# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 12:15:00 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: (2S,3R)-3-amino-2-hydroxydecanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCC[C@@H](N)[C@H](O)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
 AHY  AHY  '(2S,3R)-3-amino-2-hydroxydecanoic acid'  ligand  35  14  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_AHY
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
 AHY  C10   C  CH3   0  -0.662   7.9020   9.4742  -1.4236
 AHY  C9    C  CH2   0  -0.419   8.7285   8.2267  -1.1435
 AHY  C8    C  CH2   0  -0.407   8.0020   7.2241  -0.2549
 AHY  C7    C  CH2   0  -0.412   8.8179   5.9701   0.0315
 AHY  C6    C  CH2   0  -0.412   8.0968   4.9761   0.9334
 AHY  C5    C  CH2   0  -0.419   8.9111   3.7171   1.2033
 AHY  C4    C  CH2   0  -0.435   8.2042   2.7481   2.1440
 AHY  C3    C  CH1   0  -0.150   8.9585   1.4349   2.3300
 AHY  N3    N  NH2   0  -0.813  10.3358   1.5636   2.7852
 AHY  C2    C  CH1   0  -0.001   8.2769   0.4798   3.3442
 AHY  OH2   O  OH1   0  -0.680   9.1130  -0.6082   3.5914
 AHY  C1    C  C     0   0.510   6.9698  -0.0456   2.7878
 AHY  O     O  O     0  -0.435   6.8832  -0.9908   2.0475
 AHY  OXT   O  OH1   0  -0.590   5.9294   0.6685   3.1972
 AHY  H101  H  HCH3  0   0.216   6.9704   9.2223  -1.9341
 AHY  H102  H  HCH3  0   0.215   7.6388   9.9877  -0.4966
 AHY  H103  H  HCH3  0   0.225   8.4418  10.1829  -2.0528
 AHY  H9C1  H  HCH2  0   0.210   8.9971   7.7436  -2.0882
 AHY  H9C2  H  HCH2  0   0.210   9.6734   8.5089  -0.6690
 AHY  H8C1  H  HCH2  0   0.206   7.7332   7.7072   0.6912
 AHY  H8C2  H  HCH2  0   0.206   7.0549   6.9425  -0.7287
 AHY  H7C1  H  HCH2  0   0.207   9.7696   6.2525   0.4953
 AHY  H7C2  H  HCH2  0   0.207   9.0766   5.4812  -0.9145
 AHY  H6C1  H  HCH2  0   0.210   7.1393   4.7013   0.4778
 AHY  H6C2  H  HCH2  0   0.209   7.8512   5.4614   1.8846
 AHY  H5C1  H  HCH2  0   0.212   9.8800   4.0010   1.6251
 AHY  H5C2  H  HCH2  0   0.214   9.1265   3.2139   0.2541
 AHY  H4C1  H  HCH2  0   0.220   8.0523   3.2278   3.1179
 AHY  H4C2  H  HCH2  0   0.229   7.2061   2.5408   1.7474
 AHY  H3    H  HCH1  0   0.247   8.9997   0.9132   1.3673
 AHY  H3N1  H  HNH2  0   0.358  10.4190   2.2712   3.5066
 AHY  H3N2  H  HNH2  0   0.373  10.9443   1.8381   2.0264
 AHY  HXT   H  HOH1  0   0.482   5.1154   0.3394   2.7860
 AHY  H2O   H  HOH1  0   0.445  10.0060  -0.2288   3.4813
 AHY  H2    H  HCH1  0   0.224   8.0673   1.0499   4.2623

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
 AHY  C10  C9    single  1.522  0.020  1.522
 AHY  C10  H101  single  0.970  0.020  1.090
 AHY  C10  H102  single  0.970  0.020  1.090
 AHY  C10  H103  single  0.970  0.020  1.090
 AHY  C9   C8    single  1.524  0.020  1.524
 AHY  C9   H9C1  single  0.970  0.020  1.090
 AHY  C9   H9C2  single  0.970  0.020  1.090
 AHY  C8   C7    single  1.523  0.020  1.523
 AHY  C8   H8C1  single  0.970  0.020  1.090
 AHY  C8   H8C2  single  0.970  0.020  1.090
 AHY  C7   C6    single  1.524  0.020  1.524
 AHY  C7   H7C1  single  0.970  0.020  1.090
 AHY  C7   H7C2  single  0.970  0.020  1.090
 AHY  C6   C5    single  1.523  0.020  1.523
 AHY  C6   H6C1  single  0.970  0.020  1.090
 AHY  C6   H6C2  single  0.970  0.020  1.090
 AHY  C5   C4    single  1.524  0.020  1.524
 AHY  C5   H5C1  single  0.970  0.020  1.090
 AHY  C5   H5C2  single  0.970  0.020  1.090
 AHY  C4   C3    single  1.526  0.020  1.526
 AHY  C4   H4C1  single  0.970  0.020  1.090
 AHY  C4   H4C2  single  0.970  0.020  1.090
 AHY  C3   H3    single  0.970  0.020  1.090
 AHY  C3   N3    single  1.456  0.020  1.456
 AHY  C3   C2    single  1.551  0.020  1.551
 AHY  N3   H3N1  single  0.890  0.020  1.040
 AHY  N3   H3N2  single  0.890  0.020  1.040
 AHY  C2   H2    single  0.970  0.020  1.090
 AHY  C2   OH2   single  1.394  0.020  1.394
 AHY  C2   C1    single  1.515  0.020  1.515
 AHY  OH2  H2O   single  0.850  0.020  0.980
 AHY  C1   O     double  1.204  0.020  1.204
 AHY  C1   OXT   single  1.327  0.020  1.327
 AHY  OXT  HXT   single  0.850  0.020  0.980

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
 AHY  H103  C10  H102  107.67  3.000
 AHY  H103  C10  H101  107.61  3.000
 AHY  H102  C10  H101  107.44  3.000
 AHY  H103  C10  C9    111.71  3.000
 AHY  H102  C10  C9    111.10  3.000
 AHY  H101  C10  C9    111.11  3.000
 AHY  H9C2  C9   H9C1  106.03  3.000
 AHY  H9C2  C9   C8    109.18  3.000
 AHY  H9C1  C9   C8    109.27  3.000
 AHY  H9C2  C9   C10   109.70  3.000
 AHY  H9C1  C9   C10   109.63  3.000
 AHY  C8    C9   C10   112.80  3.000
 AHY  H8C2  C8   H8C1  105.94  3.000
 AHY  H8C2  C8   C7    109.43  3.000
 AHY  H8C1  C8   C7    109.39  3.000
 AHY  H8C2  C8   C9    109.21  3.000
 AHY  H8C1  C8   C9    109.29  3.000
 AHY  C7    C8   C9    113.32  3.000
 AHY  H7C2  C7   H7C1  105.98  3.000
 AHY  H7C2  C7   C6    109.37  3.000
 AHY  H7C1  C7   C6    109.19  3.000
 AHY  H7C2  C7   C8    109.35  3.000
 AHY  H7C1  C7   C8    109.43  3.000
 AHY  C6    C7   C8    113.26  3.000
 AHY  H6C2  C6   H6C1  106.04  3.000
 AHY  H6C2  C6   C5    109.39  3.000
 AHY  H6C1  C6   C5    109.49  3.000
 AHY  H6C2  C6   C7    109.33  3.000
 AHY  H6C1  C6   C7    109.34  3.000
 AHY  C5    C6   C7    113.02  3.000
 AHY  H5C2  C5   H5C1  106.20  3.000
 AHY  H5C2  C5   C4    109.50  3.000
 AHY  H5C1  C5   C4    109.74  3.000
 AHY  H5C2  C5   C6    109.34  3.000
 AHY  H5C1  C5   C6    109.10  3.000
 AHY  C4    C5   C6    112.75  3.000
 AHY  H4C2  C4   H4C1  106.18  3.000
 AHY  H4C2  C4   C3    109.40  3.000
 AHY  H4C1  C4   C3    109.68  3.000
 AHY  H4C2  C4   C5    108.66  3.000
 AHY  H4C1  C4   C5    109.54  3.000
 AHY  C3    C4   C5    113.15  3.000
 AHY  H3    C3   C2    107.33  3.000
 AHY  C2    C3   N3    105.40  3.000
 AHY  H3    C3   N3    106.33  3.000
 AHY  C2    C3   C4    113.11  3.000
 AHY  N3    C3   C4    115.44  3.000
 AHY  H3    C3   C4    108.75  3.000
 AHY  H3N2  N3   H3N1  107.17  3.000
 AHY  H3N2  N3   C3    111.02  3.000
 AHY  H3N1  N3   C3    111.20  3.000
 AHY  H2    C2   C1    108.77  3.000
 AHY  C1    C2   OH2   108.18  3.000
 AHY  H2    C2   OH2   111.74  3.000
 AHY  C1    C2   C3    110.65  3.000
 AHY  OH2   C2   C3    109.45  3.000
 AHY  H2    C2   C3    108.07  3.000
 AHY  H2O   OH2  C2    103.02  3.000
 AHY  OXT   C1   O     123.79  3.000
 AHY  OXT   C1   C2    112.13  3.000
 AHY  O     C1   C2    124.08  3.000
 AHY  HXT   OXT  C1    110.17  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
 AHY  CONST_01  HXT   OXT  C1  C2   180.00   0.0  0
 AHY  Var_01    C7    C8   C9  C10  179.92  30.0  3
 AHY  Var_02    C6    C7   C8  C9   179.32  30.0  3
 AHY  Var_03    C5    C6   C7  C8   179.34  30.0  3
 AHY  Var_04    C4    C5   C6  C7   178.05  30.0  3
 AHY  Var_05    C3    C4   C5  C6   175.26  30.0  3
 AHY  Var_06    H101  C10  C9  C8   -60.34  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
 AHY  chir_01  C3  C4   N3  C2  negativ
 AHY  chir_02  C2  OH2  C3  C1  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
 AHY  plan-1  C2   0.020
 AHY  plan-1  C1   0.020
 AHY  plan-1  O    0.020
 AHY  plan-1  OXT  0.020
 AHY  plan-1  HXT  0.020

