# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 07:25:12 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: N~6~-[(1R,2R)-1-({[(1R)-1-carboxy-2-methylpropyl]oxy}carbonyl)-2-sulfanylpropyl]-6-oxo-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@@H](OC(=O)[C@@H](NC(=O)CCC[C@H](N)C(O)=O)[C@@H](C)S)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
 MDZ  MDZ  N~6~-[(1R,2R)-1-({[(1R)-1-carboxy-2-methylpropyl]oxy}carbonyl)-2-sulfanylpropyl]-6-oxo-L-lysine  ligand  49  25  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_MDZ
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
 MDZ  O43   O  O      0  -0.592   0.8460   3.4114  -1.6152
 MDZ  C31   C  C      0   0.388   0.9446   3.7320  -0.4211
 MDZ  O42   O  OC    -1  -0.605   1.9841   4.0031   0.2114
 MDZ  C30   C  CH1    0  -0.066  -0.3490   3.8398   0.4103
 MDZ  O29   O  O2     0  -0.456  -1.3890   3.1252  -0.2867
 MDZ  C13   C  C      0   0.608  -2.3950   2.6136   0.3886
 MDZ  O18   O  O      0  -0.443  -2.5003   2.5847   1.5882
 MDZ  C12   C  CH1    0  -0.197  -3.4525   2.0651  -0.5694
 MDZ  C16   C  CH1    0  -0.397  -4.1193   3.2067  -1.3480
 MDZ  S17   S  S2     0  -0.235  -4.8851   4.3456  -0.1263
 MDZ  C25   C  CH3    0  -0.635  -5.1265   2.6974  -2.3633
 MDZ  N11   N  NH1    0  -0.634  -4.4270   1.2790   0.1282
 MDZ  C10   C  C      0   0.572  -4.1355   0.0583   0.6257
 MDZ  O15   O  O      0  -0.491  -3.0520  -0.4719   0.4381
 MDZ  C7    C  CH2    0  -0.588  -5.2631  -0.5896   1.3987
 MDZ  C4    C  CH2    0  -0.429  -4.9559  -1.9983   1.8814
 MDZ  C3    C  CH2    0  -0.404  -6.1516  -2.6112   2.6013
 MDZ  C2    C  CH1    0  -0.223  -5.9025  -4.0236   3.1425
 MDZ  N14   N  NH2    0  -0.797  -4.8440  -4.0018   4.1440
 MDZ  C1    C  C      0   0.384  -5.6787  -4.9991   1.9611
 MDZ  O20   O  O      0  -0.611  -4.5308  -5.4609   1.8003
 MDZ  O19   O  OC    -1  -0.623  -6.6756  -5.2248   1.2433
 MDZ  C32   C  CH1    0  -0.269  -0.8147   5.2864   0.6322
 MDZ  C37   C  CH3    0  -0.650   0.0953   6.0407   1.5950
 MDZ  C33   C  CH3    0  -0.656  -0.9829   6.0584  -0.6727
 MDZ  H30   H  HCH1   0   0.238  -0.1848   3.3685   1.3835
 MDZ  H12   H  HCH1   0   0.305  -2.9454   1.4395  -1.3104
 MDZ  H16   H  HCH1   0   0.309  -3.3331   3.7566  -1.8646
 MDZ  H251  H  HCH3   0   0.237  -5.9435   2.1518  -1.8933
 MDZ  H252  H  HCH3   0   0.243  -4.6333   2.0303  -3.0729
 MDZ  H253  H  HCH3   0   0.250  -5.5524   3.5267  -2.9273
 MDZ  H11   H  HNH1   0   0.399  -5.2928   1.7202   0.4010
 MDZ  H7C1  H  HCH2   0   0.262  -6.1553  -0.5938   0.7640
 MDZ  H7C2  H  HCH2   0   0.265  -5.5136   0.0542   2.2489
 MDZ  H4C1  H  HCH2   0   0.220  -4.0930  -1.9706   2.5510
 MDZ  H4C2  H  HCH2   0   0.225  -4.6702  -2.6190   1.0286
 MDZ  H3C1  H  HCH2   0   0.208  -6.4377  -1.9647   3.4379
 MDZ  H3C2  H  HCH2   0   0.212  -7.0102  -2.6413   1.9250
 MDZ  H2    H  HCH1   0   0.218  -6.8240  -4.3303   3.6491
 MDZ  H141  H  HNH2   0   0.327  -3.9559  -4.0322   3.6562
 MDZ  H142  H  HNH2   0   0.335  -4.8692  -4.8760   4.6551
 MDZ  H32   H  HCH1   0   0.230  -1.7996   5.2220   1.1083
 MDZ  H371  H  HCH3   0   0.221   0.2459   5.4885   2.5240
 MDZ  H372  H  HCH3   0   0.219  -0.3523   7.0022   1.8498
 MDZ  H373  H  HCH3   0   0.223   1.0738   6.2307   1.1573
 MDZ  H331  H  HCH3   0   0.231  -1.6171   5.5322  -1.3864
 MDZ  H332  H  HCH3   0   0.217  -0.0208   6.2469  -1.1529
 MDZ  H333  H  HCH3   0   0.223  -1.4433   7.0281  -0.4770
 MDZ  HS1   H  HSH1   0   0.234  -5.4566   5.1650  -1.0146

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
 MDZ  O43  C31   deloc   1.240  0.020  1.240
 MDZ  C31  O42   deloc   1.247  0.020  1.247
 MDZ  C31  C30   single  1.541  0.020  1.541
 MDZ  C30  O29   single  1.442  0.020  1.442
 MDZ  C30  C32   single  1.536  0.020  1.536
 MDZ  C30  H30   single  0.970  0.020  1.090
 MDZ  O29  C13   single  1.315  0.020  1.315
 MDZ  C13  O18   double  1.205  0.020  1.205
 MDZ  C13  C12   single  1.529  0.020  1.529
 MDZ  C12  C16   single  1.534  0.020  1.534
 MDZ  C12  N11   single  1.433  0.020  1.433
 MDZ  C12  H12   single  0.970  0.020  1.090
 MDZ  C16  S17   single  1.837  0.020  1.837
 MDZ  C16  C25   single  1.518  0.020  1.518
 MDZ  C16  H16   single  0.970  0.020  1.090
 MDZ  C25  H251  single  0.970  0.020  1.090
 MDZ  C25  H252  single  0.970  0.020  1.090
 MDZ  C25  H253  single  0.970  0.020  1.090
 MDZ  N11  C10   single  1.350  0.020  1.350
 MDZ  N11  H11   single  0.860  0.020  1.020
 MDZ  C10  O15   double  1.221  0.020  1.221
 MDZ  C10  C7    single  1.513  0.020  1.513
 MDZ  C7   C4    single  1.520  0.020  1.520
 MDZ  C7   H7C1  single  0.970  0.020  1.090
 MDZ  C7   H7C2  single  0.970  0.020  1.090
 MDZ  C4   C3    single  1.524  0.020  1.524
 MDZ  C4   H4C1  single  0.970  0.020  1.090
 MDZ  C4   H4C2  single  0.970  0.020  1.090
 MDZ  C3   C2    single  1.533  0.020  1.533
 MDZ  C3   H3C1  single  0.970  0.020  1.090
 MDZ  C3   H3C2  single  0.970  0.020  1.090
 MDZ  C2   N14   single  1.457  0.020  1.457
 MDZ  C2   C1    single  1.548  0.020  1.548
 MDZ  C2   H2    single  0.970  0.020  1.090
 MDZ  N14  H141  single  0.890  0.020  1.040
 MDZ  N14  H142  single  0.890  0.020  1.040
 MDZ  C1   O20   deloc   1.248  0.020  1.248
 MDZ  C1   O19   deloc   1.249  0.020  1.249
 MDZ  C32  C37   single  1.524  0.020  1.524
 MDZ  C32  C33   single  1.525  0.020  1.525
 MDZ  C32  H32   single  0.970  0.020  1.090
 MDZ  C37  H371  single  0.970  0.020  1.090
 MDZ  C37  H372  single  0.970  0.020  1.090
 MDZ  C37  H373  single  0.970  0.020  1.090
 MDZ  C33  H331  single  0.970  0.020  1.090
 MDZ  C33  H332  single  0.970  0.020  1.090
 MDZ  C33  H333  single  0.970  0.020  1.090
 MDZ  HS1  S17   single  1.200  0.020  1.300

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
 MDZ  C30   C31  O42   114.26  3.000
 MDZ  C30   C31  O43   118.08  3.000
 MDZ  O42   C31  O43   127.65  3.000
 MDZ  H30   C30  C32   108.84  3.000
 MDZ  H30   C30  O29   108.96  3.000
 MDZ  C32   C30  O29   108.54  3.000
 MDZ  H30   C30  C31   108.90  3.000
 MDZ  C32   C30  C31   113.47  3.000
 MDZ  O29   C30  C31   108.06  3.000
 MDZ  C13   O29  C30   119.76  3.000
 MDZ  C12   C13  O18   123.71  3.000
 MDZ  C12   C13  O29   110.30  3.000
 MDZ  O18   C13  O29   125.98  3.000
 MDZ  H12   C12  N11   109.33  3.000
 MDZ  H12   C12  C16   106.45  3.000
 MDZ  N11   C12  C16   111.08  3.000
 MDZ  H12   C12  C13   107.99  3.000
 MDZ  N11   C12  C13   111.23  3.000
 MDZ  C16   C12  C13   110.59  3.000
 MDZ  H16   C16  C25   109.32  3.000
 MDZ  H16   C16  S17   107.64  3.000
 MDZ  C25   C16  S17   112.09  3.000
 MDZ  H16   C16  C12   107.61  3.000
 MDZ  C25   C16  C12   112.22  3.000
 MDZ  S17   C16  C12   107.75  3.000
 MDZ  HS1   S17  C16    96.68  3.000
 MDZ  H253  C25  H252  107.78  3.000
 MDZ  H253  C25  H251  108.15  3.000
 MDZ  H252  C25  H251  108.26  3.000
 MDZ  H253  C25  C16   110.50  3.000
 MDZ  H252  C25  C16   109.87  3.000
 MDZ  H251  C25  C16   112.15  3.000
 MDZ  H11   N11  C10   118.74  3.000
 MDZ  H11   N11  C12   118.36  3.000
 MDZ  C10   N11  C12   121.91  3.000
 MDZ  C7    C10  O15   123.64  3.000
 MDZ  C7    C10  N11   114.50  3.000
 MDZ  O15   C10  N11   121.85  3.000
 MDZ  H7C2  C7   H7C1  105.42  3.000
 MDZ  H7C2  C7   C4    110.14  3.000
 MDZ  H7C1  C7   C4    110.19  3.000
 MDZ  H7C2  C7   C10   108.38  3.000
 MDZ  H7C1  C7   C10   108.22  3.000
 MDZ  C4    C7   C10   114.10  3.000
 MDZ  H4C2  C4   H4C1  106.63  3.000
 MDZ  H4C2  C4   C3    110.19  3.000
 MDZ  H4C1  C4   C3    109.89  3.000
 MDZ  H4C2  C4   C7    109.36  3.000
 MDZ  H4C1  C4   C7    109.31  3.000
 MDZ  C3    C4   C7    111.34  3.000
 MDZ  H3C2  C3   H3C1  106.48  3.000
 MDZ  H3C2  C3   C2    108.70  3.000
 MDZ  H3C1  C3   C2    108.46  3.000
 MDZ  H3C2  C3   C4    109.57  3.000
 MDZ  H3C1  C3   C4    109.16  3.000
 MDZ  C2    C3   C4    114.19  3.000
 MDZ  H2    C2   C1    107.34  3.000
 MDZ  H2    C2   N14   107.30  3.000
 MDZ  C1    C2   N14   115.39  3.000
 MDZ  H2    C2   C3    106.53  3.000
 MDZ  C1    C2   C3    109.55  3.000
 MDZ  N14   C2   C3    110.30  3.000
 MDZ  H142  N14  H141  103.81  3.000
 MDZ  H142  N14  C2    108.40  3.000
 MDZ  H141  N14  C2    107.77  3.000
 MDZ  O19   C1   O20   126.39  3.000
 MDZ  O19   C1   C2    115.91  3.000
 MDZ  O20   C1   C2    117.68  3.000
 MDZ  H32   C32  C33   107.60  3.000
 MDZ  H32   C32  C37   106.93  3.000
 MDZ  C33   C32  C37   110.83  3.000
 MDZ  H32   C32  C30   106.26  3.000
 MDZ  C33   C32  C30   112.74  3.000
 MDZ  C37   C32  C30   112.10  3.000
 MDZ  H373  C37  H372  107.99  3.000
 MDZ  H373  C37  H371  107.85  3.000
 MDZ  H372  C37  H371  107.69  3.000
 MDZ  H373  C37  C32   111.66  3.000
 MDZ  H372  C37  C32   109.79  3.000
 MDZ  H371  C37  C32   111.70  3.000
 MDZ  H333  C33  H332  107.29  3.000
 MDZ  H333  C33  H331  107.51  3.000
 MDZ  H332  C33  H331  107.94  3.000
 MDZ  H333  C33  C32   110.05  3.000
 MDZ  H332  C33  C32   111.50  3.000
 MDZ  H331  C33  C32   112.32  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
 MDZ  CONST_01  O15   C10  N11  C12     0.00   0.0  0
 MDZ  CONST_02  C7    C10  N11  C12   180.00   0.0  0
 MDZ  CONST_03  H11   N11  C10  O15   180.00   0.0  0
 MDZ  Var_01    O18   C13  O29  C30    -6.32  30.0  3
 MDZ  Var_02    C4    C7   C10  N11   176.41  30.0  3
 MDZ  Var_03    C3    C4   C7   C10  -177.68  30.0  3
 MDZ  Var_04    C2    C3   C4   C7   -178.76  30.0  3
 MDZ  Var_05    H371  C37  C32  C30   -51.61  30.0  3
 MDZ  Var_06    H331  C33  C32  C30    52.47  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
 MDZ  chir_01  C30  C31  O29  C32  positiv
 MDZ  chir_02  C12  N11  C16  C13  negativ
 MDZ  chir_03  C16  S17  C12  C25  negativ
 MDZ  chir_04  C2   C3   N14  C1   positiv

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
 MDZ  plan-1  C12  0.020
 MDZ  plan-1  N11  0.020
 MDZ  plan-1  C10  0.020
 MDZ  plan-1  O15  0.020
 MDZ  plan-1  C7   0.020
 MDZ  plan-1  H11  0.020
 MDZ  plan-2  O43  0.020
 MDZ  plan-2  C31  0.020
 MDZ  plan-2  O42  0.020
 MDZ  plan-2  C30  0.020
 MDZ  plan-3  C2   0.020
 MDZ  plan-3  C1   0.020
 MDZ  plan-3  O20  0.020
 MDZ  plan-3  O19  0.020
 MDZ  plan-4  O29  0.020
 MDZ  plan-4  C13  0.020
 MDZ  plan-4  O18  0.020
 MDZ  plan-4  C12  0.020

