# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 20:05:32 2021
#   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  51  25  .  2022-07-25  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.429   5.9259  35.8858  5.8789
 MDZ  C31   C  C     0   0.537   6.5642  36.8849  5.6813
 MDZ  O42   O  OH1   0  -0.573   6.6127  37.8475  6.5842
 MDZ  C30   C  CH1   0  -0.130   7.3282  37.0847  4.3806
 MDZ  O29   O  O2    0  -0.496   8.0804  38.2957  4.4776
 MDZ  C13   C  C     0   0.625   9.3945  38.2940  4.2296
 MDZ  O18   O  O     0  -0.402  10.0332  37.3241  3.9425
 MDZ  C12   C  CH1   0  -0.195   9.9495  39.7105  4.3318
 MDZ  C16   C  CH1   0  -0.401   9.5577  40.5405  3.1018
 MDZ  S17   S  S2    0  -0.226  10.2858  39.7460  1.6154
 MDZ  C25   C  CH3   0  -0.636   9.9872  41.9905  3.2405
 MDZ  N11   N  NH1   0  -0.633  11.3702  39.6764  4.5136
 MDZ  C10   C  C     0   0.566  11.9075  39.1616  5.6376
 MDZ  O15   O  O     0  -0.493  11.2076  38.7869  6.5669
 MDZ  C7    C  CH2   0  -0.567  13.4135  39.0720  5.6641
 MDZ  C4    C  CH2   0  -0.441  13.8764  37.6293  5.8651
 MDZ  C3    C  CH2   0  -0.429  15.3965  37.5379  5.9144
 MDZ  C2    C  CH1   0  -0.187  15.9113  36.0918  5.9562
 MDZ  N14   N  NH2   0  -0.803  15.4737  35.4258  7.1658
 MDZ  C1    C  C     0   0.534  17.4226  36.1427  5.8494
 MDZ  O20   O  O     0  -0.455  17.9965  36.3632  4.8098
 MDZ  O19   O  OH1   0  -0.578  18.0518  35.9544  6.9984
 MDZ  C32   C  CH1   0  -0.261   6.3767  37.1456  3.1814
 MDZ  C37   C  CH3   0  -0.668   7.1566  37.1692  1.8713
 MDZ  C33   C  CH3   0  -0.672   5.3980  38.3134  3.2682
 MDZ  H42   H  HOH1  0   0.490   7.1402  38.5997  6.2779
 MDZ  H30   H  HCH1  0   0.315   8.0017  36.2310  4.2690
 MDZ  H12   H  HCH1  0   0.313   9.4793  40.1972  5.1916
 MDZ  H16   H  HCH1  0   0.309   8.4719  40.4960  3.0091
 MDZ  H251  H  HCH3  0   0.254   9.6454  42.5708  2.3844
 MDZ  H252  H  HCH3  0   0.247   9.5434  42.4271  4.1371
 MDZ  H253  H  HCH3  0   0.241  11.0692  42.0935  3.3068
 MDZ  H11   H  HNH1  0   0.406  11.9672  39.8772  3.7254
 MDZ  H7C1  H  HCH2  0   0.255  13.8472  39.4802  4.7486
 MDZ  H7C2  H  HCH2  0   0.270  13.7740  39.6915  6.4899
 MDZ  H4C1  H  HCH2  0   0.236  13.4340  37.2471  6.7872
 MDZ  H4C2  H  HCH2  0   0.238  13.4984  37.0091  5.0465
 MDZ  H3C1  H  HCH2  0   0.241  15.8107  38.0256  5.0288
 MDZ  H3C2  H  HCH2  0   0.238  15.7715  38.0808  6.7872
 MDZ  H2    H  HCH1  0   0.247  15.5712  35.5987  5.0334
 MDZ  H141  H  HNH2  0   0.357  14.4625  35.4113  7.1859
 MDZ  H142  H  HNH2  0   0.354  15.7523  34.4526  7.1487
 MDZ  H19   H  HOH1  0   0.480  19.0081  36.0247  6.8572
 MDZ  H32   H  HCH1  0   0.258   5.8081  36.2122  3.2167
 MDZ  H371  H  HCH3  0   0.237   7.8409  36.3229  1.7950
 MDZ  H372  H  HCH3  0   0.244   6.4675  37.1167  1.0281
 MDZ  H373  H  HCH3  0   0.226   7.7411  38.0840  1.7548
 MDZ  H331  H  HCH3  0   0.238   4.7695  38.2686  4.1592
 MDZ  H332  H  HCH3  0   0.231   5.9134  39.2751  3.2659
 MDZ  H333  H  HCH3  0   0.246   4.7317  38.2985  2.4061
 MDZ  HS1   H  HSH1  0   0.238   9.9371  40.7027  0.7488

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   double  1.202  0.020  1.202
 MDZ  C31  O42   single  1.321  0.020  1.321
 MDZ  C31  C30   single  1.522  0.020  1.522
 MDZ  O42  H42   single  0.850  0.020  0.980
 MDZ  C30  O29   single  1.429  0.020  1.429
 MDZ  C30  C32   single  1.532  0.020  1.532
 MDZ  C30  H30   single  0.970  0.020  1.090
 MDZ  O29  C13   single  1.337  0.020  1.337
 MDZ  C13  O18   double  1.196  0.020  1.196
 MDZ  C13  C12   single  1.525  0.020  1.525
 MDZ  C12  C16   single  1.535  0.020  1.535
 MDZ  C12  N11   single  1.433  0.020  1.433
 MDZ  C12  H12   single  0.970  0.020  1.090
 MDZ  C16  S17   single  1.836  0.020  1.836
 MDZ  C16  C25   single  1.519  0.020  1.519
 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  1.348  0.020  1.348
 MDZ  N11  H11   single  0.860  0.020  1.020
 MDZ  C10  O15   double  1.222  0.020  1.222
 MDZ  C10  C7    single  1.509  0.020  1.509
 MDZ  C7   C4    single  1.528  0.020  1.528
 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  1.535  0.020  1.535
 MDZ  C3   H3C1  single  0.970  0.020  1.090
 MDZ  C3   H3C2  single  0.970  0.020  1.090
 MDZ  C2   N14   single  1.449  0.020  1.449
 MDZ  C2   C1    single  1.516  0.020  1.516
 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   double  1.208  0.020  1.208
 MDZ  C1   O19   single  1.324  0.020  1.324
 MDZ  O19  H19   single  0.850  0.020  0.980
 MDZ  C32  C37   single  1.525  0.020  1.525
 MDZ  C32  C33   single  1.526  0.020  1.526
 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   118.05  3.000
 MDZ  C30   C31  O43   121.08  3.000
 MDZ  O42   C31  O43   120.86  3.000
 MDZ  H42   O42  C31   111.72  3.000
 MDZ  H30   C30  C32   109.50  3.000
 MDZ  H30   C30  O29   110.15  3.000
 MDZ  C32   C30  O29   110.26  3.000
 MDZ  H30   C30  C31   107.11  3.000
 MDZ  C32   C30  C31   111.26  3.000
 MDZ  O29   C30  C31   108.51  3.000
 MDZ  C13   O29  C30   120.24  3.000
 MDZ  C12   C13  O18   125.10  3.000
 MDZ  C12   C13  O29   110.13  3.000
 MDZ  O18   C13  O29   124.76  3.000
 MDZ  H12   C12  N11   109.70  3.000
 MDZ  H12   C12  C16   106.23  3.000
 MDZ  N11   C12  C16   111.58  3.000
 MDZ  H12   C12  C13   108.02  3.000
 MDZ  N11   C12  C13   110.33  3.000
 MDZ  C16   C12  C13   110.84  3.000
 MDZ  H16   C16  C25   109.16  3.000
 MDZ  H16   C16  S17   107.96  3.000
 MDZ  C25   C16  S17   112.02  3.000
 MDZ  H16   C16  C12   107.48  3.000
 MDZ  C25   C16  C12   111.77  3.000
 MDZ  S17   C16  C12   108.28  3.000
 MDZ  HS1   S17  C16    96.41  3.000
 MDZ  H253  C25  H252  108.43  3.000
 MDZ  H253  C25  H251  108.01  3.000
 MDZ  H252  C25  H251  107.76  3.000
 MDZ  H253  C25  C16   112.14  3.000
 MDZ  H252  C25  C16   110.00  3.000
 MDZ  H251  C25  C16   110.37  3.000
 MDZ  H11   N11  C10   119.44  3.000
 MDZ  H11   N11  C12   118.87  3.000
 MDZ  C10   N11  C12   120.68  3.000
 MDZ  C7    C10  O15   122.68  3.000
 MDZ  C7    C10  N11   115.80  3.000
 MDZ  O15   C10  N11   121.52  3.000
 MDZ  H7C2  C7   H7C1  106.87  3.000
 MDZ  H7C2  C7   C4    109.61  3.000
 MDZ  H7C1  C7   C4    110.04  3.000
 MDZ  H7C2  C7   C10   107.98  3.000
 MDZ  H7C1  C7   C10   111.07  3.000
 MDZ  C4    C7   C10   111.14  3.000
 MDZ  H4C2  C4   H4C1  107.06  3.000
 MDZ  H4C2  C4   C3    109.56  3.000
 MDZ  H4C1  C4   C3    110.85  3.000
 MDZ  H4C2  C4   C7    109.38  3.000
 MDZ  H4C1  C4   C7    108.59  3.000
 MDZ  C3    C4   C7    111.29  3.000
 MDZ  H3C2  C3   H3C1  107.16  3.000
 MDZ  H3C2  C3   C2    109.31  3.000
 MDZ  H3C1  C3   C2    108.38  3.000
 MDZ  H3C2  C3   C4    109.75  3.000
 MDZ  H3C1  C3   C4    108.98  3.000
 MDZ  C2    C3   C4    113.07  3.000
 MDZ  H2    C2   C1    105.31  3.000
 MDZ  H2    C2   N14   113.64  3.000
 MDZ  C1    C2   N14   112.05  3.000
 MDZ  H2    C2   C3    107.20  3.000
 MDZ  C1    C2   C3    107.50  3.000
 MDZ  N14   C2   C3    110.76  3.000
 MDZ  H142  N14  H141  105.17  3.000
 MDZ  H142  N14  C2    110.17  3.000
 MDZ  H141  N14  C2    108.98  3.000
 MDZ  O19   C1   O20   123.18  3.000
 MDZ  O19   C1   C2    114.08  3.000
 MDZ  O20   C1   C2    122.72  3.000
 MDZ  H19   O19  C1    109.41  3.000
 MDZ  H32   C32  C33   108.53  3.000
 MDZ  H32   C32  C37   107.87  3.000
 MDZ  C33   C32  C37   111.41  3.000
 MDZ  H32   C32  C30   105.29  3.000
 MDZ  C33   C32  C30   112.59  3.000
 MDZ  C37   C32  C30   110.82  3.000
 MDZ  H373  C37  H372  107.23  3.000
 MDZ  H373  C37  H371  107.86  3.000
 MDZ  H372  C37  H371  107.76  3.000
 MDZ  H373  C37  C32   112.24  3.000
 MDZ  H372  C37  C32   109.90  3.000
 MDZ  H371  C37  C32   111.65  3.000
 MDZ  H333  C33  H332  107.41  3.000
 MDZ  H333  C33  H331  107.05  3.000
 MDZ  H332  C33  H331  108.06  3.000
 MDZ  H333  C33  C32   109.67  3.000
 MDZ  H332  C33  C32   111.80  3.000
 MDZ  H331  C33  C32   112.60  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  CONST_04  H42   O42  C31  O43   180.00   0.0  0
 MDZ  CONST_05  H19   O19  C1   C2    180.00   0.0  0
 MDZ  Var_01    O18   C13  O29  C30    -1.38  30.0  3
 MDZ  Var_02    C4    C7   C10  N11  -121.11  30.0  3
 MDZ  Var_03    C3    C4   C7   C10  -179.10  30.0  3
 MDZ  Var_04    C2    C3   C4   C7   -173.52  30.0  3
 MDZ  Var_05    H371  C37  C32  C30    55.13  30.0  3
 MDZ  Var_06    H331  C33  C32  C30   -59.65  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-2  H42  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-3  H19  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

