# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 22:50:10 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: 1,4:3,6-dianhydro-2,5-bis-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)Oc4ccc(cc4)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
 TL3  TL3  1,4:3,6-dianhydro-2,5-bis-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_TL3
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
 TL3  N1    N  N     0  -0.646   6.1521   3.4858   0.8734
 TL3  C1    C  C     0   0.329   5.9932   2.5418   0.0252
 TL3  N2    N  NH2   0  -0.805   6.8719   2.3918  -1.0067
 TL3  C2    C  CR6   0  -0.015   4.9150   1.5190   0.0846
 TL3  C3    C  CR16  0  -0.274   3.6625   1.8483   0.6065
 TL3  C4    C  CR16  0  -0.339   2.6521   0.9119   0.6792
 TL3  C5    C  CR6   0   0.401   2.8711  -0.3952   0.2390
 TL3  O1    O  O2    0  -0.476   1.8305  -1.2381   0.3701
 TL3  C6    C  CH1   0  -0.083   1.9240  -2.5684  -0.0971
 TL3  C7    C  CH2   0  -0.191   1.7480  -2.6674  -1.6033
 TL3  O2    O  O2    0  -0.490   0.3552  -2.5104  -1.8426
 TL3  C8    C  CH1   0  -0.006  -0.3642  -2.8998  -0.6982
 TL3  C9    C  CH1   0  -0.054  -1.1373  -1.7639  -0.0333
 TL3  O3    O  O2    0  -0.481  -2.4717  -1.7712  -0.4980
 TL3  C10   C  CR6   0   0.391  -3.2646  -0.7043  -0.2765
 TL3  C11   C  CR16  0  -0.357  -2.8989   0.4174   0.4652
 TL3  C12   C  CR16  0  -0.262  -3.7980   1.4602   0.6253
 TL3  C13   C  CR6   0   0.024  -5.0730   1.4145   0.0729
 TL3  C14   C  C     0   0.333  -6.0049   2.5546   0.2747
 TL3  N3    N  N     0  -0.655  -5.5194   3.7077   0.5376
 TL3  N4    N  NH2   0  -0.824  -7.3305   2.2638   0.1083
 TL3  C15   C  CR16  0  -0.274  -5.4241   0.2862  -0.6705
 TL3  C16   C  CR16  0  -0.337  -4.5361  -0.7576  -0.8478
 TL3  C17   C  CH2   0  -0.169  -1.0074  -2.0899   1.4604
 TL3  O4    O  O2    0  -0.485   0.1640  -2.8749   1.6152
 TL3  C18   C  CH1   0  -0.021   0.6543  -3.2899   0.3733
 TL3  C19   C  CR16  0  -0.361   4.1148  -0.7406  -0.2828
 TL3  C20   C  CR16  0  -0.270   5.1179   0.2164  -0.3578
 TL3  HN1   H  H     0   0.330   5.4924   3.3979   1.6373
 TL3  HN21  H  HNH2  0   0.383   7.5312   3.1418  -1.1414
 TL3  HN22  H  HNH2  0   0.391   6.5428   1.9726  -1.8602
 TL3  H3    H  HCR6  0   0.264   3.4602   2.8578   0.9430
 TL3  H4    H  HCR6  0   0.267   1.6821   1.1856   1.0749
 TL3  H6    H  HCH1  0   0.279   2.8380  -3.0527   0.2576
 TL3  H71   H  HCH2  0   0.258   2.2921  -1.9043  -2.1619
 TL3  H72   H  HCH2  0   0.235   2.0978  -3.6484  -1.9454
 TL3  H8    H  HCH1  0   0.263  -1.0472  -3.7224  -0.9372
 TL3  H9    H  HCH1  0   0.259  -0.6587  -0.8108  -0.2781
 TL3  H11   H  HCR6  0   0.272  -1.9282   0.5005   0.9345
 TL3  H12   H  HCR6  0   0.260  -3.5021   2.3240   1.2050
 TL3  HN3   H  H     0   0.322  -6.2570   4.3904   0.6893
 TL3  HN41  H  HNH2  0   0.394  -7.6427   1.3281   0.3106
 TL3  HN42  H  HNH2  0   0.390  -7.9916   2.9718   0.3862
 TL3  H15   H  HCR6  0   0.259  -6.3951   0.2182  -1.1444
 TL3  H16   H  HCR6  0   0.268  -4.8210  -1.6205  -1.4363
 TL3  H171  H  HCH2  0   0.238  -0.9199  -1.1973   2.0821
 TL3  H172  H  HCH2  0   0.231  -1.8863  -2.6509   1.7976
 TL3  H18   H  HCH1  0   0.280   0.8502  -4.3657   0.3876
 TL3  H19   H  HCR6  0   0.286   4.3315  -1.7416  -0.6296
 TL3  H20   H  HCR6  0   0.267   6.0795  -0.0808  -0.7561

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
 TL3  N1   C1    double    1.279  0.020  1.279
 TL3  N1   HN1   single    0.890  0.020  1.040
 TL3  C1   N2    single    1.364  0.020  1.364
 TL3  C1   C2    single    1.487  0.020  1.487
 TL3  N2   HN21  single    0.890  0.020  1.040
 TL3  N2   HN22  single    0.890  0.020  1.040
 TL3  C2   C3    aromatic  1.396  0.020  1.396
 TL3  C2   C20   aromatic  1.391  0.020  1.391
 TL3  C3   C4    aromatic  1.379  0.020  1.379
 TL3  C3   H3    single    0.930  0.020  1.080
 TL3  C4   C5    aromatic  1.397  0.020  1.397
 TL3  C4   H4    single    0.930  0.020  1.080
 TL3  C5   O1    single    1.345  0.020  1.345
 TL3  C5   C19   aromatic  1.392  0.020  1.392
 TL3  O1   C6    single    1.413  0.020  1.413
 TL3  C6   C7    single    1.520  0.020  1.520
 TL3  C6   C18   single    1.534  0.020  1.534
 TL3  C6   H6    single    0.970  0.020  1.090
 TL3  C7   O2    single    1.422  0.020  1.422
 TL3  C7   H71   single    0.970  0.020  1.090
 TL3  C7   H72   single    0.970  0.020  1.090
 TL3  O2   C8    single    1.407  0.020  1.407
 TL3  C8   C9    single    1.526  0.020  1.526
 TL3  C8   C18   single    1.529  0.020  1.529
 TL3  C8   H8    single    0.970  0.020  1.090
 TL3  C9   O3    single    1.413  0.020  1.413
 TL3  C9   C17   single    1.534  0.020  1.534
 TL3  C9   H9    single    0.970  0.020  1.090
 TL3  O3   C10   single    1.348  0.020  1.348
 TL3  C10  C11   aromatic  1.394  0.020  1.394
 TL3  C10  C16   aromatic  1.395  0.020  1.395
 TL3  C11  C12   aromatic  1.386  0.020  1.386
 TL3  C11  H11   single    0.930  0.020  1.080
 TL3  C12  C13   aromatic  1.390  0.020  1.390
 TL3  C12  H12   single    0.930  0.020  1.080
 TL3  C13  C14   single    1.486  0.020  1.486
 TL3  C13  C15   aromatic  1.396  0.020  1.396
 TL3  C14  N3    double    1.278  0.020  1.278
 TL3  C14  N4    single    1.367  0.020  1.367
 TL3  N3   HN3   single    0.890  0.020  1.040
 TL3  N4   HN41  single    0.890  0.020  1.040
 TL3  N4   HN42  single    0.890  0.020  1.040
 TL3  C15  C16   aromatic  1.382  0.020  1.382
 TL3  C15  H15   single    0.930  0.020  1.080
 TL3  C16  H16   single    0.930  0.020  1.080
 TL3  C17  O4    single    1.419  0.020  1.419
 TL3  C17  H171  single    0.970  0.020  1.090
 TL3  C17  H172  single    0.970  0.020  1.090
 TL3  O4   C18   single    1.398  0.020  1.398
 TL3  C18  H18   single    0.970  0.020  1.090
 TL3  C19  C20   aromatic  1.388  0.020  1.388
 TL3  C19  H19   single    0.930  0.020  1.080
 TL3  C20  H20   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
 TL3  HN1   N1   C1    110.80  3.000
 TL3  C2    C1   N2    114.94  3.000
 TL3  C2    C1   N1    124.83  3.000
 TL3  N2    C1   N1    120.20  3.000
 TL3  HN22  N2   HN21  114.25  3.000
 TL3  HN22  N2   C1    118.49  3.000
 TL3  HN21  N2   C1    116.16  3.000
 TL3  C20   C2   C3    118.08  3.000
 TL3  C20   C2   C1    121.71  3.000
 TL3  C3    C2   C1    120.20  3.000
 TL3  H3    C3   C4    118.65  3.000
 TL3  H3    C3   C2    120.23  3.000
 TL3  C4    C3   C2    121.10  3.000
 TL3  H4    C4   C5    119.48  3.000
 TL3  H4    C4   C3    120.25  3.000
 TL3  C5    C4   C3    120.26  3.000
 TL3  C19   C5   O1    124.89  3.000
 TL3  C19   C5   C4    119.36  3.000
 TL3  O1    C5   C4    115.75  3.000
 TL3  C6    O1   C5    120.42  3.000
 TL3  H6    C6   C18   112.58  3.000
 TL3  H6    C6   C7    112.92  3.000
 TL3  C18   C6   C7    100.22  3.000
 TL3  H6    C6   O1    111.41  3.000
 TL3  C18   C6   O1    106.65  3.000
 TL3  C7    C6   O1    112.42  3.000
 TL3  H72   C7   H71   107.88  3.000
 TL3  H72   C7   O2    111.03  3.000
 TL3  H71   C7   O2    108.98  3.000
 TL3  H72   C7   C6    109.31  3.000
 TL3  H71   C7   C6    113.84  3.000
 TL3  O2    C7   C6    105.85  3.000
 TL3  C8    O2   C7    109.48  3.000
 TL3  H8    C8   C18   112.13  3.000
 TL3  H8    C8   C9    109.76  3.000
 TL3  C18   C8   C9    102.82  3.000
 TL3  H8    C8   O2    110.44  3.000
 TL3  C18   C8   O2    107.46  3.000
 TL3  C9    C8   O2    114.04  3.000
 TL3  H9    C9   C17   111.46  3.000
 TL3  H9    C9   O3    110.12  3.000
 TL3  C17   C9   O3    113.51  3.000
 TL3  H9    C9   C8    109.22  3.000
 TL3  C17   C9   C8    102.89  3.000
 TL3  O3    C9   C8    109.34  3.000
 TL3  C10   O3   C9    119.83  3.000
 TL3  C16   C10  C11   119.20  3.000
 TL3  C16   C10  O3    116.03  3.000
 TL3  C11   C10  O3    124.78  3.000
 TL3  H11   C11  C12   118.31  3.000
 TL3  H11   C11  C10   121.89  3.000
 TL3  C12   C11  C10   119.79  3.000
 TL3  H12   C12  C13   119.34  3.000
 TL3  H12   C12  C11   119.03  3.000
 TL3  C13   C12  C11   121.62  3.000
 TL3  C15   C13  C14   122.32  3.000
 TL3  C15   C13  C12   117.95  3.000
 TL3  C14   C13  C12   119.73  3.000
 TL3  N4    C14  N3    125.81  3.000
 TL3  N4    C14  C13   115.35  3.000
 TL3  N3    C14  C13   118.79  3.000
 TL3  HN3   N3   C14   111.15  3.000
 TL3  HN42  N4   HN41  113.20  3.000
 TL3  HN42  N4   C14   116.93  3.000
 TL3  HN41  N4   C14   118.29  3.000
 TL3  H15   C15  C16   118.22  3.000
 TL3  H15   C15  C13   120.63  3.000
 TL3  C16   C15  C13   121.14  3.000
 TL3  H16   C16  C15   120.17  3.000
 TL3  H16   C16  C10   119.54  3.000
 TL3  C15   C16  C10   120.29  3.000
 TL3  H172  C17  H171  107.92  3.000
 TL3  H172  C17  O4    110.21  3.000
 TL3  H171  C17  O4    108.92  3.000
 TL3  H172  C17  C9    109.91  3.000
 TL3  H171  C17  C9    112.81  3.000
 TL3  O4    C17  C9    107.08  3.000
 TL3  C18   O4   C17   110.91  3.000
 TL3  H18   C18  O4    110.07  3.000
 TL3  H18   C18  C8    112.30  3.000
 TL3  O4    C18  C8    108.25  3.000
 TL3  H18   C18  C6    108.56  3.000
 TL3  O4    C18  C6    115.02  3.000
 TL3  C8    C18  C6    102.50  3.000
 TL3  H19   C19  C20   118.42  3.000
 TL3  H19   C19  C5    121.93  3.000
 TL3  C20   C19  C5    119.65  3.000
 TL3  H20   C20  C19   118.19  3.000
 TL3  H20   C20  C2    120.26  3.000
 TL3  C19   C20  C2    121.54  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
 TL3  CONST_01  C5    C4   C3   C2      0.00   0.0  0
 TL3  CONST_02  C5    C19  C20  C2      0.00   0.0  0
 TL3  CONST_03  C19   C20  C2   C3      0.00   0.0  0
 TL3  CONST_04  C19   C5   C4   C3      0.00   0.0  0
 TL3  CONST_05  C20   C2   C3   C4      0.00   0.0  0
 TL3  CONST_06  C20   C19  C5   C4      0.00   0.0  0
 TL3  CONST_07  C13   C12  C11  C10     0.00   0.0  0
 TL3  CONST_08  C13   C15  C16  C10     0.00   0.0  0
 TL3  CONST_09  C15   C16  C10  C11     0.00   0.0  0
 TL3  CONST_10  C15   C13  C12  C11     0.00   0.0  0
 TL3  CONST_11  C16   C10  C11  C12     0.00   0.0  0
 TL3  CONST_12  C16   C15  C13  C12     0.00   0.0  0
 TL3  CONST_13  C4    C3   C2   C1    180.00   0.0  0
 TL3  CONST_14  C19   C20  C2   C1    180.00   0.0  0
 TL3  CONST_15  O1    C5   C4   C3    180.00   0.0  0
 TL3  CONST_16  C20   C19  C5   O1    180.00   0.0  0
 TL3  CONST_17  C12   C11  C10  O3    180.00   0.0  0
 TL3  CONST_18  C15   C16  C10  O3    180.00   0.0  0
 TL3  CONST_19  C14   C13  C12  C11   180.00   0.0  0
 TL3  CONST_20  C16   C15  C13  C14   180.00   0.0  0
 TL3  CONST_21  H4    C4   C3   C2    180.00   0.0  0
 TL3  CONST_22  H19   C19  C20  C2    180.00   0.0  0
 TL3  CONST_23  H20   C20  C2   C3    180.00   0.0  0
 TL3  CONST_24  H3    C3   C4   C5    180.00   0.0  0
 TL3  CONST_25  H12   C12  C11  C10   180.00   0.0  0
 TL3  CONST_26  H15   C15  C16  C10   180.00   0.0  0
 TL3  CONST_27  H16   C16  C10  C11   180.00   0.0  0
 TL3  CONST_28  H11   C11  C12  C13   180.00   0.0  0
 TL3  CONST_29  HN1   N1   C1   C2      0.00   0.0  0
 TL3  CONST_30  HN21  N2   C1   C2    180.00   0.0  0
 TL3  CONST_32  HN3   N3   C14  C13   180.00   0.0  0
 TL3  CONST_34  HN42  N4   C14  C13   180.00   0.0  0
 TL3  Var_01    C19   C5   O1   C6     -3.27  30.0  2
 TL3  Var_02    C11   C10  O3   C9     -4.10  30.0  2
 TL3  Var_03    H71   C7   O2   C8   -148.08  30.0  1
 TL3  Var_04    H171  C17  O4   C18  -133.20  30.0  1
 TL3  Var_05    C3    C2   C1   N1     32.58  30.0  2
 TL3  Var_06    N3    C14  C13  C12    23.39  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
 TL3  chir_01  C6   O1  C7   C18  positiv
 TL3  chir_02  C8   O2  C18  C9   negativ
 TL3  chir_03  C9   O3  C8   C17  positiv
 TL3  chir_04  C18  O4  C6   C8   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
 TL3  plan-1  C1    0.020
 TL3  plan-1  C2    0.020
 TL3  plan-1  C3    0.020
 TL3  plan-1  C4    0.020
 TL3  plan-1  C5    0.020
 TL3  plan-1  O1    0.020
 TL3  plan-1  C19   0.020
 TL3  plan-1  C20   0.020
 TL3  plan-1  H3    0.020
 TL3  plan-1  H4    0.020
 TL3  plan-1  H19   0.020
 TL3  plan-1  H20   0.020
 TL3  plan-2  O3    0.020
 TL3  plan-2  C10   0.020
 TL3  plan-2  C11   0.020
 TL3  plan-2  C12   0.020
 TL3  plan-2  C13   0.020
 TL3  plan-2  C14   0.020
 TL3  plan-2  C15   0.020
 TL3  plan-2  C16   0.020
 TL3  plan-2  H11   0.020
 TL3  plan-2  H12   0.020
 TL3  plan-2  H15   0.020
 TL3  plan-2  H16   0.020
 TL3  plan-3  N1    0.020
 TL3  plan-3  C1    0.020
 TL3  plan-3  N2    0.020
 TL3  plan-3  C2    0.020
 TL3  plan-3  HN1   0.020
 TL3  plan-3  HN21  0.020
 TL3  plan-3  HN22  0.020
 TL3  plan-4  C13   0.020
 TL3  plan-4  C14   0.020
 TL3  plan-4  N3    0.020
 TL3  plan-4  N4    0.020
 TL3  plan-4  HN3   0.020
 TL3  plan-4  HN41  0.020
 TL3  plan-4  HN42  0.020

