# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 09:29:35 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: 3-[(3R)-1-ethyl-2,5-dioxopyrrolidin-3-yl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN1C(=O)C[C@@H](C1=O)c2cccc(c2)C(N)=O
#
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
 L7S  L7S  3-[(3R)-1-ethyl-2,5-dioxopyrrolidin-3-yl]benzamide  ligand  32  18  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_L7S
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
 L7S  C     C  CH3   0  -0.663  -4.1329   1.8373  -0.7732
 L7S  N     N  NT    0  -0.518  -2.8808  -0.2608  -0.4162
 L7S  C1    C  CH2   0  -0.321  -4.0056   0.3585  -1.0969
 L7S  N1    N  NH2   0  -0.812   5.1884   0.5830  -0.5269
 L7S  C2    C  C     0   0.555  -2.9750  -0.8539   0.8252
 L7S  O2    O  O     0  -0.480   4.3957  -1.5257  -0.5544
 L7S  C3    C  CH2   0  -0.582  -1.6045  -1.3257   1.2337
 L7S  C4    C  CH1   0  -0.522  -0.6958  -1.0005   0.0476
 L7S  C5    C  C     0   0.588  -1.6050  -0.2680  -0.9256
 L7S  C6    C  CR6   0   0.213   0.5269  -0.1786   0.3561
 L7S  C7    C  CR16  0  -0.296   0.4205   1.0115   1.0729
 L7S  C8    C  CR16  0  -0.226   1.5468   1.7719   1.3402
 L7S  C9    C  CR16  0  -0.295   2.7920   1.3612   0.8844
 L7S  C10   C  CR6   0  -0.018   2.9120   0.1797   0.1598
 L7S  C11   C  CR16  0  -0.347   1.7752  -0.5871  -0.0872
 L7S  C12   C  C     0   0.491   4.2270  -0.3332  -0.3397
 L7S  H     H  HCH3  0   0.236  -3.2396   2.3878  -1.0671
 L7S  HA    H  HCH3  0   0.244  -4.9795   2.2582  -1.3148
 L7S  HB    H  HCH3  0   0.237  -4.3022   1.9966   0.2913
 L7S  H1    H  HCH2  0   0.267  -4.9050  -0.1796  -0.8026
 L7S  H1A   H  HCH2  0   0.266  -3.8718   0.2053  -2.1666
 L7S  HN1   H  HNH2  0   0.406   6.0823   0.2958  -0.8917
 L7S  HN1A  H  HNH2  0   0.413   5.0073   1.5713  -0.5001
 L7S  H3    H  HCH2  0   0.305  -1.3109  -0.8136   2.1519
 L7S  H3A   H  HCH2  0   0.318  -1.6338  -2.3913   1.4603
 L7S  H4    H  HCH1  0   0.337  -0.3850  -1.9219  -0.4525
 L7S  H7    H  HCR6  0   0.259  -0.5438   1.3524   1.4329
 L7S  H8    H  HCR6  0   0.268   1.4574   2.6872   1.9097
 L7S  H9    H  HCR6  0   0.263   3.6601   1.9615   1.1244
 L7S  H11   H  HCR6  0   0.261   1.8659  -1.5139  -0.6398
 L7S  O     O  O     0  -0.431  -4.0001  -0.9539   1.4532
 L7S  O1    O  O     0  -0.416  -1.2826   0.2281  -1.9760

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
 L7S  C    C1    single    1.519  0.020  1.519
 L7S  N    C1    single    1.453  0.020  1.453
 L7S  N    C2    single    1.379  0.020  1.379
 L7S  N    C5    single    1.374  0.020  1.374
 L7S  O    C2    double    1.206  0.020  1.206
 L7S  N1   C12   single    1.341  0.020  1.341
 L7S  O1   C5    double    1.206  0.020  1.206
 L7S  C2   C3    single    1.506  0.020  1.506
 L7S  O2   C12   double    1.223  0.020  1.223
 L7S  C3   C4    single    1.529  0.020  1.529
 L7S  C4   C5    single    1.520  0.020  1.520
 L7S  C4   C6    single    1.505  0.020  1.505
 L7S  C6   C7    aromatic  1.393  0.020  1.393
 L7S  C6   C11   aromatic  1.386  0.020  1.386
 L7S  C7   C8    aromatic  1.385  0.020  1.385
 L7S  C8   C9    aromatic  1.388  0.020  1.388
 L7S  C9   C10   aromatic  1.391  0.020  1.391
 L7S  C10  C11   aromatic  1.393  0.020  1.393
 L7S  C10  C12   single    1.497  0.020  1.497
 L7S  C    H     single    0.970  0.020  1.090
 L7S  C    HA    single    0.970  0.020  1.090
 L7S  C    HB    single    0.970  0.020  1.090
 L7S  C1   H1    single    0.970  0.020  1.090
 L7S  C1   H1A   single    0.970  0.020  1.090
 L7S  N1   HN1   single    0.860  0.020  1.020
 L7S  N1   HN1A  single    0.860  0.020  1.020
 L7S  C3   H3    single    0.970  0.020  1.090
 L7S  C3   H3A   single    0.970  0.020  1.090
 L7S  C4   H4    single    0.970  0.020  1.090
 L7S  C7   H7    single    0.930  0.020  1.080
 L7S  C8   H8    single    0.930  0.020  1.080
 L7S  C9   H9    single    0.930  0.020  1.080
 L7S  C11  H11   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
 L7S  HB    C    HA   107.96  3.000
 L7S  HB    C    H    108.47  3.000
 L7S  HA    C    H    107.92  3.000
 L7S  HB    C    C1   111.32  3.000
 L7S  HA    C    C1   109.59  3.000
 L7S  H     C    C1   111.45  3.000
 L7S  C5    N    C2   113.27  3.000
 L7S  C5    N    C1   123.18  3.000
 L7S  C2    N    C1   123.51  3.000
 L7S  H1A   C1   H1   107.31  3.000
 L7S  H1A   C1   N    107.76  3.000
 L7S  H1    C1   N    107.59  3.000
 L7S  H1A   C1   C    110.90  3.000
 L7S  H1    C1   C    110.75  3.000
 L7S  N     C1   C    112.33  3.000
 L7S  HN1A  N1   HN1  116.75  3.000
 L7S  HN1A  N1   C12  122.60  3.000
 L7S  HN1   N1   C12  119.46  3.000
 L7S  C3    C2   O    127.32  3.000
 L7S  C3    C2   N    108.47  3.000
 L7S  O     C2   N    124.22  3.000
 L7S  H3A   C3   H3   106.92  3.000
 L7S  H3A   C3   C4   112.66  3.000
 L7S  H3    C3   C4   113.14  3.000
 L7S  H3A   C3   C2   109.77  3.000
 L7S  H3    C3   C2   109.02  3.000
 L7S  C4    C3   C2   105.30  3.000
 L7S  H4    C4   C6   108.84  3.000
 L7S  H4    C4   C5   106.46  3.000
 L7S  C6    C4   C5   110.73  3.000
 L7S  H4    C4   C3   110.15  3.000
 L7S  C6    C4   C3   116.10  3.000
 L7S  C5    C4   C3   104.10  3.000
 L7S  C4    C5   O1   126.60  3.000
 L7S  C4    C5   N    108.69  3.000
 L7S  O1    C5   N    124.70  3.000
 L7S  C11   C6   C7   119.01  3.000
 L7S  C11   C6   C4   120.33  3.000
 L7S  C7    C6   C4   120.65  3.000
 L7S  H7    C7   C8   119.11  3.000
 L7S  H7    C7   C6   120.48  3.000
 L7S  C8    C7   C6   120.41  3.000
 L7S  H8    C8   C9   119.83  3.000
 L7S  H8    C8   C7   119.93  3.000
 L7S  C9    C8   C7   120.24  3.000
 L7S  H9    C9   C10  121.15  3.000
 L7S  H9    C9   C8   118.85  3.000
 L7S  C10   C9   C8   119.98  3.000
 L7S  C12   C10  C11  117.96  3.000
 L7S  C12   C10  C9   122.72  3.000
 L7S  C11   C10  C9   119.30  3.000
 L7S  H11   C11  C10  119.55  3.000
 L7S  H11   C11  C6   119.39  3.000
 L7S  C10   C11  C6   121.05  3.000
 L7S  C10   C12  O2   120.90  3.000
 L7S  C10   C12  N1   116.24  3.000
 L7S  O2    C12  N1   122.86  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
 L7S  CONST_01  C9    C8   C7   C6     0.00   0.0  0
 L7S  CONST_02  C9    C10  C11  C6     0.00   0.0  0
 L7S  CONST_03  C10   C11  C6   C7     0.00   0.0  0
 L7S  CONST_04  C10   C9   C8   C7     0.00   0.0  0
 L7S  CONST_05  C11   C6   C7   C8     0.00   0.0  0
 L7S  CONST_06  C11   C10  C9   C8     0.00   0.0  0
 L7S  CONST_07  C8    C7   C6   C4   180.00   0.0  0
 L7S  CONST_08  C10   C11  C6   C4   180.00   0.0  0
 L7S  CONST_09  C5    N    C2   C3     0.00   0.0  0
 L7S  CONST_10  C12   C10  C11  C6   180.00   0.0  0
 L7S  CONST_11  C12   C10  C9   C8   180.00   0.0  0
 L7S  CONST_12  C5    N    C2   O    180.00   0.0  0
 L7S  CONST_13  C3    C2   N    C1   180.00   0.0  0
 L7S  CONST_14  H7    C7   C6   C4     0.00   0.0  0
 L7S  CONST_15  H11   C11  C6   C4     0.00   0.0  0
 L7S  CONST_16  H8    C8   C7   C6   180.00   0.0  0
 L7S  CONST_17  H9    C9   C8   C7   180.00   0.0  0
 L7S  CONST_18  C1    N    C2   O      0.00   0.0  0
 L7S  CONST_19  HN1   N1   C12  C10  180.00   0.0  0
 L7S  CONST_20  HN1A  N1   C12  C10    0.00   0.0  0
 L7S  Var_01    C4    C3   C2   N     -2.74  30.0  1
 L7S  Var_02    C4    C5   N    C2     2.41  30.0  1
 L7S  Var_03    C9    C10  C12  N1   -24.89  30.0  3
 L7S  Var_04    H     C    C1   N     59.90  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
 L7S  chir_01  C4  C3  C5  C6  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
 L7S  plan-1  C4    0.020
 L7S  plan-1  C6    0.020
 L7S  plan-1  C7    0.020
 L7S  plan-1  C8    0.020
 L7S  plan-1  C9    0.020
 L7S  plan-1  C10   0.020
 L7S  plan-1  C11   0.020
 L7S  plan-1  C12   0.020
 L7S  plan-1  H7    0.020
 L7S  plan-1  H8    0.020
 L7S  plan-1  H9    0.020
 L7S  plan-1  H11   0.020
 L7S  plan-2  N     0.020
 L7S  plan-2  C4    0.020
 L7S  plan-2  C5    0.020
 L7S  plan-2  O1    0.020
 L7S  plan-3  N1    0.020
 L7S  plan-3  O2    0.020
 L7S  plan-3  C10   0.020
 L7S  plan-3  C12   0.020
 L7S  plan-3  HN1   0.020
 L7S  plan-3  HN1A  0.020
 L7S  plan-4  N     0.020
 L7S  plan-4  C1    0.020
 L7S  plan-4  C2    0.020
 L7S  plan-4  C3    0.020
 L7S  plan-4  C5    0.020
 L7S  plan-4  O     0.020

