# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 20:25:23 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 2-[5-[2-(3-methoxyphenyl)ethanoylamino]-2-oxidanyl-phenyl]pyridine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(CC(=O)Nc2ccc(O)c(c2)c3cc(ccn3)C(O)=O)c1
#
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
 9CJ  9CJ  '2-[5-[2-(3-methoxyphenyl)ethanoylamino]-2-oxidanyl-phenyl]pyridine-4-carboxylic acid'  ligand  45  28  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9CJ
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
 9CJ  O4    O  O      0  -0.464   1.3390  -0.0166  -0.5533
 9CJ  C7    C  C      0   0.549   1.6955  -1.1502  -0.8219
 9CJ  C6    C  CH2    0  -0.686   3.0955  -1.4442  -1.3366
 9CJ  C5    C  CR6    0   0.153   4.1403  -0.7523  -0.5081
 9CJ  C4    C  CR16   0  -0.317   4.7206  -1.4097   0.5769
 9CJ  C3    C  CR16   0  -0.228   5.6667  -0.7577   1.3486
 9CJ  C2    C  CR16   0  -0.396   6.0515   0.5480   1.0640
 9CJ  C20   C  CR16   0  -0.392   4.5170   0.5491  -0.7972
 9CJ  C1    C  CR6    0   0.395   5.4720   1.2057  -0.0182
 9CJ  O     O  O2     0  -0.473   5.7697   2.4667  -0.3878
 9CJ  C     C  CH3    0  -0.436   6.7260   3.1824   0.3668
 9CJ  N     N  NH1    0  -0.745   0.9047  -2.2417  -0.7185
 9CJ  C8    C  CR6    0   0.387  -0.4322  -2.3287  -0.2977
 9CJ  C13   C  CR16   0  -0.428  -1.2870  -1.2451  -0.1755
 9CJ  C12   C  CR6    0  -0.071  -2.6178  -1.3959   0.2331
 9CJ  C11   C  CR6    0   0.336  -3.0918  -2.6875   0.5419
 9CJ  O3    O  OH1    0  -0.643  -4.3356  -2.9374   0.9588
 9CJ  C10   C  CR16   0  -0.337  -2.2268  -3.7758   0.4035
 9CJ  C9    C  CR16   0  -0.335  -0.9247  -3.6037  -0.0072
 9CJ  C14   C  CR6    0   0.401  -3.5036  -0.2152   0.3225
 9CJ  N1    N  N      0  -0.573  -4.7294  -0.4254   0.8176
 9CJ  C18   C  CR16   0  -0.023  -5.5857   0.5829   0.9224
 9CJ  C17   C  CR16   0  -0.390  -5.2763   1.8714   0.5341
 9CJ  C16   C  CR6    0   0.026  -4.0120   2.1215   0.0096
 9CJ  C15   C  CR16   0  -0.396  -3.1237   1.0632  -0.0909
 9CJ  C19   C  C      0   0.415  -3.6107   3.5233  -0.4560
 9CJ  O2    O  O      0  -0.579  -2.4472   3.6494  -0.8748
 9CJ  O1    O  OC    -1  -0.581  -4.4903   4.3972  -0.3733
 9CJ  H61C  H  HCH2   0   0.280   3.2900  -2.5172  -1.3724
 9CJ  H62C  H  HCH2   0   0.299   3.1335  -1.0881  -2.3698
 9CJ  H     H  HNH1   0   0.415   1.3372  -3.1274  -0.9298
 9CJ  H4    H  HCR6   0   0.248   4.4358  -2.4284   0.8094
 9CJ  H20   H  HCR6   0   0.255   4.0799   1.0703  -1.6410
 9CJ  H3    H  HCR6   0   0.258   6.1219  -1.2683   2.1875
 9CJ  H2    H  HCR6   0   0.278   6.7968   1.0258   1.6854
 9CJ  HC1   H  HCH3   0   0.259   6.8107   4.1646  -0.0919
 9CJ  HC2   H  HCH3   0   0.228   6.4159   3.3063   1.4079
 9CJ  HC3   H  HCH3   0   0.227   7.7071   2.7004   0.3474
 9CJ  H13   H  HCR6   0   0.278  -0.9154  -0.2604  -0.4013
 9CJ  H9    H  HCR6   0   0.274  -0.2793  -4.4692  -0.0997
 9CJ  H10   H  HCR6   0   0.266  -2.5944  -4.7683   0.6312
 9CJ  H15   H  HCR6   0   0.260  -2.1438   1.2556  -0.5024
 9CJ  H18   H  HCR6   0   0.272  -6.5591   0.3421   1.3320
 9CJ  H17   H  HCR6   0   0.263  -6.0051   2.6624   0.6337
 9CJ  H31   H  HOH1   0   0.472  -4.7936  -2.0544   1.0384

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
 9CJ  O4   C7    double    1.218  0.020  1.218
 9CJ  C7   C6    single    1.520  0.020  1.520
 9CJ  C7   N     single    1.352  0.020  1.352
 9CJ  C6   C5    single    1.502  0.020  1.502
 9CJ  C5   C4    aromatic  1.395  0.020  1.395
 9CJ  C5   C20   aromatic  1.385  0.020  1.385
 9CJ  C4   C3    aromatic  1.384  0.020  1.384
 9CJ  C3   C2    aromatic  1.391  0.020  1.391
 9CJ  C2   C1    aromatic  1.393  0.020  1.393
 9CJ  C20  C1    aromatic  1.396  0.020  1.396
 9CJ  C1   O     single    1.347  0.020  1.347
 9CJ  O    C     single    1.413  0.020  1.413
 9CJ  N    C8    single    1.404  0.020  1.404
 9CJ  C8   C13   aromatic  1.386  0.020  1.386
 9CJ  C8   C9    aromatic  1.397  0.020  1.397
 9CJ  C13  C12   aromatic  1.400  0.020  1.400
 9CJ  C12  C11   aromatic  1.410  0.020  1.410
 9CJ  C12  C14   single    1.479  0.020  1.479
 9CJ  C11  O3    single    1.335  0.020  1.335
 9CJ  C11  C10   aromatic  1.397  0.020  1.397
 9CJ  C10  C9    aromatic  1.376  0.020  1.376
 9CJ  C14  N1    aromatic  1.339  0.020  1.339
 9CJ  C14  C15   aromatic  1.396  0.020  1.396
 9CJ  N1   C18   aromatic  1.327  0.020  1.327
 9CJ  C18  C17   aromatic  1.381  0.020  1.381
 9CJ  C17  C16   aromatic  1.391  0.020  1.391
 9CJ  C16  C15   aromatic  1.385  0.020  1.385
 9CJ  C16  C19   single    1.531  0.020  1.531
 9CJ  C19  O2    deloc     1.243  0.020  1.243
 9CJ  C19  O1    deloc     1.243  0.020  1.243
 9CJ  O3   H31   single    0.850  0.020  0.980
 9CJ  C6   H61C  single    0.970  0.020  1.090
 9CJ  C6   H62C  single    0.970  0.020  1.090
 9CJ  N    H     single    0.860  0.020  1.020
 9CJ  C4   H4    single    0.930  0.020  1.080
 9CJ  C20  H20   single    0.930  0.020  1.080
 9CJ  C3   H3    single    0.930  0.020  1.080
 9CJ  C2   H2    single    0.930  0.020  1.080
 9CJ  C    HC1   single    0.970  0.020  1.090
 9CJ  C    HC2   single    0.970  0.020  1.090
 9CJ  C    HC3   single    0.970  0.020  1.090
 9CJ  C13  H13   single    0.930  0.020  1.080
 9CJ  C9   H9    single    0.930  0.020  1.080
 9CJ  C10  H10   single    0.930  0.020  1.080
 9CJ  C15  H15   single    0.930  0.020  1.080
 9CJ  C18  H18   single    0.930  0.020  1.080
 9CJ  C17  H17   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
 9CJ  N     C7   C6    114.11  3.000
 9CJ  N     C7   O4    124.28  3.000
 9CJ  C6    C7   O4    121.60  3.000
 9CJ  H62C  C6   H61C  106.44  3.000
 9CJ  H62C  C6   C5    110.29  3.000
 9CJ  H61C  C6   C5    110.31  3.000
 9CJ  H62C  C6   C7    106.79  3.000
 9CJ  H61C  C6   C7    111.44  3.000
 9CJ  C5    C6   C7    111.39  3.000
 9CJ  C20   C5   C4    119.47  3.000
 9CJ  C20   C5   C6    120.45  3.000
 9CJ  C4    C5   C6    120.07  3.000
 9CJ  H4    C4   C3    120.20  3.000
 9CJ  H4    C4   C5    120.06  3.000
 9CJ  C3    C4   C5    119.73  3.000
 9CJ  H3    C3   C2    119.03  3.000
 9CJ  H3    C3   C4    119.82  3.000
 9CJ  C2    C3   C4    121.15  3.000
 9CJ  H2    C2   C1    121.64  3.000
 9CJ  H2    C2   C3    119.20  3.000
 9CJ  C1    C2   C3    119.16  3.000
 9CJ  H20   C20  C1    118.95  3.000
 9CJ  H20   C20  C5    120.30  3.000
 9CJ  C1    C20  C5    120.75  3.000
 9CJ  O     C1   C20   115.98  3.000
 9CJ  O     C1   C2    124.28  3.000
 9CJ  C20   C1   C2    119.74  3.000
 9CJ  C     O    C1    118.50  3.000
 9CJ  HC3   C    HC2   108.75  3.000
 9CJ  HC3   C    HC1   108.71  3.000
 9CJ  HC2   C    HC1   108.76  3.000
 9CJ  HC3   C    O     111.99  3.000
 9CJ  HC2   C    O     111.96  3.000
 9CJ  HC1   C    O     106.56  3.000
 9CJ  H     N    C8    114.64  3.000
 9CJ  H     N    C7    116.26  3.000
 9CJ  C8    N    C7    129.04  3.000
 9CJ  C9    C8   C13   118.55  3.000
 9CJ  C9    C8   N     117.02  3.000
 9CJ  C13   C8   N     124.42  3.000
 9CJ  H13   C13  C12   119.20  3.000
 9CJ  H13   C13  C8    118.94  3.000
 9CJ  C12   C13  C8    121.86  3.000
 9CJ  C14   C12  C11   121.12  3.000
 9CJ  C14   C12  C13   120.06  3.000
 9CJ  C11   C12  C13   118.82  3.000
 9CJ  C10   C11  O3    117.51  3.000
 9CJ  C10   C11  C12   118.93  3.000
 9CJ  O3    C11  C12   123.56  3.000
 9CJ  H31   O3   C11   106.67  3.000
 9CJ  H10   C10  C9    119.91  3.000
 9CJ  H10   C10  C11   118.89  3.000
 9CJ  C9    C10  C11   121.20  3.000
 9CJ  H9    C9   C10   119.28  3.000
 9CJ  H9    C9   C8    120.08  3.000
 9CJ  C10   C9   C8    120.64  3.000
 9CJ  C15   C14  N1    120.16  3.000
 9CJ  C15   C14  C12   123.38  3.000
 9CJ  N1    C14  C12   116.45  3.000
 9CJ  C18   N1   C14   120.05  3.000
 9CJ  H18   C18  C17   121.00  3.000
 9CJ  H18   C18  N1    116.16  3.000
 9CJ  C17   C18  N1    122.84  3.000
 9CJ  H17   C17  C16   121.08  3.000
 9CJ  H17   C17  C18   120.41  3.000
 9CJ  C16   C17  C18   118.51  3.000
 9CJ  C19   C16  C15   120.62  3.000
 9CJ  C19   C16  C17   121.17  3.000
 9CJ  C15   C16  C17   118.21  3.000
 9CJ  H15   C15  C16   118.25  3.000
 9CJ  H15   C15  C14   121.52  3.000
 9CJ  C16   C15  C14   120.23  3.000
 9CJ  O1    C19  O2    127.85  3.000
 9CJ  O1    C19  C16   115.99  3.000
 9CJ  O2    C19  C16   116.16  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
 9CJ  CONST_01  C2   C3   C4   C5      0.00   0.0  0
 9CJ  CONST_02  C2   C1   C20  C5      0.00   0.0  0
 9CJ  CONST_03  C1   C20  C5   C4      0.00   0.0  0
 9CJ  CONST_04  C1   C2   C3   C4      0.00   0.0  0
 9CJ  CONST_05  C20  C5   C4   C3      0.00   0.0  0
 9CJ  CONST_06  C20  C1   C2   C3      0.00   0.0  0
 9CJ  CONST_07  C11  C12  C13  C8      0.00   0.0  0
 9CJ  CONST_08  C14  C12  C13  C8    180.00   0.0  0
 9CJ  CONST_09  C11  C10  C9   C8      0.00   0.0  0
 9CJ  CONST_10  C10  C9   C8   C13     0.00   0.0  0
 9CJ  CONST_11  C10  C11  C12  C13     0.00   0.0  0
 9CJ  CONST_12  N1   C14  C12  C13   180.00   0.0  0
 9CJ  CONST_13  C15  C14  C12  C13     0.00   0.0  0
 9CJ  CONST_14  C9   C8   C13  C12     0.00   0.0  0
 9CJ  CONST_15  C9   C10  C11  C12     0.00   0.0  0
 9CJ  CONST_16  C18  N1   C14  C12   180.00   0.0  0
 9CJ  CONST_17  C16  C15  C14  C12   180.00   0.0  0
 9CJ  CONST_18  N1   C14  C12  C11     0.00   0.0  0
 9CJ  CONST_19  C15  C14  C12  C11   180.00   0.0  0
 9CJ  CONST_20  C14  C12  C11  C10   180.00   0.0  0
 9CJ  CONST_21  C17  C18  N1   C14     0.00   0.0  0
 9CJ  CONST_22  C17  C16  C15  C14     0.00   0.0  0
 9CJ  CONST_23  C16  C15  C14  N1      0.00   0.0  0
 9CJ  CONST_24  C16  C17  C18  N1      0.00   0.0  0
 9CJ  CONST_25  C15  C14  N1   C18     0.00   0.0  0
 9CJ  CONST_26  C15  C16  C17  C18     0.00   0.0  0
 9CJ  CONST_27  C3   C4   C5   C6    180.00   0.0  0
 9CJ  CONST_28  C1   C20  C5   C6    180.00   0.0  0
 9CJ  CONST_29  O    C1   C20  C5    180.00   0.0  0
 9CJ  CONST_30  O    C1   C2   C3    180.00   0.0  0
 9CJ  CONST_31  C12  C13  C8   N     180.00   0.0  0
 9CJ  CONST_32  C10  C9   C8   N     180.00   0.0  0
 9CJ  CONST_33  O3   C11  C12  C13   180.00   0.0  0
 9CJ  CONST_34  C14  C12  C11  O3      0.00   0.0  0
 9CJ  CONST_35  C9   C10  C11  O3    180.00   0.0  0
 9CJ  CONST_36  C19  C16  C15  C14   180.00   0.0  0
 9CJ  CONST_37  C19  C16  C17  C18   180.00   0.0  0
 9CJ  CONST_38  H3   C3   C4   C5    180.00   0.0  0
 9CJ  CONST_39  H20  C20  C5   C4    180.00   0.0  0
 9CJ  CONST_40  H2   C2   C3   C4    180.00   0.0  0
 9CJ  CONST_41  H4   C4   C3   C2    180.00   0.0  0
 9CJ  CONST_42  H10  C10  C9   C8    180.00   0.0  0
 9CJ  CONST_43  H9   C9   C8   C13   180.00   0.0  0
 9CJ  CONST_44  H15  C15  C14  C12     0.00   0.0  0
 9CJ  CONST_45  H13  C13  C12  C11   180.00   0.0  0
 9CJ  CONST_46  H18  C18  N1   C14   180.00   0.0  0
 9CJ  CONST_47  H17  C17  C18  N1    180.00   0.0  0
 9CJ  CONST_48  C13  C8   N    C7      0.00   0.0  0
 9CJ  CONST_49  C9   C8   N    C7    180.00   0.0  0
 9CJ  CONST_50  H    N    C8   C13   180.00   0.0  0
 9CJ  CONST_51  C8   N    C7   O4      0.00   0.0  0
 9CJ  CONST_52  C8   N    C7   C6    180.00   0.0  0
 9CJ  Var_01    C4   C5   C6   C7     92.00  30.0  2
 9CJ  Var_02    O2   C19  C16  C17   178.09  30.0  2
 9CJ  Var_03    C5   C6   C7   O4     47.30  30.0  3
 9CJ  Var_04    HC1  C    O    C1   -179.69  30.0  3

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
 9CJ  plan-1  C6   0.020
 9CJ  plan-1  C5   0.020
 9CJ  plan-1  C4   0.020
 9CJ  plan-1  C3   0.020
 9CJ  plan-1  C2   0.020
 9CJ  plan-1  C20  0.020
 9CJ  plan-1  C1   0.020
 9CJ  plan-1  O    0.020
 9CJ  plan-1  H4   0.020
 9CJ  plan-1  H20  0.020
 9CJ  plan-1  H3   0.020
 9CJ  plan-1  H2   0.020
 9CJ  plan-2  N    0.020
 9CJ  plan-2  C8   0.020
 9CJ  plan-2  C13  0.020
 9CJ  plan-2  C12  0.020
 9CJ  plan-2  C11  0.020
 9CJ  plan-2  O3   0.020
 9CJ  plan-2  C10  0.020
 9CJ  plan-2  C9   0.020
 9CJ  plan-2  C14  0.020
 9CJ  plan-2  H13  0.020
 9CJ  plan-2  H9   0.020
 9CJ  plan-2  H10  0.020
 9CJ  plan-3  C12  0.020
 9CJ  plan-3  C14  0.020
 9CJ  plan-3  N1   0.020
 9CJ  plan-3  C18  0.020
 9CJ  plan-3  C17  0.020
 9CJ  plan-3  C16  0.020
 9CJ  plan-3  C15  0.020
 9CJ  plan-3  C19  0.020
 9CJ  plan-3  H15  0.020
 9CJ  plan-3  H18  0.020
 9CJ  plan-3  H17  0.020
 9CJ  plan-4  O4   0.020
 9CJ  plan-4  C7   0.020
 9CJ  plan-4  C6   0.020
 9CJ  plan-4  N    0.020
 9CJ  plan-4  C8   0.020
 9CJ  plan-4  H    0.020
 9CJ  plan-5  C16  0.020
 9CJ  plan-5  C19  0.020
 9CJ  plan-5  O2   0.020
 9CJ  plan-5  O1   0.020

