# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 06:09:28 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 2-[5-[(4-hydroxyphenyl)carbonylamino]-2-oxidanyl-phenyl]pyridine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccnc(c1)c2cc(NC(=O)c3ccc(O)cc3)ccc2O
#
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
 35M  35M  '2-[5-[(4-hydroxyphenyl)carbonylamino]-2-oxidanyl-phenyl]pyridine-4-carboxylic acid'  ligand  40  26  .  2022-03-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_35M
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
 35M  O3   O  O     0  -0.459   3.0678  -1.9677   0.8640
 35M  C6   C  C     0   0.524   2.9761  -0.9378   0.2192
 35M  C5   C  CR6   0  -0.070   4.1123   0.0117   0.0917
 35M  C4   C  CR16  0  -0.238   5.0863   0.0208   1.0908
 35M  C3   C  CR16  0  -0.304   6.1655   0.8779   1.0274
 35M  C2   C  CR6   0   0.372   6.3069   1.7390  -0.0606
 35M  O4   O  OH1   0  -0.604   7.3758   2.5524  -0.0758
 35M  C1   C  CR16  0  -0.343   5.3566   1.7218  -1.0775
 35M  C    C  CR16  0  -0.254   4.2710   0.8669  -0.9954
 35M  N    N  NH1   0  -0.762   1.8378  -0.5722  -0.4287
 35M  C7   C  CR6   0   0.402   0.6476  -1.3217  -0.4412
 35M  C12  C  CR16  0  -0.410  -0.5576  -0.6800  -0.2338
 35M  C11  C  CR6   0  -0.079  -1.7857  -1.3485  -0.2865
 35M  C10  C  CR6   0   0.353  -1.7727  -2.7361  -0.5462
 35M  O2   O  OH1   0  -0.631  -2.8741  -3.4819  -0.6251
 35M  C9   C  CR16  0  -0.330  -0.5477  -3.3805  -0.7399
 35M  C8   C  CR16  0  -0.262   0.6440  -2.6933  -0.6993
 35M  C13  C  CR6   0   0.425  -3.0488  -0.6241  -0.0586
 35M  N1   N  N     0  -0.562  -4.1786  -1.3289  -0.1807
 35M  C17  C  CR16  0   0.013  -5.3562  -0.7561   0.0115
 35M  C16  C  CR16  0  -0.346  -5.4972   0.5765   0.3469
 35M  C15  C  CR6   0   0.060  -4.3370   1.3307   0.4825
 35M  C14  C  CR16  0  -0.350  -3.1078   0.7301   0.2778
 35M  C18  C  C     0   0.560  -4.3581   2.7774   0.8461
 35M  O1   O  O     0  -0.416  -3.3681   3.4560   0.9331
 35M  O    O  OH1   0  -0.577  -5.5826   3.2288   1.0631
 35M  H    H  HNH1  0   0.389   1.7723   0.3773  -0.7572
 35M  H4   H  HCR6  0   0.254   4.9920  -0.6447   1.9380
 35M  HA   H  HCR6  0   0.240   3.5688   0.8639  -1.8192
 35M  H3   H  HCR6  0   0.253   6.9052   0.8855   1.8168
 35M  HB   H  HOH1  0   0.450   7.3719   3.1041  -0.8628
 35M  H1   H  HCR6  0   0.242   5.4596   2.3665  -1.9421
 35M  H12  H  HCR6  0   0.227  -0.5328   0.3816  -0.0279
 35M  H8   H  HCR6  0   0.256   1.5660  -3.2238  -0.8855
 35M  H9   H  HCR6  0   0.250  -0.5489  -4.4434  -0.9427
 35M  H14  H  HCR6  0   0.257  -2.2132   1.3229   0.3898
 35M  H17  H  HCR6  0   0.265  -6.2250  -1.3896  -0.1081
 35M  H16  H  HCR6  0   0.264  -6.4827   0.9902   0.4943
 35M  HC   H  HOH1  0   0.467  -5.5457   4.1659   1.2956
 35M  H2   H  HOH1  0   0.474  -3.6494  -2.8749  -0.4969

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
 35M  O3   C6   double    1.219  0.020  1.219
 35M  C6   C5   single    1.486  0.020  1.486
 35M  C6   N    single    1.360  0.020  1.360
 35M  C5   C4   aromatic  1.395  0.020  1.395
 35M  C5   C    aromatic  1.392  0.020  1.392
 35M  C4   C3   aromatic  1.380  0.020  1.380
 35M  C3   C2   aromatic  1.395  0.020  1.395
 35M  C2   O4   single    1.343  0.020  1.343
 35M  C2   C1   aromatic  1.392  0.020  1.392
 35M  C1   C    aromatic  1.384  0.020  1.384
 35M  N    C7   single    1.407  0.020  1.407
 35M  C7   C12  aromatic  1.381  0.020  1.381
 35M  C7   C8   aromatic  1.396  0.020  1.396
 35M  C12  C11  aromatic  1.399  0.020  1.399
 35M  C11  C10  aromatic  1.412  0.020  1.412
 35M  C11  C13  single    1.474  0.020  1.474
 35M  C10  O2   single    1.333  0.020  1.333
 35M  C10  C9   aromatic  1.398  0.020  1.398
 35M  C9   C8   aromatic  1.376  0.020  1.376
 35M  C13  N1   aromatic  1.337  0.020  1.337
 35M  C13  C14  aromatic  1.397  0.020  1.397
 35M  N1   C17  aromatic  1.323  0.020  1.323
 35M  C17  C16  aromatic  1.381  0.020  1.381
 35M  C16  C15  aromatic  1.390  0.020  1.390
 35M  C15  C14  aromatic  1.383  0.020  1.383
 35M  C15  C18  single    1.492  0.020  1.492
 35M  C18  O1   double    1.203  0.020  1.203
 35M  C18  O    single    1.323  0.020  1.323
 35M  N    H    single    0.860  0.020  1.020
 35M  C4   H4   single    0.930  0.020  1.080
 35M  C    HA   single    0.930  0.020  1.080
 35M  C3   H3   single    0.930  0.020  1.080
 35M  O4   HB   single    0.850  0.020  0.980
 35M  C1   H1   single    0.930  0.020  1.080
 35M  C12  H12  single    0.930  0.020  1.080
 35M  C8   H8   single    0.930  0.020  1.080
 35M  C9   H9   single    0.930  0.020  1.080
 35M  C14  H14  single    0.930  0.020  1.080
 35M  C17  H17  single    0.930  0.020  1.080
 35M  C16  H16  single    0.930  0.020  1.080
 35M  O    HC   single    0.850  0.020  0.980
 35M  O2   H2   single    0.850  0.020  0.980

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
 35M  N    C6   C5   115.30  3.000
 35M  N    C6   O3   122.84  3.000
 35M  C5   C6   O3   121.86  3.000
 35M  C    C5   C4   118.39  3.000
 35M  C    C5   C6   123.13  3.000
 35M  C4   C5   C6   118.45  3.000
 35M  H4   C4   C3   119.11  3.000
 35M  H4   C4   C5   119.74  3.000
 35M  C3   C4   C5   121.15  3.000
 35M  H3   C3   C2   119.71  3.000
 35M  H3   C3   C4   120.37  3.000
 35M  C2   C3   C4   119.91  3.000
 35M  C1   C2   O4   122.85  3.000
 35M  C1   C2   C3   119.54  3.000
 35M  O4   C2   C3   117.60  3.000
 35M  HB   O4   C2   110.71  3.000
 35M  H1   C1   C    119.30  3.000
 35M  H1   C1   C2   120.72  3.000
 35M  C    C1   C2   119.98  3.000
 35M  HA   C    C1   117.73  3.000
 35M  HA   C    C5   121.24  3.000
 35M  C1   C    C5   121.01  3.000
 35M  H    N    C7   116.40  3.000
 35M  H    N    C6   117.61  3.000
 35M  C7   N    C6   124.70  3.000
 35M  C8   C7   C12  118.83  3.000
 35M  C8   C7   N    121.84  3.000
 35M  C12  C7   N    119.31  3.000
 35M  H12  C12  C11  119.75  3.000
 35M  H12  C12  C7   117.68  3.000
 35M  C11  C12  C7   122.57  3.000
 35M  C13  C11  C10  121.30  3.000
 35M  C13  C11  C12  120.76  3.000
 35M  C10  C11  C12  117.93  3.000
 35M  C9   C10  O2   117.27  3.000
 35M  C9   C10  C11  119.13  3.000
 35M  O2   C10  C11  123.60  3.000
 35M  H2   O2   C10  107.19  3.000
 35M  H9   C9   C8   119.81  3.000
 35M  H9   C9   C10  118.54  3.000
 35M  C8   C9   C10  121.64  3.000
 35M  H8   C8   C9   119.27  3.000
 35M  H8   C8   C7   120.83  3.000
 35M  C9   C8   C7   119.89  3.000
 35M  C14  C13  N1   119.82  3.000
 35M  C14  C13  C11  123.37  3.000
 35M  N1   C13  C11  116.80  3.000
 35M  C17  N1   C13  120.69  3.000
 35M  H17  C17  C16  120.65  3.000
 35M  H17  C17  N1   116.42  3.000
 35M  C16  C17  N1   122.93  3.000
 35M  H16  C16  C15  122.74  3.000
 35M  H16  C16  C17  119.76  3.000
 35M  C15  C16  C17  117.50  3.000
 35M  C18  C15  C14  118.01  3.000
 35M  C18  C15  C16  122.55  3.000
 35M  C14  C15  C16  119.44  3.000
 35M  H14  C14  C15  118.87  3.000
 35M  H14  C14  C13  121.51  3.000
 35M  C15  C14  C13  119.62  3.000
 35M  O    C18  O1   123.86  3.000
 35M  O    C18  C15  112.58  3.000
 35M  O1   C18  C15  123.56  3.000
 35M  HC   O    C18  109.58  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
 35M  CONST_01  C2   C3   C4   C5      0.00   0.0  0
 35M  CONST_02  C2   C1   C    C5      0.00   0.0  0
 35M  CONST_03  C1   C    C5   C4      0.00   0.0  0
 35M  CONST_04  C1   C2   C3   C4      0.00   0.0  0
 35M  CONST_05  C    C5   C4   C3      0.00   0.0  0
 35M  CONST_06  C    C1   C2   C3      0.00   0.0  0
 35M  CONST_07  C10  C11  C12  C7      0.00   0.0  0
 35M  CONST_08  C13  C11  C12  C7    180.00   0.0  0
 35M  CONST_09  C10  C9   C8   C7      0.00   0.0  0
 35M  CONST_10  C9   C8   C7   C12     0.00   0.0  0
 35M  CONST_11  C9   C10  C11  C12     0.00   0.0  0
 35M  CONST_12  N1   C13  C11  C12   180.00   0.0  0
 35M  CONST_13  C14  C13  C11  C12     0.00   0.0  0
 35M  CONST_14  C8   C7   C12  C11     0.00   0.0  0
 35M  CONST_15  C8   C9   C10  C11     0.00   0.0  0
 35M  CONST_16  C17  N1   C13  C11   180.00   0.0  0
 35M  CONST_17  C15  C14  C13  C11   180.00   0.0  0
 35M  CONST_18  N1   C13  C11  C10     0.00   0.0  0
 35M  CONST_19  C14  C13  C11  C10   180.00   0.0  0
 35M  CONST_20  C13  C11  C10  C9    180.00   0.0  0
 35M  CONST_21  C16  C17  N1   C13     0.00   0.0  0
 35M  CONST_22  C16  C15  C14  C13     0.00   0.0  0
 35M  CONST_23  C15  C14  C13  N1      0.00   0.0  0
 35M  CONST_24  C15  C16  C17  N1      0.00   0.0  0
 35M  CONST_25  C14  C13  N1   C17     0.00   0.0  0
 35M  CONST_26  C14  C15  C16  C17     0.00   0.0  0
 35M  CONST_27  C3   C4   C5   C6    180.00   0.0  0
 35M  CONST_28  C1   C    C5   C6    180.00   0.0  0
 35M  CONST_29  O4   C2   C3   C4    180.00   0.0  0
 35M  CONST_30  C    C1   C2   O4    180.00   0.0  0
 35M  CONST_31  C11  C12  C7   N     180.00   0.0  0
 35M  CONST_32  C9   C8   C7   N     180.00   0.0  0
 35M  CONST_33  O2   C10  C11  C12   180.00   0.0  0
 35M  CONST_34  C13  C11  C10  O2      0.00   0.0  0
 35M  CONST_35  C8   C9   C10  O2    180.00   0.0  0
 35M  CONST_36  C18  C15  C14  C13   180.00   0.0  0
 35M  CONST_37  C18  C15  C16  C17   180.00   0.0  0
 35M  CONST_38  H3   C3   C4   C5    180.00   0.0  0
 35M  CONST_39  H1   C1   C    C5    180.00   0.0  0
 35M  CONST_40  HA   C    C5   C4    180.00   0.0  0
 35M  CONST_41  H4   C4   C3   C2    180.00   0.0  0
 35M  CONST_42  H9   C9   C8   C7    180.00   0.0  0
 35M  CONST_43  H8   C8   C7   C12   180.00   0.0  0
 35M  CONST_44  H14  C14  C13  C11     0.00   0.0  0
 35M  CONST_45  H12  C12  C11  C10   180.00   0.0  0
 35M  CONST_46  H17  C17  N1   C13   180.00   0.0  0
 35M  CONST_47  H16  C16  C17  N1    180.00   0.0  0
 35M  CONST_48  C7   N    C6   C5    180.00   0.0  0
 35M  CONST_52  C7   N    C6   O3      0.00   0.0  0
 35M  CONST_53  HC   O    C18  C15   180.00   0.0  0
 35M  Var_01    C4   C5   C6   O3    -24.90  30.0  2
 35M  Var_02    O1   C18  C15  C16  -177.93  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
 35M  plan-1  C6   0.020
 35M  plan-1  C5   0.020
 35M  plan-1  C4   0.020
 35M  plan-1  C3   0.020
 35M  plan-1  C2   0.020
 35M  plan-1  O4   0.020
 35M  plan-1  C1   0.020
 35M  plan-1  C    0.020
 35M  plan-1  H4   0.020
 35M  plan-1  HA   0.020
 35M  plan-1  H3   0.020
 35M  plan-1  H1   0.020
 35M  plan-2  N    0.020
 35M  plan-2  C7   0.020
 35M  plan-2  C12  0.020
 35M  plan-2  C11  0.020
 35M  plan-2  C10  0.020
 35M  plan-2  O2   0.020
 35M  plan-2  C9   0.020
 35M  plan-2  C8   0.020
 35M  plan-2  C13  0.020
 35M  plan-2  H12  0.020
 35M  plan-2  H8   0.020
 35M  plan-2  H9   0.020
 35M  plan-3  C11  0.020
 35M  plan-3  C13  0.020
 35M  plan-3  N1   0.020
 35M  plan-3  C17  0.020
 35M  plan-3  C16  0.020
 35M  plan-3  C15  0.020
 35M  plan-3  C14  0.020
 35M  plan-3  C18  0.020
 35M  plan-3  H14  0.020
 35M  plan-3  H17  0.020
 35M  plan-3  H16  0.020
 35M  plan-4  O3   0.020
 35M  plan-4  C6   0.020
 35M  plan-4  C5   0.020
 35M  plan-4  N    0.020
 35M  plan-4  C7   0.020
 35M  plan-4  H    0.020
 35M  plan-5  C15  0.020
 35M  plan-5  C18  0.020
 35M  plan-5  O1   0.020
 35M  plan-5  O    0.020
 35M  plan-5  HC   0.020

