# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 04:59:08 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: (2Z)-N-biphenyl-4-yl-2-cyano-3-cyclopropyl-3-hydroxyprop-2-enamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(/C1CC1)=C(/C#N)C(=O)Nc2ccc(cc2)c3ccccc3
#
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
 MD7  MD7  (2Z)-N-biphenyl-4-yl-2-cyano-3-cyclopropyl-3-hydroxyprop-2-enamide  ligand  39  23  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_MD7
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
 MD7  CAN   C  CH2   0  -0.456  -6.8576  -0.9194   0.7325
 MD7  CAO   C  CH2   0  -0.456  -6.8156  -1.0313  -0.7414
 MD7  CAW   C  CH1   0  -0.418  -5.8099  -0.1439  -0.0376
 MD7  CAS   C  C     0   0.534  -4.4140  -0.5621   0.0343
 MD7  OAC   O  OH1   0  -0.577  -4.1979  -1.8366   0.1610
 MD7  CAR   C  C     0  -0.353  -3.3556   0.3344  -0.0252
 MD7  CAD   C  CSP   0  -0.011  -3.5984   1.7168  -0.1587
 MD7  NAA   N  NS    0  -0.257  -3.7498   2.8577  -0.2669
 MD7  CAQ   C  C     0   0.677  -1.9843  -0.1681   0.0636
 MD7  OAB   O  O     0  -0.537  -1.7766  -1.3842   0.1949
 MD7  NAP   N  NH1   0  -0.770  -0.9864   0.7330  -0.0013
 MD7  CAT   C  CR6   0   0.352   0.3941   0.4761   0.0219
 MD7  CAK   C  CR16  0  -0.322   1.2220   1.3600  -0.6671
 MD7  CAM   C  CR16  0  -0.303   2.5944   1.1908  -0.6580
 MD7  CAJ   C  CR16  0  -0.274   0.9686  -0.5771   0.7300
 MD7  CAL   C  CR16  0  -0.309   2.3447  -0.7399   0.7219
 MD7  CAV   C  CR6   0   0.084   3.1861   0.1310   0.0303
 MD7  CAU   C  CR6   0   0.095   4.6499  -0.0554   0.0329
 MD7  CAH   C  CR16  0  -0.314   5.2080  -1.3355   0.0269
 MD7  CAF   C  CR16  0  -0.239   6.5840  -1.5124   0.0309
 MD7  CAE   C  CR16  0  -0.267   7.4303  -0.4116   0.0376
 MD7  CAG   C  CR16  0  -0.239   6.8880   0.8668   0.0419
 MD7  CAI   C  CR16  0  -0.314   5.5122   1.0432   0.0405
 MD7  HAN   H  HCH2  0   0.278  -7.6372  -0.3253   1.1892
 MD7  HANA  H  HCH2  0   0.272  -6.5234  -1.7617   1.3228
 MD7  HAO   H  HCH2  0   0.272  -6.4533  -1.9505  -1.1812
 MD7  HAOA  H  HCH2  0   0.278  -7.5647  -0.5132  -1.3245
 MD7  HAW   H  HCH1  0   0.298  -5.9721   0.9218  -0.1263
 MD7  HOAC  H  HOH1  0   0.496  -3.1936  -1.9635   0.2052
 MD7  HNAP  H  HNH1  0   0.428  -1.2364   1.6883  -0.2122
 MD7  HAK   H  HCR6  0   0.275   0.7890   2.1839  -1.2217
 MD7  HAM   H  HCR6  0   0.260   3.2075   1.8848  -1.2182
 MD7  HAJ   H  HCR6  0   0.275   0.3639  -1.2601   1.3051
 MD7  HAL   H  HCR6  0   0.259   2.7666  -1.5554   1.2960
 MD7  HAH   H  HCR6  0   0.255   4.5629  -2.2047  -0.0013
 MD7  HAF   H  HCR6  0   0.257   6.9942  -2.5140   0.0189
 MD7  HAE   H  HCR6  0   0.257   8.5038  -0.5484   0.0394
 MD7  HAG   H  HCR6  0   0.258   7.5387   1.7315   0.0540
 MD7  HAI   H  HCR6  0   0.254   5.1078   2.0479   0.0648

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
 MD7  CAN  CAO   single    1.479  0.020  1.479
 MD7  CAN  CAW   single    1.514  0.020  1.514
 MD7  CAO  CAW   single    1.515  0.020  1.515
 MD7  CAW  CAS   single    1.459  0.020  1.459
 MD7  CAS  OAC   single    1.299  0.020  1.299
 MD7  CAS  CAR   double    1.388  0.020  1.388
 MD7  CAR  CAD   single    1.410  0.020  1.410
 MD7  CAR  CAQ   single    1.463  0.020  1.463
 MD7  CAD  NAA   triple    1.156  0.020  1.156
 MD7  CAQ  OAB   double    1.241  0.020  1.241
 MD7  CAQ  NAP   single    1.346  0.020  1.346
 MD7  NAP  CAT   single    1.404  0.020  1.404
 MD7  CAT  CAK   aromatic  1.393  0.020  1.393
 MD7  CAT  CAJ   aromatic  1.393  0.020  1.393
 MD7  CAK  CAM   aromatic  1.383  0.020  1.383
 MD7  CAM  CAV   aromatic  1.395  0.020  1.395
 MD7  CAJ  CAL   aromatic  1.386  0.020  1.386
 MD7  CAL  CAV   aromatic  1.394  0.020  1.394
 MD7  CAV  CAU   single    1.476  0.020  1.476
 MD7  CAU  CAH   aromatic  1.396  0.020  1.396
 MD7  CAU  CAI   aromatic  1.397  0.020  1.397
 MD7  CAH  CAF   aromatic  1.387  0.020  1.387
 MD7  CAF  CAE   aromatic  1.389  0.020  1.389
 MD7  CAE  CAG   aromatic  1.389  0.020  1.389
 MD7  CAG  CAI   aromatic  1.387  0.020  1.387
 MD7  CAN  HAN   single    0.970  0.020  1.090
 MD7  CAN  HANA  single    0.970  0.020  1.090
 MD7  CAO  HAO   single    0.970  0.020  1.090
 MD7  CAO  HAOA  single    0.970  0.020  1.090
 MD7  CAW  HAW   single    0.970  0.020  1.090
 MD7  OAC  HOAC  single    0.850  0.020  0.980
 MD7  NAP  HNAP  single    0.860  0.020  1.020
 MD7  CAK  HAK   single    0.930  0.020  1.080
 MD7  CAM  HAM   single    0.930  0.020  1.080
 MD7  CAJ  HAJ   single    0.930  0.020  1.080
 MD7  CAL  HAL   single    0.930  0.020  1.080
 MD7  CAH  HAH   single    0.930  0.020  1.080
 MD7  CAF  HAF   single    0.930  0.020  1.080
 MD7  CAE  HAE   single    0.930  0.020  1.080
 MD7  CAG  HAG   single    0.930  0.020  1.080
 MD7  CAI  HAI   single    0.930  0.020  1.080

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
 MD7  HANA  CAN  HAN  114.84  3.000
 MD7  HANA  CAN  CAW  117.56  3.000
 MD7  HAN   CAN  CAW  115.62  3.000
 MD7  HANA  CAN  CAO  118.45  3.000
 MD7  HAN   CAN  CAO  118.88  3.000
 MD7  CAW   CAN  CAO   60.80  3.000
 MD7  HAOA  CAO  HAO  114.84  3.000
 MD7  HAOA  CAO  CAW  115.46  3.000
 MD7  HAO   CAO  CAW  117.67  3.000
 MD7  HAOA  CAO  CAN  118.78  3.000
 MD7  HAO   CAO  CAN  118.63  3.000
 MD7  CAW   CAO  CAN   60.75  3.000
 MD7  HAW   CAW  CAS  115.46  3.000
 MD7  HAW   CAW  CAO  116.08  3.000
 MD7  CAS   CAW  CAO  119.36  3.000
 MD7  HAW   CAW  CAN  116.27  3.000
 MD7  CAS   CAW  CAN  119.36  3.000
 MD7  CAO   CAW  CAN   58.45  3.000
 MD7  CAR   CAS  OAC  120.73  3.000
 MD7  CAR   CAS  CAW  122.83  3.000
 MD7  OAC   CAS  CAW  116.43  3.000
 MD7  HOAC  OAC  CAS  106.98  3.000
 MD7  CAQ   CAR  CAD  120.25  3.000
 MD7  CAQ   CAR  CAS  119.35  3.000
 MD7  CAD   CAR  CAS  120.40  3.000
 MD7  NAA   CAD  CAR  180.00  3.000
 MD7  NAP   CAQ  OAB  122.49  3.000
 MD7  NAP   CAQ  CAR  117.52  3.000
 MD7  OAB   CAQ  CAR  120.00  3.000
 MD7  HNAP  NAP  CAT  114.82  3.000
 MD7  HNAP  NAP  CAQ  117.38  3.000
 MD7  CAT   NAP  CAQ  127.27  3.000
 MD7  CAJ   CAT  CAK  119.07  3.000
 MD7  CAJ   CAT  NAP  123.51  3.000
 MD7  CAK   CAT  NAP  117.38  3.000
 MD7  HAK   CAK  CAM  119.55  3.000
 MD7  HAK   CAK  CAT  119.87  3.000
 MD7  CAM   CAK  CAT  120.59  3.000
 MD7  HAM   CAM  CAV  120.14  3.000
 MD7  HAM   CAM  CAK  118.70  3.000
 MD7  CAV   CAM  CAK  121.14  3.000
 MD7  HAJ   CAJ  CAL  119.06  3.000
 MD7  HAJ   CAJ  CAT  121.23  3.000
 MD7  CAL   CAJ  CAT  119.69  3.000
 MD7  HAL   CAL  CAV  119.88  3.000
 MD7  HAL   CAL  CAJ  118.18  3.000
 MD7  CAV   CAL  CAJ  121.92  3.000
 MD7  CAU   CAV  CAL  121.25  3.000
 MD7  CAU   CAV  CAM  121.16  3.000
 MD7  CAL   CAV  CAM  117.59  3.000
 MD7  CAI   CAU  CAH  118.32  3.000
 MD7  CAI   CAU  CAV  120.87  3.000
 MD7  CAH   CAU  CAV  120.82  3.000
 MD7  HAH   CAH  CAF  119.25  3.000
 MD7  HAH   CAH  CAU  119.86  3.000
 MD7  CAF   CAH  CAU  120.88  3.000
 MD7  HAF   CAF  CAE  120.17  3.000
 MD7  HAF   CAF  CAH  119.60  3.000
 MD7  CAE   CAF  CAH  120.23  3.000
 MD7  HAE   CAE  CAG  120.25  3.000
 MD7  HAE   CAE  CAF  120.29  3.000
 MD7  CAG   CAE  CAF  119.46  3.000
 MD7  HAG   CAG  CAI  119.66  3.000
 MD7  HAG   CAG  CAE  120.05  3.000
 MD7  CAI   CAG  CAE  120.29  3.000
 MD7  HAI   CAI  CAG  119.22  3.000
 MD7  HAI   CAI  CAU  119.95  3.000
 MD7  CAG   CAI  CAU  120.82  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
 MD7  CONST_01  CAV  CAM  CAK  CAT    0.00   0.0  0
 MD7  CONST_02  CAV  CAL  CAJ  CAT    0.00   0.0  0
 MD7  CONST_03  CAL  CAJ  CAT  CAK    0.00   0.0  0
 MD7  CONST_04  CAL  CAV  CAM  CAK    0.00   0.0  0
 MD7  CONST_05  CAU  CAV  CAM  CAK  180.00   0.0  0
 MD7  CONST_06  CAJ  CAT  CAK  CAM    0.00   0.0  0
 MD7  CONST_07  CAJ  CAL  CAV  CAM    0.00   0.0  0
 MD7  CONST_10  CAU  CAV  CAL  CAJ  180.00   0.0  0
 MD7  CONST_13  CAF  CAH  CAU  CAV  180.00   0.0  0
 MD7  CONST_14  CAG  CAI  CAU  CAV  180.00   0.0  0
 MD7  CONST_15  CAE  CAF  CAH  CAU    0.00   0.0  0
 MD7  CONST_16  CAE  CAG  CAI  CAU    0.00   0.0  0
 MD7  CONST_17  CAG  CAI  CAU  CAH    0.00   0.0  0
 MD7  CONST_18  CAG  CAE  CAF  CAH    0.00   0.0  0
 MD7  CONST_19  CAI  CAU  CAH  CAF    0.00   0.0  0
 MD7  CONST_20  CAI  CAG  CAE  CAF    0.00   0.0  0
 MD7  CONST_21  CAM  CAK  CAT  NAP  180.00   0.0  0
 MD7  CONST_22  CAL  CAJ  CAT  NAP  180.00   0.0  0
 MD7  CONST_23  HAM  CAM  CAK  CAT  180.00   0.0  0
 MD7  CONST_24  HAL  CAL  CAJ  CAT  180.00   0.0  0
 MD7  CONST_25  HAJ  CAJ  CAT  CAK  180.00   0.0  0
 MD7  CONST_26  HAK  CAK  CAT  CAJ  180.00   0.0  0
 MD7  CONST_27  HAH  CAH  CAU  CAV    0.00   0.0  0
 MD7  CONST_28  HAI  CAI  CAU  CAV    0.00   0.0  0
 MD7  CONST_29  HAF  CAF  CAH  CAU  180.00   0.0  0
 MD7  CONST_30  HAG  CAG  CAI  CAU  180.00   0.0  0
 MD7  CONST_31  HAE  CAE  CAF  CAH  180.00   0.0  0
 MD7  CONST_35  CAT  NAP  CAQ  CAR  180.00   0.0  0
 MD7  CONST_36  CAT  NAP  CAQ  OAB    0.00   0.0  0
 MD7  Var_01    CAS  CAW  CAO  CAN  108.34  30.0  1
 MD7  Var_02    OAC  CAS  CAW  CAN   32.89  30.0  3
 MD7  Var_03    CAD  CAR  CAS  CAW    0.10   0.0  2
 MD7  Var_04    OAB  CAQ  CAR  CAS   -0.22  30.0  2

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
 MD7  chir_01  CAW  CAN  CAO  CAS  both

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
 MD7  plan-1  NAP   0.020
 MD7  plan-1  CAT   0.020
 MD7  plan-1  CAK   0.020
 MD7  plan-1  CAM   0.020
 MD7  plan-1  CAJ   0.020
 MD7  plan-1  CAL   0.020
 MD7  plan-1  CAV   0.020
 MD7  plan-1  CAU   0.020
 MD7  plan-1  HAK   0.020
 MD7  plan-1  HAM   0.020
 MD7  plan-1  HAJ   0.020
 MD7  plan-1  HAL   0.020
 MD7  plan-2  CAV   0.020
 MD7  plan-2  CAU   0.020
 MD7  plan-2  CAH   0.020
 MD7  plan-2  CAF   0.020
 MD7  plan-2  CAE   0.020
 MD7  plan-2  CAG   0.020
 MD7  plan-2  CAI   0.020
 MD7  plan-2  HAH   0.020
 MD7  plan-2  HAF   0.020
 MD7  plan-2  HAE   0.020
 MD7  plan-2  HAG   0.020
 MD7  plan-2  HAI   0.020
 MD7  plan-3  CAR   0.020
 MD7  plan-3  CAQ   0.020
 MD7  plan-3  OAB   0.020
 MD7  plan-3  NAP   0.020
 MD7  plan-3  CAT   0.020
 MD7  plan-3  HNAP  0.020
 MD7  plan-4  CAW   0.020
 MD7  plan-4  CAS   0.020
 MD7  plan-4  OAC   0.020
 MD7  plan-4  CAR   0.020
 MD7  plan-4  CAD   0.020
 MD7  plan-4  CAQ   0.020

