# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 07:53:33 2021
#   Inital geometry file: a 123 line input string
#   Ligand name: N-{[(2S,3S)-3-(ethoxycarbonyl)oxiran-2-yl]carbonyl}-L-threonyl-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)O)C(=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
 042  042  N-{[(2S,3S)-3-(ethoxycarbonyl)oxiran-2-yl]carbonyl}-L-threonyl-L-isoleucine  ligand  52  26  .  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_042
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
 042  C10   C  CH2   0  -0.202  15.5212  20.4277   -5.2521
 042  C11   C  CH3   0  -0.689  16.2357  20.3056   -6.5788
 042  C3    C  CH1   0  -0.139  11.6125  19.3309   -6.6343
 042  C2    C  CH1   0  -0.130  12.3060  18.6276   -5.5415
 042  O1    O  O2    0  -0.441  11.4556  19.7208   -5.2948
 042  O4    O  O     0  -0.474  10.5276  18.3977   -8.5106
 042  N1    N  NH1   0  -0.633   9.4227  18.3367   -6.5342
 042  C5    C  CH1   0  -0.231   8.2240  17.7604   -7.0734
 042  C6    C  C     0   0.584   7.4228  18.8180   -7.8385
 042  O5    O  O     0  -0.472   7.6281  20.0130   -7.7259
 042  C12   C  CH1   0   0.027   7.3776  17.1518   -5.9508
 042  O8    O  OH1   0  -0.664   7.0801  18.2091   -5.0679
 042  C13   C  CH3   0  -0.689   8.0837  15.9947   -5.2635
 042  N2    N  NH1   0  -0.654   6.4743  18.3207   -8.6470
 042  C7    C  CH1   0  -0.121   5.5708  19.1784   -9.3756
 042  C8    C  C     0   0.526   4.7802  20.0574   -8.4166
 042  O7    O  OH1   0  -0.581   4.3488  19.3837   -7.3615
 042  C14   C  CH1   0  -0.292   4.6394  18.3281  -10.2684
 042  C16   C  CH2   0  -0.405   5.3553  17.8379  -11.5343
 042  C15   C  CH3   0  -0.674   3.3830  19.0936  -10.6816
 042  C17   C  CH3   0  -0.685   6.5581  16.9197  -11.3524
 042  O6    O  O     0  -0.438   4.5403  21.2211   -8.6157
 042  C9    C  C     0   0.594  13.7782  18.8235   -5.3488
 042  O2    O  O     0  -0.437  14.5239  17.8872   -5.2156
 042  O3    O  O2    0  -0.449  14.1240  20.0917   -5.3616
 042  H101  H  HCH2  0   0.256  15.5245  21.4580   -4.9028
 042  H102  H  HCH2  0   0.244  15.9910  19.8082   -4.4877
 042  H111  H  HCH3  0   0.240  16.2783  19.2748   -6.9280
 042  H112  H  HCH3  0   0.246  17.2597  20.6603   -6.4609
 042  H113  H  HCH3  0   0.239  15.7575  20.9158   -7.3448
 042  H3    H  HCH1  0   0.304  12.1762  20.0063   -7.2737
 042  H2    H  HCH1  0   0.304  11.9445  17.6511   -5.2281
 042  HN1   H  HNH1  0   0.407   9.3742  18.7417   -5.6104
 042  H5    H  HCH1  0   0.299   8.4895  16.9560   -7.7648
 042  H12   H  HCH1  0   0.232   6.4604  16.7623   -6.4118
 042  HO8   H  HOH1  0   0.461   6.5899  17.8576   -4.3180
 042  H131  H  HCH3  0   0.245   7.4535  15.5883   -4.4706
 042  H132  H  HCH3  0   0.234   9.0327  16.2954   -4.8186
 042  H133  H  HCH3  0   0.237   8.2748  15.1879   -5.9713
 042  HN2   H  HNH1  0   0.406   6.3015  17.3280   -8.6602
 042  H7    H  HCH1  0   0.281   6.1377  19.8600  -10.0176
 042  HO7   H  HOH1  0   0.483   3.8318  19.9648   -6.7834
 042  H14   H  HCH1  0   0.246   4.3216  17.4571   -9.6811
 042  H161  H  HCH2  0   0.224   5.6505  18.7111  -12.1253
 042  H162  H  HCH2  0   0.234   4.6110  17.3072  -12.1341
 042  H151  H  HCH3  0   0.244   2.7939  18.4847  -11.3671
 042  H152  H  HCH3  0   0.231   3.6326  20.0237  -11.1947
 042  H153  H  HCH3  0   0.239   2.7363  19.3345   -9.8375
 042  H171  H  HCH3  0   0.220   6.3085  16.0510  -10.7392
 042  H172  H  HCH3  0   0.228   7.4098  17.4215  -10.8952
 042  H173  H  HCH3  0   0.238   6.8872  16.5452  -12.3221
 042  C4    C  C     0   0.545  10.4589  18.6534   -7.3206

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
 042  C10  C11   single  1.512  0.020  1.512
 042  C10  O3    single  1.441  0.020  1.441
 042  C10  H101  single  0.970  0.020  1.090
 042  C10  H102  single  0.970  0.020  1.090
 042  C11  H111  single  0.970  0.020  1.090
 042  C11  H112  single  0.970  0.020  1.090
 042  C11  H113  single  0.970  0.020  1.090
 042  C3   C2    single  1.473  0.020  1.473
 042  C3   O1    single  1.404  0.020  1.404
 042  C3   C4    single  1.504  0.020  1.504
 042  C3   H3    single  0.970  0.020  1.090
 042  C2   O1    single  1.407  0.020  1.407
 042  C2   C9    single  1.498  0.020  1.498
 042  C2   H2    single  0.970  0.020  1.090
 042  C4   O4    double  1.219  0.020  1.219
 042  C4   N1    single  1.339  0.020  1.339
 042  N1   C5    single  1.435  0.020  1.435
 042  N1   HN1   single  0.860  0.020  1.020
 042  C5   C6    single  1.532  0.020  1.532
 042  C5   C12   single  1.532  0.020  1.532
 042  C5   H5    single  0.970  0.020  1.090
 042  C6   O5    double  1.218  0.020  1.218
 042  C6   N2    single  1.342  0.020  1.342
 042  C12  O8    single  1.409  0.020  1.409
 042  C12  C13   single  1.520  0.020  1.520
 042  C12  H12   single  0.970  0.020  1.090
 042  O8   HO8   single  0.850  0.020  0.980
 042  C13  H131  single  0.970  0.020  1.090
 042  C13  H132  single  0.970  0.020  1.090
 042  C13  H133  single  0.970  0.020  1.090
 042  N2   C7    single  1.443  0.020  1.443
 042  N2   HN2   single  0.860  0.020  1.020
 042  C7   C8    single  1.522  0.020  1.522
 042  C7   C14   single  1.545  0.020  1.545
 042  C7   H7    single  0.970  0.020  1.090
 042  C8   O7    single  1.324  0.020  1.324
 042  C8   O6    double  1.205  0.020  1.205
 042  O7   HO7   single  0.850  0.020  0.980
 042  C14  C16   single  1.535  0.020  1.535
 042  C14  C15   single  1.528  0.020  1.528
 042  C14  H14   single  0.970  0.020  1.090
 042  C16  C17   single  1.524  0.020  1.524
 042  C16  H161  single  0.970  0.020  1.090
 042  C16  H162  single  0.970  0.020  1.090
 042  C15  H151  single  0.970  0.020  1.090
 042  C15  H152  single  0.970  0.020  1.090
 042  C15  H153  single  0.970  0.020  1.090
 042  C17  H171  single  0.970  0.020  1.090
 042  C17  H172  single  0.970  0.020  1.090
 042  C17  H173  single  0.970  0.020  1.090
 042  C9   O2    double  1.204  0.020  1.204
 042  C9   O3    single  1.315  0.020  1.315

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
 042  H102  C10  H101  108.17  3.000
 042  H102  C10  O3    109.78  3.000
 042  H101  C10  O3    104.37  3.000
 042  H102  C10  C11   111.45  3.000
 042  H101  C10  C11   110.90  3.000
 042  O3    C10  C11   111.88  3.000
 042  H113  C11  H112  107.81  3.000
 042  H113  C11  H111  108.77  3.000
 042  H112  C11  H111  107.82  3.000
 042  H113  C11  C10   111.36  3.000
 042  H112  C11  C10   108.83  3.000
 042  H111  C11  C10   112.10  3.000
 042  H3    C3   C4    114.15  3.000
 042  H3    C3   O1    116.52  3.000
 042  C4    C3   O1    118.35  3.000
 042  H3    C3   C2    119.25  3.000
 042  C4    C3   C2    118.99  3.000
 042  O1    C3   C2     58.49  3.000
 042  H2    C2   C9    114.03  3.000
 042  H2    C2   O1    116.50  3.000
 042  C9    C2   O1    118.04  3.000
 042  H2    C2   C3    119.08  3.000
 042  C9    C2   C3    119.73  3.000
 042  O1    C2   C3     58.30  3.000
 042  C2    O1   C3     63.21  3.000
 042  HN1   N1   C5    117.69  3.000
 042  HN1   N1   C4    118.66  3.000
 042  C5    N1   C4    121.38  3.000
 042  H5    C5   C12   107.77  3.000
 042  H5    C5   C6    108.61  3.000
 042  C12   C5   C6    110.57  3.000
 042  H5    C5   N1    109.28  3.000
 042  C12   C5   N1    110.22  3.000
 042  C6    C5   N1    110.32  3.000
 042  N2    C6   O5    122.59  3.000
 042  N2    C6   C5    114.51  3.000
 042  O5    C6   C5    122.90  3.000
 042  H12   C12  C13   107.93  3.000
 042  H12   C12  O8    110.66  3.000
 042  C13   C12  O8    112.70  3.000
 042  H12   C12  C5    107.15  3.000
 042  C13   C12  C5    112.16  3.000
 042  O8    C12  C5    106.12  3.000
 042  HO8   O8   C12   108.77  3.000
 042  H133  C13  H132  108.45  3.000
 042  H133  C13  H131  107.29  3.000
 042  H132  C13  H131  107.99  3.000
 042  H133  C13  C12   110.57  3.000
 042  H132  C13  C12   112.27  3.000
 042  H131  C13  C12   110.11  3.000
 042  HN2   N2   C7    118.14  3.000
 042  HN2   N2   C6    119.61  3.000
 042  C7    N2   C6    121.76  3.000
 042  H7    C7   C14   108.42  3.000
 042  H7    C7   C8    106.19  3.000
 042  C14   C7   C8    111.63  3.000
 042  H7    C7   N2    109.99  3.000
 042  C14   C7   N2    110.00  3.000
 042  C8    C7   N2    110.51  3.000
 042  O6    C8   O7    123.94  3.000
 042  O6    C8   C7    123.85  3.000
 042  O7    C8   C7    112.17  3.000
 042  HO7   O7   C8    110.13  3.000
 042  H14   C14  C15   107.71  3.000
 042  H14   C14  C16   108.84  3.000
 042  C15   C14  C16   108.69  3.000
 042  H14   C14  C7    107.58  3.000
 042  C15   C14  C7    112.10  3.000
 042  C16   C14  C7    111.79  3.000
 042  H162  C16  H161  105.93  3.000
 042  H162  C16  C17   108.08  3.000
 042  H161  C16  C17   109.40  3.000
 042  H162  C16  C14   106.86  3.000
 042  H161  C16  C14   108.43  3.000
 042  C17   C16  C14   117.52  3.000
 042  H153  C15  H152  108.14  3.000
 042  H153  C15  H151  106.85  3.000
 042  H152  C15  H151  107.71  3.000
 042  H153  C15  C14   112.89  3.000
 042  H152  C15  C14   111.47  3.000
 042  H151  C15  C14   109.55  3.000
 042  H173  C17  H172  107.19  3.000
 042  H173  C17  H171  107.16  3.000
 042  H172  C17  H171  108.03  3.000
 042  H173  C17  C16   109.81  3.000
 042  H172  C17  C16   112.94  3.000
 042  H171  C17  C16   111.45  3.000
 042  O3    C9   O2    126.03  3.000
 042  O3    C9   C2    112.55  3.000
 042  O2    C9   C2    121.41  3.000
 042  C9    O3   C10   118.63  3.000
 042  N1    C4   O4    124.56  3.000
 042  N1    C4   C3    115.62  3.000
 042  O4    C4   C3    119.79  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
 042  CONST_01  C5    N1   C4   C3    180.00   0.0  0
 042  CONST_02  HN1   N1   C4   C3      0.00   0.0  0
 042  CONST_03  C5    N1   C4   O4      0.00   0.0  0
 042  CONST_04  C7    N2   C6   C5    180.00   0.0  0
 042  CONST_05  C7    N2   C6   O5      0.00   0.0  0
 042  CONST_06  HN2   N2   C6   C5      0.00   0.0  0
 042  CONST_07  HO7   O7   C8   C7    180.00   0.0  0
 042  Var_01    C9    C2   O1   C3    109.35  30.0  1
 042  Var_02    C4    C3   O1   C2    108.38  30.0  1
 042  Var_03    O2    C9   C2   C3   -131.00  30.0  3
 042  Var_04    O4    C4   C3   C2   -118.03  30.0  3
 042  Var_05    C2    C9   O3   C10  -177.03  30.0  1
 042  Var_06    H171  C17  C16  C14    54.04  30.0  3
 042  Var_07    H101  C10  O3   C9   -158.75  30.0  1
 042  Var_08    H111  C11  C10  O3    -66.18  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
 042  chir_03  C5   N1  C6   C12  positiv
 042  chir_04  C12  O8  C5   C13  negativ
 042  chir_05  C7   N2  C8   C14  positiv
 042  chir_06  C14  C7  C16  C15  positiv
 042  chir_07  C3   C2  O1   C4   both
 042  chir_08  C2   O1  C3   C9   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
 042  plan-1  C5   0.020
 042  plan-1  C6   0.020
 042  plan-1  O5   0.020
 042  plan-1  N2   0.020
 042  plan-1  C7   0.020
 042  plan-1  HN2  0.020
 042  plan-2  C3   0.020
 042  plan-2  O4   0.020
 042  plan-2  N1   0.020
 042  plan-2  C5   0.020
 042  plan-2  HN1  0.020
 042  plan-2  C4   0.020
 042  plan-3  C7   0.020
 042  plan-3  C8   0.020
 042  plan-3  O7   0.020
 042  plan-3  O6   0.020
 042  plan-3  HO7  0.020
 042  plan-4  C2   0.020
 042  plan-4  C9   0.020
 042  plan-4  O2   0.020
 042  plan-4  O3   0.020

