# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 13:56:13 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: (3,4-dihydroxy-5-nitrophenyl)(2-fluorophenyl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cc(cc(c1O)[N+]([O-])=O)C(=O)c2ccccc2F
#
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
 3M1  3M1  (3,4-dihydroxy-5-nitrophenyl)(2-fluorophenyl)methanone  ligand  28  20  .  2021-08-04  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3M1
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
 3M1  OAA   O  O      0  -0.374  -1.0542   2.3071  -1.0566
 3M1  OAB   O  O      0  -0.419   4.6744   0.2149   0.3520
 3M1  OAD   O  OH1    0  -0.602   3.4247  -2.0150   0.0391
 3M1  OAE   O  O     -1  -0.353   3.6675   2.0889   0.2629
 3M1  FAF   F  F      0  -0.298  -1.8742  -0.2789   1.6684
 3M1  CAG   C  CR16   0  -0.232  -5.0411  -0.4776  -0.0285
 3M1  CAH   C  CR16   0  -0.258  -4.7542   0.2208  -1.1955
 3M1  CAI   C  CR16   0  -0.398  -4.0674  -0.6534   0.9435
 3M1  CAJ   C  CR16   0  -0.254  -3.4878   0.7445  -1.3910
 3M1  CAK   C  CR16   0  -0.358   0.0182  -1.0652  -0.5208
 3M1  CAL   C  CR16   0  -0.355   1.2752   0.9649  -0.2314
 3M1  CAM   C  C      0   0.390  -1.1407   1.1618  -0.6690
 3M1  CAN   C  CR6    0   0.330   1.1548  -1.8243  -0.3659
 3M1  CAO   C  CR6    0   0.551  -2.8079  -0.1350   0.7176
 3M1  CAP   C  CR6    0   0.264   2.3935  -1.1992  -0.1134
 3M1  CAQ   C  CR6    0  -0.021   0.0696   0.3327  -0.4535
 3M1  CAR   C  CR6    0  -0.257  -2.4833   0.5558  -0.4415
 3M1  CAS   C  CR6    0   0.212   2.4235   0.2018  -0.0490
 3M1  NAT   N  N      1   0.364   3.6649   0.8880   0.2047
 3M1  HOAC  H  HOH1   0   0.482   1.9366  -3.5712  -0.3302
 3M1  HOAD  H  HOH1   0   0.496   4.2332  -1.4910   0.1963
 3M1  HAG   H  HCR6   0   0.279  -6.0305  -0.8840   0.1327
 3M1  HAH   H  HCR6   0   0.271  -5.5183   0.3603  -1.9476
 3M1  HAI   H  HCR6   0   0.289  -4.2821  -1.1773   1.8657
 3M1  HAJ   H  HCR6   0   0.278  -3.2614   1.2915  -2.2970
 3M1  HAK   H  HCR6   0   0.288  -0.9135  -1.5765  -0.7301
 3M1  HAL   H  HCR6   0   0.306   1.3261   2.0428  -0.1847
 3M1  OAC   O  OH1    0  -0.620   1.0726  -3.1596  -0.4566

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
 3M1  OAA  CAM   double    1.212  0.020  1.212
 3M1  OAE  NAT   single    1.202  0.020  1.202
 3M1  FAF  CAO   single    1.340  0.020  1.340
 3M1  CAG  CAH   aromatic  1.390  0.020  1.390
 3M1  CAH  CAJ   aromatic  1.384  0.020  1.384
 3M1  CAI  CAG   aromatic  1.387  0.020  1.387
 3M1  CAI  CAO   aromatic  1.381  0.020  1.381
 3M1  CAK  CAN   aromatic  1.376  0.020  1.376
 3M1  CAL  CAS   aromatic  1.391  0.020  1.391
 3M1  CAM  CAQ   single    1.483  0.020  1.483
 3M1  CAN  OAC   single    1.341  0.020  1.341
 3M1  CAN  CAP   aromatic  1.410  0.020  1.410
 3M1  CAO  CAR   aromatic  1.388  0.020  1.388
 3M1  CAP  OAD   single    1.324  0.020  1.324
 3M1  CAQ  CAK   aromatic  1.400  0.020  1.400
 3M1  CAQ  CAL   aromatic  1.379  0.020  1.379
 3M1  CAR  CAJ   aromatic  1.395  0.020  1.395
 3M1  CAR  CAM   single    1.490  0.020  1.490
 3M1  CAS  CAP   aromatic  1.403  0.020  1.403
 3M1  CAS  NAT   single    1.441  0.020  1.441
 3M1  NAT  OAB   double    1.222  0.020  1.222
 3M1  OAC  HOAC  single    0.850  0.020  0.980
 3M1  OAD  HOAD  single    0.850  0.020  0.980
 3M1  CAG  HAG   single    0.930  0.020  1.080
 3M1  CAH  HAH   single    0.930  0.020  1.080
 3M1  CAI  HAI   single    0.930  0.020  1.080
 3M1  CAJ  HAJ   single    0.930  0.020  1.080
 3M1  CAK  HAK   single    0.930  0.020  1.080
 3M1  CAL  HAL   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
 3M1  HOAD  OAD  CAP  109.45  3.000
 3M1  HAG   CAG  CAI  119.35  3.000
 3M1  HAG   CAG  CAH  120.18  3.000
 3M1  CAI   CAG  CAH  120.48  3.000
 3M1  HAH   CAH  CAJ  119.97  3.000
 3M1  HAH   CAH  CAG  120.20  3.000
 3M1  CAJ   CAH  CAG  119.83  3.000
 3M1  HAI   CAI  CAO  120.15  3.000
 3M1  HAI   CAI  CAG  121.28  3.000
 3M1  CAO   CAI  CAG  118.57  3.000
 3M1  HAJ   CAJ  CAR  119.18  3.000
 3M1  HAJ   CAJ  CAH  120.05  3.000
 3M1  CAR   CAJ  CAH  120.76  3.000
 3M1  HAK   CAK  CAQ  120.80  3.000
 3M1  HAK   CAK  CAN  118.16  3.000
 3M1  CAQ   CAK  CAN  121.01  3.000
 3M1  HAL   CAL  CAS  120.20  3.000
 3M1  HAL   CAL  CAQ  120.37  3.000
 3M1  CAS   CAL  CAQ  119.42  3.000
 3M1  CAR   CAM  CAQ  119.06  3.000
 3M1  CAR   CAM  OAA  119.82  3.000
 3M1  CAQ   CAM  OAA  121.10  3.000
 3M1  CAP   CAN  CAK  120.08  3.000
 3M1  CAP   CAN  OAC  120.49  3.000
 3M1  CAK   CAN  OAC  119.43  3.000
 3M1  CAR   CAO  CAI  122.48  3.000
 3M1  CAR   CAO  FAF  118.88  3.000
 3M1  CAI   CAO  FAF  118.63  3.000
 3M1  CAS   CAP  CAN  118.01  3.000
 3M1  CAS   CAP  OAD  126.41  3.000
 3M1  CAN   CAP  OAD  115.58  3.000
 3M1  CAM   CAQ  CAL  118.72  3.000
 3M1  CAL   CAQ  CAK  119.83  3.000
 3M1  CAM   CAQ  CAK  121.41  3.000
 3M1  CAO   CAR  CAM  122.72  3.000
 3M1  CAM   CAR  CAJ  119.32  3.000
 3M1  CAO   CAR  CAJ  117.86  3.000
 3M1  NAT   CAS  CAP  120.14  3.000
 3M1  NAT   CAS  CAL  118.24  3.000
 3M1  CAP   CAS  CAL  121.62  3.000
 3M1  CAS   NAT  OAE  119.08  3.000
 3M1  CAS   NAT  OAB  118.07  3.000
 3M1  OAE   NAT  OAB  122.85  3.000
 3M1  HOAC  OAC  CAN  111.15  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
 3M1  CONST_01  CAR  CAJ  CAH  CAG     0.00   0.0  0
 3M1  CONST_02  CAR  CAO  CAI  CAG     0.00   0.0  0
 3M1  CONST_03  CAO  CAI  CAG  CAH     0.00   0.0  0
 3M1  CONST_04  CAO  CAR  CAJ  CAH     0.00   0.0  0
 3M1  CONST_05  CAJ  CAH  CAG  CAI     0.00   0.0  0
 3M1  CONST_06  CAJ  CAR  CAO  CAI     0.00   0.0  0
 3M1  CONST_07  CAS  CAP  CAN  CAK     0.00   0.0  0
 3M1  CONST_08  CAS  CAL  CAQ  CAK     0.00   0.0  0
 3M1  CONST_09  CAN  CAP  CAS  CAL     0.00   0.0  0
 3M1  CONST_10  CAN  CAK  CAQ  CAL     0.00   0.0  0
 3M1  CONST_11  CAQ  CAK  CAN  CAP     0.00   0.0  0
 3M1  CONST_12  CAQ  CAL  CAS  CAP     0.00   0.0  0
 3M1  CONST_13  CAQ  CAK  CAN  OAC   180.00   0.0  0
 3M1  CONST_14  CAS  CAP  CAN  OAC   180.00   0.0  0
 3M1  CONST_15  CAK  CAN  CAP  OAD   180.00   0.0  0
 3M1  CONST_16  CAL  CAS  CAP  OAD   180.00   0.0  0
 3M1  CONST_17  CAG  CAI  CAO  FAF   180.00   0.0  0
 3M1  CONST_18  CAJ  CAR  CAO  FAF   180.00   0.0  0
 3M1  CONST_19  CAM  CAR  CAJ  CAH   180.00   0.0  0
 3M1  CONST_20  CAM  CAR  CAO  CAI   180.00   0.0  0
 3M1  CONST_21  CAN  CAK  CAQ  CAM   180.00   0.0  0
 3M1  CONST_22  CAS  CAL  CAQ  CAM   180.00   0.0  0
 3M1  CONST_23  NAT  CAS  CAP  CAN   180.00   0.0  0
 3M1  CONST_24  NAT  CAS  CAL  CAQ   180.00   0.0  0
 3M1  CONST_25  HAJ  CAJ  CAH  CAG   180.00   0.0  0
 3M1  CONST_26  HAI  CAI  CAG  CAH   180.00   0.0  0
 3M1  CONST_27  HAH  CAH  CAG  CAI   180.00   0.0  0
 3M1  CONST_28  HAG  CAG  CAH  CAJ   180.00   0.0  0
 3M1  CONST_29  HAL  CAL  CAQ  CAK   180.00   0.0  0
 3M1  CONST_30  HAK  CAK  CAQ  CAL   180.00   0.0  0
 3M1  CONST_31  CAL  CAS  NAT  OAB   180.00   0.0  0
 3M1  CONST_32  CAP  CAS  NAT  OAB     0.00   0.0  0
 3M1  CONST_33  CAL  CAS  NAT  OAE     0.00   0.0  0
 3M1  CONST_34  CAP  CAS  NAT  OAE   180.00   0.0  0
 3M1  Var_01    CAQ  CAM  CAR  CAJ  -133.48  30.0  2
 3M1  Var_02    CAR  CAM  CAQ  CAK    23.39  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
 3M1  plan-1  FAF  0.020
 3M1  plan-1  CAG  0.020
 3M1  plan-1  CAH  0.020
 3M1  plan-1  CAI  0.020
 3M1  plan-1  CAJ  0.020
 3M1  plan-1  CAM  0.020
 3M1  plan-1  CAO  0.020
 3M1  plan-1  CAR  0.020
 3M1  plan-1  HAG  0.020
 3M1  plan-1  HAH  0.020
 3M1  plan-1  HAI  0.020
 3M1  plan-1  HAJ  0.020
 3M1  plan-2  OAD  0.020
 3M1  plan-2  CAK  0.020
 3M1  plan-2  CAL  0.020
 3M1  plan-2  CAM  0.020
 3M1  plan-2  CAN  0.020
 3M1  plan-2  CAP  0.020
 3M1  plan-2  CAQ  0.020
 3M1  plan-2  CAS  0.020
 3M1  plan-2  NAT  0.020
 3M1  plan-2  HAK  0.020
 3M1  plan-2  HAL  0.020
 3M1  plan-2  OAC  0.020
 3M1  plan-3  OAB  0.020
 3M1  plan-3  OAE  0.020
 3M1  plan-3  CAS  0.020
 3M1  plan-3  NAT  0.020
 3M1  plan-4  OAA  0.020
 3M1  plan-4  CAM  0.020
 3M1  plan-4  CAQ  0.020
 3M1  plan-4  CAR  0.020

