# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 15:57:20 2022
#   Inital geometry file: a 127 line input string
#   Ligand name: 1,4:3,6-dianhydro-2,5-bis-O-(3-carbamimidoylphenyl)-D-glucitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1cccc(O[C@@H]2CO[C@@H]3[C@H](CO[C@H]23)Oc4cccc(c4)C(N)=N)c1
#
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
 TL1  TL1  1,4:3,6-dianhydro-2,5-bis-O-(3-carbamimidoylphenyl)-D-glucitol  ligand  50  28  .  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_TL1
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
 TL1  N1    N  N     0  -0.640   3.4175   3.3691   1.4051
 TL1  C1    C  C     0   0.330   4.4191   2.5867   1.2709
 TL1  N2    N  NH2   0  -0.802   5.6085   2.8722   1.8689
 TL1  C2    C  CR6   0   0.024   4.4212   1.3523   0.4338
 TL1  C3    C  CR16  0  -0.304   5.5427   0.9925  -0.3139
 TL1  C4    C  CR16  0  -0.228   5.4926  -0.1380  -1.1113
 TL1  C5    C  CR16  0  -0.375   4.3525  -0.9301  -1.1693
 TL1  C6    C  CR6   0   0.418   3.2394  -0.5789  -0.4099
 TL1  O1    O  O2    0  -0.479   2.0925  -1.2850  -0.3543
 TL1  C7    C  CH1   0  -0.079   1.9095  -2.4117  -1.1847
 TL1  C8    C  CH2   0  -0.195   1.5349  -2.0192  -2.6044
 TL1  O2    O  O2    0  -0.490   0.1809  -1.5922  -2.5353
 TL1  C9    C  CH1   0  -0.006  -0.4600  -2.2595  -1.4741
 TL1  C10   C  CH1   0  -0.048  -0.9827  -1.3387  -0.3771
 TL1  O3    O  O2    0  -0.486  -2.3310  -1.0136  -0.6320
 TL1  C11   C  CR6   0   0.418  -2.9263  -0.0238   0.0698
 TL1  C12   C  CR16  0  -0.372  -2.2965   0.7404   1.0487
 TL1  C13   C  CR16  0  -0.229  -3.0140   1.7360   1.6990
 TL1  C14   C  CR16  0  -0.315  -4.3448   1.9734   1.4006
 TL1  C15   C  CR6   0   0.062  -4.9768   1.2041   0.4225
 TL1  C16   C  C     0   0.338  -6.4077   1.4200   0.0619
 TL1  N3    N  N     0  -0.651  -6.7945   1.1210  -1.1183
 TL1  N4    N  NH2   0  -0.822  -7.1743   1.9755   1.0444
 TL1  C17   C  CR16  0  -0.386  -4.2615   0.2184  -0.2425
 TL1  C18   C  CH2   0  -0.174  -0.7860  -2.1934   0.8800
 TL1  O4    O  O2    0  -0.484   0.3458  -3.0095   0.6331
 TL1  C19   C  CH1   0  -0.017   0.6037  -3.0835  -0.7415
 TL1  C20   C  CR16  0  -0.400   3.2780   0.5675   0.3813
 TL1  HN1   H  H     0   0.332   2.6488   3.0741   0.8143
 TL1  HN21  H  HNH2  0   0.385   5.6067   3.6343   2.5281
 TL1  HN22  H  HNH2  0   0.394   6.2181   2.1098   2.1136
 TL1  H3    H  HCR6  0   0.261   6.4368   1.6007  -0.2934
 TL1  H4    H  HCR6  0   0.266   6.3524  -0.4133  -1.7079
 TL1  H5    H  HCR6  0   0.286   4.3552  -1.8068  -1.8025
 TL1  H7    H  HCH1  0   0.277   2.7662  -3.0896  -1.1393
 TL1  H81   H  HCH2  0   0.256   2.1401  -1.2100  -3.0152
 TL1  H82   H  HCH2  0   0.234   1.6430  -2.8884  -3.2642
 TL1  H9    H  HCH1  0   0.260  -1.2766  -2.8831  -1.8543
 TL1  H10   H  HCH1  0   0.255  -0.3667  -0.4339  -0.3433
 TL1  H12   H  HCR6  0   0.275  -1.2623   0.5827   1.3221
 TL1  H13   H  HCR6  0   0.266  -2.5164   2.3336   2.4513
 TL1  H14   H  HCR6  0   0.258  -4.8727   2.7663   1.9130
 TL1  HN3   H  H     0   0.324  -7.7920   1.2830  -1.2299
 TL1  HN41  H  HNH2  0   0.392  -8.1709   1.9985   0.8977
 TL1  HN42  H  HNH2  0   0.396  -6.9098   1.8260   2.0040
 TL1  H17   H  HCR6  0   0.263  -4.7472  -0.3771  -1.0050
 TL1  H181  H  HCH2  0   0.242  -0.6018  -1.6050   1.7800
 TL1  H182  H  HCH2  0   0.227  -1.6791  -2.8071   1.0507
 TL1  H19   H  HCH1  0   0.277   0.6186  -4.1267  -1.0709
 TL1  H20   H  HCR6  0   0.265   2.4092   0.8209   0.9775

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
 TL1  N1   C1    double    1.278  0.020  1.278
 TL1  N1   HN1   single    0.890  0.020  1.040
 TL1  C1   N2    single    1.362  0.020  1.362
 TL1  C1   C2    single    1.491  0.020  1.491
 TL1  N2   HN21  single    0.890  0.020  1.040
 TL1  N2   HN22  single    0.890  0.020  1.040
 TL1  C2   C3    aromatic  1.395  0.020  1.395
 TL1  C2   C20   aromatic  1.388  0.020  1.388
 TL1  C3   C4    aromatic  1.384  0.020  1.384
 TL1  C3   H3    single    0.930  0.020  1.080
 TL1  C4   C5    aromatic  1.389  0.020  1.389
 TL1  C4   H4    single    0.930  0.020  1.080
 TL1  C5   C6    aromatic  1.393  0.020  1.393
 TL1  C5   H5    single    0.930  0.020  1.080
 TL1  C6   O1    single    1.348  0.020  1.348
 TL1  C6   C20   aromatic  1.393  0.020  1.393
 TL1  O1   C7    single    1.412  0.020  1.412
 TL1  C7   C8    single    1.520  0.020  1.520
 TL1  C7   C19   single    1.534  0.020  1.534
 TL1  C7   H7    single    0.970  0.020  1.090
 TL1  C8   O2    single    1.421  0.020  1.421
 TL1  C8   H81   single    0.970  0.020  1.090
 TL1  C8   H82   single    0.970  0.020  1.090
 TL1  O2   C9    single    1.408  0.020  1.408
 TL1  C9   C10   single    1.525  0.020  1.525
 TL1  C9   C19   single    1.532  0.020  1.532
 TL1  C9   H9    single    0.970  0.020  1.090
 TL1  C10  O3    single    1.410  0.020  1.410
 TL1  C10  C18   single    1.533  0.020  1.533
 TL1  C10  H10   single    0.970  0.020  1.090
 TL1  O3   C11   single    1.352  0.020  1.352
 TL1  C11  C12   aromatic  1.392  0.020  1.392
 TL1  C11  C17   aromatic  1.392  0.020  1.392
 TL1  C12  C13   aromatic  1.389  0.020  1.389
 TL1  C12  H12   single    0.930  0.020  1.080
 TL1  C13  C14   aromatic  1.384  0.020  1.384
 TL1  C13  H13   single    0.930  0.020  1.080
 TL1  C14  C15   aromatic  1.396  0.020  1.396
 TL1  C14  H14   single    0.930  0.020  1.080
 TL1  C15  C16   single    1.491  0.020  1.491
 TL1  C15  C17   aromatic  1.388  0.020  1.388
 TL1  C16  N3    double    1.277  0.020  1.277
 TL1  C16  N4    single    1.364  0.020  1.364
 TL1  N3   HN3   single    0.890  0.020  1.040
 TL1  N4   HN41  single    0.890  0.020  1.040
 TL1  N4   HN42  single    0.890  0.020  1.040
 TL1  C17  H17   single    0.930  0.020  1.080
 TL1  C18  O4    single    1.417  0.020  1.417
 TL1  C18  H181  single    0.970  0.020  1.090
 TL1  C18  H182  single    0.970  0.020  1.090
 TL1  O4   C19   single    1.401  0.020  1.401
 TL1  C19  H19   single    0.970  0.020  1.090
 TL1  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
 TL1  HN1   N1   C1    110.79  3.000
 TL1  C2    C1   N2    114.76  3.000
 TL1  C2    C1   N1    124.52  3.000
 TL1  N2    C1   N1    120.67  3.000
 TL1  HN22  N2   HN21  114.52  3.000
 TL1  HN22  N2   C1    118.49  3.000
 TL1  HN21  N2   C1    116.38  3.000
 TL1  C20   C2   C3    119.75  3.000
 TL1  C20   C2   C1    119.22  3.000
 TL1  C3    C2   C1    121.02  3.000
 TL1  H3    C3   C4    120.01  3.000
 TL1  H3    C3   C2    120.62  3.000
 TL1  C4    C3   C2    119.36  3.000
 TL1  H4    C4   C5    118.94  3.000
 TL1  H4    C4   C3    119.77  3.000
 TL1  C5    C4   C3    121.29  3.000
 TL1  H5    C5   C6    121.72  3.000
 TL1  H5    C5   C4    118.99  3.000
 TL1  C6    C5   C4    119.29  3.000
 TL1  C20   C6   O1    115.54  3.000
 TL1  C20   C6   C5    119.67  3.000
 TL1  O1    C6   C5    124.78  3.000
 TL1  C7    O1   C6    120.27  3.000
 TL1  H7    C7   C19   112.54  3.000
 TL1  H7    C7   C8    113.08  3.000
 TL1  C19   C7   C8     99.97  3.000
 TL1  H7    C7   O1    111.65  3.000
 TL1  C19   C7   O1    106.86  3.000
 TL1  C8    C7   O1    112.05  3.000
 TL1  H82   C8   H81   107.86  3.000
 TL1  H82   C8   O2    111.18  3.000
 TL1  H81   C8   O2    108.90  3.000
 TL1  H82   C8   C7    109.46  3.000
 TL1  H81   C8   C7    113.99  3.000
 TL1  O2    C8   C7    105.49  3.000
 TL1  C9    O2   C8    109.14  3.000
 TL1  H9    C9   C19   112.17  3.000
 TL1  H9    C9   C10   109.76  3.000
 TL1  C19   C9   C10   102.64  3.000
 TL1  H9    C9   O2    110.33  3.000
 TL1  C19   C9   O2    107.41  3.000
 TL1  C10   C9   O2    114.34  3.000
 TL1  H10   C10  C18   111.30  3.000
 TL1  H10   C10  O3    110.67  3.000
 TL1  C18   C10  O3    113.54  3.000
 TL1  H10   C10  C9    109.17  3.000
 TL1  C18   C10  C9    102.08  3.000
 TL1  O3    C10  C9    109.69  3.000
 TL1  C11   O3   C10   119.74  3.000
 TL1  C17   C11  C12   119.73  3.000
 TL1  C17   C11  O3    115.67  3.000
 TL1  C12   C11  O3    124.59  3.000
 TL1  H12   C12  C13   118.70  3.000
 TL1  H12   C12  C11   122.03  3.000
 TL1  C13   C12  C11   119.27  3.000
 TL1  H13   C13  C14   119.82  3.000
 TL1  H13   C13  C12   118.94  3.000
 TL1  C14   C13  C12   121.24  3.000
 TL1  H14   C14  C15   121.00  3.000
 TL1  H14   C14  C13   119.53  3.000
 TL1  C15   C14  C13   119.46  3.000
 TL1  C17   C15  C16   118.78  3.000
 TL1  C17   C15  C14   119.60  3.000
 TL1  C16   C15  C14   121.61  3.000
 TL1  N4    C16  N3    126.19  3.000
 TL1  N4    C16  C15   115.08  3.000
 TL1  N3    C16  C15   118.69  3.000
 TL1  HN3   N3   C16   111.17  3.000
 TL1  HN42  N4   HN41  113.71  3.000
 TL1  HN42  N4   C16   118.58  3.000
 TL1  HN41  N4   C16   117.40  3.000
 TL1  H17   C17  C15   119.81  3.000
 TL1  H17   C17  C11   119.51  3.000
 TL1  C15   C17  C11   120.68  3.000
 TL1  H182  C18  H181  108.11  3.000
 TL1  H182  C18  O4    110.81  3.000
 TL1  H181  C18  O4    108.63  3.000
 TL1  H182  C18  C10   109.58  3.000
 TL1  H181  C18  C10   113.42  3.000
 TL1  O4    C18  C10   106.30  3.000
 TL1  C19   O4   C18   110.39  3.000
 TL1  H19   C19  O4    110.39  3.000
 TL1  H19   C19  C9    112.24  3.000
 TL1  O4    C19  C9    108.24  3.000
 TL1  H19   C19  C7    108.60  3.000
 TL1  O4    C19  C7    114.65  3.000
 TL1  C9    C19  C7    102.55  3.000
 TL1  H20   C20  C6    118.85  3.000
 TL1  H20   C20  C2    120.49  3.000
 TL1  C6    C20  C2    120.64  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
 TL1  CONST_01  C5    C4   C3   C2      0.00   0.0  0
 TL1  CONST_02  C5    C6   C20  C2      0.00   0.0  0
 TL1  CONST_03  C6    C20  C2   C3      0.00   0.0  0
 TL1  CONST_04  C6    C5   C4   C3      0.00   0.0  0
 TL1  CONST_05  C20   C2   C3   C4      0.00   0.0  0
 TL1  CONST_06  C20   C6   C5   C4      0.00   0.0  0
 TL1  CONST_07  C14   C13  C12  C11     0.00   0.0  0
 TL1  CONST_08  C14   C15  C17  C11     0.00   0.0  0
 TL1  CONST_09  C15   C17  C11  C12     0.00   0.0  0
 TL1  CONST_10  C15   C14  C13  C12     0.00   0.0  0
 TL1  CONST_11  C17   C11  C12  C13     0.00   0.0  0
 TL1  CONST_12  C17   C15  C14  C13     0.00   0.0  0
 TL1  CONST_13  C4    C3   C2   C1    180.00   0.0  0
 TL1  CONST_14  C6    C20  C2   C1    180.00   0.0  0
 TL1  CONST_15  O1    C6   C20  C2    180.00   0.0  0
 TL1  CONST_16  O1    C6   C5   C4    180.00   0.0  0
 TL1  CONST_17  C13   C12  C11  O3    180.00   0.0  0
 TL1  CONST_18  C15   C17  C11  O3    180.00   0.0  0
 TL1  CONST_19  C16   C15  C17  C11   180.00   0.0  0
 TL1  CONST_20  C16   C15  C14  C13   180.00   0.0  0
 TL1  CONST_21  H4    C4   C3   C2    180.00   0.0  0
 TL1  CONST_22  H20   C20  C2   C3    180.00   0.0  0
 TL1  CONST_23  H5    C5   C4   C3    180.00   0.0  0
 TL1  CONST_24  H3    C3   C4   C5    180.00   0.0  0
 TL1  CONST_25  H13   C13  C12  C11   180.00   0.0  0
 TL1  CONST_26  H17   C17  C11  C12   180.00   0.0  0
 TL1  CONST_27  H14   C14  C13  C12   180.00   0.0  0
 TL1  CONST_28  H12   C12  C13  C14   180.00   0.0  0
 TL1  CONST_29  HN1   N1   C1   C2      0.00   0.0  0
 TL1  CONST_30  HN21  N2   C1   C2    180.00   0.0  0
 TL1  CONST_32  HN3   N3   C16  C15   180.00   0.0  0
 TL1  CONST_33  HN41  N4   C16  C15   180.00   0.0  0
 TL1  Var_01    C20   C6   O1   C7    175.61  30.0  3
 TL1  Var_02    C12   C11  O3   C10     0.74  30.0  2
 TL1  Var_03    H81   C8   O2   C9   -151.01  30.0  1
 TL1  Var_04    H181  C18  O4   C19  -141.57  30.0  1
 TL1  Var_05    C3    C2   C1   N1    141.44  30.0  2
 TL1  Var_06    N3    C16  C15  C14   152.38  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
 TL1  chir_01  C7   O1  C8   C19  positiv
 TL1  chir_02  C9   O2  C19  C10  negativ
 TL1  chir_03  C10  O3  C9   C18  positiv
 TL1  chir_04  C19  O4  C7   C9   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
 TL1  plan-1  C1    0.020
 TL1  plan-1  C2    0.020
 TL1  plan-1  C3    0.020
 TL1  plan-1  C4    0.020
 TL1  plan-1  C5    0.020
 TL1  plan-1  C6    0.020
 TL1  plan-1  O1    0.020
 TL1  plan-1  C20   0.020
 TL1  plan-1  H3    0.020
 TL1  plan-1  H4    0.020
 TL1  plan-1  H5    0.020
 TL1  plan-1  H20   0.020
 TL1  plan-2  O3    0.020
 TL1  plan-2  C11   0.020
 TL1  plan-2  C12   0.020
 TL1  plan-2  C13   0.020
 TL1  plan-2  C14   0.020
 TL1  plan-2  C15   0.020
 TL1  plan-2  C16   0.020
 TL1  plan-2  C17   0.020
 TL1  plan-2  H12   0.020
 TL1  plan-2  H13   0.020
 TL1  plan-2  H14   0.020
 TL1  plan-2  H17   0.020
 TL1  plan-3  N1    0.020
 TL1  plan-3  C1    0.020
 TL1  plan-3  N2    0.020
 TL1  plan-3  C2    0.020
 TL1  plan-3  HN1   0.020
 TL1  plan-3  HN21  0.020
 TL1  plan-3  HN22  0.020
 TL1  plan-4  C15   0.020
 TL1  plan-4  C16   0.020
 TL1  plan-4  N3    0.020
 TL1  plan-4  N4    0.020
 TL1  plan-4  HN3   0.020
 TL1  plan-4  HN41  0.020
 TL1  plan-4  HN42  0.020

