# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 13:38:52 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: (2S)-2-amino-8,8-dihydroxy-8-[(2S)-oxiran-2-yl]octanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCCC(O)(O)[C@@H]1CO1)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
 5OM  5OM  '(2S)-2-amino-8,8-dihydroxy-8-[(2S)-oxiran-2-yl]octanoic acid'  L-peptide  34  16  .  2022-07-23  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_5OM
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
 5OM  O01  O  OH1    0  -0.665  -3.6961   1.7639  -0.0358
 5OM  C02  C  CT     0   0.480  -3.5935   0.3699   0.0124
 5OM  C03  C  CH2    0  -0.519  -2.2508  -0.1375  -0.5205
 5OM  C04  C  CH2    0  -0.414  -1.0213   0.4253   0.1825
 5OM  C05  C  CH2    0  -0.415   0.2667  -0.1804  -0.3620
 5OM  C06  C  CH2    0  -0.403   1.5221   0.3696   0.3025
 5OM  C07  C  CH2    0  -0.417   2.7962  -0.2669  -0.2360
 5OM  C08  C  CH1    0  -0.212   4.0814   0.2417   0.4223
 5OM  N09  N  NH2    0  -0.785   4.2086   1.6785   0.2281
 5OM  C27  C  C      0   0.383   5.2808  -0.6042  -0.0746
 5OM  O28  O  O      0  -0.609   6.1246  -0.0439  -0.8023
 5OM  O02  O  OH1    0  -0.666  -3.7543   0.0759   1.3673
 5OM  C30  C  CH1    0  -0.053  -4.7301  -0.2212  -0.8159
 5OM  C31  C  CH2    0  -0.249  -6.0571  -0.4385  -0.2603
 5OM  O32  O  O2     0  -0.488  -5.1580  -1.5252  -0.4674
 5OM  OXT  O  OC    -1  -0.626   5.2920  -1.8010   0.2850
 5OM  H1   H  HOH1   0   0.460  -3.2554   2.0925  -0.8257
 5OM  H2   H  HCH2   0   0.241  -2.2437  -1.2306  -0.4441
 5OM  H3   H  HCH2   0   0.233  -2.1896   0.0776  -1.5935
 5OM  H4   H  HCH2   0   0.214  -0.9825   1.5126   0.0662
 5OM  H5   H  HCH2   0   0.219  -1.0871   0.2326   1.2566
 5OM  H6   H  HCH2   0   0.207   0.2348  -1.2686  -0.2364
 5OM  H7   H  HCH2   0   0.207   0.3226  -0.0055  -1.4425
 5OM  H8   H  HCH2   0   0.211   1.5671   1.4531   0.1671
 5OM  H9   H  HCH2   0   0.199   1.4642   0.2010   1.3842
 5OM  H10  H  HCH2   0   0.214   2.7425  -1.3501  -0.1017
 5OM  H11  H  HCH2   0   0.201   2.8563  -0.0980  -1.3191
 5OM  H12  H  HCH1   0   0.204   3.9831   0.0652   1.5007
 5OM  H13  H  HNH2   0   0.332   5.0165   2.0046   0.7451
 5OM  H14  H  HNH2   0   0.321   4.4551   1.8387  -0.7424
 5OM  H16  H  HOH1   0   0.452  -3.7711  -0.8817   1.4780
 5OM  H17  H  HCH1   0   0.258  -4.6419  -0.0407  -1.8880
 5OM  H18  H  HCH2   0   0.244  -6.2648  -0.1871   0.7749
 5OM  H19  H  HCH2   0   0.244  -6.9186  -0.4107  -0.9209

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
 5OM  C30  O32  single  1.416  0.020  1.416
 5OM  C30  C31  single  1.455  0.020  1.455
 5OM  C30  C02  single  1.526  0.020  1.526
 5OM  O01  C02  single  1.399  0.020  1.399
 5OM  O32  C31  single  1.426  0.020  1.426
 5OM  C02  C03  single  1.531  0.020  1.531
 5OM  C02  O02  single  1.396  0.020  1.396
 5OM  C03  C04  single  1.524  0.020  1.524
 5OM  C27  O28  deloc   1.247  0.020  1.247
 5OM  C27  C08  single  1.549  0.020  1.549
 5OM  C04  C05  single  1.524  0.020  1.524
 5OM  C05  C06  single  1.523  0.020  1.523
 5OM  C06  C07  single  1.523  0.020  1.523
 5OM  C07  C08  single  1.531  0.020  1.531
 5OM  C08  N09  single  1.455  0.020  1.455
 5OM  C27  OXT  deloc   1.250  0.020  1.250
 5OM  O01  H1   single  0.850  0.020  0.980
 5OM  C03  H2   single  0.970  0.020  1.090
 5OM  C03  H3   single  0.970  0.020  1.090
 5OM  C04  H4   single  0.970  0.020  1.090
 5OM  C04  H5   single  0.970  0.020  1.090
 5OM  C05  H6   single  0.970  0.020  1.090
 5OM  C05  H7   single  0.970  0.020  1.090
 5OM  C06  H8   single  0.970  0.020  1.090
 5OM  C06  H9   single  0.970  0.020  1.090
 5OM  C07  H10  single  0.970  0.020  1.090
 5OM  C07  H11  single  0.970  0.020  1.090
 5OM  C08  H12  single  0.970  0.020  1.090
 5OM  N09  H13  single  0.890  0.020  1.040
 5OM  N09  H14  single  0.890  0.020  1.040
 5OM  O02  H16  single  0.850  0.020  0.980
 5OM  C30  H17  single  0.970  0.020  1.090
 5OM  C31  H18  single  0.970  0.020  1.090
 5OM  C31  H19  single  0.970  0.020  1.090

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
 5OM  H1   O01  C02  109.57  3.000
 5OM  C30  C02  O02  111.08  3.000
 5OM  O02  C02  C03  111.66  3.000
 5OM  C30  C02  C03  109.63  3.000
 5OM  O02  C02  O01  103.59  3.000
 5OM  C03  C02  O01  112.50  3.000
 5OM  C30  C02  O01  108.23  3.000
 5OM  H3   C03  H2   105.29  3.000
 5OM  H3   C03  C04  109.51  3.000
 5OM  H2   C03  C04  109.33  3.000
 5OM  H3   C03  C02  108.94  3.000
 5OM  H2   C03  C02  108.18  3.000
 5OM  C04  C03  C02  115.12  3.000
 5OM  H5   C04  H4   106.37  3.000
 5OM  H5   C04  C05  109.38  3.000
 5OM  H4   C04  C05  109.09  3.000
 5OM  H5   C04  C03  109.85  3.000
 5OM  H4   C04  C03  110.28  3.000
 5OM  C05  C04  C03  111.73  3.000
 5OM  H7   C05  H6   105.84  3.000
 5OM  H7   C05  C06  109.30  3.000
 5OM  H6   C05  C06  109.43  3.000
 5OM  H7   C05  C04  109.38  3.000
 5OM  H6   C05  C04  109.21  3.000
 5OM  C06  C05  C04  113.40  3.000
 5OM  H9   C06  H8   106.08  3.000
 5OM  H9   C06  C07  109.20  3.000
 5OM  H8   C06  C07  109.64  3.000
 5OM  H9   C06  C05  109.36  3.000
 5OM  H8   C06  C05  109.75  3.000
 5OM  C07  C06  C05  112.61  3.000
 5OM  H11  C07  H10  106.05  3.000
 5OM  H11  C07  C08  109.10  3.000
 5OM  H10  C07  C08  108.52  3.000
 5OM  H11  C07  C06  109.30  3.000
 5OM  H10  C07  C06  109.25  3.000
 5OM  C08  C07  C06  114.30  3.000
 5OM  H12  C08  C27  107.26  3.000
 5OM  H12  C08  N09  107.32  3.000
 5OM  C27  C08  N09  115.37  3.000
 5OM  H12  C08  C07  107.10  3.000
 5OM  N09  C08  C07  110.12  3.000
 5OM  C27  C08  C07  109.31  3.000
 5OM  H14  N09  H13  104.10  3.000
 5OM  H14  N09  C08  107.75  3.000
 5OM  H13  N09  C08  108.62  3.000
 5OM  OXT  C27  O28  126.30  3.000
 5OM  OXT  C27  C08  115.95  3.000
 5OM  O28  C27  C08  117.74  3.000
 5OM  H16  O02  C02  108.83  3.000
 5OM  H17  C30  O32  114.76  3.000
 5OM  H17  C30  C31  118.28  3.000
 5OM  O32  C30  C31   59.53  3.000
 5OM  H17  C30  C02  114.16  3.000
 5OM  C31  C30  C02  122.00  3.000
 5OM  O32  C30  C02  116.63  3.000
 5OM  H19  C31  H18  114.99  3.000
 5OM  H19  C31  O32  115.56  3.000
 5OM  H18  C31  O32  115.84  3.000
 5OM  H19  C31  C30  119.17  3.000
 5OM  H18  C31  C30  120.28  3.000
 5OM  O32  C31  C30   58.88  3.000
 5OM  C31  O32  C30   61.60  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
 5OM  Var_01  H18  C31  O32  C30  -111.23  30.0  1
 5OM  Var_02  H17  C30  O32  C31  -109.52  30.0  1
 5OM  Var_03  O32  C30  C02  O01  -154.13  30.0  1
 5OM  Var_04  C30  C02  C03  C04   177.49  30.0  3
 5OM  Var_05  C05  C04  C03  C02   177.23  30.0  3
 5OM  Var_06  C06  C05  C04  C03   179.25  30.0  3
 5OM  Var_07  C07  C06  C05  C04   178.90  30.0  3
 5OM  Var_08  C08  C07  C06  C05  -179.04  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
 5OM  chir_01  C08  C27  C07  N09  positiv
 5OM  chir_02  C30  O32  C31  C02  both

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
 5OM  plan-1  C08  0.020
 5OM  plan-1  C27  0.020
 5OM  plan-1  O28  0.020
 5OM  plan-1  OXT  0.020

