# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 17 22:20:19 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: 3-{[(4-hydroxy-3-methoxyphenyl)acetyl]amino}-D-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(CC(=O)NC[C@@H](N)C(O)=O)ccc1O
#
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
 0GG  0GG  3-{[(4-hydroxy-3-methoxyphenyl)acetyl]amino}-D-alanine  D-peptide  34  19  .  2022-08-09  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_0GG
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
 0GG  N4   N  NH2    0  -0.785  -3.7467   1.6266  -0.0979
 0GG  N6   N  NH1    0  -0.631  -1.8722  -0.3002   1.1404
 0GG  C31  C  CH1    0  -0.227  -4.1753   0.3604   0.4599
 0GG  C32  C  C      0   0.405  -5.3919  -0.2220  -0.2932
 0GG  C33  C  CH2    0  -0.287  -3.0840  -0.7277   0.4794
 0GG  C34  C  C      0   0.538  -0.7358   0.0504   0.5130
 0GG  C35  C  CH2    0  -0.696   0.3549   0.5492   1.4535
 0GG  C36  C  CR6    0   0.156   1.6867   0.6951   0.7839
 0GG  C37  C  CR16   0  -0.417   2.4551  -0.4380   0.5050
 0GG  C38  C  CR6    0   0.306   3.6823  -0.3255  -0.1250
 0GG  C39  C  CR6    0   0.265   4.1707   0.9418  -0.4888
 0GG  C40  C  CR16   0  -0.333   3.4116   2.0622  -0.2087
 0GG  C41  C  CR16   0  -0.333   2.1766   1.9380   0.4225
 0GG  C42  C  CH3    0  -0.432   4.0924  -2.6679  -0.1086
 0GG  O8   O  O      0  -0.601  -5.6520   0.2459  -1.4169
 0GG  O9   O  O      0  -0.485  -0.5791  -0.0144  -0.6962
 0GG  O10  O  O2     0  -0.490   4.4988  -1.3555  -0.4401
 0GG  O11  O  OH1    0  -0.634   5.3656   1.0834  -1.1011
 0GG  H4   H  HNH2   0   0.334  -2.8941   1.9301   0.3565
 0GG  H7   H  HNH1   0   0.398  -1.9059  -0.2040   2.1433
 0GG  H32  H  HCH1   0   0.215  -4.4768   0.5396   1.4988
 0GG  H33  H  HCH2   0   0.236  -2.8269  -1.0135  -0.5411
 0GG  H34  H  HCH2   0   0.239  -3.4621  -1.6178   0.9838
 0GG  H35  H  HCH2   0   0.293   0.0306   1.5132   1.8561
 0GG  H36  H  HCH2   0   0.281   0.4212  -0.1266   2.3110
 0GG  H37  H  HCR6   0   0.275   2.0767  -1.4114   0.7916
 0GG  H38  H  HCR6   0   0.261   3.7897   3.0391  -0.4838
 0GG  H39  H  HCR6   0   0.246   1.5997   2.8304   0.6318
 0GG  H40  H  HCH3   0   0.230   3.9667  -2.7933   0.9698
 0GG  H41  H  HCH3   0   0.231   3.1594  -2.9416  -0.6077
 0GG  H42  H  HCH3   0   0.262   4.8817  -3.3326  -0.4502
 0GG  H45  H  HOH1   0   0.471   5.7773   0.2202  -1.2272
 0GG  H2   H  HNH2   0   0.327  -3.5276   1.5058  -1.0787
 0GG  OXT  O  OC    -1  -0.620  -5.9858  -1.1552   0.2850

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
 0GG  N4   C31  single    1.449  0.020  1.449
 0GG  C33  C31  single    1.541  0.020  1.541
 0GG  C33  N6   single    1.445  0.020  1.445
 0GG  C31  C32  single    1.545  0.020  1.545
 0GG  C42  O10  single    1.413  0.020  1.413
 0GG  N6   C34  single    1.345  0.020  1.345
 0GG  O10  C38  single    1.352  0.020  1.352
 0GG  C35  C34  single    1.524  0.020  1.524
 0GG  C35  C36  single    1.498  0.020  1.498
 0GG  C37  C38  aromatic  1.384  0.020  1.384
 0GG  C37  C36  aromatic  1.397  0.020  1.397
 0GG  C34  O9   double    1.221  0.020  1.221
 0GG  C38  C39  aromatic  1.406  0.020  1.406
 0GG  C32  O8   deloc     1.245  0.020  1.245
 0GG  C36  C41  aromatic  1.384  0.020  1.384
 0GG  C39  O11  single    1.350  0.020  1.350
 0GG  C39  C40  aromatic  1.382  0.020  1.382
 0GG  C41  C40  aromatic  1.392  0.020  1.392
 0GG  N4   H4   single    0.890  0.020  1.040
 0GG  N6   H7   single    0.860  0.020  1.020
 0GG  C31  H32  single    0.970  0.020  1.090
 0GG  C33  H33  single    0.970  0.020  1.090
 0GG  C33  H34  single    0.970  0.020  1.090
 0GG  C35  H35  single    0.970  0.020  1.090
 0GG  C35  H36  single    0.970  0.020  1.090
 0GG  C37  H37  single    0.930  0.020  1.080
 0GG  C40  H38  single    0.930  0.020  1.080
 0GG  C41  H39  single    0.930  0.020  1.080
 0GG  C42  H40  single    0.970  0.020  1.090
 0GG  C42  H41  single    0.970  0.020  1.090
 0GG  C42  H42  single    0.970  0.020  1.090
 0GG  O11  H45  single    0.850  0.020  0.980
 0GG  N4   H2   single    0.890  0.020  1.040
 0GG  C32  OXT  deloc     1.248  0.020  1.248

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
 0GG  H2   N4   H4   106.76  3.000
 0GG  H2   N4   C31  109.44  3.000
 0GG  H4   N4   C31  109.77  3.000
 0GG  H7   N6   C34  117.88  3.000
 0GG  H7   N6   C33  117.08  3.000
 0GG  C34  N6   C33  124.92  3.000
 0GG  H32  C31  C33  107.34  3.000
 0GG  H32  C31  C32  107.87  3.000
 0GG  C33  C31  C32  107.32  3.000
 0GG  H32  C31  N4   107.66  3.000
 0GG  C32  C31  N4   112.02  3.000
 0GG  C33  C31  N4   114.36  3.000
 0GG  OXT  C32  O8   126.86  3.000
 0GG  OXT  C32  C31  115.51  3.000
 0GG  O8   C32  C31  117.58  3.000
 0GG  H34  C33  H33  107.49  3.000
 0GG  H34  C33  C31  109.67  3.000
 0GG  H33  C33  C31  109.88  3.000
 0GG  H34  C33  N6   108.70  3.000
 0GG  H33  C33  N6   107.93  3.000
 0GG  C31  C33  N6   113.00  3.000
 0GG  O9   C34  C35  122.45  3.000
 0GG  O9   C34  N6   123.83  3.000
 0GG  C35  C34  N6   113.71  3.000
 0GG  H36  C35  H35  105.90  3.000
 0GG  H36  C35  C36  110.90  3.000
 0GG  H35  C35  C36  110.02  3.000
 0GG  H36  C35  C34  108.97  3.000
 0GG  H35  C35  C34  107.66  3.000
 0GG  C36  C35  C34  113.10  3.000
 0GG  C41  C36  C37  118.78  3.000
 0GG  C41  C36  C35  121.26  3.000
 0GG  C37  C36  C35  119.95  3.000
 0GG  H37  C37  C38  120.22  3.000
 0GG  H37  C37  C36  118.94  3.000
 0GG  C38  C37  C36  120.84  3.000
 0GG  O10  C38  C39  114.62  3.000
 0GG  C39  C38  C37  119.94  3.000
 0GG  O10  C38  C37  125.44  3.000
 0GG  O11  C39  C40  119.54  3.000
 0GG  C40  C39  C38  119.17  3.000
 0GG  O11  C39  C38  121.29  3.000
 0GG  H38  C40  C41  120.34  3.000
 0GG  H38  C40  C39  119.21  3.000
 0GG  C41  C40  C39  120.45  3.000
 0GG  H39  C41  C40  119.11  3.000
 0GG  H39  C41  C36  120.06  3.000
 0GG  C40  C41  C36  120.82  3.000
 0GG  H42  C42  H41  108.86  3.000
 0GG  H42  C42  H40  108.87  3.000
 0GG  H41  C42  H40  108.88  3.000
 0GG  H42  C42  O10  106.58  3.000
 0GG  H41  C42  O10  111.77  3.000
 0GG  H40  C42  O10  111.78  3.000
 0GG  C42  O10  C38  118.63  3.000
 0GG  H45  O11  C39  110.07  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
 0GG  CONST_01  C39  C38  C37  C36     0.00   0.0  0
 0GG  CONST_02  C39  C40  C41  C36     0.00   0.0  0
 0GG  CONST_03  C40  C39  C38  C37     0.00   0.0  0
 0GG  CONST_04  C40  C41  C36  C37     0.00   0.0  0
 0GG  CONST_05  C41  C36  C37  C38     0.00   0.0  0
 0GG  CONST_06  C41  C40  C39  C38     0.00   0.0  0
 0GG  CONST_07  C38  C37  C36  C35   180.00   0.0  0
 0GG  CONST_08  C40  C41  C36  C35   180.00   0.0  0
 0GG  CONST_09  O10  C38  C37  C36   180.00   0.0  0
 0GG  CONST_10  O11  C39  C38  C37   180.00   0.0  0
 0GG  CONST_11  O10  C38  C39  C40   180.00   0.0  0
 0GG  CONST_12  O11  C39  C40  C41   180.00   0.0  0
 0GG  CONST_13  H38  C40  C41  C36   180.00   0.0  0
 0GG  CONST_14  H39  C41  C36  C37   180.00   0.0  0
 0GG  CONST_15  H37  C37  C38  C39   180.00   0.0  0
 0GG  CONST_16  C35  C34  N6   C33   180.00   0.0  0
 0GG  CONST_17  O9   C34  N6   C33     0.00   0.0  0
 0GG  CONST_18  H7   N6   C34  C35     0.00   0.0  0
 0GG  Var_01    C37  C36  C35  C34   -76.14  30.0  2
 0GG  Var_02    C36  C35  C34  N6    169.37  30.0  2
 0GG  Var_03    H40  C42  O10  C38   -61.41  30.0  3
 0GG  Var_04    C34  N6   C33  C31  -104.17  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
 0GG  chir_01  C31  N4  C33  C32  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
 0GG  plan-1  C35  0.020
 0GG  plan-1  C36  0.020
 0GG  plan-1  C37  0.020
 0GG  plan-1  C38  0.020
 0GG  plan-1  C39  0.020
 0GG  plan-1  C40  0.020
 0GG  plan-1  C41  0.020
 0GG  plan-1  O10  0.020
 0GG  plan-1  O11  0.020
 0GG  plan-1  H37  0.020
 0GG  plan-1  H38  0.020
 0GG  plan-1  H39  0.020
 0GG  plan-2  N6   0.020
 0GG  plan-2  C33  0.020
 0GG  plan-2  C34  0.020
 0GG  plan-2  C35  0.020
 0GG  plan-2  O9   0.020
 0GG  plan-2  H7   0.020
 0GG  plan-3  C31  0.020
 0GG  plan-3  C32  0.020
 0GG  plan-3  O8   0.020
 0GG  plan-3  OXT  0.020

