# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 04:03:15 2021
#   Inital geometry file: a 115 line input string
#   Ligand name: methyl 3-O-[3-(benzyloxy)-3-oxopropanoyl]-beta-D-galactopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H]1O[C@H](CO)[C@H](O)[C@H](OC(=O)CC(=O)OCc2ccccc2)[C@H]1O
#
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
 SZS  SZS  'methyl 3-O-[3-(benzyloxy)-3-oxopropanoyl]-beta-D-galactopyranoside'  ligand  48  26  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SZS
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
 SZS  C1   C  CH1   0   0.291   -9.3038  -28.6873  11.8415
 SZS  C2   C  CH1   0   0.020  -10.6558  -28.4120  11.1760
 SZS  C3   C  CH1   0  -0.038  -10.3863  -27.7481   9.8374
 SZS  C4   C  CH1   0  -0.008   -9.5109  -26.5048   9.9956
 SZS  C5   C  CH1   0  -0.017   -8.2424  -26.9098  10.7403
 SZS  C6   C  CH2   0  -0.155   -7.3224  -25.7331  10.9874
 SZS  O2   O  OH1   0  -0.654  -11.3595  -29.6005  10.9380
 SZS  O3   O  O2    0  -0.470  -11.6537  -27.3874   9.2823
 SZS  O5   O  O2    0  -0.492   -8.5689  -27.5003  11.9806
 SZS  O6   O  OH1   0  -0.669   -6.1042  -26.2186  11.4980
 SZS  O1   O  O2    0  -0.495   -9.5445  -29.2108  13.0903
 SZS  O4   O  OH1   0  -0.663  -10.1586  -25.4957  10.7257
 SZS  CAN  C  C     0   0.598  -11.8507  -27.4614   7.9702
 SZS  OAQ  O  O     0  -0.426  -11.0043  -27.7365   7.1646
 SZS  CAO  C  CH2   0  -0.679  -13.2842  -27.1171   7.6422
 SZS  CAP  C  C     0   0.589  -14.2257  -27.7347   8.6484
 SZS  OAS  O  O     0  -0.436  -14.9470  -27.1223   9.3905
 SZS  OAR  O  O2    0  -0.446  -14.1409  -29.0548   8.6025
 SZS  CAT  C  CH2   0  -0.239  -14.8665  -29.8135   9.5819
 SZS  CAU  C  CR6   0   0.061  -14.7274  -31.2613   9.2231
 SZS  CAV  C  CR16  0  -0.303  -15.8516  -32.0195   8.9166
 SZS  CAW  C  CR16  0  -0.241  -15.7303  -33.3648   8.5893
 SZS  CAX  C  CR16  0  -0.262  -14.4778  -33.9602   8.5586
 SZS  CAY  C  CR16  0  -0.242  -13.3486  -33.2071   8.8615
 SZS  CAZ  C  CR16  0  -0.288  -13.4718  -31.8672   9.1950
 SZS  H1   H  HCH1  0   0.185   -8.7351  -29.4035  11.2149
 SZS  H2   H  HCH1  0   0.234  -11.2219  -27.7238  11.8188
 SZS  H3   H  HCH1  0   0.268   -9.8761  -28.4568   9.1766
 SZS  H4   H  HCH1  0   0.250   -9.2189  -26.1555   8.9958
 SZS  H5   H  HCH1  0   0.235   -7.7097  -27.6335  10.1016
 SZS  H61  H  HCH2  0   0.209   -7.8001  -25.0271  11.6754
 SZS  H62  H  HCH2  0   0.204   -7.1832  -25.2111  10.0317
 SZS  HO2  H  HOH1  0   0.457  -11.6279  -29.9718  11.7843
 SZS  HO6  H  HOH1  0   0.457   -5.5316  -25.4650  11.6661
 SZS  H10  H  HCH3  0   0.240   -8.7942  -30.3820  14.5646
 SZS  H11  H  HCH3  0   0.214   -7.9109  -30.5003  13.0330
 SZS  H12  H  HCH3  0   0.222   -7.7056  -29.0746  14.0706
 SZS  HO4  H  HOH1  0   0.457  -10.9045  -25.1677  10.2139
 SZS  H14  H  HCH2  0   0.315  -13.5132  -27.4694   6.6365
 SZS  H15  H  HCH2  0   0.318  -13.3983  -26.0316   7.6543
 SZS  H16  H  HCH2  0   0.256  -15.9163  -29.5165   9.5917
 SZS  H17  H  HCH2  0   0.254  -14.4450  -29.6075  10.5687
 SZS  H18  H  HCR6  0   0.256  -16.8320  -31.5581   8.9341
 SZS  H19  H  HCR6  0   0.258  -16.6145  -33.9433   8.3552
 SZS  H20  H  HCR6  0   0.258  -14.3788  -35.0072   8.3028
 SZS  H21  H  HCR6  0   0.257  -12.3694  -33.6680   8.8409
 SZS  H22  H  HCR6  0   0.265  -12.5883  -31.2910   9.4413
 SZS  CAM  C  CH3   0  -0.407   -8.4254  -29.8138  13.7127

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
 SZS  CAW  CAX  aromatic  1.387  0.020  1.387
 SZS  CAW  CAV  aromatic  1.390  0.020  1.390
 SZS  CAX  CAY  aromatic  1.391  0.020  1.391
 SZS  CAV  CAU  aromatic  1.390  0.020  1.390
 SZS  CAY  CAZ  aromatic  1.386  0.020  1.386
 SZS  CAU  CAZ  aromatic  1.394  0.020  1.394
 SZS  CAU  CAT  single    1.498  0.020  1.498
 SZS  CAT  OAR  single    1.436  0.020  1.436
 SZS  CAO  CAP  single    1.510  0.020  1.510
 SZS  CAO  CAN  single    1.510  0.020  1.510
 SZS  OAR  CAP  single    1.324  0.020  1.324
 SZS  C6   O6   single    1.407  0.020  1.407
 SZS  C6   C5   single    1.514  0.020  1.514
 SZS  CAP  OAS  double    1.202  0.020  1.202
 SZS  OAQ  CAN  double    1.200  0.020  1.200
 SZS  CAN  O3   single    1.329  0.020  1.329
 SZS  C4   C5   single    1.526  0.020  1.526
 SZS  C4   O4   single    1.404  0.020  1.404
 SZS  C4   C3   single    1.529  0.020  1.529
 SZS  C5   O5   single    1.412  0.020  1.412
 SZS  O3   C3   single    1.430  0.020  1.430
 SZS  C3   C2   single    1.518  0.020  1.518
 SZS  O5   C1   single    1.403  0.020  1.403
 SZS  C1   C2   single    1.532  0.020  1.532
 SZS  C1   O1   single    1.375  0.020  1.375
 SZS  C2   O2   single    1.402  0.020  1.402
 SZS  O1   CAM  single    1.415  0.020  1.415
 SZS  C1   H1   single    0.970  0.020  1.090
 SZS  C2   H2   single    0.970  0.020  1.090
 SZS  C3   H3   single    0.970  0.020  1.090
 SZS  C4   H4   single    0.970  0.020  1.090
 SZS  C5   H5   single    0.970  0.020  1.090
 SZS  C6   H61  single    0.970  0.020  1.090
 SZS  C6   H62  single    0.970  0.020  1.090
 SZS  O2   HO2  single    0.850  0.020  0.980
 SZS  O6   HO6  single    0.850  0.020  0.980
 SZS  CAM  H10  single    0.970  0.020  1.090
 SZS  CAM  H11  single    0.970  0.020  1.090
 SZS  CAM  H12  single    0.970  0.020  1.090
 SZS  O4   HO4  single    0.850  0.020  0.980
 SZS  CAO  H14  single    0.970  0.020  1.090
 SZS  CAO  H15  single    0.970  0.020  1.090
 SZS  CAT  H16  single    0.970  0.020  1.090
 SZS  CAT  H17  single    0.970  0.020  1.090
 SZS  CAV  H18  single    0.930  0.020  1.080
 SZS  CAW  H19  single    0.930  0.020  1.080
 SZS  CAX  H20  single    0.930  0.020  1.080
 SZS  CAY  H21  single    0.930  0.020  1.080
 SZS  CAZ  H22  single    0.930  0.020  1.080

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
 SZS  H1   C1   O1   110.92  3.000
 SZS  H1   C1   O5   109.51  3.000
 SZS  O1   C1   O5   108.89  3.000
 SZS  H1   C1   C2   108.86  3.000
 SZS  O1   C1   C2   107.96  3.000
 SZS  O5   C1   C2   110.69  3.000
 SZS  H2   C2   O2   111.83  3.000
 SZS  H2   C2   C3   109.47  3.000
 SZS  O2   C2   C3   108.07  3.000
 SZS  H2   C2   C1   108.24  3.000
 SZS  O2   C2   C1   111.38  3.000
 SZS  C3   C2   C1   107.76  3.000
 SZS  H3   C3   O3   110.00  3.000
 SZS  H3   C3   C4   108.78  3.000
 SZS  O3   C3   C4   110.03  3.000
 SZS  H3   C3   C2   109.38  3.000
 SZS  O3   C3   C2   107.17  3.000
 SZS  C4   C3   C2   111.47  3.000
 SZS  H4   C4   O4   111.55  3.000
 SZS  H4   C4   C5   107.91  3.000
 SZS  O4   C4   C5   108.69  3.000
 SZS  H4   C4   C3   108.46  3.000
 SZS  O4   C4   C3   111.98  3.000
 SZS  C5   C4   C3   108.11  3.000
 SZS  H5   C5   O5   110.25  3.000
 SZS  H5   C5   C6   108.13  3.000
 SZS  O5   C5   C6   108.80  3.000
 SZS  H5   C5   C4   107.05  3.000
 SZS  O5   C5   C4   110.33  3.000
 SZS  C6   C5   C4   112.25  3.000
 SZS  H62  C6   H61  107.19  3.000
 SZS  H62  C6   O6   111.73  3.000
 SZS  H61  C6   O6   111.84  3.000
 SZS  H62  C6   C5   107.73  3.000
 SZS  H61  C6   C5   109.78  3.000
 SZS  O6   C6   C5   108.49  3.000
 SZS  HO2  O2   C2   108.54  3.000
 SZS  CAN  O3   C3   120.04  3.000
 SZS  C5   O5   C1   112.82  3.000
 SZS  HO6  O6   C6   107.98  3.000
 SZS  CAM  O1   C1   115.03  3.000
 SZS  HO4  O4   C4   109.03  3.000
 SZS  CAO  CAN  OAQ  125.15  3.000
 SZS  OAQ  CAN  O3   124.81  3.000
 SZS  CAO  CAN  O3   110.03  3.000
 SZS  H15  CAO  H14  108.04  3.000
 SZS  H15  CAO  CAP  109.52  3.000
 SZS  H14  CAO  CAP  110.59  3.000
 SZS  H15  CAO  CAN  108.88  3.000
 SZS  H14  CAO  CAN  109.03  3.000
 SZS  CAP  CAO  CAN  110.72  3.000
 SZS  OAR  CAP  OAS  124.59  3.000
 SZS  OAS  CAP  CAO  125.24  3.000
 SZS  OAR  CAP  CAO  110.17  3.000
 SZS  CAT  OAR  CAP  118.10  3.000
 SZS  H17  CAT  H16  108.16  3.000
 SZS  H17  CAT  CAU  111.26  3.000
 SZS  H16  CAT  CAU  110.77  3.000
 SZS  H17  CAT  OAR  108.76  3.000
 SZS  H16  CAT  OAR  110.40  3.000
 SZS  CAU  CAT  OAR  107.48  3.000
 SZS  CAZ  CAU  CAV  119.13  3.000
 SZS  CAZ  CAU  CAT  120.55  3.000
 SZS  CAV  CAU  CAT  120.32  3.000
 SZS  H18  CAV  CAW  119.66  3.000
 SZS  H18  CAV  CAU  119.73  3.000
 SZS  CAW  CAV  CAU  120.61  3.000
 SZS  H19  CAW  CAX  120.23  3.000
 SZS  H19  CAW  CAV  119.80  3.000
 SZS  CAX  CAW  CAV  119.97  3.000
 SZS  H20  CAX  CAY  120.07  3.000
 SZS  H20  CAX  CAW  120.20  3.000
 SZS  CAY  CAX  CAW  119.73  3.000
 SZS  H21  CAY  CAZ  119.77  3.000
 SZS  H21  CAY  CAX  119.99  3.000
 SZS  CAZ  CAY  CAX  120.24  3.000
 SZS  H22  CAZ  CAY  119.76  3.000
 SZS  H22  CAZ  CAU  119.92  3.000
 SZS  CAY  CAZ  CAU  120.32  3.000
 SZS  H12  CAM  H11  108.56  3.000
 SZS  H12  CAM  H10  108.67  3.000
 SZS  H11  CAM  H10  108.54  3.000
 SZS  H12  CAM  O1   112.14  3.000
 SZS  H11  CAM  O1   111.45  3.000
 SZS  H10  CAM  O1   107.38  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
 SZS  CONST_01  CAX  CAW  CAV  CAU     0.00   0.0  0
 SZS  CONST_02  CAX  CAY  CAZ  CAU     0.00   0.0  0
 SZS  CONST_03  CAY  CAX  CAW  CAV     0.00   0.0  0
 SZS  CONST_04  CAY  CAZ  CAU  CAV     0.00   0.0  0
 SZS  CONST_05  CAZ  CAY  CAX  CAW     0.00   0.0  0
 SZS  CONST_06  CAZ  CAU  CAV  CAW     0.00   0.0  0
 SZS  CONST_07  CAW  CAV  CAU  CAT   180.00   0.0  0
 SZS  CONST_08  CAY  CAZ  CAU  CAT   180.00   0.0  0
 SZS  CONST_09  H19  CAW  CAV  CAU   180.00   0.0  0
 SZS  CONST_10  H21  CAY  CAZ  CAU   180.00   0.0  0
 SZS  CONST_11  H20  CAX  CAW  CAV   180.00   0.0  0
 SZS  CONST_12  H22  CAZ  CAU  CAV   180.00   0.0  0
 SZS  CONST_13  H18  CAV  CAW  CAX   180.00   0.0  0
 SZS  Var_01    CAV  CAU  CAT  OAR  -118.66  30.0  2
 SZS  Var_02    CAO  CAN  O3   C3    176.36  30.0  1
 SZS  Var_03    CAU  CAT  OAR  CAP   173.91  30.0  1
 SZS  Var_04    H10  CAM  O1   C1   -166.94  30.0  3
 SZS  Var_05    CAP  CAO  CAN  O3    -40.94  30.0  1
 SZS  Var_06    OAR  CAP  CAO  CAN   -62.70  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
 SZS  chir_01  C1  O5  C2  O1  positiv
 SZS  chir_02  C2  O2  C1  C3  negativ
 SZS  chir_03  C3  O3  C4  C2  negativ
 SZS  chir_04  C4  O4  C3  C5  positiv
 SZS  chir_05  C5  O5  C4  C6  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
 SZS  plan-1  CAT  0.020
 SZS  plan-1  CAU  0.020
 SZS  plan-1  CAV  0.020
 SZS  plan-1  CAW  0.020
 SZS  plan-1  CAX  0.020
 SZS  plan-1  CAY  0.020
 SZS  plan-1  CAZ  0.020
 SZS  plan-1  H18  0.020
 SZS  plan-1  H19  0.020
 SZS  plan-1  H20  0.020
 SZS  plan-1  H21  0.020
 SZS  plan-1  H22  0.020
 SZS  plan-2  CAO  0.020
 SZS  plan-2  CAP  0.020
 SZS  plan-2  OAS  0.020
 SZS  plan-2  OAR  0.020
 SZS  plan-3  O3   0.020
 SZS  plan-3  CAN  0.020
 SZS  plan-3  OAQ  0.020
 SZS  plan-3  CAO  0.020

