# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 02:12:53 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 3-(biphenyl-4-yl)prop-2-yn-1-yl alpha-D-mannopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](OCC#Cc2ccc(cc2)c3ccccc3)[C@@H](O)[C@@H](O)[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
 FYZ  FYZ  '3-(biphenyl-4-yl)prop-2-yn-1-yl alpha-D-mannopyranoside'  ligand  49  27  .  2021-08-09  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_FYZ
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
 FYZ  O2    O  OH1   0  -0.666    5.3642   1.6495   1.5960
 FYZ  C2    C  CH1   0  -0.026    4.2144   1.4231   0.8247
 FYZ  C3    C  CH1   0   0.023    4.5811   1.5784  -0.6478
 FYZ  O3    O  OH1   0  -0.639    5.1670   2.8296  -0.9268
 FYZ  C4    C  CH1   0   0.078    5.5676   0.4962  -1.0708
 FYZ  O4    O  OH1   0  -0.641    5.8056   0.5457  -2.4561
 FYZ  C5    C  CH1   0  -0.074    4.9957  -0.8841  -0.7433
 FYZ  O5    O  O2    0  -0.445    4.6065  -0.9569   0.6184
 FYZ  C6    C  CH2   0  -0.173    6.0217  -1.9733  -0.9710
 FYZ  O6    O  OH1   0  -0.688    5.4150  -3.2271  -0.7674
 FYZ  C1    C  CH1   0   0.222    3.6933   0.0002   1.0560
 FYZ  O1    O  O2    0  -0.487    2.4571  -0.0902   0.4185
 FYZ  C7    C  CH2   0  -0.270    1.7354  -1.2805   0.6586
 FYZ  C8    C  CSP   0  -0.049    0.3189  -1.0019   0.4752
 FYZ  C9    C  CSP   0   0.095   -0.8658  -0.7958   0.4115
 FYZ  C10   C  CR6   0  -0.061   -2.2614  -0.5252   0.3228
 FYZ  C11   C  CR16  0  -0.275   -3.0366  -1.0886  -0.6930
 FYZ  C12   C  CR16  0  -0.237   -4.3933  -0.8319  -0.7631
 FYZ  C13   C  CR6   0   0.034   -5.0187  -0.0051   0.1712
 FYZ  C14   C  CR16  0  -0.237   -4.2380   0.5581   1.1817
 FYZ  C15   C  CR16  0  -0.324   -2.8821   0.3024   1.2611
 FYZ  C16   C  CR6   0   0.004   -6.4666   0.2651   0.0983
 FYZ  C21   C  CR16  0  -0.241   -6.9670   1.5409   0.3587
 FYZ  C20   C  CR16  0  -0.292   -8.3280   1.7955   0.2958
 FYZ  C19   C  CR16  0  -0.245   -9.2146   0.7773  -0.0257
 FYZ  C18   C  CR16  0  -0.223   -8.7287  -0.4962  -0.2867
 FYZ  C17   C  CR16  0  -0.209   -7.3672  -0.7494  -0.2270
 FYZ  H2    H  HOH1  0   0.457    5.0994   1.7955   2.5075
 FYZ  HA    H  HCH1  0   0.231    3.4162   2.1336   1.0774
 FYZ  H3    H  HCH1  0   0.204    3.6665   1.4472  -1.2397
 FYZ  H1    H  HCH1  0   0.220    3.5831  -0.1983   2.1322
 FYZ  HB    H  HOH1  0   0.467    4.4756   3.4381  -1.1962
 FYZ  H4    H  HCH1  0   0.195    6.5057   0.6316  -0.5106
 FYZ  HC    H  HOH1  0   0.475    6.0564   1.4497  -2.6717
 FYZ  H5    H  HCH1  0   0.233    4.1357  -1.0698  -1.4037
 FYZ  H61C  H  HCH2  0   0.246    6.4111  -1.8729  -1.9895
 FYZ  H62C  H  HCH2  0   0.211    6.8650  -1.8118  -0.2857
 FYZ  H6    H  HOH1  0   0.443    6.0742  -3.9003  -0.9522
 FYZ  H71C  H  HCH2  0   0.196    2.0529  -2.0853  -0.0129
 FYZ  H72C  H  HCH2  0   0.248    1.8984  -1.6395   1.6833
 FYZ  H11   H  HCR6  0   0.265   -2.5675  -1.7248  -1.4312
 FYZ  H15   H  HCR6  0   0.226   -2.2956   0.7368   2.0594
 FYZ  H12   H  HCR6  0   0.255   -4.9705  -1.2608  -1.5722
 FYZ  H14   H  HCR6  0   0.273   -4.7032   1.1817   1.9346
 FYZ  H21   H  HCR6  0   0.255   -6.2832   2.3490   0.5869
 FYZ  H17   H  HCR6  0   0.222   -7.0031  -1.7528  -0.4101
 FYZ  H20   H  HCR6  0   0.237   -8.6960   2.7937   0.4939
 FYZ  H19   H  HCR6  0   0.270  -10.2775   0.9743  -0.0718
 FYZ  H18   H  HCR6  0   0.221   -9.4127  -1.2988  -0.5298

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
 FYZ  O2   C2    single    1.403  0.020  1.403
 FYZ  C2   C3    single    1.525  0.020  1.525
 FYZ  C2   C1    single    1.533  0.020  1.533
 FYZ  C3   O3    single    1.409  0.020  1.409
 FYZ  C3   C4    single    1.524  0.020  1.524
 FYZ  C4   O4    single    1.407  0.020  1.407
 FYZ  C4   C5    single    1.530  0.020  1.530
 FYZ  C5   O5    single    1.418  0.020  1.418
 FYZ  C5   C6    single    1.514  0.020  1.514
 FYZ  O5   C1    single    1.393  0.020  1.393
 FYZ  C6   O6    single    1.408  0.020  1.408
 FYZ  C1   O1    single    1.394  0.020  1.394
 FYZ  O1   C7    single    1.413  0.020  1.413
 FYZ  C7   C8    single    1.455  0.020  1.455
 FYZ  C8   C9    triple    1.204  0.020  1.204
 FYZ  C9   C10   single    1.424  0.020  1.424
 FYZ  C10  C11   aromatic  1.396  0.020  1.396
 FYZ  C10  C15   aromatic  1.397  0.020  1.397
 FYZ  C11  C12   aromatic  1.382  0.020  1.382
 FYZ  C12  C13   aromatic  1.396  0.020  1.396
 FYZ  C13  C14   aromatic  1.396  0.020  1.396
 FYZ  C13  C16   single    1.475  0.020  1.475
 FYZ  C14  C15   aromatic  1.382  0.020  1.382
 FYZ  C16  C21   aromatic  1.395  0.020  1.395
 FYZ  C16  C17   aromatic  1.395  0.020  1.395
 FYZ  C21  C20   aromatic  1.386  0.020  1.386
 FYZ  C20  C19   aromatic  1.388  0.020  1.388
 FYZ  C19  C18   aromatic  1.388  0.020  1.388
 FYZ  C18  C17   aromatic  1.386  0.020  1.386
 FYZ  O2   H2    single    0.850  0.020  0.980
 FYZ  C2   HA    single    0.970  0.020  1.090
 FYZ  C3   H3    single    0.970  0.020  1.090
 FYZ  C1   H1    single    0.970  0.020  1.090
 FYZ  O3   HB    single    0.850  0.020  0.980
 FYZ  C4   H4    single    0.970  0.020  1.090
 FYZ  O4   HC    single    0.850  0.020  0.980
 FYZ  C5   H5    single    0.970  0.020  1.090
 FYZ  C6   H61C  single    0.970  0.020  1.090
 FYZ  C6   H62C  single    0.970  0.020  1.090
 FYZ  O6   H6    single    0.850  0.020  0.980
 FYZ  C7   H71C  single    0.970  0.020  1.090
 FYZ  C7   H72C  single    0.970  0.020  1.090
 FYZ  C11  H11   single    0.930  0.020  1.080
 FYZ  C15  H15   single    0.930  0.020  1.080
 FYZ  C12  H12   single    0.930  0.020  1.080
 FYZ  C14  H14   single    0.930  0.020  1.080
 FYZ  C21  H21   single    0.930  0.020  1.080
 FYZ  C17  H17   single    0.930  0.020  1.080
 FYZ  C20  H20   single    0.930  0.020  1.080
 FYZ  C19  H19   single    0.930  0.020  1.080
 FYZ  C18  H18   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
 FYZ  H2    O2   C2    108.68  3.000
 FYZ  HA    C2   C1    108.59  3.000
 FYZ  HA    C2   C3    109.33  3.000
 FYZ  C1    C2   C3    108.78  3.000
 FYZ  HA    C2   O2    111.39  3.000
 FYZ  C1    C2   O2    110.21  3.000
 FYZ  C3    C2   O2    108.50  3.000
 FYZ  H3    C3   C4    107.75  3.000
 FYZ  H3    C3   O3    110.24  3.000
 FYZ  C4    C3   O3    107.84  3.000
 FYZ  H3    C3   C2    107.95  3.000
 FYZ  C4    C3   C2    110.56  3.000
 FYZ  O3    C3   C2    112.42  3.000
 FYZ  HB    O3   C3    108.60  3.000
 FYZ  H4    C4   C5    108.70  3.000
 FYZ  H4    C4   O4    110.65  3.000
 FYZ  C5    C4   O4    107.81  3.000
 FYZ  H4    C4   C3    108.84  3.000
 FYZ  C5    C4   C3    109.83  3.000
 FYZ  O4    C4   C3    110.97  3.000
 FYZ  HC    O4   C4    107.32  3.000
 FYZ  H5    C5   C6    108.55  3.000
 FYZ  H5    C5   O5    110.69  3.000
 FYZ  C6    C5   O5    107.07  3.000
 FYZ  H5    C5   C4    108.43  3.000
 FYZ  C6    C5   C4    111.33  3.000
 FYZ  O5    C5   C4    110.77  3.000
 FYZ  C1    O5   C5    116.50  3.000
 FYZ  H62C  C6   H61C  107.08  3.000
 FYZ  H62C  C6   O6    111.81  3.000
 FYZ  H61C  C6   O6    111.69  3.000
 FYZ  H62C  C6   C5    108.70  3.000
 FYZ  H61C  C6   C5    108.36  3.000
 FYZ  O6    C6   C5    109.09  3.000
 FYZ  H6    O6   C6    107.51  3.000
 FYZ  H1    C1   O1    110.30  3.000
 FYZ  H1    C1   O5    104.42  3.000
 FYZ  O1    C1   O5    113.14  3.000
 FYZ  H1    C1   C2    110.44  3.000
 FYZ  O1    C1   C2    107.02  3.000
 FYZ  O5    C1   C2    111.56  3.000
 FYZ  C7    O1   C1    115.47  3.000
 FYZ  H72C  C7   H71C  106.80  3.000
 FYZ  H72C  C7   C8    108.95  3.000
 FYZ  H71C  C7   C8    110.22  3.000
 FYZ  H72C  C7   O1    111.00  3.000
 FYZ  H71C  C7   O1    111.52  3.000
 FYZ  C8    C7   O1    108.34  3.000
 FYZ  C9    C8   C7    180.00  3.000
 FYZ  C10   C9   C8    180.00  3.000
 FYZ  C15   C10  C11   118.75  3.000
 FYZ  C15   C10  C9    120.41  3.000
 FYZ  C11   C10  C9    120.84  3.000
 FYZ  H11   C11  C12   120.02  3.000
 FYZ  H11   C11  C10   119.54  3.000
 FYZ  C12   C11  C10   120.45  3.000
 FYZ  H12   C12  C13   119.75  3.000
 FYZ  H12   C12  C11   119.18  3.000
 FYZ  C13   C12  C11   121.05  3.000
 FYZ  C16   C13  C14   120.73  3.000
 FYZ  C16   C13  C12   121.03  3.000
 FYZ  C14   C13  C12   118.24  3.000
 FYZ  H14   C14  C15   119.21  3.000
 FYZ  H14   C14  C13   119.71  3.000
 FYZ  C15   C14  C13   121.05  3.000
 FYZ  H15   C15  C14   120.00  3.000
 FYZ  H15   C15  C10   119.53  3.000
 FYZ  C14   C15  C10   120.47  3.000
 FYZ  C17   C16  C21   118.49  3.000
 FYZ  C17   C16  C13   120.80  3.000
 FYZ  C21   C16  C13   120.70  3.000
 FYZ  H21   C21  C20   119.51  3.000
 FYZ  H21   C21  C16   119.69  3.000
 FYZ  C20   C21  C16   120.78  3.000
 FYZ  H20   C20  C19   120.13  3.000
 FYZ  H20   C20  C21   119.67  3.000
 FYZ  C19   C20  C21   120.20  3.000
 FYZ  H19   C19  C18   120.20  3.000
 FYZ  H19   C19  C20   120.25  3.000
 FYZ  C18   C19  C20   119.55  3.000
 FYZ  H18   C18  C17   119.67  3.000
 FYZ  H18   C18  C19   120.10  3.000
 FYZ  C17   C18  C19   120.23  3.000
 FYZ  H17   C17  C18   119.48  3.000
 FYZ  H17   C17  C16   119.75  3.000
 FYZ  C18   C17  C16   120.75  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
 FYZ  CONST_01  C13  C12  C11  C10    0.00   0.0  0
 FYZ  CONST_02  C13  C14  C15  C10    0.00   0.0  0
 FYZ  CONST_03  C14  C15  C10  C11    0.00   0.0  0
 FYZ  CONST_04  C14  C13  C12  C11    0.00   0.0  0
 FYZ  CONST_05  C16  C13  C12  C11  180.00   0.0  0
 FYZ  CONST_06  C15  C10  C11  C12    0.00   0.0  0
 FYZ  CONST_07  C15  C14  C13  C12    0.00   0.0  0
 FYZ  CONST_10  C20  C21  C16  C13  180.00   0.0  0
 FYZ  CONST_11  C18  C17  C16  C13  180.00   0.0  0
 FYZ  CONST_14  C16  C13  C14  C15  180.00   0.0  0
 FYZ  CONST_15  C19  C20  C21  C16    0.00   0.0  0
 FYZ  CONST_16  C19  C18  C17  C16    0.00   0.0  0
 FYZ  CONST_17  C18  C17  C16  C21    0.00   0.0  0
 FYZ  CONST_18  C18  C19  C20  C21    0.00   0.0  0
 FYZ  CONST_19  C17  C16  C21  C20    0.00   0.0  0
 FYZ  CONST_20  C17  C18  C19  C20    0.00   0.0  0
 FYZ  CONST_21  C12  C11  C10  C9   180.00   0.0  0
 FYZ  CONST_22  C14  C15  C10  C9   180.00   0.0  0
 FYZ  CONST_23  H12  C12  C11  C10  180.00   0.0  0
 FYZ  CONST_24  H14  C14  C15  C10  180.00   0.0  0
 FYZ  CONST_25  H15  C15  C10  C11  180.00   0.0  0
 FYZ  CONST_26  H11  C11  C12  C13  180.00   0.0  0
 FYZ  CONST_27  H21  C21  C16  C13    0.00   0.0  0
 FYZ  CONST_28  H17  C17  C16  C13    0.00   0.0  0
 FYZ  CONST_29  H20  C20  C21  C16  180.00   0.0  0
 FYZ  CONST_30  H18  C18  C17  C16  180.00   0.0  0
 FYZ  CONST_31  H19  C19  C20  C21  180.00   0.0  0
 FYZ  Var_01    C8   C7   O1   C1   154.46  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
 FYZ  chir_01  C2  O2  C3  C1  negativ
 FYZ  chir_02  C3  O3  C2  C4  positiv
 FYZ  chir_03  C4  O4  C5  C3  positiv
 FYZ  chir_04  C5  O5  C4  C6  negativ
 FYZ  chir_05  C1  O5  O1  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
 FYZ  plan-1  C8   0.020
 FYZ  plan-1  C9   0.020
 FYZ  plan-1  C10  0.020
 FYZ  plan-1  C11  0.020
 FYZ  plan-1  C12  0.020
 FYZ  plan-1  C13  0.020
 FYZ  plan-1  C14  0.020
 FYZ  plan-1  C15  0.020
 FYZ  plan-1  C16  0.020
 FYZ  plan-1  H11  0.020
 FYZ  plan-1  H15  0.020
 FYZ  plan-1  H12  0.020
 FYZ  plan-1  H14  0.020
 FYZ  plan-2  C13  0.020
 FYZ  plan-2  C16  0.020
 FYZ  plan-2  C21  0.020
 FYZ  plan-2  C20  0.020
 FYZ  plan-2  C19  0.020
 FYZ  plan-2  C18  0.020
 FYZ  plan-2  C17  0.020
 FYZ  plan-2  H21  0.020
 FYZ  plan-2  H17  0.020
 FYZ  plan-2  H20  0.020
 FYZ  plan-2  H19  0.020
 FYZ  plan-2  H18  0.020

