# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 12:28:08 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 2-amino-2-deoxy-4,6-O-[(1R)-3-phenylpropylidene]-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](CCc3ccccc3)O[C@H]2[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
 04O  04O  2-amino-2-deoxy-4,6-O-[(1R)-3-phenylpropylidene]-alpha-D-glucopyranose  ligand  42  21  .  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_04O
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
 04O  C11   C  CH1   0   0.245  -4.5060  -0.7056  -0.0407
 04O  O11   O  OH1   0  -0.658  -4.6250  -0.9301  -1.4057
 04O  C16   C  CR6   0   0.131   4.2298  -0.2051   0.2714
 04O  C21   C  CH1   0  -0.138  -4.2672   0.7882   0.2045
 04O  N21   N  NH2   0  -0.811  -5.2970   1.5796  -0.4440
 04O  C26   C  CR16  0  -0.309   4.8589   0.9095   0.8227
 04O  C31   C  CH1   0   0.018  -2.8799   1.2188  -0.2896
 04O  O31   O  OH1   0  -0.673  -2.6028   2.5556   0.0580
 04O  C36   C  CR16  0  -0.240   6.0863   1.3462   0.3423
 04O  C41   C  CH1   0   0.004  -1.8641   0.3169   0.3750
 04O  O41   O  O2    0  -0.501  -0.5559   0.5922  -0.0750
 04O  C46   C  CR16  0  -0.274   6.7058   0.6726  -0.7029
 04O  C51   C  CH1   0   0.012  -2.1931  -1.1395   0.0636
 04O  O51   O  O2    0  -0.503  -3.4757  -1.4758   0.5388
 04O  C56   C  CR16  0  -0.240   6.0887  -0.4393  -1.2610
 04O  C61   C  CH2   0  -0.222  -1.1425  -2.0081   0.7353
 04O  O61   O  O2    0  -0.491   0.1332  -1.5857   0.2930
 04O  C66   C  CR16  0  -0.312   4.8609  -0.8718  -0.7765
 04O  CBJ   C  CH1   0   0.316   0.3823  -0.2333   0.5622
 04O  H11   H  HCH1  0   0.236  -5.4119  -1.0201   0.4922
 04O  H21   H  HCH1  0   0.225  -4.2696   0.9079   1.2998
 04O  HN21  H  HNH2  0   0.350  -6.2123   1.2544  -0.1554
 04O  HN2A  H  HNH2  0   0.347  -5.2423   2.5327  -0.1071
 04O  H26   H  HCR6  0   0.246   4.3840   1.4421   1.6395
 04O  H31   H  HCH1  0   0.222  -2.8263   1.0813  -1.3779
 04O  HO31  H  HOH1  0   0.457  -2.9594   3.1311  -0.6243
 04O  H35   H  HCH2  0   0.249   1.9052   1.1982   0.2124
 04O  H35A  H  HCH2  0   0.244   1.8090  -0.0467  -1.0250
 04O  H36   H  HCR6  0   0.253   6.5615   2.2115   0.7867
 04O  H41   H  HCH1  0   0.221  -1.9199   0.4618   1.4684
 04O  H45   H  HCH2  0   0.251   2.7545  -1.7154   0.5861
 04O  H45A  H  HCH2  0   0.244   2.8009  -0.4867   1.8379
 04O  H46   H  HCR6  0   0.253   7.6639   1.0094  -1.0773
 04O  H51   H  HCH1  0   0.230  -2.1232  -1.2896  -1.0223
 04O  H56   H  HCR6  0   0.253   6.5653  -0.9742  -2.0728
 04O  H61   H  HCH2  0   0.215  -1.2272  -1.9248   1.8283
 04O  H61A  H  HCH2  0   0.255  -1.2520  -3.0590   0.4645
 04O  H66   H  HCR6  0   0.246   4.3865  -1.7412  -1.2173
 04O  HBJ   H  HCH1  0   0.192   0.3184  -0.0677   1.6536
 04O  H2    H  HOH1  0   0.462  -4.9531  -1.8248  -1.5475
 04O  C35   C  CH2   0  -0.490   1.7606   0.1268   0.0541
 04O  C45   C  CH2   0  -0.516   2.8769  -0.6449   0.7585

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
 04O  C11  O11   single    1.388  0.020  1.388
 04O  C11  C21   single    1.532  0.020  1.532
 04O  C11  O51   single    1.411  0.020  1.411
 04O  C16  C26   aromatic  1.394  0.020  1.394
 04O  C16  C45   single    1.504  0.020  1.504
 04O  C16  C66   aromatic  1.393  0.020  1.393
 04O  C21  N21   single    1.452  0.020  1.452
 04O  C21  C31   single    1.534  0.020  1.534
 04O  C26  C36   aromatic  1.389  0.020  1.389
 04O  C31  O31   single    1.409  0.020  1.409
 04O  C31  C41   single    1.512  0.020  1.512
 04O  C35  C45   single    1.529  0.020  1.529
 04O  C35  CBJ   single    1.512  0.020  1.512
 04O  C36  C46   aromatic  1.389  0.020  1.389
 04O  C41  O41   single    1.410  0.020  1.410
 04O  C41  C51   single    1.525  0.020  1.525
 04O  O41  CBJ   single    1.403  0.020  1.403
 04O  C46  C56   aromatic  1.389  0.020  1.389
 04O  C51  O51   single    1.409  0.020  1.409
 04O  C51  C61   single    1.520  0.020  1.520
 04O  C56  C66   aromatic  1.389  0.020  1.389
 04O  C61  O61   single    1.415  0.020  1.415
 04O  O61  CBJ   single    1.401  0.020  1.401
 04O  C11  H11   single    0.970  0.020  1.090
 04O  C21  H21   single    0.970  0.020  1.090
 04O  N21  HN21  single    0.890  0.020  1.040
 04O  N21  HN2A  single    0.890  0.020  1.040
 04O  C26  H26   single    0.930  0.020  1.080
 04O  C31  H31   single    0.970  0.020  1.090
 04O  O31  HO31  single    0.850  0.020  0.980
 04O  C35  H35   single    0.970  0.020  1.090
 04O  C35  H35A  single    0.970  0.020  1.090
 04O  C36  H36   single    0.930  0.020  1.080
 04O  C41  H41   single    0.970  0.020  1.090
 04O  C45  H45   single    0.970  0.020  1.090
 04O  C45  H45A  single    0.970  0.020  1.090
 04O  C46  H46   single    0.930  0.020  1.080
 04O  C51  H51   single    0.970  0.020  1.090
 04O  C56  H56   single    0.930  0.020  1.080
 04O  C61  H61   single    0.970  0.020  1.090
 04O  C61  H61A  single    0.970  0.020  1.090
 04O  C66  H66   single    0.930  0.020  1.080
 04O  CBJ  HBJ   single    0.970  0.020  1.090
 04O  O11  H2    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
 04O  H11   C11  O51   104.30  3.000
 04O  H11   C11  C21   109.29  3.000
 04O  O51   C11  C21   110.65  3.000
 04O  H11   C11  O11   111.12  3.000
 04O  O51   C11  O11   112.22  3.000
 04O  C21   C11  O11   109.16  3.000
 04O  H2    O11  C11   108.91  3.000
 04O  C66   C16  C45   120.75  3.000
 04O  C66   C16  C26   118.42  3.000
 04O  C45   C16  C26   120.79  3.000
 04O  H21   C21  C31   106.95  3.000
 04O  H21   C21  N21   112.54  3.000
 04O  C31   C21  N21   110.16  3.000
 04O  H21   C21  C11   105.34  3.000
 04O  C31   C21  C11   111.28  3.000
 04O  N21   C21  C11   110.45  3.000
 04O  HN2A  N21  HN21  104.84  3.000
 04O  HN2A  N21  C21   109.05  3.000
 04O  HN21  N21  C21   109.79  3.000
 04O  H26   C26  C36   119.55  3.000
 04O  H26   C26  C16   119.54  3.000
 04O  C36   C26  C16   120.91  3.000
 04O  H31   C31  C41   109.16  3.000
 04O  H31   C31  O31   110.71  3.000
 04O  C41   C31  O31   108.99  3.000
 04O  H31   C31  C21   109.15  3.000
 04O  C41   C31  C21   107.37  3.000
 04O  O31   C31  C21   111.39  3.000
 04O  HO31  O31  C31   108.67  3.000
 04O  H36   C36  C46   120.04  3.000
 04O  H36   C36  C26   119.83  3.000
 04O  C46   C36  C26   120.14  3.000
 04O  H41   C41  C51   108.45  3.000
 04O  H41   C41  O41   109.70  3.000
 04O  C51   C41  O41   108.74  3.000
 04O  H41   C41  C31   108.84  3.000
 04O  C51   C41  C31   109.56  3.000
 04O  O41   C41  C31   111.49  3.000
 04O  CBJ   O41  C41   111.13  3.000
 04O  H46   C46  C56   120.23  3.000
 04O  H46   C46  C36   120.27  3.000
 04O  C56   C46  C36   119.50  3.000
 04O  H51   C51  C61   108.35  3.000
 04O  H51   C51  O51   111.02  3.000
 04O  C61   C51  O51   110.11  3.000
 04O  H51   C51  C41   108.58  3.000
 04O  C61   C51  C41   107.85  3.000
 04O  O51   C51  C41   110.83  3.000
 04O  C51   O51  C11   113.33  3.000
 04O  H56   C56  C66   119.79  3.000
 04O  H56   C56  C46   120.08  3.000
 04O  C66   C56  C46   120.13  3.000
 04O  H61A  C61  H61   108.19  3.000
 04O  H61A  C61  O61   107.49  3.000
 04O  H61   C61  O61   110.96  3.000
 04O  H61A  C61  C51   111.81  3.000
 04O  H61   C61  C51   110.05  3.000
 04O  O61   C61  C51   108.33  3.000
 04O  CBJ   O61  C61   112.85  3.000
 04O  H66   C66  C56   119.65  3.000
 04O  H66   C66  C16   119.43  3.000
 04O  C56   C66  C16   120.92  3.000
 04O  HBJ   CBJ  O61   108.90  3.000
 04O  HBJ   CBJ  O41   108.76  3.000
 04O  O61   CBJ  O41   111.21  3.000
 04O  HBJ   CBJ  C35   110.41  3.000
 04O  O61   CBJ  C35   109.10  3.000
 04O  O41   CBJ  C35   108.47  3.000
 04O  H35A  C35  H35   107.01  3.000
 04O  H35A  C35  CBJ   109.51  3.000
 04O  H35   C35  CBJ   107.78  3.000
 04O  H35A  C35  C45   110.00  3.000
 04O  H35   C35  C45   109.36  3.000
 04O  CBJ   C35  C45   112.98  3.000
 04O  H45A  C45  H45   106.86  3.000
 04O  H45A  C45  C35   109.33  3.000
 04O  H45   C45  C35   109.91  3.000
 04O  H45A  C45  C16   109.87  3.000
 04O  H45   C45  C16   109.68  3.000
 04O  C35   C45  C16   111.10  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
 04O  CONST_01  C46  C36  C26  C16     0.00   0.0  0
 04O  CONST_02  C46  C56  C66  C16     0.00   0.0  0
 04O  CONST_03  C56  C66  C16  C26     0.00   0.0  0
 04O  CONST_04  C56  C46  C36  C26     0.00   0.0  0
 04O  CONST_05  C66  C16  C26  C36     0.00   0.0  0
 04O  CONST_06  C66  C56  C46  C36     0.00   0.0  0
 04O  CONST_07  C45  C16  C26  C36   180.00   0.0  0
 04O  CONST_08  C56  C66  C16  C45   180.00   0.0  0
 04O  CONST_09  H36  C36  C26  C16   180.00   0.0  0
 04O  CONST_10  H56  C56  C66  C16   180.00   0.0  0
 04O  CONST_11  H66  C66  C16  C26   180.00   0.0  0
 04O  CONST_12  H46  C46  C36  C26   180.00   0.0  0
 04O  CONST_13  H26  C26  C36  C46   180.00   0.0  0
 04O  Var_01    H61  C61  O61  CBJ   -63.10  30.0  1
 04O  Var_02    CBJ  C35  C45  C16  -177.12  30.0  1
 04O  Var_03    C35  C45  C16  C26    84.55  30.0  2

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
 04O  chir_01  C11  O11  C21  O51  positiv
 04O  chir_02  C21  N21  C11  C31  negativ
 04O  chir_03  C31  O31  C21  C41  positiv
 04O  chir_04  C41  O41  C51  C31  positiv
 04O  chir_05  C51  O51  C41  C61  negativ
 04O  chir_06  CBJ  O41  O61  C35  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
 04O  plan-1  C16  0.020
 04O  plan-1  C26  0.020
 04O  plan-1  C36  0.020
 04O  plan-1  C46  0.020
 04O  plan-1  C56  0.020
 04O  plan-1  C66  0.020
 04O  plan-1  H26  0.020
 04O  plan-1  H36  0.020
 04O  plan-1  H46  0.020
 04O  plan-1  H56  0.020
 04O  plan-1  H66  0.020
 04O  plan-1  C45  0.020

