# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 22:34:00 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 2-{[3-(3,4-dimethylphenoxy)phenyl]carbamoyl}-4-nitrobenzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(Oc2cccc(NC(=O)c3cc(ccc3C(O)=O)[N+]([O-])=O)c2)cc1C
#
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
 2BJ  2BJ  '2-{[3-(3,4-dimethylphenoxy)phenyl]carbamoyl}-4-nitrobenzoic acid'  ligand  47  30  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2BJ
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
 2BJ  C1    C  CR6    0  -0.066   3.4158  -0.3427  -0.2470
 2BJ  N1    N  N      1   0.328   6.2309   1.5087  -1.8186
 2BJ  O1    O  O      0  -0.377   5.6005   2.2022  -2.5815
 2BJ  C2    C  CR6    0  -0.085   4.0908  -1.1741   0.6473
 2BJ  N2    N  NH1    0  -0.717   1.2704   0.3621   0.5349
 2BJ  O2    O  O     -1  -0.376   7.4351   1.5344  -1.7227
 2BJ  C3    C  CR16   0  -0.281   5.4783  -1.0909   0.7217
 2BJ  O3    O  O      0  -0.566   2.1446  -2.3627   1.1944
 2BJ  C4    C  CR16   0  -0.258   6.1945  -0.2196  -0.0775
 2BJ  O4    O  OC    -1  -0.572   3.9830  -2.7468   2.4037
 2BJ  C5    C  CR6    0   0.258   5.4974   0.5866  -0.9649
 2BJ  O5    O  O      0  -0.456   1.4055  -0.8248  -1.4119
 2BJ  C6    C  CR16   0  -0.286   4.1164   0.5364  -1.0603
 2BJ  O6    O  O2     0  -0.519  -3.2644   0.0423  -0.9421
 2BJ  C7    C  C      0   0.412   3.3369  -2.1894   1.5027
 2BJ  C8    C  C      0   0.503   1.9205  -0.3514  -0.4175
 2BJ  C9    C  CR6    0   0.391  -0.0979   0.5657   0.7051
 2BJ  C10   C  CR16   0  -0.366  -0.4945   1.2060   1.8851
 2BJ  C11   C  CR16   0  -0.235  -1.8328   1.4541   2.1150
 2BJ  C12   C  CR16   0  -0.365  -2.8087   1.0821   1.1976
 2BJ  C13   C  CR6    0   0.303  -4.6122   0.2614  -0.7788
 2BJ  C14   C  CR6    0   0.396  -2.4038   0.4496   0.0303
 2BJ  C15   C  CR16   0  -0.421  -1.0599   0.1874  -0.2263
 2BJ  C16   C  CR16   0  -0.311  -5.1850   1.4230  -1.2626
 2BJ  C17   C  CR16   0  -0.299  -6.5558   1.5969  -1.1260
 2BJ  C18   C  CR6    0   0.064  -7.3584   0.6406  -0.5132
 2BJ  C19   C  CH3    0  -0.733  -8.8355   0.8633  -0.3727
 2BJ  C20   C  CR6    0   0.075  -6.7625  -0.5327  -0.0265
 2BJ  C21   C  CH3    0  -0.736  -7.5915  -1.5917   0.6373
 2BJ  C22   C  CR16   0  -0.351  -5.3897  -0.7078  -0.1637
 2BJ  HN2   H  HNH1   0   0.416   1.8404   0.6921   1.2989
 2BJ  H3    H  HCR6   0   0.271   6.0069  -1.7283   1.4164
 2BJ  H4    H  HCR6   0   0.297   7.2715  -0.1773  -0.0048
 2BJ  H6    H  HCR6   0   0.299   3.5878   1.1747  -1.7550
 2BJ  H10   H  HCR6   0   0.267   0.2470   1.5032   2.6166
 2BJ  H11   H  HCR6   0   0.264  -2.1312   1.9482   3.0302
 2BJ  H12   H  HCR6   0   0.276  -3.8498   1.2864   1.4042
 2BJ  H15   H  HCR6   0   0.289  -0.7866  -0.3027  -1.1470
 2BJ  H16   H  HCR6   0   0.267  -4.5780   2.1793  -1.7441
 2BJ  H17   H  HCR6   0   0.252  -7.0099   2.5033  -1.5077
 2BJ  H19   H  HCH3   0   0.243  -9.4120   0.0561  -0.8288
 2BJ  H19A  H  HCH3   0   0.244  -9.1355   0.9089   0.6768
 2BJ  H19B  H  HCH3   0   0.250  -9.1403   1.7962  -0.8445
 2BJ  H21   H  HCH3   0   0.246  -8.3453  -1.9957  -0.0418
 2BJ  H21A  H  HCH3   0   0.253  -6.9762  -2.4224   0.9794
 2BJ  H21B  H  HCH3   0   0.245  -8.1282  -1.1967   1.5023
 2BJ  H22   H  HCR6   0   0.261  -4.9209  -1.6102   0.2115

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
 2BJ  C1   C8    single    1.505  0.020  1.505
 2BJ  N1   C5    single    1.455  0.020  1.455
 2BJ  N1   O2    single    1.208  0.020  1.208
 2BJ  O1   N1    double    1.209  0.020  1.209
 2BJ  C2   C1    aromatic  1.395  0.020  1.395
 2BJ  C2   C7    single    1.527  0.020  1.527
 2BJ  N2   C9    single    1.394  0.020  1.394
 2BJ  N2   HN2   single    0.860  0.020  1.020
 2BJ  C3   C2    aromatic  1.392  0.020  1.392
 2BJ  C3   H3    single    0.930  0.020  1.080
 2BJ  O3   C7    deloc     1.244  0.020  1.244
 2BJ  C4   C3    aromatic  1.382  0.020  1.382
 2BJ  C4   C5    aromatic  1.387  0.020  1.387
 2BJ  C4   H4    single    0.930  0.020  1.080
 2BJ  C5   C6    aromatic  1.385  0.020  1.385
 2BJ  C6   C1    aromatic  1.387  0.020  1.387
 2BJ  C6   H6    single    0.930  0.020  1.080
 2BJ  O6   C13   single    1.375  0.020  1.375
 2BJ  C7   O4    deloc     1.241  0.020  1.241
 2BJ  C8   N2    single    1.356  0.020  1.356
 2BJ  C8   O5    double    1.216  0.020  1.216
 2BJ  C9   C10   aromatic  1.400  0.020  1.400
 2BJ  C9   C15   aromatic  1.391  0.020  1.391
 2BJ  C10  C11   aromatic  1.380  0.020  1.380
 2BJ  C10  H10   single    0.930  0.020  1.080
 2BJ  C11  C12   aromatic  1.390  0.020  1.390
 2BJ  C11  H11   single    0.930  0.020  1.080
 2BJ  C12  H12   single    0.930  0.020  1.080
 2BJ  C13  C16   aromatic  1.383  0.020  1.383
 2BJ  C14  O6    single    1.361  0.020  1.361
 2BJ  C14  C12   aromatic  1.388  0.020  1.388
 2BJ  C15  C14   aromatic  1.393  0.020  1.393
 2BJ  C15  H15   single    0.930  0.020  1.080
 2BJ  C16  C17   aromatic  1.389  0.020  1.389
 2BJ  C16  H16   single    0.930  0.020  1.080
 2BJ  C17  H17   single    0.930  0.020  1.080
 2BJ  C18  C17   aromatic  1.391  0.020  1.391
 2BJ  C18  C19   single    1.500  0.020  1.500
 2BJ  C19  H19   single    0.970  0.020  1.090
 2BJ  C19  H19A  single    0.970  0.020  1.090
 2BJ  C19  H19B  single    0.970  0.020  1.090
 2BJ  C20  C18   aromatic  1.403  0.020  1.403
 2BJ  C21  C20   single    1.500  0.020  1.500
 2BJ  C21  H21   single    0.970  0.020  1.090
 2BJ  C21  H21A  single    0.970  0.020  1.090
 2BJ  C21  H21B  single    0.970  0.020  1.090
 2BJ  C22  C13   aromatic  1.386  0.020  1.386
 2BJ  C22  C20   aromatic  1.391  0.020  1.391
 2BJ  C22  H22   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
 2BJ  C8    C1   C6    116.04  3.000
 2BJ  C6    C1   C2    120.59  3.000
 2BJ  C8    C1   C2    123.36  3.000
 2BJ  C5    N1   O2    118.00  3.000
 2BJ  O2    N1   O1    123.90  3.000
 2BJ  C5    N1   O1    118.10  3.000
 2BJ  C7    C2   C3    120.13  3.000
 2BJ  C3    C2   C1    118.75  3.000
 2BJ  C7    C2   C1    121.10  3.000
 2BJ  HN2   N2   C9    114.48  3.000
 2BJ  HN2   N2   C8    115.67  3.000
 2BJ  C9    N2   C8    129.30  3.000
 2BJ  H3    C3   C4    119.34  3.000
 2BJ  C4    C3   C2    121.54  3.000
 2BJ  H3    C3   C2    119.12  3.000
 2BJ  H4    C4   C5    121.43  3.000
 2BJ  H4    C4   C3    120.15  3.000
 2BJ  C5    C4   C3    118.42  3.000
 2BJ  C6    C5   C4    121.61  3.000
 2BJ  C6    C5   N1    119.02  3.000
 2BJ  C4    C5   N1    119.36  3.000
 2BJ  H6    C6   C5    120.68  3.000
 2BJ  H6    C6   C1    120.24  3.000
 2BJ  C5    C6   C1    119.08  3.000
 2BJ  C14   O6   C13   119.15  3.000
 2BJ  O4    C7   O3    128.07  3.000
 2BJ  O4    C7   C2    116.64  3.000
 2BJ  O3    C7   C2    115.29  3.000
 2BJ  O5    C8   N2    125.19  3.000
 2BJ  O5    C8   C1    121.05  3.000
 2BJ  N2    C8   C1    113.18  3.000
 2BJ  C15   C9   C10   119.52  3.000
 2BJ  C15   C9   N2    123.86  3.000
 2BJ  C10   C9   N2    116.61  3.000
 2BJ  H10   C10  C11   120.13  3.000
 2BJ  H10   C10  C9    120.05  3.000
 2BJ  C11   C10  C9    119.82  3.000
 2BJ  H11   C11  C12   119.13  3.000
 2BJ  H11   C11  C10   119.36  3.000
 2BJ  C12   C11  C10   121.51  3.000
 2BJ  H12   C12  C14   121.86  3.000
 2BJ  C14   C12  C11   118.18  3.000
 2BJ  H12   C12  C11   119.96  3.000
 2BJ  C22   C13  C16   120.68  3.000
 2BJ  C22   C13  O6    119.40  3.000
 2BJ  C16   C13  O6    119.89  3.000
 2BJ  C15   C14  C12   121.47  3.000
 2BJ  C15   C14  O6    114.96  3.000
 2BJ  C12   C14  O6    123.56  3.000
 2BJ  H15   C15  C14   119.17  3.000
 2BJ  H15   C15  C9    121.33  3.000
 2BJ  C14   C15  C9    119.50  3.000
 2BJ  H16   C16  C17   120.65  3.000
 2BJ  H16   C16  C13   120.68  3.000
 2BJ  C17   C16  C13   118.67  3.000
 2BJ  H17   C17  C18   119.26  3.000
 2BJ  C18   C17  C16   121.80  3.000
 2BJ  H17   C17  C16   118.94  3.000
 2BJ  C20   C18  C19   120.64  3.000
 2BJ  C20   C18  C17   118.87  3.000
 2BJ  C19   C18  C17   120.49  3.000
 2BJ  H19B  C19  H19A  107.67  3.000
 2BJ  H19B  C19  H19   107.73  3.000
 2BJ  H19A  C19  H19   106.69  3.000
 2BJ  H19B  C19  C18   111.23  3.000
 2BJ  H19A  C19  C18   111.50  3.000
 2BJ  H19   C19  C18   111.78  3.000
 2BJ  C22   C20  C21   120.03  3.000
 2BJ  C22   C20  C18   119.36  3.000
 2BJ  C21   C20  C18   120.61  3.000
 2BJ  H21B  C21  H21A  107.75  3.000
 2BJ  H21B  C21  H21   106.69  3.000
 2BJ  H21A  C21  H21   107.65  3.000
 2BJ  H21B  C21  C20   111.52  3.000
 2BJ  H21A  C21  C20   111.43  3.000
 2BJ  H21   C21  C20   111.56  3.000
 2BJ  H22   C22  C20   119.84  3.000
 2BJ  H22   C22  C13   119.54  3.000
 2BJ  C20   C22  C13   120.62  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
 2BJ  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 2BJ  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 2BJ  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 2BJ  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 2BJ  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 2BJ  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 2BJ  CONST_07  C12  C11  C10  C9      0.00   0.0  0
 2BJ  CONST_08  C12  C14  C15  C9      0.00   0.0  0
 2BJ  CONST_09  C14  C15  C9   C10     0.00   0.0  0
 2BJ  CONST_10  C14  C12  C11  C10     0.00   0.0  0
 2BJ  CONST_11  C15  C9   C10  C11     0.00   0.0  0
 2BJ  CONST_12  C15  C14  C12  C11     0.00   0.0  0
 2BJ  CONST_13  C18  C17  C16  C13     0.00   0.0  0
 2BJ  CONST_14  C18  C20  C22  C13     0.00   0.0  0
 2BJ  CONST_15  C20  C22  C13  C16     0.00   0.0  0
 2BJ  CONST_16  C20  C18  C17  C16     0.00   0.0  0
 2BJ  CONST_17  C22  C13  C16  C17     0.00   0.0  0
 2BJ  CONST_18  C22  C20  C18  C17     0.00   0.0  0
 2BJ  CONST_19  N1   C5   C6   C1    180.00   0.0  0
 2BJ  CONST_20  C3   C4   C5   N1    180.00   0.0  0
 2BJ  CONST_21  C11  C10  C9   N2    180.00   0.0  0
 2BJ  CONST_22  C14  C15  C9   N2    180.00   0.0  0
 2BJ  CONST_23  C8   C1   C2   C3    180.00   0.0  0
 2BJ  CONST_24  C7   C2   C3   C4    180.00   0.0  0
 2BJ  CONST_25  C8   C1   C6   C5    180.00   0.0  0
 2BJ  CONST_26  C7   C2   C1   C6    180.00   0.0  0
 2BJ  CONST_27  C17  C16  C13  O6    180.00   0.0  0
 2BJ  CONST_28  C20  C22  C13  O6    180.00   0.0  0
 2BJ  CONST_29  C11  C12  C14  O6    180.00   0.0  0
 2BJ  CONST_30  C9   C15  C14  O6    180.00   0.0  0
 2BJ  CONST_31  C21  C20  C22  C13   180.00   0.0  0
 2BJ  CONST_32  C19  C18  C17  C16   180.00   0.0  0
 2BJ  CONST_33  C21  C20  C18  C17   180.00   0.0  0
 2BJ  CONST_34  C22  C20  C18  C19   180.00   0.0  0
 2BJ  CONST_35  H3   C3   C2   C1    180.00   0.0  0
 2BJ  CONST_36  H6   C6   C1   C2    180.00   0.0  0
 2BJ  CONST_37  H4   C4   C3   C2    180.00   0.0  0
 2BJ  CONST_38  H11  C11  C10  C9    180.00   0.0  0
 2BJ  CONST_39  H15  C15  C9   C10   180.00   0.0  0
 2BJ  CONST_40  H12  C12  C11  C10   180.00   0.0  0
 2BJ  CONST_41  H10  C10  C11  C12   180.00   0.0  0
 2BJ  CONST_42  H17  C17  C16  C13   180.00   0.0  0
 2BJ  CONST_43  H22  C22  C13  C16   180.00   0.0  0
 2BJ  CONST_44  H16  C16  C17  C18   180.00   0.0  0
 2BJ  CONST_45  C9   N2   C8   C1    180.00   0.0  0
 2BJ  CONST_46  C4   C5   N1   O1    180.00   0.0  0
 2BJ  CONST_47  C6   C5   N1   O1      0.00   0.0  0
 2BJ  CONST_48  C4   C5   N1   O2      0.00   0.0  0
 2BJ  CONST_49  C6   C5   N1   O2    180.00   0.0  0
 2BJ  CONST_50  C10  C9   N2   C8    180.00   0.0  0
 2BJ  CONST_51  C15  C9   N2   C8      0.00   0.0  0
 2BJ  CONST_52  HN2  N2   C9   C10     0.00   0.0  0
 2BJ  CONST_53  C9   N2   C8   O5      0.00   0.0  0
 2BJ  Var_01    C15  C14  O6   C13  -179.84  30.0  1
 2BJ  Var_02    C16  C13  O6   C14    91.35  30.0  2
 2BJ  Var_03    O3   C7   C2   C1     10.86  30.0  2
 2BJ  Var_04    N2   C8   C1   C2     80.92  30.0  2
 2BJ  Var_05    H19  C19  C18  C17   123.42  30.0  2
 2BJ  Var_06    H21  C21  C20  C18    61.12  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
 2BJ  plan-1  C1   0.020
 2BJ  plan-1  N1   0.020
 2BJ  plan-1  C2   0.020
 2BJ  plan-1  C3   0.020
 2BJ  plan-1  C4   0.020
 2BJ  plan-1  C5   0.020
 2BJ  plan-1  C6   0.020
 2BJ  plan-1  C7   0.020
 2BJ  plan-1  C8   0.020
 2BJ  plan-1  H3   0.020
 2BJ  plan-1  H4   0.020
 2BJ  plan-1  H6   0.020
 2BJ  plan-2  N2   0.020
 2BJ  plan-2  O6   0.020
 2BJ  plan-2  C9   0.020
 2BJ  plan-2  C10  0.020
 2BJ  plan-2  C11  0.020
 2BJ  plan-2  C12  0.020
 2BJ  plan-2  C14  0.020
 2BJ  plan-2  C15  0.020
 2BJ  plan-2  H10  0.020
 2BJ  plan-2  H11  0.020
 2BJ  plan-2  H12  0.020
 2BJ  plan-2  H15  0.020
 2BJ  plan-3  O6   0.020
 2BJ  plan-3  C13  0.020
 2BJ  plan-3  C16  0.020
 2BJ  plan-3  C17  0.020
 2BJ  plan-3  C18  0.020
 2BJ  plan-3  C19  0.020
 2BJ  plan-3  C20  0.020
 2BJ  plan-3  C21  0.020
 2BJ  plan-3  C22  0.020
 2BJ  plan-3  H16  0.020
 2BJ  plan-3  H17  0.020
 2BJ  plan-3  H22  0.020
 2BJ  plan-4  C1   0.020
 2BJ  plan-4  N2   0.020
 2BJ  plan-4  O5   0.020
 2BJ  plan-4  C8   0.020
 2BJ  plan-4  C9   0.020
 2BJ  plan-4  HN2  0.020
 2BJ  plan-5  N1   0.020
 2BJ  plan-5  O1   0.020
 2BJ  plan-5  O2   0.020
 2BJ  plan-5  C5   0.020
 2BJ  plan-6  C2   0.020
 2BJ  plan-6  O3   0.020
 2BJ  plan-6  O4   0.020
 2BJ  plan-6  C7   0.020

