# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 13:27:50 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: 2,4-diamino-1,2,4,6-tetradeoxy-1,6-diphenyl-D-glucitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccccc1)[C@@H](O)[C@H](N)[C@H](O)Cc2ccccc2
#
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
 078  078  2,4-diamino-1,2,4,6-tetradeoxy-1,6-diphenyl-D-glucitol  ligand  46  22  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_078
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
 078  C27  C  CR16  0  -0.310  -5.1374   0.9697  -0.1159
 078  C28  C  CR16  0  -0.240  -6.4034   0.7962   0.4276
 078  C29  C  CR16  0  -0.275  -6.9513  -0.4766   0.5228
 078  C30  C  CR16  0  -0.242  -6.2238  -1.5692   0.0692
 078  C31  C  CR16  0  -0.321  -4.9565  -1.3893  -0.4696
 078  C26  C  CR6   0   0.162  -4.3954  -0.1185  -0.5715
 078  C25  C  CH2   0  -0.557  -3.0146   0.0824  -1.1250
 078  C24  C  CH1   0   0.059  -1.9486   0.0939  -0.0235
 078  O5   O  OH1   0  -0.658  -1.9849  -1.0984   0.7274
 078  C23  C  CH1   0  -0.151  -0.5449   0.3734  -0.5872
 078  N3   N  NH2   0  -0.819  -0.5722   1.6163  -1.3465
 078  C22  C  CH1   0   0.043   0.5315   0.3177   0.5140
 078  O4   O  OH1   0  -0.672   0.3889   1.3719   1.4456
 078  C14  C  CH1   0  -0.097   1.9597   0.2458  -0.0500
 078  C15  C  CH2   0  -0.526   2.9423  -0.2266   1.0379
 078  C16  C  CR6   0   0.134   4.3439  -0.3666   0.5187
 078  C17  C  CR16  0  -0.305   4.7115  -1.4835  -0.2317
 078  C18  C  CR16  0  -0.239   5.9919  -1.6046  -0.7526
 078  C19  C  CR16  0  -0.274   6.9320  -0.6049  -0.5318
 078  C20  C  CR16  0  -0.240   6.5797   0.5122   0.2130
 078  C21  C  CR16  0  -0.323   5.2953   0.6289   0.7303
 078  N2   N  NH2   0  -0.799   2.3398   1.5039  -0.6791
 078  H1   H  HCR6  0   0.243  -4.7215   1.9680  -0.1944
 078  H2   H  HCR6  0   0.251  -6.9637   1.6566   0.7713
 078  H3   H  HCR6  0   0.252  -7.9390  -0.6165   0.9429
 078  H4   H  HCR6  0   0.251  -6.6431  -2.5651   0.1364
 078  H5   H  HCR6  0   0.242  -4.4026  -2.2490  -0.8278
 078  H6   H  HCH2  0   0.242  -2.7776  -0.7108  -1.8427
 078  H7   H  HCH2  0   0.257  -2.9658   1.0216  -1.6769
 078  H8   H  HCH1  0   0.225  -2.1937   0.8901   0.6895
 078  H9   H  HOH1  0   0.442  -1.8222  -1.8393   0.1329
 078  H10  H  HCH1  0   0.217  -0.3123  -0.4386  -1.2908
 078  H11  H  HNH2  0   0.333  -0.9975   2.3617  -0.8068
 078  H12  H  HNH2  0   0.364   0.3839   1.9008  -1.5408
 078  H14  H  HCH1  0   0.229   0.3780  -0.6028   1.0835
 078  H15  H  HOH1  0   0.432   0.3440   2.2019   0.9579
 078  H16  H  HCH1  0   0.237   1.9486  -0.5154  -0.8382
 078  H17  H  HCH2  0   0.243   2.9227   0.4817   1.8712
 078  H18  H  HCH2  0   0.242   2.5962  -1.1877   1.4290
 078  H19  H  HCR6  0   0.245   3.9858  -2.2700  -0.4066
 078  H20  H  HCR6  0   0.252   6.2585  -2.4815  -1.3290
 078  H21  H  HCR6  0   0.253   7.9322  -0.6980  -0.9349
 078  H22  H  HCR6  0   0.253   7.3064   1.2939   0.3949
 078  H23  H  HCR6  0   0.245   5.0310   1.5020   1.3160
 078  H24  H  HNH2  0   0.342   2.5354   2.2033   0.0287
 078  H25  H  HNH2  0   0.361   3.2037   1.3858  -1.1933

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
 078  C29  C28  aromatic  1.389  0.020  1.389
 078  C29  C30  aromatic  1.389  0.020  1.389
 078  C28  C27  aromatic  1.389  0.020  1.389
 078  C30  C31  aromatic  1.389  0.020  1.389
 078  C27  C26  aromatic  1.394  0.020  1.394
 078  C31  C26  aromatic  1.393  0.020  1.393
 078  C26  C25  single    1.501  0.020  1.501
 078  O5   C24  single    1.410  0.020  1.410
 078  C25  C24  single    1.533  0.020  1.533
 078  C24  C23  single    1.538  0.020  1.538
 078  C23  N3   single    1.457  0.020  1.457
 078  C23  C22  single    1.541  0.020  1.541
 078  C22  C14  single    1.537  0.020  1.537
 078  C22  O4   single    1.414  0.020  1.414
 078  C14  C15  single    1.540  0.020  1.540
 078  C14  N2   single    1.457  0.020  1.457
 078  C17  C18  aromatic  1.388  0.020  1.388
 078  C17  C16  aromatic  1.395  0.020  1.395
 078  C15  C16  single    1.501  0.020  1.501
 078  C18  C19  aromatic  1.390  0.020  1.390
 078  C16  C21  aromatic  1.393  0.020  1.393
 078  C19  C20  aromatic  1.388  0.020  1.388
 078  C21  C20  aromatic  1.390  0.020  1.390
 078  C27  H1   single    0.930  0.020  1.080
 078  C28  H2   single    0.930  0.020  1.080
 078  C29  H3   single    0.930  0.020  1.080
 078  C30  H4   single    0.930  0.020  1.080
 078  C31  H5   single    0.930  0.020  1.080
 078  C25  H6   single    0.970  0.020  1.090
 078  C25  H7   single    0.970  0.020  1.090
 078  C24  H8   single    0.970  0.020  1.090
 078  O5   H9   single    0.850  0.020  0.980
 078  C23  H10  single    0.970  0.020  1.090
 078  N3   H11  single    0.890  0.020  1.040
 078  N3   H12  single    0.890  0.020  1.040
 078  C22  H14  single    0.970  0.020  1.090
 078  O4   H15  single    0.850  0.020  0.980
 078  C14  H16  single    0.970  0.020  1.090
 078  C15  H17  single    0.970  0.020  1.090
 078  C15  H18  single    0.970  0.020  1.090
 078  C17  H19  single    0.930  0.020  1.080
 078  C18  H20  single    0.930  0.020  1.080
 078  C19  H21  single    0.930  0.020  1.080
 078  C20  H22  single    0.930  0.020  1.080
 078  C21  H23  single    0.930  0.020  1.080
 078  N2   H24  single    0.890  0.020  1.040
 078  N2   H25  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
 078  H1   C27  C26  119.41  3.000
 078  H1   C27  C28  119.54  3.000
 078  C26  C27  C28  121.05  3.000
 078  H2   C28  C29  120.15  3.000
 078  H2   C28  C27  119.79  3.000
 078  C29  C28  C27  120.06  3.000
 078  H3   C29  C30  120.21  3.000
 078  H3   C29  C28  120.33  3.000
 078  C30  C29  C28  119.46  3.000
 078  H4   C30  C31  119.78  3.000
 078  H4   C30  C29  120.03  3.000
 078  C31  C30  C29  120.19  3.000
 078  H5   C31  C26  119.58  3.000
 078  H5   C31  C30  119.47  3.000
 078  C26  C31  C30  120.94  3.000
 078  C25  C26  C31  121.31  3.000
 078  C25  C26  C27  120.38  3.000
 078  C31  C26  C27  118.30  3.000
 078  H7   C25  H6   106.40  3.000
 078  H7   C25  C24  109.03  3.000
 078  H6   C25  C24  109.01  3.000
 078  H7   C25  C26  110.06  3.000
 078  H6   C25  C26  110.09  3.000
 078  C24  C25  C26  112.07  3.000
 078  H8   C24  C23  108.08  3.000
 078  H8   C24  O5   105.19  3.000
 078  C23  C24  O5   111.86  3.000
 078  H8   C24  C25  108.50  3.000
 078  C23  C24  C25  111.87  3.000
 078  O5   C24  C25  111.01  3.000
 078  H9   O5   C24  108.51  3.000
 078  H10  C23  C22  106.43  3.000
 078  H10  C23  N3   107.49  3.000
 078  C22  C23  N3   114.61  3.000
 078  H10  C23  C24  107.07  3.000
 078  C22  C23  C24  111.65  3.000
 078  N3   C23  C24  109.21  3.000
 078  H12  N3   H11  106.90  3.000
 078  H12  N3   C23  108.72  3.000
 078  H11  N3   C23  110.96  3.000
 078  H14  C22  C14  106.39  3.000
 078  H14  C22  O4   105.69  3.000
 078  C14  C22  O4   111.73  3.000
 078  H14  C22  C23  107.74  3.000
 078  O4   C22  C23  111.92  3.000
 078  C14  C22  C23  112.86  3.000
 078  H15  O4   C22  108.27  3.000
 078  H16  C14  N2   106.97  3.000
 078  H16  C14  C15  107.55  3.000
 078  N2   C14  C15  113.79  3.000
 078  H16  C14  C22  106.67  3.000
 078  N2   C14  C22  111.12  3.000
 078  C15  C14  C22  110.36  3.000
 078  H18  C15  H17  106.91  3.000
 078  H18  C15  C16  109.70  3.000
 078  H17  C15  C16  109.91  3.000
 078  H18  C15  C14  108.67  3.000
 078  H17  C15  C14  109.15  3.000
 078  C16  C15  C14  112.33  3.000
 078  C21  C16  C17  118.29  3.000
 078  C21  C16  C15  121.23  3.000
 078  C17  C16  C15  120.45  3.000
 078  H19  C17  C18  119.59  3.000
 078  H19  C17  C16  119.42  3.000
 078  C18  C17  C16  121.00  3.000
 078  H20  C18  C19  120.04  3.000
 078  H20  C18  C17  119.85  3.000
 078  C19  C18  C17  120.11  3.000
 078  H21  C19  C20  120.24  3.000
 078  H21  C19  C18  120.26  3.000
 078  C20  C19  C18  119.50  3.000
 078  H22  C20  C21  119.82  3.000
 078  H22  C20  C19  120.06  3.000
 078  C21  C20  C19  120.12  3.000
 078  H23  C21  C20  119.61  3.000
 078  H23  C21  C16  119.41  3.000
 078  C20  C21  C16  120.98  3.000
 078  H25  N2   H24  105.69  3.000
 078  H25  N2   C14  109.95  3.000
 078  H24  N2   C14  110.14  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
 078  CONST_01  C30  C29  C28  C27    0.00   0.0  0
 078  CONST_02  C30  C31  C26  C27    0.00   0.0  0
 078  CONST_03  C31  C30  C29  C28    0.00   0.0  0
 078  CONST_04  C31  C26  C27  C28    0.00   0.0  0
 078  CONST_05  C26  C27  C28  C29    0.00   0.0  0
 078  CONST_06  C26  C31  C30  C29    0.00   0.0  0
 078  CONST_07  C19  C18  C17  C16    0.00   0.0  0
 078  CONST_08  C19  C20  C21  C16    0.00   0.0  0
 078  CONST_09  C20  C19  C18  C17    0.00   0.0  0
 078  CONST_10  C20  C21  C16  C17    0.00   0.0  0
 078  CONST_11  C21  C16  C17  C18    0.00   0.0  0
 078  CONST_12  C21  C20  C19  C18    0.00   0.0  0
 078  CONST_13  C25  C26  C27  C28  180.00   0.0  0
 078  CONST_14  C25  C26  C31  C30  180.00   0.0  0
 078  CONST_15  C18  C17  C16  C15  180.00   0.0  0
 078  CONST_16  C20  C21  C16  C15  180.00   0.0  0
 078  CONST_17  H3   C29  C28  C27  180.00   0.0  0
 078  CONST_18  H5   C31  C26  C27  180.00   0.0  0
 078  CONST_19  H4   C30  C29  C28  180.00   0.0  0
 078  CONST_20  H1   C27  C28  C29  180.00   0.0  0
 078  CONST_21  H2   C28  C29  C30  180.00   0.0  0
 078  CONST_22  H20  C18  C17  C16  180.00   0.0  0
 078  CONST_23  H22  C20  C21  C16  180.00   0.0  0
 078  CONST_24  H21  C19  C18  C17  180.00   0.0  0
 078  CONST_25  H23  C21  C16  C17  180.00   0.0  0
 078  CONST_26  H19  C17  C18  C19  180.00   0.0  0
 078  Var_01    C24  C25  C26  C27   85.66  30.0  2
 078  Var_02    C17  C16  C15  C14  -78.51  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
 078  chir_01  C24  O5  C25  C23  positiv
 078  chir_02  C23  N3  C22  C24  negativ
 078  chir_03  C22  O4  C23  C14  negativ
 078  chir_04  C14  N2  C15  C22  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
 078  plan-1  C27  0.020
 078  plan-1  C28  0.020
 078  plan-1  C29  0.020
 078  plan-1  C30  0.020
 078  plan-1  C31  0.020
 078  plan-1  C26  0.020
 078  plan-1  C25  0.020
 078  plan-1  H1   0.020
 078  plan-1  H2   0.020
 078  plan-1  H3   0.020
 078  plan-1  H4   0.020
 078  plan-1  H5   0.020
 078  plan-2  C15  0.020
 078  plan-2  C16  0.020
 078  plan-2  C17  0.020
 078  plan-2  C18  0.020
 078  plan-2  C19  0.020
 078  plan-2  C20  0.020
 078  plan-2  C21  0.020
 078  plan-2  H19  0.020
 078  plan-2  H20  0.020
 078  plan-2  H21  0.020
 078  plan-2  H22  0.020
 078  plan-2  H23  0.020

