# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 17:55:00 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: 4-[(2R,5S)-2,5-diamino-5-hydroxypentyl]phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](O)CC[C@@H](N)Cc1ccc(O)cc1
#
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
 AHT  AHT  4-[(2R,5S)-2,5-diamino-5-hydroxypentyl]phenol  peptide  33  15  .  2022-03-11  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_AHT
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
 AHT  N     N  NH2   0  -0.779  -0.5062   1.6823  -0.2068
 AHT  CA    C  CH1   0  -0.083  -0.7434   0.2793   0.0939
 AHT  C     C  CH2   0  -0.415  -2.1681  -0.0563   0.5501
 AHT  CB    C  CH2   0  -0.508   0.2655  -0.1932   1.1485
 AHT  CG    C  CR6   0   0.137   1.6886  -0.1741   0.6706
 AHT  CD1   C  CR16  0  -0.287   2.4769   0.9717   0.7582
 AHT  CD2   C  CR16  0  -0.307   2.2611  -1.3032   0.0935
 AHT  CE1   C  CR16  0  -0.328   3.7824   0.9941   0.2936
 AHT  CE2   C  CR16  0  -0.371   3.5663  -1.3009  -0.3814
 AHT  CZ    C  CR6   0   0.332   4.3365  -0.1468  -0.2829
 AHT  OH    O  OH1   0  -0.638   5.6138  -0.0790  -0.7192
 AHT  C1    C  CH2   0  -0.481  -3.2419   0.3726  -0.4394
 AHT  C2    C  CH1   0   0.150  -4.6559  -0.0193  -0.0245
 AHT  O2    O  OH1   0  -0.669  -4.7741  -1.4179   0.1897
 AHT  N2    N  NH2   0  -0.802  -5.6002   0.5281  -0.9604
 AHT  H     H  HNH2  0   0.348  -1.0965   1.9803  -0.9732
 AHT  H2    H  HNH2  0   0.332  -0.7775   2.2491   0.5893
 AHT  HA    H  HCH1  0   0.221  -0.5473  -0.2808  -0.8287
 AHT  HC1   H  HCH2  0   0.216  -2.2338  -1.1346   0.7189
 AHT  HC2   H  HCH2  0   0.209  -2.3578   0.4178   1.5215
 AHT  HB2   H  HCH2  0   0.232   0.1580   0.4361   2.0391
 AHT  HB3   H  HCH2  0   0.238  -0.0023  -1.2079   1.4549
 AHT  HD1   H  HCR6  0   0.237   2.0662   1.8687   1.2036
 AHT  HD2   H  HCR6  0   0.245   1.6792  -2.2149   0.0147
 AHT  HE1   H  HCR6  0   0.256   4.3777   1.8954   0.3771
 AHT  HE2   H  HCR6  0   0.264   3.9809  -2.2015  -0.8212
 AHT  HH    H  HOH1  0   0.471   5.8939  -0.9322  -1.0681
 AHT  H11   H  HCH2  0   0.223  -3.2227   1.4576  -0.5648
 AHT  H12   H  HCH2  0   0.220  -3.0282  -0.0550  -1.4285
 AHT  HC22  H  HCH1  0   0.214  -4.8736   0.4188   0.9541
 AHT  HO2   H  HOH1  0   0.435  -4.4740  -1.8717  -0.6063
 AHT  HN21  H  HNH2  0   0.339  -5.4222   0.1901  -1.8991
 AHT  HN22  H  HNH2  0   0.349  -6.5441   0.2520  -0.7210

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
 AHT  N    CA    single    1.458  0.019  1.458
 AHT  N    H     single    0.860  0.020  0.860
 AHT  N    H2    single    0.890  0.020  1.040
 AHT  CA   C     single    1.525  0.021  1.525
 AHT  CA   CB    single    1.521  0.033  1.521
 AHT  CA   HA    single    0.970  0.020  0.970
 AHT  C    C1    single    1.522  0.020  1.522
 AHT  C    HC1   single    0.970  0.020  1.090
 AHT  C    HC2   single    0.970  0.020  1.090
 AHT  CB   CG    single    1.501  0.020  1.501
 AHT  CB   HB2   single    0.970  0.020  1.090
 AHT  CB   HB3   single    0.970  0.020  1.090
 AHT  CG   CD1   aromatic  1.394  0.020  1.394
 AHT  CG   CD2   aromatic  1.391  0.020  1.391
 AHT  CD1  CE1   aromatic  1.386  0.020  1.386
 AHT  CD1  HD1   single    0.930  0.020  1.080
 AHT  CD2  CE2   aromatic  1.389  0.020  1.389
 AHT  CD2  HD2   single    0.930  0.020  1.080
 AHT  CE1  CZ    aromatic  1.393  0.020  1.393
 AHT  CE1  HE1   single    0.930  0.020  1.080
 AHT  CE2  CZ    aromatic  1.391  0.020  1.391
 AHT  CE2  HE2   single    0.930  0.020  1.080
 AHT  CZ   OH    single    1.351  0.020  1.351
 AHT  OH   HH    single    0.850  0.020  0.980
 AHT  C1   C2    single    1.525  0.020  1.525
 AHT  C1   H11   single    0.970  0.020  1.090
 AHT  C1   H12   single    0.970  0.020  1.090
 AHT  C2   O2    single    1.420  0.020  1.420
 AHT  C2   N2    single    1.438  0.020  1.438
 AHT  C2   HC22  single    0.970  0.020  1.090
 AHT  O2   HO2   single    0.850  0.020  0.980
 AHT  N2   HN21  single    0.890  0.020  1.040
 AHT  N2   HN22  single    0.890  0.020  1.040

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
 AHT  H2    N    H     105.89  3.000
 AHT  H2    N    CA    109.46  3.000
 AHT  H     N    CA    114.00  3.000
 AHT  HA    CA   CB    109.00  3.000
 AHT  HA    CA   C     110.00  3.000
 AHT  CB    CA   C     110.50  1.500
 AHT  HA    CA   N     110.00  3.000
 AHT  CB    CA   N     110.40  1.500
 AHT  C     CA   N     111.00  2.800
 AHT  HC2   C    HC1   106.21  3.000
 AHT  HC2   C    C1    109.38  3.000
 AHT  HC1   C    C1    109.63  3.000
 AHT  HC2   C    CA    109.23  3.000
 AHT  HC1   C    CA    108.52  3.000
 AHT  C1    C    CA    113.61  3.000
 AHT  HB3   CB   HB2   106.33  3.000
 AHT  HB3   CB   CG    109.46  3.000
 AHT  HB2   CB   CG    110.14  3.000
 AHT  HB3   CB   CA    108.51  3.000
 AHT  HB2   CB   CA    108.50  3.000
 AHT  CG    CB   CA    113.62  3.000
 AHT  CD2   CG   CD1   117.42  3.000
 AHT  CD2   CG   CB    120.78  3.000
 AHT  CD1   CG   CB    121.78  3.000
 AHT  HD1   CD1  CE1   118.82  3.000
 AHT  HD1   CD1  CG    119.51  3.000
 AHT  CE1   CD1  CG    121.67  3.000
 AHT  HD2   CD2  CE2   118.74  3.000
 AHT  HD2   CD2  CG    119.45  3.000
 AHT  CE2   CD2  CG    121.81  3.000
 AHT  HE1   CE1  CZ    119.65  3.000
 AHT  HE1   CE1  CD1   120.34  3.000
 AHT  CZ    CE1  CD1   120.01  3.000
 AHT  HE2   CE2  CZ    120.39  3.000
 AHT  HE2   CE2  CD2   119.77  3.000
 AHT  CZ    CE2  CD2   119.83  3.000
 AHT  OH    CZ   CE2   122.83  3.000
 AHT  OH    CZ   CE1   117.93  3.000
 AHT  CE2   CZ   CE1   119.24  3.000
 AHT  HH    OH   CZ    110.32  3.000
 AHT  H12   C1   H11   106.25  3.000
 AHT  H12   C1   C2    108.99  3.000
 AHT  H11   C1   C2    107.63  3.000
 AHT  H12   C1   C     109.78  3.000
 AHT  H11   C1   C     110.01  3.000
 AHT  C2    C1   C     113.88  3.000
 AHT  HC22  C2   N2    107.40  3.000
 AHT  HC22  C2   O2    104.06  3.000
 AHT  N2    C2   O2    114.74  3.000
 AHT  HC22  C2   C1    108.96  3.000
 AHT  N2    C2   C1    109.51  3.000
 AHT  O2    C2   C1    111.80  3.000
 AHT  HO2   O2   C2    108.25  3.000
 AHT  HN22  N2   HN21  106.98  3.000
 AHT  HN22  N2   C2    110.77  3.000
 AHT  HN21  N2   C2    111.14  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
 AHT  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 AHT  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 AHT  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 AHT  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 AHT  CONST_05  CE1  CD1  CG   CD2    0.00   0.0  0
 AHT  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 AHT  CONST_07  CE1  CD1  CG   CB   180.00   0.0  0
 AHT  CONST_08  CE2  CD2  CG   CB   180.00   0.0  0
 AHT  CONST_09  OH   CZ   CE1  CD1  180.00   0.0  0
 AHT  CONST_10  OH   CZ   CE2  CD2  180.00   0.0  0
 AHT  CONST_11  HE1  CE1  CD1  CG   180.00   0.0  0
 AHT  CONST_12  HE2  CE2  CD2  CG   180.00   0.0  0
 AHT  CONST_13  HD2  CD2  CG   CD1  180.00   0.0  0
 AHT  CONST_14  HD1  CD1  CG   CD2  180.00   0.0  0
 AHT  Var_01    CD1  CG   CB   CA    86.39  30.0  2
 AHT  Var_02    C2   C1   C    CA   177.14  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
 AHT  chir_01  CA  N   C   CB  positiv
 AHT  chir_02  C2  O2  N2  C1  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
 AHT  plan-1  CB   0.020
 AHT  plan-1  CG   0.020
 AHT  plan-1  CD1  0.020
 AHT  plan-1  CD2  0.020
 AHT  plan-1  CE1  0.020
 AHT  plan-1  CE2  0.020
 AHT  plan-1  CZ   0.020
 AHT  plan-1  OH   0.020
 AHT  plan-1  HD1  0.020
 AHT  plan-1  HD2  0.020
 AHT  plan-1  HE1  0.020
 AHT  plan-1  HE2  0.020

