# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 22:48:33 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: N-(methoxycarbonyl)-beta-D-glucopyranosylamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)N[C@@H]1O[C@H](CO)[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
 CR1  CR1  N-(methoxycarbonyl)-beta-D-glucopyranosylamine  D-saccharide  31  16  .  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_CR1
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
 CR1  C2    C  CR16  0  -0.026  -1.5565   0.2386  -0.5245
 CR1  O2    O  OH1   0  -0.664  -2.7457  -0.3457  -0.0588
 CR1  C4    C  CR16  0   0.035   0.0227   0.2207  -2.4737
 CR1  C5    C  CR16  0  -0.014   1.1249  -0.1682  -1.4875
 CR1  C6    C  CH2   0  -0.156   2.4773   0.3659  -1.9099
 CR1  C1    C  CR16  0   0.204  -0.3599  -0.1553   0.3448
 CR1  C3    C  CR16  0  -0.004  -1.3252  -0.2556  -1.9459
 CR1  O3    O  OH1   0  -0.671  -2.3148   0.2075  -2.8326
 CR1  O4    O  OH1   0  -0.672   0.3195  -0.3664  -3.7164
 CR1  O5    O  O     0  -0.488   0.8273   0.3596  -0.2122
 CR1  N2    N  NH1   0  -0.707  -0.5117   0.3629   1.6608
 CR1  O6    O  OH1   0  -0.670   3.4506  -0.1027  -1.0076
 CR1  C7    C  C     0   0.757   0.0161  -0.2578   2.7473
 CR1  O7    O  O     0  -0.505   0.5088  -1.3636   2.7492
 CR1  C8    C  CH3   0  -0.419   0.3788  -0.0185   5.0568
 CR1  O8    O  O2    0  -0.475  -0.1077   0.5111   3.8264
 CR1  H21   H  HCR6  0   0.227  -1.6287   1.3374  -0.5403
 CR1  H1O2  H  HOH1  0   0.457  -3.0116   0.0952   0.7544
 CR1  H41   H  HCR6  0   0.213  -0.0005   1.3196  -2.5504
 CR1  H51   H  HCR6  0   0.221   1.1765  -1.2686  -1.4376
 CR1  H61   H  HCH2  0   0.213   2.6762   0.0289  -2.9322
 CR1  H62   H  HCH2  0   0.196   2.4360   1.4638  -1.9325
 CR1  H11   H  HCR6  0   0.232  -0.3087  -1.2499   0.4061
 CR1  H31   H  HCR6  0   0.216  -1.3056  -1.3577  -1.9240
 CR1  H1O3  H  HOH1  0   0.457  -3.1509  -0.2107  -2.6045
 CR1  H1O4  H  HOH1  0   0.455  -0.3658  -0.1106  -4.3426
 CR1  H1N2  H  HNH1  0   0.404  -0.7783   1.3328   1.7574
 CR1  H1O6  H  HOH1  0   0.457   4.3095   0.2013  -1.3140
 CR1  H81   H  HCH3  0   0.251   0.2017   0.7521   5.8013
 CR1  H82   H  HCH3  0   0.238  -0.1569  -0.9228   5.3444
 CR1  H83   H  HCH3  0   0.238   1.4463  -0.2319   5.0085

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
 CR1  C2  O2    single  1.404  0.020  1.404
 CR1  C2  C1    single  1.531  0.020  1.531
 CR1  C2  C3    single  1.523  0.020  1.523
 CR1  C2  H21   single  0.970  0.020  1.090
 CR1  O2  H1O2  single  0.850  0.020  0.980
 CR1  C4  C5    single  1.529  0.020  1.529
 CR1  C4  C3    single  1.524  0.020  1.524
 CR1  C4  O4    single  1.406  0.020  1.406
 CR1  C4  H41   single  0.970  0.020  1.090
 CR1  C5  C6    single  1.514  0.020  1.514
 CR1  C5  O5    single  1.412  0.020  1.412
 CR1  C5  H51   single  0.970  0.020  1.090
 CR1  C6  O6    single  1.408  0.020  1.408
 CR1  C6  H61   single  0.970  0.020  1.090
 CR1  C6  H62   single  0.970  0.020  1.090
 CR1  C1  O5    single  1.409  0.020  1.409
 CR1  C1  N2    single  1.422  0.020  1.422
 CR1  C1  H11   single  0.970  0.020  1.090
 CR1  C3  O3    single  1.407  0.020  1.407
 CR1  C3  H31   single  0.970  0.020  1.090
 CR1  O3  H1O3  single  0.850  0.020  0.980
 CR1  O4  H1O4  single  0.850  0.020  0.980
 CR1  N2  C7    single  1.358  0.020  1.358
 CR1  N2  H1N2  single  0.860  0.020  1.020
 CR1  O6  H1O6  single  0.850  0.020  0.980
 CR1  C7  O7    double  1.211  0.020  1.211
 CR1  C7  O8    single  1.331  0.020  1.331
 CR1  C8  O8    single  1.425  0.020  1.425
 CR1  C8  H81   single  0.970  0.020  1.090
 CR1  C8  H82   single  0.970  0.020  1.090
 CR1  C8  H83   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
 CR1  H21   C2  C3   108.69  3.000
 CR1  H21   C2  C1   108.43  3.000
 CR1  C3    C2  C1   109.14  3.000
 CR1  H21   C2  O2   111.36  3.000
 CR1  C3    C2  O2   107.65  3.000
 CR1  C1    C2  O2   111.50  3.000
 CR1  H1O2  O2  C2   108.87  3.000
 CR1  H41   C4  O4   111.06  3.000
 CR1  H41   C4  C3   108.50  3.000
 CR1  O4    C4  C3   111.24  3.000
 CR1  H41   C4  C5   108.28  3.000
 CR1  O4    C4  C5   108.16  3.000
 CR1  C3    C4  C5   109.55  3.000
 CR1  H51   C5  O5   110.00  3.000
 CR1  H51   C5  C6   108.83  3.000
 CR1  O5    C5  C6   107.96  3.000
 CR1  H51   C5  C4   108.46  3.000
 CR1  O5    C5  C4   109.61  3.000
 CR1  C6    C5  C4   111.97  3.000
 CR1  H62   C6  H61  107.17  3.000
 CR1  H62   C6  O6   111.83  3.000
 CR1  H61   C6  O6   111.75  3.000
 CR1  H62   C6  C5   108.94  3.000
 CR1  H61   C6  C5   108.32  3.000
 CR1  O6    C6  C5   108.74  3.000
 CR1  H11   C1  N2   108.47  3.000
 CR1  H11   C1  O5   110.32  3.000
 CR1  N2    C1  O5   108.81  3.000
 CR1  H11   C1  C2   108.96  3.000
 CR1  N2    C1  C2   110.38  3.000
 CR1  O5    C1  C2   109.89  3.000
 CR1  H31   C3  O3   110.74  3.000
 CR1  H31   C3  C4   107.68  3.000
 CR1  O3    C3  C4   107.51  3.000
 CR1  H31   C3  C2   107.97  3.000
 CR1  O3    C3  C2   112.00  3.000
 CR1  C4    C3  C2   110.87  3.000
 CR1  H1O3  O3  C3   108.58  3.000
 CR1  H1O4  O4  C4   108.28  3.000
 CR1  C1    O5  C5   113.46  3.000
 CR1  H1N2  N2  C7   117.69  3.000
 CR1  H1N2  N2  C1   117.80  3.000
 CR1  C7    N2  C1   122.15  3.000
 CR1  H1O6  O6  C6   107.95  3.000
 CR1  O8    C7  O7   124.36  3.000
 CR1  O8    C7  N2   110.40  3.000
 CR1  O7    C7  N2   125.23  3.000
 CR1  H83   C8  H82  109.32  3.000
 CR1  H83   C8  H81  109.22  3.000
 CR1  H82   C8  H81  109.13  3.000
 CR1  H83   C8  O8   111.65  3.000
 CR1  H82   C8  O8   111.61  3.000
 CR1  H81   C8  O8   105.81  3.000
 CR1  C8    O8  C7   116.98  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
 CR1  Var_01  O7   C7  N2  C1   -9.63  30.0  2
 CR1  Var_02  H81  C8  O8  C7  179.24  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
 CR1  chir_01  C2  O2  C1  C3  negativ
 CR1  chir_02  C4  O4  C3  C5  negativ
 CR1  chir_03  C5  O5  C4  C6  negativ
 CR1  chir_04  C1  O5  N2  C2  negativ
 CR1  chir_05  C3  O3  C2  C4  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
 CR1  plan-1  N2  0.020
 CR1  plan-1  C7  0.020
 CR1  plan-1  O7  0.020
 CR1  plan-1  O8  0.020

