# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 12:51:40 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: 3-[(2S,4S,5R)-5,6-dichloro-2,4-dimethylhexanoyl]-4-hydroxy-5,6-dimethoxypyridin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC1=C(OC)C(=C(C(=O)N1)C(=O)[C@@H](C)C[C@H](C)[C@@H](Cl)CCl)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
 AT5  AT5  3-[(2S,4S,5R)-5,6-dichloro-2,4-dimethylhexanoyl]-4-hydroxy-5,6-dimethoxypyridin-2(1H)-one  ligand  44  23  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AT5
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
 AT5  O5    O   O     0  -0.412   0.1208  -1.8046   0.1387
 AT5  C7    C   C     0   0.440   0.3849  -0.6224   0.0298
 AT5  C8    C   CH1   0  -0.397  -0.7182   0.3860  -0.2554
 AT5  C11   C   CH2   0  -0.387  -2.0943  -0.2719  -0.1734
 AT5  C12   C   CH1   0  -0.244  -3.2687   0.7056  -0.2886
 AT5  C17   C   CH3   0  -0.676  -3.2544   1.7785   0.7942
 AT5  C13   C   CH1   0  -0.253  -4.5878  -0.0682  -0.3599
 AT5  CL12  CL  CL    0  -0.156  -4.9174  -0.9505   1.1850
 AT5  C14   C   CH2   0  -0.440  -5.7693   0.8203  -0.6759
 AT5  CL16  CL  CL    0  -0.151  -7.2509  -0.1366  -0.9901
 AT5  C10   C   CH3   0  -0.670  -0.4651   1.0463  -1.6155
 AT5  C6    C   CR6   0  -0.425   1.7907  -0.1619   0.1165
 AT5  C5    C   CR6   0   0.516   2.1271   1.1445   0.6082
 AT5  N4    N   NR16  0  -0.758   3.4924   1.4447   0.6458
 AT5  C3    C   CR6   0   0.636   4.4894   0.6226   0.2735
 AT5  C2    C   CR6   0   0.035   4.1840  -0.6368  -0.1792
 AT5  C1    C   CR6   0   0.469   2.8320  -1.0236  -0.2499
 AT5  O1    O   OH1   0  -0.576   2.5710  -2.2296  -0.7278
 AT5  O2    O   O2    0  -0.495   5.1466  -1.5113  -0.5851
 AT5  CM2   C   CH3   0  -0.416   5.7892  -2.2154   0.4806
 AT5  O3    O   O2    0  -0.437   5.7473   0.9968   0.3307
 AT5  CM3   C   CH3   0  -0.473   6.0974   2.3095   0.7707
 AT5  O4    O   OC    0  -0.485   1.3609   2.0146   1.0105
 AT5  H8    H   HCH1  0   0.275  -0.6422   1.1606   0.5078
 AT5  H111  H   HCH2  0   0.227  -2.1892  -1.0238  -0.9629
 AT5  H112  H   HCH2  0   0.230  -2.1782  -0.8081   0.7747
 AT5  H12   H   HCH1  0   0.254  -3.2110   1.2036  -1.2641
 AT5  H171  H   HCH3  0   0.244  -2.3611   2.3974   0.7158
 AT5  H172  H   HCH3  0   0.241  -4.1065   2.4532   0.7159
 AT5  H173  H   HCH3  0   0.229  -3.2627   1.3371   1.7913
 AT5  H13   H   HCH1  0   0.309  -4.5027  -0.8418  -1.1241
 AT5  H141  H   HCH2  0   0.296  -5.9958   1.5085   0.1344
 AT5  H142  H   HCH2  0   0.300  -5.5591   1.3919  -1.5789
 AT5  H101  H   HCH3  0   0.240  -1.1848   1.8441  -1.7972
 AT5  H102  H   HCH3  0   0.244   0.5266   1.4920  -1.6782
 AT5  H103  H   HCH3  0   0.227  -0.5597   0.3209  -2.4256
 AT5  HN4   H   HNR6  0   0.443   3.7053   2.3685   1.0024
 AT5  HO1   H   HOH1  0   0.482   3.3963  -2.6358  -1.0341
 AT5  HM21  H   HCH3  0   0.236   6.3665  -1.5401   1.1134
 AT5  HM22  H   HCH3  0   0.229   5.0659  -2.7494   1.1008
 AT5  HM23  H   HCH3  0   0.249   6.4648  -2.9350   0.0234
 AT5  HM31  H   HCH3  0   0.259   5.6866   3.0728   0.1085
 AT5  HM32  H   HCH3  0   0.257   5.7708   2.4862   1.7963
 AT5  HM33  H   HCH3  0   0.285   7.1806   2.3539   0.7330

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
 AT5  O5   C7    double    1.216  0.020  1.216
 AT5  C7   C8    single    1.522  0.020  1.522
 AT5  C7   C6    single    1.482  0.020  1.482
 AT5  C8   C11   single    1.527  0.020  1.527
 AT5  C8   C10   single    1.533  0.020  1.533
 AT5  C8   H8    single    0.970  0.020  1.090
 AT5  C11  C12   single    1.532  0.020  1.532
 AT5  C11  H111  single    0.970  0.020  1.090
 AT5  C11  H112  single    0.970  0.020  1.090
 AT5  C12  C17   single    1.524  0.020  1.524
 AT5  C12  C13   single    1.531  0.020  1.531
 AT5  C12  H12   single    0.970  0.020  1.090
 AT5  C17  H171  single    0.970  0.020  1.090
 AT5  C17  H172  single    0.970  0.020  1.090
 AT5  C17  H173  single    0.970  0.020  1.090
 AT5  C13  CL12  single    1.809  0.020  1.809
 AT5  C13  C14   single    1.512  0.020  1.512
 AT5  C13  H13   single    0.970  0.020  1.090
 AT5  C14  CL16  single    1.792  0.020  1.792
 AT5  C14  H141  single    0.970  0.020  1.090
 AT5  C14  H142  single    0.970  0.020  1.090
 AT5  C10  H101  single    0.970  0.020  1.090
 AT5  C10  H102  single    0.970  0.020  1.090
 AT5  C10  H103  single    0.970  0.020  1.090
 AT5  C6   C5    aromatic  1.436  0.020  1.436
 AT5  C6   C1    aromatic  1.400  0.020  1.400
 AT5  C5   N4    aromatic  1.398  0.020  1.398
 AT5  C5   O4    double    1.227  0.020  1.227
 AT5  N4   C3    aromatic  1.345  0.020  1.345
 AT5  N4   HN4   single    0.860  0.020  1.020
 AT5  C3   C2    aromatic  1.373  0.020  1.373
 AT5  C3   O3    single    1.314  0.020  1.314
 AT5  C2   C1    aromatic  1.408  0.020  1.408
 AT5  C2   O2    single    1.362  0.020  1.362
 AT5  C1   O1    single    1.323  0.020  1.323
 AT5  O1   HO1   single    0.850  0.020  0.980
 AT5  O2   CM2   single    1.430  0.020  1.430
 AT5  CM2  HM21  single    0.970  0.020  1.090
 AT5  CM2  HM22  single    0.970  0.020  1.090
 AT5  CM2  HM23  single    0.970  0.020  1.090
 AT5  O3   CM3   single    1.428  0.020  1.428
 AT5  CM3  HM31  single    0.970  0.020  1.090
 AT5  CM3  HM32  single    0.970  0.020  1.090
 AT5  CM3  HM33  single    0.970  0.020  1.090

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
 AT5  C6    C7   C8    119.52  3.000
 AT5  C6    C7   O5    120.19  3.000
 AT5  C8    C7   O5    120.24  3.000
 AT5  H8    C8   C10   107.68  3.000
 AT5  H8    C8   C11   109.35  3.000
 AT5  C10   C8   C11   112.45  3.000
 AT5  H8    C8   C7    106.81  3.000
 AT5  C10   C8   C7    109.40  3.000
 AT5  C11   C8   C7    110.95  3.000
 AT5  H112  C11  H111  106.39  3.000
 AT5  H112  C11  C12   108.63  3.000
 AT5  H111  C11  C12   108.52  3.000
 AT5  H112  C11  C8    109.10  3.000
 AT5  H111  C11  C8    109.60  3.000
 AT5  C12   C11  C8    114.31  3.000
 AT5  H12   C12  C13   103.50  3.000
 AT5  H12   C12  C17   108.16  3.000
 AT5  C13   C12  C17   113.38  3.000
 AT5  H12   C12  C11   108.43  3.000
 AT5  C13   C12  C11   109.97  3.000
 AT5  C17   C12  C11   112.86  3.000
 AT5  H173  C17  H172  108.08  3.000
 AT5  H173  C17  H171  107.58  3.000
 AT5  H172  C17  H171  106.51  3.000
 AT5  H173  C17  C12   111.38  3.000
 AT5  H172  C17  C12   112.18  3.000
 AT5  H171  C17  C12   110.88  3.000
 AT5  H13   C13  C14   109.35  3.000
 AT5  H13   C13  CL12  105.46  3.000
 AT5  C14   C13  CL12  108.83  3.000
 AT5  H13   C13  C12   108.89  3.000
 AT5  C14   C13  C12   112.72  3.000
 AT5  CL12  C13  C12   111.33  3.000
 AT5  H142  C14  H141  109.03  3.000
 AT5  H142  C14  CL16  107.13  3.000
 AT5  H141  C14  CL16  107.25  3.000
 AT5  H142  C14  C13   109.32  3.000
 AT5  H141  C14  C13   112.28  3.000
 AT5  CL16  C14  C13   111.66  3.000
 AT5  H103  C10  H102  107.95  3.000
 AT5  H103  C10  H101  107.79  3.000
 AT5  H102  C10  H101  106.99  3.000
 AT5  H103  C10  C8    110.97  3.000
 AT5  H102  C10  C8    112.19  3.000
 AT5  H101  C10  C8    110.75  3.000
 AT5  C1    C6   C5    118.38  3.000
 AT5  C1    C6   C7    119.92  3.000
 AT5  C5    C6   C7    121.67  3.000
 AT5  O4    C5   N4    116.65  3.000
 AT5  O4    C5   C6    127.67  3.000
 AT5  N4    C5   C6    115.67  3.000
 AT5  HN4   N4   C3    119.95  3.000
 AT5  HN4   N4   C5    114.23  3.000
 AT5  C3    N4   C5    125.81  3.000
 AT5  O3    C3   C2    119.26  3.000
 AT5  O3    C3   N4    121.58  3.000
 AT5  C2    C3   N4    119.16  3.000
 AT5  O2    C2   C1    119.15  3.000
 AT5  O2    C2   C3    122.00  3.000
 AT5  C1    C2   C3    118.83  3.000
 AT5  O1    C1   C2    117.25  3.000
 AT5  O1    C1   C6    120.58  3.000
 AT5  C2    C1   C6    122.13  3.000
 AT5  HO1   O1   C1    109.16  3.000
 AT5  CM2   O2   C2    114.30  3.000
 AT5  HM23  CM2  HM22  109.06  3.000
 AT5  HM23  CM2  HM21  108.95  3.000
 AT5  HM22  CM2  HM21  108.90  3.000
 AT5  HM23  CM2  O2    106.95  3.000
 AT5  HM22  CM2  O2    111.49  3.000
 AT5  HM21  CM2  O2    111.43  3.000
 AT5  CM3   O3   C3    120.67  3.000
 AT5  HM33  CM3  HM32  108.97  3.000
 AT5  HM33  CM3  HM31  109.04  3.000
 AT5  HM32  CM3  HM31  110.16  3.000
 AT5  HM33  CM3  O3    105.77  3.000
 AT5  HM32  CM3  O3    111.42  3.000
 AT5  HM31  CM3  O3    111.34  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
 AT5  CONST_01  C3    N4   C5  C6     0.00   0.0  0
 AT5  CONST_02  C3    C2   C1  C6     0.00   0.0  0
 AT5  CONST_03  C2    C1   C6  C5     0.00   0.0  0
 AT5  CONST_04  C2    C3   N4  C5     0.00   0.0  0
 AT5  CONST_05  C1    C6   C5  N4     0.00   0.0  0
 AT5  CONST_06  C1    C2   C3  N4     0.00   0.0  0
 AT5  CONST_07  N4    C5   C6  C7   180.00   0.0  0
 AT5  CONST_08  C2    C1   C6  C7   180.00   0.0  0
 AT5  CONST_09  O2    C2   C1  C6   180.00   0.0  0
 AT5  CONST_10  O1    C1   C6  C5   180.00   0.0  0
 AT5  CONST_11  O3    C3   N4  C5   180.00   0.0  0
 AT5  CONST_12  O2    C2   C3  N4   180.00   0.0  0
 AT5  CONST_13  O4    C5   N4  C3   180.00   0.0  0
 AT5  CONST_14  O1    C1   C2  C3   180.00   0.0  0
 AT5  CONST_15  O4    C5   C6  C1   180.00   0.0  0
 AT5  CONST_16  O3    C3   C2  C1   180.00   0.0  0
 AT5  CONST_17  HN4   N4   C5  C6   180.00   0.0  0
 AT5  Var_01    C5    C6   C7  O5  -150.55  30.0  2
 AT5  Var_02    HM31  CM3  O3  C3   -62.23  30.0  3
 AT5  Var_03    HM21  CM2  O2  C2   -65.88  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
 AT5  chir_01  C8   C7    C11  C10  positiv
 AT5  chir_02  C12  C13   C17  C11  negativ
 AT5  chir_03  C13  CL12  C12  C14  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
 AT5  plan-1  C7   0.020
 AT5  plan-1  C6   0.020
 AT5  plan-1  C5   0.020
 AT5  plan-1  N4   0.020
 AT5  plan-1  C3   0.020
 AT5  plan-1  C2   0.020
 AT5  plan-1  C1   0.020
 AT5  plan-1  O1   0.020
 AT5  plan-1  O2   0.020
 AT5  plan-1  O3   0.020
 AT5  plan-1  O4   0.020
 AT5  plan-1  HN4  0.020
 AT5  plan-2  O5   0.020
 AT5  plan-2  C7   0.020
 AT5  plan-2  C8   0.020
 AT5  plan-2  C6   0.020

