# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 17:38:38 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: 2-deoxy-2-{[(2E)-3-(3,4-dichlorophenyl)prop-2-enoyl]amino}-alpha-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](O)[C@H](NC(=O)\C=C\c2ccc(Cl)c(Cl)c2)[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
 62C  62C  2-deoxy-2-{[(2E)-3-(3,4-dichlorophenyl)prop-2-enoyl]amino}-alpha-D-glucopyranose  ligand  41  24  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_62C
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
 62C  C4    C   CH1   0  -0.007  -5.1394  -0.6786   0.8168
 62C  C5    C   CH1   0  -0.018  -5.7251  -0.1833  -0.5091
 62C  C6    C   CH2   0  -0.163  -7.1930   0.1626  -0.3856
 62C  C8    C   C     0   0.583  -0.6192   0.8102   0.6926
 62C  C10   C   C1    0  -0.424   0.7604   0.4516   0.2833
 62C  C13   C   CR16  0  -0.305   4.1954   1.5828   1.1313
 62C  C15   C   CR6   0  -0.021   5.9380   0.3703   0.0177
 62C  C17   C   CR16  0  -0.278   3.6364  -0.2686  -0.2858
 62C  C16   C   CR6   0   0.034   4.9782  -0.4626  -0.5543
 62C  CL2   CL  CL    0  -0.087   7.6095   0.1379  -0.3099
 62C  C14   C   CR16  0  -0.202   5.5393   1.3939   0.8622
 62C  C12   C   CR6   0   0.155   3.2228   0.7623   0.5591
 62C  C11   C   C1    0  -0.231   1.8183   1.0171   0.8680
 62C  O9    O   O     0  -0.495  -0.8580   1.5820   1.6126
 62C  N7    N   NH1   0  -0.661  -1.5724   0.2192  -0.0523
 62C  C2    C   CH1   0  -0.156  -2.9858   0.3828   0.1603
 62C  C1    C   CH1   0   0.267  -3.6707   0.8632  -1.1219
 62C  O1    O   OH1   0  -0.668  -3.3551  -0.0337  -2.1388
 62C  C3    C   CH1   0   0.047  -3.6374  -0.8994   0.6710
 62C  O3    O   OH1   0  -0.663  -3.0368  -1.2300   1.8956
 62C  O4    O   OH1   0  -0.673  -5.7071  -1.9090   1.2097
 62C  O5    O   O2    0  -0.499  -5.0485   0.9944  -0.9223
 62C  O6    O   OH1   0  -0.669  -7.6884   0.5159  -1.6544
 62C  H41   H   HCH1  0   0.224  -5.3000   0.0927   1.5849
 62C  H51   H   HCH1  0   0.225  -5.6110  -0.9784  -1.2589
 62C  H61   H   HCH2  0   0.204  -7.7199  -0.7089   0.0201
 62C  H62   H   HCH2  0   0.197  -7.3101   0.9781   0.3421
 62C  H101  H   H     0   0.276   0.8738  -0.2746  -0.5136
 62C  H171  H   HCR6  0   0.285   2.9165  -0.9374  -0.7378
 62C  H141  H   HCR6  0   0.294   6.2807   2.0417   1.3088
 62C  H111  H   H     0   0.268   1.6436   1.7548   1.6449
 62C  H71   H   HNH1  0   0.401  -1.2874  -0.4041  -0.7919
 62C  H21   H   HCH1  0   0.279  -3.1200   1.1631   0.9125
 62C  H11   H   HCH1  0   0.245  -3.3200   1.8730  -1.3602
 62C  H12   H   HOH1  0   0.468  -3.5493   0.3694  -2.9919
 62C  H31   H   HCH1  0   0.214  -3.4822  -1.7008  -0.0688
 62C  H32   H   HOH1  0   0.451  -3.4466  -2.0415   2.2134
 62C  H42   H   HOH1  0   0.463  -6.4809  -1.7405   1.7541
 62C  H63   H   HOH1  0   0.457  -8.6328   0.6739  -1.5706
 62C  H131  H   HCR6  0   0.276   3.8995   2.3874   1.7921
 62C  CL1   CL  CL    0  -0.090   5.4508  -1.7471  -1.5996

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
 62C  O3   C3    single    1.403  0.020  1.403
 62C  CL2  C15   single    1.719  0.020  1.719
 62C  C14  C13   aromatic  1.383  0.020  1.383
 62C  C14  C15   aromatic  1.386  0.020  1.386
 62C  C13  C12   aromatic  1.395  0.020  1.395
 62C  C15  C16   aromatic  1.394  0.020  1.394
 62C  O4   C4    single    1.411  0.020  1.411
 62C  C3   C4    single    1.525  0.020  1.525
 62C  C3   C2    single    1.526  0.020  1.526
 62C  C4   C5    single    1.532  0.020  1.532
 62C  N7   C2    single    1.439  0.020  1.439
 62C  N7   C8    single    1.346  0.020  1.346
 62C  C10  C8    single    1.483  0.020  1.483
 62C  C10  C11   double    1.334  0.020  1.334
 62C  C12  C11   single    1.461  0.020  1.461
 62C  C12  C17   aromatic  1.396  0.020  1.396
 62C  C16  C17   aromatic  1.382  0.020  1.382
 62C  C16  CL1   single    1.722  0.020  1.722
 62C  C2   C1    single    1.531  0.020  1.531
 62C  C8   O9    double    1.224  0.020  1.224
 62C  C5   C6    single    1.513  0.020  1.513
 62C  C5   O5    single    1.420  0.020  1.420
 62C  C1   O1    single    1.392  0.020  1.392
 62C  C1   O5    single    1.398  0.020  1.398
 62C  O6   C6    single    1.407  0.020  1.407
 62C  C4   H41   single    0.970  0.020  1.090
 62C  C5   H51   single    0.970  0.020  1.090
 62C  C6   H61   single    0.970  0.020  1.090
 62C  C6   H62   single    0.970  0.020  1.090
 62C  C10  H101  single    0.930  0.020  1.080
 62C  C13  H131  single    0.930  0.020  1.080
 62C  C17  H171  single    0.930  0.020  1.080
 62C  C14  H141  single    0.930  0.020  1.080
 62C  C11  H111  single    0.930  0.020  1.080
 62C  N7   H71   single    0.860  0.020  1.020
 62C  C2   H21   single    0.970  0.020  1.090
 62C  C1   H11   single    0.970  0.020  1.090
 62C  O1   H12   single    0.850  0.020  0.980
 62C  C3   H31   single    0.970  0.020  1.090
 62C  O3   H32   single    0.850  0.020  0.980
 62C  O4   H42   single    0.850  0.020  0.980
 62C  O6   H63   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
 62C  H41   C4   O4   110.99  3.000
 62C  H41   C4   C3   108.18  3.000
 62C  O4    C4   C3   107.25  3.000
 62C  H41   C4   C5   108.77  3.000
 62C  C3    C4   C5   109.91  3.000
 62C  O4    C4   C5   111.66  3.000
 62C  H51   C5   O5   110.62  3.000
 62C  H51   C5   C6   108.77  3.000
 62C  O5    C5   C6   107.25  3.000
 62C  H51   C5   C4   108.48  3.000
 62C  O5    C5   C4   109.75  3.000
 62C  C6    C5   C4   111.97  3.000
 62C  H62   C6   H61  107.07  3.000
 62C  H62   C6   O6   111.91  3.000
 62C  H61   C6   O6   111.35  3.000
 62C  H62   C6   C5   109.08  3.000
 62C  H61   C6   C5   108.35  3.000
 62C  O6    C6   C5   108.99  3.000
 62C  N7    C8   O9   123.66  3.000
 62C  O9    C8   C10  122.77  3.000
 62C  N7    C8   C10  113.56  3.000
 62C  H101  C10  C11  121.54  3.000
 62C  H101  C10  C8   117.52  3.000
 62C  C11   C10  C8   120.93  3.000
 62C  H131  C13  C12  119.80  3.000
 62C  H131  C13  C14  119.07  3.000
 62C  C12   C13  C14  121.14  3.000
 62C  C14   C15  CL2  119.72  3.000
 62C  C14   C15  C16  119.57  3.000
 62C  CL2   C15  C16  120.71  3.000
 62C  H171  C17  C12  120.83  3.000
 62C  H171  C17  C16  118.57  3.000
 62C  C12   C17  C16  120.59  3.000
 62C  CL1   C16  C17  119.28  3.000
 62C  CL1   C16  C15  120.39  3.000
 62C  C17   C16  C15  120.33  3.000
 62C  H141  C14  C15  119.81  3.000
 62C  H141  C14  C13  120.26  3.000
 62C  C15   C14  C13  119.93  3.000
 62C  C11   C12  C17  122.81  3.000
 62C  C17   C12  C13  118.43  3.000
 62C  C11   C12  C13  118.76  3.000
 62C  H111  C11  C12  115.13  3.000
 62C  H111  C11  C10  118.30  3.000
 62C  C12   C11  C10  126.57  3.000
 62C  H71   N7   C2   117.15  3.000
 62C  H71   N7   C8   118.49  3.000
 62C  C2    N7   C8   124.32  3.000
 62C  H21   C2   C3   108.50  3.000
 62C  H21   C2   C1   107.32  3.000
 62C  C3    C2   C1   110.66  3.000
 62C  H21   C2   N7   107.69  3.000
 62C  C1    C2   N7   110.58  3.000
 62C  C3    C2   N7   111.93  3.000
 62C  H11   C1   O5   105.07  3.000
 62C  H11   C1   O1   111.25  3.000
 62C  O5    C1   O1   112.84  3.000
 62C  H11   C1   C2   109.17  3.000
 62C  O5    C1   C2   110.53  3.000
 62C  O1    C1   C2   107.95  3.000
 62C  H12   O1   C1   109.37  3.000
 62C  H31   C3   O3   110.75  3.000
 62C  H31   C3   C2   109.04  3.000
 62C  O3    C3   C2   107.89  3.000
 62C  H31   C3   C4   107.96  3.000
 62C  C2    C3   C4   109.32  3.000
 62C  O3    C3   C4   111.85  3.000
 62C  H32   O3   C3   107.72  3.000
 62C  H42   O4   C4   109.20  3.000
 62C  C1    O5   C5   115.68  3.000
 62C  H63   O6   C6   107.97  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
 62C  CONST_01  C16   C15  C14  C13     0.00   0.0  0
 62C  CONST_02  C16   C17  C12  C13     0.00   0.0  0
 62C  CONST_03  C12   C13  C14  C15     0.00   0.0  0
 62C  CONST_04  C12   C17  C16  C15     0.00   0.0  0
 62C  CONST_05  C14   C13  C12  C17     0.00   0.0  0
 62C  CONST_06  C14   C15  C16  C17     0.00   0.0  0
 62C  CONST_07  CL2   C15  C14  C13   180.00   0.0  0
 62C  CONST_08  CL2   C15  C16  C17   180.00   0.0  0
 62C  CONST_09  C14   C15  C16  CL1   180.00   0.0  0
 62C  CONST_10  C12   C17  C16  CL1   180.00   0.0  0
 62C  CONST_11  C11   C12  C17  C16   180.00   0.0  0
 62C  CONST_12  C11   C12  C13  C14   180.00   0.0  0
 62C  CONST_13  H171  C17  C12  C13   180.00   0.0  0
 62C  CONST_14  H131  C13  C14  C15   180.00   0.0  0
 62C  CONST_15  H141  C14  C15  C16   180.00   0.0  0
 62C  CONST_16  C2    N7   C8   C10   180.00   0.0  0
 62C  CONST_17  C2    N7   C8   O9      0.00   0.0  0
 62C  CONST_18  H71   N7   C8   C10     0.00   0.0  0
 62C  Var_01    C13   C12  C11  C10   170.74  30.0  2
 62C  Var_02    C12   C11  C10  C8   -179.66   0.0  2
 62C  Var_03    N7    C8   C10  C11   175.84  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
 62C  chir_01  C4  O4  C3  C5  negativ
 62C  chir_02  C5  O5  C4  C6  negativ
 62C  chir_03  C2  N7  C1  C3  negativ
 62C  chir_04  C1  O5  O1  C2  positiv
 62C  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
 62C  plan-1  C13   0.020
 62C  plan-1  C15   0.020
 62C  plan-1  C17   0.020
 62C  plan-1  C16   0.020
 62C  plan-1  CL2   0.020
 62C  plan-1  C14   0.020
 62C  plan-1  C12   0.020
 62C  plan-1  C11   0.020
 62C  plan-1  H171  0.020
 62C  plan-1  H141  0.020
 62C  plan-1  H131  0.020
 62C  plan-1  CL1   0.020
 62C  plan-2  C8    0.020
 62C  plan-2  C10   0.020
 62C  plan-2  O9    0.020
 62C  plan-2  N7    0.020
 62C  plan-2  C2    0.020
 62C  plan-2  H71   0.020
 62C  plan-3  C8    0.020
 62C  plan-3  C10   0.020
 62C  plan-3  C12   0.020
 62C  plan-3  C11   0.020
 62C  plan-3  H101  0.020
 62C  plan-3  H111  0.020

