# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 17:21:50 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  35  16  .  2022-07-23  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.663  -3.6759   1.7301  -0.1254
 5OM  C02  C  CT    0   0.479  -3.5553   0.3416  -0.0078
 5OM  C03  C  CH2   0  -0.518  -2.2075  -0.1741  -0.5203
 5OM  C04  C  CH2   0  -0.414  -0.9844   0.4208   0.1665
 5OM  C05  C  CH2   0  -0.419   0.3087  -0.1757  -0.3754
 5OM  C06  C  CH2   0  -0.407   1.5573   0.3940   0.2855
 5OM  C07  C  CH2   0  -0.432   2.8301  -0.2403  -0.2588
 5OM  C08  C  CH1   0  -0.206   4.1035   0.2692   0.4308
 5OM  N09  N  NH2   0  -0.776   4.2447   1.6949   0.2609
 5OM  C27  C  C     0   0.520   5.2981  -0.5251  -0.0814
 5OM  O28  O  O     0  -0.442   6.1493  -0.0882  -0.8155
 5OM  O02  O  OH1   0  -0.666  -3.7078   0.1172   1.3605
 5OM  C30  C  CH1   0  -0.054  -4.6855  -0.3092  -0.8002
 5OM  C31  C  CH2   0  -0.249  -6.0070  -0.5181  -0.2288
 5OM  O32  O  O2    0  -0.488  -5.0916  -1.5994  -0.3818
 5OM  OXT  O  OH1   0  -0.595   5.2934  -1.7788   0.3596
 5OM  H1   H  HOH1  0   0.459  -3.2989   2.0149  -0.9640
 5OM  H2   H  HCH2  0   0.240  -2.1918  -1.2641  -0.4092
 5OM  H3   H  HCH2  0   0.234  -2.1465   0.0068  -1.5996
 5OM  H4   H  HCH2  0   0.217  -0.9651   1.5062   0.0323
 5OM  H5   H  HCH2  0   0.220  -1.0412   0.2443   1.2439
 5OM  H6   H  HCH2  0   0.211   0.2900  -1.2629  -0.2407
 5OM  H7   H  HCH2  0   0.212   0.3626  -0.0080  -1.4569
 5OM  H8   H  HCH2  0   0.222   1.5914   1.4762   0.1424
 5OM  H9   H  HCH2  0   0.211   1.5059   0.2286   1.3673
 5OM  H10  H  HCH2  0   0.238   2.7651  -1.3247  -0.1421
 5OM  H11  H  HCH2  0   0.228   2.9060  -0.0511  -1.3355
 5OM  H12  H  HCH1  0   0.264   4.0095   0.0595   1.5017
 5OM  H13  H  HNH2  0   0.353   5.0592   2.0321   0.7576
 5OM  H14  H  HNH2  0   0.342   4.3954   1.9168  -0.7158
 5OM  H16  H  HOH1  0   0.453  -3.6850  -0.8324   1.5244
 5OM  H17  H  HCH1  0   0.258  -4.6033  -0.1850  -1.8808
 5OM  H18  H  HCH2  0   0.244  -6.2165  -0.2154   0.7921
 5OM  H19  H  HCH2  0   0.244  -6.8706  -0.5389  -0.8871
 5OM  H20  H  HOH1  0   0.480   6.0419  -2.2664  -0.0154

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  1.425  0.020  1.425
 5OM  C02  C03  single  1.531  0.020  1.531
 5OM  C02  O02  single  1.395  0.020  1.395
 5OM  C03  C04  single  1.524  0.020  1.524
 5OM  C27  O28  double  1.206  0.020  1.206
 5OM  C27  C08  single  1.523  0.020  1.523
 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  1.535  0.020  1.535
 5OM  C08  N09  single  1.443  0.020  1.443
 5OM  C27  OXT  single  1.329  0.020  1.329
 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
 5OM  OXT  H20  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
 5OM  H1   O01  C02  109.46  3.000
 5OM  C30  C02  O02  111.09  3.000
 5OM  O02  C02  C03  111.74  3.000
 5OM  C30  C02  C03  109.54  3.000
 5OM  O02  C02  O01  103.46  3.000
 5OM  C03  C02  O01  112.46  3.000
 5OM  C30  C02  O01  108.41  3.000
 5OM  H3   C03  H2   105.26  3.000
 5OM  H3   C03  C04  109.56  3.000
 5OM  H2   C03  C04  109.34  3.000
 5OM  H3   C03  C02  108.84  3.000
 5OM  H2   C03  C02  108.28  3.000
 5OM  C04  C03  C02  115.10  3.000
 5OM  H5   C04  H4   106.38  3.000
 5OM  H5   C04  C05  109.35  3.000
 5OM  H4   C04  C05  109.26  3.000
 5OM  H5   C04  C03  109.84  3.000
 5OM  H4   C04  C03  110.26  3.000
 5OM  C05  C04  C03  111.60  3.000
 5OM  H7   C05  H6   105.90  3.000
 5OM  H7   C05  C06  109.31  3.000
 5OM  H6   C05  C06  109.38  3.000
 5OM  H7   C05  C04  109.44  3.000
 5OM  H6   C05  C04  109.28  3.000
 5OM  C06  C05  C04  113.26  3.000
 5OM  H9   C06  H8   106.28  3.000
 5OM  H9   C06  C07  109.23  3.000
 5OM  H8   C06  C07  109.87  3.000
 5OM  H9   C06  C05  109.48  3.000
 5OM  H8   C06  C05  109.83  3.000
 5OM  C07  C06  C05  111.98  3.000
 5OM  H11  C07  H10  106.28  3.000
 5OM  H11  C07  C08  109.06  3.000
 5OM  H10  C07  C08  109.32  3.000
 5OM  H11  C07  C06  109.71  3.000
 5OM  H10  C07  C06  108.99  3.000
 5OM  C08  C07  C06  113.24  3.000
 5OM  H12  C08  C27  107.23  3.000
 5OM  H12  C08  N09  108.22  3.000
 5OM  C27  C08  N09  113.52  3.000
 5OM  H12  C08  C07  107.72  3.000
 5OM  N09  C08  C07  110.87  3.000
 5OM  C27  C08  C07  109.05  3.000
 5OM  H14  N09  H13  106.29  3.000
 5OM  H14  N09  C08  110.16  3.000
 5OM  H13  N09  C08  110.51  3.000
 5OM  OXT  C27  O28  123.11  3.000
 5OM  OXT  C27  C08  112.19  3.000
 5OM  O28  C27  C08  124.70  3.000
 5OM  H16  O02  C02  108.82  3.000
 5OM  H17  C30  O32  114.72  3.000
 5OM  H17  C30  C31  118.29  3.000
 5OM  O32  C30  C31   59.51  3.000
 5OM  H17  C30  C02  114.21  3.000
 5OM  C31  C30  C02  122.01  3.000
 5OM  O32  C30  C02  116.59  3.000
 5OM  H19  C31  H18  114.96  3.000
 5OM  H19  C31  O32  115.54  3.000
 5OM  H18  C31  O32  115.89  3.000
 5OM  H19  C31  C30  119.14  3.000
 5OM  H18  C31  C30  120.32  3.000
 5OM  O32  C31  C30   58.89  3.000
 5OM  C31  O32  C30   61.61  3.000
 5OM  H20  OXT  C27  110.10  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  CONST_01  H20  OXT  C27  C08   180.00   0.0  0
 5OM  Var_01    H18  C31  O32  C30  -111.25  30.0  1
 5OM  Var_02    H17  C30  O32  C31  -109.53  30.0  1
 5OM  Var_03    O32  C30  C02  O01  -154.12  30.0  1
 5OM  Var_04    C30  C02  C03  C04   178.70  30.0  2
 5OM  Var_05    C05  C04  C03  C02   178.35  30.0  3
 5OM  Var_06    C06  C05  C04  C03   179.96  30.0  3
 5OM  Var_07    C07  C06  C05  C04   178.93  30.0  3
 5OM  Var_08    C08  C07  C06  C05  -177.50  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
 5OM  plan-1  H20  0.020

