# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 05:15:21 2021
#   Inital geometry file: a 100 line input string
#   Ligand name: N-(carboxycarbonyl)-S-(naphthalen-2-ylmethyl)-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H](CSCc1ccc2ccccc2c1)NC(=O)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
 MD3  MD3  N-(carboxycarbonyl)-S-(naphthalen-2-ylmethyl)-L-cysteine  L-peptide  38  23  .  2022-03-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MD3
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
 MD3  C16   C  CR16  0  -0.306  -2.3467   3.7355   5.9096
 MD3  N     N  NH1   0  -0.611  -3.4354   1.3402   1.8282
 MD3  O05   O  O     0  -0.407  -1.3730   0.2153   3.2125
 MD3  SG    S  S2    0  -0.013  -3.0203   3.8770  -0.1282
 MD3  C01   C  C     0   0.462  -2.3915   0.4745   3.7961
 MD3  OXT   O  OH1   0  -0.578  -4.0959  -0.2500  -0.2294
 MD3  C02   C  C     0   0.468  -3.6670   0.9312   3.0799
 MD3  O     O  O     0  -0.425  -4.6659   1.5369  -1.4432
 MD3  CA    C  CH1   0  -0.221  -4.4829   1.7662   0.9411
 MD3  O03   O  O     0  -0.447  -4.7503   0.8788   3.6251
 MD3  C     C  C     0   0.568  -4.4170   1.0209  -0.3850
 MD3  O04   O  OH1   0  -0.561  -2.5856   0.3875   5.0895
 MD3  CB    C  CH2   0  -0.551  -4.5056   3.2714   0.7259
 MD3  C06   C  CH2   0  -0.675  -2.3429   5.0336   1.1089
 MD3  C07   C  CR6   0   0.159  -1.7239   4.3533   2.2875
 MD3  C08   C  CR16  0  -0.290  -0.4913   3.6707   2.1315
 MD3  C09   C  CR16  0  -0.282   0.1089   3.0560   3.1907
 MD3  C10   C  CR66  0   0.092  -0.4914   3.0696   4.4729
 MD3  C11   C  CR16  0  -0.374  -2.3238   4.3727   3.5179
 MD3  C12   C  CR66  0   0.123  -1.7347   3.7307   4.6351
 MD3  C13   C  CR16  0  -0.310   0.0988   2.4289   5.5855
 MD3  C14   C  CR16  0  -0.270  -0.5162   2.4501   6.8093
 MD3  C15   C  CR16  0  -0.250  -1.7513   3.1114   6.9720
 MD3  H16   H  HCR6  0   0.253  -3.2965   4.2416   6.0348
 MD3  H2    H  HNH1  0   0.415  -2.4791   1.4009   1.5078
 MD3  HXT   H  HOH1  0   0.489  -4.0886  -0.7013  -1.0875
 MD3  HA    H  HCH1  0   0.329  -5.4378   1.4837   1.3980
 MD3  HO04  H  HOH1  0   0.491  -1.7640   0.1351   5.5394
 MD3  HB2   H  HCH2  0   0.297  -4.5871   3.7654   1.6938
 MD3  HB3   H  HCH2  0   0.295  -5.3860   3.5503   0.1489
 MD3  H06   H  HCH2  0   0.302  -1.5985   5.6127   0.5590
 MD3  H06A  H  HCH2  0   0.296  -3.1290   5.7252   1.4125
 MD3  H08   H  HCR6  0   0.254  -0.0221   3.6424   1.1552
 MD3  H09   H  HCR6  0   0.252   1.0541   2.5436   3.0584
 MD3  H11   H  HCR6  0   0.252  -3.2632   4.8974   3.6561
 MD3  H13   H  HCR6  0   0.256   1.0460   1.9191   5.4561
 MD3  H14   H  HCR6  0   0.260  -0.0564   1.9587   7.6569
 MD3  H15   H  HCR6  0   0.258  -2.2275   3.1226   7.9438

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
 MD3  C12  C16   aromatic  1.414  0.020  1.414
 MD3  C16  C15   aromatic  1.369  0.020  1.369
 MD3  C16  H16   single    0.930  0.020  1.080
 MD3  CA   N     single    1.458  0.019  1.458
 MD3  N    C02   single    1.337  0.020  1.337
 MD3  N    H2    single    0.860  0.020  1.020
 MD3  O05  C01   double    1.202  0.020  1.202
 MD3  SG   CB    single    1.817  0.020  1.817
 MD3  SG   C06   single    1.824  0.020  1.824
 MD3  C02  C01   single    1.532  0.020  1.532
 MD3  C01  O04   single    1.311  0.020  1.311
 MD3  OXT  C     single    1.320  0.020  1.320
 MD3  OXT  HXT   single    0.850  0.020  0.980
 MD3  C02  O03   double    1.214  0.020  1.214
 MD3  O    C     double    1.231  0.020  1.231
 MD3  C    CA    single    1.525  0.021  1.525
 MD3  CA   CB    single    1.530  0.020  1.530
 MD3  CA   HA    single    0.970  0.020  0.970
 MD3  O04  HO04  single    0.850  0.020  0.980
 MD3  CB   HB2   single    0.970  0.020  1.090
 MD3  CB   HB3   single    0.970  0.020  1.090
 MD3  C06  C07   single    1.495  0.020  1.495
 MD3  C06  H06   single    0.970  0.020  1.090
 MD3  C06  H06A  single    0.970  0.020  1.090
 MD3  C08  C07   aromatic  1.418  0.020  1.418
 MD3  C07  C11   aromatic  1.369  0.020  1.369
 MD3  C08  C09   aromatic  1.364  0.020  1.364
 MD3  C08  H08   single    0.930  0.020  1.080
 MD3  C09  C10   aromatic  1.416  0.020  1.416
 MD3  C09  H09   single    0.930  0.020  1.080
 MD3  C10  C12   aromatic  1.417  0.020  1.417
 MD3  C10  C13   aromatic  1.413  0.020  1.413
 MD3  C11  C12   aromatic  1.417  0.020  1.417
 MD3  C11  H11   single    0.930  0.020  1.080
 MD3  C13  C14   aromatic  1.370  0.020  1.370
 MD3  C13  H13   single    0.930  0.020  1.080
 MD3  C14  C15   aromatic  1.410  0.020  1.410
 MD3  C14  H14   single    0.930  0.020  1.080
 MD3  C15  H15   single    0.930  0.020  1.080

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
 MD3  H16   C16  C15  120.31  3.000
 MD3  H16   C16  C12  119.03  3.000
 MD3  C15   C16  C12  120.66  3.000
 MD3  H2    N    CA   118.45  3.000
 MD3  H2    N    C02  118.63  3.000
 MD3  CA    N    C02  122.84  3.000
 MD3  C06   SG   CB   101.31  3.000
 MD3  O04   C01  C02  110.96  3.000
 MD3  O04   C01  O05  126.17  3.000
 MD3  C02   C01  O05  122.86  3.000
 MD3  HXT   OXT  C    110.22  3.000
 MD3  O03   C02  C01  121.33  3.000
 MD3  O03   C02  N    126.03  3.000
 MD3  C01   C02  N    112.62  3.000
 MD3  HA    CA   CB   109.00  3.000
 MD3  HA    CA   C    109.00  3.000
 MD3  CB    CA   C    110.10  1.900
 MD3  HA    CA   N    110.00  3.000
 MD3  CB    CA   N    110.50  1.700
 MD3  C     CA   N    111.00  2.800
 MD3  CA    C    O    120.80  1.700
 MD3  CA    C    OXT  112.28  3.000
 MD3  O     C    OXT  124.53  3.000
 MD3  HO04  O04  C01  110.45  3.000
 MD3  HB3   CB   HB2  107.10  3.000
 MD3  HB3   CB   CA   109.91  3.000
 MD3  HB2   CB   CA   108.91  3.000
 MD3  HB3   CB   SG   109.05  3.000
 MD3  HB2   CB   SG   109.12  3.000
 MD3  CA    CB   SG   112.59  3.000
 MD3  H06A  C06  H06  107.18  3.000
 MD3  H06A  C06  C07  111.58  3.000
 MD3  H06   C06  C07  110.86  3.000
 MD3  H06A  C06  SG   108.87  3.000
 MD3  H06   C06  SG   104.35  3.000
 MD3  C07   C06  SG   113.57  3.000
 MD3  C11   C07  C08  119.12  3.000
 MD3  C11   C07  C06  121.37  3.000
 MD3  C08   C07  C06  119.50  3.000
 MD3  H08   C08  C09  119.83  3.000
 MD3  H08   C08  C07  119.22  3.000
 MD3  C09   C08  C07  120.95  3.000
 MD3  H09   C09  C10  119.02  3.000
 MD3  H09   C09  C08  120.16  3.000
 MD3  C10   C09  C08  120.82  3.000
 MD3  C13   C10  C12  119.19  3.000
 MD3  C13   C10  C09  122.11  3.000
 MD3  C12   C10  C09  118.69  3.000
 MD3  H11   C11  C12  118.61  3.000
 MD3  H11   C11  C07  120.05  3.000
 MD3  C12   C11  C07  121.34  3.000
 MD3  C11   C12  C10  119.07  3.000
 MD3  C11   C12  C16  121.96  3.000
 MD3  C10   C12  C16  118.98  3.000
 MD3  H13   C13  C14  120.43  3.000
 MD3  H13   C13  C10  118.98  3.000
 MD3  C14   C13  C10  120.59  3.000
 MD3  H14   C14  C15  119.64  3.000
 MD3  H14   C14  C13  120.13  3.000
 MD3  C15   C14  C13  120.23  3.000
 MD3  H15   C15  C14  119.58  3.000
 MD3  H15   C15  C16  120.06  3.000
 MD3  C14   C15  C16  120.35  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
 MD3  CONST_01  C09   C10  C12  C16  180.00   0.0  0
 MD3  CONST_02  C13   C10  C12  C16    0.00   0.0  0
 MD3  CONST_03  C07   C11  C12  C16  180.00   0.0  0
 MD3  CONST_04  C13   C14  C15  C16    0.00   0.0  0
 MD3  CONST_05  C10   C09  C08  C07    0.00   0.0  0
 MD3  CONST_06  C10   C12  C11  C07    0.00   0.0  0
 MD3  CONST_07  C12   C11  C07  C08    0.00   0.0  0
 MD3  CONST_08  C12   C10  C09  C08    0.00   0.0  0
 MD3  CONST_09  C13   C10  C09  C08  180.00   0.0  0
 MD3  CONST_10  C11   C07  C08  C09    0.00   0.0  0
 MD3  CONST_11  C11   C12  C10  C09    0.00   0.0  0
 MD3  CONST_12  C14   C13  C10  C09  180.00   0.0  0
 MD3  CONST_13  C15   C16  C12  C10    0.00   0.0  0
 MD3  CONST_14  C15   C14  C13  C10    0.00   0.0  0
 MD3  CONST_15  C15   C16  C12  C11  180.00   0.0  0
 MD3  CONST_16  C13   C10  C12  C11  180.00   0.0  0
 MD3  CONST_17  C14   C15  C16  C12    0.00   0.0  0
 MD3  CONST_18  C14   C13  C10  C12    0.00   0.0  0
 MD3  CONST_19  C09   C08  C07  C06  180.00   0.0  0
 MD3  CONST_20  C12   C11  C07  C06  180.00   0.0  0
 MD3  CONST_21  H11   C11  C12  C16    0.00   0.0  0
 MD3  CONST_22  H14   C14  C15  C16  180.00   0.0  0
 MD3  CONST_23  H09   C09  C08  C07  180.00   0.0  0
 MD3  CONST_24  H13   C13  C10  C09    0.00   0.0  0
 MD3  CONST_25  H08   C08  C09  C10  180.00   0.0  0
 MD3  CONST_26  H16   C16  C12  C10  180.00   0.0  0
 MD3  CONST_27  H15   C15  C16  C12  180.00   0.0  0
 MD3  CONST_28  CA    N    C02  C01  180.00   0.0  0
 MD3  CONST_29  O03   C02  N    CA     0.00   0.0  0
 MD3  CONST_30  H2    N    C02  C01    0.00   0.0  0
 MD3  CONST_31  HO04  O04  C01  O05    0.00   0.0  0
 MD3  CONST_32  HXT   OXT  C    O      0.00   0.0  0
 MD3  Var_01    C08   C07  C06  SG    71.44  30.0  2
 MD3  Var_02    C07   C06  SG   CB    73.04  30.0  3
 MD3  Var_03    O05   C01  C02  N    -16.40  30.0  2
 MD3  Var_04    HB2   CB   SG   C06    1.19  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
 MD3  chir_01  CA  N  C  CB  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
 MD3  plan-1  C16   0.020
 MD3  plan-1  C06   0.020
 MD3  plan-1  C07   0.020
 MD3  plan-1  C08   0.020
 MD3  plan-1  C09   0.020
 MD3  plan-1  C10   0.020
 MD3  plan-1  C11   0.020
 MD3  plan-1  C12   0.020
 MD3  plan-1  C13   0.020
 MD3  plan-1  C14   0.020
 MD3  plan-1  C15   0.020
 MD3  plan-1  H16   0.020
 MD3  plan-1  H08   0.020
 MD3  plan-1  H09   0.020
 MD3  plan-1  H11   0.020
 MD3  plan-1  H13   0.020
 MD3  plan-1  H14   0.020
 MD3  plan-1  H15   0.020
 MD3  plan-2  N     0.020
 MD3  plan-2  C01   0.020
 MD3  plan-2  C02   0.020
 MD3  plan-2  CA    0.020
 MD3  plan-2  O03   0.020
 MD3  plan-2  H2    0.020
 MD3  plan-3  O05   0.020
 MD3  plan-3  C01   0.020
 MD3  plan-3  C02   0.020
 MD3  plan-3  O04   0.020
 MD3  plan-3  HO04  0.020
 MD3  plan-4  OXT   0.020
 MD3  plan-4  O     0.020
 MD3  plan-4  CA    0.020
 MD3  plan-4  C     0.020
 MD3  plan-4  HXT   0.020

