# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 03:06:29 2022
#   Inital geometry file: a 129 line input string
#   Ligand name: (2S)-2-azanyl-3-[2,4-dihydroxy-5-[[(E,2S)-1-oxo-5-phenoxy-pent-3-en-2-yl]amino]phenyl]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1cc(N[C@H](C=O)\C=C\COc2ccccc2)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
 P2Q  P2Q  '(2S)-2-azanyl-3-[2,4-dihydroxy-5-[[(E,2S)-1-oxo-5-phenoxy-pent-3-en-2-yl]amino]phenyl]propanoic acid'  L-peptide  49  28  .  2016-04-26  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_P2Q
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
 P2Q  C     C  C      0   0.409  37.3792   4.8062  56.5760
 P2Q  N     N  NH2    0  -0.810  37.1750   3.1402  58.4061
 P2Q  O     O  O      0  -0.599  37.4609   5.6466  57.4934
 P2Q  C1    C  CH1    0  -0.248  35.0819  -1.2530  60.2138
 P2Q  C2    C  C1     0  -0.192  35.4065   0.1378  60.6812
 P2Q  C3    C  C1     0  -0.233  36.5229   0.4677  61.3185
 P2Q  C4    C  CH2    0  -0.242  36.8234   1.8592  61.7621
 P2Q  C5    C  C1     0   0.171  34.0493  -1.8186  61.1626
 P2Q  C6    C  CR6    0   0.385  37.2625   2.9911  63.8093
 P2Q  C7    C  CR16   0  -0.382  37.4772   4.2093  63.1686
 P2Q  C8    C  CR16   0  -0.239  37.8061   5.3322  63.9217
 P2Q  C9    C  CR16   0  -0.280  37.9225   5.2605  65.3002
 P2Q  CA    C  CH1    0  -0.207  37.4115   3.3095  56.9793
 P2Q  CB    C  CH2    0  -0.476  36.3851   2.4949  56.1793
 P2Q  CG    C  CR6    0   0.012  36.3997   1.0324  56.5264
 P2Q  CZ    C  CR6    0   0.336  36.4580  -1.6785  57.2950
 P2Q  C10   C  CR16   0  -0.239  37.7044   4.0406  65.9333
 P2Q  C11   C  CR16   0  -0.344  37.3777   2.9142  65.1994
 P2Q  NAS   N  NH1    0  -0.692  34.5870  -1.2398  58.8555
 P2Q  OAT   O  O2     0  -0.470  36.9397   1.8449  63.1767
 P2Q  OAZ   O  OH1    0  -0.627  36.5564  -2.9855  57.6151
 P2Q  CD1   C  CR16   0  -0.327  35.5079   0.5082  57.4504
 P2Q  CD2   C  CR6    0   0.327  37.3327   0.1461  55.9749
 P2Q  CE1   C  CR6    0   0.133  35.5098  -0.8210  57.8620
 P2Q  CE2   C  CR16   0  -0.480  37.3526  -1.1928  56.3467
 P2Q  OXT   O  OC    -1  -0.607  37.3095   5.0424  55.3535
 P2Q  H     H  HNH2   0   0.334  37.5514   2.2524  58.7120
 P2Q  HNA   H  HNH2   0   0.333  37.6804   3.8622  58.9021
 P2Q  H1    H  HCH1   0   0.272  35.9791  -1.8799  60.3662
 P2Q  H2    H  H      0   0.272  34.6474   0.8898  60.4828
 P2Q  H3    H  H      0   0.261  37.2842  -0.2835  61.5091
 P2Q  H4    H  HCH2   0   0.234  37.7628   2.1970  61.3079
 P2Q  H4A   H  HCH2   0   0.239  36.0325   2.5449  61.4390
 P2Q  H5    H  H      0   0.210  34.3868  -1.8391  62.2135
 P2Q  H7    H  HCR6   0   0.279  37.3933   4.3063  62.0944
 P2Q  H8    H  HCR6   0   0.256  37.9710   6.2729  63.4119
 P2Q  H9    H  HCR6   0   0.250  38.1787   6.1395  65.8763
 P2Q  HA    H  HCH1   0   0.199  38.4124   2.9497  56.6860
 P2Q  HB    H  HCH2   0   0.221  35.3885   2.8939  56.3891
 P2Q  HBA   H  HCH2   0   0.225  36.5667   2.6442  55.1157
 P2Q  H10   H  HCR6   0   0.254  37.7899   3.9638  67.0098
 P2Q  H11   H  HCR6   0   0.258  37.2092   1.9655  65.6941
 P2Q  HOAD  H  HOH1   0   0.471  38.8033  -0.0585  54.7698
 P2Q  HNAS  H  HNH1   0   0.365  34.0543  -2.0671  58.6215
 P2Q  HOAZ  H  HOH1   0   0.466  35.8939  -3.2275  58.2718
 P2Q  HD1   H  HCR6   0   0.239  34.7644   1.1651  57.8862
 P2Q  HE2   H  HCR6   0   0.266  38.0755  -1.8724  55.9065
 P2Q  OAD   O  OH1    0  -0.630  38.2064   0.6363  55.0690
 P2Q  OC5   O  O      0  -0.358  32.9653  -2.2218  60.8337

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
 P2Q  C    CA    single    1.525  0.021  1.525
 P2Q  C    O     deloc     1.231  0.020  1.231
 P2Q  C    OXT   deloc     1.247  0.020  1.247
 P2Q  CA   N     single    1.458  0.019  1.458
 P2Q  N    H     single    0.860  0.020  0.860
 P2Q  N    HNA   single    0.890  0.020  1.040
 P2Q  NAS  C1    single    1.446  0.020  1.446
 P2Q  C1   C2    single    1.503  0.020  1.503
 P2Q  C1   C5    single    1.512  0.020  1.512
 P2Q  C1   H1    single    0.970  0.020  1.090
 P2Q  C2   C3    double    1.327  0.020  1.327
 P2Q  C2   H2    single    0.930  0.020  1.080
 P2Q  C3   C4    single    1.491  0.020  1.491
 P2Q  C3   H3    single    0.930  0.020  1.080
 P2Q  C4   OAT   single    1.419  0.020  1.419
 P2Q  C4   H4    single    0.970  0.020  1.090
 P2Q  C4   H4A   single    0.970  0.020  1.090
 P2Q  OC5  C5    double    1.202  0.020  1.202
 P2Q  C5   H5    single    0.930  0.020  1.080
 P2Q  OAT  C6    single    1.348  0.020  1.348
 P2Q  C7   C6    aromatic  1.393  0.020  1.393
 P2Q  C6   C11   aromatic  1.397  0.020  1.397
 P2Q  C7   C8    aromatic  1.392  0.020  1.392
 P2Q  C7   H7    single    0.930  0.020  1.080
 P2Q  C8   C9    aromatic  1.385  0.020  1.385
 P2Q  C8   H8    single    0.930  0.020  1.080
 P2Q  C9   C10   aromatic  1.392  0.020  1.392
 P2Q  C9   H9    single    0.930  0.020  1.080
 P2Q  CB   CA    single    1.530  0.020  1.530
 P2Q  CA   HA    single    0.970  0.020  0.970
 P2Q  CB   CG    single    1.503  0.020  1.503
 P2Q  CB   HB    single    0.970  0.020  1.090
 P2Q  CB   HBA   single    0.970  0.020  1.090
 P2Q  CD2  CG    aromatic  1.400  0.020  1.400
 P2Q  CG   CD1   aromatic  1.387  0.020  1.387
 P2Q  CE2  CZ    aromatic  1.391  0.020  1.391
 P2Q  CZ   OAZ   single    1.349  0.020  1.349
 P2Q  CZ   CE1   aromatic  1.399  0.020  1.399
 P2Q  C11  C10   aromatic  1.384  0.020  1.384
 P2Q  C10  H10   single    0.930  0.020  1.080
 P2Q  C11  H11   single    0.930  0.020  1.080
 P2Q  OAD  CD2   single    1.351  0.020  1.351
 P2Q  OAD  HOAD  single    0.850  0.020  0.980
 P2Q  CE1  NAS   single    1.419  0.020  1.419
 P2Q  NAS  HNAS  single    0.890  0.020  1.040
 P2Q  OAZ  HOAZ  single    0.850  0.020  0.980
 P2Q  CD1  CE1   aromatic  1.391  0.020  1.391
 P2Q  CD1  HD1   single    0.930  0.020  1.080
 P2Q  CD2  CE2   aromatic  1.390  0.020  1.390
 P2Q  CE2  HE2   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
 P2Q  OXT   C    CA   116.04  3.000
 P2Q  OXT   C    O    126.68  3.000
 P2Q  CA    C    O    120.80  1.700
 P2Q  HNA   N    H    107.00  3.000
 P2Q  HNA   N    CA   108.44  3.000
 P2Q  H     N    CA   114.00  3.000
 P2Q  H1    C1   NAS  114.38  3.000
 P2Q  H1    C1   C5   104.82  3.000
 P2Q  NAS   C1   C5   111.05  3.000
 P2Q  H1    C1   C2   107.86  3.000
 P2Q  C5    C1   C2   107.37  3.000
 P2Q  NAS   C1   C2   110.96  3.000
 P2Q  H2    C2   C3   120.21  3.000
 P2Q  H2    C2   C1   115.64  3.000
 P2Q  C3    C2   C1   124.14  3.000
 P2Q  H3    C3   C4   116.87  3.000
 P2Q  H3    C3   C2   120.12  3.000
 P2Q  C4    C3   C2   122.98  3.000
 P2Q  H4A   C4   H4   107.67  3.000
 P2Q  H4A   C4   OAT  111.06  3.000
 P2Q  H4    C4   OAT  110.22  3.000
 P2Q  H4A   C4   C3   110.54  3.000
 P2Q  H4    C4   C3   109.68  3.000
 P2Q  OAT   C4   C3   107.67  3.000
 P2Q  H5    C5   OC5  121.99  3.000
 P2Q  H5    C5   C1   113.30  3.000
 P2Q  OC5   C5   C1   124.71  3.000
 P2Q  OAT   C6   C11  116.09  3.000
 P2Q  C11   C6   C7   119.55  3.000
 P2Q  OAT   C6   C7   124.36  3.000
 P2Q  H7    C7   C8   118.90  3.000
 P2Q  H7    C7   C6   121.55  3.000
 P2Q  C8    C7   C6   119.55  3.000
 P2Q  H8    C8   C9   120.05  3.000
 P2Q  H8    C8   C7   118.84  3.000
 P2Q  C9    C8   C7   121.11  3.000
 P2Q  H9    C9   C10  120.47  3.000
 P2Q  H9    C9   C8   120.52  3.000
 P2Q  C10   C9   C8   119.01  3.000
 P2Q  HA    CA   CB   109.00  3.000
 P2Q  HA    CA   N    110.00  3.000
 P2Q  CB    CA   N    110.50  1.700
 P2Q  HA    CA   C    109.00  3.000
 P2Q  CB    CA   C    110.10  1.900
 P2Q  N     CA   C    111.00  2.800
 P2Q  HBA   CB   HB   106.81  3.000
 P2Q  HBA   CB   CG   110.93  3.000
 P2Q  HB    CB   CG   108.63  3.000
 P2Q  HBA   CB   CA   108.94  3.000
 P2Q  HB    CB   CA   108.40  3.000
 P2Q  CG    CB   CA   112.92  3.000
 P2Q  CD2   CG   CD1  116.85  3.000
 P2Q  CD1   CG   CB   121.02  3.000
 P2Q  CD2   CG   CB   122.10  3.000
 P2Q  CE2   CZ   CE1  119.89  3.000
 P2Q  CE1   CZ   OAZ  123.18  3.000
 P2Q  CE2   CZ   OAZ  116.94  3.000
 P2Q  H10   C10  C11  119.23  3.000
 P2Q  H10   C10  C9   120.15  3.000
 P2Q  C11   C10  C9   120.62  3.000
 P2Q  H11   C11  C10  120.50  3.000
 P2Q  H11   C11  C6   119.33  3.000
 P2Q  C10   C11  C6   120.17  3.000
 P2Q  HNAS  NAS  CE1  114.95  3.000
 P2Q  HNAS  NAS  C1   112.97  3.000
 P2Q  CE1   NAS  C1   115.97  3.000
 P2Q  C6    OAT  C4   118.60  3.000
 P2Q  HOAZ  OAZ  CZ   110.78  3.000
 P2Q  HD1   CD1  CE1  117.46  3.000
 P2Q  HD1   CD1  CG   118.68  3.000
 P2Q  CE1   CD1  CG   123.86  3.000
 P2Q  CE2   CD2  OAD  121.32  3.000
 P2Q  CE2   CD2  CG   120.94  3.000
 P2Q  OAD   CD2  CG   117.74  3.000
 P2Q  CD1   CE1  NAS  119.21  3.000
 P2Q  CD1   CE1  CZ   117.82  3.000
 P2Q  NAS   CE1  CZ   122.94  3.000
 P2Q  HE2   CE2  CD2  120.29  3.000
 P2Q  HE2   CE2  CZ   119.08  3.000
 P2Q  CD2   CE2  CZ   120.63  3.000
 P2Q  HOAD  OAD  CD2  110.32  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
 P2Q  CONST_01  C9   C8   C7   C6     0.00   0.0  0
 P2Q  CONST_02  C9   C10  C11  C6     0.00   0.0  0
 P2Q  CONST_03  C10  C11  C6   C7     0.00   0.0  0
 P2Q  CONST_04  C10  C9   C8   C7     0.00   0.0  0
 P2Q  CONST_05  C11  C6   C7   C8     0.00   0.0  0
 P2Q  CONST_06  C11  C10  C9   C8     0.00   0.0  0
 P2Q  CONST_07  CZ   CE2  CD2  CG     0.00   0.0  0
 P2Q  CONST_08  CZ   CE1  CD1  CG     0.00   0.0  0
 P2Q  CONST_09  CE2  CD2  CG   CD1    0.00   0.0  0
 P2Q  CONST_10  CE2  CZ   CE1  CD1    0.00   0.0  0
 P2Q  CONST_11  CE1  CD1  CG   CD2    0.00   0.0  0
 P2Q  CONST_12  CE1  CZ   CE2  CD2    0.00   0.0  0
 P2Q  CONST_13  OAT  C6   C7   C8   180.00   0.0  0
 P2Q  CONST_14  CE2  CD2  CG   CB   180.00   0.0  0
 P2Q  CONST_15  CE1  CD1  CG   CB   180.00   0.0  0
 P2Q  CONST_16  NAS  CE1  CD1  CG   180.00   0.0  0
 P2Q  CONST_17  OAD  CD2  CE2  CZ   180.00   0.0  0
 P2Q  CONST_18  OAT  C6   C11  C10  180.00   0.0  0
 P2Q  CONST_19  CD1  CG   CD2  OAD  180.00   0.0  0
 P2Q  CONST_20  CE2  CZ   CE1  NAS  180.00   0.0  0
 P2Q  CONST_21  CD2  CE2  CZ   OAZ  180.00   0.0  0
 P2Q  CONST_22  CD1  CE1  CZ   OAZ  180.00   0.0  0
 P2Q  CONST_23  H8   C8   C7   C6   180.00   0.0  0
 P2Q  CONST_24  H10  C10  C11  C6   180.00   0.0  0
 P2Q  CONST_25  H11  C11  C6   C7   180.00   0.0  0
 P2Q  CONST_26  H9   C9   C8   C7   180.00   0.0  0
 P2Q  CONST_27  H7   C7   C8   C9   180.00   0.0  0
 P2Q  CONST_28  HE2  CE2  CD2  CG   180.00   0.0  0
 P2Q  CONST_29  HD1  CD1  CE1  CZ   180.00   0.0  0
 P2Q  Var_01    C7   C6   OAT  C4     0.84  30.0  2
 P2Q  Var_02    CD2  CG   CB   CA   -81.79  30.0  2
 P2Q  Var_03    H4   C4   OAT  C6    57.88  30.0  2
 P2Q  Var_04    C4   C3   C2   C1   179.53   0.0  2
 P2Q  Var_05    OAT  C4   C3   C2   118.37  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
 P2Q  chir_01  C1  NAS  C2  C5  negativ
 P2Q  chir_02  CA  N    CB  C   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
 P2Q  plan-1  C6    0.020
 P2Q  plan-1  C7    0.020
 P2Q  plan-1  C8    0.020
 P2Q  plan-1  C9    0.020
 P2Q  plan-1  C10   0.020
 P2Q  plan-1  C11   0.020
 P2Q  plan-1  OAT   0.020
 P2Q  plan-1  H7    0.020
 P2Q  plan-1  H8    0.020
 P2Q  plan-1  H9    0.020
 P2Q  plan-1  H10   0.020
 P2Q  plan-1  H11   0.020
 P2Q  plan-2  CB    0.020
 P2Q  plan-2  CG    0.020
 P2Q  plan-2  CZ    0.020
 P2Q  plan-2  NAS   0.020
 P2Q  plan-2  OAZ   0.020
 P2Q  plan-2  CD1   0.020
 P2Q  plan-2  CD2   0.020
 P2Q  plan-2  CE1   0.020
 P2Q  plan-2  CE2   0.020
 P2Q  plan-2  HD1   0.020
 P2Q  plan-2  HE2   0.020
 P2Q  plan-2  OAD   0.020
 P2Q  plan-3  C1    0.020
 P2Q  plan-3  NAS   0.020
 P2Q  plan-3  CE1   0.020
 P2Q  plan-3  HNAS  0.020
 P2Q  plan-4  C     0.020
 P2Q  plan-4  O     0.020
 P2Q  plan-4  CA    0.020
 P2Q  plan-4  OXT   0.020
 P2Q  plan-5  C1    0.020
 P2Q  plan-5  C2    0.020
 P2Q  plan-5  C3    0.020
 P2Q  plan-5  C4    0.020
 P2Q  plan-5  H2    0.020
 P2Q  plan-5  H3    0.020
 P2Q  plan-6  C1    0.020
 P2Q  plan-6  C5    0.020
 P2Q  plan-6  H5    0.020
 P2Q  plan-6  OC5   0.020

