# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 00:12:31 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: methyl [(2S,3R,4S,5S,6R)-2-carbamoyl-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]carbamate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)N[C@@]1(O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O)C(N)=O
#
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
 CRA  CRA  'methyl [(2S,3R,4S,5S,6R)-2-carbamoyl-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]carbamate (non-preferred name)'  D-saccharide  35  19  .  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_CRA
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
 CRA  N1    N  NH2   0  -0.785  -1.1903   2.5339  -0.2074
 CRA  C2    C  CR16  0   0.010   1.4255  -0.1639  -0.0024
 CRA  O2    O  OH1   0  -0.664   2.4665   0.4995   0.6537
 CRA  C4    C  CR16  0   0.007   0.4385  -1.0139  -2.1218
 CRA  C5    C  CR16  0  -0.044  -0.8547  -0.2918  -1.7339
 CRA  C6    C  CH2   0  -0.153  -2.0891  -1.0373  -2.1906
 CRA  C1    C  CR6   0   0.348   0.0936   0.5485   0.2936
 CRA  C3    C  CR16  0  -0.004   1.6383  -0.3036  -1.5058
 CRA  O3    O  OH1   0  -0.674   2.8204  -1.0476  -1.6832
 CRA  O4    O  OH1   0  -0.671   0.6195  -1.0221  -3.5203
 CRA  O5    O  O     0  -0.487  -0.9492  -0.1686  -0.3215
 CRA  N2    N  NH1   0  -0.734  -0.1865   0.6164   1.6998
 CRA  C7    C  C     0   0.762  -0.2423  -0.4482   2.5405
 CRA  O7    O  O     0  -0.496  -0.0616  -1.6071   2.2449
 CRA  C8    C  CH3   0  -0.417  -0.6163  -1.0256   4.7888
 CRA  O8    O  O2    0  -0.478  -0.5345  -0.0302   3.7725
 CRA  C9    C  C     0   0.456   0.0517   2.0320  -0.1879
 CRA  O9    O  O     0  -0.437   1.0466   2.6691  -0.4718
 CRA  H1N1  H  HNH2  0   0.412  -2.0033   1.9528  -0.0832
 CRA  H2N1  H  HNH2  0   0.409  -1.3422   3.4809  -0.5158
 CRA  H21   H  HCR6  0   0.253   1.3105  -1.1815   0.3891
 CRA  H1O2  H  HOH1  0   0.455   3.2141  -0.1029   0.7060
 CRA  H41   H  HCR6  0   0.226   0.4031  -2.0380  -1.7239
 CRA  H51   H  HCR6  0   0.231  -0.8536   0.7008  -2.2112
 CRA  H61   H  HCH2  0   0.203  -1.9964  -1.2358  -3.2650
 CRA  H62   H  HCH2  0   0.205  -2.1249  -2.0107  -1.6828
 CRA  H31   H  HCR6  0   0.222   1.7367   0.6884  -1.9688
 CRA  H1O3  H  HOH1  0   0.454   3.0175  -1.0779  -2.6249
 CRA  H1O4  H  HOH1  0   0.461   0.2135  -1.8120  -3.8875
 CRA  H1N2  H  HNH1  0   0.415  -0.4273   1.5132   2.0944
 CRA  H1O6  H  HOH1  0   0.458  -4.0018  -0.7544  -2.1664
 CRA  H81   H  HCH3  0   0.251  -0.8239  -0.4902   5.7107
 CRA  H82   H  HCH3  0   0.237  -1.4233  -1.7322   4.5958
 CRA  H83   H  HCH3  0   0.237   0.3217  -1.5700   4.8946
 CRA  O6    O  OH1   0  -0.667  -3.2226  -0.2539  -1.9080

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
 CRA  N1  C9    single  1.340  0.020  1.340
 CRA  N1  H1N1  single  0.860  0.020  1.020
 CRA  N1  H2N1  single  0.860  0.020  1.020
 CRA  C2  O2    single  1.398  0.020  1.398
 CRA  C2  C1    single  1.539  0.020  1.539
 CRA  C2  C3    single  1.525  0.020  1.525
 CRA  C2  H21   single  0.970  0.020  1.090
 CRA  O2  H1O2  single  0.850  0.020  0.980
 CRA  C4  C5    single  1.531  0.020  1.531
 CRA  C4  C3    single  1.524  0.020  1.524
 CRA  C4  O4    single  1.410  0.020  1.410
 CRA  C4  H41   single  0.970  0.020  1.090
 CRA  C5  C6    single  1.513  0.020  1.513
 CRA  C5  O5    single  1.421  0.020  1.421
 CRA  C5  H51   single  0.970  0.020  1.090
 CRA  C6  O6    single  1.407  0.020  1.407
 CRA  C6  H61   single  0.970  0.020  1.090
 CRA  C6  H62   single  0.970  0.020  1.090
 CRA  C1  O5    single  1.407  0.020  1.407
 CRA  C1  N2    single  1.435  0.020  1.435
 CRA  C1  C9    single  1.560  0.020  1.560
 CRA  C3  O3    single  1.408  0.020  1.408
 CRA  C3  H31   single  0.970  0.020  1.090
 CRA  O3  H1O3  single  0.850  0.020  0.980
 CRA  O4  H1O4  single  0.850  0.020  0.980
 CRA  N2  C7    single  1.358  0.020  1.358
 CRA  N2  H1N2  single  0.860  0.020  1.020
 CRA  O6  H1O6  single  0.850  0.020  0.980
 CRA  C7  O7    double  1.210  0.020  1.210
 CRA  C7  O8    single  1.333  0.020  1.333
 CRA  C8  O8    single  1.425  0.020  1.425
 CRA  C8  H81   single  0.970  0.020  1.090
 CRA  C8  H82   single  0.970  0.020  1.090
 CRA  C8  H83   single  0.970  0.020  1.090
 CRA  C9  O9    double  1.215  0.020  1.215

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
 CRA  H2N1  N1  H1N1  117.28  3.000
 CRA  H2N1  N1  C9    119.77  3.000
 CRA  H1N1  N1  C9    122.04  3.000
 CRA  H21   C2  C3    106.36  3.000
 CRA  H21   C2  C1    105.68  3.000
 CRA  C3    C2  C1    110.66  3.000
 CRA  H21   C2  O2    110.54  3.000
 CRA  C3    C2  O2    113.72  3.000
 CRA  C1    C2  O2    109.54  3.000
 CRA  H1O2  O2  C2    107.89  3.000
 CRA  H41   C4  O4    110.96  3.000
 CRA  H41   C4  C3    108.25  3.000
 CRA  O4    C4  C3    107.60  3.000
 CRA  H41   C4  C5    108.69  3.000
 CRA  O4    C4  C5    111.25  3.000
 CRA  C3    C4  C5    110.04  3.000
 CRA  H51   C5  O5    110.65  3.000
 CRA  H51   C5  C6    108.31  3.000
 CRA  O5    C5  C6    106.77  3.000
 CRA  H51   C5  C4    108.33  3.000
 CRA  O5    C5  C4    110.42  3.000
 CRA  C6    C5  C4    112.35  3.000
 CRA  H62   C6  H61   107.18  3.000
 CRA  H62   C6  O6    111.99  3.000
 CRA  H61   C6  O6    111.46  3.000
 CRA  H62   C6  C5    108.89  3.000
 CRA  H61   C6  C5    108.42  3.000
 CRA  O6    C6  C5    108.81  3.000
 CRA  C9    C1  N2    104.60  3.000
 CRA  C9    C1  O5    109.25  3.000
 CRA  N2    C1  O5    107.92  3.000
 CRA  C9    C1  C2    113.83  3.000
 CRA  N2    C1  C2    112.28  3.000
 CRA  O5    C1  C2    108.74  3.000
 CRA  H31   C3  O3    110.41  3.000
 CRA  H31   C3  C4    108.71  3.000
 CRA  O3    C3  C4    111.33  3.000
 CRA  H31   C3  C2    110.19  3.000
 CRA  O3    C3  C2    106.85  3.000
 CRA  C4    C3  C2    109.35  3.000
 CRA  H1O3  O3  C3    108.17  3.000
 CRA  H1O4  O4  C4    109.24  3.000
 CRA  C1    O5  C5    115.43  3.000
 CRA  H1N2  N2  C7    116.43  3.000
 CRA  H1N2  N2  C1    118.14  3.000
 CRA  C7    N2  C1    125.28  3.000
 CRA  O8    C7  O7    123.97  3.000
 CRA  O8    C7  N2    109.59  3.000
 CRA  O7    C7  N2    126.43  3.000
 CRA  H83   C8  H82   109.30  3.000
 CRA  H83   C8  H81   109.18  3.000
 CRA  H82   C8  H81   109.17  3.000
 CRA  H83   C8  O8    111.64  3.000
 CRA  H82   C8  O8    111.66  3.000
 CRA  H81   C8  O8    105.79  3.000
 CRA  C8    O8  C7    116.92  3.000
 CRA  O9    C9  C1    123.27  3.000
 CRA  O9    C9  N1    124.01  3.000
 CRA  C1    C9  N1    112.68  3.000
 CRA  H1O6  O6  C6    108.01  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
 CRA  CONST_01  H1N1  N1  C9  C1    0.00   0.0  0
 CRA  CONST_02  H2N1  N1  C9  C1  180.00   0.0  0
 CRA  Var_01    O7    C7  N2  C1    0.36  30.0  2
 CRA  Var_02    H81   C8  O8  C7  178.00  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
 CRA  chir_01  C2  O2  C1  C3  negativ
 CRA  chir_02  C4  O4  C3  C5  negativ
 CRA  chir_03  C5  O5  C4  C6  negativ
 CRA  chir_04  C1  O5  C9  C2  positiv
 CRA  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
 CRA  plan-1  N1    0.020
 CRA  plan-1  C1    0.020
 CRA  plan-1  C9    0.020
 CRA  plan-1  O9    0.020
 CRA  plan-1  H1N1  0.020
 CRA  plan-1  H2N1  0.020
 CRA  plan-2  N2    0.020
 CRA  plan-2  C7    0.020
 CRA  plan-2  O7    0.020
 CRA  plan-2  O8    0.020

