# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jul 20 23:20:07 2020
#   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  51  26  .  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_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  -0.185  -5.5719   3.2592   0.2958
 042  C11   C  CH3    0  -0.690  -5.1949   4.3380   1.2799
 042  C3    C  CH1    0  -0.135  -3.3841  -0.8652  -0.5330
 042  C2    C  CH1    0  -0.141  -4.2211  -0.1552   0.4478
 042  O1    O  O2     0  -0.437  -4.5689  -1.4230  -0.0386
 042  O4    O  O      0  -0.476  -2.0826  -2.1954   0.9528
 042  N1    N  NH1    0  -0.652  -1.0426  -1.1819  -0.7945
 042  C5    C  CH1    0  -0.261   0.3133  -1.5433  -0.4667
 042  C6    C  C      0   0.585   1.2065  -0.3193  -0.6435
 042  O5    O  O      0  -0.497   0.8870   0.6070  -1.3751
 042  C12   C  CH1    0   0.046   0.8282  -2.6933  -1.3616
 042  O8    O  OH1    0  -0.655   0.7538  -2.3399  -2.7212
 042  C13   C  CH3    0  -0.694   0.1055  -3.9981  -1.0737
 042  N2    N  NH1    0  -0.639   2.3429  -0.3563   0.0576
 042  C7    C  CH1    0  -0.134   3.4396   0.5480  -0.2220
 042  C8    C  C      0   0.408   3.9695   0.3666  -1.6671
 042  O7    O  OC    -1  -0.610   4.5416   1.3601  -2.1607
 042  C14   C  CH1    0  -0.274   4.5439   0.3417   0.8331
 042  C16   C  CH2    0  -0.408   5.5235   1.5171   0.8543
 042  C15   C  CH3    0  -0.666   5.2704  -0.9936   0.6740
 042  C17   C  CH3    0  -0.672   6.4914   1.4812   2.0304
 042  O6    O  O      0  -0.589   3.8068  -0.7459  -2.1951
 042  C9    C  C      0   0.600  -5.0628   0.9767  -0.0574
 042  O2    O  O      0  -0.441  -5.7826   0.8968  -1.0180
 042  O3    O  O2     0  -0.451  -4.8794   2.0539   0.6763
 042  H101  H  HCH2   0   0.243  -6.6479   3.0768   0.3055
 042  H102  H  HCH2   0   0.243  -5.2832   3.5348  -0.7201
 042  H111  H  HCH3   0   0.239  -5.5016   4.0832   2.2939
 042  H112  H  HCH3   0   0.239  -4.1220   4.5292   1.2750
 042  H113  H  HCH3   0   0.242  -5.6994   5.2623   0.9999
 042  H3    H  HCH1   0   0.299  -3.4104  -0.5403  -1.5720
 042  H2    H  HCH1   0   0.300  -3.8952  -0.1051   1.4840
 042  HN1   H  HNH1   0   0.405  -1.1576  -0.5166  -1.5456
 042  H5    H  HCH1   0   0.286   0.3462  -1.8743   0.5738
 042  H12   H  HCH1   0   0.239   1.8923  -2.8176  -1.1439
 042  HO8   H  HOH1   0   0.442  -0.1657  -2.4049  -3.0012
 042  H131  H  HCH3   0   0.228  -0.9603  -3.9253  -1.3005
 042  H132  H  HCH3   0   0.245   0.5230  -4.8014  -1.6815
 042  H133  H  HCH3   0   0.235   0.2058  -4.2820  -0.0264
 042  HN2   H  HNH1   0   0.391   2.5461  -1.1945   0.5801
 042  H7    H  HCH1   0   0.230   3.0697   1.5716  -0.1110
 042  H14   H  HCH1   0   0.223   4.0341   0.3338   1.8063
 042  H161  H  HCH2   0   0.220   6.0816   1.5444  -0.0837
 042  H162  H  HCH2   0   0.214   4.9503   2.4482   0.8937
 042  H151  H  HCH3   0   0.231   5.9170  -1.1857   1.5302
 042  H152  H  HCH3   0   0.221   4.5852  -1.8394   0.5973
 042  H153  H  HCH3   0   0.222   5.8958  -1.0000  -0.2203
 042  H171  H  HCH3   0   0.214   5.9576   1.4300   2.9819
 042  H172  H  HCH3   0   0.221   7.1624   0.6233   1.9821
 042  H173  H  HCH3   0   0.228   7.1118   2.3780   2.0493
 042  C4    C  C      0   0.566  -2.1068  -1.4947  -0.0425

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  1.508  0.020  1.508
 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  1.472  0.020  1.472
 042  C3   O1    single  1.400  0.020  1.400
 042  C3   C4    single  1.506  0.020  1.506
 042  C3   H3    single  0.970  0.020  1.090
 042  C2   O1    single  1.402  0.020  1.402
 042  C2   C9    single  1.498  0.020  1.498
 042  C2   H2    single  0.970  0.020  1.090
 042  C4   O4    double  1.217  0.020  1.217
 042  C4   N1    single  1.340  0.020  1.340
 042  N1   C5    single  1.441  0.020  1.441
 042  N1   HN1   single  0.860  0.020  1.020
 042  C5   C6    single  1.526  0.020  1.526
 042  C5   C12   single  1.545  0.020  1.545
 042  C5   H5    single  0.970  0.020  1.090
 042  C6   O5    double  1.223  0.020  1.223
 042  C6   N2    single  1.336  0.020  1.336
 042  C12  O8    single  1.407  0.020  1.407
 042  C12  C13   single  1.519  0.020  1.519
 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  1.449  0.020  1.449
 042  N2   HN2   single  0.860  0.020  1.020
 042  C7   C8    single  1.550  0.020  1.550
 042  C7   C14   single  1.541  0.020  1.541
 042  C7   H7    single  0.970  0.020  1.090
 042  C8   O7    deloc   1.248  0.020  1.248
 042  C8   O6    deloc   1.242  0.020  1.242
 042  C14  C16   single  1.530  0.020  1.530
 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  1.203  0.020  1.203
 042  C9   O3    single  1.316  0.020  1.316

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  108.14  3.000
 042  H102  C10  O3    109.26  3.000
 042  H101  C10  O3    109.36  3.000
 042  H102  C10  C11   111.14  3.000
 042  H101  C10  C11   111.11  3.000
 042  O3    C10  C11   107.81  3.000
 042  H113  C11  H112  107.81  3.000
 042  H113  C11  H111  107.89  3.000
 042  H112  C11  H111  108.80  3.000
 042  H113  C11  C10   108.87  3.000
 042  H112  C11  C10   111.64  3.000
 042  H111  C11  C10   111.69  3.000
 042  H3    C3   C4    117.13  3.000
 042  H3    C3   O1    115.81  3.000
 042  C4    C3   O1    115.87  3.000
 042  H3    C3   C2    118.56  3.000
 042  C4    C3   C2    117.83  3.000
 042  O1    C3   C2     58.37  3.000
 042  H2    C2   C9    117.05  3.000
 042  H2    C2   O1    116.53  3.000
 042  C9    C2   O1    115.27  3.000
 042  H2    C2   C3    119.12  3.000
 042  C9    C2   C3    117.34  3.000
 042  O1    C2   C3     58.24  3.000
 042  C2    O1   C3     63.39  3.000
 042  HN1   N1   C5    116.21  3.000
 042  HN1   N1   C4    118.72  3.000
 042  C5    N1   C4    124.13  3.000
 042  H5    C5   C12   108.42  3.000
 042  H5    C5   C6    109.62  3.000
 042  C12   C5   C6    109.57  3.000
 042  H5    C5   N1    108.73  3.000
 042  C12   C5   N1    111.61  3.000
 042  C6    C5   N1    108.87  3.000
 042  N2    C6   O5    123.87  3.000
 042  N2    C6   C5    114.52  3.000
 042  O5    C6   C5    121.61  3.000
 042  H12   C12  C13   109.13  3.000
 042  H12   C12  O8    105.81  3.000
 042  C13   C12  O8    111.95  3.000
 042  H12   C12  C5    107.07  3.000
 042  C13   C12  C5    111.77  3.000
 042  O8    C12  C5    110.79  3.000
 042  HO8   O8   C12   108.33  3.000
 042  H133  C13  H132  107.97  3.000
 042  H133  C13  H131  107.87  3.000
 042  H132  C13  H131  107.88  3.000
 042  H133  C13  C12   111.23  3.000
 042  H132  C13  C12   110.18  3.000
 042  H131  C13  C12   111.57  3.000
 042  HN2   N2   C7    117.79  3.000
 042  HN2   N2   C6    117.81  3.000
 042  C7    N2   C6    121.70  3.000
 042  H7    C7   C14   107.35  3.000
 042  H7    C7   C8    108.65  3.000
 042  C14   C7   C8    112.19  3.000
 042  H7    C7   N2    107.97  3.000
 042  C14   C7   N2    109.07  3.000
 042  C8    C7   N2    111.45  3.000
 042  O6    C8   O7    127.21  3.000
 042  O6    C8   C7    117.16  3.000
 042  O7    C8   C7    115.61  3.000
 042  H14   C14  C15   107.85  3.000
 042  H14   C14  C16   106.88  3.000
 042  C15   C14  C16   111.60  3.000
 042  H14   C14  C7    105.96  3.000
 042  C15   C14  C7    112.73  3.000
 042  C16   C14  C7    111.43  3.000
 042  H162  C16  H161  106.11  3.000
 042  H162  C16  C17   108.97  3.000
 042  H161  C16  C17   109.82  3.000
 042  H162  C16  C14   108.59  3.000
 042  H161  C16  C14   109.54  3.000
 042  C17   C16  C14   113.53  3.000
 042  H153  C15  H152  107.33  3.000
 042  H153  C15  H151  107.62  3.000
 042  H152  C15  H151  106.92  3.000
 042  H153  C15  C14   111.28  3.000
 042  H152  C15  C14   112.70  3.000
 042  H151  C15  C14   110.74  3.000
 042  H173  C17  H172  107.32  3.000
 042  H173  C17  H171  107.55  3.000
 042  H172  C17  H171  107.61  3.000
 042  H173  C17  C16   110.82  3.000
 042  H172  C17  C16   112.04  3.000
 042  H171  C17  C16   111.29  3.000
 042  O3    C9   O2    125.65  3.000
 042  O3    C9   C2    110.62  3.000
 042  O2    C9   C2    123.72  3.000
 042  C9    O3   C10   118.05  3.000
 042  N1    C4   O4    125.26  3.000
 042  N1    C4   C3    113.15  3.000
 042  O4    C4   C3    121.58  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  Var_01    C9    C2   O1   C3   107.76  30.0  1
 042  Var_02    C4    C3   O1   C2   108.10  30.0  1
 042  Var_03    O2    C9   C2   C3    49.61  30.0  3
 042  Var_04    O4    C4   C3   C2    48.39  30.0  3
 042  Var_05    C2    C9   O3   C10  177.44  30.0  1
 042  Var_06    H171  C17  C16  C14  -55.67  30.0  3
 042  Var_07    H101  C10  O3   C9    59.30  30.0  1
 042  Var_08    H111  C11  C10  O3   -61.73  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-4  C2   0.020
 042  plan-4  C9   0.020
 042  plan-4  O2   0.020
 042  plan-4  O3   0.020

