# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 02:27:30 2022
#   Inital geometry file: a 133 line input string
#   Ligand name: (2S)-2-azanyl-3-[2,4-dihydroxy-5-[[(E)-1-oxo-6-phenyl-hex-2-en-3-yl]amino]phenyl]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1cc(NC(/CCCc2ccccc2)=C/C=O)c(O)cc1O)C(O)=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
 P3Q  P3Q  '(2S)-2-azanyl-3-[2,4-dihydroxy-5-[[(E)-1-oxo-6-phenyl-hex-2-en-3-yl]amino]phenyl]propanoic acid'  L-peptide  51  28  .  2012-08-28  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_P3Q
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
 P3Q  C     C  C      0   0.405  -2.6592   5.0630  27.5108
 P3Q  N     N  NH2    0  -0.806  -1.7594   3.7571  25.5957
 P3Q  O     O  O      0  -0.596  -2.4603   6.0578  26.7866
 P3Q  C1    C  C      0   0.410   2.6137  -0.4240  25.9879
 P3Q  C2    C  CH2    0  -0.563   3.7381  -0.5463  24.9955
 P3Q  C3    C  CH2    0  -0.409   4.2474   0.8261  24.5489
 P3Q  C4    C  CH2    0  -0.507   5.3555   0.7043  23.5031
 P3Q  C5    C  CR6    0   0.134   5.8580   2.0498  23.0620
 P3Q  C6    C  CR16   0  -0.310   6.9070   2.6760  23.7321
 P3Q  C7    C  CR16   0  -0.237   7.3458   3.9371  23.3505
 P3Q  C8    C  CR16   0  -0.273   6.7387   4.5949  22.2884
 P3Q  C9    C  CR16   0  -0.237   5.6914   3.9814  21.6132
 P3Q  CA    C  CH1    0  -0.203  -2.4018   3.6624  26.8965
 P3Q  CB    C  CH2    0  -0.477  -1.5398   2.8121  27.8423
 P3Q  CG    C  CR6    0   0.012  -1.2673   1.4303  27.3188
 P3Q  CZ    C  CR6    0   0.331  -0.7390  -1.1433  26.2843
 P3Q  C10   C  CR16   0  -0.310   5.2566   2.7204  21.9990
 P3Q  C11   C  C1     0  -0.496   2.8035  -0.3273  27.3440
 P3Q  C12   C  C1     0   0.118   4.0888  -0.3354  27.9627
 P3Q  O12   O  O      0  -0.468   4.2877  -0.2421  29.1685
 P3Q  OAZ   O  OH1    0  -0.618  -0.4369  -2.3537  25.7824
 P3Q  CD1   C  CR16   0  -0.300  -0.0975   1.1420  26.6331
 P3Q  CD2   C  CR6    0   0.338  -2.1924   0.3873  27.4612
 P3Q  CE1   C  CR6    0   0.180   0.1888  -0.1165  26.1181
 P3Q  CE2   C  CR16   0  -0.518  -1.9307  -0.8807  26.9524
 P3Q  OXT   O  OC    -1  -0.609  -3.0744   5.0683  28.6869
 P3Q  HN    H  HNH2   0   0.331  -1.9651   2.9339  25.0458
 P3Q  HNA   H  HNH2   0   0.332  -2.1460   4.5500  25.1020
 P3Q  H2    H  HCH2   0   0.265   4.5605  -1.1271  25.4118
 P3Q  H2A   H  HCH2   0   0.269   3.3865  -1.1050  24.1234
 P3Q  H3    H  HCH2   0   0.242   3.4192   1.4119  24.1409
 P3Q  H3A   H  HCH2   0   0.240   4.6205   1.3770  25.4161
 P3Q  H4    H  HCH2   0   0.244   6.1787   0.1170  23.9189
 P3Q  H4A   H  HCH2   0   0.244   4.9777   0.1478  22.6411
 P3Q  H6    H  HCR6   0   0.244   7.3893   2.1679  24.5596
 P3Q  H7    H  HCR6   0   0.250   8.1650   4.4051  23.8818
 P3Q  H8    H  HCR6   0   0.251   7.0809   5.5768  21.9879
 P3Q  H9    H  HCR6   0   0.250   5.2137   4.4847  20.7822
 P3Q  HA    H  HCH1   0   0.199  -3.3918   3.1813  26.8349
 P3Q  HB    H  HCH2   0   0.225  -0.5838   3.3231  27.9877
 P3Q  HBA   H  HCH2   0   0.228  -2.0238   2.7650  28.8172
 P3Q  H10   H  HCR6   0   0.244   4.4414   2.2476  21.4628
 P3Q  H11   H  H      0   0.247   1.9446  -0.2172  27.9955
 P3Q  H12   H  H      0   0.155   4.9556  -0.4283  27.2832
 P3Q  HOAD  H  HOH1   0   0.474  -3.9020  -0.1241  28.1538
 P3Q  HOAZ  H  HOH1   0   0.477  -1.1568  -2.9751  25.9409
 P3Q  HD1   H  HCR6   0   0.252   0.6356   1.9282  26.4961
 P3Q  HE2   H  HCR6   0   0.279  -2.6592  -1.6760  27.0830
 P3Q  HNAE  H  HNH1   0   0.402   1.3349  -0.5136  24.4277
 P3Q  OAD   O  OH1    0  -0.625  -3.3405   0.6585  28.1124
 P3Q  NAE   N  NH1    0  -0.709   1.3955  -0.3556  25.4227

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
 P3Q  CA   C     single    1.525  0.021  1.525
 P3Q  C    O     deloc     1.231  0.020  1.231
 P3Q  C    OXT   deloc     1.247  0.020  1.247
 P3Q  N    CA    single    1.458  0.019  1.458
 P3Q  N    HN    single    0.890  0.020  1.040
 P3Q  N    HNA   single    0.890  0.020  1.040
 P3Q  C2   C1    single    1.505  0.020  1.505
 P3Q  NAE  C1    single    1.345  0.020  1.345
 P3Q  C1   C11   double    1.373  0.020  1.373
 P3Q  C3   C2    single    1.530  0.020  1.530
 P3Q  C2   H2    single    0.970  0.020  1.090
 P3Q  C2   H2A   single    0.970  0.020  1.090
 P3Q  C4   C3    single    1.529  0.020  1.529
 P3Q  C3   H3    single    0.970  0.020  1.090
 P3Q  C3   H3A   single    0.970  0.020  1.090
 P3Q  C5   C4    single    1.502  0.020  1.502
 P3Q  C4   H4    single    0.970  0.020  1.090
 P3Q  C4   H4A   single    0.970  0.020  1.090
 P3Q  C10  C5    aromatic  1.393  0.020  1.393
 P3Q  C5   C6    aromatic  1.393  0.020  1.393
 P3Q  C7   C6    aromatic  1.389  0.020  1.389
 P3Q  C6   H6    single    0.930  0.020  1.080
 P3Q  C8   C7    aromatic  1.389  0.020  1.389
 P3Q  C7   H7    single    0.930  0.020  1.080
 P3Q  C9   C8    aromatic  1.389  0.020  1.389
 P3Q  C8   H8    single    0.930  0.020  1.080
 P3Q  C9   C10   aromatic  1.389  0.020  1.389
 P3Q  C9   H9    single    0.930  0.020  1.080
 P3Q  CA   CB    single    1.530  0.020  1.530
 P3Q  CA   HA    single    0.970  0.020  0.970
 P3Q  CG   CB    single    1.503  0.020  1.503
 P3Q  CB   HB    single    0.970  0.020  1.090
 P3Q  CB   HBA   single    0.970  0.020  1.090
 P3Q  CD1  CG    aromatic  1.386  0.020  1.386
 P3Q  CD2  CG    aromatic  1.401  0.020  1.401
 P3Q  OAZ  CZ    single    1.345  0.020  1.345
 P3Q  CZ   CE1   aromatic  1.394  0.020  1.394
 P3Q  CZ   CE2   aromatic  1.391  0.020  1.391
 P3Q  C10  H10   single    0.930  0.020  1.080
 P3Q  C11  C12   single    1.427  0.020  1.427
 P3Q  C11  H11   single    0.930  0.020  1.080
 P3Q  C12  O12   double    1.226  0.020  1.226
 P3Q  C12  H12   single    0.930  0.020  1.080
 P3Q  CD2  OAD   single    1.347  0.020  1.347
 P3Q  OAD  HOAD  single    0.850  0.020  0.980
 P3Q  NAE  CE1   single    1.413  0.020  1.413
 P3Q  OAZ  HOAZ  single    0.850  0.020  0.980
 P3Q  CE1  CD1   aromatic  1.390  0.020  1.390
 P3Q  CD1  HD1   single    0.930  0.020  1.080
 P3Q  CE2  CD2   aromatic  1.391  0.020  1.391
 P3Q  CE2  HE2   single    0.930  0.020  1.080
 P3Q  NAE  HNAE  single    0.860  0.020  1.020

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
 P3Q  OXT   C    CA   115.63  3.000
 P3Q  OXT   C    O    126.70  3.000
 P3Q  CA    C    O    120.80  1.700
 P3Q  HNA   N    HN   107.17  3.000
 P3Q  HNA   N    CA   108.60  3.000
 P3Q  HN    N    CA   110.10  3.000
 P3Q  NAE   C1   C11  122.47  3.000
 P3Q  C11   C1   C2   123.64  3.000
 P3Q  NAE   C1   C2   113.82  3.000
 P3Q  H2A   C2   H2   105.97  3.000
 P3Q  H2A   C2   C3   109.41  3.000
 P3Q  H2    C2   C3   109.78  3.000
 P3Q  H2A   C2   C1   109.10  3.000
 P3Q  H2    C2   C1   110.82  3.000
 P3Q  C3    C2   C1   111.60  3.000
 P3Q  H3A   C3   H3   106.54  3.000
 P3Q  H3A   C3   C4   109.60  3.000
 P3Q  H3    C3   C4   109.66  3.000
 P3Q  H3A   C3   C2   109.51  3.000
 P3Q  H3    C3   C2   109.71  3.000
 P3Q  C4    C3   C2   111.68  3.000
 P3Q  H4A   C4   H4   106.65  3.000
 P3Q  H4A   C4   C5   109.87  3.000
 P3Q  H4    C4   C5   109.93  3.000
 P3Q  H4A   C4   C3   109.23  3.000
 P3Q  H4    C4   C3   109.17  3.000
 P3Q  C5    C4   C3   111.84  3.000
 P3Q  C10   C5   C6   118.40  3.000
 P3Q  C6    C5   C4   120.87  3.000
 P3Q  C10   C5   C4   120.71  3.000
 P3Q  H6    C6   C7   119.65  3.000
 P3Q  H6    C6   C5   119.42  3.000
 P3Q  C7    C6   C5   120.92  3.000
 P3Q  H7    C7   C8   120.08  3.000
 P3Q  H7    C7   C6   119.79  3.000
 P3Q  C8    C7   C6   120.13  3.000
 P3Q  H8    C8   C9   120.27  3.000
 P3Q  H8    C8   C7   120.24  3.000
 P3Q  C9    C8   C7   119.48  3.000
 P3Q  H9    C9   C10  119.82  3.000
 P3Q  H9    C9   C8   120.03  3.000
 P3Q  C10   C9   C8   120.14  3.000
 P3Q  HA    CA   CB   109.00  3.000
 P3Q  HA    CA   N    110.00  3.000
 P3Q  CB    CA   N    110.50  1.700
 P3Q  HA    CA   C    109.00  3.000
 P3Q  CB    CA   C    110.10  1.900
 P3Q  N     CA   C    111.00  2.800
 P3Q  HBA   CB   HB   106.83  3.000
 P3Q  HBA   CB   CG   110.65  3.000
 P3Q  HB    CB   CG   108.51  3.000
 P3Q  HBA   CB   CA   108.99  3.000
 P3Q  HB    CB   CA   108.28  3.000
 P3Q  CG    CB   CA   113.34  3.000
 P3Q  CD2   CG   CD1  116.91  3.000
 P3Q  CD2   CG   CB   121.96  3.000
 P3Q  CD1   CG   CB   121.10  3.000
 P3Q  CE2   CZ   CE1  119.23  3.000
 P3Q  CE2   CZ   OAZ  122.80  3.000
 P3Q  CE1   CZ   OAZ  117.97  3.000
 P3Q  H10   C10  C9   119.61  3.000
 P3Q  H10   C10  C5   119.47  3.000
 P3Q  C9    C10  C5   120.92  3.000
 P3Q  H11   C11  C12  116.99  3.000
 P3Q  H11   C11  C1   119.44  3.000
 P3Q  C12   C11  C1   123.55  3.000
 P3Q  H12   C12  O12  118.95  3.000
 P3Q  H12   C12  C11  116.12  3.000
 P3Q  O12   C12  C11  124.92  3.000
 P3Q  HOAZ  OAZ  CZ   110.55  3.000
 P3Q  HD1   CD1  CE1  118.09  3.000
 P3Q  HD1   CD1  CG   118.85  3.000
 P3Q  CE1   CD1  CG   123.06  3.000
 P3Q  CE2   CD2  OAD  121.37  3.000
 P3Q  CE2   CD2  CG   121.13  3.000
 P3Q  OAD   CD2  CG   117.50  3.000
 P3Q  CD1   CE1  NAE  120.77  3.000
 P3Q  CD1   CE1  CZ   119.07  3.000
 P3Q  NAE   CE1  CZ   120.16  3.000
 P3Q  HE2   CE2  CD2  119.81  3.000
 P3Q  HE2   CE2  CZ   119.60  3.000
 P3Q  CD2   CE2  CZ   120.59  3.000
 P3Q  HOAD  OAD  CD2  110.71  3.000
 P3Q  HNAE  NAE  CE1  117.41  3.000
 P3Q  HNAE  NAE  C1   117.44  3.000
 P3Q  CE1   NAE  C1   125.12  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
 P3Q  CONST_01  C8   C9   C10  C5      0.00   0.0  0
 P3Q  CONST_02  C8   C7   C6   C5      0.00   0.0  0
 P3Q  CONST_03  C9   C10  C5   C6      0.00   0.0  0
 P3Q  CONST_04  C9   C8   C7   C6      0.00   0.0  0
 P3Q  CONST_05  C10  C5   C6   C7      0.00   0.0  0
 P3Q  CONST_06  C10  C9   C8   C7      0.00   0.0  0
 P3Q  CONST_07  CZ   CE1  CD1  CG      0.00   0.0  0
 P3Q  CONST_08  CZ   CE2  CD2  CG      0.00   0.0  0
 P3Q  CONST_09  CE2  CD2  CG   CD1     0.00   0.0  0
 P3Q  CONST_10  CE2  CZ   CE1  CD1     0.00   0.0  0
 P3Q  CONST_11  CE1  CD1  CG   CD2     0.00   0.0  0
 P3Q  CONST_12  CE1  CZ   CE2  CD2     0.00   0.0  0
 P3Q  CONST_13  C9   C10  C5   C4    180.00   0.0  0
 P3Q  CONST_14  C7   C6   C5   C4    180.00   0.0  0
 P3Q  CONST_15  CE1  CD1  CG   CB    180.00   0.0  0
 P3Q  CONST_16  CE2  CD2  CG   CB    180.00   0.0  0
 P3Q  CONST_17  NAE  CE1  CD1  CG    180.00   0.0  0
 P3Q  CONST_18  OAD  CD2  CE2  CZ    180.00   0.0  0
 P3Q  CONST_19  CD1  CG   CD2  OAD   180.00   0.0  0
 P3Q  CONST_20  CE2  CZ   CE1  NAE   180.00   0.0  0
 P3Q  CONST_21  CD1  CE1  CZ   OAZ   180.00   0.0  0
 P3Q  CONST_22  CD2  CE2  CZ   OAZ   180.00   0.0  0
 P3Q  CONST_23  H9   C9   C10  C5    180.00   0.0  0
 P3Q  CONST_24  H7   C7   C6   C5    180.00   0.0  0
 P3Q  CONST_25  H10  C10  C5   C6    180.00   0.0  0
 P3Q  CONST_26  H8   C8   C7   C6    180.00   0.0  0
 P3Q  CONST_27  H6   C6   C7   C8    180.00   0.0  0
 P3Q  CONST_28  HE2  CE2  CD2  CG    180.00   0.0  0
 P3Q  CONST_29  HD1  CD1  CE1  CZ    180.00   0.0  0
 P3Q  CONST_33  CE1  NAE  C1   C2    180.00   0.0  0
 P3Q  CONST_34  CE1  NAE  C1   C11     0.00   0.0  0
 P3Q  Var_01    C10  C5   C4   C3    -88.61  30.0  2
 P3Q  Var_02    CD1  CG   CB   CA     95.79  30.0  2
 P3Q  Var_03    C5   C4   C3   C2    179.99  30.0  1
 P3Q  Var_04    C12  C11  C1   C2     -0.15   0.0  2
 P3Q  Var_05    C4   C3   C2   C1   -177.95  30.0  2
 P3Q  Var_06    O12  C12  C11  C1    179.50  30.0  2

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
 P3Q  chir_01  CA  C  N  CB  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
 P3Q  plan-1  C4    0.020
 P3Q  plan-1  C5    0.020
 P3Q  plan-1  C6    0.020
 P3Q  plan-1  C7    0.020
 P3Q  plan-1  C8    0.020
 P3Q  plan-1  C9    0.020
 P3Q  plan-1  C10   0.020
 P3Q  plan-1  H6    0.020
 P3Q  plan-1  H7    0.020
 P3Q  plan-1  H8    0.020
 P3Q  plan-1  H9    0.020
 P3Q  plan-1  H10   0.020
 P3Q  plan-2  CB    0.020
 P3Q  plan-2  CG    0.020
 P3Q  plan-2  CZ    0.020
 P3Q  plan-2  OAZ   0.020
 P3Q  plan-2  CD1   0.020
 P3Q  plan-2  CD2   0.020
 P3Q  plan-2  CE1   0.020
 P3Q  plan-2  CE2   0.020
 P3Q  plan-2  HD1   0.020
 P3Q  plan-2  HE2   0.020
 P3Q  plan-2  OAD   0.020
 P3Q  plan-2  NAE   0.020
 P3Q  plan-3  C1    0.020
 P3Q  plan-3  CE1   0.020
 P3Q  plan-3  HNAE  0.020
 P3Q  plan-3  NAE   0.020
 P3Q  plan-4  C     0.020
 P3Q  plan-4  O     0.020
 P3Q  plan-4  CA    0.020
 P3Q  plan-4  OXT   0.020
 P3Q  plan-5  C1    0.020
 P3Q  plan-5  C2    0.020
 P3Q  plan-5  C11   0.020
 P3Q  plan-5  C12   0.020
 P3Q  plan-5  H11   0.020
 P3Q  plan-5  NAE   0.020
 P3Q  plan-6  C11   0.020
 P3Q  plan-6  C12   0.020
 P3Q  plan-6  O12   0.020
 P3Q  plan-6  H12   0.020

