# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 00:24:08 2022
#   Inital geometry file: a 115 line input string
#   Ligand name: (2~{R},3~{S},4~{R},5~{S},6~{S})-2-[2-[4-(1-azanyl-2-methyl-propan-2-yl)phenyl]ethynyl]-6-methyl-oxane-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1O[C@H](C#Cc2ccc(cc2)C(C)(C)CN)[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
 VJT  VJT  "(2-(4-(beta-L-fucopyranosylethynyl)phenyl)-2-methylpropan-1-amine"
  ligand  48  23  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_VJT
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
 VJT  N1   N  NH2   0  -0.794  6.6024   8.5263   1.8486
 VJT  C4   C  CH1   0   0.012  6.0668  15.1186  11.2108
 VJT  C5   C  CH1   0   0.013  7.2480  14.4381  10.5290
 VJT  C6   C  CH3   0  -0.679  8.4643  15.3294  10.3878
 VJT  C7   C  CSP   0   0.130  5.6525  12.5545   7.8910
 VJT  C10  C  CR16  0  -0.275  4.3961  10.6477   5.1739
 VJT  C13  C  CR16  0  -0.300  5.8227  11.7538   3.0847
 VJT  C15  C  CT    0  -0.169  4.8020  10.1778   1.3871
 VJT  C17  C  CH3   0  -0.639  4.4474  11.3224   0.4300
 VJT  O5   O  O2    0  -0.490  6.8853  13.9892   9.2327
 VJT  C3   C  CH1   0  -0.038  4.8767  14.1561  11.2353
 VJT  C2   C  CH1   0   0.041  4.5694  13.6364   9.8370
 VJT  C1   C  CH1   0  -0.159  5.8543  13.0340   9.2533
 VJT  O2   O  OH1   0  -0.664  3.5967  12.6266   9.8457
 VJT  O3   O  OH1   0  -0.667  3.7095  14.7867  11.7166
 VJT  O4   O  OH1   0  -0.667  5.7549  16.3056  10.5264
 VJT  C9   C  CR6   0  -0.149  5.2896  11.6848   5.4365
 VJT  C11  C  CR16  0  -0.321  4.2282  10.1720   3.8822
 VJT  C12  C  CR6   0   0.171  4.9339  10.7100   2.8079
 VJT  C14  C  CR16  0  -0.279  6.0016  12.2368   4.3677
 VJT  C18  C  CH2   0  -0.254  6.1580   9.5841   0.9580
 VJT  C16  C  CH3   0  -0.665  3.7192   9.1065   1.2662
 VJT  H1   H  HNH2  0   0.348  7.3980   8.0539   1.4397
 VJT  H2   H  HNH2  0   0.342  6.9365   8.9275   2.7161
 VJT  H4   H  HCH1  0   0.219  6.3631  15.3253  12.2518
 VJT  H6   H  HCH3  0   0.232  8.7672  15.7026  11.3661
 VJT  H7   H  HCH3  0   0.240  9.3025  14.7707   9.9714
 VJT  H8   H  HCH3  0   0.234  8.2664  16.1846   9.7433
 VJT  H9   H  HCR6  0   0.254  3.8334  10.2055   5.9860
 VJT  H10  H  HCR6  0   0.256  6.3998  12.2010   2.2850
 VJT  H11  H  HCH3  0   0.232  3.4913  11.7730   0.6999
 VJT  H12  H  HCH3  0   0.230  5.1989  12.1130   0.4229
 VJT  H13  H  HCH3  0   0.229  4.3608  10.9450  -0.5910
 VJT  H14  H  HCH1  0   0.225  5.1502  13.2974  11.8655
 VJT  H15  H  HCH1  0   0.216  4.2681  14.4788   9.1984
 VJT  H16  H  HCH1  0   0.249  6.1412  12.1744   9.8844
 VJT  H17  H  HOH1  0   0.453  2.7912  12.9876  10.2305
 VJT  H18  H  HOH1  0   0.460  3.7599  14.8423  12.6765
 VJT  H19  H  HOH1  0   0.446  4.9130  16.6266  10.8688
 VJT  H20  H  HCR6  0   0.256  3.5290   9.3621   3.7272
 VJT  H21  H  HCR6  0   0.254  6.7011  13.0431   4.5472
 VJT  H22  H  HCH2  0   0.202  6.8863  10.4018   0.8530
 VJT  H23  H  HCH2  0   0.226  6.0351   9.1599  -0.0427
 VJT  H24  H  HCH3  0   0.232  3.9414   8.2271   1.8689
 VJT  H25  H  HCH3  0   0.227  2.7401   9.4882   1.5615
 VJT  H26  H  HCH3  0   0.234  3.6429   8.7811   0.2273
 VJT  C8   C  CSP   0   0.127  5.4812  12.1622   6.7655
 VJT  H5   H  HCH1  0   0.221  7.5181  13.5713  11.1531

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
 VJT  C17  C15  single    1.534  0.020  1.534
 VJT  C18  N1   single    1.452  0.020  1.452
 VJT  C18  C15  single    1.541  0.020  1.541
 VJT  C16  C15  single    1.528  0.020  1.528
 VJT  C15  C12  single    1.523  0.020  1.523
 VJT  C12  C13  aromatic  1.399  0.020  1.399
 VJT  C12  C11  aromatic  1.393  0.020  1.393
 VJT  C13  C14  aromatic  1.383  0.020  1.383
 VJT  C11  C10  aromatic  1.387  0.020  1.387
 VJT  C14  C9   aromatic  1.398  0.020  1.398
 VJT  C10  C9   aromatic  1.394  0.020  1.394
 VJT  C9   C8   single    1.425  0.020  1.425
 VJT  C8   C7   triple    1.204  0.020  1.204
 VJT  C7   C1   single    1.458  0.020  1.458
 VJT  C1   O5   single    1.406  0.020  1.406
 VJT  C1   C2   single    1.534  0.020  1.534
 VJT  O5   C5   single    1.419  0.020  1.419
 VJT  C2   O2   single    1.402  0.020  1.402
 VJT  C2   C3   single    1.523  0.020  1.523
 VJT  O4   C4   single    1.405  0.020  1.405
 VJT  C6   C5   single    1.515  0.020  1.515
 VJT  C5   C4   single    1.524  0.020  1.524
 VJT  C3   C4   single    1.531  0.020  1.531
 VJT  C3   O3   single    1.411  0.020  1.411
 VJT  N1   H1   single    0.890  0.020  1.040
 VJT  N1   H2   single    0.890  0.020  1.040
 VJT  C4   H4   single    0.970  0.020  1.090
 VJT  C5   H5   single    0.970  0.020  1.090
 VJT  C6   H6   single    0.970  0.020  1.090
 VJT  C6   H7   single    0.970  0.020  1.090
 VJT  C6   H8   single    0.970  0.020  1.090
 VJT  C10  H9   single    0.930  0.020  1.080
 VJT  C13  H10  single    0.930  0.020  1.080
 VJT  C17  H11  single    0.970  0.020  1.090
 VJT  C17  H12  single    0.970  0.020  1.090
 VJT  C17  H13  single    0.970  0.020  1.090
 VJT  C3   H14  single    0.970  0.020  1.090
 VJT  C2   H15  single    0.970  0.020  1.090
 VJT  C1   H16  single    0.970  0.020  1.090
 VJT  O2   H17  single    0.850  0.020  0.980
 VJT  O3   H18  single    0.850  0.020  0.980
 VJT  O4   H19  single    0.850  0.020  0.980
 VJT  C11  H20  single    0.930  0.020  1.080
 VJT  C14  H21  single    0.930  0.020  1.080
 VJT  C18  H22  single    0.970  0.020  1.090
 VJT  C18  H23  single    0.970  0.020  1.090
 VJT  C16  H24  single    0.970  0.020  1.090
 VJT  C16  H25  single    0.970  0.020  1.090
 VJT  C16  H26  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
 VJT  H2   N1   H1   105.78  3.000
 VJT  H2   N1   C18  109.74  3.000
 VJT  H1   N1   C18  109.44  3.000
 VJT  H4   C4   O4   111.18  3.000
 VJT  H4   C4   C3   108.17  3.000
 VJT  O4   C4   C3   111.49  3.000
 VJT  H4   C4   C5   107.34  3.000
 VJT  C3   C4   C5   109.20  3.000
 VJT  O4   C4   C5   109.35  3.000
 VJT  H5   C5   O5   109.35  3.000
 VJT  H5   C5   C6   108.60  3.000
 VJT  O5   C5   C6   107.83  3.000
 VJT  H5   C5   C4   106.73  3.000
 VJT  C6   C5   C4   113.66  3.000
 VJT  O5   C5   C4   110.60  3.000
 VJT  H8   C6   H7   108.44  3.000
 VJT  H8   C6   H6   108.23  3.000
 VJT  H7   C6   H6   107.74  3.000
 VJT  H8   C6   C5   111.80  3.000
 VJT  H7   C6   C5   110.59  3.000
 VJT  H6   C6   C5   109.93  3.000
 VJT  C1   C7   C8   180.00  3.000
 VJT  H9   C10  C11  119.72  3.000
 VJT  H9   C10  C9   119.73  3.000
 VJT  C11  C10  C9   120.55  3.000
 VJT  H10  C13  C14  118.17  3.000
 VJT  H10  C13  C12  120.05  3.000
 VJT  C14  C13  C12  121.78  3.000
 VJT  C16  C15  C18  109.35  3.000
 VJT  C16  C15  C12  112.34  3.000
 VJT  C18  C15  C12  108.55  3.000
 VJT  C12  C15  C17  109.97  3.000
 VJT  C16  C15  C17  108.07  3.000
 VJT  C18  C15  C17  108.49  3.000
 VJT  H13  C17  H12  107.40  3.000
 VJT  H13  C17  H11  107.74  3.000
 VJT  H12  C17  H11  107.82  3.000
 VJT  H13  C17  C15  110.12  3.000
 VJT  H12  C17  C15  112.69  3.000
 VJT  H11  C17  C15  110.88  3.000
 VJT  C1   O5   C5   112.90  3.000
 VJT  H14  C3   O3   111.04  3.000
 VJT  H14  C3   C2   108.05  3.000
 VJT  O3   C3   C2   107.38  3.000
 VJT  H14  C3   C4   107.87  3.000
 VJT  O3   C3   C4   111.56  3.000
 VJT  C2   C3   C4   110.90  3.000
 VJT  H15  C2   O2   111.43  3.000
 VJT  H15  C2   C1   108.02  3.000
 VJT  O2   C2   C1   107.49  3.000
 VJT  H15  C2   C3   109.10  3.000
 VJT  O2   C2   C3   112.34  3.000
 VJT  C1   C2   C3   108.31  3.000
 VJT  H16  C1   C2   107.80  3.000
 VJT  H16  C1   O5   110.29  3.000
 VJT  C2   C1   O5   110.67  3.000
 VJT  H16  C1   C7   108.29  3.000
 VJT  C2   C1   C7   111.63  3.000
 VJT  O5   C1   C7   108.13  3.000
 VJT  H17  O2   C2   108.22  3.000
 VJT  H18  O3   C3   108.82  3.000
 VJT  H19  O4   C4   107.59  3.000
 VJT  C14  C9   C10  118.45  3.000
 VJT  C10  C9   C8   120.73  3.000
 VJT  C14  C9   C8   120.82  3.000
 VJT  H20  C11  C12  120.41  3.000
 VJT  H20  C11  C10  117.96  3.000
 VJT  C12  C11  C10  121.63  3.000
 VJT  C11  C12  C15  122.72  3.000
 VJT  C11  C12  C13  117.22  3.000
 VJT  C15  C12  C13  120.03  3.000
 VJT  H21  C14  C9   119.77  3.000
 VJT  H21  C14  C13  119.85  3.000
 VJT  C9   C14  C13  120.38  3.000
 VJT  H23  C18  H22  105.98  3.000
 VJT  H23  C18  C15  107.77  3.000
 VJT  H22  C18  C15  108.82  3.000
 VJT  H23  C18  N1   108.24  3.000
 VJT  H22  C18  N1   113.41  3.000
 VJT  C15  C18  N1   112.28  3.000
 VJT  H26  C16  H25  107.40  3.000
 VJT  H26  C16  H24  107.48  3.000
 VJT  H25  C16  H24  108.40  3.000
 VJT  H26  C16  C15  109.51  3.000
 VJT  H25  C16  C15  111.66  3.000
 VJT  H24  C16  C15  112.20  3.000
 VJT  C9   C8   C7   180.00  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
 VJT  CONST_01  C13  C12  C11  C10     0.00   0.0  0
 VJT  CONST_02  C13  C14  C9   C10     0.00   0.0  0
 VJT  CONST_03  C12  C13  C14  C9      0.00   0.0  0
 VJT  CONST_04  C12  C11  C10  C9      0.00   0.0  0
 VJT  CONST_05  C14  C13  C12  C11     0.00   0.0  0
 VJT  CONST_06  C14  C9   C10  C11     0.00   0.0  0
 VJT  CONST_07  C13  C14  C9   C8    180.00   0.0  0
 VJT  CONST_08  C11  C10  C9   C8    180.00   0.0  0
 VJT  CONST_09  C15  C12  C11  C10   180.00   0.0  0
 VJT  CONST_10  C14  C13  C12  C15   180.00   0.0  0
 VJT  CONST_11  H21  C14  C9   C10   180.00   0.0  0
 VJT  CONST_12  H20  C11  C12  C13   180.00   0.0  0
 VJT  CONST_13  H10  C13  C14  C9    180.00   0.0  0
 VJT  CONST_14  H20  C11  C10  C9    180.00   0.0  0
 VJT  CONST_15  H10  C13  C12  C11   180.00   0.0  0
 VJT  CONST_16  H21  C14  C13  C12   180.00   0.0  0
 VJT  CONST_17  H9   C10  C11  C12   180.00   0.0  0
 VJT  CONST_18  H9   C10  C9   C14   180.00   0.0  0
 VJT  Var_01    C17  C15  C12  C13   -55.80  30.0  2
 VJT  Var_02    C18  C15  C12  C13    62.75  30.0  2
 VJT  Var_03    C16  C15  C12  C13  -176.20  30.0  2
 VJT  Var_04    C11  C12  C15  C17   126.26  30.0  2
 VJT  Var_05    C9   C8   C7   C1   -166.58  30.0  3
 VJT  Var_06    C18  C15  C12  C11  -115.19  30.0  2
 VJT  Var_07    C16  C15  C12  C11     5.86  30.0  2
 VJT  Var_08    C12  C15  C18  N1     58.01  30.0  3
 VJT  Var_09    H11  C17  C15  C12   -61.35  30.0  3
 VJT  Var_10    H12  C17  C15  C12    59.62  30.0  3
 VJT  Var_11    H13  C17  C15  C12   179.51  30.0  3
 VJT  Var_12    H22  C18  C15  C12   -68.37  30.0  2
 VJT  Var_13    H23  C18  C15  C12   177.12  30.0  2
 VJT  Var_14    H24  C16  C15  C12   -62.50  30.0  3
 VJT  Var_15    H25  C16  C15  C12    59.43  30.0  3
 VJT  Var_16    H26  C16  C15  C12   178.25  30.0  3
 VJT  Var_17    C17  C15  C18  N1    177.49  30.0  3
 VJT  Var_18    C16  C15  C18  N1    -64.86  30.0  3
 VJT  Var_19    H1   N1   C18  C15   169.58  30.0  3
 VJT  Var_20    H2   N1   C18  C15   -74.76  30.0  3
 VJT  Var_21    H22  C18  C15  C17    51.10  30.0  2
 VJT  Var_22    H23  C18  C15  C17   -63.40  30.0  2
 VJT  Var_23    H24  C16  C15  C17   176.01  30.0  3
 VJT  Var_24    H25  C16  C15  C17   -62.06  30.0  3
 VJT  Var_25    H26  C16  C15  C17    56.75  30.0  3
 VJT  Var_26    H11  C17  C15  C18  -179.93  30.0  3
 VJT  Var_27    H12  C17  C15  C18   -58.97  30.0  3
 VJT  Var_28    H13  C17  C15  C18    60.92  30.0  3
 VJT  Var_29    H24  C16  C15  C18    58.10  30.0  3
 VJT  Var_30    H25  C16  C15  C18  -179.98  30.0  3
 VJT  Var_31    H26  C16  C15  C18   -61.16  30.0  3
 VJT  Var_32    H11  C17  C15  C16    61.60  30.0  3
 VJT  Var_33    H12  C17  C15  C16  -177.43  30.0  3
 VJT  Var_34    H13  C17  C15  C16   -57.54  30.0  3
 VJT  Var_35    H22  C18  C15  C16   168.75  30.0  2
 VJT  Var_36    H23  C18  C15  C16    54.25  30.0  2

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
 VJT  chir_01  C4  O4  C5  C3  positiv
 VJT  chir_02  C5  O5  C4  C6  positiv
 VJT  chir_03  C3  O3  C4  C2  positiv
 VJT  chir_04  C2  O2  C3  C1  negativ
 VJT  chir_05  C1  O5  C7  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
 VJT  plan-1  C7   0.020
 VJT  plan-1  C10  0.020
 VJT  plan-1  C13  0.020
 VJT  plan-1  C15  0.020
 VJT  plan-1  C9   0.020
 VJT  plan-1  C11  0.020
 VJT  plan-1  C12  0.020
 VJT  plan-1  C14  0.020
 VJT  plan-1  H9   0.020
 VJT  plan-1  H10  0.020
 VJT  plan-1  H20  0.020
 VJT  plan-1  H21  0.020
 VJT  plan-1  C8   0.020

