# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 13:48:04 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  46  24  .  2022-07-25  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.442  -8.8219   0.4618   0.6859
 EYZ  C    C  C     0   0.520  -8.0388   0.0723  -0.1445
 EYZ  CA   C  CH1   0  -0.206  -6.7313   0.7694  -0.4966
 EYZ  N    N  NH2   0  -0.776  -6.6788   2.1469  -0.0712
 EYZ  CB   C  CH2   0  -0.431  -5.5621  -0.0270   0.0990
 EYZ  CAD  C  CH2   0  -0.414  -4.2040   0.4763  -0.3700
 EYZ  CAE  C  CH2   0  -0.463  -3.0603  -0.3425   0.2137
 EYZ  CAF  C  CH2   0  -0.246  -1.7064   0.1407  -0.2822
 EYZ  NAG  N  NH1   0  -0.640  -0.6363  -0.6797   0.2467
 EYZ  CAL  C  C     0   0.573   0.5167  -0.9034  -0.3932
 EYZ  OAK  O  O     0  -0.498   0.7948  -0.4034  -1.4754
 EYZ  CAJ  C  CH2   0  -0.579   1.4574  -1.8748   0.2985
 EYZ  CAM  C  CH1   0  -0.495   2.8988  -1.4115   0.1648
 EYZ  CAN  C  C     0   0.591   3.9354  -2.4109   0.6072
 EYZ  OAP  O  O     0  -0.434   4.9829  -2.5804   0.0358
 EYZ  OAO  O  OH1   0  -0.585   3.5860  -3.0508   1.7136
 EYZ  SAQ  S  S2    0   0.035   3.1228   0.0978   1.1867
 EYZ  CAR  C  CR6   0  -0.128   4.3951   0.9380   0.2853
 EYZ  CAS  C  CR16  0  -0.239   5.6825   1.0081   0.8061
 EYZ  CAT  C  CR16  0  -0.246   6.6671   1.7077   0.1201
 EYZ  CAU  C  CR16  0  -0.252   6.3698   2.3277  -1.0856
 EYZ  CAV  C  CR16  0  -0.246   5.0830   2.2532  -1.6069
 EYZ  CAW  C  CR16  0  -0.224   4.0926   1.5679  -0.9196
 EYZ  H2   H  HCH1  0   0.265  -6.6335   0.7434  -1.5871
 EYZ  H3   H  HNH2  0   0.354  -7.4122   2.6840  -0.5154
 EYZ  H4   H  HNH2  0   0.343  -6.8438   2.2120   0.9260
 EYZ  H6   H  HCH2  0   0.230  -5.6201   0.0207   1.1920
 EYZ  H7   H  HCH2  0   0.241  -5.6645  -1.0812  -0.1684
 EYZ  H8   H  HCH2  0   0.219  -4.1623   0.4294  -1.4634
 EYZ  H9   H  HCH2  0   0.229  -4.0862   1.5282  -0.1011
 EYZ  H10  H  HCH2  0   0.229  -3.0936  -0.2894   1.3071
 EYZ  H11  H  HCH2  0   0.230  -3.1843  -1.3964  -0.0528
 EYZ  H12  H  HCH2  0   0.239  -1.6714   0.0936  -1.3711
 EYZ  H13  H  HCH2  0   0.233  -1.5577   1.1891  -0.0038
 EYZ  H14  H  HNH1  0   0.401  -0.7700  -1.0859   1.1591
 EYZ  H15  H  HCH2  0   0.278   1.1804  -2.0271   1.3429
 EYZ  H16  H  HCH2  0   0.305   1.3452  -2.8447  -0.1969
 EYZ  H17  H  HCH1  0   0.328   3.1045  -1.1431  -0.8703
 EYZ  H18  H  HOH1  0   0.487   4.2902  -3.6592   1.9835
 EYZ  H19  H  HCR6  0   0.268   5.9152   0.5197   1.7434
 EYZ  H20  H  HCR6  0   0.264   7.6684   1.7620   0.5267
 EYZ  H21  H  HCR6  0   0.264   7.1385   2.8714  -1.6188
 EYZ  H22  H  HCR6  0   0.264   4.8475   2.7375  -2.5454
 EYZ  H23  H  HCR6  0   0.269   3.0865   1.5143  -1.3170
 EYZ  O1   O  OH1   0  -0.594  -8.2204  -1.0387  -0.8503
 EYZ  H1   H  HOH1  0   0.480  -9.0431  -1.4734  -0.5798

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    double    1.206  0.020  1.206
 EYZ  C    CA   single    1.523  0.020  1.523
 EYZ  CA   N    single    1.443  0.020  1.443
 EYZ  CA   CB   single    1.535  0.020  1.535
 EYZ  CB   CAD  single    1.522  0.020  1.522
 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    1.338  0.020  1.338
 EYZ  CAL  OAK  double    1.224  0.020  1.224
 EYZ  CAL  CAJ  single    1.519  0.020  1.519
 EYZ  CAJ  CAM  single    1.520  0.020  1.520
 EYZ  CAM  CAN  single    1.506  0.020  1.506
 EYZ  CAM  SAQ  single    1.836  0.020  1.836
 EYZ  CAN  OAP  double    1.205  0.020  1.205
 EYZ  CAN  OAO  single    1.325  0.020  1.325
 EYZ  SAQ  CAR  single    1.771  0.020  1.771
 EYZ  CAR  CAS  aromatic  1.390  0.020  1.390
 EYZ  CAR  CAW  aromatic  1.393  0.020  1.393
 EYZ  CAS  CAT  aromatic  1.389  0.020  1.389
 EYZ  CAT  CAU  aromatic  1.388  0.020  1.388
 EYZ  CAU  CAV  aromatic  1.390  0.020  1.390
 EYZ  CAV  CAW  aromatic  1.387  0.020  1.387
 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  OAO  H18  single    0.850  0.020  0.980
 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   single    1.329  0.020  1.329
 EYZ  O1   H1   single    0.850  0.020  0.980

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   112.16  3.000
 EYZ  O1   C    O    123.17  3.000
 EYZ  CA   C    O    124.67  3.000
 EYZ  H2   CA   CB   107.82  3.000
 EYZ  H2   CA   N    108.24  3.000
 EYZ  CB   CA   N    110.69  3.000
 EYZ  H2   CA   C    107.22  3.000
 EYZ  CB   CA   C    109.08  3.000
 EYZ  N    CA   C    113.58  3.000
 EYZ  H4   N    H3   106.27  3.000
 EYZ  H4   N    CA   110.23  3.000
 EYZ  H3   N    CA   110.55  3.000
 EYZ  H7   CB   H6   106.33  3.000
 EYZ  H7   CB   CAD  109.10  3.000
 EYZ  H6   CB   CAD  109.89  3.000
 EYZ  H7   CB   CA   109.53  3.000
 EYZ  H6   CB   CA   108.92  3.000
 EYZ  CAD  CB   CA   112.86  3.000
 EYZ  H9   CAD  H8   106.44  3.000
 EYZ  H9   CAD  CAE  110.03  3.000
 EYZ  H8   CAD  CAE  109.33  3.000
 EYZ  H9   CAD  CB   109.80  3.000
 EYZ  H8   CAD  CB   109.11  3.000
 EYZ  CAE  CAD  CB   111.97  3.000
 EYZ  H11  CAE  H10  106.64  3.000
 EYZ  H11  CAE  CAF  109.12  3.000
 EYZ  H10  CAE  CAF  109.71  3.000
 EYZ  H11  CAE  CAD  109.84  3.000
 EYZ  H10  CAE  CAD  109.50  3.000
 EYZ  CAF  CAE  CAD  111.89  3.000
 EYZ  H13  CAF  H12  106.91  3.000
 EYZ  H13  CAF  NAG  110.44  3.000
 EYZ  H12  CAF  NAG  108.45  3.000
 EYZ  H13  CAF  CAE  110.01  3.000
 EYZ  H12  CAF  CAE  109.90  3.000
 EYZ  NAG  CAF  CAE  111.02  3.000
 EYZ  H14  NAG  CAL  118.69  3.000
 EYZ  H14  NAG  CAF  117.45  3.000
 EYZ  CAL  NAG  CAF  123.84  3.000
 EYZ  CAJ  CAL  OAK  121.54  3.000
 EYZ  CAJ  CAL  NAG  115.02  3.000
 EYZ  OAK  CAL  NAG  123.40  3.000
 EYZ  H16  CAJ  H15  106.47  3.000
 EYZ  H16  CAJ  CAM  109.11  3.000
 EYZ  H15  CAJ  CAM  111.56  3.000
 EYZ  H16  CAJ  CAL  107.28  3.000
 EYZ  H15  CAJ  CAL  111.59  3.000
 EYZ  CAM  CAJ  CAL  110.63  3.000
 EYZ  H17  CAM  SAQ  107.66  3.000
 EYZ  H17  CAM  CAN  108.23  3.000
 EYZ  SAQ  CAM  CAN  107.33  3.000
 EYZ  H17  CAM  CAJ  109.75  3.000
 EYZ  SAQ  CAM  CAJ  108.49  3.000
 EYZ  CAN  CAM  CAJ  115.12  3.000
 EYZ  OAO  CAN  OAP  123.86  3.000
 EYZ  OAO  CAN  CAM  112.59  3.000
 EYZ  OAP  CAN  CAM  123.52  3.000
 EYZ  H18  OAO  CAN  110.13  3.000
 EYZ  CAR  SAQ  CAM  101.20  3.000
 EYZ  CAW  CAR  CAS  120.15  3.000
 EYZ  CAW  CAR  SAQ  119.92  3.000
 EYZ  CAS  CAR  SAQ  119.89  3.000
 EYZ  H19  CAS  CAT  120.17  3.000
 EYZ  H19  CAS  CAR  120.05  3.000
 EYZ  CAT  CAS  CAR  119.78  3.000
 EYZ  H20  CAT  CAU  120.15  3.000
 EYZ  H20  CAT  CAS  119.71  3.000
 EYZ  CAU  CAT  CAS  120.14  3.000
 EYZ  H21  CAU  CAV  119.98  3.000
 EYZ  H21  CAU  CAT  120.02  3.000
 EYZ  CAV  CAU  CAT  120.00  3.000
 EYZ  H22  CAV  CAW  119.71  3.000
 EYZ  H22  CAV  CAU  120.18  3.000
 EYZ  CAW  CAV  CAU  120.11  3.000
 EYZ  H23  CAW  CAV  120.41  3.000
 EYZ  H23  CAW  CAR  119.78  3.000
 EYZ  CAV  CAW  CAR  119.81  3.000
 EYZ  H1   O1   C    110.05  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  CONST_17  H1   O1   C    O       0.00   0.0  0
 EYZ  CONST_18  H18  OAO  CAN  CAM   180.00   0.0  0
 EYZ  Var_01    CAS  CAR  SAQ  CAM  -108.22  30.0  2
 EYZ  Var_02    CAE  CAD  CB   CA   -179.01  30.0  3
 EYZ  Var_03    CAF  CAE  CAD  CB    178.63  30.0  3
 EYZ  Var_04    NAG  CAF  CAE  CAD  -177.98  30.0  3
 EYZ  Var_05    CAL  NAG  CAF  CAE   149.88  30.0  3
 EYZ  Var_06    CAM  CAJ  CAL  NAG  -141.06  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-3  H1   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
 EYZ  plan-4  H18  0.020

