# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 16:54:16 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: N-{[(2S,3S)-3-(ethoxycarbonyl)oxiran-2-yl]carbonyl}-L-isoleucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)[C@H]1O[C@@H]1C(=O)N[C@@H]([C@@H](C)CC)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
 59A  59A  N-{[(2S,3S)-3-(ethoxycarbonyl)oxiran-2-yl]carbonyl}-L-isoleucine  ligand  38  19  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_59A
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
 59A  C2    C  CH1   0  -0.142   2.4546  -0.7001   0.2173
 59A  O1    O  O2    0  -0.437   2.0969  -1.6405   1.1939
 59A  C3    C  CH1   0  -0.144   1.2484  -0.5357   1.0444
 59A  C4    C  C     0   0.591  -0.0824  -0.8254   0.4069
 59A  O4    O  O     0  -0.479  -0.2442  -1.7712  -0.3449
 59A  N1    N  NH1   0  -0.666  -1.0473   0.0466   0.7184
 59A  C5    C  CH1   0  -0.127  -2.3771  -0.0811   0.1761
 59A  C6    C  C     0   0.540  -2.3164   0.0090  -1.3412
 59A  O5    O  OH1   0  -0.585  -3.2714  -0.7101  -1.9123
 59A  C10   C  CH1   0  -0.296  -3.2984   0.9997   0.7842
 59A  C12   C  CH2   0  -0.415  -4.7733   0.7158   0.4846
 59A  C11   C  CH3   0  -0.671  -2.8995   2.4188   0.3842
 59A  C13   C  CH3   0  -0.671  -5.7228   1.5515   1.3331
 59A  OA    O  O     0  -0.434  -1.5228   0.6767  -1.9510
 59A  C7    C  C     0   0.605   3.6436   0.1490   0.5512
 59A  O2    O  O     0  -0.441   4.0584   0.3070   1.6693
 59A  O3    O  O2    0  -0.451   4.1396   0.6990  -0.5365
 59A  C8    C  CH2   0  -0.186   5.2602   1.5942  -0.3957
 59A  C9    C  CH3   0  -0.690   5.6617   2.0496  -1.7762
 59A  H2    H  HCH1  0   0.299   2.3470  -1.0129  -0.8184
 59A  H3    H  HCH1  0   0.298   1.2657   0.1885   1.8570
 59A  HN1   H  HNH1  0   0.415  -0.8583   0.7852   1.3777
 59A  H5    H  HCH1  0   0.292  -2.7844  -1.0592   0.4496
 59A  HO5   H  HOH1  0   0.482  -3.2487  -0.5882  -2.8738
 59A  H10   H  HCH1  0   0.257  -3.1645   0.8953   1.8679
 59A  H121  H  HCH2  0   0.225  -4.9811   0.8960  -0.5732
 59A  H122  H  HCH2  0   0.231  -4.9786  -0.3427   0.6653
 59A  H111  H  HCH3  0   0.247  -3.4387   3.1478   0.9869
 59A  H112  H  HCH3  0   0.235  -1.8366   2.6146   0.5281
 59A  H113  H  HCH3  0   0.229  -3.1352   2.6215  -0.6614
 59A  H131  H  HCH3  0   0.235  -6.7595   1.2904   1.1207
 59A  H132  H  HCH3  0   0.222  -5.5518   1.3845   2.3981
 59A  H133  H  HCH3  0   0.226  -5.6127   2.6195   1.1432
 59A  H81   H  HCH2  0   0.244   6.0806   1.0730   0.1001
 59A  H82   H  HCH2  0   0.243   4.9676   2.4396   0.2298
 59A  H91   H  HCH3  0   0.243   6.4994   2.7407  -1.6910
 59A  H92   H  HCH3  0   0.239   5.9813   1.2130  -2.3975
 59A  H93   H  HCH3  0   0.239   4.8484   2.5702  -2.2812

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
 59A  C2   O1    single  1.402  0.020  1.402
 59A  C2   C3    single  1.472  0.020  1.472
 59A  C2   C7    single  1.499  0.020  1.499
 59A  C2   H2    single  0.970  0.020  1.090
 59A  O1   C3    single  1.401  0.020  1.401
 59A  C3   C4    single  1.504  0.020  1.504
 59A  C3   H3    single  0.970  0.020  1.090
 59A  C4   O4    double  1.219  0.020  1.219
 59A  C4   N1    single  1.337  0.020  1.337
 59A  N1   C5    single  1.442  0.020  1.442
 59A  N1   HN1   single  0.860  0.020  1.020
 59A  C5   C6    single  1.521  0.020  1.521
 59A  C5   C10   single  1.545  0.020  1.545
 59A  C5   H5    single  0.970  0.020  1.090
 59A  C6   O5    single  1.325  0.020  1.325
 59A  C6   OA    double  1.203  0.020  1.203
 59A  O5   HO5   single  0.850  0.020  0.980
 59A  C10  C12   single  1.531  0.020  1.531
 59A  C10  C11   single  1.527  0.020  1.527
 59A  C10  H10   single  0.970  0.020  1.090
 59A  C12  C13   single  1.523  0.020  1.523
 59A  C12  H121  single  0.970  0.020  1.090
 59A  C12  H122  single  0.970  0.020  1.090
 59A  C11  H111  single  0.970  0.020  1.090
 59A  C11  H112  single  0.970  0.020  1.090
 59A  C11  H113  single  0.970  0.020  1.090
 59A  C13  H131  single  0.970  0.020  1.090
 59A  C13  H132  single  0.970  0.020  1.090
 59A  C13  H133  single  0.970  0.020  1.090
 59A  C7   O2    double  1.203  0.020  1.203
 59A  C7   O3    single  1.316  0.020  1.316
 59A  O3   C8    single  1.441  0.020  1.441
 59A  C8   C9    single  1.508  0.020  1.508
 59A  C8   H81   single  0.970  0.020  1.090
 59A  C8   H82   single  0.970  0.020  1.090
 59A  C9   H91   single  0.970  0.020  1.090
 59A  C9   H92   single  0.970  0.020  1.090
 59A  C9   H93   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
 59A  H2    C2   C7    116.98  3.000
 59A  H2    C2   C3    119.10  3.000
 59A  C7    C2   C3    117.50  3.000
 59A  H2    C2   O1    116.44  3.000
 59A  C7    C2   O1    115.29  3.000
 59A  C3    C2   O1     58.29  3.000
 59A  C3    O1   C2     63.34  3.000
 59A  H3    C3   C4    117.30  3.000
 59A  H3    C3   O1    115.80  3.000
 59A  C4    C3   O1    115.42  3.000
 59A  H3    C3   C2    118.74  3.000
 59A  C4    C3   C2    117.75  3.000
 59A  O1    C3   C2     58.37  3.000
 59A  N1    C4   O4    123.62  3.000
 59A  N1    C4   C3    114.47  3.000
 59A  O4    C4   C3    121.90  3.000
 59A  HN1   N1   C5    118.94  3.000
 59A  HN1   N1   C4    119.66  3.000
 59A  C5    N1   C4    121.34  3.000
 59A  H5    C5   C10   107.76  3.000
 59A  H5    C5   C6    108.49  3.000
 59A  C10   C5   C6    112.02  3.000
 59A  H5    C5   N1    109.18  3.000
 59A  C10   C5   N1    109.88  3.000
 59A  C6    C5   N1    109.46  3.000
 59A  OA    C6   O5    123.93  3.000
 59A  OA    C6   C5    124.39  3.000
 59A  O5    C6   C5    111.66  3.000
 59A  HO5   O5   C6    110.03  3.000
 59A  H10   C10  C11   108.38  3.000
 59A  H10   C10  C12   107.05  3.000
 59A  C11   C10  C12   111.87  3.000
 59A  H10   C10  C5    104.45  3.000
 59A  C11   C10  C5    113.03  3.000
 59A  C12   C10  C5    111.57  3.000
 59A  H122  C12  H121  106.49  3.000
 59A  H122  C12  C13   108.79  3.000
 59A  H121  C12  C13   109.28  3.000
 59A  H122  C12  C10   109.14  3.000
 59A  H121  C12  C10   109.99  3.000
 59A  C13   C12  C10   112.93  3.000
 59A  H113  C11  H112  107.68  3.000
 59A  H113  C11  H111  107.41  3.000
 59A  H112  C11  H111  106.82  3.000
 59A  H113  C11  C10   111.55  3.000
 59A  H112  C11  C10   112.77  3.000
 59A  H111  C11  C10   110.35  3.000
 59A  H133  C13  H132  107.70  3.000
 59A  H133  C13  H131  107.26  3.000
 59A  H132  C13  H131  107.61  3.000
 59A  H133  C13  C12   112.18  3.000
 59A  H132  C13  C12   111.22  3.000
 59A  H131  C13  C12   110.66  3.000
 59A  O3    C7   O2    125.69  3.000
 59A  O3    C7   C2    110.59  3.000
 59A  O2    C7   C2    123.72  3.000
 59A  C8    O3   C7    118.16  3.000
 59A  H82   C8   H81   108.12  3.000
 59A  H82   C8   C9    111.22  3.000
 59A  H81   C8   C9    111.11  3.000
 59A  H82   C8   O3    109.19  3.000
 59A  H81   C8   O3    109.41  3.000
 59A  C9    C8   O3    107.76  3.000
 59A  H93   C9   H92   108.74  3.000
 59A  H93   C9   H91   107.89  3.000
 59A  H92   C9   H91   107.82  3.000
 59A  H93   C9   C8    111.71  3.000
 59A  H92   C9   C8    111.60  3.000
 59A  H91   C9   C8    108.94  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
 59A  CONST_01  C5    N1   C4   C3    180.00   0.0  0
 59A  CONST_02  HN1   N1   C4   C3      0.00   0.0  0
 59A  CONST_03  C5    N1   C4   O4      0.00   0.0  0
 59A  CONST_04  HO5   O5   C6   C5    180.00   0.0  0
 59A  Var_01    C4    C3   O1   C2    108.22  30.0  1
 59A  Var_02    O4    C4   C3   C2     40.60  30.0  3
 59A  Var_03    O2    C7   C2   O1    -19.63  30.0  3
 59A  Var_04    C9    C8   O3   C7    178.26  30.0  3
 59A  Var_05    H131  C13  C12  C10  -177.60  30.0  3
 59A  Var_06    H91   C9   C8   O3    179.14  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
 59A  chir_03  C5   N1  C6   C10  positiv
 59A  chir_04  C10  C5  C12  C11  positiv
 59A  chir_05  C2   O1  C3   C7   both
 59A  chir_06  C3   O1  C2   C4   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
 59A  plan-1  C3   0.020
 59A  plan-1  C4   0.020
 59A  plan-1  O4   0.020
 59A  plan-1  N1   0.020
 59A  plan-1  C5   0.020
 59A  plan-1  HN1  0.020
 59A  plan-2  C5   0.020
 59A  plan-2  C6   0.020
 59A  plan-2  O5   0.020
 59A  plan-2  OA   0.020
 59A  plan-2  HO5  0.020
 59A  plan-3  C2   0.020
 59A  plan-3  C7   0.020
 59A  plan-3  O2   0.020
 59A  plan-3  O3   0.020

