# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 06:51:39 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: ({3-[(3-nitrobenzyl)carbamoyl]biphenyl-4-yl}oxy)acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)COc1ccc(cc1C(=O)NCc2cccc(c2)[N+]([O-])=O)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
 3UH  3UH  '({3-[(3-nitrobenzyl)carbamoyl]biphenyl-4-yl}oxy)acetic 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_3UH
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
 3UH  O1   O  O2     0  -0.427  -3.3058  -1.6925   0.2142
 3UH  C2   C  CH2    0  -0.329  -4.7041  -1.8997   0.3225
 3UH  C3   C  C      0   0.382  -5.0371  -3.4007   0.2980
 3UH  O4   O  O      0  -0.517  -4.1047  -4.2132   0.2400
 3UH  O6   O  OC    -1  -0.743  -6.2608  -3.6324   0.3467
 3UH  C9   C  CR6    0   0.383  -2.8336  -0.4445   0.2329
 3UH  C10  C  CR6    0  -0.101  -1.4473  -0.2931   0.0836
 3UH  C11  C  C      0   0.560  -0.5440  -1.4842   0.0173
 3UH  N12  N  NH1    0  -0.627   0.2381  -1.5140  -1.0803
 3UH  C14  C  CH2    0  -0.336   1.3223  -2.4398  -1.2833
 3UH  C15  C  C      0  -0.019   2.6767  -1.7801  -1.1675
 3UH  C16  C  C1     0  -0.253   2.8997  -0.7772  -0.2346
 3UH  C17  C  C      0   0.195   4.1525  -0.1919  -0.1484
 3UH  N18  N  N      1   0.300   4.3599   0.8752   0.8214
 3UH  O19  O  O     -1  -0.211   3.4083   1.2553   1.4627
 3UH  O20  O  O      0  -0.502   5.4733   1.3301   0.9349
 3UH  C21  C  C1     0  -0.272   5.2069  -0.5834  -0.9601
 3UH  C22  C  C1     0  -0.160   4.9791  -1.5892  -1.8836
 3UH  C23  C  C1     0  -0.237   3.7264  -2.1779  -1.9893
 3UH  O30  O  O      0  -0.499  -0.4967  -2.3135   0.9094
 3UH  C31  C  CR16   0  -0.339  -0.8871   0.9738   0.0599
 3UH  C33  C  CR6    0   0.079  -1.6571   2.1271   0.2078
 3UH  C34  C  CR6    0   0.012  -1.0299   3.4628   0.2157
 3UH  C35  C  CR16   0  -0.337   0.2386   3.6545   0.7689
 3UH  C36  C  CR16   0  -0.204   0.8304   4.9090   0.7773
 3UH  C38  C  CR16   0  -0.267   0.1633   6.0011   0.2382
 3UH  C39  C  CR16   0  -0.237  -1.0991   5.8250  -0.3132
 3UH  C40  C  CR16   0  -0.282  -1.6877   4.5690  -0.3269
 3UH  C45  C  CR16   0  -0.308  -3.0309   1.9590   0.3550
 3UH  C47  C  CR16   0  -0.360  -3.6174   0.7021   0.3600
 3UH  H1   H  HCH2   0   0.242  -5.0846  -1.4663   1.2556
 3UH  H2   H  HCH2   0   0.270  -5.2303  -1.4025  -0.5013
 3UH  H4   H  HNH1   0   0.400   0.0915  -0.8142  -1.7909
 3UH  H5   H  HCH2   0   0.244   1.2371  -3.2410  -0.5486
 3UH  H6   H  HCH2   0   0.299   1.2265  -2.9035  -2.2662
 3UH  H7   H  H      0   0.305   2.1042  -0.4566   0.4221
 3UH  H8   H  H      0   0.287   6.1783  -0.1173  -0.8895
 3UH  H9   H  H      0   0.282   5.7817  -1.9075  -2.5344
 3UH  H10  H  H      0   0.290   3.5640  -2.9534  -2.7278
 3UH  H11  H  HCR6   0   0.226   0.1837   1.0695  -0.0785
 3UH  H12  H  HCR6   0   0.253   0.7646   2.8214   1.2192
 3UH  H13  H  HCR6   0   0.265   1.8111   5.0351   1.2176
 3UH  H14  H  HCR6   0   0.239   0.6221   6.9812   0.2498
 3UH  H15  H  HCR6   0   0.256  -1.6261   6.6673  -0.7425
 3UH  H16  H  HCR6   0   0.258  -2.6626   4.4469  -0.7827
 3UH  H17  H  HCR6   0   0.261  -3.6715   2.8219   0.4862
 3UH  H18  H  HCR6   0   0.280  -4.6899   0.6338   0.4743

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
 3UH  O20  N18  double    1.208  0.020  1.208
 3UH  N18  O19  single    1.209  0.020  1.209
 3UH  N18  C17  single    1.457  0.020  1.457
 3UH  C21  C17  aromatic  1.387  0.020  1.387
 3UH  C21  C22  aromatic  1.384  0.020  1.384
 3UH  C17  C16  aromatic  1.385  0.020  1.385
 3UH  C22  C23  aromatic  1.388  0.020  1.388
 3UH  C16  C15  aromatic  1.388  0.020  1.388
 3UH  C23  C15  aromatic  1.391  0.020  1.391
 3UH  C15  C14  single    1.511  0.020  1.511
 3UH  C14  N12  single    1.440  0.020  1.440
 3UH  O30  C11  double    1.219  0.020  1.219
 3UH  N12  C11  single    1.348  0.020  1.348
 3UH  C11  C10  single    1.496  0.020  1.496
 3UH  C36  C35  aromatic  1.387  0.020  1.387
 3UH  C36  C38  aromatic  1.389  0.020  1.389
 3UH  C35  C34  aromatic  1.397  0.020  1.397
 3UH  C38  C39  aromatic  1.389  0.020  1.389
 3UH  C31  C10  aromatic  1.385  0.020  1.385
 3UH  C31  C33  aromatic  1.395  0.020  1.395
 3UH  C10  C9   aromatic  1.403  0.020  1.403
 3UH  C34  C33  single    1.476  0.020  1.476
 3UH  C34  C40  aromatic  1.397  0.020  1.397
 3UH  C39  C40  aromatic  1.387  0.020  1.387
 3UH  C33  C45  aromatic  1.392  0.020  1.392
 3UH  O4   C3   deloc     1.238  0.020  1.238
 3UH  C9   O1   single    1.335  0.020  1.335
 3UH  C9   C47  aromatic  1.395  0.020  1.395
 3UH  O1   C2   single    1.418  0.020  1.418
 3UH  C45  C47  aromatic  1.387  0.020  1.387
 3UH  C3   C2   single    1.538  0.020  1.538
 3UH  C3   O6   deloc     1.246  0.020  1.246
 3UH  C2   H1   single    0.970  0.020  1.090
 3UH  C2   H2   single    0.970  0.020  1.090
 3UH  N12  H4   single    0.860  0.020  1.020
 3UH  C14  H5   single    0.970  0.020  1.090
 3UH  C14  H6   single    0.970  0.020  1.090
 3UH  C16  H7   single    0.930  0.020  1.080
 3UH  C21  H8   single    0.930  0.020  1.080
 3UH  C22  H9   single    0.930  0.020  1.080
 3UH  C23  H10  single    0.930  0.020  1.080
 3UH  C31  H11  single    0.930  0.020  1.080
 3UH  C35  H12  single    0.930  0.020  1.080
 3UH  C36  H13  single    0.930  0.020  1.080
 3UH  C38  H14  single    0.930  0.020  1.080
 3UH  C39  H15  single    0.930  0.020  1.080
 3UH  C40  H16  single    0.930  0.020  1.080
 3UH  C45  H17  single    0.930  0.020  1.080
 3UH  C47  H18  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
 3UH  C9   O1   C2   118.98  3.000
 3UH  H2   C2   H1   107.07  3.000
 3UH  H2   C2   C3   109.07  3.000
 3UH  H1   C2   C3   108.92  3.000
 3UH  H2   C2   O1   110.46  3.000
 3UH  H1   C2   O1   110.45  3.000
 3UH  C3   C2   O1   110.79  3.000
 3UH  O6   C3   O4   128.26  3.000
 3UH  O6   C3   C2   113.16  3.000
 3UH  O4   C3   C2   118.57  3.000
 3UH  C47  C9   C10  118.46  3.000
 3UH  C47  C9   O1   124.84  3.000
 3UH  C10  C9   O1   116.69  3.000
 3UH  C31  C10  C11  118.89  3.000
 3UH  C31  C10  C9   120.01  3.000
 3UH  C11  C10  C9   121.03  3.000
 3UH  O30  C11  N12  123.94  3.000
 3UH  N12  C11  C10  113.82  3.000
 3UH  O30  C11  C10  122.18  3.000
 3UH  H4   N12  C14  117.15  3.000
 3UH  H4   N12  C11  118.31  3.000
 3UH  C14  N12  C11  124.46  3.000
 3UH  H6   C14  H5   106.72  3.000
 3UH  H6   C14  C15  109.47  3.000
 3UH  H5   C14  C15  109.83  3.000
 3UH  H6   C14  N12  109.52  3.000
 3UH  H5   C14  N12  108.58  3.000
 3UH  C15  C14  N12  112.54  3.000
 3UH  C23  C15  C16  118.85  3.000
 3UH  C23  C15  C14  120.41  3.000
 3UH  C16  C15  C14  120.74  3.000
 3UH  H7   C16  C17  120.18  3.000
 3UH  H7   C16  C15  120.31  3.000
 3UH  C17  C16  C15  119.51  3.000
 3UH  C21  C17  N18  119.22  3.000
 3UH  C21  C17  C16  122.12  3.000
 3UH  N18  C17  C16  118.67  3.000
 3UH  O20  N18  O19  123.87  3.000
 3UH  O19  N18  C17  118.12  3.000
 3UH  O20  N18  C17  118.01  3.000
 3UH  H8   C21  C22  120.35  3.000
 3UH  H8   C21  C17  121.58  3.000
 3UH  C22  C21  C17  118.06  3.000
 3UH  H9   C22  C23  119.95  3.000
 3UH  H9   C22  C21  119.55  3.000
 3UH  C23  C22  C21  120.49  3.000
 3UH  H10  C23  C22  119.40  3.000
 3UH  H10  C23  C15  119.63  3.000
 3UH  C22  C23  C15  120.97  3.000
 3UH  H11  C31  C33  119.08  3.000
 3UH  H11  C31  C10  118.84  3.000
 3UH  C33  C31  C10  122.08  3.000
 3UH  C45  C33  C34  121.89  3.000
 3UH  C45  C33  C31  117.15  3.000
 3UH  C34  C33  C31  120.96  3.000
 3UH  C40  C34  C35  118.21  3.000
 3UH  C40  C34  C33  120.97  3.000
 3UH  C35  C34  C33  120.81  3.000
 3UH  H12  C35  C36  119.07  3.000
 3UH  H12  C35  C34  119.99  3.000
 3UH  C36  C35  C34  120.92  3.000
 3UH  H13  C36  C38  120.10  3.000
 3UH  H13  C36  C35  119.63  3.000
 3UH  C38  C36  C35  120.27  3.000
 3UH  H14  C38  C39  120.30  3.000
 3UH  H14  C38  C36  120.30  3.000
 3UH  C39  C38  C36  119.41  3.000
 3UH  H15  C39  C40  119.62  3.000
 3UH  H15  C39  C38  120.09  3.000
 3UH  C40  C39  C38  120.30  3.000
 3UH  H16  C40  C39  119.22  3.000
 3UH  H16  C40  C34  119.88  3.000
 3UH  C39  C40  C34  120.89  3.000
 3UH  H17  C45  C47  118.14  3.000
 3UH  H17  C45  C33  120.04  3.000
 3UH  C47  C45  C33  121.82  3.000
 3UH  H18  C47  C45  118.51  3.000
 3UH  H18  C47  C9   121.03  3.000
 3UH  C45  C47  C9   120.46  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
 3UH  CONST_01  C33  C31  C10  C9      0.00   0.0  0
 3UH  CONST_02  C33  C45  C47  C9      0.00   0.0  0
 3UH  CONST_03  C34  C33  C31  C10   180.00   0.0  0
 3UH  CONST_04  C45  C33  C31  C10     0.00   0.0  0
 3UH  CONST_05  C45  C47  C9   C10     0.00   0.0  0
 3UH  CONST_06  C21  C17  C16  C15     0.00   0.0  0
 3UH  CONST_07  C21  C22  C23  C15     0.00   0.0  0
 3UH  CONST_08  C22  C21  C17  C16     0.00   0.0  0
 3UH  CONST_09  C22  C23  C15  C16     0.00   0.0  0
 3UH  CONST_10  C23  C22  C21  C17     0.00   0.0  0
 3UH  CONST_11  C23  C15  C16  C17     0.00   0.0  0
 3UH  CONST_12  C47  C9   C10  C31     0.00   0.0  0
 3UH  CONST_15  C47  C45  C33  C31     0.00   0.0  0
 3UH  CONST_16  C36  C35  C34  C33   180.00   0.0  0
 3UH  CONST_17  C39  C40  C34  C33   180.00   0.0  0
 3UH  CONST_18  C38  C36  C35  C34     0.00   0.0  0
 3UH  CONST_19  C47  C45  C33  C34   180.00   0.0  0
 3UH  CONST_20  C38  C39  C40  C34     0.00   0.0  0
 3UH  CONST_21  C39  C38  C36  C35     0.00   0.0  0
 3UH  CONST_23  C39  C40  C34  C35     0.00   0.0  0
 3UH  CONST_24  C40  C34  C35  C36     0.00   0.0  0
 3UH  CONST_25  C40  C39  C38  C36     0.00   0.0  0
 3UH  CONST_27  C31  C10  C9   O1    180.00   0.0  0
 3UH  CONST_28  C45  C47  C9   O1    180.00   0.0  0
 3UH  CONST_29  C33  C31  C10  C11   180.00   0.0  0
 3UH  CONST_30  C47  C9   C10  C11   180.00   0.0  0
 3UH  CONST_31  C17  C16  C15  C14   180.00   0.0  0
 3UH  CONST_32  C22  C23  C15  C14   180.00   0.0  0
 3UH  CONST_33  N18  C17  C16  C15   180.00   0.0  0
 3UH  CONST_34  C22  C21  C17  N18   180.00   0.0  0
 3UH  CONST_35  H11  C31  C10  C9    180.00   0.0  0
 3UH  CONST_36  H17  C45  C47  C9    180.00   0.0  0
 3UH  CONST_37  H18  C47  C9   C10   180.00   0.0  0
 3UH  CONST_38  H9   C22  C23  C15   180.00   0.0  0
 3UH  CONST_39  H8   C21  C17  C16   180.00   0.0  0
 3UH  CONST_40  H10  C23  C15  C16   180.00   0.0  0
 3UH  CONST_41  H7   C16  C17  C21   180.00   0.0  0
 3UH  CONST_42  H12  C35  C34  C33     0.00   0.0  0
 3UH  CONST_43  H16  C40  C34  C33     0.00   0.0  0
 3UH  CONST_44  H13  C36  C35  C34   180.00   0.0  0
 3UH  CONST_45  H15  C39  C40  C34   180.00   0.0  0
 3UH  CONST_46  H14  C38  C36  C35   180.00   0.0  0
 3UH  CONST_47  O20  N18  C17  C16   180.00   0.0  0
 3UH  CONST_48  O19  N18  C17  C16     0.00   0.0  0
 3UH  CONST_49  C21  C17  N18  O19   180.00   0.0  0
 3UH  CONST_50  C21  C17  N18  O20     0.00   0.0  0
 3UH  CONST_51  C14  N12  C11  C10   180.00   0.0  0
 3UH  CONST_52  H4   N12  C11  C10     0.00   0.0  0
 3UH  CONST_53  O30  C11  N12  C14     0.00   0.0  0
 3UH  Var_01    C10  C9   O1   C2   -178.21  30.0  2
 3UH  Var_02    O30  C11  C10  C9    -57.71  30.0  2
 3UH  Var_03    C16  C15  C14  N12    36.96  30.0  2
 3UH  Var_04    C15  C14  N12  C11  -107.66  30.0  2
 3UH  Var_05    H1   C2   O1   C9    -58.52  30.0  3
 3UH  Var_06    O4   C3   C2   O1      2.48  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
 3UH  plan-1  C14  0.020
 3UH  plan-1  C15  0.020
 3UH  plan-1  C16  0.020
 3UH  plan-1  C17  0.020
 3UH  plan-1  N18  0.020
 3UH  plan-1  C21  0.020
 3UH  plan-1  C22  0.020
 3UH  plan-1  C23  0.020
 3UH  plan-1  H7   0.020
 3UH  plan-1  H8   0.020
 3UH  plan-1  H9   0.020
 3UH  plan-1  H10  0.020
 3UH  plan-2  O1   0.020
 3UH  plan-2  C9   0.020
 3UH  plan-2  C10  0.020
 3UH  plan-2  C11  0.020
 3UH  plan-2  C31  0.020
 3UH  plan-2  C33  0.020
 3UH  plan-2  C34  0.020
 3UH  plan-2  C45  0.020
 3UH  plan-2  C47  0.020
 3UH  plan-2  H11  0.020
 3UH  plan-2  H17  0.020
 3UH  plan-2  H18  0.020
 3UH  plan-3  C33  0.020
 3UH  plan-3  C34  0.020
 3UH  plan-3  C35  0.020
 3UH  plan-3  C36  0.020
 3UH  plan-3  C38  0.020
 3UH  plan-3  C39  0.020
 3UH  plan-3  C40  0.020
 3UH  plan-3  H12  0.020
 3UH  plan-3  H13  0.020
 3UH  plan-3  H14  0.020
 3UH  plan-3  H15  0.020
 3UH  plan-3  H16  0.020
 3UH  plan-4  C10  0.020
 3UH  plan-4  C11  0.020
 3UH  plan-4  N12  0.020
 3UH  plan-4  C14  0.020
 3UH  plan-4  O30  0.020
 3UH  plan-4  H4   0.020
 3UH  plan-5  C17  0.020
 3UH  plan-5  N18  0.020
 3UH  plan-5  O19  0.020
 3UH  plan-5  O20  0.020
 3UH  plan-6  C2   0.020
 3UH  plan-6  C3   0.020
 3UH  plan-6  O4   0.020
 3UH  plan-6  O6   0.020

