# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 12:01:02 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: 2-amino-4,6-O-benzylidene-2-deoxy-alpha-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1[C@@H](O)O[C@@H]2CO[C@H](O[C@H]2[C@@H]1O)c3ccccc3
#
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
 04N  04N  2-amino-4,6-O-benzylidene-2-deoxy-alpha-D-glucopyranose  ligand  36  19  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_04N
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
 04N  C1    C  CH1   0   0.243  -3.5773  -0.7397  -0.1839
 04N  O1    O  OH1   0  -0.658  -3.6933  -0.6360  -1.5637
 04N  C2    C  CH1   0  -0.139  -3.3444   0.6542   0.4065
 04N  N2    N  NH2   0  -0.812  -4.3671   1.5804  -0.0493
 04N  C3    C  CH1   0   0.020  -1.9518   1.1922   0.0493
 04N  O3    O  OH1   0  -0.672  -1.6856   2.4045   0.7145
 04N  C4    C  CH1   0   0.014  -0.9400   0.1577   0.4864
 04N  O4    O  O2    0  -0.503   0.3727   0.5345   0.1275
 04N  C5    C  CH1   0   0.013  -1.2635  -1.1790  -0.1738
 04N  O5    O  O2    0  -0.503  -2.5461  -1.6216   0.2019
 04N  C6    C  CH2   0  -0.224  -0.2130  -2.1851   0.2652
 04N  O6    O  O2    0  -0.489   1.0630  -1.6633  -0.0620
 04N  CAL   C  CR16  0  -0.262   5.3026   0.7589  -0.4817
 04N  CAM   C  CR16  0  -0.244   5.0552  -0.4665   0.1253
 04N  CAN   C  CR16  0  -0.239   4.2449   1.6121  -0.7584
 04N  CAO   C  CR16  0  -0.277   3.7575  -0.8328   0.4481
 04N  CAP   C  CR16  0  -0.302   2.9435   1.2461  -0.4351
 04N  CBC   C  CR6   0  -0.016   2.6914   0.0193   0.1679
 04N  CBP   C  CH1   0   0.320   1.3009  -0.4201   0.5428
 04N  H1    H  HCH1  0   0.238  -4.4832  -1.1725   0.2577
 04N  H2    H  HCH1  0   0.228  -3.3635   0.5135   1.4989
 04N  HN2   H  HNH2  0   0.351  -5.2835   1.1611   0.0561
 04N  HN2A  H  HNH2  0   0.349  -4.3783   2.3874   0.5616
 04N  H3    H  HCH1  0   0.221  -1.8831   1.3226  -1.0393
 04N  HO3   H  HOH1  0   0.456  -2.0937   3.1202   0.2186
 04N  H4    H  HCH1  0   0.227  -1.0051   0.0325   1.5809
 04N  H5    H  HCH1  0   0.233  -1.1897  -1.0581  -1.2628
 04N  H6    H  HCH2  0   0.219  -0.2953  -2.3719   1.3451
 04N  H6A   H  HCH2  0   0.258  -0.3195  -3.1365  -0.2571
 04N  HAM   H  HCR6  0   0.257   5.8746  -1.1377   0.3485
 04N  HAN   H  HCR6  0   0.257   4.4295   2.5687  -1.2300
 04N  HAO   H  HCR6  0   0.253   3.5775  -1.7880   0.9259
 04N  HAP   H  HCR6  0   0.255   2.1326   1.9263  -0.6560
 04N  HBP   H  HCH1  0   0.210   1.2257  -0.5396   1.6393
 04N  H7    H  HOH1  0   0.462  -4.0136  -1.4741  -1.9148
 04N  HAL   H  HCR6  0   0.258   6.3150   1.0475  -0.7329

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
 04N  C1   O1    single    1.388  0.020  1.388
 04N  C1   C2    single    1.532  0.020  1.532
 04N  C1   O5    single    1.411  0.020  1.411
 04N  C2   N2    single    1.453  0.020  1.453
 04N  C2   C3    single    1.535  0.020  1.535
 04N  C3   O3    single    1.408  0.020  1.408
 04N  C3   C4    single    1.512  0.020  1.512
 04N  C4   O4    single    1.412  0.020  1.412
 04N  C4   C5    single    1.525  0.020  1.525
 04N  O4   CBP   single    1.395  0.020  1.395
 04N  C5   O5    single    1.408  0.020  1.408
 04N  C5   C6    single    1.519  0.020  1.519
 04N  C6   O6    single    1.417  0.020  1.417
 04N  O6   CBP   single    1.403  0.020  1.403
 04N  CAL  CAM   aromatic  1.390  0.020  1.390
 04N  CAL  CAN   aromatic  1.387  0.020  1.387
 04N  CAM  CAO   aromatic  1.387  0.020  1.387
 04N  CAN  CAP   aromatic  1.390  0.020  1.390
 04N  CAO  CBC   aromatic  1.393  0.020  1.393
 04N  CAP  CBC   aromatic  1.390  0.020  1.390
 04N  CBC  CBP   single    1.506  0.020  1.506
 04N  C1   H1    single    0.970  0.020  1.090
 04N  C2   H2    single    0.970  0.020  1.090
 04N  N2   HN2   single    0.890  0.020  1.040
 04N  N2   HN2A  single    0.890  0.020  1.040
 04N  C3   H3    single    0.970  0.020  1.090
 04N  O3   HO3   single    0.850  0.020  0.980
 04N  C4   H4    single    0.970  0.020  1.090
 04N  C5   H5    single    0.970  0.020  1.090
 04N  C6   H6    single    0.970  0.020  1.090
 04N  C6   H6A   single    0.970  0.020  1.090
 04N  CAL  HAL   single    0.930  0.020  1.080
 04N  CAM  HAM   single    0.930  0.020  1.080
 04N  CAN  HAN   single    0.930  0.020  1.080
 04N  CAO  HAO   single    0.930  0.020  1.080
 04N  CAP  HAP   single    0.930  0.020  1.080
 04N  CBP  HBP   single    0.970  0.020  1.090
 04N  O1   H7    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
 04N  H1    C1   O5   104.30  3.000
 04N  H1    C1   C2   109.24  3.000
 04N  O5    C1   C2   110.63  3.000
 04N  H1    C1   O1   111.14  3.000
 04N  O5    C1   O1   112.30  3.000
 04N  C2    C1   O1   109.14  3.000
 04N  H7    O1   C1   108.96  3.000
 04N  H2    C2   C3   106.93  3.000
 04N  H2    C2   N2   112.35  3.000
 04N  C3    C2   N2   110.01  3.000
 04N  H2    C2   C1   105.28  3.000
 04N  C3    C2   C1   111.54  3.000
 04N  N2    C2   C1   110.62  3.000
 04N  HN2A  N2   HN2  104.89  3.000
 04N  HN2A  N2   C2   109.06  3.000
 04N  HN2   N2   C2   109.89  3.000
 04N  H3    C3   C4   109.02  3.000
 04N  H3    C3   O3   110.74  3.000
 04N  C4    C3   O3   109.03  3.000
 04N  H3    C3   C2   109.20  3.000
 04N  C4    C3   C2   107.46  3.000
 04N  O3    C3   C2   111.30  3.000
 04N  HO3   O3   C3   108.47  3.000
 04N  H4    C4   C5   108.50  3.000
 04N  H4    C4   O4   109.70  3.000
 04N  C5    C4   O4   108.72  3.000
 04N  H4    C4   C3   108.96  3.000
 04N  C5    C4   C3   109.43  3.000
 04N  O4    C4   C3   111.48  3.000
 04N  CBP   O4   C4   111.12  3.000
 04N  H5    C5   C6   108.24  3.000
 04N  H5    C5   O5   111.13  3.000
 04N  C6    C5   O5   110.16  3.000
 04N  H5    C5   C4   108.57  3.000
 04N  C6    C5   C4   107.97  3.000
 04N  O5    C5   C4   110.68  3.000
 04N  C5    O5   C1   113.36  3.000
 04N  H6A   C6   H6   108.36  3.000
 04N  H6A   C6   O6   107.37  3.000
 04N  H6    C6   O6   110.91  3.000
 04N  H6A   C6   C5   111.82  3.000
 04N  H6    C6   C5   110.17  3.000
 04N  O6    C6   C5   108.18  3.000
 04N  CBP   O6   C6   112.30  3.000
 04N  HAL   CAL  CAN  120.20  3.000
 04N  HAL   CAL  CAM  120.20  3.000
 04N  CAN   CAL  CAM  119.59  3.000
 04N  HAM   CAM  CAO  119.78  3.000
 04N  HAM   CAM  CAL  120.14  3.000
 04N  CAO   CAM  CAL  120.08  3.000
 04N  HAN   CAN  CAP  119.59  3.000
 04N  HAN   CAN  CAL  120.04  3.000
 04N  CAP   CAN  CAL  120.38  3.000
 04N  HAO   CAO  CBC  120.07  3.000
 04N  HAO   CAO  CAM  119.42  3.000
 04N  CBC   CAO  CAM  120.51  3.000
 04N  HAP   CAP  CBC  120.52  3.000
 04N  HAP   CAP  CAN  119.28  3.000
 04N  CBC   CAP  CAN  120.21  3.000
 04N  CBP   CBC  CAP  122.22  3.000
 04N  CBP   CBC  CAO  118.56  3.000
 04N  CAP   CBC  CAO  119.23  3.000
 04N  HBP   CBP  CBC  109.96  3.000
 04N  HBP   CBP  O6   108.68  3.000
 04N  CBC   CBP  O6   107.93  3.000
 04N  HBP   CBP  O4   108.91  3.000
 04N  CBC   CBP  O4   109.92  3.000
 04N  O6    CBP  O4   111.43  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
 04N  CONST_01  CBC  CAO  CAM  CAL    0.00   0.0  0
 04N  CONST_02  CBC  CAP  CAN  CAL    0.00   0.0  0
 04N  CONST_03  CAP  CAN  CAL  CAM    0.00   0.0  0
 04N  CONST_04  CAP  CBC  CAO  CAM    0.00   0.0  0
 04N  CONST_05  CAO  CAM  CAL  CAN    0.00   0.0  0
 04N  CONST_06  CAO  CBC  CAP  CAN    0.00   0.0  0
 04N  CONST_07  CBP  CBC  CAO  CAM  180.00   0.0  0
 04N  CONST_08  CBP  CBC  CAP  CAN  180.00   0.0  0
 04N  CONST_09  HAO  CAO  CAM  CAL  180.00   0.0  0
 04N  CONST_10  HAP  CAP  CAN  CAL  180.00   0.0  0
 04N  CONST_11  HAN  CAN  CAL  CAM  180.00   0.0  0
 04N  CONST_12  HAM  CAM  CAL  CAN  180.00   0.0  0
 04N  CONST_13  HAL  CAL  CAM  CAO  180.00   0.0  0
 04N  Var_01    H6   C6   O6   CBP  -62.75  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
 04N  chir_01  C1   O1  C2  O5   positiv
 04N  chir_02  C2   N2  C1  C3   negativ
 04N  chir_03  C3   O3  C2  C4   positiv
 04N  chir_04  C4   O4  C5  C3   positiv
 04N  chir_05  C5   O5  C4  C6   negativ
 04N  chir_06  CBP  O4  O6  CBC  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
 04N  plan-1  CAL  0.020
 04N  plan-1  CAM  0.020
 04N  plan-1  CAN  0.020
 04N  plan-1  CAO  0.020
 04N  plan-1  CAP  0.020
 04N  plan-1  CBC  0.020
 04N  plan-1  CBP  0.020
 04N  plan-1  HAM  0.020
 04N  plan-1  HAN  0.020
 04N  plan-1  HAO  0.020
 04N  plan-1  HAP  0.020
 04N  plan-1  HAL  0.020

