# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 03:43:30 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  37  19  .  2022-09-22  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

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  -0.144   2.4505  -0.7001   0.1610
 59A  O1    O  O2     0  -0.443   2.0683  -1.6180   1.1500
 59A  C3    C  CH1    0  -0.148   1.2331  -0.5058   0.9644
 59A  C4    C  C      0   0.583  -0.0969  -0.7944   0.3179
 59A  O4    O  O      0  -0.497  -0.2361  -1.7410  -0.4420
 59A  N1    N  NH1    0  -0.655  -1.0647   0.0528   0.6597
 59A  C5    C  CH1    0  -0.124  -2.3829   0.0042   0.0602
 59A  C6    C  C      0   0.411  -2.3324   0.2755  -1.4651
 59A  O5    O  OC    -1  -0.608  -3.2560  -0.2348  -2.1294
 59A  C10   C  CH1    0  -0.282  -3.3034   0.9937   0.8004
 59A  C12   C  CH2    0  -0.406  -4.7785   0.7259   0.4902
 59A  C11   C  CH3    0  -0.666  -2.9301   2.4532   0.5437
 59A  C13   C  CH3    0  -0.673  -5.7378   1.5079   1.3784
 59A  OA    O  O      0  -0.599  -1.4092   0.9930  -1.8846
 59A  C7    C  C      0   0.603   3.6460   0.1364   0.4990
 59A  O2    O  O      0  -0.443   4.0453   0.3104   1.6209
 59A  O3    O  O2     0  -0.452   4.1726   0.6587  -0.5889
 59A  C8    C  CH2    0  -0.186   5.3066   1.5345  -0.4386
 59A  C9    C  CH3    0  -0.690   5.7389   1.9693  -1.8165
 59A  H2    H  HCH1   0   0.295   2.3557  -1.0310  -0.8702
 59A  H3    H  HCH1   0   0.289   1.2525   0.2328   1.7643
 59A  HN1   H  HNH1   0   0.398  -0.8388   0.8174   1.2761
 59A  H5    H  HCH1   0   0.232  -2.7848  -1.0012   0.2199
 59A  H10   H  HCH1   0   0.225  -3.1627   0.7924   1.8712
 59A  H121  H  HCH2   0   0.220  -4.9788   0.9537  -0.5584
 59A  H122  H  HCH2   0   0.215  -4.9750  -0.3432   0.6134
 59A  H111  H  HCH3   0   0.231  -3.4778   3.1161   1.2128
 59A  H112  H  HCH3   0   0.223  -1.8694   2.6494   0.7061
 59A  H113  H  HCH3   0   0.222  -3.1632   2.7492  -0.4800
 59A  H131  H  HCH3   0   0.229  -6.7723   1.2369   1.1648
 59A  H132  H  HCH3   0   0.215  -5.5570   1.3050   2.4361
 59A  H133  H  HCH3   0   0.221  -5.6499   2.5847   1.2304
 59A  H81   H  HCH2   0   0.243   6.1095   1.0039   0.0757
 59A  H82   H  HCH2   0   0.242   5.0202   2.3916   0.1738
 59A  H91   H  HCH3   0   0.242   6.5897   2.6434  -1.7241
 59A  H92   H  HCH3   0   0.239   6.0505   1.1209  -2.4256
 59A  H93   H  HCH3   0   0.239   4.9447   2.5023  -2.3386

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  1.471  0.020  1.471
 59A  C2   C7    single  1.498  0.020  1.498
 59A  C2   H2    single  0.970  0.020  1.090
 59A  O1   C3    single  1.403  0.020  1.403
 59A  C3   C4    single  1.507  0.020  1.507
 59A  C3   H3    single  0.970  0.020  1.090
 59A  C4   O4    double  1.222  0.020  1.222
 59A  C4   N1    single  1.331  0.020  1.331
 59A  N1   C5    single  1.449  0.020  1.449
 59A  N1   HN1   single  0.860  0.020  1.020
 59A  C5   C6    single  1.550  0.020  1.550
 59A  C5   C10   single  1.541  0.020  1.541
 59A  C5   H5    single  0.970  0.020  1.090
 59A  C6   O5    deloc   1.247  0.020  1.247
 59A  C6   OA    deloc   1.242  0.020  1.242
 59A  C10  C12   single  1.531  0.020  1.531
 59A  C10  C11   single  1.528  0.020  1.528
 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  1.317  0.020  1.317
 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    119.07  3.000
 59A  C7    C2   C3    117.61  3.000
 59A  H2    C2   O1    116.48  3.000
 59A  C7    C2   O1    115.08  3.000
 59A  C3    C2   O1     58.40  3.000
 59A  C3    O1   C2     63.26  3.000
 59A  H3    C3   C4    117.44  3.000
 59A  H3    C3   O1    115.46  3.000
 59A  C4    C3   O1    115.49  3.000
 59A  H3    C3   C2    118.42  3.000
 59A  C4    C3   C2    118.08  3.000
 59A  O1    C3   C2     58.34  3.000
 59A  N1    C4   O4    124.75  3.000
 59A  N1    C4   C3    114.19  3.000
 59A  O4    C4   C3    121.06  3.000
 59A  HN1   N1   C5    118.85  3.000
 59A  HN1   N1   C4    118.49  3.000
 59A  C5    N1   C4    122.28  3.000
 59A  H5    C5   C10   107.49  3.000
 59A  H5    C5   C6    108.44  3.000
 59A  C10   C5   C6    112.32  3.000
 59A  H5    C5   N1    107.73  3.000
 59A  C10   C5   N1    108.86  3.000
 59A  C6    C5   N1    111.81  3.000
 59A  OA    C6   O5    127.37  3.000
 59A  OA    C6   C5    117.24  3.000
 59A  O5    C6   C5    115.37  3.000
 59A  H10   C10  C11   107.91  3.000
 59A  H10   C10  C12   106.79  3.000
 59A  C11   C10  C12   111.62  3.000
 59A  H10   C10  C5    105.90  3.000
 59A  C11   C10  C5    112.75  3.000
 59A  C12   C10  C5    111.46  3.000
 59A  H122  C12  H121  106.22  3.000
 59A  H122  C12  C13   108.84  3.000
 59A  H121  C12  C13   109.72  3.000
 59A  H122  C12  C10   108.74  3.000
 59A  H121  C12  C10   109.57  3.000
 59A  C13   C12  C10   113.50  3.000
 59A  H113  C11  H112  107.38  3.000
 59A  H113  C11  H111  107.68  3.000
 59A  H112  C11  H111  106.73  3.000
 59A  H113  C11  C10   111.39  3.000
 59A  H112  C11  C10   112.60  3.000
 59A  H111  C11  C10   110.80  3.000
 59A  H133  C13  H132  107.55  3.000
 59A  H133  C13  H131  107.17  3.000
 59A  H132  C13  H131  107.50  3.000
 59A  H133  C13  C12   112.15  3.000
 59A  H132  C13  C12   111.41  3.000
 59A  H131  C13  C12   110.83  3.000
 59A  O3    C7   O2    125.47  3.000
 59A  O3    C7   C2    110.75  3.000
 59A  O2    C7   C2    123.78  3.000
 59A  C8    O3   C7    118.01  3.000
 59A  H82   C8   H81   108.09  3.000
 59A  H82   C8   C9    111.18  3.000
 59A  H81   C8   C9    111.09  3.000
 59A  H82   C8   O3    109.23  3.000
 59A  H81   C8   O3    109.44  3.000
 59A  C9    C8   O3    107.79  3.000
 59A  H93   C9   H92   108.75  3.000
 59A  H93   C9   H91   107.89  3.000
 59A  H92   C9   H91   107.80  3.000
 59A  H93   C9   C8    111.71  3.000
 59A  H92   C9   C8    111.60  3.000
 59A  H91   C9   C8    108.95  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  Var_01    C4    C3   O1   C2    108.59  30.0  1
 59A  Var_02    O4    C4   C3   C2     38.63  30.0  3
 59A  Var_03    O2    C7   C2   O1    -19.86  30.0  3
 59A  Var_04    C9    C8   O3   C7    178.68  30.0  3
 59A  Var_05    H131  C13  C12  C10  -176.34  30.0  3
 59A  Var_06    H91   C9   C8   O3    179.32  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-3  C2   0.020
 59A  plan-3  C7   0.020
 59A  plan-3  O2   0.020
 59A  plan-3  O3   0.020

