# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 03:18:04 2022
#   Inital geometry file: a 68 line input string
#   Ligand name: N-methyl-S-[(1R)-1-methylpropyl]-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@@H](C)SC[C@H](NC)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
 NYB  NYB  N-methyl-S-[(1R)-1-methylpropyl]-L-cysteine  L-peptide  28  12  .  2012-08-28  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NYB
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
 NYB  N     N  NH1    0  -0.583   2.5911   1.1712  17.3901
 NYB  CA    C  CH1    0  -0.216   1.4753   2.0326  17.7334
 NYB  CB    C  CH2    0  -0.533   0.8499   1.8366  19.1191
 NYB  SG    S  S2     0  -0.028   1.7144   2.6653  20.4931
 NYB  CD    C  CH1    0  -0.368   1.6637   1.3770  21.7924
 NYB  CE1   C  CH3    0  -0.652   1.9819   2.0752  23.1086
 NYB  CE2   C  CH2    0  -0.397   2.6119   0.2174  21.5007
 NYB  CF    C  CH3    0  -0.664   2.4697  -0.9455  22.4763
 NYB  CN    C  CH3    0  -0.528   3.8630   1.4051  18.0441
 NYB  C     C  C      0   0.410   1.7527   3.5276  17.4104
 NYB  O     O  O      0  -0.589   1.2393   4.3579  18.1873
 NYB  OXT   O  OC    -1  -0.600   2.4175   3.7731  16.3887
 NYB  H     H  HNH1   0   0.333   2.3172   0.2071  17.5275
 NYB  HA    H  HCH1   0   0.231   0.6720   1.7418  17.0393
 NYB  HN1   H  HCH3   0   0.211   4.6123   0.7446  17.6021
 NYB  HN2   H  HCH3   0   0.216   4.1936   2.4276  17.8626
 NYB  HN3   H  HCH3   0   0.205   3.8755   1.2429  19.1255
 NYB  HB1   H  HCH2   0   0.245  -0.1797   2.1963  19.1029
 NYB  HB2   H  HCH2   0   0.250   0.8046   0.7686  19.3450
 NYB  HD    H  HCH1   0   0.245   0.6378   0.9959  21.8338
 NYB  HE11  H  HCH3   0   0.238   1.9313   1.3778  23.9451
 NYB  HE12  H  HCH3   0   0.223   2.9878   2.5003  23.0924
 NYB  HE13  H  HCH3   0   0.235   1.2774   2.8822  23.3092
 NYB  HE21  H  HCH2   0   0.229   2.4303  -0.1523  20.4881
 NYB  HE22  H  HCH2   0   0.214   3.6398   0.5921  21.5071
 NYB  HF1   H  HCH3   0   0.231   3.1179  -1.7736  22.1878
 NYB  HF2   H  HCH3   0   0.222   2.7373  -0.6638  23.4949
 NYB  HF3   H  HCH3   0   0.218   1.4448  -1.3209  22.4945

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
 NYB  N    CA    single  1.458  0.019  1.458
 NYB  N    CN    single  1.449  0.020  1.449
 NYB  CA   CB    single  1.530  0.020  1.530
 NYB  CA   C     single  1.525  0.021  1.525
 NYB  CB   SG    single  1.823  0.020  1.823
 NYB  SG   CD    single  1.830  0.020  1.830
 NYB  CD   CE1   single  1.523  0.020  1.523
 NYB  CD   CE2   single  1.526  0.020  1.526
 NYB  CE2  CF    single  1.525  0.020  1.525
 NYB  C    O     deloc   1.231  0.020  1.231
 NYB  C    OXT   deloc   1.243  0.020  1.243
 NYB  N    H     single  0.860  0.020  0.860
 NYB  CA   HA    single  0.970  0.020  0.970
 NYB  CN   HN1   single  0.970  0.020  1.090
 NYB  CN   HN2   single  0.970  0.020  1.090
 NYB  CN   HN3   single  0.970  0.020  1.090
 NYB  CB   HB1   single  0.970  0.020  1.090
 NYB  CB   HB2   single  0.970  0.020  1.090
 NYB  CD   HD    single  0.970  0.020  1.090
 NYB  CE1  HE11  single  0.970  0.020  1.090
 NYB  CE1  HE12  single  0.970  0.020  1.090
 NYB  CE1  HE13  single  0.970  0.020  1.090
 NYB  CE2  HE21  single  0.970  0.020  1.090
 NYB  CE2  HE22  single  0.970  0.020  1.090
 NYB  CF   HF1   single  0.970  0.020  1.090
 NYB  CF   HF2   single  0.970  0.020  1.090
 NYB  CF   HF3   single  0.970  0.020  1.090

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
 NYB  H     N    CN    109.27  3.000
 NYB  H     N    CA    114.00  3.000
 NYB  CN    N    CA    118.18  3.000
 NYB  HA    CA   C     109.00  3.000
 NYB  HA    CA   CB    109.00  3.000
 NYB  C     CA   CB    110.10  1.900
 NYB  HA    CA   N     110.00  3.000
 NYB  C     CA   N     111.00  2.800
 NYB  CB    CA   N     110.50  1.700
 NYB  HB2   CB   HB1   106.63  3.000
 NYB  HB2   CB   SG    107.95  3.000
 NYB  HB1   CB   SG    108.00  3.000
 NYB  HB2   CB   CA    109.20  3.000
 NYB  HB1   CB   CA    109.24  3.000
 NYB  SG    CB   CA    115.46  3.000
 NYB  CD    SG   CB    101.66  3.000
 NYB  HD    CD   CE2   108.95  3.000
 NYB  HD    CD   CE1   108.81  3.000
 NYB  CE2   CD   CE1   112.56  3.000
 NYB  HD    CD   SG    107.32  3.000
 NYB  CE2   CD   SG    112.45  3.000
 NYB  CE1   CD   SG    106.56  3.000
 NYB  HE13  CE1  HE12  108.05  3.000
 NYB  HE13  CE1  HE11  107.60  3.000
 NYB  HE12  CE1  HE11  107.65  3.000
 NYB  HE13  CE1  CD    111.31  3.000
 NYB  HE12  CE1  CD    110.97  3.000
 NYB  HE11  CE1  CD    111.10  3.000
 NYB  HE22  CE2  HE21  106.10  3.000
 NYB  HE22  CE2  CF    110.19  3.000
 NYB  HE21  CE2  CF    108.62  3.000
 NYB  HE22  CE2  CD    108.81  3.000
 NYB  HE21  CE2  CD    109.32  3.000
 NYB  CF    CE2  CD    113.54  3.000
 NYB  HF3   CF   HF2   107.68  3.000
 NYB  HF3   CF   HF1   107.54  3.000
 NYB  HF2   CF   HF1   107.31  3.000
 NYB  HF3   CF   CE2   111.13  3.000
 NYB  HF2   CF   CE2   112.21  3.000
 NYB  HF1   CF   CE2   110.76  3.000
 NYB  HN3   CN   HN2   107.47  3.000
 NYB  HN3   CN   HN1   107.62  3.000
 NYB  HN2   CN   HN1   106.97  3.000
 NYB  HN3   CN   N     115.62  3.000
 NYB  HN2   CN   N     110.03  3.000
 NYB  HN1   CN   N     108.78  3.000
 NYB  OXT   C    O     126.89  3.000
 NYB  OXT   C    CA    117.13  3.000
 NYB  O     C    CA    120.80  1.700

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
 NYB  Var_01  HN1  CN  N    CA  -174.27  30.0  3
 NYB  Var_02  HB1  CB  SG   CD    99.52  30.0  1
 NYB  Var_03  HF1  CF  CE2  CD   176.20  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
 NYB  chir_01  CA  N   CB   C    negativ
 NYB  chir_02  CD  SG  CE2  CE1  negativ

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
 NYB  plan-1  CA   0.020
 NYB  plan-1  C    0.020
 NYB  plan-1  O    0.020
 NYB  plan-1  OXT  0.020

