# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 22:04:13 2022
#   Inital geometry file: a 96 line input string
#   Ligand name: (4S)-4-{[4-(2,5-dioxopyrrolidin-1-yl)phenyl]amino}-4-hydroxybutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H](CCC(O)=O)Nc1ccc(cc1)N2C(=O)CCC2=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
 PDM  PDM  '(4S)-4-{[4-(2,5-dioxopyrrolidin-1-yl)phenyl]amino}-4-hydroxybutanoic acid'  ligand  36  21  .  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_PDM
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
 PDM  CP1   C  CR6    0   0.283   0.0931   0.0623   2.4397
 PDM  CP2   C  CR16   0  -0.255   1.0710   0.9173   1.9482
 PDM  CP3   C  CR16   0  -0.360   1.2171   1.0994   0.5876
 PDM  CP4   C  CR6    0   0.408   0.3857   0.4319  -0.3276
 PDM  CP5   C  CR16   0  -0.358  -0.6058  -0.4189   0.1848
 PDM  CP6   C  CR16   0  -0.255  -0.7382  -0.6007   1.5510
 PDM  CP7   C  CH1    0   0.188  -0.2682   0.0924  -2.6967
 PDM  CP8   C  CH2    0  -0.479   0.4131   0.2766  -4.0474
 PDM  CP9   C  CH2    0  -0.582  -0.3530  -0.3647  -5.1908
 PDM  C10   C  C      0   0.415   0.2797  -0.1989  -6.5843
 PDM  C11   C  CR5    0   0.542  -0.9414   0.6086   4.6095
 PDM  NP1   N  NR5    0  -0.650  -0.0581  -0.1242   3.8374
 PDM  NP2   N  NH1    0  -0.726   0.5921   0.6062  -1.6688
 PDM  OP3   O  OH1    0  -0.660  -1.5642   0.6488  -2.6647
 PDM  OP4   O  OC    -1  -0.631  -0.3036  -0.7890  -7.5178
 PDM  OP5   O  O      0  -0.609   1.3045   0.5041  -6.6818
 PDM  C12   C  CH2    0  -0.594  -0.8223   0.1334   6.0338
 PDM  C14   C  CR5    0   0.541   0.6622  -1.0575   4.5607
 PDM  C13   C  CH2    0  -0.594   0.2358  -0.9621   6.0022
 PDM  HP2   H  HCR6   0   0.265   1.7232   1.4442   2.6334
 PDM  HP3   H  HCR6   0   0.263   1.9905   1.7628   0.2186
 PDM  HP5   H  HCR6   0   0.270  -1.2869  -0.9395  -0.4731
 PDM  HP6   H  HCR6   0   0.264  -1.5081  -1.2629   1.9270
 PDM  HP7   H  HCH1   0   0.223  -0.4225  -0.9759  -2.5167
 PDM  HP81  H  HCH2   0   0.223   0.5484   1.3482  -4.2336
 PDM  HP82  H  HCH2   0   0.230   1.4157  -0.1518  -3.9839
 PDM  HP91  H  HCH2   0   0.222  -0.4735  -1.4365  -4.9973
 PDM  HP92  H  HCH2   0   0.229  -1.3713   0.0335  -5.2334
 PDM  HP2N  H  HNH1   0   0.382   1.1904   1.3754  -1.9280
 PDM  HP3O  H  HOH1   0   0.441  -1.5005   1.5755  -2.9236
 PDM  H121  H  HCH2   0   0.304  -0.5465   0.9755   6.6693
 PDM  H122  H  HCH2   0   0.304  -1.7950  -0.2222   6.3743
 PDM  H131  H  HCH2   0   0.304   1.1060  -0.7326   6.6176
 PDM  H132  H  HCH2   0   0.303  -0.1427  -1.9313   6.3279
 PDM  OP2   O  O      0  -0.423   1.4810  -1.7986   4.0791
 PDM  OP1   O  O      0  -0.429  -1.6642   1.4694   4.1753

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
 PDM  CP1  CP2   aromatic  1.389  0.020  1.389
 PDM  CP1  CP6   aromatic  1.386  0.020  1.386
 PDM  CP1  NP1   single    1.418  0.020  1.418
 PDM  CP2  CP3   aromatic  1.380  0.020  1.380
 PDM  CP2  HP2   single    0.930  0.020  1.080
 PDM  CP3  CP4   aromatic  1.405  0.020  1.405
 PDM  CP3  HP3   single    0.930  0.020  1.080
 PDM  CP4  CP5   aromatic  1.403  0.020  1.403
 PDM  CP4  NP2   single    1.368  0.020  1.368
 PDM  CP5  CP6   aromatic  1.385  0.020  1.385
 PDM  CP5  HP5   single    0.930  0.020  1.080
 PDM  CP6  HP6   single    0.930  0.020  1.080
 PDM  CP7  CP8   single    1.524  0.020  1.524
 PDM  CP7  NP2   single    1.436  0.020  1.436
 PDM  CP7  OP3   single    1.411  0.020  1.411
 PDM  CP7  HP7   single    0.970  0.020  1.090
 PDM  CP8  CP9   single    1.518  0.020  1.518
 PDM  CP8  HP81  single    0.970  0.020  1.090
 PDM  CP8  HP82  single    0.970  0.020  1.090
 PDM  CP9  C10   single    1.539  0.020  1.539
 PDM  CP9  HP91  single    0.970  0.020  1.090
 PDM  CP9  HP92  single    0.970  0.020  1.090
 PDM  C10  OP4   deloc     1.249  0.020  1.249
 PDM  C10  OP5   deloc     1.246  0.020  1.246
 PDM  C11  NP1   single    1.383  0.020  1.383
 PDM  C11  OP1   double    1.205  0.020  1.205
 PDM  C11  C12   single    1.506  0.020  1.506
 PDM  NP1  C14   single    1.383  0.020  1.383
 PDM  NP2  HP2N  single    0.890  0.020  1.040
 PDM  OP2  C14   double    1.205  0.020  1.205
 PDM  OP3  HP3O  single    0.850  0.020  0.980
 PDM  C12  C13   single    1.523  0.020  1.523
 PDM  C12  H121  single    0.970  0.020  1.090
 PDM  C12  H122  single    0.970  0.020  1.090
 PDM  C14  C13   single    1.506  0.020  1.506
 PDM  C13  H131  single    0.970  0.020  1.090
 PDM  C13  H132  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
 PDM  NP1   CP1  CP6   120.34  3.000
 PDM  NP1   CP1  CP2   120.32  3.000
 PDM  CP6   CP1  CP2   119.33  3.000
 PDM  HP2   CP2  CP3   119.72  3.000
 PDM  HP2   CP2  CP1   119.98  3.000
 PDM  CP3   CP2  CP1   120.30  3.000
 PDM  HP3   CP3  CP4   119.43  3.000
 PDM  HP3   CP3  CP2   119.46  3.000
 PDM  CP4   CP3  CP2   121.10  3.000
 PDM  NP2   CP4  CP5   122.80  3.000
 PDM  NP2   CP4  CP3   119.25  3.000
 PDM  CP5   CP4  CP3   117.93  3.000
 PDM  HP5   CP5  CP6   118.51  3.000
 PDM  HP5   CP5  CP4   121.00  3.000
 PDM  CP6   CP5  CP4   120.49  3.000
 PDM  HP6   CP6  CP5   119.40  3.000
 PDM  HP6   CP6  CP1   119.76  3.000
 PDM  CP5   CP6  CP1   120.84  3.000
 PDM  HP7   CP7  OP3   104.58  3.000
 PDM  HP7   CP7  NP2   108.43  3.000
 PDM  OP3   CP7  NP2   113.15  3.000
 PDM  HP7   CP7  CP8   109.08  3.000
 PDM  OP3   CP7  CP8   112.53  3.000
 PDM  NP2   CP7  CP8   108.87  3.000
 PDM  HP82  CP8  HP81  106.27  3.000
 PDM  HP82  CP8  CP9   109.96  3.000
 PDM  HP81  CP8  CP9   110.32  3.000
 PDM  HP82  CP8  CP7   108.14  3.000
 PDM  HP81  CP8  CP7   108.90  3.000
 PDM  CP9   CP8  CP7   113.00  3.000
 PDM  HP92  CP9  HP91  105.10  3.000
 PDM  HP92  CP9  C10   107.94  3.000
 PDM  HP91  CP9  C10   108.08  3.000
 PDM  HP92  CP9  CP8   110.19  3.000
 PDM  HP91  CP9  CP8   109.61  3.000
 PDM  C10   CP9  CP8   115.39  3.000
 PDM  OP5   C10  OP4   126.30  3.000
 PDM  OP5   C10  CP9   118.00  3.000
 PDM  OP4   C10  CP9   115.70  3.000
 PDM  C12   C11  OP1   127.84  3.000
 PDM  C12   C11  NP1   108.08  3.000
 PDM  OP1   C11  NP1   124.08  3.000
 PDM  C14   NP1  C11   113.46  3.000
 PDM  C14   NP1  CP1   123.27  3.000
 PDM  C11   NP1  CP1   123.27  3.000
 PDM  HP2N  NP2  CP7   116.39  3.000
 PDM  HP2N  NP2  CP4   116.02  3.000
 PDM  CP7   NP2  CP4   124.47  3.000
 PDM  HP3O  OP3  CP7   108.19  3.000
 PDM  H122  C12  H121  107.20  3.000
 PDM  H122  C12  C13   113.05  3.000
 PDM  H121  C12  C13   113.07  3.000
 PDM  H122  C12  C11   109.13  3.000
 PDM  H121  C12  C11   109.12  3.000
 PDM  C13   C12  C11   105.20  3.000
 PDM  C13   C14  OP2   127.87  3.000
 PDM  C13   C14  NP1   108.08  3.000
 PDM  OP2   C14  NP1   124.05  3.000
 PDM  H132  C13  H131  107.19  3.000
 PDM  H132  C13  C14   109.14  3.000
 PDM  H131  C13  C14   109.12  3.000
 PDM  H132  C13  C12   113.08  3.000
 PDM  H131  C13  C12   113.03  3.000
 PDM  C14   C13  C12   105.19  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
 PDM  CONST_01  CP4   CP3  CP2  CP1    0.00   0.0  0
 PDM  CONST_02  CP4   CP5  CP6  CP1    0.00   0.0  0
 PDM  CONST_03  CP5   CP6  CP1  CP2    0.00   0.0  0
 PDM  CONST_04  CP5   CP4  CP3  CP2    0.00   0.0  0
 PDM  CONST_05  CP6   CP1  CP2  CP3    0.00   0.0  0
 PDM  CONST_06  CP6   CP5  CP4  CP3    0.00   0.0  0
 PDM  CONST_07  NP1   CP1  CP2  CP3  180.00   0.0  0
 PDM  CONST_08  NP1   CP1  CP6  CP5  180.00   0.0  0
 PDM  CONST_09  C12   C11  NP1  CP1  180.00   0.0  0
 PDM  CONST_10  C14   NP1  C11  C12    0.00   0.0  0
 PDM  CONST_11  NP2   CP4  CP3  CP2  180.00   0.0  0
 PDM  CONST_12  NP2   CP4  CP5  CP6  180.00   0.0  0
 PDM  CONST_13  OP1   C11  NP1  CP1    0.00   0.0  0
 PDM  CONST_14  C14   NP1  C11  OP1  180.00   0.0  0
 PDM  CONST_15  HP3   CP3  CP2  CP1  180.00   0.0  0
 PDM  CONST_16  HP5   CP5  CP6  CP1  180.00   0.0  0
 PDM  CONST_17  HP6   CP6  CP1  CP2  180.00   0.0  0
 PDM  CONST_18  HP2   CP2  CP3  CP4  180.00   0.0  0
 PDM  CONST_19  CP7   NP2  CP4  CP3  180.00   0.0  0
 PDM  CONST_20  CP7   NP2  CP4  CP5    0.00   0.0  0
 PDM  CONST_21  HP2N  NP2  CP4  CP3    0.00   0.0  0
 PDM  Var_01    C13   C14  NP1  CP1  179.88  30.0  1
 PDM  Var_02    C11   NP1  CP1  CP2   93.51  30.0  2
 PDM  Var_03    C14   C13  C12  C11   -0.16  30.0  1
 PDM  Var_04    C13   C12  C11  NP1    0.06  30.0  1
 PDM  Var_05    C12   C13  C14  NP1    0.21  30.0  1
 PDM  Var_06    C10   CP9  CP8  CP7  179.39  30.0  3
 PDM  Var_07    OP4   C10  CP9  CP8  176.02  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
 PDM  chir_01  CP7  CP8  NP2  OP3  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
 PDM  plan-1  CP1   0.020
 PDM  plan-1  CP2   0.020
 PDM  plan-1  CP3   0.020
 PDM  plan-1  CP4   0.020
 PDM  plan-1  CP5   0.020
 PDM  plan-1  CP6   0.020
 PDM  plan-1  NP1   0.020
 PDM  plan-1  NP2   0.020
 PDM  plan-1  HP2   0.020
 PDM  plan-1  HP3   0.020
 PDM  plan-1  HP5   0.020
 PDM  plan-1  HP6   0.020
 PDM  plan-2  CP4   0.020
 PDM  plan-2  CP7   0.020
 PDM  plan-2  NP2   0.020
 PDM  plan-2  HP2N  0.020
 PDM  plan-3  NP1   0.020
 PDM  plan-3  C14   0.020
 PDM  plan-3  C13   0.020
 PDM  plan-3  OP2   0.020
 PDM  plan-4  CP1   0.020
 PDM  plan-4  C11   0.020
 PDM  plan-4  NP1   0.020
 PDM  plan-4  C12   0.020
 PDM  plan-4  C14   0.020
 PDM  plan-4  OP1   0.020
 PDM  plan-5  CP9   0.020
 PDM  plan-5  C10   0.020
 PDM  plan-5  OP4   0.020
 PDM  plan-5  OP5   0.020

