# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue Jul  7 19:38:25 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H](O)[C@H]2O)[C@H](N)[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
 XXX  XXX  '(1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside'  D-saccharide  48  22  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_XXX
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
 XXX  O3    O  OH1   0  -0.725   1.6271   2.3801   0.0569
 XXX  C4    C  CH1   0   0.022   2.0036   1.1142   0.5333
 XXX  C5    C  CH1   0   0.068   3.5252   1.0316   0.4612
 XXX  O4    O  OH1   0  -0.675   4.1162   2.0418   1.2442
 XXX  C6    C  CH1   0  -0.116   4.0124  -0.3308   0.9388
 XXX  N1    N  NH2   0  -0.786   5.4648  -0.3932   0.8929
 XXX  C7    C  CH2   0  -0.468   3.3270  -1.4271   0.1216
 XXX  C8    C  CH1   0  -0.092   1.8059  -1.3830   0.1974
 XXX  N2    N  NH2   0  -0.826   1.2492  -2.4155  -0.6634
 XXX  C9    C  CH1   0   0.034   1.3330  -0.0081  -0.2541
 XXX  O5    O  O2    0  -0.516  -0.0591   0.1395  -0.0397
 XXX  C10   C  CH1   0   0.264  -0.9300   0.2082  -1.1193
 XXX  O6    O  O2    0  -0.497  -1.6857  -0.9606  -1.2264
 XXX  C11   C  CH1   0   0.013  -2.4789  -1.2591  -0.0881
 XXX  C12   C  CH2   0  -0.307  -3.1165  -2.6159  -0.3254
 XXX  N3    N  NH2   0  -0.792  -2.0944  -3.6526  -0.3334
 XXX  C13   C  CH1   0   0.043  -3.4818  -0.1289   0.1375
 XXX  O7    O  OH1   0  -0.674  -4.2211  -0.4218   1.2978
 XXX  C14   C  CH1   0  -0.009  -2.7391   1.2011   0.2756
 XXX  O8    O  OH1   0  -0.679  -3.6768   2.2580   0.3803
 XXX  C15   C  CH1   0  -0.110  -1.8498   1.4209  -0.9418
 XXX  N4    N  NH2   0  -0.826  -1.0530   2.6320  -0.8068
 XXX  HO3   H  HOH1  0   0.463   0.6500   2.4248  -0.0779
 XXX  H4    H  HCH1  0   0.185   1.7149   0.9909   1.5928
 XXX  H5    H  HCH1  0   0.185   3.8210   1.1434  -0.5978
 XXX  HO4   H  HOH1  0   0.443   3.7025   2.8758   0.9965
 XXX  H6    H  HCH1  0   0.221   3.7172  -0.4444   1.9895
 XXX  HN11  H  HNH2  0   0.344   5.7640  -1.3009   1.2288
 XXX  HN12  H  HNH2  0   0.333   5.7730  -0.3484  -0.0728
 XXX  H71   H  HCH2  0   0.242   3.6806  -2.4031   0.4679
 XXX  H72   H  HCH2  0   0.218   3.6319  -1.3393  -0.9283
 XXX  H8    H  HCH1  0   0.199   1.5111  -1.5043   1.2534
 XXX  HN21  H  HNH2  0   0.341   1.5881  -3.3182  -0.3531
 XXX  HN22  H  HNH2  0   0.356   0.2394  -2.4626  -0.5781
 XXX  H9    H  HCH1  0   0.215   1.5655   0.1053  -1.3237
 XXX  H10   H  HCH1  0   0.243  -0.3754   0.2927  -2.0624
 XXX  H11   H  HCH1  0   0.217  -1.8455  -1.3362   0.8082
 XXX  H121  H  HCH2  0   0.223  -3.6208  -2.6076  -1.2959
 XXX  H122  H  HCH2  0   0.215  -3.8942  -2.7738   0.4301
 XXX  HN31  H  HNH2  0   0.342  -1.7750  -3.8144   0.6136
 XXX  HN32  H  HNH2  0   0.352  -2.5021  -4.5272  -0.6373
 XXX  H13   H  HCH1  0   0.203  -4.1394  -0.0655  -0.7453
 XXX  HO7   H  HOH1  0   0.450  -4.8641   0.2831   1.4276
 XXX  H14   H  HCH1  0   0.231  -2.1115   1.1622   1.1748
 XXX  HO8   H  HOH1  0   0.463  -3.6093   2.6535   1.2526
 XXX  H15   H  HCH1  0   0.234  -2.4986   1.4599  -1.8286
 XXX  HN41  H  HNH2  0   0.368  -0.7652   2.9481  -1.7257
 XXX  HN42  H  HNH2  0   0.366  -1.6299   3.3782  -0.4366

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
 XXX  O3   C4    single  1.404  0.020  1.404
 XXX  O3   HO3   single  0.850  0.020  0.980
 XXX  C4   C5    single  1.526  0.020  1.526
 XXX  C4   C9    single  1.526  0.020  1.526
 XXX  C4   H4    single  0.970  0.020  1.090
 XXX  C5   O4    single  1.408  0.020  1.408
 XXX  C5   C6    single  1.524  0.020  1.524
 XXX  C5   H5    single  0.970  0.020  1.090
 XXX  O4   HO4   single  0.850  0.020  0.980
 XXX  C6   N1    single  1.454  0.020  1.454
 XXX  C6   C7    single  1.530  0.020  1.530
 XXX  C6   H6    single  0.970  0.020  1.090
 XXX  N1   HN11  single  0.890  0.020  1.040
 XXX  N1   HN12  single  0.890  0.020  1.040
 XXX  C7   C8    single  1.524  0.020  1.524
 XXX  C7   H71   single  0.970  0.020  1.090
 XXX  C7   H72   single  0.970  0.020  1.090
 XXX  C8   N2    single  1.455  0.020  1.455
 XXX  C8   C9    single  1.522  0.020  1.522
 XXX  C8   H8    single  0.970  0.020  1.090
 XXX  N2   HN21  single  0.890  0.020  1.040
 XXX  N2   HN22  single  0.890  0.020  1.040
 XXX  C9   O5    single  1.416  0.020  1.416
 XXX  C9   H9    single  0.970  0.020  1.090
 XXX  O5   C10   single  1.389  0.020  1.389
 XXX  C10  O6    single  1.396  0.020  1.396
 XXX  C10  C15   single  1.532  0.020  1.532
 XXX  C10  H10   single  0.970  0.020  1.090
 XXX  O6   C11   single  1.419  0.020  1.419
 XXX  C11  C12   single  1.518  0.020  1.518
 XXX  C11  C13   single  1.528  0.020  1.528
 XXX  C11  H11   single  0.970  0.020  1.090
 XXX  C12  N3    single  1.456  0.020  1.456
 XXX  C12  H121  single  0.970  0.020  1.090
 XXX  C12  H122  single  0.970  0.020  1.090
 XXX  N3   HN31  single  0.890  0.020  1.040
 XXX  N3   HN32  single  0.890  0.020  1.040
 XXX  C13  O7    single  1.407  0.020  1.407
 XXX  C13  C14   single  1.530  0.020  1.530
 XXX  C13  H13   single  0.970  0.020  1.090
 XXX  O7   HO7   single  0.850  0.020  0.980
 XXX  C14  O8    single  1.417  0.020  1.417
 XXX  C14  C15   single  1.524  0.020  1.524
 XXX  C14  H14   single  0.970  0.020  1.090
 XXX  O8   HO8   single  0.850  0.020  0.980
 XXX  C15  N4    single  1.456  0.020  1.456
 XXX  C15  H15   single  0.970  0.020  1.090
 XXX  N4   HN41  single  0.890  0.020  1.040
 XXX  N4   HN42  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
 XXX  HO3   O3   C4    110.64  3.000
 XXX  H4    C4   C9    107.33  3.000
 XXX  H4    C4   C5    107.45  3.000
 XXX  C9    C4   C5    111.97  3.000
 XXX  H4    C4   O3    110.85  3.000
 XXX  C9    C4   O3    111.72  3.000
 XXX  C5    C4   O3    107.47  3.000
 XXX  H5    C5   C6    107.77  3.000
 XXX  H5    C5   O4    110.36  3.000
 XXX  C6    C5   O4    109.44  3.000
 XXX  H5    C5   C4    107.87  3.000
 XXX  C6    C5   C4    110.64  3.000
 XXX  O4    C5   C4    110.70  3.000
 XXX  HO4   O4   C5    107.32  3.000
 XXX  H6    C6   C7    108.47  3.000
 XXX  H6    C6   N1    107.13  3.000
 XXX  C7    C6   N1    113.57  3.000
 XXX  H6    C6   C5    107.86  3.000
 XXX  C7    C6   C5    109.27  3.000
 XXX  N1    C6   C5    110.35  3.000
 XXX  HN12  N1   HN11  105.39  3.000
 XXX  HN12  N1   C6    109.36  3.000
 XXX  HN11  N1   C6    108.84  3.000
 XXX  H72   C7   H71   106.53  3.000
 XXX  H72   C7   C8    108.83  3.000
 XXX  H71   C7   C8    109.43  3.000
 XXX  H72   C7   C6    109.24  3.000
 XXX  H71   C7   C6    108.99  3.000
 XXX  C8    C7   C6    113.58  3.000
 XXX  H8    C8   C9    107.47  3.000
 XXX  H8    C8   N2    112.71  3.000
 XXX  C9    C8   N2    110.28  3.000
 XXX  H8    C8   C7    108.13  3.000
 XXX  C9    C8   C7    108.76  3.000
 XXX  N2    C8   C7    109.39  3.000
 XXX  HN22  N2   HN21  105.42  3.000
 XXX  HN22  N2   C8    111.35  3.000
 XXX  HN21  N2   C8    108.86  3.000
 XXX  H9    C9   O5    110.13  3.000
 XXX  H9    C9   C8    108.40  3.000
 XXX  O5    C9   C8    110.77  3.000
 XXX  H9    C9   C4    109.44  3.000
 XXX  O5    C9   C4    106.09  3.000
 XXX  C8    C9   C4    112.00  3.000
 XXX  C10   O5   C9    120.26  3.000
 XXX  H10   C10  C15   109.99  3.000
 XXX  H10   C10  O6    105.79  3.000
 XXX  C15   C10  O6    110.28  3.000
 XXX  H10   C10  O5    110.80  3.000
 XXX  C15   C10  O5    109.00  3.000
 XXX  O6    C10  O5    110.96  3.000
 XXX  C11   O6   C10   114.65  3.000
 XXX  H11   C11  C13   108.02  3.000
 XXX  H11   C11  C12   107.86  3.000
 XXX  C13   C11  C12   114.12  3.000
 XXX  H11   C11  O6    110.27  3.000
 XXX  C13   C11  O6    109.25  3.000
 XXX  C12   C11  O6    107.30  3.000
 XXX  H122  C12  H121  106.61  3.000
 XXX  H122  C12  N3    113.55  3.000
 XXX  H121  C12  N3    108.92  3.000
 XXX  H122  C12  C11   108.61  3.000
 XXX  H121  C12  C11   109.00  3.000
 XXX  N3    C12  C11   110.02  3.000
 XXX  HN32  N3   HN31  105.66  3.000
 XXX  HN32  N3   C12   109.53  3.000
 XXX  HN31  N3   C12   109.28  3.000
 XXX  H13   C13  C14   108.17  3.000
 XXX  H13   C13  O7    111.03  3.000
 XXX  C14   C13  O7    111.21  3.000
 XXX  H13   C13  C11   108.41  3.000
 XXX  C14   C13  C11   109.75  3.000
 XXX  O7    C13  C11   108.23  3.000
 XXX  HO7   O7   C13   108.05  3.000
 XXX  H14   C14  C15   109.04  3.000
 XXX  H14   C14  O8    110.15  3.000
 XXX  C15   C14  O8    109.74  3.000
 XXX  H14   C14  C13   108.72  3.000
 XXX  C15   C14  C13   109.67  3.000
 XXX  O8    C14  C13   109.51  3.000
 XXX  HO8   O8   C14   109.14  3.000
 XXX  H15   C15  N4    111.60  3.000
 XXX  H15   C15  C14   107.77  3.000
 XXX  N4    C15  C14   111.43  3.000
 XXX  H15   C15  C10   106.79  3.000
 XXX  N4    C15  C10   109.91  3.000
 XXX  C14   C15  C10   109.19  3.000
 XXX  HN42  N4   HN41  105.27  3.000
 XXX  HN42  N4   C15   109.56  3.000
 XXX  HN41  N4   C15   109.31  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
 XXX  Var_01  HN31  N3  C12  C11  73.70  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
 XXX  chir_01  C4   O3  C5   C9   positiv
 XXX  chir_02  C5   O4  C4   C6   positiv
 XXX  chir_03  C6   N1  C7   C5   positiv
 XXX  chir_04  C8   N2  C9   C7   positiv
 XXX  chir_05  C9   O5  C4   C8   negativ
 XXX  chir_06  C10  O6  O5   C15  positiv
 XXX  chir_07  C11  O6  C12  C13  positiv
 XXX  chir_08  C13  O7  C11  C14  positiv
 XXX  chir_09  C14  O8  C13  C15  negativ
 XXX  chir_10  C15  N4  C14  C10  positiv

