# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 14:15:21 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: 5-[2,4-dihydroxy-6-(4-nitrophenoxy)phenyl]-N-(1-methylpiperidin-4-yl)-1,2-oxazole-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCC(CC1)NC(=O)c2cc(on2)c3c(O)cc(O)cc3Oc4ccc(cc4)[N+]([O-])=O
#
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
 9UN  9UN  5-[2,4-dihydroxy-6-(4-nitrophenoxy)phenyl]-N-(1-methylpiperidin-4-yl)-1,2-oxazole-3-carboxamide  ligand  55  33  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9UN
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
 9UN  C1    C  CR16   0  -0.481   3.2255  -4.5947   0.3022
 9UN  C2    C  CR6    0   0.362   2.0035  -3.9330   0.3659
 9UN  C3    C  CR6    0  -0.208   1.8286  -2.6998  -0.2745
 9UN  C4    C  CR6    0   0.360   2.9241  -2.1597  -0.9610
 9UN  C5    C  CR16   0  -0.440   4.1402  -2.7949  -1.0348
 9UN  C6    C  CR6    0   0.397   4.2821  -4.0328  -0.4001
 9UN  O7    O  OH1    0  -0.619   5.4753  -4.6295  -0.4952
 9UN  O8    O  OH1    0  -0.605   1.0238  -4.5404   1.0457
 9UN  O9    O  O2     0  -0.502   2.7837  -0.9595  -1.6049
 9UN  C10   C  CR6    0   0.353   2.4432   0.1341  -0.8770
 9UN  C11   C  CR16   0  -0.310   1.6946   1.1119  -1.5239
 9UN  C12   C  CR16   0  -0.260   1.3156   2.2484  -0.8390
 9UN  C13   C  CR6    0   0.241   1.6885   2.3954   0.4908
 9UN  C14   C  CR16   0  -0.257   2.4483   1.4297   1.1371
 9UN  C15   C  CR16   0  -0.301   2.8299   0.2946   0.4504
 9UN  N16   N  N      1   0.328   1.2822   3.5817   1.2159
 9UN  O17   O  O      0  -0.383   0.6398   4.4192   0.6248
 9UN  O18   O  O     -1  -0.383   1.6038   3.6784   2.3779
 9UN  C19   C  CR5    0   0.380   0.5517  -2.0007  -0.2361
 9UN  O20   O  O      0  -0.312  -0.0327  -1.7027  -1.4100
 9UN  N21   N  N      0  -0.152  -1.1673  -1.0117  -1.1943
 9UN  C22   C  CR5    0   0.133  -1.2954  -0.9030   0.0963
 9UN  C23   C  CR15   0  -0.470  -0.2206  -1.5245   0.7724
 9UN  C24   C  C      0   0.538  -2.4382  -0.1812   0.7276
 9UN  O25   O  O      0  -0.473  -2.5462  -0.1801   1.9440
 9UN  N26   N  NH1    0  -0.653  -3.2614   0.4348  -0.1236
 9UN  C27   C  CH1    0  -0.073  -4.4501   1.1609   0.2794
 9UN  C28   C  CH2    0  -0.448  -4.6924   2.3306  -0.6648
 9UN  C29   C  CH2    0  -0.281  -5.9757   3.0565  -0.2915
 9UN  N30   N  NT     0  -0.409  -7.1129   2.1564  -0.2893
 9UN  C31   C  CH2    0  -0.282  -6.9233   1.0699   0.6533
 9UN  C32   C  CH2    0  -0.430  -5.6808   0.2595   0.3190
 9UN  C33   C  CH3    0  -0.518  -8.3436   2.8685  -0.0310
 9UN  H1    H  HCR6   0   0.290   3.3350  -5.5532   0.7961
 9UN  H5    H  HCR6   0   0.288   4.9684  -2.3419  -1.5631
 9UN  HO7   H  HOH1   0   0.483   5.4810  -5.4644  -0.0125
 9UN  HO8   H  HOH1   0   0.481   0.1876  -4.0617   0.9802
 9UN  H11   H  HCR6   0   0.292   1.4030   0.9760  -2.5564
 9UN  H12   H  HCR6   0   0.303   0.7248   2.9991  -1.3426
 9UN  H14   H  HCR6   0   0.304   2.7492   1.5512   2.1672
 9UN  H15   H  HCR6   0   0.301   3.4241  -0.4550   0.9558
 9UN  H23   H  HCR5   0   0.307  -0.0266  -1.5584   1.8309
 9UN  HN26  H  HNH1   0   0.407  -3.0889   0.3338  -1.1135
 9UN  H27   H  HCH1   0   0.246  -4.2709   1.5563   1.2830
 9UN  H28   H  HCH2   0   0.248  -3.8531   3.0277  -0.6258
 9UN  H28A  H  HCH2   0   0.227  -4.7683   1.9647  -1.6941
 9UN  H29   H  HCH2   0   0.189  -5.8446   3.5440   0.6918
 9UN  H29A  H  HCH2   0   0.240  -6.1613   3.8549  -1.0133
 9UN  H31   H  HCH2   0   0.189  -6.8470   1.4448   1.6906
 9UN  H31A  H  HCH2   0   0.239  -7.8017   0.4213   0.6213
 9UN  H32   H  HCH2   0   0.223  -5.8069  -0.2246  -0.6538
 9UN  H32A  H  HCH2   0   0.242  -5.5468  -0.5280   1.0635
 9UN  H33   H  HCH3   0   0.232  -8.4923   3.6460  -0.7821
 9UN  H33A  H  HCH3   0   0.232  -9.1922   2.1848  -0.0853
 9UN  H33B  H  HCH3   0   0.190  -8.3661   3.3514   0.9590

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
 9UN  C1   C2    aromatic  1.391  0.020  1.391
 9UN  C1   C6    aromatic  1.388  0.020  1.388
 9UN  C2   C3    aromatic  1.401  0.020  1.401
 9UN  C2   O8    single    1.338  0.020  1.338
 9UN  C3   C4    aromatic  1.401  0.020  1.401
 9UN  C3   C19   single    1.456  0.020  1.456
 9UN  C4   C5    aromatic  1.374  0.020  1.374
 9UN  C4   O9    single    1.369  0.020  1.369
 9UN  C5   C6    aromatic  1.398  0.020  1.398
 9UN  C6   O7    single    1.337  0.020  1.337
 9UN  O9   C10   single    1.357  0.020  1.357
 9UN  C10  C11   aromatic  1.391  0.020  1.391
 9UN  C10  C15   aromatic  1.392  0.020  1.392
 9UN  C11  C12   aromatic  1.380  0.020  1.380
 9UN  C12  C13   aromatic  1.389  0.020  1.389
 9UN  C13  C14   aromatic  1.388  0.020  1.388
 9UN  C13  N16   single    1.449  0.020  1.449
 9UN  C14  C15   aromatic  1.381  0.020  1.381
 9UN  N16  O17   double    1.210  0.020  1.210
 9UN  N16  O18   single    1.210  0.020  1.210
 9UN  C19  O20   aromatic  1.345  0.020  1.345
 9UN  C19  C23   aromatic  1.357  0.020  1.357
 9UN  O20  N21   aromatic  1.346  0.020  1.346
 9UN  N21  C22   aromatic  1.301  0.020  1.301
 9UN  C22  C23   aromatic  1.414  0.020  1.414
 9UN  C22  C24   single    1.492  0.020  1.492
 9UN  C24  O25   double    1.221  0.020  1.221
 9UN  C24  N26   single    1.335  0.020  1.335
 9UN  N26  C27   single    1.450  0.020  1.450
 9UN  C27  C28   single    1.523  0.020  1.523
 9UN  C27  C32   single    1.526  0.020  1.526
 9UN  C28  C29   single    1.521  0.020  1.521
 9UN  C29  N30   single    1.450  0.020  1.450
 9UN  N30  C31   single    1.451  0.020  1.451
 9UN  N30  C33   single    1.445  0.020  1.445
 9UN  C31  C32   single    1.521  0.020  1.521
 9UN  C1   H1    single    0.930  0.020  1.080
 9UN  C5   H5    single    0.930  0.020  1.080
 9UN  O7   HO7   single    0.850  0.020  0.980
 9UN  O8   HO8   single    0.850  0.020  0.980
 9UN  C11  H11   single    0.930  0.020  1.080
 9UN  C12  H12   single    0.930  0.020  1.080
 9UN  C14  H14   single    0.930  0.020  1.080
 9UN  C15  H15   single    0.930  0.020  1.080
 9UN  C23  H23   single    0.930  0.020  1.080
 9UN  N26  HN26  single    0.860  0.020  1.020
 9UN  C27  H27   single    0.970  0.020  1.090
 9UN  C28  H28   single    0.970  0.020  1.090
 9UN  C28  H28A  single    0.970  0.020  1.090
 9UN  C29  H29   single    0.970  0.020  1.090
 9UN  C29  H29A  single    0.970  0.020  1.090
 9UN  C31  H31   single    0.970  0.020  1.090
 9UN  C31  H31A  single    0.970  0.020  1.090
 9UN  C32  H32   single    0.970  0.020  1.090
 9UN  C32  H32A  single    0.970  0.020  1.090
 9UN  C33  H33   single    0.970  0.020  1.090
 9UN  C33  H33A  single    0.970  0.020  1.090
 9UN  C33  H33B  single    0.970  0.020  1.090

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
 9UN  H1    C1   C6    120.78  3.000
 9UN  H1    C1   C2    119.25  3.000
 9UN  C6    C1   C2    119.97  3.000
 9UN  O8    C2   C3    122.72  3.000
 9UN  O8    C2   C1    116.77  3.000
 9UN  C3    C2   C1    120.51  3.000
 9UN  C19   C3   C4    120.89  3.000
 9UN  C19   C3   C2    121.35  3.000
 9UN  C4    C3   C2    117.76  3.000
 9UN  O9    C4   C5    118.08  3.000
 9UN  O9    C4   C3    119.21  3.000
 9UN  C5    C4   C3    122.69  3.000
 9UN  H5    C5   C6    120.97  3.000
 9UN  H5    C5   C4    120.68  3.000
 9UN  C6    C5   C4    118.34  3.000
 9UN  O7    C6   C5    116.95  3.000
 9UN  O7    C6   C1    122.32  3.000
 9UN  C5    C6   C1    120.72  3.000
 9UN  HO7   O7   C6    110.84  3.000
 9UN  HO8   O8   C2    111.99  3.000
 9UN  C10   O9   C4    118.68  3.000
 9UN  C15   C10  C11   120.79  3.000
 9UN  C15   C10  O9    122.33  3.000
 9UN  C11   C10  O9    116.88  3.000
 9UN  H11   C11  C12   120.22  3.000
 9UN  H11   C11  C10   120.05  3.000
 9UN  C12   C11  C10   119.73  3.000
 9UN  H12   C12  C13   121.32  3.000
 9UN  H12   C12  C11   119.42  3.000
 9UN  C13   C12  C11   119.25  3.000
 9UN  N16   C13  C14   119.35  3.000
 9UN  N16   C13  C12   119.38  3.000
 9UN  C14   C13  C12   121.27  3.000
 9UN  H14   C14  C15   119.34  3.000
 9UN  H14   C14  C13   121.21  3.000
 9UN  C15   C14  C13   119.45  3.000
 9UN  H15   C15  C14   119.29  3.000
 9UN  H15   C15  C10   121.21  3.000
 9UN  C14   C15  C10   119.50  3.000
 9UN  O18   N16  O17   123.73  3.000
 9UN  O18   N16  C13   118.15  3.000
 9UN  O17   N16  C13   118.12  3.000
 9UN  C23   C19  O20   108.90  3.000
 9UN  C23   C19  C3    133.42  3.000
 9UN  O20   C19  C3    117.67  3.000
 9UN  N21   O20  C19   109.88  3.000
 9UN  C22   N21  O20   106.55  3.000
 9UN  C24   C22  C23   126.35  3.000
 9UN  C24   C22  N21   122.37  3.000
 9UN  C23   C22  N21   111.27  3.000
 9UN  H23   C23  C22   128.39  3.000
 9UN  H23   C23  C19   128.12  3.000
 9UN  C22   C23  C19   103.39  3.000
 9UN  N26   C24  O25   125.47  3.000
 9UN  N26   C24  C22   115.21  3.000
 9UN  O25   C24  C22   119.32  3.000
 9UN  HN26  N26  C27   117.56  3.000
 9UN  HN26  N26  C24   118.26  3.000
 9UN  C27   N26  C24   124.01  3.000
 9UN  H27   C27  C32   108.78  3.000
 9UN  H27   C27  C28   108.51  3.000
 9UN  C32   C27  C28   109.97  3.000
 9UN  H27   C27  N26   107.56  3.000
 9UN  C32   C27  N26   111.87  3.000
 9UN  C28   C27  N26   110.04  3.000
 9UN  H28A  C28  H28   107.47  3.000
 9UN  H28A  C28  C29   109.37  3.000
 9UN  H28   C28  C29   109.58  3.000
 9UN  H28A  C28  C27   109.71  3.000
 9UN  H28   C28  C27   110.25  3.000
 9UN  C29   C28  C27   110.41  3.000
 9UN  H29A  C29  H29   106.60  3.000
 9UN  H29A  C29  N30   108.75  3.000
 9UN  H29   C29  N30   111.43  3.000
 9UN  H29A  C29  C28   109.28  3.000
 9UN  H29   C29  C28   109.19  3.000
 9UN  N30   C29  C28   111.45  3.000
 9UN  C33   N30  C31   111.36  3.000
 9UN  C33   N30  C29   111.23  3.000
 9UN  C31   N30  C29   111.31  3.000
 9UN  H31A  C31  H31   106.52  3.000
 9UN  H31A  C31  C32   109.52  3.000
 9UN  H31   C31  C32   109.30  3.000
 9UN  H31A  C31  N30   108.70  3.000
 9UN  H31   C31  N30   111.38  3.000
 9UN  C32   C31  N30   111.29  3.000
 9UN  H32A  C32  H32   107.53  3.000
 9UN  H32A  C32  C31   109.56  3.000
 9UN  H32   C32  C31   109.70  3.000
 9UN  H32A  C32  C27   110.16  3.000
 9UN  H32   C32  C27   109.35  3.000
 9UN  C31   C32  C27   110.48  3.000
 9UN  H33B  C33  H33A  107.67  3.000
 9UN  H33B  C33  H33   107.66  3.000
 9UN  H33A  C33  H33   107.83  3.000
 9UN  H33B  C33  N30   113.20  3.000
 9UN  H33A  C33  N30   110.16  3.000
 9UN  H33   C33  N30   110.13  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
 9UN  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 9UN  CONST_02  C19   C3   C2   C1    180.00   0.0  0
 9UN  CONST_03  C4    C5   C6   C1      0.00   0.0  0
 9UN  CONST_04  C5    C6   C1   C2      0.00   0.0  0
 9UN  CONST_05  C5    C4   C3   C2      0.00   0.0  0
 9UN  CONST_08  C6    C1   C2   C3      0.00   0.0  0
 9UN  CONST_09  C6    C5   C4   C3      0.00   0.0  0
 9UN  CONST_10  N21   O20  C19  C3    180.00   0.0  0
 9UN  CONST_11  C22   C23  C19  C3    180.00   0.0  0
 9UN  CONST_14  C19   C3   C4   C5    180.00   0.0  0
 9UN  CONST_15  C13   C12  C11  C10     0.00   0.0  0
 9UN  CONST_16  C13   C14  C15  C10     0.00   0.0  0
 9UN  CONST_17  C14   C15  C10  C11     0.00   0.0  0
 9UN  CONST_18  C14   C13  C12  C11     0.00   0.0  0
 9UN  CONST_19  C15   C10  C11  C12     0.00   0.0  0
 9UN  CONST_20  C15   C14  C13  C12     0.00   0.0  0
 9UN  CONST_21  C22   N21  O20  C19     0.00   0.0  0
 9UN  CONST_22  N21   C22  C23  C19     0.00   0.0  0
 9UN  CONST_23  C22   C23  C19  O20     0.00   0.0  0
 9UN  CONST_24  C23   C22  N21  O20     0.00   0.0  0
 9UN  CONST_25  C23   C19  O20  N21     0.00   0.0  0
 9UN  CONST_26  O7    C6   C1   C2    180.00   0.0  0
 9UN  CONST_27  O9    C4   C3   C2    180.00   0.0  0
 9UN  CONST_28  O8    C2   C3   C4    180.00   0.0  0
 9UN  CONST_29  O7    C6   C5   C4    180.00   0.0  0
 9UN  CONST_30  O8    C2   C1   C6    180.00   0.0  0
 9UN  CONST_31  O9    C4   C5   C6    180.00   0.0  0
 9UN  CONST_32  C19   C3   C2   O8      0.00   0.0  0
 9UN  CONST_33  C19   C3   C4   O9      0.00   0.0  0
 9UN  CONST_34  C12   C11  C10  O9    180.00   0.0  0
 9UN  CONST_35  C14   C15  C10  O9    180.00   0.0  0
 9UN  CONST_36  N16   C13  C12  C11   180.00   0.0  0
 9UN  CONST_37  N16   C13  C14  C15   180.00   0.0  0
 9UN  CONST_38  C24   C22  C23  C19   180.00   0.0  0
 9UN  CONST_39  C24   C22  N21  O20   180.00   0.0  0
 9UN  CONST_40  H5    C5   C6   C1    180.00   0.0  0
 9UN  CONST_41  H1    C1   C2   C3    180.00   0.0  0
 9UN  CONST_42  H23   C23  C19  C3      0.00   0.0  0
 9UN  CONST_43  H12   C12  C11  C10   180.00   0.0  0
 9UN  CONST_44  H14   C14  C15  C10   180.00   0.0  0
 9UN  CONST_45  H15   C15  C10  C11   180.00   0.0  0
 9UN  CONST_46  H11   C11  C12  C13   180.00   0.0  0
 9UN  CONST_47  C27   N26  C24  C22   180.00   0.0  0
 9UN  CONST_48  O17   N16  C13  C12     0.00   0.0  0
 9UN  CONST_49  O18   N16  C13  C12   180.00   0.0  0
 9UN  CONST_50  O17   N16  C13  C14   180.00   0.0  0
 9UN  CONST_51  O18   N16  C13  C14     0.00   0.0  0
 9UN  CONST_52  C27   N26  C24  O25     0.00   0.0  0
 9UN  CONST_53  HN26  N26  C24  C22     0.00   0.0  0
 9UN  Var_01    N30   C29  C28  C27   -56.57  30.0  1
 9UN  Var_02    N30   C31  C32  C27    56.57  30.0  1
 9UN  Var_03    C31   N30  C29  C28    59.42  30.0  1
 9UN  Var_04    C32   C31  N30  C29   -59.38  30.0  1
 9UN  Var_05    C11   C10  O9   C4   -149.33  30.0  2
 9UN  Var_06    O25   C24  C22  N21   175.72  30.0  2
 9UN  Var_07    H33   C33  N30  C29    58.21  30.0  3

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
 9UN  chir_01  C27  N26  C28  C32  negativ

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
 9UN  plan-1  C3    0.020
 9UN  plan-1  C19   0.020
 9UN  plan-1  O20   0.020
 9UN  plan-1  N21   0.020
 9UN  plan-1  C22   0.020
 9UN  plan-1  C23   0.020
 9UN  plan-1  C24   0.020
 9UN  plan-1  H23   0.020
 9UN  plan-2  C1    0.020
 9UN  plan-2  C2    0.020
 9UN  plan-2  C3    0.020
 9UN  plan-2  C4    0.020
 9UN  plan-2  C5    0.020
 9UN  plan-2  C6    0.020
 9UN  plan-2  O7    0.020
 9UN  plan-2  O8    0.020
 9UN  plan-2  O9    0.020
 9UN  plan-2  C19   0.020
 9UN  plan-2  H1    0.020
 9UN  plan-2  H5    0.020
 9UN  plan-3  O9    0.020
 9UN  plan-3  C10   0.020
 9UN  plan-3  C11   0.020
 9UN  plan-3  C12   0.020
 9UN  plan-3  C13   0.020
 9UN  plan-3  C14   0.020
 9UN  plan-3  C15   0.020
 9UN  plan-3  N16   0.020
 9UN  plan-3  H11   0.020
 9UN  plan-3  H12   0.020
 9UN  plan-3  H14   0.020
 9UN  plan-3  H15   0.020
 9UN  plan-4  C22   0.020
 9UN  plan-4  C24   0.020
 9UN  plan-4  O25   0.020
 9UN  plan-4  N26   0.020
 9UN  plan-4  C27   0.020
 9UN  plan-4  HN26  0.020
 9UN  plan-5  C13   0.020
 9UN  plan-5  N16   0.020
 9UN  plan-5  O17   0.020
 9UN  plan-5  O18   0.020

