# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 23:06:06 2022
#   Inital geometry file: a 107 line input string
#   Ligand name: 2-(acetylamino)-3-O-[(2S,3S)-2-carboxy-3,4-dihydroxybutan-2-yl]-2-deoxy-alpha-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@H]1[C@@H](O)O[C@H](CO)[C@@H](O)[C@@H]1O[C@@](C)([C@@H](O)CO)C(O)=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
 UDC  UDC  2-(acetylamino)-3-O-[(2S,3S)-2-carboxy-3,4-dihydroxybutan-2-yl]-2-deoxy-alpha-D-glucopyranose  D-saccharide  46  24  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UDC
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
 UDC  C1    C  CH1    0   0.264   4.2135  -0.1090  -4.8506
 UDC  O1    O  OH1    0  -0.666   5.3033  -0.9280  -5.1420
 UDC  C2    C  CH1    0  -0.147   3.7706  -0.4008  -3.4194
 UDC  N2    N  NH1    0  -0.621   4.8576  -0.1737  -2.5053
 UDC  C3    C  CH1    0   0.046   3.1682  -1.8081  -3.2895
 UDC  O3    O  O2     0  -0.529   2.7151  -1.8838  -1.9591
 UDC  C4    C  CH1    0   0.029   2.0420  -1.9514  -4.3320
 UDC  O4    O  OH1    0  -0.718   1.5396  -3.2492  -4.4459
 UDC  C5    C  CH1    0  -0.000   2.5661  -1.5774  -5.7243
 UDC  O5    O  O2     0  -0.499   3.1480  -0.2839  -5.7334
 UDC  C6    C  CH2    0  -0.183   1.4994  -1.5947  -6.7997
 UDC  O6    O  OH1    0  -0.669   0.4649  -0.6978  -6.4688
 UDC  C7    C  C      0   0.511   4.7958   0.6656  -1.4533
 UDC  O7    O  O      0  -0.493   3.8189   1.3549  -1.1975
 UDC  C8    C  CH3    0  -0.783   6.0382   0.7172  -0.5976
 UDC  CBN   C  CT     0   0.063   2.4905  -3.1089  -1.2461
 UDC  CBO   C  C      0   0.488   0.9330  -3.2473  -1.2110
 UDC  OBP   O  OC    -1  -0.555   0.3214  -2.7360  -0.2682
 UDC  OBQ   O  O      0  -0.617   0.3948  -3.8166  -2.2012
 UDC  CBR   C  CH3    0  -0.730   3.1698  -4.3283  -1.8521
 UDC  CBS   C  CH1    0   0.034   3.0199  -2.8234   0.1784
 UDC  OBT   O  OH1    0  -0.678   2.6535  -3.8455   1.0749
 UDC  CBU   C  CH2    0  -0.217   4.5292  -2.5804   0.2730
 UDC  OBV   O  OH1    0  -0.673   5.2088  -3.8218   0.3676
 UDC  H1    H  HCH1   0   0.235   4.4837   0.9501  -4.9345
 UDC  HO1   H  HOH1   0   0.462   5.7445  -0.6034  -5.9350
 UDC  H2    H  HCH1   0   0.268   2.9898   0.3232  -3.1774
 UDC  HN2   H  HNH1   0   0.395   5.6949  -0.7181  -2.6390
 UDC  H3    H  HCH1   0   0.216   3.9390  -2.5621  -3.4952
 UDC  H4    H  HCH1   0   0.187   1.2549  -1.2345  -4.0463
 UDC  HO4   H  HOH1   0   0.461   1.0842  -3.5008  -3.5948
 UDC  H5    H  HCH1   0   0.216   3.3121  -2.3310  -6.0151
 UDC  H61   H  HCH2   0   0.205   1.9741  -1.3284  -7.7543
 UDC  H62   H  HCH2   0   0.208   1.1358  -2.6218  -6.9038
 UDC  HO6   H  HOH1   0   0.453  -0.2514  -0.8240  -7.0968
 UDC  H81   H  HCH3   0   0.268   6.4389   1.7311  -0.6019
 UDC  H82   H  HCH3   0   0.264   5.7738   0.4791   0.4327
 UDC  H83   H  HCH3   0   0.246   6.8243   0.0352  -0.9165
 UDC  HBR   H  HCH3   0   0.236   3.0023  -5.1920  -1.2080
 UDC  HBRA  H  HCH3   0   0.235   2.7807  -4.5784  -2.8344
 UDC  HBRB  H  HCH3   0   0.236   4.2471  -4.1946  -1.9476
 UDC  HBS   H  HCH1   0   0.220   2.5332  -1.9005   0.5062
 UDC  HOBT  H  HOH1   0   0.436   3.4114  -4.4421   1.1236
 UDC  HBU   H  HCH2   0   0.213   4.8758  -2.0053  -0.5887
 UDC  HBUA  H  HCH2   0   0.222   4.7209  -1.9740   1.1650
 UDC  HOBV  H  HOH1   0   0.461   5.9824  -3.7069   0.9248

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
 UDC  O5   C1    single  1.395  0.020  1.395
 UDC  O1   C1    single  1.394  0.020  1.394
 UDC  C1   C2    single  1.526  0.020  1.526
 UDC  C1   H1    single  0.970  0.020  1.090
 UDC  O1   HO1   single  0.850  0.020  0.980
 UDC  C2   C3    single  1.536  0.020  1.536
 UDC  C2   N2    single  1.438  0.020  1.438
 UDC  C2   H2    single  0.970  0.020  1.090
 UDC  N2   C7    single  1.347  0.020  1.347
 UDC  N2   HN2   single  0.860  0.020  1.020
 UDC  C4   C3    single  1.541  0.020  1.541
 UDC  C3   O3    single  1.407  0.020  1.407
 UDC  C3   H3    single  0.970  0.020  1.090
 UDC  O3   CBN   single  1.435  0.020  1.435
 UDC  C5   C4    single  1.534  0.020  1.534
 UDC  O4   C4    single  1.396  0.020  1.396
 UDC  C4   H4    single  0.970  0.020  1.090
 UDC  O4   HO4   single  0.850  0.020  0.980
 UDC  C6   C5    single  1.515  0.020  1.515
 UDC  C5   O5    single  1.418  0.020  1.418
 UDC  C5   H5    single  0.970  0.020  1.090
 UDC  C6   O6    single  1.409  0.020  1.409
 UDC  C6   H61   single  0.970  0.020  1.090
 UDC  C6   H62   single  0.970  0.020  1.090
 UDC  O6   HO6   single  0.850  0.020  0.980
 UDC  O7   C7    double  1.223  0.020  1.223
 UDC  C7   C8    single  1.509  0.020  1.509
 UDC  C8   H81   single  0.970  0.020  1.090
 UDC  C8   H82   single  0.970  0.020  1.090
 UDC  C8   H83   single  0.970  0.020  1.090
 UDC  CBR  CBN   single  1.522  0.020  1.522
 UDC  CBN  CBO   single  1.564  0.020  1.564
 UDC  CBN  CBS   single  1.546  0.020  1.546
 UDC  OBQ  CBO   deloc   1.263  0.020  1.263
 UDC  CBO  OBP   deloc   1.235  0.020  1.235
 UDC  CBR  HBR   single  0.970  0.020  1.090
 UDC  CBR  HBRA  single  0.970  0.020  1.090
 UDC  CBR  HBRB  single  0.970  0.020  1.090
 UDC  CBU  CBS   single  1.532  0.020  1.532
 UDC  CBS  OBT   single  1.408  0.020  1.408
 UDC  CBS  HBS   single  0.970  0.020  1.090
 UDC  OBT  HOBT  single  0.850  0.020  0.980
 UDC  CBU  OBV   single  1.418  0.020  1.418
 UDC  CBU  HBU   single  0.970  0.020  1.090
 UDC  CBU  HBUA  single  0.970  0.020  1.090
 UDC  OBV  HOBV  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
 UDC  H1    C1   O5    105.13  3.000
 UDC  H1    C1   C2    109.14  3.000
 UDC  O5    C1   C2    110.35  3.000
 UDC  H1    C1   O1    111.04  3.000
 UDC  C2    C1   O1    108.09  3.000
 UDC  O5    C1   O1    113.04  3.000
 UDC  HO1   O1   C1    109.39  3.000
 UDC  H2    C2   C3    107.95  3.000
 UDC  H2    C2   N2    107.15  3.000
 UDC  C3    C2   N2    112.78  3.000
 UDC  H2    C2   C1    106.77  3.000
 UDC  N2    C2   C1    110.27  3.000
 UDC  C3    C2   C1    111.61  3.000
 UDC  HN2   N2   C7    118.57  3.000
 UDC  HN2   N2   C2    117.28  3.000
 UDC  C7    N2   C2    124.06  3.000
 UDC  H3    C3   C4    108.81  3.000
 UDC  H3    C3   O3    111.49  3.000
 UDC  C4    C3   O3    113.53  3.000
 UDC  H3    C3   C2    109.75  3.000
 UDC  O3    C3   C2    104.80  3.000
 UDC  C4    C3   C2    108.33  3.000
 UDC  CBN   O3   C3    124.46  3.000
 UDC  H4    C4   C5    108.70  3.000
 UDC  H4    C4   O4    111.63  3.000
 UDC  C5    C4   O4    105.99  3.000
 UDC  H4    C4   C3    106.62  3.000
 UDC  O4    C4   C3    113.86  3.000
 UDC  C5    C4   C3    109.98  3.000
 UDC  HO4   O4   C4    109.21  3.000
 UDC  H5    C5   C6    106.39  3.000
 UDC  H5    C5   O5    110.19  3.000
 UDC  C6    C5   O5    107.15  3.000
 UDC  H5    C5   C4    107.74  3.000
 UDC  O5    C5   C4    111.61  3.000
 UDC  C6    C5   C4    113.64  3.000
 UDC  C5    O5   C1    115.07  3.000
 UDC  H62   C6   H61   106.76  3.000
 UDC  H62   C6   O6    112.08  3.000
 UDC  H61   C6   O6    111.53  3.000
 UDC  H62   C6   C5    108.20  3.000
 UDC  H61   C6   C5    108.04  3.000
 UDC  O6    C6   C5    110.07  3.000
 UDC  HO6   O6   C6    108.08  3.000
 UDC  C8    C7   O7    121.32  3.000
 UDC  C8    C7   N2    115.23  3.000
 UDC  O7    C7   N2    123.45  3.000
 UDC  H83   C8   H82   108.38  3.000
 UDC  H83   C8   H81   108.43  3.000
 UDC  H82   C8   H81   107.21  3.000
 UDC  H83   C8   C7    114.01  3.000
 UDC  H82   C8   C7    109.19  3.000
 UDC  H81   C8   C7    109.40  3.000
 UDC  CBS   CBN  CBR   111.23  3.000
 UDC  CBS   CBN  CBO   109.67  3.000
 UDC  CBR   CBN  CBO   112.49  3.000
 UDC  CBS   CBN  O3    104.27  3.000
 UDC  CBO   CBN  O3    104.04  3.000
 UDC  CBR   CBN  O3    114.60  3.000
 UDC  OBQ   CBO  OBP   125.06  3.000
 UDC  OBP   CBO  CBN   118.28  3.000
 UDC  OBQ   CBO  CBN   116.54  3.000
 UDC  HBRB  CBR  HBRA  107.66  3.000
 UDC  HBRB  CBR  HBR   107.50  3.000
 UDC  HBRA  CBR  HBR   107.27  3.000
 UDC  HBRB  CBR  CBN   112.21  3.000
 UDC  HBRA  CBR  CBN   112.64  3.000
 UDC  HBR   CBR  CBN   109.32  3.000
 UDC  HBS   CBS  CBU   106.62  3.000
 UDC  HBS   CBS  OBT   107.81  3.000
 UDC  CBU   CBS  OBT   109.40  3.000
 UDC  HBS   CBS  CBN   106.24  3.000
 UDC  OBT   CBS  CBN   111.31  3.000
 UDC  CBU   CBS  CBN   115.06  3.000
 UDC  HOBT  OBT  CBS   106.05  3.000
 UDC  HBUA  CBU  HBU   107.17  3.000
 UDC  HBUA  CBU  OBV   110.27  3.000
 UDC  HBU   CBU  OBV   111.18  3.000
 UDC  HBUA  CBU  CBS   108.10  3.000
 UDC  HBU   CBU  CBS   110.33  3.000
 UDC  OBV   CBU  CBS   109.72  3.000
 UDC  HOBV  OBV  CBU   108.66  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
 UDC  CONST_01  O7   C7  N2  C2    0.00   0.0  0
 UDC  CONST_02  C8   C7  N2  C2  180.00   0.0  0
 UDC  CONST_03  HN2  N2  C7  O7  180.00   0.0  0
 UDC  Var_01    H81  C8  C7  N2  119.33  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
 UDC  chir_01  C1   O5   O1   C2   positiv
 UDC  chir_02  C2   N2   C3   C1   positiv
 UDC  chir_03  C3   O3   C4   C2   negativ
 UDC  chir_04  C4   O4   C5   C3   positiv
 UDC  chir_05  C5   O5   C4   C6   negativ
 UDC  chir_06  CBN  CBS  CBO  CBR  positiv
 UDC  chir_07  CBS  OBT  CBN  CBU  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
 UDC  plan-1  C2   0.020
 UDC  plan-1  N2   0.020
 UDC  plan-1  C7   0.020
 UDC  plan-1  O7   0.020
 UDC  plan-1  C8   0.020
 UDC  plan-1  HN2  0.020
 UDC  plan-2  CBN  0.020
 UDC  plan-2  CBO  0.020
 UDC  plan-2  OBP  0.020
 UDC  plan-2  OBQ  0.020

