# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 23 20:03:05 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: 3-hydroxy-5-(3-nitrophenoxy)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cc(O)cc(Oc2cccc(c2)[N+]([O-])=O)c1
#
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
 1R2  1R2  '3-hydroxy-5-(3-nitrophenoxy)benzoic acid'  ligand  28  20  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1R2
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
 1R2  OAA  O  O      0  -0.588  -3.8263  -2.5515   0.6192
 1R2  CAN  C  C      0   0.411  -4.2099  -1.3687   0.5652
 1R2  OAC  O  OC    -1  -0.588  -5.3312  -0.9273   0.8770
 1R2  CAR  C  CR6    0  -0.088  -3.1911  -0.3481   0.0608
 1R2  CAK  C  CR16   0  -0.381  -1.8959  -0.7493  -0.2542
 1R2  CAJ  C  CR16   0  -0.435  -3.5499   0.9866  -0.0816
 1R2  CAO  C  CR6    0   0.384  -2.6293   1.9233  -0.5428
 1R2  OAD  O  OH1    0  -0.634  -2.9368   3.2258  -0.7025
 1R2  CAI  C  CR16   0  -0.391  -1.3325   1.5289  -0.8589
 1R2  CAQ  C  CR6    0   0.328  -0.9935   0.1949  -0.7082
 1R2  OAM  O  O2     0  -0.512   0.2790  -0.2068  -1.0566
 1R2  CAP  C  CR6    0   0.390   1.2871  -0.0379  -0.1699
 1R2  CAL  C  CR16   0  -0.362   2.5650  -0.2986  -0.6495
 1R2  CAS  C  CR6    0   0.267   3.6372  -0.1571   0.2138
 1R2  NAT  N  N      1   0.329   4.9772  -0.4297  -0.2941
 1R2  OAE  O  O     -1  -0.374   5.9104  -0.2618   0.4540
 1R2  OAB  O  O      0  -0.375   5.0869  -0.8084  -1.4357
 1R2  CAH  C  CR16   0  -0.284   3.4851   0.2373   1.5348
 1R2  CAF  C  CR16   0  -0.242   2.2017   0.4907   1.9868
 1R2  CAG  C  CR16   0  -0.316   1.1018   0.3585   1.1511
 1R2  H2   H  HCR6   0   0.258  -1.6005  -1.7846  -0.1502
 1R2  H3   H  HCR6   0   0.263  -4.5582   1.2945   0.1703
 1R2  H4   H  HOH1   0   0.475  -3.8539   3.3859  -0.4540
 1R2  H5   H  HCR6   0   0.279  -0.6081   2.2497  -1.2191
 1R2  H6   H  HCR6   0   0.308   2.6998  -0.6031  -1.6779
 1R2  H7   H  HCR6   0   0.296   4.3309   0.3438   2.1964
 1R2  H8   H  HCR6   0   0.284   2.0497   0.7968   3.0126
 1R2  H9   H  HCR6   0   0.298   0.1131   0.5641   1.5382

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
 1R2  OAE  NAT  single    1.208  0.020  1.208
 1R2  CAH  CAF  aromatic  1.384  0.020  1.384
 1R2  CAH  CAS  aromatic  1.387  0.020  1.387
 1R2  OAA  CAN  deloc     1.245  0.020  1.245
 1R2  NAT  CAS  single    1.459  0.020  1.459
 1R2  NAT  OAB  double    1.208  0.020  1.208
 1R2  CAF  CAG  aromatic  1.388  0.020  1.388
 1R2  CAS  CAL  aromatic  1.384  0.020  1.384
 1R2  CAN  CAR  single    1.528  0.020  1.528
 1R2  CAN  OAC  deloc     1.245  0.020  1.245
 1R2  CAJ  CAR  aromatic  1.389  0.020  1.389
 1R2  CAJ  CAO  aromatic  1.392  0.020  1.392
 1R2  CAG  CAP  aromatic  1.392  0.020  1.392
 1R2  CAR  CAK  aromatic  1.392  0.020  1.392
 1R2  OAD  CAO  single    1.348  0.020  1.348
 1R2  CAL  CAP  aromatic  1.390  0.020  1.390
 1R2  CAO  CAI  aromatic  1.392  0.020  1.392
 1R2  CAP  OAM  single    1.353  0.020  1.353
 1R2  CAK  CAQ  aromatic  1.383  0.020  1.383
 1R2  CAI  CAQ  aromatic  1.385  0.020  1.385
 1R2  CAQ  OAM  single    1.379  0.020  1.379
 1R2  CAK  H2   single    0.930  0.020  1.080
 1R2  CAJ  H3   single    0.930  0.020  1.080
 1R2  OAD  H4   single    0.850  0.020  0.980
 1R2  CAI  H5   single    0.930  0.020  1.080
 1R2  CAL  H6   single    0.930  0.020  1.080
 1R2  CAH  H7   single    0.930  0.020  1.080
 1R2  CAF  H8   single    0.930  0.020  1.080
 1R2  CAG  H9   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
 1R2  CAR  CAN  OAC  116.53  3.000
 1R2  OAC  CAN  OAA  127.14  3.000
 1R2  CAR  CAN  OAA  116.34  3.000
 1R2  CAJ  CAR  CAK  119.60  3.000
 1R2  CAK  CAR  CAN  120.18  3.000
 1R2  CAJ  CAR  CAN  120.22  3.000
 1R2  H2   CAK  CAQ  120.46  3.000
 1R2  H2   CAK  CAR  120.55  3.000
 1R2  CAQ  CAK  CAR  118.99  3.000
 1R2  H3   CAJ  CAO  120.07  3.000
 1R2  H3   CAJ  CAR  119.29  3.000
 1R2  CAO  CAJ  CAR  120.64  3.000
 1R2  CAI  CAO  OAD  117.35  3.000
 1R2  CAI  CAO  CAJ  120.05  3.000
 1R2  OAD  CAO  CAJ  122.60  3.000
 1R2  H4   OAD  CAO  110.31  3.000
 1R2  H5   CAI  CAQ  120.89  3.000
 1R2  H5   CAI  CAO  120.66  3.000
 1R2  CAQ  CAI  CAO  118.45  3.000
 1R2  OAM  CAQ  CAI  118.62  3.000
 1R2  OAM  CAQ  CAK  119.09  3.000
 1R2  CAI  CAQ  CAK  122.26  3.000
 1R2  CAP  OAM  CAQ  119.05  3.000
 1R2  CAG  CAP  CAL  120.23  3.000
 1R2  CAL  CAP  OAM  115.82  3.000
 1R2  CAG  CAP  OAM  123.95  3.000
 1R2  H6   CAL  CAS  121.72  3.000
 1R2  H6   CAL  CAP  119.72  3.000
 1R2  CAS  CAL  CAP  118.56  3.000
 1R2  CAH  CAS  NAT  119.05  3.000
 1R2  NAT  CAS  CAL  118.39  3.000
 1R2  CAH  CAS  CAL  122.56  3.000
 1R2  OAB  NAT  OAE  123.98  3.000
 1R2  OAB  NAT  CAS  118.11  3.000
 1R2  OAE  NAT  CAS  117.91  3.000
 1R2  H7   CAH  CAF  120.56  3.000
 1R2  H7   CAH  CAS  121.73  3.000
 1R2  CAF  CAH  CAS  117.70  3.000
 1R2  H8   CAF  CAG  119.13  3.000
 1R2  H8   CAF  CAH  119.48  3.000
 1R2  CAG  CAF  CAH  121.38  3.000
 1R2  H9   CAG  CAF  119.40  3.000
 1R2  H9   CAG  CAP  121.04  3.000
 1R2  CAF  CAG  CAP  119.56  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
 1R2  CONST_01  CAI  CAO  CAJ  CAR    0.00   0.0  0
 1R2  CONST_02  CAI  CAQ  CAK  CAR    0.00   0.0  0
 1R2  CONST_03  CAO  CAJ  CAR  CAK    0.00   0.0  0
 1R2  CONST_04  CAO  CAI  CAQ  CAK    0.00   0.0  0
 1R2  CONST_05  CAQ  CAK  CAR  CAJ    0.00   0.0  0
 1R2  CONST_06  CAQ  CAI  CAO  CAJ    0.00   0.0  0
 1R2  CONST_07  CAH  CAF  CAG  CAP    0.00   0.0  0
 1R2  CONST_08  CAH  CAS  CAL  CAP    0.00   0.0  0
 1R2  CONST_09  CAF  CAH  CAS  CAL    0.00   0.0  0
 1R2  CONST_10  CAF  CAG  CAP  CAL    0.00   0.0  0
 1R2  CONST_11  CAG  CAF  CAH  CAS    0.00   0.0  0
 1R2  CONST_12  CAG  CAP  CAL  CAS    0.00   0.0  0
 1R2  CONST_13  CAO  CAJ  CAR  CAN  180.00   0.0  0
 1R2  CONST_14  CAQ  CAK  CAR  CAN  180.00   0.0  0
 1R2  CONST_15  OAD  CAO  CAJ  CAR  180.00   0.0  0
 1R2  CONST_16  OAM  CAQ  CAK  CAR  180.00   0.0  0
 1R2  CONST_17  OAM  CAQ  CAI  CAO  180.00   0.0  0
 1R2  CONST_18  CAQ  CAI  CAO  OAD  180.00   0.0  0
 1R2  CONST_19  CAF  CAG  CAP  OAM  180.00   0.0  0
 1R2  CONST_20  CAS  CAL  CAP  OAM  180.00   0.0  0
 1R2  CONST_21  NAT  CAS  CAL  CAP  180.00   0.0  0
 1R2  CONST_22  CAF  CAH  CAS  NAT  180.00   0.0  0
 1R2  CONST_23  H3   CAJ  CAR  CAK  180.00   0.0  0
 1R2  CONST_24  H5   CAI  CAQ  CAK  180.00   0.0  0
 1R2  CONST_25  H2   CAK  CAR  CAJ  180.00   0.0  0
 1R2  CONST_26  H8   CAF  CAG  CAP  180.00   0.0  0
 1R2  CONST_27  H7   CAH  CAS  CAL  180.00   0.0  0
 1R2  CONST_28  H9   CAG  CAP  CAL  180.00   0.0  0
 1R2  CONST_29  H6   CAL  CAS  CAH  180.00   0.0  0
 1R2  CONST_30  OAE  NAT  CAS  CAL  180.00   0.0  0
 1R2  CONST_31  OAB  NAT  CAS  CAL    0.00   0.0  0
 1R2  CONST_32  CAH  CAS  NAT  OAE    0.00   0.0  0
 1R2  CONST_33  CAH  CAS  NAT  OAB  180.00   0.0  0
 1R2  Var_01    CAG  CAP  OAM  CAQ    8.78  30.0  2
 1R2  Var_02    CAJ  CAR  CAN  OAA  177.48  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
 1R2  plan-1  CAN  0.020
 1R2  plan-1  CAR  0.020
 1R2  plan-1  CAK  0.020
 1R2  plan-1  CAJ  0.020
 1R2  plan-1  CAO  0.020
 1R2  plan-1  OAD  0.020
 1R2  plan-1  CAI  0.020
 1R2  plan-1  CAQ  0.020
 1R2  plan-1  OAM  0.020
 1R2  plan-1  H2   0.020
 1R2  plan-1  H3   0.020
 1R2  plan-1  H5   0.020
 1R2  plan-2  OAM  0.020
 1R2  plan-2  CAP  0.020
 1R2  plan-2  CAL  0.020
 1R2  plan-2  CAS  0.020
 1R2  plan-2  NAT  0.020
 1R2  plan-2  CAH  0.020
 1R2  plan-2  CAF  0.020
 1R2  plan-2  CAG  0.020
 1R2  plan-2  H6   0.020
 1R2  plan-2  H7   0.020
 1R2  plan-2  H8   0.020
 1R2  plan-2  H9   0.020
 1R2  plan-3  CAS  0.020
 1R2  plan-3  NAT  0.020
 1R2  plan-3  OAE  0.020
 1R2  plan-3  OAB  0.020
 1R2  plan-4  OAA  0.020
 1R2  plan-4  CAN  0.020
 1R2  plan-4  OAC  0.020
 1R2  plan-4  CAR  0.020

