# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 00:13:30 2021
#   Inital geometry file: a 89 line input string
#   Ligand name: 1-[2-(2-oxidanylidenepyrrolidin-1-yl)ethyl]-3-phenyl-urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NCCN1CCCC1=O)Nc2ccccc2
#
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
 S6V  S6V  1-[2-(2-oxidanylidenepyrrolidin-1-yl)ethyl]-3-phenyl-urea  ligand  35  18  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_S6V
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
 S6V  N1   N  NH1   0  -0.780  14.9685   -9.4608   -9.5536
 S6V  N3   N  NR5   0  -0.450  13.8206   -6.2175  -11.8567
 S6V  C4   C  CR6   0   0.373  16.1959  -10.1212   -9.5324
 S6V  C5   C  CR16  0  -0.314  17.0459  -10.2366  -10.6355
 S6V  C6   C  CR16  0  -0.246  18.2629  -10.8921  -10.5030
 S6V  C7   C  C     0   0.732  14.1763   -9.1923  -10.6428
 S6V  C8   C  CH2   0  -0.303  12.1561   -7.9757  -11.3091
 S6V  C10  C  CH2   0  -0.261  14.3092   -6.4125  -13.2095
 S6V  C13  C  CR5   0   0.529  14.7935   -5.9529  -10.9602
 S6V  C1   C  CR16  0  -0.278  18.6657  -11.4309   -9.2897
 S6V  C11  C  CH2   0  -0.479  15.6963   -5.7688  -13.1709
 S6V  C12  C  CH2   0  -0.576  16.1083   -5.8942  -11.7081
 S6V  C2   C  CR16  0  -0.245  17.8270  -11.3029   -8.1900
 S6V  C3   C  CR16  0  -0.349  16.6067  -10.6597   -8.3089
 S6V  C9   C  CH2   0  -0.313  12.4551   -6.4867  -11.4916
 S6V  N2   N  NH1   0  -0.666  12.9984   -8.5977  -10.3179
 S6V  O1   O  O     0  -0.512  14.4875   -9.4864  -11.7877
 S6V  O2   O  O     0  -0.501  14.6351   -5.8029   -9.7586
 S6V  H1   H  HNH1  0   0.405  14.5708   -9.2850   -8.6437
 S6V  H2   H  HCR6  0   0.270  16.7689   -9.8213  -11.5905
 S6V  H3   H  HCR6  0   0.255  18.9061  -10.9739  -11.3701
 S6V  H4   H  HCH2  0   0.259  11.1138   -8.0811  -11.0033
 S6V  H5   H  HCH2  0   0.254  12.2620   -8.5133  -12.2495
 S6V  H6   H  HCH2  0   0.246  13.6440   -5.9319  -13.9284
 S6V  H7   H  HCH2  0   0.241  14.3626   -7.4759  -13.4546
 S6V  H8   H  HCR6  0   0.252  19.6166  -11.9394   -9.2010
 S6V  H9   H  HCH2  0   0.253  16.3905   -6.2491  -13.8577
 S6V  H10  H  HCH2  0   0.248  15.6246   -4.7169  -13.4502
 S6V  H11  H  HCH2  0   0.264  16.6506   -6.8255  -11.5162
 S6V  H12  H  HCH2  0   0.271  16.7333   -5.0784  -11.3468
 S6V  H13  H  HCR6  0   0.257  18.1190  -11.7102   -7.2305
 S6V  H14  H  HCR6  0   0.265  15.9609  -10.5748   -7.4424
 S6V  H15  H  HCH2  0   0.255  12.2321   -5.9518  -10.5679
 S6V  H16  H  HCH2  0   0.255  11.7938   -6.0853  -12.2630
 S6V  H17  H  HNH1  0   0.392  12.8731   -8.2703   -9.3728

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
 S6V  C11  C10  single    1.530  0.020  1.530
 S6V  C11  C12  single    1.525  0.020  1.525
 S6V  C10  N3   single    1.451  0.020  1.451
 S6V  N3   C9   single    1.439  0.020  1.439
 S6V  N3   C13  single    1.349  0.020  1.349
 S6V  C12  C13  single    1.514  0.020  1.514
 S6V  O1   C7   double    1.222  0.020  1.222
 S6V  C9   C8   single    1.530  0.020  1.530
 S6V  C8   N2   single    1.442  0.020  1.442
 S6V  C13  O2   double    1.221  0.020  1.221
 S6V  C7   N2   single    1.359  0.020  1.359
 S6V  C7   N1   single    1.373  0.020  1.373
 S6V  C5   C6   aromatic  1.389  0.020  1.389
 S6V  C5   C4   aromatic  1.397  0.020  1.397
 S6V  C6   C1   aromatic  1.387  0.020  1.387
 S6V  N1   C4   single    1.394  0.020  1.394
 S6V  C4   C3   aromatic  1.398  0.020  1.398
 S6V  C1   C2   aromatic  1.389  0.020  1.389
 S6V  C3   C2   aromatic  1.385  0.020  1.385
 S6V  N1   H1   single    0.860  0.020  1.020
 S6V  C5   H2   single    0.930  0.020  1.080
 S6V  C6   H3   single    0.930  0.020  1.080
 S6V  C8   H4   single    0.970  0.020  1.090
 S6V  C8   H5   single    0.970  0.020  1.090
 S6V  C10  H6   single    0.970  0.020  1.090
 S6V  C10  H7   single    0.970  0.020  1.090
 S6V  C1   H8   single    0.930  0.020  1.080
 S6V  C11  H9   single    0.970  0.020  1.090
 S6V  C11  H10  single    0.970  0.020  1.090
 S6V  C12  H11  single    0.970  0.020  1.090
 S6V  C12  H12  single    0.970  0.020  1.090
 S6V  C2   H13  single    0.930  0.020  1.080
 S6V  C3   H14  single    0.930  0.020  1.080
 S6V  C9   H15  single    0.970  0.020  1.090
 S6V  C9   H16  single    0.970  0.020  1.090
 S6V  N2   H17  single    0.890  0.020  1.040

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
 S6V  H1   N1   C7   117.01  3.000
 S6V  H1   N1   C4   114.59  3.000
 S6V  C7   N1   C4   127.78  3.000
 S6V  C9   N3   C13  123.54  3.000
 S6V  C13  N3   C10  113.76  3.000
 S6V  C9   N3   C10  122.05  3.000
 S6V  C3   C4   C5   118.70  3.000
 S6V  C3   C4   N1   117.03  3.000
 S6V  C5   C4   N1   124.24  3.000
 S6V  H2   C5   C6   119.46  3.000
 S6V  H2   C5   C4   120.76  3.000
 S6V  C6   C5   C4   119.79  3.000
 S6V  H3   C6   C1   119.91  3.000
 S6V  H3   C6   C5   118.68  3.000
 S6V  C1   C6   C5   121.41  3.000
 S6V  O1   C7   N2   123.36  3.000
 S6V  N2   C7   N1   113.32  3.000
 S6V  O1   C7   N1   123.30  3.000
 S6V  H5   C8   H4   106.70  3.000
 S6V  H5   C8   N2   108.91  3.000
 S6V  H4   C8   N2   108.88  3.000
 S6V  H5   C8   C9   111.02  3.000
 S6V  H4   C8   C9   108.31  3.000
 S6V  N2   C8   C9   112.82  3.000
 S6V  H7   C10  H6   108.10  3.000
 S6V  H7   C10  C11  111.77  3.000
 S6V  H6   C10  C11  112.59  3.000
 S6V  H7   C10  N3   110.87  3.000
 S6V  H6   C10  N3   110.47  3.000
 S6V  C11  C10  N3   103.02  3.000
 S6V  O2   C13  C12  126.44  3.000
 S6V  O2   C13  N3   125.76  3.000
 S6V  C12  C13  N3   107.80  3.000
 S6V  H8   C1   C2   120.60  3.000
 S6V  H8   C1   C6   120.62  3.000
 S6V  C2   C1   C6   118.78  3.000
 S6V  H10  C11  H9   107.82  3.000
 S6V  H10  C11  C12  110.04  3.000
 S6V  H9   C11  C12  113.38  3.000
 S6V  H10  C11  C10  109.86  3.000
 S6V  H9   C11  C10  112.14  3.000
 S6V  C12  C11  C10  103.57  3.000
 S6V  H12  C12  H11  107.14  3.000
 S6V  H12  C12  C11  114.31  3.000
 S6V  H11  C12  C11  111.84  3.000
 S6V  H12  C12  C13  111.31  3.000
 S6V  H11  C12  C13  108.10  3.000
 S6V  C11  C12  C13  104.03  3.000
 S6V  H13  C2   C3   119.25  3.000
 S6V  H13  C2   C1   120.29  3.000
 S6V  C3   C2   C1   120.46  3.000
 S6V  H14  C3   C2   119.53  3.000
 S6V  H14  C3   C4   119.61  3.000
 S6V  C2   C3   C4   120.86  3.000
 S6V  H16  C9   H15  107.11  3.000
 S6V  H16  C9   C8   108.88  3.000
 S6V  H15  C9   C8   109.66  3.000
 S6V  H16  C9   N3   109.06  3.000
 S6V  H15  C9   N3   108.49  3.000
 S6V  C8   C9   N3   113.45  3.000
 S6V  H17  N2   C8   115.58  3.000
 S6V  H17  N2   C7   118.30  3.000
 S6V  C8   N2   C7   122.06  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
 S6V  CONST_01  C1   C6   C5   C4     0.00   0.0  0
 S6V  CONST_02  C1   C2   C3   C4     0.00   0.0  0
 S6V  CONST_03  C2   C1   C6   C5     0.00   0.0  0
 S6V  CONST_04  C2   C3   C4   C5     0.00   0.0  0
 S6V  CONST_05  C3   C4   C5   C6     0.00   0.0  0
 S6V  CONST_06  C3   C2   C1   C6     0.00   0.0  0
 S6V  CONST_07  C12  C13  N3   C10    0.00   0.0  0
 S6V  CONST_08  C6   C5   C4   N1   180.00   0.0  0
 S6V  CONST_09  C2   C3   C4   N1   180.00   0.0  0
 S6V  CONST_10  O2   C13  N3   C10  180.00   0.0  0
 S6V  CONST_11  C9   N3   C13  C12  180.00   0.0  0
 S6V  CONST_12  H3   C6   C5   C4   180.00   0.0  0
 S6V  CONST_13  H13  C2   C3   C4   180.00   0.0  0
 S6V  CONST_14  H8   C1   C6   C5   180.00   0.0  0
 S6V  CONST_15  H14  C3   C4   C5   180.00   0.0  0
 S6V  CONST_16  H2   C5   C6   C1   180.00   0.0  0
 S6V  CONST_19  O2   C13  N3   C9     0.00   0.0  0
 S6V  CONST_20  H1   N1   C4   C5   180.00   0.0  0
 S6V  CONST_21  O1   C7   N1   C4     0.00   0.0  0
 S6V  CONST_22  N2   C7   N1   C4   180.00   0.0  0
 S6V  CONST_24  C8   N2   C7   N1   180.00   0.0  0
 S6V  CONST_25  H17  N2   C7   O1   180.00   0.0  0
 S6V  Var_01    C12  C11  C10  N3    26.86  30.0  1
 S6V  Var_02    C11  C12  C13  N3    15.47  30.0  1
 S6V  Var_03    C13  C12  C11  C10  -25.90  30.0  1
 S6V  Var_04    C11  C10  N3   C13  -18.84  30.0  1
 S6V  Var_05    C10  N3   C9   C8    77.75  30.0  2
 S6V  Var_06    N2   C8   C9   N3    57.56  30.0  3
 S6V  Var_07    C9   C8   N2   C7   -91.63  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
 S6V  plan-1  N1   0.020
 S6V  plan-1  C4   0.020
 S6V  plan-1  C5   0.020
 S6V  plan-1  C6   0.020
 S6V  plan-1  C1   0.020
 S6V  plan-1  C2   0.020
 S6V  plan-1  C3   0.020
 S6V  plan-1  H2   0.020
 S6V  plan-1  H3   0.020
 S6V  plan-1  H8   0.020
 S6V  plan-1  H13  0.020
 S6V  plan-1  H14  0.020
 S6V  plan-2  N1   0.020
 S6V  plan-2  C4   0.020
 S6V  plan-2  C7   0.020
 S6V  plan-2  C8   0.020
 S6V  plan-2  N2   0.020
 S6V  plan-2  O1   0.020
 S6V  plan-2  H1   0.020
 S6V  plan-2  H17  0.020
 S6V  plan-3  N3   0.020
 S6V  plan-3  C10  0.020
 S6V  plan-3  C13  0.020
 S6V  plan-3  C12  0.020
 S6V  plan-3  C9   0.020
 S6V  plan-3  O2   0.020

