  CAE    0.00   0.0  0
 5S9  CONST_12  CAH  CAO  CAN  FAD  180.00   0.0  0
 5S9  CONST_13  CAM  CAI  CAN  FAD  180.00   0.0  0
 5S9  CONST_14  FAC  CAM  CAI  CAN  180.00   0.0  0
 5S9  CONST_15  NAK  CAO  CAN  CAI  180.00   0.0  0
 5S9  CONST_16  CAH  CAG  CAM  FAC  180.00   0.0  0
 5S9  CONST_17  NAK  CAO  CAH  CAG  180.00   0.0  0
 5S9  CONST_18  NAJ  NAQ  CAP  CAL  180.00   0.0  0
 5S9  CONST_19  CAE  CAF  CAP  CAL  180.00   0.0  0
 5S9  CONST_20  CAA  NAQ  CAP  CAF  180.00   0.0  0
 5S9  CONST_21  CAA  NAQ  NAJ  CAE  180.00   0.0  0
 5S9  CONST_22  H3   CAH  CAO  CAN  180.00   0.0  0
 5S9  CONST_23  H2   CAG  CAM  CAI  180.00   0.0  0
 5S9  CONST_24  H1   CAI  CAM  CAG  180.00   0.0  0
 5S9  CONST_25  H6   CAE  CAF  CAP  180.00   0.0  0
 5S9  CONST_26  H5   CAF  CAE  NAJ  180.00   0.0  0
 5S9  CONST_27  CAP  CAL  NAK  CAO  180.00   0.0  0
 5S9  CONST_31  OAB  CAL  NAK  CAO    0.00   0.0  0
 5S9  Var_01    NAQ  CAP  CAL  NAK   35.78  30.0  3
 5S9  Var_02    H7   CAA  NAQ  CAP  -87.41  30.0  2

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
 5S9  plan-1  CAL  0.020
 5S9  plan-1  CAP  0.020
 5S9  plan-1  CAF  0.020
 5S9  plan-1  CAE  0.020
 5S9  plan-1  NAJ  0.020
 5S9  plan-1  NAQ  0.020
 5S9  plan-1  CAA  0.020
 5S9  plan-1  H5   0.020
 5S9  plan-1  H6   0.020
 5S9  plan-2  FAD  0.020
 5S9  plan-2  CAN  0.020
 5S9  plan-2  CAI  0.020
 5S9  plan-2  CAM  0.020
 5S9  plan-2  FAC  0.020
 5S9  plan-2  CAG  0.020
 5S9  plan-2  CAH  0.020
 5S9  plan-2  CAO  0.020
 5S9  plan-2  NAK  0.020
 5S9  plan-2  H1   0.020
 5S9  plan-2  H2   0.020
 5S9  plan-2  H3   0.020
 5S9  plan-3  CAO  0.020
 5S9  plan-3  NAK  0.020
 5S9  plan-3  CAL  0.020
 5S9  plan-3  OAB  0.020
 5S9  plan-3  CAP  0.020
 5S9  plan-3  H4   0.020

