# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 14:22:56 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: N-(4-aminobutanoyl)-S-(4-methoxybenzyl)-L-cysteinylglycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(CSC[C@H](NC(=O)CCCN)C(=O)NCC(O)=O)cc1
#
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
 ABY  ABY  N-(4-aminobutanoyl)-S-(4-methoxybenzyl)-L-cysteinylglycine  ligand  50  26  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ABY
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
 ABY  C7'   C  CH3    0  -0.437   0.6562  -0.1584   8.5110
 ABY  O4'   O  O2     0  -0.470   0.8466   0.7323   7.4300
 ABY  C4'   C  CR6    0   0.371   0.1823   0.5017   6.2819
 ABY  C5'   C  CR16   0  -0.328   0.4058   1.4112   5.2444
 ABY  C6'   C  CR16   0  -0.267  -0.2301   1.2489   4.0293
 ABY  C1'   C  CR6    0   0.085  -1.1099   0.1880   3.8092
 ABY  C2'   C  CR16   0  -0.277  -1.3214  -0.7092   4.8461
 ABY  C3'   C  CR16   0  -0.371  -0.6911  -0.5629   6.0771
 ABY  C'    C  CH2    0  -0.619  -1.7677   0.0058   2.4766
 ABY  SG2   S  S2     0  -0.012  -0.5822  -0.8074   1.3549
 ABY  CB2   C  CH2    0  -0.583  -1.5550  -0.7838  -0.1801
 ABY  CA2   C  CH1    0  -0.163  -0.6944  -1.2181  -1.3629
 ABY  N2    N  NH1    0  -0.660   0.4229  -0.3220  -1.5207
 ABY  CD1   C  C      0   0.569   1.4389  -0.6012  -2.3662
 ABY  OE1   O  O      0  -0.483   1.4276  -1.5978  -3.0706
 ABY  CG1   C  CH2    0  -0.587   2.5481   0.4251  -2.3909
 ABY  CB1   C  CH2    0  -0.425   3.8613  -0.1127  -2.9361
 ABY  CA1   C  CH2    0  -0.272   4.9481   0.9515  -2.9350
 ABY  N1    N  NH2    0  -0.800   6.1865   0.4227  -3.4872
 ABY  C2    C  C      0   0.536  -1.5991  -1.2908  -2.5993
 ABY  O2    O  O      0  -0.508  -2.2707  -2.2947  -2.8063
 ABY  N3    N  NH1    0  -0.619  -1.6436  -0.1933  -3.3464
 ABY  CA3   C  CH2    0  -0.410  -2.4717  -0.0352  -4.5129
 ABY  C3    C  C      0   0.399  -2.2728   1.3621  -5.1356
 ABY  O31   O  O      0  -0.597  -1.4605   2.1217  -4.5736
 ABY  O32   O  OC    -1  -0.609  -2.9522   1.5917  -6.1504
 ABY  H7'1  H  HCH3   0   0.260   1.2883   0.1979   9.3206
 ABY  H7'2  H  HCH3   0   0.228  -0.3814  -0.1683   8.8552
 ABY  H7'3  H  HCH3   0   0.228   0.9525  -1.1793   8.2563
 ABY  H5'   H  HCR6   0   0.262   1.0821   2.2424   5.4013
 ABY  H6'   H  HCR6   0   0.255  -0.0407   1.9625   3.2358
 ABY  H2'   H  HCR6   0   0.257  -1.9976  -1.5437   4.7037
 ABY  H3'   H  HCR6   0   0.279  -0.8938  -1.2868   6.8545
 ABY  H'1   H  HCH2   0   0.284  -2.6641  -0.6100   2.5586
 ABY  H'2   H  HCH2   0   0.285  -2.0522   0.9648   2.0403
 ABY  HB21  H  HCH2   0   0.296  -2.4036  -1.4618  -0.0915
 ABY  HB22  H  HCH2   0   0.280  -1.9403   0.2263  -0.3417
 ABY  HA2   H  HCH1   0   0.281  -0.3341  -2.2358  -1.1854
 ABY  HN2   H  HNH1   0   0.404   0.5010   0.4687  -0.8994
 ABY  HG11  H  HCH2   0   0.272   2.2046   1.2643  -3.0068
 ABY  HG12  H  HCH2   0   0.256   2.6883   0.8349  -1.3867
 ABY  HB11  H  HCH2   0   0.225   4.1896  -0.9653  -2.3334
 ABY  HB12  H  HCH2   0   0.227   3.7244  -0.4812  -3.9543
 ABY  HA11  H  HCH2   0   0.215   4.6268   1.7911  -3.5581
 ABY  HA12  H  HCH2   0   0.190   5.0571   1.3517  -1.9163
 ABY  HN11  H  HNH2   0   0.346   6.8847   1.1546  -3.5129
 ABY  HN12  H  HNH2   0   0.338   6.5565  -0.2829  -2.8618
 ABY  HN3   H  HNH1   0   0.387  -1.0604   0.6046  -3.1321
 ABY  HA31  H  HCH2   0   0.243  -2.2382  -0.7960  -5.2644
 ABY  HA32  H  HCH2   0   0.242  -3.5284  -0.1654  -4.2596

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
 ABY  C7'  O4'   single    1.414  0.020  1.414
 ABY  C7'  H7'1  single    0.970  0.020  1.090
 ABY  C7'  H7'2  single    0.970  0.020  1.090
 ABY  C7'  H7'3  single    0.970  0.020  1.090
 ABY  O4'  C4'   single    1.346  0.020  1.346
 ABY  C4'  C5'   aromatic  1.398  0.020  1.398
 ABY  C4'  C3'   aromatic  1.392  0.020  1.392
 ABY  C5'  C6'   aromatic  1.381  0.020  1.381
 ABY  C5'  H5'   single    0.930  0.020  1.080
 ABY  C6'  C1'   aromatic  1.396  0.020  1.396
 ABY  C6'  H6'   single    0.930  0.020  1.080
 ABY  C1'  C2'   aromatic  1.387  0.020  1.387
 ABY  C1'  C'    single    1.497  0.020  1.497
 ABY  C2'  C3'   aromatic  1.391  0.020  1.391
 ABY  C2'  H2'   single    0.930  0.020  1.080
 ABY  C3'  H3'   single    0.930  0.020  1.080
 ABY  C'   SG2   single    1.823  0.020  1.823
 ABY  C'   H'1   single    0.970  0.020  1.090
 ABY  C'   H'2   single    0.970  0.020  1.090
 ABY  SG2  CB2   single    1.817  0.020  1.817
 ABY  CB2  CA2   single    1.526  0.020  1.526
 ABY  CB2  HB21  single    0.970  0.020  1.090
 ABY  CB2  HB22  single    0.970  0.020  1.090
 ABY  CA2  N2    single    1.441  0.020  1.441
 ABY  CA2  C2    single    1.534  0.020  1.534
 ABY  CA2  HA2   single    0.970  0.020  1.090
 ABY  N2   CD1   single    1.351  0.020  1.351
 ABY  N2   HN2   single    0.860  0.020  1.020
 ABY  CD1  OE1   double    1.220  0.020  1.220
 ABY  CD1  CG1   single    1.511  0.020  1.511
 ABY  CG1  CB1   single    1.520  0.020  1.520
 ABY  CG1  HG11  single    0.970  0.020  1.090
 ABY  CG1  HG12  single    0.970  0.020  1.090
 ABY  CB1  CA1   single    1.521  0.020  1.521
 ABY  CB1  HB11  single    0.970  0.020  1.090
 ABY  CB1  HB12  single    0.970  0.020  1.090
 ABY  CA1  N1    single    1.455  0.020  1.455
 ABY  CA1  HA11  single    0.970  0.020  1.090
 ABY  CA1  HA12  single    0.970  0.020  1.090
 ABY  N1   HN11  single    0.890  0.020  1.040
 ABY  N1   HN12  single    0.890  0.020  1.040
 ABY  C2   O2    double    1.225  0.020  1.225
 ABY  C2   N3    single    1.328  0.020  1.328
 ABY  N3   CA3   single    1.439  0.020  1.439
 ABY  N3   HN3   single    0.860  0.020  1.020
 ABY  CA3  C3    single    1.543  0.020  1.543
 ABY  CA3  HA31  single    0.970  0.020  1.090
 ABY  CA3  HA32  single    0.970  0.020  1.090
 ABY  C3   O31   deloc     1.246  0.020  1.246
 ABY  C3   O32   deloc     1.243  0.020  1.243

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
 ABY  H7'3  C7'  H7'2  108.79  3.000
 ABY  H7'3  C7'  H7'1  108.78  3.000
 ABY  H7'2  C7'  H7'1  108.68  3.000
 ABY  H7'3  C7'  O4'   111.95  3.000
 ABY  H7'2  C7'  O4'   111.99  3.000
 ABY  H7'1  C7'  O4'   106.54  3.000
 ABY  C4'   O4'  C7'   118.54  3.000
 ABY  C3'   C4'  C5'   119.26  3.000
 ABY  C3'   C4'  O4'   124.47  3.000
 ABY  C5'   C4'  O4'   116.27  3.000
 ABY  H5'   C5'  C6'   120.34  3.000
 ABY  H5'   C5'  C4'   119.46  3.000
 ABY  C6'   C5'  C4'   120.20  3.000
 ABY  H6'   C6'  C1'   119.68  3.000
 ABY  H6'   C6'  C5'   119.10  3.000
 ABY  C1'   C6'  C5'   121.21  3.000
 ABY  C'    C1'  C2'   121.30  3.000
 ABY  C'    C1'  C6'   120.65  3.000
 ABY  C2'   C1'  C6'   118.03  3.000
 ABY  H2'   C2'  C3'   118.70  3.000
 ABY  H2'   C2'  C1'   119.67  3.000
 ABY  C3'   C2'  C1'   121.63  3.000
 ABY  H3'   C3'  C2'   118.75  3.000
 ABY  H3'   C3'  C4'   121.59  3.000
 ABY  C2'   C3'  C4'   119.67  3.000
 ABY  H'2   C'   H'1   108.18  3.000
 ABY  H'2   C'   SG2   108.38  3.000
 ABY  H'1   C'   SG2   109.20  3.000
 ABY  H'2   C'   C1'   111.31  3.000
 ABY  H'1   C'   C1'   111.28  3.000
 ABY  SG2   C'   C1'   108.43  3.000
 ABY  CB2   SG2  C'     99.54  3.000
 ABY  HB22  CB2  HB21  108.21  3.000
 ABY  HB22  CB2  CA2   110.32  3.000
 ABY  HB21  CB2  CA2   108.98  3.000
 ABY  HB22  CB2  SG2   108.99  3.000
 ABY  HB21  CB2  SG2   109.88  3.000
 ABY  CA2   CB2  SG2   110.43  3.000
 ABY  HA2   CA2  C2    106.31  3.000
 ABY  HA2   CA2  N2    109.93  3.000
 ABY  C2    CA2  N2    113.49  3.000
 ABY  HA2   CA2  CB2   108.95  3.000
 ABY  C2    CA2  CB2   107.79  3.000
 ABY  N2    CA2  CB2   110.20  3.000
 ABY  HN2   N2   CD1   119.30  3.000
 ABY  HN2   N2   CA2   118.69  3.000
 ABY  CD1   N2   CA2   121.54  3.000
 ABY  CG1   CD1  OE1   123.50  3.000
 ABY  CG1   CD1  N2    114.95  3.000
 ABY  OE1   CD1  N2    121.54  3.000
 ABY  HG12  CG1  HG11  105.62  3.000
 ABY  HG12  CG1  CB1   110.56  3.000
 ABY  HG11  CG1  CB1   109.88  3.000
 ABY  HG12  CG1  CD1   109.49  3.000
 ABY  HG11  CG1  CD1   107.40  3.000
 ABY  CB1   CG1  CD1   113.55  3.000
 ABY  HB12  CB1  HB11  106.75  3.000
 ABY  HB12  CB1  CA1   109.06  3.000
 ABY  HB11  CB1  CA1   109.29  3.000
 ABY  HB12  CB1  CG1   110.22  3.000
 ABY  HB11  CB1  CG1   109.70  3.000
 ABY  CA1   CB1  CG1   111.69  3.000
 ABY  HA12  CA1  HA11  106.10  3.000
 ABY  HA12  CA1  N1    113.54  3.000
 ABY  HA11  CA1  N1    108.22  3.000
 ABY  HA12  CA1  CB1   109.03  3.000
 ABY  HA11  CA1  CB1   109.07  3.000
 ABY  N1    CA1  CB1   110.70  3.000
 ABY  HN12  N1   HN11  105.51  3.000
 ABY  HN12  N1   CA1   109.25  3.000
 ABY  HN11  N1   CA1   109.51  3.000
 ABY  N3    C2   O2    124.29  3.000
 ABY  N3    C2   CA2   115.72  3.000
 ABY  O2    C2   CA2   119.89  3.000
 ABY  HN3   N3   CA3   114.64  3.000
 ABY  HN3   N3   C2    120.89  3.000
 ABY  CA3   N3   C2    124.46  3.000
 ABY  HA32  CA3  HA31  106.39  3.000
 ABY  HA32  CA3  C3    109.01  3.000
 ABY  HA31  CA3  C3    108.96  3.000
 ABY  HA32  CA3  N3    110.78  3.000
 ABY  HA31  CA3  N3    110.94  3.000
 ABY  C3    CA3  N3    110.63  3.000
 ABY  O32   C3   O31   127.74  3.000
 ABY  O32   C3   CA3   115.24  3.000
 ABY  O31   C3   CA3   117.01  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
 ABY  CONST_01  C1'   C6'  C5'  C4'     0.00   0.0  0
 ABY  CONST_02  C1'   C2'  C3'  C4'     0.00   0.0  0
 ABY  CONST_03  C2'   C3'  C4'  C5'     0.00   0.0  0
 ABY  CONST_04  C2'   C1'  C6'  C5'     0.00   0.0  0
 ABY  CONST_05  C3'   C4'  C5'  C6'     0.00   0.0  0
 ABY  CONST_06  C3'   C2'  C1'  C6'     0.00   0.0  0
 ABY  CONST_07  C6'   C5'  C4'  O4'   180.00   0.0  0
 ABY  CONST_08  C2'   C3'  C4'  O4'   180.00   0.0  0
 ABY  CONST_09  C'    C1'  C6'  C5'   180.00   0.0  0
 ABY  CONST_10  C'    C1'  C2'  C3'   180.00   0.0  0
 ABY  CONST_11  H6'   C6'  C5'  C4'   180.00   0.0  0
 ABY  CONST_12  H2'   C2'  C3'  C4'   180.00   0.0  0
 ABY  CONST_13  H3'   C3'  C4'  C5'   180.00   0.0  0
 ABY  CONST_14  H5'   C5'  C6'  C1'   180.00   0.0  0
 ABY  CONST_15  OE1   CD1  N2   CA2     0.00   0.0  0
 ABY  CONST_16  CG1   CD1  N2   CA2   180.00   0.0  0
 ABY  CONST_17  CA3   N3   C2   CA2   180.00   0.0  0
 ABY  CONST_18  CA3   N3   C2   O2      0.00   0.0  0
 ABY  CONST_19  HN3   N3   C2   CA2     0.00   0.0  0
 ABY  CONST_20  HN2   N2   CD1  OE1   180.00   0.0  0
 ABY  Var_01    C5'   C4'  O4'  C7'  -179.98  30.0  2
 ABY  Var_02    SG2   C'   C1'  C6'    80.47  30.0  2
 ABY  Var_03    H7'1  C7'  O4'  C4'   179.12  30.0  3
 ABY  Var_04    CA2   CB2  SG2  C'    170.95  30.0  3
 ABY  Var_05    CB1   CG1  CD1  N2    159.53  30.0  3
 ABY  Var_06    CA1   CB1  CG1  CD1  -179.70  30.0  3
 ABY  Var_07    N1    CA1  CB1  CG1  -178.77  30.0  3
 ABY  Var_08    C3    CA3  N3   C2   -179.98  30.0  3
 ABY  Var_09    O31   C3   CA3  N3      0.20  30.0  3
 ABY  Var_10    HN11  N1   CA1  CB1   177.71  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
 ABY  chir_01  CA2  CB2  N2  C2  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
 ABY  plan-1  O4'  0.020
 ABY  plan-1  C4'  0.020
 ABY  plan-1  C5'  0.020
 ABY  plan-1  C6'  0.020
 ABY  plan-1  C1'  0.020
 ABY  plan-1  C2'  0.020
 ABY  plan-1  C3'  0.020
 ABY  plan-1  C'   0.020
 ABY  plan-1  H5'  0.020
 ABY  plan-1  H6'  0.020
 ABY  plan-1  H2'  0.020
 ABY  plan-1  H3'  0.020
 ABY  plan-2  CA2  0.020
 ABY  plan-2  N2   0.020
 ABY  plan-2  CD1  0.020
 ABY  plan-2  OE1  0.020
 ABY  plan-2  CG1  0.020
 ABY  plan-2  HN2  0.020
 ABY  plan-3  CA2  0.020
 ABY  plan-3  C2   0.020
 ABY  plan-3  O2   0.020
 ABY  plan-3  N3   0.020
 ABY  plan-3  CA3  0.020
 ABY  plan-3  HN3  0.020
 ABY  plan-4  CA3  0.020
 ABY  plan-4  C3   0.020
 ABY  plan-4  O31  0.020
 ABY  plan-4  O32  0.020

