# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 16:26:10 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: N-[3-(methoxymethyl)phenyl]-N'-(5-methyl-1,2-oxazol-3-yl)urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCc1cccc(NC(=O)Nc2cc(C)on2)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
 N6D  N6D  N-[3-(methoxymethyl)phenyl]-N'-(5-methyl-1,2-oxazol-3-yl)urea  ligand  34  19  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_N6D
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
 N6D  N1   N  NH1   0  -0.777   1.9730   0.7827   0.0314
 N6D  C4   C  CR16  0  -0.235  -2.8126  -2.3515   0.6268
 N6D  C5   C  CR16  0  -0.322  -1.5528  -1.7747   0.5290
 N6D  C6   C  CR6   0   0.397  -1.4437  -0.3925   0.3763
 N6D  C7   C  C     0   0.753   1.0125  -0.1997   0.0758
 N6D  C8   C  CR5   0   0.497   3.3141   0.5726  -0.1847
 N6D  C10  C  CR5   0   0.440   5.3143  -0.1997  -0.5497
 N6D  N    N  NH1   0  -0.794  -0.2362   0.3046   0.2874
 N6D  C    C  CH3   0  -0.398  -6.7015   1.4003  -1.1861
 N6D  O    O  O2    0  -0.482  -5.5375   0.6345  -0.9998
 N6D  C11  C  CH3   0  -0.747   6.5850  -0.9155  -0.8000
 N6D  C12  C  CR16  0  -0.402  -2.6096   0.3768   0.3331
 N6D  C2   C  CR6   0   0.100  -3.8638  -0.2037   0.4385
 N6D  C3   C  CR16  0  -0.309  -3.9649  -1.5845   0.5819
 N6D  C9   C  CR15  0  -0.517   4.0381  -0.6301  -0.4036
 N6D  N2   N  N     0  -0.228   4.1009   1.6155  -0.2023
 N6D  O1   O  O     0  -0.487   1.2700  -1.3801  -0.0595
 N6D  O2   O  O     0  -0.339   5.3568   1.1277  -0.4313
 N6D  H1   H  HNH1  0   0.418   1.7067   1.7468   0.1704
 N6D  H2   H  HCR6  0   0.259  -2.8851  -3.4248   0.7459
 N6D  H3   H  HCR6  0   0.279  -0.6790  -2.4025   0.5800
 N6D  H4   H  HNH1  0   0.417  -0.3318   1.3086   0.3108
 N6D  H5   H  HCH3  0   0.204  -6.5513   2.4521  -0.9142
 N6D  H6   H  HCH3  0   0.236  -6.9689   1.3525  -2.2411
 N6D  H7   H  HCH3  0   0.205  -7.5450   1.0194  -0.5977
 N6D  H8   H  HCH2  0   0.215  -4.8808   1.6714   0.6683
 N6D  H9   H  HCH2  0   0.214  -5.8786   0.2548   1.0061
 N6D  H10  H  HCH3  0   0.270   7.0531  -0.5783  -1.7256
 N6D  H11  H  HCH3  0   0.270   7.2956  -0.7524   0.0109
 N6D  H12  H  HCH3  0   0.268   6.3979  -1.9833  -0.8805
 N6D  H13  H  HCR6  0   0.266  -2.5323   1.4533   0.2197
 N6D  H14  H  HCR6  0   0.251  -4.9371  -2.0541   0.6683
 N6D  H15  H  HCR5  0   0.288   3.6818  -1.6418  -0.4446
 N6D  C1   C  CH2   0  -0.210  -5.0976   0.6457   0.3393

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
 N6D  C11  C10  single    1.480  0.020  1.480
 N6D  O2   C10  aromatic  1.333  0.020  1.333
 N6D  O2   N2   aromatic  1.367  0.020  1.367
 N6D  C10  C9   aromatic  1.355  0.020  1.355
 N6D  N2   C8   aromatic  1.306  0.020  1.306
 N6D  C9   C8   aromatic  1.421  0.020  1.421
 N6D  C8   N1   single    1.375  0.020  1.375
 N6D  N1   C7   single    1.375  0.020  1.375
 N6D  O1   C7   double    1.216  0.020  1.216
 N6D  C7   N    single    1.363  0.020  1.363
 N6D  N    C6   single    1.397  0.020  1.397
 N6D  C5   C6   aromatic  1.395  0.020  1.395
 N6D  C5   C4   aromatic  1.389  0.020  1.389
 N6D  C6   C12  aromatic  1.397  0.020  1.397
 N6D  C4   C3   aromatic  1.385  0.020  1.385
 N6D  C12  C2   aromatic  1.386  0.020  1.386
 N6D  C3   C2   aromatic  1.392  0.020  1.392
 N6D  C2   C1   single    1.501  0.020  1.501
 N6D  C1   O    single    1.410  0.020  1.410
 N6D  O    C    single    1.406  0.020  1.406
 N6D  N1   H1   single    0.860  0.020  1.020
 N6D  C4   H2   single    0.930  0.020  1.080
 N6D  C5   H3   single    0.930  0.020  1.080
 N6D  N    H4   single    0.860  0.020  1.020
 N6D  C    H5   single    0.970  0.020  1.090
 N6D  C    H6   single    0.970  0.020  1.090
 N6D  C    H7   single    0.970  0.020  1.090
 N6D  C1   H8   single    0.970  0.020  1.090
 N6D  C1   H9   single    0.970  0.020  1.090
 N6D  C11  H10  single    0.970  0.020  1.090
 N6D  C11  H11  single    0.970  0.020  1.090
 N6D  C11  H12  single    0.970  0.020  1.090
 N6D  C12  H13  single    0.930  0.020  1.080
 N6D  C3   H14  single    0.930  0.020  1.080
 N6D  C9   H15  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
 N6D  H1   N1   C8   115.14  3.000
 N6D  H1   N1   C7   119.58  3.000
 N6D  C8   N1   C7   125.28  3.000
 N6D  H2   C4   C3   119.80  3.000
 N6D  H2   C4   C5   118.71  3.000
 N6D  C3   C4   C5   121.49  3.000
 N6D  H3   C5   C6   121.29  3.000
 N6D  H3   C5   C4   119.37  3.000
 N6D  C6   C5   C4   119.35  3.000
 N6D  C12  C6   N    116.39  3.000
 N6D  C12  C6   C5   118.93  3.000
 N6D  N    C6   C5   124.68  3.000
 N6D  O1   C7   N    124.78  3.000
 N6D  N    C7   N1   112.37  3.000
 N6D  O1   C7   N1   122.84  3.000
 N6D  N2   C8   C9   111.52  3.000
 N6D  C9   C8   N1   130.60  3.000
 N6D  N2   C8   N1   117.88  3.000
 N6D  O2   C10  C9   109.68  3.000
 N6D  C9   C10  C11  132.33  3.000
 N6D  O2   C10  C11  117.98  3.000
 N6D  H4   N    C7   117.30  3.000
 N6D  H4   N    C6   114.40  3.000
 N6D  C7   N    C6   128.10  3.000
 N6D  H7   C    H6   108.40  3.000
 N6D  H7   C    H5   107.78  3.000
 N6D  H6   C    H5   108.40  3.000
 N6D  H7   C    O    112.12  3.000
 N6D  H6   C    O    107.92  3.000
 N6D  H5   C    O    112.10  3.000
 N6D  C1   O    C    112.34  3.000
 N6D  H12  C11  H11  108.31  3.000
 N6D  H12  C11  H10  108.35  3.000
 N6D  H11  C11  H10  107.77  3.000
 N6D  H12  C11  C10  109.87  3.000
 N6D  H11  C11  C10  111.19  3.000
 N6D  H10  C11  C10  111.26  3.000
 N6D  H13  C12  C2   119.20  3.000
 N6D  H13  C12  C6   119.33  3.000
 N6D  C2   C12  C6   121.47  3.000
 N6D  C3   C2   C12  119.27  3.000
 N6D  C3   C2   C1   120.56  3.000
 N6D  C12  C2   C1   120.11  3.000
 N6D  H14  C3   C2   120.23  3.000
 N6D  H14  C3   C4   120.27  3.000
 N6D  C2   C3   C4   119.49  3.000
 N6D  H15  C9   C10  127.45  3.000
 N6D  H15  C9   C8   129.39  3.000
 N6D  C10  C9   C8   103.16  3.000
 N6D  O2   N2   C8   105.71  3.000
 N6D  N2   O2   C10  109.93  3.000
 N6D  H9   C1   H8   106.90  3.000
 N6D  H9   C1   C2   110.05  3.000
 N6D  H8   C1   C2   110.26  3.000
 N6D  H9   C1   O    110.60  3.000
 N6D  H8   C1   O    110.69  3.000
 N6D  C2   C1   O    108.35  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
 N6D  CONST_01  C12  C6   C5   C4     0.00   0.0  0
 N6D  CONST_02  C12  C2   C3   C4     0.00   0.0  0
 N6D  CONST_03  C2   C12  C6   C5     0.00   0.0  0
 N6D  CONST_04  C2   C3   C4   C5     0.00   0.0  0
 N6D  CONST_05  C3   C4   C5   C6     0.00   0.0  0
 N6D  CONST_06  C3   C2   C12  C6     0.00   0.0  0
 N6D  CONST_07  C10  O2   N2   C8     0.00   0.0  0
 N6D  CONST_08  O2   C10  C9   C8     0.00   0.0  0
 N6D  CONST_09  N2   C8   C9   C10    0.00   0.0  0
 N6D  CONST_10  N2   O2   C10  C9     0.00   0.0  0
 N6D  CONST_11  O2   N2   C8   C9     0.00   0.0  0
 N6D  CONST_12  O2   N2   C8   N1   180.00   0.0  0
 N6D  CONST_13  C10  C9   C8   N1   180.00   0.0  0
 N6D  CONST_14  N    C6   C5   C4   180.00   0.0  0
 N6D  CONST_15  C1   C2   C3   C4   180.00   0.0  0
 N6D  CONST_16  C1   C2   C12  C6   180.00   0.0  0
 N6D  CONST_17  C11  C10  C9   C8   180.00   0.0  0
 N6D  CONST_18  C2   C12  C6   N    180.00   0.0  0
 N6D  CONST_19  N2   O2   C10  C11  180.00   0.0  0
 N6D  CONST_20  H13  C12  C6   C5   180.00   0.0  0
 N6D  CONST_21  H14  C3   C4   C5   180.00   0.0  0
 N6D  CONST_22  H2   C4   C5   C6   180.00   0.0  0
 N6D  CONST_23  H3   C5   C6   C12  180.00   0.0  0
 N6D  CONST_24  H15  C9   C8   N2   180.00   0.0  0
 N6D  CONST_25  C7   N    C6   C5     0.00   0.0  0
 N6D  CONST_26  N2   C8   N1   C7   180.00   0.0  0
 N6D  CONST_27  C9   C8   N1   C7     0.00   0.0  0
 N6D  CONST_28  C12  C6   N    C7   180.00   0.0  0
 N6D  CONST_29  H4   N    C6   C5   180.00   0.0  0
 N6D  CONST_30  H1   N1   C8   C9   180.00   0.0  0
 N6D  CONST_31  O1   C7   N    C6     0.00   0.0  0
 N6D  CONST_32  O1   C7   N1   C8     0.00   0.0  0
 N6D  CONST_33  C6   N    C7   N1   180.00   0.0  0
 N6D  CONST_34  N    C7   N1   C8   180.00   0.0  0
 N6D  Var_01    C12  C2   C1   O     93.88  30.0  2
 N6D  Var_02    H10  C11  C10  C9   120.53  30.0  2
 N6D  Var_03    C2   C1   O    C    179.53  30.0  1
 N6D  Var_04    H5   C    O    C1    59.97  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
 N6D  plan-1  N1   0.020
 N6D  plan-1  C8   0.020
 N6D  plan-1  C10  0.020
 N6D  plan-1  C11  0.020
 N6D  plan-1  C9   0.020
 N6D  plan-1  N2   0.020
 N6D  plan-1  O2   0.020
 N6D  plan-1  H15  0.020
 N6D  plan-2  C4   0.020
 N6D  plan-2  C5   0.020
 N6D  plan-2  C6   0.020
 N6D  plan-2  N    0.020
 N6D  plan-2  C12  0.020
 N6D  plan-2  C2   0.020
 N6D  plan-2  C3   0.020
 N6D  plan-2  H2   0.020
 N6D  plan-2  H3   0.020
 N6D  plan-2  H13  0.020
 N6D  plan-2  H14  0.020
 N6D  plan-2  C1   0.020
 N6D  plan-3  N1   0.020
 N6D  plan-3  C6   0.020
 N6D  plan-3  C7   0.020
 N6D  plan-3  C8   0.020
 N6D  plan-3  N    0.020
 N6D  plan-3  O1   0.020
 N6D  plan-3  H1   0.020
 N6D  plan-3  H4   0.020

