# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 13:08:54 2022
#   Inital geometry file: a 81 line input string
#   Ligand name: 3-{[(3-methyl-1,2,4-oxadiazol-5-yl)methyl]carbamoyl}benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1noc(CNC(=O)c2cccc(c2)C(O)=O)n1
#
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
 W6M  W6M  '3-{[(3-methyl-1,2,4-oxadiazol-5-yl)methyl]carbamoyl}benzoic acid'  ligand  29  19  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_W6M
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
 W6M  C10   C  CR6    0  -0.009  -49.6226  -29.3352   5.8923
 W6M  C13   C  CR16   0  -0.288  -46.8781  -29.1490   5.5186
 W6M  C15   C  C      0   0.401  -47.1605  -28.7715   3.0186
 W6M  C02   C  CR5    0   0.307  -53.9934  -27.2530   8.7357
 W6M  C05   C  CR5    0   0.520  -53.5600  -29.0511   7.7995
 W6M  C06   C  CH2    0  -0.404  -52.9870  -30.3151   7.2475
 W6M  C08   C  C      0   0.533  -51.1042  -29.3987   6.0386
 W6M  C11   C  CR16   0  -0.301  -48.7621  -29.4622   6.9810
 W6M  C12   C  CR16   0  -0.229  -47.3919  -29.3648   6.7892
 W6M  C14   C  CR6    0  -0.081  -47.7236  -29.0138   4.4196
 W6M  C18   C  CR16   0  -0.321  -49.0951  -29.0987   4.6259
 W6M  N03   N  N      0  -0.155  -55.1397  -27.6432   8.2717
 W6M  N07   N  NH1    0  -0.646  -51.5780  -30.2029   7.0122
 W6M  N19   N  N      0  -0.445  -52.9685  -28.1168   8.4598
 W6M  O04   O  O      0  -0.330  -54.8554  -28.8331   7.6479
 W6M  O09   O  O      0  -0.472  -51.8562  -28.7640   5.3139
 W6M  O16   O  OC    -1  -0.584  -45.9209  -28.7021   2.9284
 W6M  O17   O  O      0  -0.583  -47.9937  -28.6684   2.0992
 W6M  H131  H  HCR6   0   0.248  -45.8079  -29.0798   5.3752
 W6M  H011  H  HCH3   0   0.262  -54.7557  -25.4612   9.5960
 W6M  H012  H  HCH3   0   0.266  -53.4161  -26.2009  10.4852
 W6M  H013  H  HCH3   0   0.267  -53.1002  -25.3455   8.9814
 W6M  H061  H  HCH2   0   0.291  -53.5289  -30.5932   6.3407
 W6M  H062  H  HCH2   0   0.315  -53.1503  -31.1161   7.9705
 W6M  H111  H  HCR6   0   0.257  -49.1458  -29.6068   7.9835
 W6M  H121  H  HCR6   0   0.255  -46.7251  -29.4528   7.6372
 W6M  H181  H  HCR6   0   0.245  -49.7616  -28.9891   3.7809
 W6M  H071  H  HNH1   0   0.417  -50.9587  -30.7882   7.5472
 W6M  C01   C  CH3    0  -0.738  -53.8130  -25.9925   9.4919

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
 W6M  O17  C15   deloc     1.245  0.020  1.245
 W6M  O16  C15   deloc     1.245  0.020  1.245
 W6M  C15  C14   single    1.529  0.020  1.529
 W6M  C14  C18   aromatic  1.389  0.020  1.389
 W6M  C14  C13   aromatic  1.393  0.020  1.393
 W6M  C18  C10   aromatic  1.392  0.020  1.392
 W6M  O09  C08   double    1.222  0.020  1.222
 W6M  C13  C12   aromatic  1.387  0.020  1.387
 W6M  C10  C08   single    1.490  0.020  1.490
 W6M  C10  C11   aromatic  1.394  0.020  1.394
 W6M  C08  N07   single    1.349  0.020  1.349
 W6M  C12  C11   aromatic  1.387  0.020  1.387
 W6M  N07  C06   single    1.433  0.020  1.433
 W6M  O04  C05   aromatic  1.322  0.020  1.322
 W6M  O04  N03   aromatic  1.373  0.020  1.373
 W6M  C06  C05   single    1.493  0.020  1.493
 W6M  C05  N19   aromatic  1.288  0.020  1.288
 W6M  N03  C02   aromatic  1.297  0.020  1.297
 W6M  N19  C02   aromatic  1.368  0.020  1.368
 W6M  C02  C01   single    1.481  0.020  1.481
 W6M  C13  H131  single    0.930  0.020  1.080
 W6M  C01  H011  single    0.970  0.020  1.090
 W6M  C01  H012  single    0.970  0.020  1.090
 W6M  C01  H013  single    0.970  0.020  1.090
 W6M  C06  H061  single    0.970  0.020  1.090
 W6M  C06  H062  single    0.970  0.020  1.090
 W6M  C11  H111  single    0.930  0.020  1.080
 W6M  C12  H121  single    0.930  0.020  1.080
 W6M  C18  H181  single    0.930  0.020  1.080
 W6M  N07  H071  single    0.860  0.020  1.020

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
 W6M  C18   C10  C11   119.49  3.000
 W6M  C11   C10  C08   122.23  3.000
 W6M  C18   C10  C08   118.25  3.000
 W6M  H131  C13  C14   119.31  3.000
 W6M  H131  C13  C12   119.84  3.000
 W6M  C14   C13  C12   120.84  3.000
 W6M  O17   C15  O16   127.46  3.000
 W6M  O16   C15  C14   116.23  3.000
 W6M  O17   C15  C14   116.31  3.000
 W6M  N19   C02  N03   113.58  3.000
 W6M  N19   C02  C01   123.30  3.000
 W6M  N03   C02  C01   123.13  3.000
 W6M  O04   C05  N19   112.90  3.000
 W6M  N19   C05  C06   128.85  3.000
 W6M  O04   C05  C06   118.23  3.000
 W6M  H062  C06  H061  106.79  3.000
 W6M  H062  C06  N07   108.26  3.000
 W6M  H061  C06  N07   111.80  3.000
 W6M  H062  C06  C05   108.60  3.000
 W6M  H061  C06  C05   109.39  3.000
 W6M  N07   C06  C05   111.82  3.000
 W6M  O09   C08  N07   121.44  3.000
 W6M  N07   C08  C10   116.46  3.000
 W6M  O09   C08  C10   122.11  3.000
 W6M  H111  C11  C12   119.17  3.000
 W6M  H111  C11  C10   121.10  3.000
 W6M  C12   C11  C10   119.71  3.000
 W6M  H121  C12  C11   119.64  3.000
 W6M  H121  C12  C13   120.13  3.000
 W6M  C11   C12  C13   120.23  3.000
 W6M  C18   C14  C15   120.60  3.000
 W6M  C18   C14  C13   118.43  3.000
 W6M  C15   C14  C13   120.97  3.000
 W6M  H181  C18  C14   119.08  3.000
 W6M  H181  C18  C10   119.62  3.000
 W6M  C14   C18  C10   121.29  3.000
 W6M  O04   N03  C02   103.90  3.000
 W6M  H071  N07  C08   120.96  3.000
 W6M  H071  N07  C06   118.19  3.000
 W6M  C08   N07  C06   120.71  3.000
 W6M  C05   N19  C02   102.55  3.000
 W6M  N03   O04  C05   107.07  3.000
 W6M  H013  C01  H012  107.60  3.000
 W6M  H013  C01  H011  108.78  3.000
 W6M  H012  C01  H011  108.79  3.000
 W6M  H013  C01  C02   110.23  3.000
 W6M  H012  C01  C02   110.30  3.000
 W6M  H011  C01  C02   111.06  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
 W6M  CONST_01  C13   C14  C18  C10    0.00   0.0  0
 W6M  CONST_02  C13   C12  C11  C10    0.00   0.0  0
 W6M  CONST_03  C05   O04  N03  C02    0.00   0.0  0
 W6M  CONST_04  O04   C05  N19  C02    0.00   0.0  0
 W6M  CONST_05  N03   C02  N19  C05    0.00   0.0  0
 W6M  CONST_06  C14   C18  C10  C11    0.00   0.0  0
 W6M  CONST_07  C14   C13  C12  C11    0.00   0.0  0
 W6M  CONST_08  C18   C14  C13  C12    0.00   0.0  0
 W6M  CONST_09  C18   C10  C11  C12    0.00   0.0  0
 W6M  CONST_10  N19   C05  O04  N03    0.00   0.0  0
 W6M  CONST_11  O04   N03  C02  N19    0.00   0.0  0
 W6M  CONST_12  C15   C14  C18  C10  180.00   0.0  0
 W6M  CONST_13  C12   C13  C14  C15  180.00   0.0  0
 W6M  CONST_14  O04   N03  C02  C01  180.00   0.0  0
 W6M  CONST_15  C05   N19  C02  C01  180.00   0.0  0
 W6M  CONST_16  C06   C05  N19  C02  180.00   0.0  0
 W6M  CONST_17  N03   O04  C05  C06  180.00   0.0  0
 W6M  CONST_18  C14   C18  C10  C08  180.00   0.0  0
 W6M  CONST_19  C12   C11  C10  C08  180.00   0.0  0
 W6M  CONST_20  H121  C12  C11  C10  180.00   0.0  0
 W6M  CONST_21  H181  C18  C14  C13  180.00   0.0  0
 W6M  CONST_22  H111  C11  C12  C13  180.00   0.0  0
 W6M  CONST_23  H131  C13  C12  C11  180.00   0.0  0
 W6M  CONST_24  C06   N07  C08  C10  180.00   0.0  0
 W6M  CONST_25  H071  N07  C08  C10    0.00   0.0  0
 W6M  CONST_26  O09   C08  N07  C06    0.00   0.0  0
 W6M  Var_01    O17   C15  C14  C13  179.76  30.0  2
 W6M  Var_02    O09   C08  C10  C11  147.92  30.0  2
 W6M  Var_03    O04   C05  C06  N07  157.51  30.0  2
 W6M  Var_04    H011  C01  C02  N03    0.01  30.0  2
 W6M  Var_05    C08   N07  C06  C05  -68.47  30.0  1

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
 W6M  plan-1  C02   0.020
 W6M  plan-1  C05   0.020
 W6M  plan-1  C06   0.020
 W6M  plan-1  N03   0.020
 W6M  plan-1  N19   0.020
 W6M  plan-1  O04   0.020
 W6M  plan-1  C01   0.020
 W6M  plan-2  C10   0.020
 W6M  plan-2  C13   0.020
 W6M  plan-2  C15   0.020
 W6M  plan-2  C08   0.020
 W6M  plan-2  C11   0.020
 W6M  plan-2  C12   0.020
 W6M  plan-2  C14   0.020
 W6M  plan-2  C18   0.020
 W6M  plan-2  H131  0.020
 W6M  plan-2  H111  0.020
 W6M  plan-2  H121  0.020
 W6M  plan-2  H181  0.020
 W6M  plan-3  C10   0.020
 W6M  plan-3  C06   0.020
 W6M  plan-3  C08   0.020
 W6M  plan-3  N07   0.020
 W6M  plan-3  O09   0.020
 W6M  plan-3  H071  0.020
 W6M  plan-4  C15   0.020
 W6M  plan-4  C14   0.020
 W6M  plan-4  O16   0.020
 W6M  plan-4  O17   0.020

