# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 22:21:57 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  39  26  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.471   3.3445  -2.2496  -0.1279
 35M  C6   C  C      0   0.526   3.0760  -1.0590  -0.1709
 35M  C5   C  CR6    0  -0.073   4.1356  -0.0194  -0.0584
 35M  C4   C  CR16   0  -0.250   5.3443  -0.3719   0.5397
 35M  C3   C  CR16   0  -0.371   6.3715   0.5437   0.6738
 35M  C2   C  CR6    0   0.361   6.2152   1.8416   0.1884
 35M  O4   O  OH1    0  -0.621   7.1760   2.7727   0.2812
 35M  C1   C  CR16   0  -0.323   5.0189   2.2028  -0.4303
 35M  C    C  CR16   0  -0.282   3.9961   1.2809  -0.5471
 35M  N    N  NH1    0  -0.768   1.8123  -0.5850  -0.3097
 35M  C7   C  C      0   0.381   0.6250  -1.3228  -0.4246
 35M  C12  C  C1     0  -0.390  -0.5574  -0.6935  -0.0437
 35M  C11  C  C      0  -0.028  -1.7956  -1.3162  -0.1385
 35M  C10  C  C      0   0.314  -1.8542  -2.6222  -0.6391
 35M  O2   O  OH1    0  -0.619  -3.0570  -3.2140  -0.7649
 35M  C9   C  C1     0  -0.377  -0.6762  -3.2523  -1.0250
 35M  C8   C  C1     0  -0.298   0.5533  -2.6203  -0.9243
 35M  C13  C  CR6    0   0.224  -3.0101  -0.5782   0.2779
 35M  N1   N  N      0  -0.415  -3.8477  -1.1885   1.1149
 35M  C17  C  CR16   0  -0.083  -4.9194  -0.5184   1.5170
 35M  C16  C  CR16   0  -0.358  -5.2129   0.7771   1.1201
 35M  C15  C  CR6    0   0.006  -4.3489   1.4216   0.2439
 35M  C14  C  CR16   0  -0.363  -3.2307   0.7175  -0.1824
 35M  C18  C  C      0   0.403  -4.6170   2.8469  -0.2379
 35M  O1   O  O      0  -0.583  -3.8117   3.3066  -1.0668
 35M  O    O  OC    -1  -0.584  -5.6138   3.4102   0.2471
 35M  H    H  HNH1   0   0.418   1.6778   0.4040  -0.1699
 35M  H4   H  HCR6   0   0.265   5.4855  -1.3759   0.9172
 35M  HA   H  HCR6   0   0.262   3.0929   1.5953  -1.0552
 35M  H3   H  HCR6   0   0.278   7.2962   0.2466   1.1549
 35M  HB   H  HOH1   0   0.479   7.9547   2.4182   0.7258
 35M  H1   H  HCR6   0   0.273   4.8976   3.2034  -0.8252
 35M  H12  H  H      0   0.271  -0.5157   0.3145   0.3548
 35M  H8   H  H      0   0.277   1.4371  -3.1467  -1.2465
 35M  H9   H  H      0   0.273  -0.7138  -4.2585  -1.4282
 35M  H14  H  HCR6   0   0.257  -2.5369   1.1735  -0.8758
 35M  H17  H  HCR6   0   0.255  -5.5818  -1.0402   2.1997
 35M  H16  H  HCR6   0   0.256  -6.1006   1.2715   1.4889
 35M  H2   H  HOH1   0   0.475  -2.9556  -4.0845  -1.1659

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    1.221  0.020  1.221
 35M  C6   C5   single    1.489  0.020  1.489
 35M  C6   N    single    1.357  0.020  1.357
 35M  C5   C4   aromatic  1.394  0.020  1.394
 35M  C5   C    aromatic  1.396  0.020  1.396
 35M  C4   C3   aromatic  1.383  0.020  1.383
 35M  C3   C2   aromatic  1.394  0.020  1.394
 35M  C2   O4   single    1.341  0.020  1.341
 35M  C2   C1   aromatic  1.394  0.020  1.394
 35M  C1   C    aromatic  1.382  0.020  1.382
 35M  N    C7   single    1.403  0.020  1.403
 35M  C7   C12  aromatic  1.393  0.020  1.393
 35M  C7   C8   aromatic  1.392  0.020  1.392
 35M  C12  C11  aromatic  1.389  0.020  1.389
 35M  C11  C10  aromatic  1.400  0.020  1.400
 35M  C11  C13  single    1.481  0.020  1.481
 35M  C10  O2   single    1.346  0.020  1.346
 35M  C10  C9   aromatic  1.391  0.020  1.391
 35M  C9   C8   aromatic  1.386  0.020  1.386
 35M  C13  N1   aromatic  1.332  0.020  1.332
 35M  C13  C14  aromatic  1.393  0.020  1.393
 35M  N1   C17  aromatic  1.326  0.020  1.326
 35M  C17  C16  aromatic  1.386  0.020  1.386
 35M  C16  C15  aromatic  1.389  0.020  1.389
 35M  C15  C14  aromatic  1.388  0.020  1.388
 35M  C15  C18  single    1.528  0.020  1.528
 35M  C18  O1   deloc     1.244  0.020  1.244
 35M  C18  O    deloc     1.243  0.020  1.243
 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  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   115.26  3.000
 35M  N    C6   O3   123.30  3.000
 35M  C5   C6   O3   121.44  3.000
 35M  C    C5   C4   118.19  3.000
 35M  C    C5   C6   123.56  3.000
 35M  C4   C5   C6   118.23  3.000
 35M  H4   C4   C3   118.93  3.000
 35M  H4   C4   C5   119.84  3.000
 35M  C3   C4   C5   121.23  3.000
 35M  H3   C3   C2   120.34  3.000
 35M  H3   C3   C4   119.70  3.000
 35M  C2   C3   C4   119.96  3.000
 35M  C1   C2   O4   117.74  3.000
 35M  C1   C2   C3   119.45  3.000
 35M  O4   C2   C3   122.81  3.000
 35M  HB   O4   C2   110.81  3.000
 35M  H1   C1   C    120.18  3.000
 35M  H1   C1   C2   119.83  3.000
 35M  C    C1   C2   119.98  3.000
 35M  HA   C    C1   117.60  3.000
 35M  HA   C    C5   121.20  3.000
 35M  C1   C    C5   121.18  3.000
 35M  H    N    C7   114.50  3.000
 35M  H    N    C6   116.93  3.000
 35M  C7   N    C6   127.81  3.000
 35M  C8   C7   C12  118.40  3.000
 35M  C8   C7   N    124.28  3.000
 35M  C12  C7   N    117.29  3.000
 35M  H12  C12  C11  118.41  3.000
 35M  H12  C12  C7   119.20  3.000
 35M  C11  C12  C7   122.38  3.000
 35M  C13  C11  C10  122.09  3.000
 35M  C13  C11  C12  119.24  3.000
 35M  C10  C11  C12  118.67  3.000
 35M  C9   C10  O2   122.12  3.000
 35M  C9   C10  C11  119.12  3.000
 35M  O2   C10  C11  118.74  3.000
 35M  H2   O2   C10  110.00  3.000
 35M  H9   C9   C8   118.74  3.000
 35M  H9   C9   C10  119.61  3.000
 35M  C8   C9   C10  121.64  3.000
 35M  H8   C8   C9   118.87  3.000
 35M  H8   C8   C7   121.34  3.000
 35M  C9   C8   C7   119.78  3.000
 35M  C14  C13  N1   122.30  3.000
 35M  C14  C13  C11  120.04  3.000
 35M  N1   C13  C11  117.65  3.000
 35M  C17  N1   C13  117.85  3.000
 35M  H17  C17  C16  120.02  3.000
 35M  H17  C17  N1   116.18  3.000
 35M  C16  C17  N1   123.80  3.000
 35M  H16  C16  C15  120.92  3.000
 35M  H16  C16  C17  120.24  3.000
 35M  C15  C16  C17  118.85  3.000
 35M  C18  C15  C14  121.16  3.000
 35M  C18  C15  C16  121.50  3.000
 35M  C14  C15  C16  117.34  3.000
 35M  H14  C14  C15  119.97  3.000
 35M  H14  C14  C13  120.17  3.000
 35M  C15  C14  C13  119.86  3.000
 35M  O    C18  O1   127.70  3.000
 35M  O    C18  C15  116.11  3.000
 35M  O1   C18  C15  116.19  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_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_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_51  H    N    C7   C12     0.00   0.0  0
 35M  CONST_52  C7   N    C6   O3      0.00   0.0  0
 35M  Var_01    C4   C5   C6   O3    -21.56  30.0  2
 35M  Var_02    O1   C18  C15  C16  -176.91  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

