# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 08:04:02 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: (3S)-3-[3-(aminomethyl)phenyl]-1-ethylpyrrolidine-2,5-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN1C(=O)C[C@H](C1=O)c2cccc(CN)c2
#
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
 L71  L71  (3S)-3-[3-(aminomethyl)phenyl]-1-ethylpyrrolidine-2,5-dione  ligand  33  17  .  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_L71
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
 L71  C     C  CH3   0  -0.663   4.5524   1.6270   0.0166
 L71  N     N  NT    0  -0.519   2.5650   0.1687   0.1521
 L71  C1    C  CH2   0  -0.321   3.7331   0.6645   0.8595
 L71  N1    N  NH2   0  -0.795  -4.5395   1.4637  -1.2393
 L71  C2    C  C     0   0.554   2.6026  -0.9222  -0.6896
 L71  C3    C  CH2   0  -0.573   1.2201  -1.1475  -1.2401
 L71  C4    C  CH1   0  -0.525   0.3855   0.0256  -0.7217
 L71  C5    C  C     0   0.589   1.3281   0.7665   0.2107
 L71  C6    C  CR6   0   0.214  -0.9039  -0.3455  -0.0391
 L71  C7    C  CR16  0  -0.313  -0.8938  -1.1536   1.0953
 L71  C8    C  CR16  0  -0.228  -2.0867  -1.4934   1.7134
 L71  C9    C  CR16  0  -0.317  -3.2941  -1.0340   1.2037
 L71  C10   C  CR6   0   0.099  -3.3244  -0.2348   0.0656
 L71  C11   C  CH2   0  -0.331  -4.6460   0.2159  -0.5063
 L71  C12   C  CR16  0  -0.372  -2.1177   0.1072  -0.5406
 L71  H     H  HCH3  0   0.243   5.4333   1.9446   0.5737
 L71  HA    H  HCH3  0   0.236   4.8908   1.1559  -0.9057
 L71  HB    H  HCH3  0   0.236   3.9785   2.5167  -0.2411
 L71  H1    H  HCH2  0   0.265   4.3315  -0.1957   1.1560
 L71  H1A   H  HCH2  0   0.266   3.3876   1.1472   1.7719
 L71  HN1   H  HNH2  0   0.356  -5.4174   1.6516  -1.7050
 L71  HN1A  H  HNH2  0   0.345  -4.3966   2.2283  -0.5914
 L71  H3    H  HCH2  0   0.311   1.2565  -1.1945  -2.3281
 L71  H3A   H  HCH2  0   0.305   0.8541  -2.1145  -0.8890
 L71  H4    H  HCH1  0   0.331   0.1654   0.7154  -1.5414
 L71  H7    H  HCR6  0   0.250   0.0418  -1.5163   1.5067
 L71  H8    H  HCR6  0   0.256  -2.0767  -2.1128   2.6010
 L71  H9    H  HCR6  0   0.248  -4.2209  -1.2978   1.7000
 L71  H11   H  HCH2  0   0.216  -5.3857   0.2376   0.3050
 L71  H11A  H  HCH2  0   0.244  -4.9962  -0.5505  -1.2046
 L71  H12   H  HCR6  0   0.248  -2.1315   0.7422  -1.4180
 L71  O     O  O     0  -0.433   3.5949  -1.5729  -0.9100
 L71  O1    O  O     0  -0.419   1.0620   1.7264   0.8905

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
 L71  C    C1    single    1.519  0.020  1.519
 L71  N    C1    single    1.453  0.020  1.453
 L71  N    C2    single    1.378  0.020  1.378
 L71  N    C5    single    1.375  0.020  1.375
 L71  O    C2    double    1.207  0.020  1.207
 L71  N1   C11   single    1.451  0.020  1.451
 L71  O1   C5    double    1.206  0.020  1.206
 L71  C2   C3    single    1.505  0.020  1.505
 L71  C3   C4    single    1.530  0.020  1.530
 L71  C4   C5    single    1.519  0.020  1.519
 L71  C4   C6    single    1.505  0.020  1.505
 L71  C6   C7    aromatic  1.393  0.020  1.393
 L71  C6   C12   aromatic  1.389  0.020  1.389
 L71  C7   C8    aromatic  1.386  0.020  1.386
 L71  C8   C9    aromatic  1.389  0.020  1.389
 L71  C9   C10   aromatic  1.391  0.020  1.391
 L71  C10  C11   single    1.509  0.020  1.509
 L71  C10  C12   aromatic  1.393  0.020  1.393
 L71  C    H     single    0.970  0.020  1.090
 L71  C    HA    single    0.970  0.020  1.090
 L71  C    HB    single    0.970  0.020  1.090
 L71  C1   H1    single    0.970  0.020  1.090
 L71  C1   H1A   single    0.970  0.020  1.090
 L71  N1   HN1   single    0.890  0.020  1.040
 L71  N1   HN1A  single    0.890  0.020  1.040
 L71  C3   H3    single    0.970  0.020  1.090
 L71  C3   H3A   single    0.970  0.020  1.090
 L71  C4   H4    single    0.970  0.020  1.090
 L71  C7   H7    single    0.930  0.020  1.080
 L71  C8   H8    single    0.930  0.020  1.080
 L71  C9   H9    single    0.930  0.020  1.080
 L71  C11  H11   single    0.970  0.020  1.090
 L71  C11  H11A  single    0.970  0.020  1.090
 L71  C12  H12   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
 L71  HB    C    HA   108.45  3.000
 L71  HB    C    H    107.97  3.000
 L71  HA    C    H    107.92  3.000
 L71  HB    C    C1   111.37  3.000
 L71  HA    C    C1   111.30  3.000
 L71  H     C    C1   109.69  3.000
 L71  C5    N    C2   113.24  3.000
 L71  C5    N    C1   123.65  3.000
 L71  C2    N    C1   123.06  3.000
 L71  H1A   C1   H1   107.25  3.000
 L71  H1A   C1   N    107.72  3.000
 L71  H1    C1   N    107.74  3.000
 L71  H1A   C1   C    110.81  3.000
 L71  H1    C1   C    110.80  3.000
 L71  N     C1   C    112.31  3.000
 L71  HN1A  N1   HN1  106.08  3.000
 L71  HN1A  N1   C11  109.67  3.000
 L71  HN1   N1   C11  109.18  3.000
 L71  C3    C2   O    127.42  3.000
 L71  C3    C2   N    108.47  3.000
 L71  O     C2   N    124.10  3.000
 L71  H3A   C3   H3   107.10  3.000
 L71  H3A   C3   C4   112.78  3.000
 L71  H3    C3   C4   112.92  3.000
 L71  H3A   C3   C2   108.84  3.000
 L71  H3    C3   C2   109.94  3.000
 L71  C4    C3   C2   105.21  3.000
 L71  H4    C4   C6   108.84  3.000
 L71  H4    C4   C5   106.10  3.000
 L71  C6    C4   C5   111.93  3.000
 L71  H4    C4   C3   109.84  3.000
 L71  C6    C4   C3   115.59  3.000
 L71  C5    C4   C3   104.09  3.000
 L71  C4    C5   O1   126.69  3.000
 L71  C4    C5   N    108.66  3.000
 L71  O1    C5   N    124.65  3.000
 L71  C12   C6   C7   119.30  3.000
 L71  C12   C6   C4   120.29  3.000
 L71  C7    C6   C4   120.40  3.000
 L71  H7    C7   C8   119.44  3.000
 L71  H7    C7   C6   120.61  3.000
 L71  C8    C7   C6   119.95  3.000
 L71  H8    C8   C9   119.89  3.000
 L71  H8    C8   C7   119.87  3.000
 L71  C9    C8   C7   120.24  3.000
 L71  H9    C9   C10  119.72  3.000
 L71  H9    C9   C8   119.66  3.000
 L71  C10   C9   C8   120.62  3.000
 L71  C12   C10  C11  121.36  3.000
 L71  C12   C10  C9   118.57  3.000
 L71  C11   C10  C9   120.05  3.000
 L71  H11A  C11  H11  105.65  3.000
 L71  H11A  C11  C10  108.24  3.000
 L71  H11   C11  C10  108.41  3.000
 L71  H11A  C11  N1   107.66  3.000
 L71  H11   C11  N1   113.93  3.000
 L71  C10   C11  N1   112.58  3.000
 L71  H12   C12  C10  119.04  3.000
 L71  H12   C12  C6   119.64  3.000
 L71  C10   C12  C6   121.32  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
 L71  CONST_01  C9   C8   C7   C6      0.00   0.0  0
 L71  CONST_02  C9   C10  C12  C6      0.00   0.0  0
 L71  CONST_03  C10  C12  C6   C7      0.00   0.0  0
 L71  CONST_04  C10  C9   C8   C7      0.00   0.0  0
 L71  CONST_05  C12  C6   C7   C8      0.00   0.0  0
 L71  CONST_06  C12  C10  C9   C8      0.00   0.0  0
 L71  CONST_07  C8   C7   C6   C4    180.00   0.0  0
 L71  CONST_08  C10  C12  C6   C4    180.00   0.0  0
 L71  CONST_09  C5   N    C2   C3      0.00   0.0  0
 L71  CONST_10  C11  C10  C12  C6    180.00   0.0  0
 L71  CONST_11  C11  C10  C9   C8    180.00   0.0  0
 L71  CONST_12  C5   N    C2   O     180.00   0.0  0
 L71  CONST_13  C3   C2   N    C1    180.00   0.0  0
 L71  CONST_14  H7   C7   C6   C4      0.00   0.0  0
 L71  CONST_15  H12  C12  C6   C4      0.00   0.0  0
 L71  CONST_16  H8   C8   C7   C6    180.00   0.0  0
 L71  CONST_17  H9   C9   C8   C7    180.00   0.0  0
 L71  CONST_18  C1   N    C2   O       0.00   0.0  0
 L71  Var_01    C4   C3   C2   N       5.14  30.0  1
 L71  Var_02    C4   C5   N    C2     -1.22  30.0  1
 L71  Var_03    C9   C10  C11  N1    153.21  30.0  2
 L71  Var_04    H    C    C1   N    -178.06  30.0  3
 L71  Var_05    HN1  N1   C11  C10   172.25  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
 L71  chir_01  C4  C3  C5  C6  positiv

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
 L71  plan-1  C4   0.020
 L71  plan-1  C6   0.020
 L71  plan-1  C7   0.020
 L71  plan-1  C8   0.020
 L71  plan-1  C9   0.020
 L71  plan-1  C10  0.020
 L71  plan-1  C11  0.020
 L71  plan-1  C12  0.020
 L71  plan-1  H7   0.020
 L71  plan-1  H8   0.020
 L71  plan-1  H9   0.020
 L71  plan-1  H12  0.020
 L71  plan-2  N    0.020
 L71  plan-2  C1   0.020
 L71  plan-2  C2   0.020
 L71  plan-2  C3   0.020
 L71  plan-2  C5   0.020
 L71  plan-2  O    0.020
 L71  plan-3  N    0.020
 L71  plan-3  C4   0.020
 L71  plan-3  C5   0.020
 L71  plan-3  O1   0.020

