# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 00:03:36 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 2-[5-[(5-methyl-1,2-oxazol-3-yl)carbonylamino]-2-oxidanyl-phenyl]pyridine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1onc(c1)C(=O)Nc2ccc(O)c(c2)c3cc(ccn3)C(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
 6Z1  6Z1  '2-[5-[(5-methyl-1,2-oxazol-3-yl)carbonylamino]-2-oxidanyl-phenyl]pyridine-4-carboxylic acid'  ligand  37  25  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6Z1
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
 6Z1  O3   O  O      0  -0.453   3.7663  -2.0170  -0.3649
 6Z1  C4   C  C      0   0.528   3.3689  -0.8808  -0.1793
 6Z1  C3   C  CR5    0   0.142   4.3467   0.2145   0.0678
 6Z1  C2   C  CR15   0  -0.491   5.7513   0.0863   0.1446
 6Z1  N2   N  N      0  -0.173   3.9711   1.4490   0.2434
 6Z1  O4   O  O      0  -0.322   5.1009   2.1603   0.4409
 6Z1  C1   C  CR5    0   0.431   6.1706   1.3530   0.3837
 6Z1  C    C  CH3    0  -0.747   7.5044   1.9595   0.5817
 6Z1  N    N  NH1    0  -0.759   2.0823  -0.4840  -0.1714
 6Z1  C5   C  CR6    0   0.383   0.9253  -1.2607  -0.3275
 6Z1  C10  C  CR16   0  -0.392  -0.2873  -0.6544  -0.0073
 6Z1  C9   C  CR6    0  -0.028  -1.5016  -1.3174  -0.1235
 6Z1  C8   C  CR6    0   0.318  -1.5044  -2.6381  -0.5903
 6Z1  O2   O  OH1    0  -0.617  -2.6842  -3.2664  -0.7439
 6Z1  C7   C  CR16   0  -0.374  -0.2958  -3.2441  -0.9136
 6Z1  C6   C  CR16   0  -0.305   0.9114  -2.5749  -0.7865
 6Z1  C11  C  CR6    0   0.225  -2.7506  -0.6086   0.2382
 6Z1  N1   N  N      0  -0.414  -3.5916  -1.2262   1.0662
 6Z1  C15  C  CR16   0  -0.083  -4.6941  -0.5816   1.4236
 6Z1  C14  C  CR16   0  -0.357  -5.0175   0.6942   0.9876
 6Z1  C13  C  CR6    0   0.005  -4.1503   1.3459   0.1200
 6Z1  C12  C  CR16   0  -0.363  -2.9984   0.6684  -0.2584
 6Z1  C16  C  C      0   0.403  -4.4503   2.7499  -0.4045
 6Z1  O1   O  O      0  -0.583  -3.6290   3.2225  -1.2100
 6Z1  O    O  OC    -1  -0.584  -5.4870   3.2846   0.0257
 6Z1  H    H  HNH1   0   0.425   1.9210   0.4949   0.0233
 6Z1  H2   H  HCR5   0   0.288   6.3521  -0.8004   0.0410
 6Z1  HC1  H  HCH3   0   0.273   7.6962   2.7429  -0.1519
 6Z1  HC2  H  HCH3   0   0.274   7.5913   2.4024   1.5746
 6Z1  HC3  H  HCH3   0   0.271   8.2719   1.1968   0.4783
 6Z1  H10  H  HCR6   0   0.274  -0.2889   0.3647   0.3635
 6Z1  H6   H  HCR6   0   0.284   1.8218  -3.0869  -1.0518
 6Z1  H7   H  HCR6   0   0.275  -0.2898  -4.2627  -1.2858
 6Z1  H12  H  HCR6   0   0.257  -2.3003   1.1316  -0.9429
 6Z1  H15  H  HCR6   0   0.256  -5.3583  -1.1083   2.1007
 6Z1  H14  H  HCR6   0   0.256  -5.9307   1.1668   1.3213
 6Z1  H16  H  HOH1   0   0.476  -2.5443  -4.1477  -1.1084

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
 6Z1  O3   C4   double    1.218  0.020  1.218
 6Z1  C4   C3   single    1.489  0.020  1.489
 6Z1  C4   N    single    1.346  0.020  1.346
 6Z1  C3   C2   aromatic  1.413  0.020  1.413
 6Z1  C3   N2   aromatic  1.302  0.020  1.302
 6Z1  C2   C1   aromatic  1.356  0.020  1.356
 6Z1  N2   O4   aromatic  1.350  0.020  1.350
 6Z1  O4   C1   aromatic  1.341  0.020  1.341
 6Z1  C1   C    single    1.479  0.020  1.479
 6Z1  N    C5   single    1.402  0.020  1.402
 6Z1  C5   C10  aromatic  1.393  0.020  1.393
 6Z1  C5   C6   aromatic  1.392  0.020  1.392
 6Z1  C10  C9   aromatic  1.388  0.020  1.388
 6Z1  C9   C8   aromatic  1.401  0.020  1.401
 6Z1  C9   C11  single    1.481  0.020  1.481
 6Z1  C8   O2   single    1.346  0.020  1.346
 6Z1  C8   C7   aromatic  1.390  0.020  1.390
 6Z1  C7   C6   aromatic  1.386  0.020  1.386
 6Z1  C11  N1   aromatic  1.332  0.020  1.332
 6Z1  C11  C12  aromatic  1.392  0.020  1.392
 6Z1  N1   C15  aromatic  1.326  0.020  1.326
 6Z1  C15  C14  aromatic  1.386  0.020  1.386
 6Z1  C14  C13  aromatic  1.389  0.020  1.389
 6Z1  C13  C12  aromatic  1.389  0.020  1.389
 6Z1  C13  C16  single    1.528  0.020  1.528
 6Z1  C16  O1   deloc     1.244  0.020  1.244
 6Z1  C16  O    deloc     1.243  0.020  1.243
 6Z1  O2   H16  single    0.850  0.020  0.980
 6Z1  N    H    single    0.860  0.020  1.020
 6Z1  C2   H2   single    0.930  0.020  1.080
 6Z1  C    HC1  single    0.970  0.020  1.090
 6Z1  C    HC2  single    0.970  0.020  1.090
 6Z1  C    HC3  single    0.970  0.020  1.090
 6Z1  C10  H10  single    0.930  0.020  1.080
 6Z1  C6   H6   single    0.930  0.020  1.080
 6Z1  C7   H7   single    0.930  0.020  1.080
 6Z1  C12  H12  single    0.930  0.020  1.080
 6Z1  C15  H15  single    0.930  0.020  1.080
 6Z1  C14  H14  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
 6Z1  N    C4   C3   114.19  3.000
 6Z1  N    C4   O3   125.99  3.000
 6Z1  C3   C4   O3   119.82  3.000
 6Z1  N2   C3   C2   111.44  3.000
 6Z1  N2   C3   C4   122.03  3.000
 6Z1  C2   C3   C4   126.53  3.000
 6Z1  H2   C2   C1   127.90  3.000
 6Z1  H2   C2   C3   128.66  3.000
 6Z1  C1   C2   C3   103.43  3.000
 6Z1  O4   N2   C3   106.14  3.000
 6Z1  C1   O4   N2   110.12  3.000
 6Z1  C    C1   O4   117.83  3.000
 6Z1  C    C1   C2   133.31  3.000
 6Z1  O4   C1   C2   108.86  3.000
 6Z1  HC3  C    HC2  108.38  3.000
 6Z1  HC3  C    HC1  108.42  3.000
 6Z1  HC2  C    HC1  107.86  3.000
 6Z1  HC3  C    C1   109.65  3.000
 6Z1  HC2  C    C1   111.13  3.000
 6Z1  HC1  C    C1   111.30  3.000
 6Z1  H    N    C5   115.21  3.000
 6Z1  H    N    C4   116.04  3.000
 6Z1  C5   N    C4   128.65  3.000
 6Z1  C6   C5   C10  118.56  3.000
 6Z1  C6   C5   N    124.59  3.000
 6Z1  C10  C5   N    116.85  3.000
 6Z1  H10  C10  C9   118.43  3.000
 6Z1  H10  C10  C5   119.27  3.000
 6Z1  C9   C10  C5   122.30  3.000
 6Z1  C11  C9   C8   122.07  3.000
 6Z1  C11  C9   C10  119.25  3.000
 6Z1  C8   C9   C10  118.68  3.000
 6Z1  C7   C8   O2   122.15  3.000
 6Z1  C7   C8   C9   119.13  3.000
 6Z1  O2   C8   C9   118.69  3.000
 6Z1  H16  O2   C8   110.06  3.000
 6Z1  H7   C7   C6   118.69  3.000
 6Z1  H7   C7   C8   119.62  3.000
 6Z1  C6   C7   C8   121.69  3.000
 6Z1  H6   C6   C7   118.94  3.000
 6Z1  H6   C6   C5   121.41  3.000
 6Z1  C7   C6   C5   119.65  3.000
 6Z1  C12  C11  N1   122.31  3.000
 6Z1  C12  C11  C9   120.13  3.000
 6Z1  N1   C11  C9   117.54  3.000
 6Z1  C15  N1   C11  117.84  3.000
 6Z1  H15  C15  C14  120.01  3.000
 6Z1  H15  C15  N1   116.18  3.000
 6Z1  C14  C15  N1   123.81  3.000
 6Z1  H14  C14  C13  121.00  3.000
 6Z1  H14  C14  C15  120.15  3.000
 6Z1  C13  C14  C15  118.85  3.000
 6Z1  C16  C13  C12  121.15  3.000
 6Z1  C16  C13  C14  121.52  3.000
 6Z1  C12  C13  C14  117.33  3.000
 6Z1  H12  C12  C13  119.91  3.000
 6Z1  H12  C12  C11  120.23  3.000
 6Z1  C13  C12  C11  119.85  3.000
 6Z1  O    C16  O1   127.69  3.000
 6Z1  O    C16  C13  116.10  3.000
 6Z1  O1   C16  C13  116.21  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
 6Z1  CONST_01  O4   C1   C2   C3      0.00   0.0  0
 6Z1  CONST_02  C1   O4   N2   C3      0.00   0.0  0
 6Z1  CONST_03  O4   N2   C3   C2      0.00   0.0  0
 6Z1  CONST_04  N2   O4   C1   C2      0.00   0.0  0
 6Z1  CONST_05  C1   C2   C3   N2      0.00   0.0  0
 6Z1  CONST_06  C8   C9   C10  C5      0.00   0.0  0
 6Z1  CONST_07  C11  C9   C10  C5    180.00   0.0  0
 6Z1  CONST_08  C8   C7   C6   C5      0.00   0.0  0
 6Z1  CONST_09  C7   C6   C5   C10     0.00   0.0  0
 6Z1  CONST_10  C7   C8   C9   C10     0.00   0.0  0
 6Z1  CONST_13  C6   C5   C10  C9      0.00   0.0  0
 6Z1  CONST_14  C6   C7   C8   C9      0.00   0.0  0
 6Z1  CONST_15  C15  N1   C11  C9    180.00   0.0  0
 6Z1  CONST_16  C13  C12  C11  C9    180.00   0.0  0
 6Z1  CONST_19  C11  C9   C8   C7    180.00   0.0  0
 6Z1  CONST_20  C14  C15  N1   C11     0.00   0.0  0
 6Z1  CONST_21  C14  C13  C12  C11     0.00   0.0  0
 6Z1  CONST_22  C13  C12  C11  N1      0.00   0.0  0
 6Z1  CONST_23  C13  C14  C15  N1      0.00   0.0  0
 6Z1  CONST_24  C12  C11  N1   C15     0.00   0.0  0
 6Z1  CONST_25  C12  C13  C14  C15     0.00   0.0  0
 6Z1  CONST_26  C1   C2   C3   C4    180.00   0.0  0
 6Z1  CONST_27  O4   N2   C3   C4    180.00   0.0  0
 6Z1  CONST_28  C    C1   C2   C3    180.00   0.0  0
 6Z1  CONST_29  C    C1   O4   N2    180.00   0.0  0
 6Z1  CONST_30  C9   C10  C5   N     180.00   0.0  0
 6Z1  CONST_31  C7   C6   C5   N     180.00   0.0  0
 6Z1  CONST_32  O2   C8   C9   C10   180.00   0.0  0
 6Z1  CONST_33  C11  C9   C8   O2      0.00   0.0  0
 6Z1  CONST_34  C6   C7   C8   O2    180.00   0.0  0
 6Z1  CONST_35  C16  C13  C12  C11   180.00   0.0  0
 6Z1  CONST_36  C16  C13  C14  C15   180.00   0.0  0
 6Z1  CONST_37  H2   C2   C3   N2    180.00   0.0  0
 6Z1  CONST_38  H7   C7   C6   C5    180.00   0.0  0
 6Z1  CONST_39  H6   C6   C5   C10   180.00   0.0  0
 6Z1  CONST_40  H12  C12  C11  C9      0.00   0.0  0
 6Z1  CONST_41  H10  C10  C9   C8    180.00   0.0  0
 6Z1  CONST_42  H15  C15  N1   C11   180.00   0.0  0
 6Z1  CONST_43  H14  C14  C15  N1    180.00   0.0  0
 6Z1  CONST_44  C5   N    C4   C3    180.00   0.0  0
 6Z1  CONST_45  C10  C5   N    C4    180.00   0.0  0
 6Z1  CONST_46  C6   C5   N    C4      0.00   0.0  0
 6Z1  CONST_47  H    N    C5   C10     0.00   0.0  0
 6Z1  CONST_48  C5   N    C4   O3      0.00   0.0  0
 6Z1  Var_01    C2   C3   C4   O3     -1.47  30.0  2
 6Z1  Var_02    O1   C16  C13  C14  -177.71  30.0  2
 6Z1  Var_03    HC1  C    C1   C2    121.87  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
 6Z1  plan-1  C4   0.020
 6Z1  plan-1  C3   0.020
 6Z1  plan-1  C2   0.020
 6Z1  plan-1  N2   0.020
 6Z1  plan-1  O4   0.020
 6Z1  plan-1  C1   0.020
 6Z1  plan-1  C    0.020
 6Z1  plan-1  H2   0.020
 6Z1  plan-2  N    0.020
 6Z1  plan-2  C5   0.020
 6Z1  plan-2  C10  0.020
 6Z1  plan-2  C9   0.020
 6Z1  plan-2  C8   0.020
 6Z1  plan-2  O2   0.020
 6Z1  plan-2  C7   0.020
 6Z1  plan-2  C6   0.020
 6Z1  plan-2  C11  0.020
 6Z1  plan-2  H10  0.020
 6Z1  plan-2  H6   0.020
 6Z1  plan-2  H7   0.020
 6Z1  plan-3  C9   0.020
 6Z1  plan-3  C11  0.020
 6Z1  plan-3  N1   0.020
 6Z1  plan-3  C15  0.020
 6Z1  plan-3  C14  0.020
 6Z1  plan-3  C13  0.020
 6Z1  plan-3  C12  0.020
 6Z1  plan-3  C16  0.020
 6Z1  plan-3  H12  0.020
 6Z1  plan-3  H15  0.020
 6Z1  plan-3  H14  0.020
 6Z1  plan-4  O3   0.020
 6Z1  plan-4  C4   0.020
 6Z1  plan-4  C3   0.020
 6Z1  plan-4  N    0.020
 6Z1  plan-4  C5   0.020
 6Z1  plan-4  H    0.020
 6Z1  plan-5  C13  0.020
 6Z1  plan-5  C16  0.020
 6Z1  plan-5  O1   0.020
 6Z1  plan-5  O    0.020

