# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 11:00:46 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: (2~{S})-2-azanyl-6-[[(3~{R})-4-oxidanyl-4-oxidanylidene-3-phenylsulfanyl-butanoyl]amino]hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCNC(=O)C[C@@H](Sc1ccccc1)C(O)=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
 EYZ  EYZ  '(2~{S})-2-azanyl-6-[[(3~{R})-4-oxidanyl-4-oxidanylidene-3-phenylsulfanyl-butanoyl]amino]hexanoic acid'  ligand  44  24  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_EYZ
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
 EYZ  O    O  O      0  -0.609  -8.6051   0.6224   1.5826
 EYZ  C    C  C      0   0.383  -8.0459   0.0928   0.6018
 EYZ  CA   C  CH1    0  -0.209  -6.7965   0.7990   0.0185
 EYZ  N    N  NH2    0  -0.786  -6.5965   2.1739   0.4524
 EYZ  CB   C  CH2    0  -0.418  -5.5546  -0.0376   0.3370
 EYZ  CAD  C  CH2    0  -0.407  -4.2714   0.4813  -0.2986
 EYZ  CAE  C  CH2    0  -0.463  -3.0732  -0.4032   0.0191
 EYZ  CAF  C  CH2    0  -0.241  -1.7878   0.1107  -0.6107
 EYZ  NAG  N  NH1    0  -0.638  -0.6755  -0.7564  -0.2821
 EYZ  CAL  C  C      0   0.557   0.4330  -0.8724  -1.0249
 EYZ  OAK  O  O      0  -0.505   0.6231  -0.2302  -2.0501
 EYZ  CAJ  C  CH2    0  -0.582   1.4306  -1.9008  -0.5293
 EYZ  CAM  C  CH1    0  -0.484   2.8660  -1.3833  -0.5279
 EYZ  CAN  C  C      0   0.445   3.8329  -2.5500  -0.2056
 EYZ  OAP  O  O      0  -0.599   4.5701  -2.9179  -1.1408
 EYZ  OAO  O  OC    -1  -0.587   3.7567  -3.0324   0.9351
 EYZ  SAQ  S  S2     0   0.039   2.9306  -0.0522   0.7095
 EYZ  CAR  C  CR6    0  -0.100   4.3760   0.8651   0.3012
 EYZ  CAS  C  CR16   0  -0.274   4.5359   2.0956   0.9448
 EYZ  CAT  C  CR16   0  -0.243   5.6515   2.8779   0.6949
 EYZ  CAU  C  CR16   0  -0.273   6.6218   2.4545  -0.2060
 EYZ  CAV  C  CR16   0  -0.240   6.4624   1.2348  -0.8467
 EYZ  CAW  C  CR16   0  -0.267   5.3523   0.4364  -0.5968
 EYZ  H2   H  HCH1   0   0.205  -6.9095   0.8136  -1.0725
 EYZ  H3   H  HNH2   0   0.333  -7.3972   2.7241   0.1646
 EYZ  H4   H  HNH2   0   0.321  -6.6361   2.1904   1.4658
 EYZ  H6   H  HCH2   0   0.203  -5.4253  -0.0839   1.4260
 EYZ  H7   H  HCH2   0   0.217  -5.7311  -1.0644   0.0076
 EYZ  H8   H  HCH2   0   0.206  -4.4044   0.5371  -1.3848
 EYZ  H9   H  HCH2   0   0.217  -4.0809   1.5025   0.0394
 EYZ  H10  H  HCH2   0   0.222  -2.9455  -0.4633   1.1055
 EYZ  H11  H  HCH2   0   0.225  -3.2608  -1.4235  -0.3299
 EYZ  H12  H  HCH2   0   0.235  -1.8931   0.1498  -1.6958
 EYZ  H13  H  HCH2   0   0.228  -1.5904   1.1335  -0.2727
 EYZ  H14  H  HNH1   0   0.398  -0.7356  -1.2861   0.5725
 EYZ  H15  H  HCH2   0   0.263   1.1661  -2.2791   0.4600
 EYZ  H16  H  HCH2   0   0.290   1.3794  -2.7550  -1.2124
 EYZ  H17  H  HCH1   0   0.274   3.0893  -0.9500  -1.5043
 EYZ  H19  H  HCR6   0   0.260   3.7817   2.4467   1.6393
 EYZ  H20  H  HCR6   0   0.258   5.7575   3.8281   1.2024
 EYZ  H21  H  HCR6   0   0.254   7.4898   3.0693  -0.4042
 EYZ  H22  H  HCR6   0   0.256   7.2116   0.8882  -1.5472
 EYZ  H23  H  HCR6   0   0.262   5.2710  -0.5197  -1.0957
 EYZ  O1   O  OC    -1  -0.626  -8.3792  -0.9758   0.0466

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
 EYZ  O    C    deloc     1.247  0.020  1.247
 EYZ  C    CA   single    1.549  0.020  1.549
 EYZ  CA   N    single    1.456  0.020  1.456
 EYZ  CA   CB   single    1.531  0.020  1.531
 EYZ  CB   CAD  single    1.523  0.020  1.523
 EYZ  CAD  CAE  single    1.523  0.020  1.523
 EYZ  CAE  CAF  single    1.521  0.020  1.521
 EYZ  CAF  NAG  single    1.448  0.020  1.448
 EYZ  NAG  CAL  single    1.339  0.020  1.339
 EYZ  CAL  OAK  double    1.225  0.020  1.225
 EYZ  CAL  CAJ  single    1.516  0.020  1.516
 EYZ  CAJ  CAM  single    1.526  0.020  1.526
 EYZ  CAM  CAN  single    1.549  0.020  1.549
 EYZ  CAM  SAQ  single    1.819  0.020  1.819
 EYZ  CAN  OAP  deloc     1.246  0.020  1.246
 EYZ  CAN  OAO  deloc     1.241  0.020  1.241
 EYZ  SAQ  CAR  single    1.760  0.020  1.760
 EYZ  CAR  CAS  aromatic  1.398  0.020  1.398
 EYZ  CAR  CAW  aromatic  1.394  0.020  1.394
 EYZ  CAS  CAT  aromatic  1.385  0.020  1.385
 EYZ  CAT  CAU  aromatic  1.390  0.020  1.390
 EYZ  CAU  CAV  aromatic  1.387  0.020  1.387
 EYZ  CAV  CAW  aromatic  1.390  0.020  1.390
 EYZ  CA   H2   single    0.970  0.020  1.090
 EYZ  N    H3   single    0.890  0.020  1.040
 EYZ  N    H4   single    0.890  0.020  1.040
 EYZ  CB   H6   single    0.970  0.020  1.090
 EYZ  CB   H7   single    0.970  0.020  1.090
 EYZ  CAD  H8   single    0.970  0.020  1.090
 EYZ  CAD  H9   single    0.970  0.020  1.090
 EYZ  CAE  H10  single    0.970  0.020  1.090
 EYZ  CAE  H11  single    0.970  0.020  1.090
 EYZ  CAF  H12  single    0.970  0.020  1.090
 EYZ  CAF  H13  single    0.970  0.020  1.090
 EYZ  NAG  H14  single    0.860  0.020  1.020
 EYZ  CAJ  H15  single    0.970  0.020  1.090
 EYZ  CAJ  H16  single    0.970  0.020  1.090
 EYZ  CAM  H17  single    0.970  0.020  1.090
 EYZ  CAS  H19  single    0.930  0.020  1.080
 EYZ  CAT  H20  single    0.930  0.020  1.080
 EYZ  CAU  H21  single    0.930  0.020  1.080
 EYZ  CAV  H22  single    0.930  0.020  1.080
 EYZ  CAW  H23  single    0.930  0.020  1.080
 EYZ  C    O1   deloc     1.250  0.020  1.250

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
 EYZ  O1   C    CA   115.96  3.000
 EYZ  O1   C    O    126.37  3.000
 EYZ  CA   C    O    117.66  3.000
 EYZ  H2   CA   CB   107.32  3.000
 EYZ  H2   CA   N    107.34  3.000
 EYZ  CB   CA   N    110.04  3.000
 EYZ  H2   CA   C    107.31  3.000
 EYZ  CB   CA   C    109.08  3.000
 EYZ  N    CA   C    115.42  3.000
 EYZ  H4   N    H3   104.13  3.000
 EYZ  H4   N    CA   107.92  3.000
 EYZ  H3   N    CA   108.65  3.000
 EYZ  H7   CB   H6   106.17  3.000
 EYZ  H7   CB   CAD  109.29  3.000
 EYZ  H6   CB   CAD  109.22  3.000
 EYZ  H7   CB   CA   108.65  3.000
 EYZ  H6   CB   CA   108.97  3.000
 EYZ  CAD  CB   CA   114.23  3.000
 EYZ  H9   CAD  H8   106.28  3.000
 EYZ  H9   CAD  CAE  109.95  3.000
 EYZ  H8   CAD  CAE  109.38  3.000
 EYZ  H9   CAD  CB   109.65  3.000
 EYZ  H8   CAD  CB   109.19  3.000
 EYZ  CAE  CAD  CB   112.21  3.000
 EYZ  H11  CAE  H10  106.56  3.000
 EYZ  H11  CAE  CAF  109.14  3.000
 EYZ  H10  CAE  CAF  109.31  3.000
 EYZ  H11  CAE  CAD  109.88  3.000
 EYZ  H10  CAE  CAD  109.30  3.000
 EYZ  CAF  CAE  CAD  112.48  3.000
 EYZ  H13  CAF  H12  106.91  3.000
 EYZ  H13  CAF  NAG  110.53  3.000
 EYZ  H12  CAF  NAG  108.74  3.000
 EYZ  H13  CAF  CAE  109.89  3.000
 EYZ  H12  CAF  CAE  110.03  3.000
 EYZ  NAG  CAF  CAE  110.67  3.000
 EYZ  H14  NAG  CAL  118.31  3.000
 EYZ  H14  NAG  CAF  117.49  3.000
 EYZ  CAL  NAG  CAF  124.18  3.000
 EYZ  CAJ  CAL  OAK  121.82  3.000
 EYZ  CAJ  CAL  NAG  114.96  3.000
 EYZ  OAK  CAL  NAG  123.18  3.000
 EYZ  H16  CAJ  H15  106.48  3.000
 EYZ  H16  CAJ  CAM  108.01  3.000
 EYZ  H15  CAJ  CAM  110.16  3.000
 EYZ  H16  CAJ  CAL  107.12  3.000
 EYZ  H15  CAJ  CAL  111.83  3.000
 EYZ  CAM  CAJ  CAL  112.91  3.000
 EYZ  H17  CAM  SAQ  108.11  3.000
 EYZ  H17  CAM  CAN  110.94  3.000
 EYZ  SAQ  CAM  CAN  112.80  3.000
 EYZ  H17  CAM  CAJ  109.05  3.000
 EYZ  SAQ  CAM  CAJ  106.40  3.000
 EYZ  CAN  CAM  CAJ  109.38  3.000
 EYZ  OAO  CAN  OAP  127.69  3.000
 EYZ  OAO  CAN  CAM  116.47  3.000
 EYZ  OAP  CAN  CAM  115.81  3.000
 EYZ  CAR  SAQ  CAM  104.64  3.000
 EYZ  CAW  CAR  CAS  119.15  3.000
 EYZ  CAW  CAR  SAQ  124.36  3.000
 EYZ  CAS  CAR  SAQ  116.48  3.000
 EYZ  H19  CAS  CAT  119.55  3.000
 EYZ  H19  CAS  CAR  120.05  3.000
 EYZ  CAT  CAS  CAR  120.41  3.000
 EYZ  H20  CAT  CAU  120.19  3.000
 EYZ  H20  CAT  CAS  119.34  3.000
 EYZ  CAU  CAT  CAS  120.47  3.000
 EYZ  H21  CAU  CAV  120.48  3.000
 EYZ  H21  CAU  CAT  120.37  3.000
 EYZ  CAV  CAU  CAT  119.15  3.000
 EYZ  H22  CAV  CAW  119.02  3.000
 EYZ  H22  CAV  CAU  120.06  3.000
 EYZ  CAW  CAV  CAU  120.92  3.000
 EYZ  H23  CAW  CAV  119.01  3.000
 EYZ  H23  CAW  CAR  121.08  3.000
 EYZ  CAV  CAW  CAR  119.90  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
 EYZ  CONST_01  CAU  CAT  CAS  CAR     0.00   0.0  0
 EYZ  CONST_02  CAU  CAV  CAW  CAR     0.00   0.0  0
 EYZ  CONST_03  CAV  CAW  CAR  CAS     0.00   0.0  0
 EYZ  CONST_04  CAV  CAU  CAT  CAS     0.00   0.0  0
 EYZ  CONST_05  CAW  CAR  CAS  CAT     0.00   0.0  0
 EYZ  CONST_06  CAW  CAV  CAU  CAT     0.00   0.0  0
 EYZ  CONST_07  CAT  CAS  CAR  SAQ   180.00   0.0  0
 EYZ  CONST_08  CAV  CAW  CAR  SAQ   180.00   0.0  0
 EYZ  CONST_09  H20  CAT  CAS  CAR   180.00   0.0  0
 EYZ  CONST_10  H22  CAV  CAW  CAR   180.00   0.0  0
 EYZ  CONST_11  H23  CAW  CAR  CAS   180.00   0.0  0
 EYZ  CONST_12  H21  CAU  CAT  CAS   180.00   0.0  0
 EYZ  CONST_13  H19  CAS  CAT  CAU   180.00   0.0  0
 EYZ  CONST_14  OAK  CAL  NAG  CAF     0.00   0.0  0
 EYZ  CONST_15  CAJ  CAL  NAG  CAF   180.00   0.0  0
 EYZ  CONST_16  H14  NAG  CAL  OAK   180.00   0.0  0
 EYZ  Var_01    CAS  CAR  SAQ  CAM   168.61  30.0  2
 EYZ  Var_02    CAE  CAD  CB   CA   -178.57  30.0  3
 EYZ  Var_03    CAF  CAE  CAD  CB   -179.90  30.0  3
 EYZ  Var_04    NAG  CAF  CAE  CAD   179.89  30.0  3
 EYZ  Var_05    CAL  NAG  CAF  CAE   155.01  30.0  3
 EYZ  Var_06    CAM  CAJ  CAL  NAG  -134.41  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
 EYZ  chir_01  CA   C    N    CB   negativ
 EYZ  chir_02  CAM  CAJ  CAN  SAQ  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
 EYZ  plan-1  SAQ  0.020
 EYZ  plan-1  CAR  0.020
 EYZ  plan-1  CAS  0.020
 EYZ  plan-1  CAT  0.020
 EYZ  plan-1  CAU  0.020
 EYZ  plan-1  CAV  0.020
 EYZ  plan-1  CAW  0.020
 EYZ  plan-1  H19  0.020
 EYZ  plan-1  H20  0.020
 EYZ  plan-1  H21  0.020
 EYZ  plan-1  H22  0.020
 EYZ  plan-1  H23  0.020
 EYZ  plan-2  CAF  0.020
 EYZ  plan-2  NAG  0.020
 EYZ  plan-2  CAL  0.020
 EYZ  plan-2  OAK  0.020
 EYZ  plan-2  CAJ  0.020
 EYZ  plan-2  H14  0.020
 EYZ  plan-3  O    0.020
 EYZ  plan-3  C    0.020
 EYZ  plan-3  CA   0.020
 EYZ  plan-3  O1   0.020
 EYZ  plan-4  CAM  0.020
 EYZ  plan-4  CAN  0.020
 EYZ  plan-4  OAP  0.020
 EYZ  plan-4  OAO  0.020

