# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 12:18:37 2021
#   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  30  19  .  2022-08-11  2023-02-16
;
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  -0.012  -49.6287  -29.4290   5.9511
 W6M  C13   C  CR16  0  -0.257  -46.8780  -29.2963   5.5212
 W6M  C15   C  C     0   0.540  -47.2902  -28.7308   3.0977
 W6M  C02   C  CR5   0   0.309  -53.9709  -27.1560   8.6418
 W6M  C05   C  CR5   0   0.521  -53.5491  -29.0127   7.8232
 W6M  C06   C  CH2   0  -0.402  -52.9900  -30.3220   7.3745
 W6M  C08   C  C     0   0.558  -51.1105  -29.4644   6.1288
 W6M  C11   C  CR16  0  -0.282  -48.7395  -29.6620   6.9981
 W6M  C12   C  CR16  0  -0.226  -47.3720  -29.5923   6.7813
 W6M  C14   C  CR6   0  -0.063  -47.7608  -29.0563   4.4691
 W6M  C18   C  CR16  0  -0.282  -49.1313  -29.1135   4.6931
 W6M  N03   N  N     0  -0.159  -55.0931  -27.5170   8.1010
 W6M  N07   N  NH1   0  -0.651  -51.5799  -30.2353   7.1254
 W6M  N19   N  N     0  -0.444  -52.9701  -28.0766   8.4915
 W6M  O04   O  O     0  -0.331  -54.8158  -28.7465   7.5553
 W6M  O09   O  O     0  -0.473  -51.8594  -28.8282   5.4028
 W6M  O16   O  OH1   0  -0.592  -45.9705  -28.6762   3.0058
 W6M  O17   O  O     0  -0.434  -48.0306  -28.5346   2.1648
 W6M  H131  H  HCR6  0   0.278  -45.8085  -29.2513   5.3710
 W6M  H011  H  HCH3  0   0.263  -54.7207  -25.3040   9.3768
 W6M  H012  H  HCH3  0   0.267  -53.4579  -26.0427  10.3734
 W6M  H013  H  HCH3  0   0.268  -53.0307  -25.2674   8.8534
 W6M  H061  H  HCH2  0   0.293  -53.5390  -30.6705   6.4971
 W6M  H062  H  HCH2  0   0.317  -53.1489  -31.0578   8.1639
 W6M  H111  H  HCR6  0   0.272  -49.0976  -29.8754   7.9971
 W6M  H121  H  HCR6  0   0.277  -46.6882  -29.7657   7.6007
 W6M  H181  H  HCR6  0   0.270  -49.8174  -28.9192   3.8798
 W6M  H071  H  HNH1  0   0.423  -50.9673  -30.8290   7.6583
 W6M  H1    H  HOH1  0   0.490  -45.7084  -28.4555   2.0995
 W6M  C01   C  CH3   0  -0.739  -53.7918  -25.8682   9.3510

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   double    1.207  0.020  1.207
 W6M  O16  C15   single    1.324  0.020  1.324
 W6M  C15  C14   single    1.486  0.020  1.486
 W6M  C14  C18   aromatic  1.390  0.020  1.390
 W6M  C14  C13   aromatic  1.394  0.020  1.394
 W6M  C18  C10   aromatic  1.389  0.020  1.389
 W6M  O09  C08   double    1.222  0.020  1.222
 W6M  C13  C12   aromatic  1.385  0.020  1.385
 W6M  C10  C08   single    1.493  0.020  1.493
 W6M  C10  C11   aromatic  1.393  0.020  1.393
 W6M  C08  N07   single    1.345  0.020  1.345
 W6M  C12  C11   aromatic  1.386  0.020  1.386
 W6M  N07  C06   single    1.434  0.020  1.434
 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
 W6M  O16  H1    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
 W6M  C18   C10  C11   119.34  3.000
 W6M  C11   C10  C08   122.69  3.000
 W6M  C18   C10  C08   117.95  3.000
 W6M  H131  C13  C14   120.96  3.000
 W6M  H131  C13  C12   119.21  3.000
 W6M  C14   C13  C12   119.83  3.000
 W6M  O17   C15  O16   123.44  3.000
 W6M  O16   C15  C14   112.88  3.000
 W6M  O17   C15  C14   123.68  3.000
 W6M  N19   C02  N03   113.57  3.000
 W6M  N19   C02  C01   123.32  3.000
 W6M  N03   C02  C01   123.11  3.000
 W6M  O04   C05  N19   112.93  3.000
 W6M  N19   C05  C06   128.70  3.000
 W6M  O04   C05  C06   118.34  3.000
 W6M  H062  C06  H061  107.04  3.000
 W6M  H062  C06  N07   108.04  3.000
 W6M  H061  C06  N07   111.96  3.000
 W6M  H062  C06  C05   108.64  3.000
 W6M  H061  C06  C05   109.45  3.000
 W6M  N07   C06  C05   111.55  3.000
 W6M  O09   C08  N07   121.67  3.000
 W6M  N07   C08  C10   116.64  3.000
 W6M  O09   C08  C10   121.69  3.000
 W6M  H111  C11  C12   118.72  3.000
 W6M  H111  C11  C10   121.02  3.000
 W6M  C12   C11  C10   120.24  3.000
 W6M  H121  C12  C11   119.82  3.000
 W6M  H121  C12  C13   119.87  3.000
 W6M  C11   C12  C13   120.31  3.000
 W6M  C18   C14  C15   118.04  3.000
 W6M  C18   C14  C13   119.71  3.000
 W6M  C15   C14  C13   122.25  3.000
 W6M  H181  C18  C14   119.80  3.000
 W6M  H181  C18  C10   119.64  3.000
 W6M  C14   C18  C10   120.56  3.000
 W6M  O04   N03  C02   103.90  3.000
 W6M  H071  N07  C08   121.23  3.000
 W6M  H071  N07  C06   118.10  3.000
 W6M  C08   N07  C06   120.43  3.000
 W6M  C05   N19  C02   102.55  3.000
 W6M  N03   O04  C05   107.05  3.000
 W6M  H1    O16  C15   110.12  3.000
 W6M  H013  C01  H012  107.62  3.000
 W6M  H013  C01  H011  108.75  3.000
 W6M  H012  C01  H011  108.83  3.000
 W6M  H013  C01  C02   110.18  3.000
 W6M  H012  C01  C02   110.31  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  H1    O16  C15  C14  180.00   0.0  0
 W6M  CONST_27  O09   C08  N07  C06    0.00   0.0  0
 W6M  Var_01    O17   C15  C14  C13  179.06  30.0  3
 W6M  Var_02    O09   C08  C10  C11  153.54  30.0  2
 W6M  Var_03    O04   C05  C06  N07  151.62  30.0  2
 W6M  Var_04    H011  C01  C02  N03    1.76  30.0  2
 W6M  Var_05    C08   N07  C06  C05  -65.27  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
 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
 W6M  plan-4  H1    0.020

