# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 20:09:00 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: N-[(cyclohexylcarbonyl)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)C2CCCCC2)[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
 F58  F58  N-[(cyclohexylcarbonyl)carbamoyl]-beta-D-glucopyranosylamine  D-saccharide  47  23  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_F58
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
 F58  C1    C  CH1   0   0.209   1.7541   0.2382  -0.2690
 F58  N1    N  NH1   0  -0.734   0.3698   0.2437   0.0626
 F58  C2    C  CH1   0  -0.027   2.4097   1.5536   0.1600
 F58  N2    N  NH1   0  -0.749  -1.8419  -0.2873  -0.1580
 F58  O2    O  OH1   0  -0.663   1.8808   2.6444  -0.5488
 F58  C3    C  CH1   0  -0.006   3.9006   1.4851  -0.1399
 F58  O3    O  OH1   0  -0.671   4.5918   2.6023   0.3645
 F58  C4    C  CH1   0   0.034   4.5176   0.2414   0.4899
 F58  O4    O  OH1   0  -0.671   5.8568   0.0810   0.0946
 F58  C5    C  CH1   0  -0.014   3.7374  -0.9987   0.0511
 F58  O5    O  O2    0  -0.488   2.3731  -0.8455   0.3841
 F58  C6    C  CH2   0  -0.157   4.2417  -2.2538   0.7313
 F58  O6    O  OH1   0  -0.670   3.5500  -3.3617   0.2069
 F58  C7    C  C     0   0.760  -0.5758  -0.3357  -0.7289
 F58  O7    O  O     0  -0.476  -0.3430  -0.8159  -1.8161
 F58  C8    C  C     0   0.591  -3.0267  -0.6882  -0.7427
 F58  O8    O  O     0  -0.423  -3.0898  -1.2106  -1.8304
 F58  C9    C  CH1   0  -0.421  -4.2420  -0.3769   0.1095
 F58  C10   C  CH2   0  -0.412  -5.4841  -1.1096  -0.3902
 F58  C11   C  CH2   0  -0.438  -6.7006  -0.7713   0.4655
 F58  C12   C  CH2   0  -0.430  -6.9507   0.7319   0.5044
 F58  C13   C  CH2   0  -0.432  -5.7124   1.4759   0.9911
 F58  C14   C  CH2   0  -0.424  -4.4877   1.1422   0.1458
 F58  H1    H  HCH1  0   0.236   1.8488   0.1327  -1.3567
 F58  HN1   H  HNH1  0   0.408   0.1219   0.5417   0.9951
 F58  H2    H  HCH1  0   0.226   2.2742   1.6743   1.2464
 F58  HN2   H  HNH1  0   0.422  -1.9207   0.1221   0.7619
 F58  HO2   H  HOH1  0   0.456   0.9860   2.8147  -0.2384
 F58  H3    H  HCH1  0   0.219   4.0257   1.4083  -1.2317
 F58  HO3   H  HOH1  0   0.458   4.3740   3.3681  -0.1759
 F58  H4    H  HCH1  0   0.213   4.4349   0.3302   1.5852
 F58  HO4   H  HOH1  0   0.455   6.3488   0.8560   0.3850
 F58  H5    H  HCH1  0   0.224   3.8487  -1.1138  -1.0400
 F58  H6    H  HCH2  0   0.213   5.3202  -2.3304   0.5595
 F58  H6A   H  HCH2  0   0.197   4.0937  -2.1548   1.8158
 F58  HO6   H  HOH1  0   0.457   3.9100  -4.1552   0.6129
 F58  H9    H  HCH1  0   0.265  -4.0287  -0.7044   1.1358
 F58  H10   H  HCH2  0   0.220  -5.6818  -0.8211  -1.4266
 F58  H10A  H  HCH2  0   0.237  -5.3125  -2.1883  -0.3888
 F58  H11   H  HCH2  0   0.232  -7.5784  -1.2937   0.0783
 F58  H11A  H  HCH2  0   0.213  -6.5452  -1.1403   1.4854
 F58  H12   H  HCH2  0   0.212  -7.2122   1.0818  -0.5001
 F58  H12A  H  HCH2  0   0.230  -7.8038   0.9595   1.1478
 F58  H13   H  HCH2  0   0.234  -5.8831   2.5547   0.9747
 F58  H13A  H  HCH2  0   0.216  -5.5133   1.2056   2.0337
 F58  H14   H  HCH2  0   0.241  -3.6143   1.6684   0.5387
 F58  H14A  H  HCH2  0   0.229  -4.6372   1.5024  -0.8778

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
 F58  C1   N1    single  1.424  0.020  1.424
 F58  C1   C2    single  1.531  0.020  1.531
 F58  C1   O5    single  1.409  0.020  1.409
 F58  N1   C7    single  1.362  0.020  1.362
 F58  C2   O2    single  1.404  0.020  1.404
 F58  C2   C3    single  1.522  0.020  1.522
 F58  N2   C7    single  1.390  0.020  1.390
 F58  N2   C8    single  1.381  0.020  1.381
 F58  C3   O3    single  1.407  0.020  1.407
 F58  C3   C4    single  1.524  0.020  1.524
 F58  C4   O4    single  1.406  0.020  1.406
 F58  C4   C5    single  1.529  0.020  1.529
 F58  C5   O5    single  1.413  0.020  1.413
 F58  C5   C6    single  1.514  0.020  1.514
 F58  C6   O6    single  1.408  0.020  1.408
 F58  C7   O7    double  1.211  0.020  1.211
 F58  C8   O8    double  1.208  0.020  1.208
 F58  C8   C9    single  1.517  0.020  1.517
 F58  C9   C10   single  1.526  0.020  1.526
 F58  C9   C14   single  1.539  0.020  1.539
 F58  C10  C11   single  1.525  0.020  1.525
 F58  C11  C12   single  1.524  0.020  1.524
 F58  C12  C13   single  1.524  0.020  1.524
 F58  C13  C14   single  1.525  0.020  1.525
 F58  C1   H1    single  0.970  0.020  1.090
 F58  N1   HN1   single  0.860  0.020  1.020
 F58  C2   H2    single  0.970  0.020  1.090
 F58  N2   HN2   single  0.860  0.020  1.020
 F58  O2   HO2   single  0.850  0.020  0.980
 F58  C3   H3    single  0.970  0.020  1.090
 F58  O3   HO3   single  0.850  0.020  0.980
 F58  C4   H4    single  0.970  0.020  1.090
 F58  O4   HO4   single  0.850  0.020  0.980
 F58  C5   H5    single  0.970  0.020  1.090
 F58  C6   H6    single  0.970  0.020  1.090
 F58  C6   H6A   single  0.970  0.020  1.090
 F58  O6   HO6   single  0.850  0.020  0.980
 F58  C9   H9    single  0.970  0.020  1.090
 F58  C10  H10   single  0.970  0.020  1.090
 F58  C10  H10A  single  0.970  0.020  1.090
 F58  C11  H11   single  0.970  0.020  1.090
 F58  C11  H11A  single  0.970  0.020  1.090
 F58  C12  H12   single  0.970  0.020  1.090
 F58  C12  H12A  single  0.970  0.020  1.090
 F58  C13  H13   single  0.970  0.020  1.090
 F58  C13  H13A  single  0.970  0.020  1.090
 F58  C14  H14   single  0.970  0.020  1.090
 F58  C14  H14A  single  0.970  0.020  1.090

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
 F58  H1    C1   O5   110.36  3.000
 F58  H1    C1   C2   108.88  3.000
 F58  O5    C1   C2   110.05  3.000
 F58  H1    C1   N1   108.38  3.000
 F58  O5    C1   N1   108.80  3.000
 F58  C2    C1   N1   110.36  3.000
 F58  HN1   N1   C7   119.44  3.000
 F58  HN1   N1   C1   117.06  3.000
 F58  C7    N1   C1   122.54  3.000
 F58  H2    C2   C3   108.65  3.000
 F58  H2    C2   O2   111.50  3.000
 F58  C3    C2   O2   107.72  3.000
 F58  H2    C2   C1   108.53  3.000
 F58  C3    C2   C1   108.99  3.000
 F58  O2    C2   C1   111.39  3.000
 F58  HN2   N2   C8   115.88  3.000
 F58  HN2   N2   C7   117.34  3.000
 F58  C8    N2   C7   126.71  3.000
 F58  HO2   O2   C2   108.96  3.000
 F58  H3    C3   C4   107.86  3.000
 F58  H3    C3   O3   110.78  3.000
 F58  C4    C3   O3   107.51  3.000
 F58  H3    C3   C2   108.04  3.000
 F58  C4    C3   C2   110.59  3.000
 F58  O3    C3   C2   112.00  3.000
 F58  HO3   O3   C3   108.62  3.000
 F58  H4    C4   C5   108.19  3.000
 F58  H4    C4   O4   111.11  3.000
 F58  C5    C4   O4   108.23  3.000
 F58  H4    C4   C3   108.33  3.000
 F58  C5    C4   C3   109.66  3.000
 F58  O4    C4   C3   111.25  3.000
 F58  HO4   O4   C4   108.07  3.000
 F58  H5    C5   C6   108.93  3.000
 F58  H5    C5   O5   110.01  3.000
 F58  C6    C5   O5   107.80  3.000
 F58  H5    C5   C4   108.48  3.000
 F58  C6    C5   C4   111.92  3.000
 F58  O5    C5   C4   109.70  3.000
 F58  C5    O5   C1   113.48  3.000
 F58  H6A   C6   H6   107.09  3.000
 F58  H6A   C6   O6   111.86  3.000
 F58  H6    C6   O6   111.75  3.000
 F58  H6A   C6   C5   108.90  3.000
 F58  H6    C6   C5   108.40  3.000
 F58  O6    C6   C5   108.75  3.000
 F58  HO6   O6   C6   107.96  3.000
 F58  O7    C7   N2   123.89  3.000
 F58  O7    C7   N1   123.83  3.000
 F58  N2    C7   N1   112.26  3.000
 F58  C9    C8   O8   123.56  3.000
 F58  C9    C8   N2   112.96  3.000
 F58  O8    C8   N2   123.47  3.000
 F58  H9    C9   C14  107.66  3.000
 F58  H9    C9   C10  108.72  3.000
 F58  C14   C9   C10  110.59  3.000
 F58  H9    C9   C8   107.95  3.000
 F58  C14   C9   C8   110.10  3.000
 F58  C10   C9   C8   111.69  3.000
 F58  H10A  C10  H10  106.86  3.000
 F58  H10A  C10  C11  110.10  3.000
 F58  H10   C10  C11  109.20  3.000
 F58  H10A  C10  C9   110.24  3.000
 F58  H10   C10  C9   109.31  3.000
 F58  C11   C10  C9   111.04  3.000
 F58  H11A  C11  H11  106.43  3.000
 F58  H11A  C11  C12  109.37  3.000
 F58  H11   C11  C12  110.41  3.000
 F58  H11A  C11  C10  109.54  3.000
 F58  H11   C11  C10  109.63  3.000
 F58  C12   C11  C10  111.34  3.000
 F58  H12A  C12  H12  106.68  3.000
 F58  H12A  C12  C13  110.16  3.000
 F58  H12   C12  C13  109.32  3.000
 F58  H12A  C12  C11  110.40  3.000
 F58  H12   C12  C11  109.32  3.000
 F58  C13   C12  C11  110.87  3.000
 F58  H13A  C13  H13  106.64  3.000
 F58  H13A  C13  C14  109.13  3.000
 F58  H13   C13  C14  109.47  3.000
 F58  H13A  C13  C12  109.33  3.000
 F58  H13   C13  C12  110.50  3.000
 F58  C14   C13  C12  111.63  3.000
 F58  H14A  C14  H14  106.66  3.000
 F58  H14A  C14  C13  109.66  3.000
 F58  H14   C14  C13  109.71  3.000
 F58  H14A  C14  C9   108.92  3.000
 F58  H14   C14  C9   110.86  3.000
 F58  C13   C14  C9   110.93  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
 F58  CONST_01  O7   C7   N1   C1     0.00   0.0  0
 F58  CONST_02  C9   C8   N2   C7   180.00   0.0  0
 F58  CONST_03  N2   C7   N1   C1   180.00   0.0  0
 F58  CONST_04  HN2  N2   C8   C9     0.00   0.0  0
 F58  CONST_05  O8   C8   N2   C7     0.00   0.0  0
 F58  CONST_06  C8   N2   C7   O7     0.00   0.0  0
 F58  CONST_07  C8   N2   C7   N1   180.00   0.0  0
 F58  CONST_08  HN1  N1   C7   O7   180.00   0.0  0
 F58  Var_01    C12  C11  C10  C9    56.57  30.0  1
 F58  Var_02    C12  C13  C14  C9   -55.55  30.0  1
 F58  Var_03    C13  C12  C11  C10  -55.73  30.0  1
 F58  Var_04    C14  C13  C12  C11   55.42  30.0  1

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
 F58  chir_01  C1  N1  C2   O5   negativ
 F58  chir_02  C2  O2  C1   C3   negativ
 F58  chir_03  C3  O3  C2   C4   positiv
 F58  chir_04  C4  O4  C5   C3   positiv
 F58  chir_05  C5  O5  C4   C6   negativ
 F58  chir_06  C9  C8  C10  C14  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
 F58  plan-1  C1   0.020
 F58  plan-1  N1   0.020
 F58  plan-1  N2   0.020
 F58  plan-1  C7   0.020
 F58  plan-1  O7   0.020
 F58  plan-1  C8   0.020
 F58  plan-1  O8   0.020
 F58  plan-1  C9   0.020
 F58  plan-1  HN1  0.020
 F58  plan-1  HN2  0.020

