# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 01:55:22 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: 1,4:3,6-dianhydro-5-O-(3-carbamimidoylphenyl)-2-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
 TL2  TL2  1,4:3,6-dianhydro-5-O-(3-carbamimidoylphenyl)-2-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_TL2
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
 TL2  N     N  N     0  -0.655  -7.5156   2.2844   1.1654
 TL2  C1    C  C     0   0.332  -7.1795   1.4025   0.3031
 TL2  C2    C  CR6   0   0.025  -5.8488   0.7526   0.4263
 TL2  C3    C  CR16  0  -0.257  -5.2020   0.7297   1.6636
 TL2  C4    C  CR16  0  -0.341  -3.9664   0.1353   1.8122
 TL2  C5    C  CR16  0  -0.279  -5.2016   0.1737  -0.6593
 TL2  C6    C  CR16  0  -0.364  -3.9540  -0.4231  -0.5283
 TL2  C7    C  CR6   0   0.392  -3.3306  -0.4522   0.7154
 TL2  O8    O  O2    0  -0.483  -2.1369  -1.0264   0.9624
 TL2  C9    C  CH1   0  -0.048  -1.4060  -1.6144  -0.1003
 TL2  C10   C  CH2   0  -0.210  -0.6838  -0.5647  -0.9301
 TL2  O11   O  O2    0  -0.481   0.4376  -0.1915  -0.1502
 TL2  C11   C  CR15  0  -0.024  -0.2399  -2.3552   0.5547
 TL2  C12   C  CR15  0  -0.048   0.8530  -1.2789   0.6459
 TL2  C13   C  CR15  0  -0.035   2.0812  -1.9917   0.0577
 TL2  O14   O  O2    0  -0.480   2.9478  -1.1652  -0.6732
 TL2  O15   O  O     0  -0.489   0.2505  -3.3921  -0.2719
 TL2  C16   C  CR16  0  -0.376   3.8759  -0.1852   1.3476
 TL2  C17   C  CH2   0  -0.194   1.4599  -3.0087  -0.8918
 TL2  C18   C  CR6   0   0.420   3.7677  -0.3028  -0.0355
 TL2  C20   C  CR16  0  -0.388   4.5561   0.4959  -0.8600
 TL2  N22   N  N     0  -0.651   5.8057   2.5084  -2.4007
 TL2  N23   N  NH2   0  -0.821   7.4518   2.6926  -0.7241
 TL2  C24   C  CR16  0  -0.230   4.7741   0.7296   1.8822
 TL2  C25   C  CR16  0  -0.316   5.5657   1.5209   1.0670
 TL2  C26   C  CR6   0   0.062   5.4568   1.4018  -0.3193
 TL2  N27   N  NH2   0  -0.824  -7.9211   1.0200  -0.7803
 TL2  HN    H  H     0   0.322  -8.4578   2.6247   0.9938
 TL2  H3    H  HCR6  0   0.257  -5.6837   1.1787   2.5216
 TL2  H4    H  HCR6  0   0.266  -3.4845   0.1121   2.7816
 TL2  H5    H  HCR6  0   0.262  -5.6494   0.1957  -1.6447
 TL2  H6    H  HCR6  0   0.284  -3.4951  -0.8517  -1.4083
 TL2  H9    H  HCH1  0   0.281  -2.0316  -2.2880  -0.6930
 TL2  H101  H  HCH2  0   0.232  -0.3906  -0.9912  -1.8969
 TL2  H102  H  HCH2  0   0.263  -1.2791   0.3271  -1.1335
 TL2  H11   H  HCR5  0   0.278  -0.5268  -2.7789   1.5195
 TL2  H12   H  HCR5  0   0.278   1.0165  -0.9252   1.6652
 TL2  H13   H  HCR5  0   0.261   2.6120  -2.5161   0.8616
 TL2  H16   H  HCR6  0   0.282   3.2822  -0.7864   2.0218
 TL2  H171  H  HCH2  0   0.223   1.2922  -2.5593  -1.8786
 TL2  H172  H  HCH2  0   0.258   2.0791  -3.8960  -1.0270
 TL2  H20   H  HCR6  0   0.262   4.4696   0.4017  -1.9348
 TL2  H22   H  H     0   0.324   6.4641   3.0606  -2.9438
 TL2  H231  H  HNH2  0   0.396   7.9036   2.1453  -0.0102
 TL2  H232  H  HNH2  0   0.392   8.0927   3.1465  -1.3553
 TL2  H24   H  HCR6  0   0.265   4.8481   0.8249   2.9575
 TL2  H25   H  HCR6  0   0.257   6.2415   2.2379   1.5139
 TL2  H271  H  HNH2  0   0.393  -7.7958   0.0864  -1.1363
 TL2  H272  H  HNH2  0   0.390  -8.8797   1.3296  -0.8094
 TL2  C21   C  C     0   0.338   6.2736   2.2401  -1.2427

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
 TL2  N    C1    double    1.278  0.020  1.278
 TL2  N    HN    single    0.890  0.020  1.040
 TL2  C1   C2    single    1.486  0.020  1.486
 TL2  C1   N27   single    1.367  0.020  1.367
 TL2  C2   C3    aromatic  1.396  0.020  1.396
 TL2  C2   C5    aromatic  1.390  0.020  1.390
 TL2  C3   C4    aromatic  1.379  0.020  1.379
 TL2  C3   H3    single    0.930  0.020  1.080
 TL2  C4   C7    aromatic  1.397  0.020  1.397
 TL2  C4   H4    single    0.930  0.020  1.080
 TL2  C5   C6    aromatic  1.389  0.020  1.389
 TL2  C5   H5    single    0.930  0.020  1.080
 TL2  C6   C7    aromatic  1.392  0.020  1.392
 TL2  C6   H6    single    0.930  0.020  1.080
 TL2  C7   O8    single    1.347  0.020  1.347
 TL2  O8   C9    single    1.417  0.020  1.417
 TL2  C9   C10   single    1.520  0.020  1.520
 TL2  C9   C11   single    1.529  0.020  1.529
 TL2  C9   H9    single    0.970  0.020  1.090
 TL2  C10  O11   single    1.416  0.020  1.416
 TL2  C10  H101  single    0.970  0.020  1.090
 TL2  C10  H102  single    0.970  0.020  1.090
 TL2  O11  C12   single    1.410  0.020  1.410
 TL2  C11  C12   single    1.537  0.020  1.537
 TL2  C11  O15   single    1.414  0.020  1.414
 TL2  C11  H11   single    0.970  0.020  1.090
 TL2  C12  C13   single    1.537  0.020  1.537
 TL2  C12  H12   single    0.970  0.020  1.090
 TL2  C13  O14   single    1.403  0.020  1.403
 TL2  C13  C17   single    1.524  0.020  1.524
 TL2  C13  H13   single    0.970  0.020  1.090
 TL2  O14  C18   single    1.350  0.020  1.350
 TL2  O15  C17   single    1.412  0.020  1.412
 TL2  C16  C18   aromatic  1.392  0.020  1.392
 TL2  C16  C24   aromatic  1.389  0.020  1.389
 TL2  C16  H16   single    0.930  0.020  1.080
 TL2  C17  H171  single    0.970  0.020  1.090
 TL2  C17  H172  single    0.970  0.020  1.090
 TL2  C18  C20   aromatic  1.393  0.020  1.393
 TL2  C20  C26   aromatic  1.387  0.020  1.387
 TL2  C20  H20   single    0.930  0.020  1.080
 TL2  C21  N22   double    1.277  0.020  1.277
 TL2  C21  N23   single    1.364  0.020  1.364
 TL2  C21  C26   single    1.491  0.020  1.491
 TL2  N22  H22   single    0.890  0.020  1.040
 TL2  N23  H231  single    0.890  0.020  1.040
 TL2  N23  H232  single    0.890  0.020  1.040
 TL2  C24  C25   aromatic  1.385  0.020  1.385
 TL2  C24  H24   single    0.930  0.020  1.080
 TL2  C25  C26   aromatic  1.396  0.020  1.396
 TL2  C25  H25   single    0.930  0.020  1.080
 TL2  N27  H271  single    0.890  0.020  1.040
 TL2  N27  H272  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
 TL2  HN    N    C1    111.15  3.000
 TL2  N27   C1   C2    115.40  3.000
 TL2  N27   C1   N     125.79  3.000
 TL2  C2    C1   N     118.76  3.000
 TL2  C5    C2   C3    118.00  3.000
 TL2  C5    C2   C1    122.29  3.000
 TL2  C3    C2   C1    119.70  3.000
 TL2  H3    C3   C4    119.51  3.000
 TL2  H3    C3   C2    119.33  3.000
 TL2  C4    C3   C2    121.17  3.000
 TL2  H4    C4   C7    119.42  3.000
 TL2  H4    C4   C3    120.29  3.000
 TL2  C7    C4   C3    120.29  3.000
 TL2  H5    C5   C6    117.78  3.000
 TL2  H5    C5   C2    120.65  3.000
 TL2  C6    C5   C2    121.56  3.000
 TL2  H6    C6   C7    121.94  3.000
 TL2  H6    C6   C5    118.34  3.000
 TL2  C7    C6   C5    119.71  3.000
 TL2  O8    C7   C6    124.72  3.000
 TL2  O8    C7   C4    116.00  3.000
 TL2  C6    C7   C4    119.27  3.000
 TL2  C9    O8   C7    119.75  3.000
 TL2  H9    C9   C11   111.72  3.000
 TL2  H9    C9   C10   113.65  3.000
 TL2  C11   C9   C10   101.89  3.000
 TL2  H9    C9   O8    111.52  3.000
 TL2  C11   C9   O8    105.85  3.000
 TL2  C10   C9   O8    111.57  3.000
 TL2  H102  C10  H101  107.42  3.000
 TL2  H102  C10  O11   108.62  3.000
 TL2  H101  C10  O11   112.10  3.000
 TL2  H102  C10  C9    114.00  3.000
 TL2  H101  C10  C9    109.86  3.000
 TL2  O11   C10  C9    104.92  3.000
 TL2  C12   O11  C10   109.94  3.000
 TL2  H11   C11  O15   108.85  3.000
 TL2  H11   C11  C12   113.97  3.000
 TL2  O15   C11  C12   107.56  3.000
 TL2  H11   C11  C9    111.47  3.000
 TL2  O15   C11  C9    111.68  3.000
 TL2  C12   C11  C9    103.21  3.000
 TL2  H12   C12  C13   112.84  3.000
 TL2  H12   C12  C11   112.89  3.000
 TL2  C13   C12  C11   102.76  3.000
 TL2  H12   C12  O11   108.75  3.000
 TL2  C13   C12  O11   112.15  3.000
 TL2  C11   C12  O11   107.28  3.000
 TL2  H13   C13  C17   109.57  3.000
 TL2  H13   C13  O14   111.38  3.000
 TL2  C17   C13  O14   108.68  3.000
 TL2  H13   C13  C12   109.15  3.000
 TL2  C17   C13  C12   102.84  3.000
 TL2  O14   C13  C12   114.82  3.000
 TL2  C18   O14  C13   120.36  3.000
 TL2  C17   O15  C11   110.77  3.000
 TL2  H16   C16  C24   118.78  3.000
 TL2  H16   C16  C18   122.00  3.000
 TL2  C24   C16  C18   119.22  3.000
 TL2  H172  C17  H171  107.98  3.000
 TL2  H172  C17  O15   108.65  3.000
 TL2  H171  C17  O15   112.03  3.000
 TL2  H172  C17  C13   112.88  3.000
 TL2  H171  C17  C13   110.45  3.000
 TL2  O15   C17  C13   104.88  3.000
 TL2  C20   C18  C16   119.72  3.000
 TL2  C20   C18  O14   115.50  3.000
 TL2  C16   C18  O14   124.77  3.000
 TL2  H20   C20  C26   119.72  3.000
 TL2  H20   C20  C18   119.53  3.000
 TL2  C26   C20  C18   120.75  3.000
 TL2  H22   N22  C21   111.17  3.000
 TL2  H232  N23  H231  113.81  3.000
 TL2  H232  N23  C21   117.42  3.000
 TL2  H231  N23  C21   118.48  3.000
 TL2  H24   C24  C25   119.71  3.000
 TL2  H24   C24  C16   118.99  3.000
 TL2  C25   C24  C16   121.30  3.000
 TL2  H25   C25  C26   121.04  3.000
 TL2  H25   C25  C24   119.52  3.000
 TL2  C26   C25  C24   119.43  3.000
 TL2  C25   C26  C21   121.63  3.000
 TL2  C25   C26  C20   119.58  3.000
 TL2  C21   C26  C20   118.78  3.000
 TL2  H272  N27  H271  113.14  3.000
 TL2  H272  N27  C1    116.93  3.000
 TL2  H271  N27  C1    118.16  3.000
 TL2  C26   C21  N23   115.10  3.000
 TL2  C26   C21  N22   118.61  3.000
 TL2  N23   C21  N22   126.24  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
 TL2  CONST_01  C7    C4   C3   C2     0.00   0.0  0
 TL2  CONST_02  C7    C6   C5   C2     0.00   0.0  0
 TL2  CONST_03  C6    C5   C2   C3     0.00   0.0  0
 TL2  CONST_04  C6    C7   C4   C3     0.00   0.0  0
 TL2  CONST_05  C5    C2   C3   C4     0.00   0.0  0
 TL2  CONST_06  C5    C6   C7   C4     0.00   0.0  0
 TL2  CONST_07  C26   C20  C18  C16    0.00   0.0  0
 TL2  CONST_08  C26   C25  C24  C16    0.00   0.0  0
 TL2  CONST_09  C25   C24  C16  C18    0.00   0.0  0
 TL2  CONST_10  C25   C26  C20  C18    0.00   0.0  0
 TL2  CONST_11  C24   C16  C18  C20    0.00   0.0  0
 TL2  CONST_12  C24   C25  C26  C20    0.00   0.0  0
 TL2  CONST_13  C4    C3   C2   C1   180.00   0.0  0
 TL2  CONST_14  C6    C5   C2   C1   180.00   0.0  0
 TL2  CONST_15  O8    C7   C4   C3   180.00   0.0  0
 TL2  CONST_16  O8    C7   C6   C5   180.00   0.0  0
 TL2  CONST_17  C24   C16  C18  O14  180.00   0.0  0
 TL2  CONST_18  C26   C20  C18  O14  180.00   0.0  0
 TL2  CONST_19  C21   C26  C20  C18  180.00   0.0  0
 TL2  CONST_20  C24   C25  C26  C21  180.00   0.0  0
 TL2  CONST_21  H4    C4   C3   C2   180.00   0.0  0
 TL2  CONST_22  H6    C6   C5   C2   180.00   0.0  0
 TL2  CONST_23  H5    C5   C2   C3   180.00   0.0  0
 TL2  CONST_24  H3    C3   C2   C5   180.00   0.0  0
 TL2  CONST_25  H20   C20  C18  C16  180.00   0.0  0
 TL2  CONST_26  H25   C25  C24  C16  180.00   0.0  0
 TL2  CONST_27  H24   C24  C16  C18  180.00   0.0  0
 TL2  CONST_28  H16   C16  C18  C20  180.00   0.0  0
 TL2  CONST_29  HN    N    C1   C2   180.00   0.0  0
 TL2  CONST_31  H272  N27  C1   C2   180.00   0.0  0
 TL2  CONST_32  H22   N22  C21  C26  180.00   0.0  0
 TL2  CONST_34  H232  N23  C21  C26  180.00   0.0  0
 TL2  Var_01    C13   C17  O15  C11   27.23  30.0  1
 TL2  Var_02    C16   C18  O14  C13    2.64  30.0  2
 TL2  Var_03    H101  C10  O11  C12  -89.39  30.0  1
 TL2  Var_04    C3    C2   C1   N     22.60  30.0  2
 TL2  Var_05    N22   C21  C26  C20   27.15  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
 TL2  chir_01  C9   O8   C10  C11  negativ
 TL2  chir_02  C11  O15  C9   C12  positiv
 TL2  chir_03  C12  O11  C13  C11  positiv
 TL2  chir_04  C13  O14  C12  C17  negativ

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
 TL2  plan-1  C1    0.020
 TL2  plan-1  C2    0.020
 TL2  plan-1  C3    0.020
 TL2  plan-1  C4    0.020
 TL2  plan-1  C5    0.020
 TL2  plan-1  C6    0.020
 TL2  plan-1  C7    0.020
 TL2  plan-1  O8    0.020
 TL2  plan-1  H3    0.020
 TL2  plan-1  H4    0.020
 TL2  plan-1  H5    0.020
 TL2  plan-1  H6    0.020
 TL2  plan-2  O14   0.020
 TL2  plan-2  C16   0.020
 TL2  plan-2  C18   0.020
 TL2  plan-2  C20   0.020
 TL2  plan-2  C24   0.020
 TL2  plan-2  C25   0.020
 TL2  plan-2  C26   0.020
 TL2  plan-2  H16   0.020
 TL2  plan-2  H20   0.020
 TL2  plan-2  H24   0.020
 TL2  plan-2  H25   0.020
 TL2  plan-2  C21   0.020
 TL2  plan-3  N     0.020
 TL2  plan-3  C1    0.020
 TL2  plan-3  C2    0.020
 TL2  plan-3  N27   0.020
 TL2  plan-3  HN    0.020
 TL2  plan-3  H271  0.020
 TL2  plan-3  H272  0.020
 TL2  plan-4  N22   0.020
 TL2  plan-4  N23   0.020
 TL2  plan-4  C26   0.020
 TL2  plan-4  H22   0.020
 TL2  plan-4  H231  0.020
 TL2  plan-4  H232  0.020
 TL2  plan-4  C21   0.020

