# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 20:06:45 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: N-[(1H-indol-2-ylcarbonyl)carbamoyl]-beta-D-glucopyranosylamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](NC(=O)NC(=O)c2[nH]c3ccccc3c2)[C@H](O)[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
 N85  N85  N-[(1H-indol-2-ylcarbonyl)carbamoyl]-beta-D-glucopyranosylamine  ligand  45  26  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_N85
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
 N85  N1    N  NH1   0  -0.735   1.0964  -0.4895   0.4648
 N85  C2    C  C     0   0.770   0.2493   0.3036   1.1766
 N85  O2    O  O     0  -0.470   0.6079   1.1093   2.0050
 N85  N3    N  NH1   0  -0.768  -1.0850   0.0772   0.8468
 N85  C4    C  C     0   0.535  -2.1783   0.6105   1.4952
 N85  O4    O  O     0  -0.416  -2.1271   1.1854   2.5590
 N85  C5    C  CR5   0   0.199  -3.4591   0.4054   0.8017
 N85  C7    C  CR15  0  -0.381  -4.7012   0.4753   1.3746
 N85  C8    C  CR56  0   0.065  -5.6449   0.1848   0.3524
 N85  C9    C  CR16  0  -0.333  -7.0450   0.1004   0.3154
 N85  C1'   C  CH1   0   0.205   2.5083  -0.3034   0.4912
 N85  C10   C  CR16  0  -0.269  -7.6578  -0.1948  -0.8817
 N85  C11   C  CR16  0  -0.274  -6.9032  -0.4106  -2.0517
 N85  C12   C  CR16  0  -0.307  -5.5268  -0.3393  -2.0471
 N85  C16   C  CR56  0   0.351  -4.9075  -0.0453  -0.8303
 N85  C2'   C  CH1   0  -0.027   3.2281  -1.6395   0.2918
 N85  O2'   O  OH1   0  -0.663   2.9738  -2.5254   1.3507
 N85  C3'   C  CH1   0  -0.006   4.7294  -1.3863   0.2527
 N85  O3'   O  OH1   0  -0.671   5.4532  -2.5493  -0.0678
 N85  N30   N  NR15  0  -0.744  -3.5861   0.0778  -0.5278
 N85  C4'   C  CH1   0   0.035   5.0710  -0.3289  -0.7907
 N85  O4'   O  OH1   0  -0.672   6.4292   0.0276  -0.7304
 N85  C5'   C  CH1   0  -0.015   4.2361   0.9277  -0.5378
 N85  O5'   O  O2    0  -0.487   2.8640   0.5920  -0.5359
 N85  C6'   C  CH2   0  -0.156   4.4551   1.9752  -1.6087
 N85  O6'   O  OH1   0  -0.670   3.7120   3.1246  -1.2810
 N85  HN1   H  HNH1  0   0.409   0.7246  -1.0560  -0.2842
 N85  HN3   H  HNH1  0   0.423  -1.2683  -0.5703   0.0942
 N85  H7    H  HCR5  0   0.265  -4.9070   0.6830   2.4126
 N85  H9    H  HCR6  0   0.254  -7.6303   0.2683   1.2106
 N85  H1'   H  HCH1  0   0.237   2.7860   0.1070   1.4699
 N85  H10   H  HCR6  0   0.254  -8.7367  -0.2614  -0.9312
 N85  H11   H  HCR6  0   0.258  -7.4177  -0.6422  -2.9752
 N85  H12   H  HCR6  0   0.266  -4.9506  -0.5099  -2.9472
 N85  H2'   H  HCH1  0   0.227   2.9175  -2.0641  -0.6759
 N85  HO2'  H  HOH1  0   0.457   2.0664  -2.8392   1.2855
 N85  H3'   H  HCH1  0   0.218   5.0323  -0.9960   1.2375
 N85  HO3'  H  HOH1  0   0.457   5.4029  -3.1570   0.6765
 N85  HN30  H  HNR5  0   0.418  -2.8501   0.0950  -1.2159
 N85  H4'   H  HCH1  0   0.213   4.8083  -0.7223  -1.7861
 N85  HO4'  H  HOH1  0   0.455   6.9541  -0.7625  -0.8950
 N85  H5'   H  HCH1  0   0.224   4.5221   1.3467   0.4415
 N85  H6'   H  HCH2  0   0.214   5.5269   2.1888  -1.6681
 N85  H6'A  H  HCH2  0   0.195   4.1541   1.5584  -2.5802
 N85  HO6'  H  HOH1  0   0.457   3.9416   3.8148  -1.9095

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
 N85  N1   C2    single    1.361  0.020  1.361
 N85  N1   C1'   single    1.424  0.020  1.424
 N85  C2   O2    double    1.210  0.020  1.210
 N85  C2   N3    single    1.393  0.020  1.393
 N85  N3   C4    single    1.378  0.020  1.378
 N85  C4   O4    double    1.210  0.020  1.210
 N85  C4   C5    single    1.471  0.020  1.471
 N85  C5   C7    aromatic  1.370  0.020  1.370
 N85  C5   N30   aromatic  1.375  0.020  1.375
 N85  C7   C8    aromatic  1.421  0.020  1.421
 N85  C8   C9    aromatic  1.403  0.020  1.403
 N85  C8   C16   aromatic  1.413  0.020  1.413
 N85  C9   C10   aromatic  1.377  0.020  1.377
 N85  C1'  C2'   single    1.531  0.020  1.531
 N85  C1'  O5'   single    1.408  0.020  1.408
 N85  C10  C11   aromatic  1.409  0.020  1.409
 N85  C11  C12   aromatic  1.378  0.020  1.378
 N85  C12  C16   aromatic  1.397  0.020  1.397
 N85  C16  N30   aromatic  1.361  0.020  1.361
 N85  C2'  O2'   single    1.404  0.020  1.404
 N85  C2'  C3'   single    1.523  0.020  1.523
 N85  C3'  O3'   single    1.407  0.020  1.407
 N85  C3'  C4'   single    1.524  0.020  1.524
 N85  C4'  O4'   single    1.405  0.020  1.405
 N85  C4'  C5'   single    1.530  0.020  1.530
 N85  C5'  O5'   single    1.413  0.020  1.413
 N85  C5'  C6'   single    1.514  0.020  1.514
 N85  C6'  O6'   single    1.407  0.020  1.407
 N85  N1   HN1   single    0.860  0.020  1.020
 N85  N3   HN3   single    0.860  0.020  1.020
 N85  C7   H7    single    0.930  0.020  1.080
 N85  C9   H9    single    0.930  0.020  1.080
 N85  C1'  H1'   single    0.970  0.020  1.090
 N85  C10  H10   single    0.930  0.020  1.080
 N85  C11  H11   single    0.930  0.020  1.080
 N85  C12  H12   single    0.930  0.020  1.080
 N85  C2'  H2'   single    0.970  0.020  1.090
 N85  O2'  HO2'  single    0.850  0.020  0.980
 N85  C3'  H3'   single    0.970  0.020  1.090
 N85  O3'  HO3'  single    0.850  0.020  0.980
 N85  N30  HN30  single    0.860  0.020  1.020
 N85  C4'  H4'   single    0.970  0.020  1.090
 N85  O4'  HO4'  single    0.850  0.020  0.980
 N85  C5'  H5'   single    0.970  0.020  1.090
 N85  C6'  H6'   single    0.970  0.020  1.090
 N85  C6'  H6'A  single    0.970  0.020  1.090
 N85  O6'  HO6'  single    0.850  0.020  0.980

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
 N85  HN1   N1   C1'  116.87  3.000
 N85  HN1   N1   C2   119.04  3.000
 N85  C1'   N1   C2   122.08  3.000
 N85  N3    C2   O2   123.66  3.000
 N85  N3    C2   N1   112.18  3.000
 N85  O2    C2   N1   124.16  3.000
 N85  HN3   N3   C4   117.05  3.000
 N85  HN3   N3   C2   117.04  3.000
 N85  C4    N3   C2   125.84  3.000
 N85  C5    C4   O4   121.17  3.000
 N85  C5    C4   N3   114.52  3.000
 N85  O4    C4   N3   124.30  3.000
 N85  N30   C5   C7   109.44  3.000
 N85  N30   C5   C4   124.71  3.000
 N85  C7    C5   C4   125.83  3.000
 N85  H7    C7   C8   127.23  3.000
 N85  H7    C7   C5   125.84  3.000
 N85  C8    C7   C5   106.91  3.000
 N85  C16   C8   C9   119.28  3.000
 N85  C16   C8   C7   106.79  3.000
 N85  C9    C8   C7   133.94  3.000
 N85  H9    C9   C10  120.76  3.000
 N85  H9    C9   C8   120.55  3.000
 N85  C10   C9   C8   118.68  3.000
 N85  H1'   C1'  O5'  110.42  3.000
 N85  H1'   C1'  C2'  108.89  3.000
 N85  O5'   C1'  C2'  109.95  3.000
 N85  H1'   C1'  N1   108.44  3.000
 N85  O5'   C1'  N1   108.66  3.000
 N85  C2'   C1'  N1   110.47  3.000
 N85  H10   C10  C11  119.11  3.000
 N85  H10   C10  C9   119.79  3.000
 N85  C11   C10  C9   121.10  3.000
 N85  H11   C11  C12  119.26  3.000
 N85  H11   C11  C10  119.13  3.000
 N85  C12   C11  C10  121.61  3.000
 N85  H12   C12  C16  121.44  3.000
 N85  H12   C12  C11  121.38  3.000
 N85  C16   C12  C11  117.18  3.000
 N85  N30   C16  C12  130.03  3.000
 N85  N30   C16  C8   107.81  3.000
 N85  C12   C16  C8   122.15  3.000
 N85  H2'   C2'  C3'  108.63  3.000
 N85  H2'   C2'  O2'  111.61  3.000
 N85  C3'   C2'  O2'  107.63  3.000
 N85  H2'   C2'  C1'  108.56  3.000
 N85  C3'   C2'  C1'  108.77  3.000
 N85  O2'   C2'  C1'  111.55  3.000
 N85  HO2'  O2'  C2'  109.00  3.000
 N85  H3'   C3'  C4'  107.72  3.000
 N85  H3'   C3'  O3'  110.79  3.000
 N85  C4'   C3'  O3'  107.59  3.000
 N85  H3'   C3'  C2'  107.88  3.000
 N85  C4'   C3'  C2'  110.72  3.000
 N85  O3'   C3'  C2'  112.07  3.000
 N85  HO3'  O3'  C3'  108.61  3.000
 N85  HN30  N30  C16  123.97  3.000
 N85  HN30  N30  C5   126.06  3.000
 N85  C16   N30  C5   109.03  3.000
 N85  H4'   C4'  C5'  108.21  3.000
 N85  H4'   C4'  O4'  111.08  3.000
 N85  C5'   C4'  O4'  108.18  3.000
 N85  H4'   C4'  C3'  108.49  3.000
 N85  C5'   C4'  C3'  109.53  3.000
 N85  O4'   C4'  C3'  111.29  3.000
 N85  HO4'  O4'  C4'  108.15  3.000
 N85  H5'   C5'  C6'  109.13  3.000
 N85  H5'   C5'  O5'  109.94  3.000
 N85  C6'   C5'  O5'  107.81  3.000
 N85  H5'   C5'  C4'  108.50  3.000
 N85  C6'   C5'  C4'  111.86  3.000
 N85  O5'   C5'  C4'  109.58  3.000
 N85  C5'   O5'  C1'  113.42  3.000
 N85  H6'A  C6'  H6'  107.11  3.000
 N85  H6'A  C6'  O6'  111.77  3.000
 N85  H6'   C6'  O6'  111.73  3.000
 N85  H6'A  C6'  C5'  108.86  3.000
 N85  H6'   C6'  C5'  108.37  3.000
 N85  O6'   C6'  C5'  108.90  3.000
 N85  HO6'  O6'  C6'  107.94  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
 N85  CONST_01  C9    C8   C7   C5   180.00   0.0  0
 N85  CONST_02  C16   C8   C7   C5     0.00   0.0  0
 N85  CONST_03  C8    C16  N30  C5     0.00   0.0  0
 N85  CONST_04  C12   C16  N30  C5   180.00   0.0  0
 N85  CONST_05  C16   N30  C5   C7     0.00   0.0  0
 N85  CONST_06  C10   C9   C8   C7   180.00   0.0  0
 N85  CONST_07  C12   C16  C8   C7   180.00   0.0  0
 N85  CONST_08  N30   C16  C8   C7     0.00   0.0  0
 N85  CONST_09  N30   C5   C7   C8     0.00   0.0  0
 N85  CONST_10  C11   C10  C9   C8     0.00   0.0  0
 N85  CONST_11  C11   C12  C16  C8     0.00   0.0  0
 N85  CONST_12  C12   C16  C8   C9     0.00   0.0  0
 N85  CONST_13  N30   C16  C8   C9   180.00   0.0  0
 N85  CONST_14  C12   C11  C10  C9     0.00   0.0  0
 N85  CONST_15  C16   C8   C9   C10    0.00   0.0  0
 N85  CONST_16  C16   C12  C11  C10    0.00   0.0  0
 N85  CONST_17  N30   C16  C12  C11  180.00   0.0  0
 N85  CONST_18  C8    C7   C5   C4   180.00   0.0  0
 N85  CONST_19  C16   N30  C5   C4   180.00   0.0  0
 N85  CONST_20  HN30  N30  C5   C7   180.00   0.0  0
 N85  CONST_21  H9    C9   C8   C7     0.00   0.0  0
 N85  CONST_22  H10   C10  C9   C8   180.00   0.0  0
 N85  CONST_23  H12   C12  C16  C8   180.00   0.0  0
 N85  CONST_24  H7    C7   C8   C9     0.00   0.0  0
 N85  CONST_25  H11   C11  C10  C9   180.00   0.0  0
 N85  CONST_26  C5    C4   N3   C2   180.00   0.0  0
 N85  CONST_27  C1'   N1   C2   O2     0.00   0.0  0
 N85  CONST_28  C1'   N1   C2   N3   180.00   0.0  0
 N85  CONST_29  HN3   N3   C4   C5     0.00   0.0  0
 N85  CONST_30  O4    C4   N3   C2     0.00   0.0  0
 N85  CONST_31  C4    N3   C2   O2     0.00   0.0  0
 N85  CONST_32  C4    N3   C2   N1   180.00   0.0  0
 N85  CONST_33  HN1   N1   C2   O2   180.00   0.0  0
 N85  Var_01    C7    C5   C4   N3   159.93  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
 N85  chir_01  C1'  N1   C2'  O5'  negativ
 N85  chir_02  C2'  O2'  C1'  C3'  negativ
 N85  chir_03  C3'  O3'  C2'  C4'  positiv
 N85  chir_04  C4'  O4'  C5'  C3'  positiv
 N85  chir_05  C5'  O5'  C4'  C6'  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
 N85  plan-1  C4    0.020
 N85  plan-1  C5    0.020
 N85  plan-1  C7    0.020
 N85  plan-1  C8    0.020
 N85  plan-1  C9    0.020
 N85  plan-1  C10   0.020
 N85  plan-1  C11   0.020
 N85  plan-1  C12   0.020
 N85  plan-1  C16   0.020
 N85  plan-1  N30   0.020
 N85  plan-1  H7    0.020
 N85  plan-1  H9    0.020
 N85  plan-1  H10   0.020
 N85  plan-1  H11   0.020
 N85  plan-1  H12   0.020
 N85  plan-1  HN30  0.020
 N85  plan-2  N1    0.020
 N85  plan-2  C2    0.020
 N85  plan-2  O2    0.020
 N85  plan-2  N3    0.020
 N85  plan-2  C4    0.020
 N85  plan-2  O4    0.020
 N85  plan-2  C5    0.020
 N85  plan-2  C1'   0.020
 N85  plan-2  HN1   0.020
 N85  plan-2  HN3   0.020

