# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 09:33:19 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: 2-[2-[2-hydroxy-2-oxoethyl-[(3-methoxy-2-oxidanyl-phenyl)methyl]amino]ethyl-[(2-methylsulfanylphenyl)methyl]amino]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(CN(CCN(CC(O)=O)Cc2ccccc2SC)CC(O)=O)c1O
#
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
 9YH  9YH  '2-[2-[2-hydroxy-2-oxoethyl-[(3-methoxy-2-oxidanyl-phenyl)methyl]amino]ethyl-[(2-methylsulfanylphenyl)methyl]amino]ethanoic acid'  ligand  57  31  .  2021-08-06  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9YH
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
 9YH  CBC  C  CH3    0  -0.428   7.2197   2.6534  -0.9995
 9YH  OAX  O  O2     0  -0.495   6.2266   1.7221  -1.3757
 9YH  CAR  C  CR6    0   0.305   5.1218   1.6096  -0.6008
 9YH  CAS  C  CR6    0   0.232   4.2136   0.6240  -1.0200
 9YH  OAY  O  OH1    0  -0.632   4.4654  -0.1138  -2.1262
 9YH  CAQ  C  CR16   0  -0.393   4.8511   2.3720   0.5243
 9YH  CAE  C  CR16   0  -0.262   3.6703   2.1518   1.2280
 9YH  CAF  C  CR16   0  -0.303   2.7797   1.1782   0.8139
 9YH  CAG  C  CR6    0  -0.035   3.0391   0.3965  -0.3115
 9YH  CAH  C  CH2    0  -0.294   2.0608  -0.6649  -0.7782
 9YH  N    N  NT     0  -0.418   1.1442  -1.0597   0.2609
 9YH  CA   C  CH2    0  -0.452   1.6845  -2.0250   1.1855
 9YH  C    C  C      0   0.400   1.9056  -3.4733   0.6946
 9YH  OXT  O  OC    -1  -0.630   2.3362  -4.2525   1.5704
 9YH  O    O  O      0  -0.602   1.6510  -3.7565  -0.4916
 9YH  CAJ  C  CH2    0  -0.270  -0.2439  -1.2574  -0.0927
 9YH  CAK  C  CH2    0  -0.274  -1.1701  -0.7182   0.9952
 9YH  NAL  N  NT     0  -0.398  -2.5682  -0.9666   0.6845
 9YH  CAT  C  CH2    0  -0.422  -2.9567  -2.3161   1.0373
 9YH  CAZ  C  C      0   0.383  -4.2668  -2.8523   0.4251
 9YH  OBD  O  OC    -1  -0.634  -4.6781  -3.9135   0.9443
 9YH  OBA  O  O      0  -0.580  -4.7822  -2.2411  -0.5247
 9YH  CAM  C  CH2    0  -0.324  -3.4685  -0.0090   1.2965
 9YH  CAN  C  C      0   0.085  -3.1515   1.4211   0.9532
 9YH  CAO  C  C1     0  -0.303  -2.9299   2.3343   1.9774
 9YH  CAP  C  C1     0  -0.259  -2.6553   3.6714   1.7244
 9YH  CAW  C  C1     0  -0.258  -2.5865   4.1055   0.4112
 9YH  CAV  C  C1     0  -0.250  -2.7946   3.2110  -0.6299
 9YH  CAU  C  C      0  -0.162  -3.0833   1.8706  -0.3764
 9YH  SBB  S  S2     0   0.085  -3.3756   0.7083  -1.6745
 9YH  CBE  C  CH3    0  -0.809  -3.6520   1.7913  -3.0957
 9YH  H1   H  HCH3   0   0.228   6.8398   3.6782  -1.0087
 9YH  H2   H  HCH3   0   0.228   7.6251   2.4367  -0.0076
 9YH  H3   H  HCH3   0   0.260   8.0185   2.5690  -1.7318
 9YH  H4   H  HOH1   0   0.469   5.3367   0.1076  -2.4766
 9YH  H5   H  HCR6   0   0.275   5.5418   3.1333   0.8619
 9YH  H6   H  HCR6   0   0.245   3.4571   2.7477   2.1058
 9YH  H7   H  HCR6   0   0.246   1.8637   0.9972   1.3606
 9YH  H8   H  HCH2   0   0.239   1.4892  -0.2544  -1.6164
 9YH  H9   H  HCH2   0   0.220   2.6113  -1.5168  -1.1926
 9YH  H11  H  HCH2   0   0.231   2.6437  -1.6502   1.5628
 9YH  H12  H  HCH2   0   0.231   1.0408  -2.0727   2.0701
 9YH  H14  H  HCH2   0   0.218  -0.4705  -0.7012  -1.0050
 9YH  H15  H  HCH2   0   0.196  -0.4682  -2.3083  -0.3145
 9YH  H16  H  HCH2   0   0.188  -0.8957  -1.1279   1.9820
 9YH  H17  H  HCH2   0   0.230  -0.9967   0.3572   1.0575
 9YH  H19  H  HCH2   0   0.238  -2.1658  -3.0013   0.7150
 9YH  H20  H  HCH2   0   0.183  -3.0143  -2.4381   2.1342
 9YH  H22  H  HCH2   0   0.252  -4.4791  -0.2401   0.9498
 9YH  H23  H  HCH2   0   0.202  -3.4829  -0.1049   2.3970
 9YH  H24  H  H      0   0.246  -2.9771   1.9828   3.0016
 9YH  H25  H  H      0   0.250  -2.4939   4.3598   2.5434
 9YH  H26  H  H      0   0.253  -2.3675   5.1412   0.1851
 9YH  H27  H  H      0   0.259  -2.7294   3.5776  -1.6447
 9YH  H28  H  HCH3   0   0.264  -4.4367   2.5229  -2.9073
 9YH  H29  H  HCH3   0   0.262  -2.7466   2.3039  -3.4170
 9YH  H30  H  HCH3   0   0.284  -3.9759   1.1377  -3.9045

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
 9YH  OBA  CAZ  deloc     1.242  0.020  1.242
 9YH  CAF  CAE  aromatic  1.383  0.020  1.383
 9YH  CAF  CAG  aromatic  1.395  0.020  1.395
 9YH  CAH  CAG  single    1.517  0.020  1.517
 9YH  CAH  N    single    1.441  0.020  1.441
 9YH  CAE  CAQ  aromatic  1.392  0.020  1.392
 9YH  CAG  CAS  aromatic  1.390  0.020  1.390
 9YH  CAZ  OBD  deloc     1.251  0.020  1.251
 9YH  CAZ  CAT  single    1.542  0.020  1.542
 9YH  CAJ  N    single    1.446  0.020  1.446
 9YH  CAJ  CAK  single    1.527  0.020  1.527
 9YH  N    CA   single    1.442  0.020  1.442
 9YH  CAQ  CAR  aromatic  1.386  0.020  1.386
 9YH  CAT  NAL  single    1.448  0.020  1.448
 9YH  CAS  CAR  aromatic  1.404  0.020  1.404
 9YH  CAS  OAY  single    1.353  0.020  1.353
 9YH  CAK  NAL  single    1.454  0.020  1.454
 9YH  CA   C    single    1.545  0.020  1.545
 9YH  CAR  OAX  single    1.354  0.020  1.354
 9YH  NAL  CAM  single    1.450  0.020  1.450
 9YH  OAX  CBC  single    1.412  0.020  1.412
 9YH  C    O    deloc     1.246  0.020  1.246
 9YH  C    OXT  deloc     1.249  0.020  1.249
 9YH  CAO  CAP  aromatic  1.388  0.020  1.388
 9YH  CAO  CAN  aromatic  1.390  0.020  1.390
 9YH  CAP  CAW  aromatic  1.385  0.020  1.385
 9YH  CAM  CAN  single    1.505  0.020  1.505
 9YH  CBE  SBB  single    1.808  0.020  1.808
 9YH  CAN  CAU  aromatic  1.405  0.020  1.405
 9YH  CAW  CAV  aromatic  1.388  0.020  1.388
 9YH  CAU  CAV  aromatic  1.394  0.020  1.394
 9YH  CAU  SBB  single    1.767  0.020  1.767
 9YH  CBC  H1   single    0.970  0.020  1.090
 9YH  CBC  H2   single    0.970  0.020  1.090
 9YH  CBC  H3   single    0.970  0.020  1.090
 9YH  OAY  H4   single    0.850  0.020  0.980
 9YH  CAQ  H5   single    0.930  0.020  1.080
 9YH  CAE  H6   single    0.930  0.020  1.080
 9YH  CAF  H7   single    0.930  0.020  1.080
 9YH  CAH  H8   single    0.970  0.020  1.090
 9YH  CAH  H9   single    0.970  0.020  1.090
 9YH  CA   H11  single    0.970  0.020  1.090
 9YH  CA   H12  single    0.970  0.020  1.090
 9YH  CAJ  H14  single    0.970  0.020  1.090
 9YH  CAJ  H15  single    0.970  0.020  1.090
 9YH  CAK  H16  single    0.970  0.020  1.090
 9YH  CAK  H17  single    0.970  0.020  1.090
 9YH  CAT  H19  single    0.970  0.020  1.090
 9YH  CAT  H20  single    0.970  0.020  1.090
 9YH  CAM  H22  single    0.970  0.020  1.090
 9YH  CAM  H23  single    0.970  0.020  1.090
 9YH  CAO  H24  single    0.930  0.020  1.080
 9YH  CAP  H25  single    0.930  0.020  1.080
 9YH  CAW  H26  single    0.930  0.020  1.080
 9YH  CAV  H27  single    0.930  0.020  1.080
 9YH  CBE  H28  single    0.970  0.020  1.090
 9YH  CBE  H29  single    0.970  0.020  1.090
 9YH  CBE  H30  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
 9YH  H3   CBC  H2   108.87  3.000
 9YH  H3   CBC  H1   108.81  3.000
 9YH  H2   CBC  H1   108.81  3.000
 9YH  H3   CBC  OAX  106.62  3.000
 9YH  H2   CBC  OAX  111.82  3.000
 9YH  H1   CBC  OAX  111.81  3.000
 9YH  CAR  OAX  CBC  118.42  3.000
 9YH  CAQ  CAR  CAS  120.14  3.000
 9YH  CAS  CAR  OAX  114.53  3.000
 9YH  CAQ  CAR  OAX  125.33  3.000
 9YH  CAG  CAS  OAY  118.98  3.000
 9YH  OAY  CAS  CAR  120.42  3.000
 9YH  CAG  CAS  CAR  120.60  3.000
 9YH  H4   OAY  CAS  109.86  3.000
 9YH  H5   CAQ  CAE  119.68  3.000
 9YH  H5   CAQ  CAR  121.05  3.000
 9YH  CAE  CAQ  CAR  119.28  3.000
 9YH  H6   CAE  CAF  120.24  3.000
 9YH  H6   CAE  CAQ  119.34  3.000
 9YH  CAF  CAE  CAQ  120.42  3.000
 9YH  H7   CAF  CAG  118.13  3.000
 9YH  H7   CAF  CAE  120.78  3.000
 9YH  CAG  CAF  CAE  121.09  3.000
 9YH  CAH  CAG  CAF  121.36  3.000
 9YH  CAH  CAG  CAS  120.16  3.000
 9YH  CAF  CAG  CAS  118.47  3.000
 9YH  H9   CAH  H8   105.33  3.000
 9YH  H9   CAH  N    112.29  3.000
 9YH  H8   CAH  N    108.84  3.000
 9YH  H9   CAH  CAG  109.65  3.000
 9YH  H8   CAH  CAG  108.06  3.000
 9YH  N    CAH  CAG  112.34  3.000
 9YH  CAJ  N    CA   115.15  3.000
 9YH  CA   N    CAH  114.06  3.000
 9YH  CAJ  N    CAH  118.15  3.000
 9YH  H12  CA   H11  104.55  3.000
 9YH  H12  CA   C    107.45  3.000
 9YH  H11  CA   C    107.73  3.000
 9YH  H12  CA   N    109.08  3.000
 9YH  H11  CA   N    108.63  3.000
 9YH  C    CA   N    118.52  3.000
 9YH  O    C    OXT  126.61  3.000
 9YH  OXT  C    CA   114.29  3.000
 9YH  O    C    CA   119.10  3.000
 9YH  H15  CAJ  H14  106.05  3.000
 9YH  H15  CAJ  CAK  110.99  3.000
 9YH  H14  CAJ  CAK  106.83  3.000
 9YH  H15  CAJ  N    112.12  3.000
 9YH  H14  CAJ  N    109.50  3.000
 9YH  CAK  CAJ  N    111.08  3.000
 9YH  H17  CAK  H16  105.99  3.000
 9YH  H17  CAK  NAL  109.48  3.000
 9YH  H16  CAK  NAL  111.53  3.000
 9YH  H17  CAK  CAJ  106.99  3.000
 9YH  H16  CAK  CAJ  110.81  3.000
 9YH  NAL  CAK  CAJ  111.76  3.000
 9YH  CAM  NAL  CAT  110.25  3.000
 9YH  CAM  NAL  CAK  113.21  3.000
 9YH  CAT  NAL  CAK  111.42  3.000
 9YH  H20  CAT  H19  105.11  3.000
 9YH  H20  CAT  CAZ  108.13  3.000
 9YH  H19  CAT  CAZ  106.21  3.000
 9YH  H20  CAT  NAL  111.02  3.000
 9YH  H19  CAT  NAL  108.53  3.000
 9YH  CAZ  CAT  NAL  117.08  3.000
 9YH  OBA  CAZ  OBD  126.78  3.000
 9YH  OBD  CAZ  CAT  114.17  3.000
 9YH  OBA  CAZ  CAT  119.02  3.000
 9YH  H23  CAM  H22  106.60  3.000
 9YH  H23  CAM  CAN  108.21  3.000
 9YH  H22  CAM  CAN  108.87  3.000
 9YH  H23  CAM  NAL  111.79  3.000
 9YH  H22  CAM  NAL  107.49  3.000
 9YH  CAN  CAM  NAL  113.62  3.000
 9YH  CAU  CAN  CAO  118.65  3.000
 9YH  CAU  CAN  CAM  122.02  3.000
 9YH  CAO  CAN  CAM  119.33  3.000
 9YH  H24  CAO  CAP  119.55  3.000
 9YH  H24  CAO  CAN  118.45  3.000
 9YH  CAP  CAO  CAN  122.00  3.000
 9YH  H25  CAP  CAW  120.72  3.000
 9YH  H25  CAP  CAO  120.29  3.000
 9YH  CAW  CAP  CAO  118.99  3.000
 9YH  H26  CAW  CAV  119.35  3.000
 9YH  H26  CAW  CAP  120.53  3.000
 9YH  CAV  CAW  CAP  120.11  3.000
 9YH  H27  CAV  CAU  120.61  3.000
 9YH  H27  CAV  CAW  118.45  3.000
 9YH  CAU  CAV  CAW  120.94  3.000
 9YH  SBB  CAU  CAV  122.21  3.000
 9YH  SBB  CAU  CAN  118.47  3.000
 9YH  CAV  CAU  CAN  119.31  3.000
 9YH  CBE  SBB  CAU  102.05  3.000
 9YH  H30  CBE  H29  108.10  3.000
 9YH  H30  CBE  H28  108.50  3.000
 9YH  H29  CBE  H28  109.50  3.000
 9YH  H30  CBE  SBB  105.65  3.000
 9YH  H29  CBE  SBB  112.76  3.000
 9YH  H28  CBE  SBB  112.12  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
 9YH  CONST_01  CAF  CAE  CAQ  CAR     0.00   0.0  0
 9YH  CONST_02  CAF  CAG  CAS  CAR     0.00   0.0  0
 9YH  CONST_03  CAE  CAF  CAG  CAS     0.00   0.0  0
 9YH  CONST_04  CAE  CAQ  CAR  CAS     0.00   0.0  0
 9YH  CONST_05  CAG  CAF  CAE  CAQ     0.00   0.0  0
 9YH  CONST_06  CAG  CAS  CAR  CAQ     0.00   0.0  0
 9YH  CONST_07  CAW  CAP  CAO  CAN     0.00   0.0  0
 9YH  CONST_08  CAW  CAV  CAU  CAN     0.00   0.0  0
 9YH  CONST_09  CAV  CAW  CAP  CAO     0.00   0.0  0
 9YH  CONST_10  CAV  CAU  CAN  CAO     0.00   0.0  0
 9YH  CONST_11  CAU  CAN  CAO  CAP     0.00   0.0  0
 9YH  CONST_12  CAU  CAV  CAW  CAP     0.00   0.0  0
 9YH  CONST_13  CAE  CAQ  CAR  OAX   180.00   0.0  0
 9YH  CONST_14  CAG  CAS  CAR  OAX   180.00   0.0  0
 9YH  CONST_15  CAH  CAG  CAS  CAR   180.00   0.0  0
 9YH  CONST_16  CAF  CAG  CAS  OAY   180.00   0.0  0
 9YH  CONST_17  CAQ  CAR  CAS  OAY   180.00   0.0  0
 9YH  CONST_18  CAH  CAG  CAF  CAE   180.00   0.0  0
 9YH  CONST_19  CAP  CAO  CAN  CAM   180.00   0.0  0
 9YH  CONST_20  CAV  CAU  CAN  CAM   180.00   0.0  0
 9YH  CONST_21  SBB  CAU  CAN  CAO   180.00   0.0  0
 9YH  CONST_22  SBB  CAU  CAV  CAW   180.00   0.0  0
 9YH  CONST_23  H6   CAE  CAQ  CAR   180.00   0.0  0
 9YH  CONST_24  H7   CAF  CAG  CAS   180.00   0.0  0
 9YH  CONST_25  H5   CAQ  CAR  CAS   180.00   0.0  0
 9YH  CONST_26  H25  CAP  CAO  CAN   180.00   0.0  0
 9YH  CONST_27  H27  CAV  CAU  CAN   180.00   0.0  0
 9YH  CONST_28  H26  CAW  CAP  CAO   180.00   0.0  0
 9YH  CONST_29  H24  CAO  CAP  CAW   180.00   0.0  0
 9YH  Var_01    CAQ  CAR  OAX  CBC     2.37  30.0  2
 9YH  Var_02    N    CAH  CAG  CAS   161.59  30.0  2
 9YH  Var_03    CAO  CAN  CAM  NAL  -124.26  30.0  2
 9YH  Var_04    CAJ  N    CAH  CAG   138.48  30.0  3
 9YH  Var_05    CAN  CAM  NAL  CAK    55.72  30.0  3
 9YH  Var_06    H1   CBC  OAX  CAR   -62.44  30.0  3
 9YH  Var_07    H28  CBE  SBB  CAU   -54.32  30.0  3
 9YH  Var_08    CAK  CAJ  N    CAH  -140.32  30.0  1
 9YH  Var_09    C    CA   N    CAH   -71.25  30.0  3
 9YH  Var_10    NAL  CAK  CAJ  N    -177.26  30.0  3
 9YH  Var_11    O    C    CA   N       2.17  30.0  3
 9YH  Var_12    CAT  NAL  CAK  CAJ    81.47  30.0  3
 9YH  Var_13    CAZ  CAT  NAL  CAK  -163.57  30.0  1
 9YH  Var_14    OBA  CAZ  CAT  NAL    14.22  30.0  3

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
 9YH  plan-1  OAX  0.020
 9YH  plan-1  CAR  0.020
 9YH  plan-1  CAS  0.020
 9YH  plan-1  OAY  0.020
 9YH  plan-1  CAQ  0.020
 9YH  plan-1  CAE  0.020
 9YH  plan-1  CAF  0.020
 9YH  plan-1  CAG  0.020
 9YH  plan-1  CAH  0.020
 9YH  plan-1  H5   0.020
 9YH  plan-1  H6   0.020
 9YH  plan-1  H7   0.020
 9YH  plan-2  CAM  0.020
 9YH  plan-2  CAN  0.020
 9YH  plan-2  CAO  0.020
 9YH  plan-2  CAP  0.020
 9YH  plan-2  CAW  0.020
 9YH  plan-2  CAV  0.020
 9YH  plan-2  CAU  0.020
 9YH  plan-2  SBB  0.020
 9YH  plan-2  H24  0.020
 9YH  plan-2  H25  0.020
 9YH  plan-2  H26  0.020
 9YH  plan-2  H27  0.020
 9YH  plan-3  CA   0.020
 9YH  plan-3  C    0.020
 9YH  plan-3  OXT  0.020
 9YH  plan-3  O    0.020
 9YH  plan-4  CAT  0.020
 9YH  plan-4  CAZ  0.020
 9YH  plan-4  OBD  0.020
 9YH  plan-4  OBA  0.020

