# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 23:45:07 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: 1-[2-methyl-1,3-bis(oxidanyl)propan-2-yl]-3-phenyl-urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(CO)(CO)NC(=O)Nc1ccccc1
#
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
 AYV  AYV  1-[2-methyl-1,3-bis(oxidanyl)propan-2-yl]-3-phenyl-urea  ligand  32  16  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_AYV
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
 AYV  N1   N  NH1   0  -0.709   1.2043  -0.5327  -0.1682
 AYV  C4   C  CH2   0  -0.131   2.8378   1.3188  -0.0148
 AYV  C5   C  C     0   0.744   0.0307   0.0085   0.2363
 AYV  C6   C  CR6   0   0.370  -2.4004  -0.2117  -0.2274
 AYV  C7   C  CR16  0  -0.348  -3.3266  -1.1829  -0.6199
 AYV  C8   C  CR16  0  -0.246  -4.6864  -0.9713  -0.4657
 AYV  C10  C  CR16  0  -0.249  -4.2375   1.1780   0.4785
 AYV  C1   C  CH3   0  -0.659   2.6805  -0.3767   1.8063
 AYV  C2   C  CT    0   0.058   2.5312  -0.1459   0.3032
 AYV  C3   C  CH2   0  -0.163   3.4807  -1.0862  -0.4566
 AYV  O1   O  OH1   0  -0.665   4.8088  -0.7711  -0.1327
 AYV  O2   O  OH1   0  -0.674   2.6892   1.5395  -1.3971
 AYV  O3   O  O     0  -0.516  -0.0751   0.8399   1.1252
 AYV  N2   N  NH1   0  -0.786  -1.0527  -0.4883  -0.4566
 AYV  C9   C  CR16  0  -0.278  -5.1547   0.2111   0.0922
 AYV  C11  C  CR16  0  -0.308  -2.8717   0.9840   0.3197
 AYV  H1   H  HNH1  0   0.394   1.1827  -1.1034  -0.9987
 AYV  H2   H  HCH2  0   0.211   2.1639   1.9551   0.5679
 AYV  H3   H  HCH2  0   0.204   3.8557   1.5390   0.3271
 AYV  H4   H  HCR6  0   0.265  -2.9746  -2.1148  -1.0472
 AYV  H5   H  HCR6  0   0.256  -5.3809  -1.7408  -0.7779
 AYV  H6   H  HCR6  0   0.255  -4.5846   2.1101   0.9058
 AYV  H7   H  HCH3  0   0.232   2.4372  -1.4100   2.0571
 AYV  H8   H  HCH3  0   0.234   3.7053  -0.1858   2.1232
 AYV  H9   H  HCH3  0   0.245   2.0262   0.2756   2.3796
 AYV  H10  H  HCH2  0   0.215   3.2289  -2.1174  -0.1752
 AYV  H11  H  HCH2  0   0.210   3.2997  -0.9937  -1.5360
 AYV  H12  H  HOH1  0   0.460   5.3785  -1.4365  -0.5278
 AYV  H13  H  HOH1  0   0.455   2.8905   2.4622  -1.5747
 AYV  H14  H  HNH1  0   0.405  -0.8876  -1.2872  -1.0498
 AYV  H15  H  HCR6  0   0.252  -6.2160   0.3778   0.2194
 AYV  H16  H  HCR6  0   0.267  -2.1886   1.7635   0.6154

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
 AYV  C8   C9   aromatic  1.389  0.020  1.389
 AYV  C8   C7   aromatic  1.385  0.020  1.385
 AYV  C9   C10  aromatic  1.388  0.020  1.388
 AYV  C7   C6   aromatic  1.398  0.020  1.398
 AYV  C10  C11  aromatic  1.389  0.020  1.389
 AYV  C6   C11  aromatic  1.397  0.020  1.397
 AYV  C6   N2   single    1.395  0.020  1.395
 AYV  N2   C5   single    1.379  0.020  1.379
 AYV  O2   C4   single    1.408  0.020  1.408
 AYV  N1   C5   single    1.354  0.020  1.354
 AYV  N1   C2   single    1.460  0.020  1.460
 AYV  C5   O3   double    1.222  0.020  1.222
 AYV  O1   C3   single    1.403  0.020  1.403
 AYV  C4   C2   single    1.530  0.020  1.530
 AYV  C2   C3   single    1.537  0.020  1.537
 AYV  C2   C1   single    1.528  0.020  1.528
 AYV  N1   H1   single    0.860  0.020  1.020
 AYV  C4   H2   single    0.970  0.020  1.090
 AYV  C4   H3   single    0.970  0.020  1.090
 AYV  C7   H4   single    0.930  0.020  1.080
 AYV  C8   H5   single    0.930  0.020  1.080
 AYV  C10  H6   single    0.930  0.020  1.080
 AYV  C1   H7   single    0.970  0.020  1.090
 AYV  C1   H8   single    0.970  0.020  1.090
 AYV  C1   H9   single    0.970  0.020  1.090
 AYV  C3   H10  single    0.970  0.020  1.090
 AYV  C3   H11  single    0.970  0.020  1.090
 AYV  O1   H12  single    0.850  0.020  0.980
 AYV  O2   H13  single    0.850  0.020  0.980
 AYV  N2   H14  single    0.860  0.020  1.020
 AYV  C9   H15  single    0.930  0.020  1.080
 AYV  C11  H16  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
 AYV  H1   N1   C2   115.82  3.000
 AYV  H1   N1   C5   116.99  3.000
 AYV  C2   N1   C5   125.82  3.000
 AYV  H3   C4   H2   106.79  3.000
 AYV  H3   C4   O2   111.89  3.000
 AYV  H2   C4   O2   111.51  3.000
 AYV  H3   C4   C2   108.27  3.000
 AYV  H2   C4   C2   108.81  3.000
 AYV  O2   C4   C2   109.45  3.000
 AYV  N2   C5   O3   122.88  3.000
 AYV  O3   C5   N1   124.35  3.000
 AYV  N2   C5   N1   112.76  3.000
 AYV  C11  C6   N2   124.07  3.000
 AYV  N2   C6   C7   117.14  3.000
 AYV  C11  C6   C7   118.75  3.000
 AYV  H4   C7   C8   119.62  3.000
 AYV  H4   C7   C6   119.52  3.000
 AYV  C8   C7   C6   120.87  3.000
 AYV  H5   C8   C9   120.32  3.000
 AYV  H5   C8   C7   119.29  3.000
 AYV  C9   C8   C7   120.40  3.000
 AYV  H6   C10  C11  118.74  3.000
 AYV  H6   C10  C9   119.87  3.000
 AYV  C11  C10  C9   121.39  3.000
 AYV  H9   C1   H8   107.91  3.000
 AYV  H9   C1   H7   108.23  3.000
 AYV  H8   C1   H7   107.99  3.000
 AYV  H9   C1   C2   111.67  3.000
 AYV  H8   C1   C2   110.58  3.000
 AYV  H7   C1   C2   110.33  3.000
 AYV  C3   C2   C1   109.48  3.000
 AYV  C1   C2   C4   109.24  3.000
 AYV  C3   C2   C4   111.05  3.000
 AYV  C1   C2   N1   111.49  3.000
 AYV  C3   C2   N1   103.86  3.000
 AYV  C4   C2   N1   111.62  3.000
 AYV  H11  C3   H10  107.04  3.000
 AYV  H11  C3   O1   111.35  3.000
 AYV  H10  C3   O1   111.64  3.000
 AYV  H11  C3   C2   109.42  3.000
 AYV  H10  C3   C2   107.82  3.000
 AYV  O1   C3   C2   109.46  3.000
 AYV  H12  O1   C3   108.11  3.000
 AYV  H13  O2   C4   108.05  3.000
 AYV  H14  N2   C6   114.33  3.000
 AYV  H14  N2   C5   116.90  3.000
 AYV  C6   N2   C5   127.24  3.000
 AYV  H15  C9   C10  120.56  3.000
 AYV  H15  C9   C8   120.61  3.000
 AYV  C10  C9   C8   118.83  3.000
 AYV  H16  C11  C10  119.40  3.000
 AYV  H16  C11  C6   120.84  3.000
 AYV  C10  C11  C6   119.76  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
 AYV  CONST_01  C9   C8   C7   C6     0.00   0.0  0
 AYV  CONST_02  C9   C10  C11  C6     0.00   0.0  0
 AYV  CONST_03  C10  C9   C8   C7     0.00   0.0  0
 AYV  CONST_04  C10  C11  C6   C7     0.00   0.0  0
 AYV  CONST_05  C11  C10  C9   C8     0.00   0.0  0
 AYV  CONST_06  C11  C6   C7   C8     0.00   0.0  0
 AYV  CONST_07  N2   C6   C7   C8   180.00   0.0  0
 AYV  CONST_08  N2   C6   C11  C10  180.00   0.0  0
 AYV  CONST_09  H5   C8   C7   C6   180.00   0.0  0
 AYV  CONST_10  H6   C10  C11  C6   180.00   0.0  0
 AYV  CONST_11  H15  C9   C8   C7   180.00   0.0  0
 AYV  CONST_12  H16  C11  C6   C7   180.00   0.0  0
 AYV  CONST_13  H4   C7   C8   C9   180.00   0.0  0
 AYV  CONST_16  H14  N2   C6   C7     0.00   0.0  0
 AYV  CONST_17  O3   C5   N2   C6     0.00   0.0  0
 AYV  CONST_18  C6   N2   C5   N1   180.00   0.0  0
 AYV  CONST_19  O3   C5   N1   C2     0.00   0.0  0
 AYV  CONST_20  N2   C5   N1   C2   180.00   0.0  0
 AYV  CONST_21  H1   N1   C5   O3   180.00   0.0  0
 AYV  Var_01    O2   C4   C2   N1   -55.68  30.0  3
 AYV  Var_02    O1   C3   C2   N1   177.33  30.0  3
 AYV  Var_03    C5   N1   C2   C4   -61.26  30.0  1
 AYV  Var_04    H7   C1   C2   N1    54.51  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
 AYV  plan-1  C6   0.020
 AYV  plan-1  C7   0.020
 AYV  plan-1  C8   0.020
 AYV  plan-1  C10  0.020
 AYV  plan-1  N2   0.020
 AYV  plan-1  C9   0.020
 AYV  plan-1  C11  0.020
 AYV  plan-1  H4   0.020
 AYV  plan-1  H5   0.020
 AYV  plan-1  H6   0.020
 AYV  plan-1  H15  0.020
 AYV  plan-1  H16  0.020
 AYV  plan-2  N1   0.020
 AYV  plan-2  C5   0.020
 AYV  plan-2  C6   0.020
 AYV  plan-2  C2   0.020
 AYV  plan-2  O3   0.020
 AYV  plan-2  N2   0.020
 AYV  plan-2  H1   0.020
 AYV  plan-2  H14  0.020

