# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 04:17:58 2021
#   Inital geometry file: a 95 line input string
#   Ligand name: (3~{S})-~{N}-methoxy-1-(4-methoxyphenyl)-~{N}-methyl-5-oxidanylidene-pyrrolidine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CON(C)C(=O)[C@@H]1CN(C(=O)C1)c2ccc(OC)cc2
#
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
 SO7  SO7  (3~{S})-~{N}-methoxy-1-(4-methoxyphenyl)-~{N}-methyl-5-oxidanylidene-pyrrolidine-3-carboxamide  ligand  38  20  .  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_SO7
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
 SO7  N1   N  NT    0  -0.198  51.1731  116.9674  31.8934
 SO7  C4   C  CR6   0   0.377  43.7394  117.1318  35.3978
 SO7  C5   C  CH3   0  -0.437  41.9737  117.6623  36.8895
 SO7  C6   C  CR16  0  -0.339  44.4702  116.1492  34.7292
 SO7  C7   C  CR16  0  -0.290  45.5105  116.4998  33.8898
 SO7  C8   C  CH2   0  -0.247  48.1325  117.3604  32.7853
 SO7  C10  C  CH2   0  -0.565  48.1709  119.0806  31.1177
 SO7  C13  C  CH3   0  -0.519  52.1203  116.0111  31.3706
 SO7  N    N  NR5   0  -0.578  46.9313  118.1761  32.8583
 SO7  C    C  CR5   0   0.520  46.8833  119.1433  31.9029
 SO7  O    O  O     0  -0.473  45.9513  119.8969  31.7016
 SO7  C1   C  CR6   0   0.330  45.8584  117.8373  33.7048
 SO7  C11  C  C     0   0.563  50.1113  117.4422  31.2054
 SO7  C12  C  CH3   0  -0.401  52.0700  118.0523  33.7238
 SO7  C2   C  CR16  0  -0.274  45.1409  118.8130  34.3850
 SO7  C3   C  CR16  0  -0.381  44.0850  118.4689  35.2191
 SO7  C9   C  CR15  0  -0.438  49.1010  118.2545  31.9941
 SO7  O2   O  O     0  -0.475  49.9802  117.2205  30.0126
 SO7  O3   O  O2    0  -0.382  51.1535  117.0651  33.2610
 SO7  H1   H  HCH3  0   0.260  41.2224  117.1116  37.4497
 SO7  H2   H  HCH3  0   0.228  42.5838  118.2361  37.5920
 SO7  H3   H  HCH3  0   0.228  41.4692  118.3571  36.2131
 SO7  H4   H  HCR6  0   0.266  44.2115  115.1063  34.8628
 SO7  H5   H  HCR6  0   0.271  46.0501  115.7164  33.3736
 SO7  H6   H  HCH2  0   0.255  47.9366  116.4190  32.2615
 SO7  H7   H  HCH2  0   0.272  48.4981  117.1239  33.7827
 SO7  H8   H  HCH2  0   0.287  48.5492  120.0781  30.8977
 SO7  H9   H  HCH2  0   0.285  47.9628  118.5888  30.1636
 SO7  H10  H  HCH3  0   0.250  53.1197  116.2379  31.7394
 SO7  H11  H  HCH3  0   0.251  51.8562  114.9926  31.6599
 SO7  H12  H  HCH3  0   0.262  52.1368  116.0787  30.2879
 SO7  H13  H  HCH3  0   0.250  52.0048  118.0333  34.8094
 SO7  H14  H  HCH3  0   0.232  53.0959  117.8241  33.4269
 SO7  H15  H  HCH3  0   0.228  51.8050  119.0484  33.3636
 SO7  H16  H  HCR6  0   0.268  45.4047  119.8562  34.2862
 SO7  H17  H  HCR6  0   0.281  43.5538  119.2615  35.7280
 SO7  H18  H  HCR5  0   0.307  49.6008  118.9243  32.6961
 SO7  O1   O  O2    0  -0.471  42.7370  116.7018  36.1881

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
 SO7  O2   C11  double    1.220  0.020  1.220
 SO7  C11  N1   single    1.351  0.020  1.351
 SO7  C11  C9   single    1.517  0.020  1.517
 SO7  C13  N1   single    1.444  0.020  1.444
 SO7  C10  C9   single    1.522  0.020  1.522
 SO7  C10  C    single    1.509  0.020  1.509
 SO7  N1   O3   single    1.371  0.020  1.371
 SO7  C9   C8   single    1.537  0.020  1.537
 SO7  C    O    double    1.215  0.020  1.215
 SO7  C    N    single    1.360  0.020  1.360
 SO7  C8   N    single    1.454  0.020  1.454
 SO7  N    C1   single    1.408  0.020  1.408
 SO7  O3   C12  single    1.424  0.020  1.424
 SO7  C1   C2   aromatic  1.389  0.020  1.389
 SO7  C1   C7   aromatic  1.394  0.020  1.394
 SO7  C2   C3   aromatic  1.389  0.020  1.389
 SO7  C7   C6   aromatic  1.382  0.020  1.382
 SO7  C3   C4   aromatic  1.392  0.020  1.392
 SO7  C6   C4   aromatic  1.395  0.020  1.395
 SO7  C4   O1   single    1.347  0.020  1.347
 SO7  C5   O1   single    1.413  0.020  1.413
 SO7  C5   H1   single    0.970  0.020  1.090
 SO7  C5   H2   single    0.970  0.020  1.090
 SO7  C5   H3   single    0.970  0.020  1.090
 SO7  C6   H4   single    0.930  0.020  1.080
 SO7  C7   H5   single    0.930  0.020  1.080
 SO7  C8   H6   single    0.970  0.020  1.090
 SO7  C8   H7   single    0.970  0.020  1.090
 SO7  C10  H8   single    0.970  0.020  1.090
 SO7  C10  H9   single    0.970  0.020  1.090
 SO7  C13  H10  single    0.970  0.020  1.090
 SO7  C13  H11  single    0.970  0.020  1.090
 SO7  C13  H12  single    0.970  0.020  1.090
 SO7  C12  H13  single    0.970  0.020  1.090
 SO7  C12  H14  single    0.970  0.020  1.090
 SO7  C12  H15  single    0.970  0.020  1.090
 SO7  C2   H16  single    0.930  0.020  1.080
 SO7  C3   H17  single    0.930  0.020  1.080
 SO7  C9   H18  single    0.970  0.020  1.090

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
 SO7  O3   N1   C11  118.13  3.000
 SO7  O3   N1   C13  114.69  3.000
 SO7  C11  N1   C13  124.32  3.000
 SO7  O1   C4   C3   124.51  3.000
 SO7  O1   C4   C6   116.49  3.000
 SO7  C3   C4   C6   119.00  3.000
 SO7  H3   C5   H2   108.76  3.000
 SO7  H3   C5   H1   108.78  3.000
 SO7  H2   C5   H1   108.70  3.000
 SO7  H3   C5   O1   111.97  3.000
 SO7  H2   C5   O1   111.98  3.000
 SO7  H1   C5   O1   106.54  3.000
 SO7  H4   C6   C7   119.95  3.000
 SO7  H4   C6   C4   119.61  3.000
 SO7  C7   C6   C4   120.44  3.000
 SO7  H5   C7   C1   120.44  3.000
 SO7  H5   C7   C6   118.77  3.000
 SO7  C1   C7   C6   120.78  3.000
 SO7  H7   C8   H6   108.17  3.000
 SO7  H7   C8   C9   112.73  3.000
 SO7  H6   C8   C9   111.50  3.000
 SO7  H7   C8   N    110.70  3.000
 SO7  H6   C8   N    111.01  3.000
 SO7  C9   C8   N    102.71  3.000
 SO7  H9   C10  H8   107.57  3.000
 SO7  H9   C10  C9   112.00  3.000
 SO7  H8   C10  C9   113.65  3.000
 SO7  H9   C10  C    108.08  3.000
 SO7  H8   C10  C    111.30  3.000
 SO7  C9   C10  C    104.14  3.000
 SO7  H12  C13  H11  109.06  3.000
 SO7  H12  C13  H10  108.12  3.000
 SO7  H11  C13  H10  109.07  3.000
 SO7  H12  C13  N1   109.27  3.000
 SO7  H11  C13  N1   111.31  3.000
 SO7  H10  C13  N1   109.96  3.000
 SO7  C1   N    C    124.51  3.000
 SO7  C1   N    C8   121.65  3.000
 SO7  C    N    C8   113.13  3.000
 SO7  O    C    N    125.74  3.000
 SO7  N    C    C10  107.80  3.000
 SO7  O    C    C10  126.43  3.000
 SO7  C2   C1   N    121.26  3.000
 SO7  C2   C1   C7   118.68  3.000
 SO7  N    C1   C7   120.05  3.000
 SO7  O2   C11  C9   122.26  3.000
 SO7  C9   C11  N1   116.52  3.000
 SO7  O2   C11  N1   121.21  3.000
 SO7  H15  C12  H14  109.20  3.000
 SO7  H15  C12  H13  109.31  3.000
 SO7  H14  C12  H13  108.91  3.000
 SO7  H15  C12  O3   111.65  3.000
 SO7  H14  C12  O3   111.79  3.000
 SO7  H13  C12  O3   105.88  3.000
 SO7  H16  C2   C3   118.67  3.000
 SO7  H16  C2   C1   120.48  3.000
 SO7  C3   C2   C1   120.85  3.000
 SO7  H17  C3   C2   118.32  3.000
 SO7  H17  C3   C4   121.44  3.000
 SO7  C2   C3   C4   120.24  3.000
 SO7  H18  C9   C11  110.97  3.000
 SO7  H18  C9   C10  108.49  3.000
 SO7  C11  C9   C10  113.46  3.000
 SO7  H18  C9   C8   108.33  3.000
 SO7  C10  C9   C8   103.13  3.000
 SO7  C11  C9   C8   112.06  3.000
 SO7  C12  O3   N1   111.37  3.000
 SO7  C5   O1   C4   118.43  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
 SO7  CONST_01  C1   C2   C3   C4      0.00   0.0  0
 SO7  CONST_02  C1   C7   C6   C4      0.00   0.0  0
 SO7  CONST_03  C2   C1   C7   C6      0.00   0.0  0
 SO7  CONST_04  C2   C3   C4   C6      0.00   0.0  0
 SO7  CONST_05  C3   C2   C1   C7      0.00   0.0  0
 SO7  CONST_06  C3   C4   C6   C7      0.00   0.0  0
 SO7  CONST_07  N    C1   C7   C6    180.00   0.0  0
 SO7  CONST_08  C3   C2   C1   N     180.00   0.0  0
 SO7  CONST_09  C10  C    N    C8      0.00   0.0  0
 SO7  CONST_10  C1   N    C    C10   180.00   0.0  0
 SO7  CONST_11  O1   C4   C6   C7    180.00   0.0  0
 SO7  CONST_12  O1   C4   C3   C2    180.00   0.0  0
 SO7  CONST_13  O    C    N    C8    180.00   0.0  0
 SO7  CONST_14  C1   N    C    O       0.00   0.0  0
 SO7  CONST_15  H16  C2   C3   C4    180.00   0.0  0
 SO7  CONST_16  H5   C7   C6   C4    180.00   0.0  0
 SO7  CONST_17  H17  C3   C4   C6    180.00   0.0  0
 SO7  CONST_18  H4   C6   C7   C1    180.00   0.0  0
 SO7  CONST_19  C9   C11  N1   C13   180.00   0.0  0
 SO7  CONST_20  O3   N1   C11  C9      0.00   0.0  0
 SO7  CONST_21  O2   C11  N1   C13     0.00   0.0  0
 SO7  CONST_22  O3   N1   C11  O2    180.00   0.0  0
 SO7  Var_01    C    N    C1   C7    132.60  30.0  2
 SO7  Var_02    C9   C10  C    N     -16.17  30.0  1
 SO7  Var_03    C9   C8   N    C      20.70  30.0  1
 SO7  Var_04    C3   C4   O1   C5      0.07  30.0  2
 SO7  Var_05    H1   C5   O1   C4    179.38  30.0  3
 SO7  Var_06    H13  C12  O3   N1   -178.28  30.0  3
 SO7  Var_07    H10  C13  N1   C11   143.96  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 SO7  chir_01  C9  C11  C10  C8  negativ

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
 SO7  plan-1  C4   0.020
 SO7  plan-1  C6   0.020
 SO7  plan-1  C7   0.020
 SO7  plan-1  N    0.020
 SO7  plan-1  C1   0.020
 SO7  plan-1  C2   0.020
 SO7  plan-1  C3   0.020
 SO7  plan-1  H4   0.020
 SO7  plan-1  H5   0.020
 SO7  plan-1  H16  0.020
 SO7  plan-1  H17  0.020
 SO7  plan-1  O1   0.020
 SO7  plan-2  N1   0.020
 SO7  plan-2  C13  0.020
 SO7  plan-2  C11  0.020
 SO7  plan-2  C9   0.020
 SO7  plan-2  O2   0.020
 SO7  plan-2  O3   0.020
 SO7  plan-3  C8   0.020
 SO7  plan-3  C10  0.020
 SO7  plan-3  N    0.020
 SO7  plan-3  C    0.020
 SO7  plan-3  O    0.020
 SO7  plan-3  C1   0.020

