# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 22:33:37 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: 1,4:3,6-dianhydro-2-O-(3-carbamimidoylphenyl)-5-O-(4-carbamimidoylphenyl)-D-glucitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc(O[C@@H]2CO[C@@H]3[C@H](CO[C@H]23)Oc4cccc(c4)C(N)=N)cc1
#
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
 TL4  TL4  1,4:3,6-dianhydro-2-O-(3-carbamimidoylphenyl)-5-O-(4-carbamimidoylphenyl)-D-glucitol  ligand  50  28  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TL4
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
 TL4  C4    C  CR6   0   0.026  -5.2348  -1.0684   0.6707
 TL4  C5    C  CR16  0  -0.259  -4.0647  -1.1441   1.4291
 TL4  C6    C  CR16  0  -0.338  -2.9510  -0.4007   1.0989
 TL4  C7    C  CR6   0   0.395  -2.9786   0.4599  -0.0016
 TL4  O8    O  O2    0  -0.474  -1.8497   1.1566  -0.2333
 TL4  C9    C  CH1   0  -0.079  -1.7514   1.9827  -1.3750
 TL4  C10   C  CH2   0  -0.194  -1.4996   1.1808  -2.6417
 TL4  O11   O  O2    0  -0.490  -0.1354   0.7869  -2.5787
 TL4  C12   C  CH1   0  -0.006   0.5853   1.7325  -1.8255
 TL4  C13   C  CH1   0  -0.049   1.2316   1.1702  -0.5637
 TL4  O14   O  O2    0  -0.486   2.5613   0.7948  -0.8458
 TL4  C15   C  CR6   0   0.416   3.2728   0.0954   0.0656
 TL4  C16   C  CR16  0  -0.372   2.7660  -0.3823   1.2716
 TL4  C17   C  CR16  0  -0.229   3.5976  -1.1038   2.1183
 TL4  C18   C  CR16  0  -0.316   4.9161  -1.3612   1.7835
 TL4  C19   C  CR6   0   0.063   5.4231  -0.8824   0.5748
 TL4  C20   C  C     0   0.336   6.8398  -1.1176   0.1742
 TL4  N21   N  N     0  -0.650   7.4066  -0.2712  -0.5963
 TL4  N22   N  NH2   0  -0.821   7.4233  -2.2203   0.7286
 TL4  C23   C  CR16  0  -0.386   4.6006  -0.1537  -0.2723
 TL4  C24   C  CH2   0  -0.174   1.1239   2.3512   0.4081
 TL4  O25   O  O2    0  -0.483  -0.0409   3.0685   0.0384
 TL4  C26   C  CH1   0  -0.018  -0.4238   2.7410  -1.2678
 TL4  C27   C  CR16  0  -0.363  -4.1401   0.5545  -0.7622
 TL4  C28   C  CR16  0  -0.278  -5.2507  -0.2059  -0.4195
 TL4  N1    N  N     0  -0.655  -6.5270  -2.2753   2.2660
 TL4  C2    C  C     0   0.332  -6.4169  -1.8828   1.0544
 TL4  N3    N  NH2   0  -0.824  -7.3270  -2.0988   0.0570
 TL4  H5    H  HCR6  0   0.257  -4.0293  -1.8049   2.2845
 TL4  H6    H  HCR6  0   0.264  -2.0472  -0.4780   1.6902
 TL4  H9    H  HCH1  0   0.278  -2.6097   2.6551  -1.4574
 TL4  H101  H  HCH2  0   0.257  -2.1231   0.2899  -2.7305
 TL4  H102  H  HCH2  0   0.234  -1.6884   1.8127  -3.5177
 TL4  H12   H  HCH1  0   0.261   1.3478   2.2169  -2.4458
 TL4  H13   H  HCH1  0   0.256   0.6506   0.3106  -0.2140
 TL4  H16   H  HCR6  0   0.275   1.7420  -0.2098   1.5736
 TL4  H17   H  HCR6  0   0.266   3.2028  -1.4652   3.0585
 TL4  H18   H  HCR6  0   0.258   5.5432  -1.9085   2.4742
 TL4  H21   H  H     0   0.324   8.3563  -0.5558  -0.8208
 TL4  H221  H  HNH2  0   0.395   6.8369  -3.0001   0.9765
 TL4  H222  H  HNH2  0   0.392   8.3276  -2.4903   0.3755
 TL4  H23   H  HCR6  0   0.263   4.9921   0.2224  -1.2086
 TL4  H241  H  HCH2  0   0.243   1.0289   2.0463   1.4511
 TL4  H242  H  HCH2  0   0.227   2.0145   2.9848   0.3173
 TL4  H26   H  HCH1  0   0.277  -0.4871   3.6425  -1.8851
 TL4  H27   H  HCR6  0   0.285  -4.2116   1.2143  -1.6154
 TL4  H28   H  HCR6  0   0.261  -6.1446  -0.0931  -1.0191
 TL4  HN1   H  H     0   0.322  -7.3552  -2.8513   2.3912
 TL4  HN31  H  HNH2  0   0.394  -6.9943  -2.1395  -0.8923
 TL4  HN32  H  HNH2  0   0.390  -8.0692  -2.7532   0.2478

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
 TL4  C4   C5    aromatic  1.396  0.020  1.396
 TL4  C4   C28   aromatic  1.390  0.020  1.390
 TL4  C4   C2    single    1.486  0.020  1.486
 TL4  C5   C6    aromatic  1.379  0.020  1.379
 TL4  C5   H5    single    0.930  0.020  1.080
 TL4  C6   C7    aromatic  1.397  0.020  1.397
 TL4  C6   H6    single    0.930  0.020  1.080
 TL4  C7   O8    single    1.347  0.020  1.347
 TL4  C7   C27   aromatic  1.392  0.020  1.392
 TL4  O8   C9    single    1.413  0.020  1.413
 TL4  C9   C10   single    1.520  0.020  1.520
 TL4  C9   C26   single    1.533  0.020  1.533
 TL4  C9   H9    single    0.970  0.020  1.090
 TL4  C10  O11   single    1.421  0.020  1.421
 TL4  C10  H101  single    0.970  0.020  1.090
 TL4  C10  H102  single    0.970  0.020  1.090
 TL4  O11  C12   single    1.407  0.020  1.407
 TL4  C12  C13   single    1.525  0.020  1.525
 TL4  C12  C26   single    1.532  0.020  1.532
 TL4  C12  H12   single    0.970  0.020  1.090
 TL4  C13  O14   single    1.410  0.020  1.410
 TL4  C13  C24   single    1.533  0.020  1.533
 TL4  C13  H13   single    0.970  0.020  1.090
 TL4  O14  C15   single    1.351  0.020  1.351
 TL4  C15  C16   aromatic  1.393  0.020  1.393
 TL4  C15  C23   aromatic  1.393  0.020  1.393
 TL4  C16  C17   aromatic  1.389  0.020  1.389
 TL4  C16  H16   single    0.930  0.020  1.080
 TL4  C17  C18   aromatic  1.384  0.020  1.384
 TL4  C17  H17   single    0.930  0.020  1.080
 TL4  C18  C19   aromatic  1.395  0.020  1.395
 TL4  C18  H18   single    0.930  0.020  1.080
 TL4  C19  C20   single    1.491  0.020  1.491
 TL4  C19  C23   aromatic  1.387  0.020  1.387
 TL4  C20  N21   double    1.277  0.020  1.277
 TL4  C20  N22   single    1.365  0.020  1.365
 TL4  N21  H21   single    0.890  0.020  1.040
 TL4  N22  H221  single    0.890  0.020  1.040
 TL4  N22  H222  single    0.890  0.020  1.040
 TL4  C23  H23   single    0.930  0.020  1.080
 TL4  C24  O25   single    1.417  0.020  1.417
 TL4  C24  H241  single    0.970  0.020  1.090
 TL4  C24  H242  single    0.970  0.020  1.090
 TL4  O25  C26   single    1.400  0.020  1.400
 TL4  C26  H26   single    0.970  0.020  1.090
 TL4  C27  C28   aromatic  1.389  0.020  1.389
 TL4  C27  H27   single    0.930  0.020  1.080
 TL4  C28  H28   single    0.930  0.020  1.080
 TL4  N1   C2    double    1.278  0.020  1.278
 TL4  N1   HN1   single    0.890  0.020  1.040
 TL4  C2   N3    single    1.367  0.020  1.367
 TL4  N3   HN31  single    0.890  0.020  1.040
 TL4  N3   HN32  single    0.890  0.020  1.040

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
 TL4  C2    C4   C28   122.24  3.000
 TL4  C2    C4   C5    119.78  3.000
 TL4  C28   C4   C5    117.98  3.000
 TL4  H5    C5   C6    119.49  3.000
 TL4  H5    C5   C4    119.35  3.000
 TL4  C6    C5   C4    121.16  3.000
 TL4  H6    C6   C7    119.38  3.000
 TL4  H6    C6   C5    120.32  3.000
 TL4  C7    C6   C5    120.31  3.000
 TL4  C27   C7   O8    124.78  3.000
 TL4  C27   C7   C6    119.26  3.000
 TL4  O8    C7   C6    115.95  3.000
 TL4  C9    O8   C7    119.99  3.000
 TL4  H9    C9   C26   112.39  3.000
 TL4  H9    C9   C10   113.06  3.000
 TL4  C26   C9   C10   100.13  3.000
 TL4  H9    C9   O8    111.46  3.000
 TL4  C26   C9   O8    107.04  3.000
 TL4  C10   C9   O8    112.12  3.000
 TL4  H102  C10  H101  107.89  3.000
 TL4  H102  C10  O11   111.13  3.000
 TL4  H101  C10  O11   109.01  3.000
 TL4  H102  C10  C9    109.46  3.000
 TL4  H101  C10  C9    113.82  3.000
 TL4  O11   C10  C9    105.56  3.000
 TL4  C12   O11  C10   109.21  3.000
 TL4  H12   C12  C26   111.93  3.000
 TL4  H12   C12  C13   109.66  3.000
 TL4  C26   C12  C13   102.75  3.000
 TL4  H12   C12  O11   110.51  3.000
 TL4  C26   C12  O11   107.45  3.000
 TL4  C13   C12  O11   114.33  3.000
 TL4  H13   C13  C24   111.41  3.000
 TL4  H13   C13  O14   110.81  3.000
 TL4  C24   C13  O14   113.46  3.000
 TL4  H13   C13  C12   109.20  3.000
 TL4  C24   C13  C12   102.16  3.000
 TL4  O14   C13  C12   109.41  3.000
 TL4  C15   O14  C13   119.96  3.000
 TL4  C23   C15  C16   119.72  3.000
 TL4  C23   C15  O14   115.53  3.000
 TL4  C16   C15  O14   124.75  3.000
 TL4  H16   C16  C17   118.66  3.000
 TL4  H16   C16  C15   122.12  3.000
 TL4  C17   C16  C15   119.22  3.000
 TL4  H17   C17  C18   119.71  3.000
 TL4  H17   C17  C16   119.00  3.000
 TL4  C18   C17  C16   121.29  3.000
 TL4  H18   C18  C19   121.07  3.000
 TL4  H18   C18  C17   119.46  3.000
 TL4  C19   C18  C17   119.45  3.000
 TL4  C23   C19  C20   118.83  3.000
 TL4  C23   C19  C18   119.58  3.000
 TL4  C20   C19  C18   121.59  3.000
 TL4  N22   C20  N21   126.20  3.000
 TL4  N22   C20  C19   115.12  3.000
 TL4  N21   C20  C19   118.63  3.000
 TL4  H21   N21  C20   111.25  3.000
 TL4  H222  N22  H221  113.67  3.000
 TL4  H222  N22  C20   117.24  3.000
 TL4  H221  N22  C20   118.47  3.000
 TL4  H23   C23  C19   119.75  3.000
 TL4  H23   C23  C15   119.51  3.000
 TL4  C19   C23  C15   120.73  3.000
 TL4  H242  C24  H241  108.14  3.000
 TL4  H242  C24  O25   110.70  3.000
 TL4  H241  C24  O25   108.63  3.000
 TL4  H242  C24  C13   109.60  3.000
 TL4  H241  C24  C13   113.38  3.000
 TL4  O25   C24  C13   106.40  3.000
 TL4  C26   O25  C24   110.48  3.000
 TL4  H26   C26  O25   110.45  3.000
 TL4  H26   C26  C12   112.03  3.000
 TL4  O25   C26  C12   108.27  3.000
 TL4  H26   C26  C9    108.54  3.000
 TL4  O25   C26  C9    114.71  3.000
 TL4  C12   C26  C9    102.67  3.000
 TL4  H27   C27  C28   118.43  3.000
 TL4  H27   C27  C7    121.88  3.000
 TL4  C28   C27  C7    119.69  3.000
 TL4  H28   C28  C27   117.82  3.000
 TL4  H28   C28  C4    120.57  3.000
 TL4  C27   C28  C4    121.60  3.000
 TL4  HN1   N1   C2    111.16  3.000
 TL4  N3    C2   N1    125.83  3.000
 TL4  N3    C2   C4    115.33  3.000
 TL4  N1    C2   C4    118.79  3.000
 TL4  HN32  N3   HN31  113.31  3.000
 TL4  HN32  N3   C2    117.05  3.000
 TL4  HN31  N3   C2    118.31  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
 TL4  CONST_01  C7    C6   C5   C4      0.00   0.0  0
 TL4  CONST_02  C7    C27  C28  C4      0.00   0.0  0
 TL4  CONST_03  C27   C28  C4   C5      0.00   0.0  0
 TL4  CONST_04  C27   C7   C6   C5      0.00   0.0  0
 TL4  CONST_05  C28   C4   C5   C6      0.00   0.0  0
 TL4  CONST_06  C28   C27  C7   C6      0.00   0.0  0
 TL4  CONST_07  C18   C17  C16  C15     0.00   0.0  0
 TL4  CONST_08  C18   C19  C23  C15     0.00   0.0  0
 TL4  CONST_09  C19   C23  C15  C16     0.00   0.0  0
 TL4  CONST_10  C19   C18  C17  C16     0.00   0.0  0
 TL4  CONST_11  C23   C15  C16  C17     0.00   0.0  0
 TL4  CONST_12  C23   C19  C18  C17     0.00   0.0  0
 TL4  CONST_13  O8    C7   C6   C5    180.00   0.0  0
 TL4  CONST_14  C2    C4   C5   C6    180.00   0.0  0
 TL4  CONST_15  C28   C27  C7   O8    180.00   0.0  0
 TL4  CONST_16  C17   C16  C15  O14   180.00   0.0  0
 TL4  CONST_17  C19   C23  C15  O14   180.00   0.0  0
 TL4  CONST_18  C20   C19  C23  C15   180.00   0.0  0
 TL4  CONST_19  C20   C19  C18  C17   180.00   0.0  0
 TL4  CONST_20  C2    C4   C28  C27   180.00   0.0  0
 TL4  CONST_21  H6    C6   C5   C4    180.00   0.0  0
 TL4  CONST_22  H27   C27  C28  C4    180.00   0.0  0
 TL4  CONST_23  H28   C28  C4   C5    180.00   0.0  0
 TL4  CONST_24  H5    C5   C6   C7    180.00   0.0  0
 TL4  CONST_25  H17   C17  C16  C15   180.00   0.0  0
 TL4  CONST_26  H23   C23  C15  C16   180.00   0.0  0
 TL4  CONST_27  H18   C18  C17  C16   180.00   0.0  0
 TL4  CONST_28  H16   C16  C17  C18   180.00   0.0  0
 TL4  CONST_29  HN1   N1   C2   C4    180.00   0.0  0
 TL4  CONST_31  HN32  N3   C2   C4    180.00   0.0  0
 TL4  CONST_32  H21   N21  C20  C19   180.00   0.0  0
 TL4  CONST_34  H222  N22  C20  C19   180.00   0.0  0
 TL4  Var_01    C27   C7   O8   C9     -5.00  30.0  2
 TL4  Var_02    C16   C15  O14  C13     4.51  30.0  2
 TL4  Var_03    H101  C10  O11  C12  -150.57  30.0  1
 TL4  Var_04    H241  C24  O25  C26  -141.13  30.0  1
 TL4  Var_05    N1    C2   C4   C5     23.35  30.0  2
 TL4  Var_06    N21   C20  C19  C18  -151.99  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
 TL4  chir_01  C9   O8   C10  C26  positiv
 TL4  chir_02  C12  O11  C26  C13  negativ
 TL4  chir_03  C13  O14  C12  C24  positiv
 TL4  chir_04  C26  O25  C9   C12  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
 TL4  plan-1  C4    0.020
 TL4  plan-1  C5    0.020
 TL4  plan-1  C6    0.020
 TL4  plan-1  C7    0.020
 TL4  plan-1  O8    0.020
 TL4  plan-1  C27   0.020
 TL4  plan-1  C28   0.020
 TL4  plan-1  C2    0.020
 TL4  plan-1  H5    0.020
 TL4  plan-1  H6    0.020
 TL4  plan-1  H27   0.020
 TL4  plan-1  H28   0.020
 TL4  plan-2  O14   0.020
 TL4  plan-2  C15   0.020
 TL4  plan-2  C16   0.020
 TL4  plan-2  C17   0.020
 TL4  plan-2  C18   0.020
 TL4  plan-2  C19   0.020
 TL4  plan-2  C20   0.020
 TL4  plan-2  C23   0.020
 TL4  plan-2  H16   0.020
 TL4  plan-2  H17   0.020
 TL4  plan-2  H18   0.020
 TL4  plan-2  H23   0.020
 TL4  plan-3  C19   0.020
 TL4  plan-3  C20   0.020
 TL4  plan-3  N21   0.020
 TL4  plan-3  N22   0.020
 TL4  plan-3  H21   0.020
 TL4  plan-3  H221  0.020
 TL4  plan-3  H222  0.020
 TL4  plan-4  C4    0.020
 TL4  plan-4  N1    0.020
 TL4  plan-4  C2    0.020
 TL4  plan-4  N3    0.020
 TL4  plan-4  HN1   0.020
 TL4  plan-4  HN31  0.020
 TL4  plan-4  HN32  0.020

