# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 07:28:57 2020
#   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  36  23  .  2022-03-22  2022-07-25
;
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  -0.313  -5.1635  -1.2390   1.3374
 MD3  N     N  NH1    0  -0.598   3.0921  -0.3282   0.0691
 MD3  O05   O  O      0  -0.593   3.5303  -2.7037   1.1504
 MD3  SG    S  S2     0  -0.018   0.2008   0.6425  -0.0993
 MD3  C01   C  C      0   0.329   4.0626  -2.5528   0.0340
 MD3  OXT   O  OC    -1  -0.615   4.0397   3.1375  -0.2685
 MD3  C02   C  C      0   0.361   3.8852  -1.1519  -0.6235
 MD3  O     O  O      0  -0.585   5.0536   1.4305   0.7529
 MD3  CA    C  CH1    0  -0.194   2.9119   1.0578  -0.2644
 MD3  O03   O  O      0  -0.512   4.4059  -0.8608  -1.6922
 MD3  C     C  C      0   0.418   4.1296   1.9542   0.1146
 MD3  O04   O  OC    -1  -0.581   4.7176  -3.3702  -0.6239
 MD3  CB    C  CH2    0  -0.569   1.6600   1.5967   0.4143
 MD3  C06   C  CH2    0  -0.621  -1.0941   1.5673   0.7885
 MD3  C07   C  CR6    0   0.115  -2.4321   1.0841   0.3213
 MD3  C08   C  CR16   0  -0.281  -2.9499   1.5488  -0.9122
 MD3  C09   C  CR16   0  -0.299  -4.1587   1.1132  -1.3748
 MD3  C10   C  CR66   0   0.100  -4.9218   0.1770  -0.6364
 MD3  C11   C  CR16   0  -0.364  -3.1528   0.1733   1.0481
 MD3  C12   C  CR66   0   0.135  -4.4071  -0.3010   0.5961
 MD3  C13   C  CR16   0  -0.310  -6.1767  -0.2943  -1.0871
 MD3  C14   C  CR16   0  -0.259  -6.8869  -1.2022  -0.3488
 MD3  C15   C  CR16   0  -0.259  -6.3741  -1.6800   0.8755
 MD3  H16   H  HCR6   0   0.254  -4.7711  -1.6052   2.2785
 MD3  H2    H  HNH1   0   0.380   2.8080  -0.6619   0.9776
 MD3  HA    H  HCH1   0   0.244   2.7753   1.1358  -1.3472
 MD3  HB2   H  HCH2   0   0.278   1.5214   2.6407   0.1370
 MD3  HB3   H  HCH2   0   0.263   1.7576   1.5456   1.5025
 MD3  H06   H  HCH2   0   0.281  -0.9765   1.4190   1.8626
 MD3  H06A  H  HCH2   0   0.280  -0.9711   2.6314   0.5766
 MD3  H08   H  HCR6   0   0.255  -2.3753   2.2636  -1.4890
 MD3  H09   H  HCR6   0   0.255  -4.5464   1.4830  -2.3165
 MD3  H11   H  HCR6   0   0.252  -2.7648  -0.1950   1.9917
 MD3  H13   H  HCR6   0   0.255  -6.5696   0.0737  -2.0274
 MD3  H14   H  HCR6   0   0.258  -7.8463  -1.5578  -0.7010
 MD3  H15   H  HCR6   0   0.258  -6.9446  -2.3983   1.4498

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  1.415  0.020  1.415
 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   deloc     1.246  0.020  1.246
 MD3  SG   CB    single    1.818  0.020  1.818
 MD3  SG   C06   single    1.822  0.020  1.822
 MD3  C02  C01   single    1.558  0.020  1.558
 MD3  C01  O04   deloc     1.237  0.020  1.237
 MD3  OXT  C     deloc     1.247  0.020  1.247
 MD3  C02  O03   double    1.224  0.020  1.224
 MD3  O    C     deloc     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  CB   HB2   single    0.970  0.020  1.090
 MD3  CB   HB3   single    0.970  0.020  1.090
 MD3  C06  C07   single    1.497  0.020  1.497
 MD3  C06  H06   single    0.970  0.020  1.090
 MD3  C06  H06A  single    0.970  0.020  1.090
 MD3  C08  C07   aromatic  1.416  0.020  1.416
 MD3  C07  C11   aromatic  1.370  0.020  1.370
 MD3  C08  C09   aromatic  1.366  0.020  1.366
 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  1.419  0.020  1.419
 MD3  C10  C13   aromatic  1.414  0.020  1.414
 MD3  C11  C12   aromatic  1.415  0.020  1.415
 MD3  C11  H11   single    0.930  0.020  1.080
 MD3  C13  C14   aromatic  1.369  0.020  1.369
 MD3  C13  H13   single    0.930  0.020  1.080
 MD3  C14  C15   aromatic  1.411  0.020  1.411
 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  120.30  3.000
 MD3  H16   C16  C12  119.05  3.000
 MD3  C15   C16  C12  120.64  3.000
 MD3  H2    N    CA   119.53  3.000
 MD3  H2    N    C02  115.46  3.000
 MD3  CA    N    C02  123.26  3.000
 MD3  C06   SG   CB    99.58  3.000
 MD3  O04   C01  C02  115.48  3.000
 MD3  O04   C01  O05  128.51  3.000
 MD3  C02   C01  O05  116.01  3.000
 MD3  O03   C02  C01  122.28  3.000
 MD3  O03   C02  N    123.93  3.000
 MD3  C01   C02  N    113.77  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  114.50  3.000
 MD3  O     C    OXT  127.81  3.000
 MD3  HB3   CB   HB2  108.02  3.000
 MD3  HB3   CB   CA   110.71  3.000
 MD3  HB2   CB   CA   109.30  3.000
 MD3  HB3   CB   SG   109.16  3.000
 MD3  HB2   CB   SG   109.22  3.000
 MD3  CA    CB   SG   110.39  3.000
 MD3  H06A  C06  H06  108.15  3.000
 MD3  H06A  C06  C07  110.77  3.000
 MD3  H06   C06  C07  111.08  3.000
 MD3  H06A  C06  SG   108.67  3.000
 MD3  H06   C06  SG   109.52  3.000
 MD3  C07   C06  SG   108.61  3.000
 MD3  C11   C07  C08  119.20  3.000
 MD3  C11   C07  C06  121.27  3.000
 MD3  C08   C07  C06  119.51  3.000
 MD3  H08   C08  C09  119.97  3.000
 MD3  H08   C08  C07  119.09  3.000
 MD3  C09   C08  C07  120.93  3.000
 MD3  H09   C09  C10  119.09  3.000
 MD3  H09   C09  C08  120.15  3.000
 MD3  C10   C09  C08  120.76  3.000
 MD3  C13   C10  C12  119.11  3.000
 MD3  C13   C10  C09  122.17  3.000
 MD3  C12   C10  C09  118.71  3.000
 MD3  H11   C11  C12  118.77  3.000
 MD3  H11   C11  C07  119.93  3.000
 MD3  C12   C11  C07  121.30  3.000
 MD3  C11   C12  C10  119.09  3.000
 MD3  C11   C12  C16  121.92  3.000
 MD3  C10   C12  C16  118.99  3.000
 MD3  H13   C13  C14  120.34  3.000
 MD3  H13   C13  C10  119.02  3.000
 MD3  C14   C13  C10  120.63  3.000
 MD3  H14   C14  C15  119.56  3.000
 MD3  H14   C14  C13  120.16  3.000
 MD3  C15   C14  C13  120.28  3.000
 MD3  H15   C15  C14  119.59  3.000
 MD3  H15   C15  C16  120.07  3.000
 MD3  C14   C15  C16  120.34  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  Var_01    C08  C07  C06  SG   -79.15  30.0  2
 MD3  Var_02    C07  C06  SG   CB   170.59  30.0  3
 MD3  Var_03    O05  C01  C02  N     -4.71  30.0  2
 MD3  Var_04    HB2  CB   SG   C06  -56.96  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-4  OXT  0.020
 MD3  plan-4  O    0.020
 MD3  plan-4  CA   0.020
 MD3  plan-4  C    0.020

