# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 02:27:11 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: (5R)-5-[(1S)-1-(acetylamino)-3-methylbutyl]-2,5-anhydro-3,4-dideoxy-4-(methoxycarbonyl)-L-threo-pentonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@@H]1C[C@@H](O[C@H]1[C@H](CC(C)C)NC(C)=O)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
 ABW  ABW  '(5R)-5-[(1S)-1-(acetylamino)-3-methylbutyl]-2,5-anhydro-3,4-dideoxy-4-(methoxycarbonyl)-L-threo-pentonic acid'  ligand  44  21  .  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_ABW
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
 ABW  C1    C  CH1   0  -0.412  -0.0787   1.2964  -0.6140
 ABW  C13   C  CH1   0   0.110  -0.3497  -0.0735   0.0154
 ABW  O6    O  O2    0  -0.480  -1.4717  -0.5396  -0.7051
 ABW  C3    C  CH1   0  -0.062  -2.3351   0.5319  -0.9563
 ABW  C4    C  CH2   0  -0.503  -1.5056   1.8300  -0.8051
 ABW  C5    C  C     0   0.509  -3.5015   0.5136   0.0113
 ABW  O1    O  OH1   0  -0.592  -4.4099   1.4145  -0.3384
 ABW  O2    O  O     0  -0.425  -3.5920  -0.2063   0.9698
 ABW  N2    N  NH1   0  -0.640   2.0425  -0.4304   0.2384
 ABW  C6    C  C     0   0.523   3.0083  -0.1074  -0.6470
 ABW  C7    C  CH3   0  -0.782   4.2611   0.4719  -0.0412
 ABW  O4    O  O     0  -0.497   2.8959  -0.2785  -1.8522
 ABW  C8    C  CH1   0  -0.115   0.7936  -1.0822  -0.1089
 ABW  C2    C  CH2   0  -0.414   0.6198  -2.3080   0.7923
 ABW  C9    C  CH1   0  -0.244  -0.6025  -3.1956   0.5508
 ABW  C10   C  CH3   0  -0.659  -0.6117  -3.7864  -0.8553
 ABW  C15   C  CH3   0  -0.651  -0.6224  -4.3078   1.5954
 ABW  C14   C  C     0   0.603   0.7425   2.2004   0.2650
 ABW  O3    O  O     0  -0.446   0.5293   2.3733   1.4401
 ABW  O5    O  O2    0  -0.447   1.7098   2.8112  -0.4009
 ABW  C16   C  CH3   0  -0.431   2.5299   3.7273   0.3264
 ABW  H1    H  HCH1  0   0.292   0.4040   1.1657  -1.5850
 ABW  H13   H  HCH1  0   0.224  -0.6006   0.0597   1.0790
 ABW  H3    H  HCH1  0   0.293  -2.7281   0.4316  -1.9727
 ABW  H41   H  HCH2  0   0.273  -1.8206   2.4113   0.0629
 ABW  H42   H  HCH2  0   0.287  -1.5935   2.4708  -1.6793
 ABW  HO1   H  HOH1  0   0.486  -5.1439   1.4201   0.2945
 ABW  HN2   H  HNH1  0   0.400   2.2462  -0.3211   1.2199
 ABW  H71   H  HCH3  0   0.247   4.1547   0.7463   1.0068
 ABW  H72   H  HCH3  0   0.276   5.0671  -0.2588  -0.1199
 ABW  H73   H  HCH3  0   0.264   4.5651   1.3519  -0.6054
 ABW  H8    H  HCH1  0   0.259   0.8705  -1.3823  -1.1558
 ABW  H21   H  HCH2  0   0.233   1.5198  -2.9242   0.6901
 ABW  H22   H  HCH2  0   0.225   0.6045  -1.9614   1.8328
 ABW  H9    H  HCH1  0   0.232  -1.5080  -2.5964   0.6788
 ABW  H101  H  HCH3  0   0.229  -0.6940  -3.0192  -1.6246
 ABW  H102  H  HCH3  0   0.210   0.3018  -4.3563  -1.0451
 ABW  H103  H  HCH3  0   0.225  -1.4549  -4.4678  -0.9843
 ABW  H151  H  HCH3  0   0.224  -0.6383  -3.9042   2.6096
 ABW  H152  H  HCH3  0   0.226  -1.5010  -4.9440   1.4777
 ABW  H153  H  HCH3  0   0.212   0.2609  -4.9449   1.5059
 ABW  H161  H  HCH3  0   0.247   1.9403   4.5431   0.7439
 ABW  H162  H  HCH3  0   0.237   3.0707   3.2281   1.1304
 ABW  H163  H  HCH3  0   0.254   3.2403   4.1267  -0.3910

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
 ABW  C1   C13   single  1.532  0.020  1.532
 ABW  C1   C4    single  1.535  0.020  1.535
 ABW  C1   C14   single  1.505  0.020  1.505
 ABW  C1   H1    single  0.970  0.020  1.090
 ABW  C13  O6    single  1.413  0.020  1.413
 ABW  C13  C8    single  1.530  0.020  1.530
 ABW  C13  H13   single  0.970  0.020  1.090
 ABW  O6   C3    single  1.399  0.020  1.399
 ABW  C3   C4    single  1.548  0.020  1.548
 ABW  C3   C5    single  1.516  0.020  1.516
 ABW  C3   H3    single  0.970  0.020  1.090
 ABW  C4   H41   single  0.970  0.020  1.090
 ABW  C4   H42   single  0.970  0.020  1.090
 ABW  C5   O1    single  1.326  0.020  1.326
 ABW  C5   O2    double  1.202  0.020  1.202
 ABW  O1   HO1   single  0.850  0.020  0.980
 ABW  N2   C6    single  1.349  0.020  1.349
 ABW  N2   C8    single  1.451  0.020  1.451
 ABW  N2   HN2   single  0.860  0.020  1.020
 ABW  C6   C7    single  1.507  0.020  1.507
 ABW  C6   O4    double  1.222  0.020  1.222
 ABW  C7   H71   single  0.970  0.020  1.090
 ABW  C7   H72   single  0.970  0.020  1.090
 ABW  C7   H73   single  0.970  0.020  1.090
 ABW  C8   C2    single  1.531  0.020  1.531
 ABW  C8   H8    single  0.970  0.020  1.090
 ABW  C2   C9    single  1.530  0.020  1.530
 ABW  C2   H21   single  0.970  0.020  1.090
 ABW  C2   H22   single  0.970  0.020  1.090
 ABW  C9   C10   single  1.525  0.020  1.525
 ABW  C9   C15   single  1.526  0.020  1.526
 ABW  C9   H9    single  0.970  0.020  1.090
 ABW  C10  H101  single  0.970  0.020  1.090
 ABW  C10  H102  single  0.970  0.020  1.090
 ABW  C10  H103  single  0.970  0.020  1.090
 ABW  C15  H151  single  0.970  0.020  1.090
 ABW  C15  H152  single  0.970  0.020  1.090
 ABW  C15  H153  single  0.970  0.020  1.090
 ABW  C14  O3    double  1.207  0.020  1.207
 ABW  C14  O5    single  1.324  0.020  1.324
 ABW  O5   C16   single  1.428  0.020  1.428
 ABW  C16  H161  single  0.970  0.020  1.090
 ABW  C16  H162  single  0.970  0.020  1.090
 ABW  C16  H163  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
 ABW  H1    C1   C14   110.49  3.000
 ABW  H1    C1   C4    109.98  3.000
 ABW  C14   C1   C4    111.78  3.000
 ABW  H1    C1   C13   109.67  3.000
 ABW  C14   C1   C13   113.19  3.000
 ABW  C4    C1   C13   101.39  3.000
 ABW  H13   C13  C8    109.18  3.000
 ABW  H13   C13  O6    110.59  3.000
 ABW  C8    C13  O6    109.55  3.000
 ABW  H13   C13  C1    109.22  3.000
 ABW  C8    C13  C1    115.09  3.000
 ABW  O6    C13  C1    103.07  3.000
 ABW  C3    O6   C13   109.22  3.000
 ABW  H3    C3   C5    108.39  3.000
 ABW  H3    C3   C4    111.10  3.000
 ABW  C5    C3   C4    111.11  3.000
 ABW  H3    C3   O6    108.56  3.000
 ABW  C5    C3   O6    110.56  3.000
 ABW  C4    C3   O6    107.10  3.000
 ABW  H42   C4   H41   107.59  3.000
 ABW  H42   C4   C3    111.85  3.000
 ABW  H41   C4   C3    111.70  3.000
 ABW  H42   C4   C1    112.33  3.000
 ABW  H41   C4   C1    110.77  3.000
 ABW  C3    C4   C1    102.63  3.000
 ABW  O2    C5   O1    124.43  3.000
 ABW  O2    C5   C3    125.04  3.000
 ABW  O1    C5   C3    110.52  3.000
 ABW  HO1   O1   C5    110.52  3.000
 ABW  HN2   N2   C8    117.09  3.000
 ABW  HN2   N2   C6    117.92  3.000
 ABW  C8    N2   C6    124.51  3.000
 ABW  O4    C6   C7    121.77  3.000
 ABW  O4    C6   N2    123.20  3.000
 ABW  C7    C6   N2    115.03  3.000
 ABW  H73   C7   H72   107.33  3.000
 ABW  H73   C7   H71   108.81  3.000
 ABW  H72   C7   H71   108.09  3.000
 ABW  H73   C7   C6    109.54  3.000
 ABW  H72   C7   C6    109.13  3.000
 ABW  H71   C7   C6    113.74  3.000
 ABW  H8    C8   C2    110.63  3.000
 ABW  H8    C8   N2    107.00  3.000
 ABW  C2    C8   N2    108.45  3.000
 ABW  H8    C8   C13   108.17  3.000
 ABW  C2    C8   C13   113.28  3.000
 ABW  N2    C8   C13   109.13  3.000
 ABW  H22   C2   H21   106.12  3.000
 ABW  H22   C2   C9    108.78  3.000
 ABW  H21   C2   C9    108.38  3.000
 ABW  H22   C2   C8    107.88  3.000
 ABW  H21   C2   C8    107.59  3.000
 ABW  C9    C2   C8    117.53  3.000
 ABW  H9    C9   C15   107.97  3.000
 ABW  H9    C9   C10   108.37  3.000
 ABW  C15   C9   C10   110.41  3.000
 ABW  H9    C9   C2    108.98  3.000
 ABW  C15   C9   C2    108.98  3.000
 ABW  C10   C9   C2    112.03  3.000
 ABW  H103  C10  H102  107.42  3.000
 ABW  H103  C10  H101  107.31  3.000
 ABW  H102  C10  H101  107.91  3.000
 ABW  H103  C10  C9    110.82  3.000
 ABW  H102  C10  C9    110.92  3.000
 ABW  H101  C10  C9    112.25  3.000
 ABW  H153  C15  H152  107.58  3.000
 ABW  H153  C15  H151  107.66  3.000
 ABW  H152  C15  H151  107.70  3.000
 ABW  H153  C15  C9    111.00  3.000
 ABW  H152  C15  C9    111.21  3.000
 ABW  H151  C15  C9    111.51  3.000
 ABW  O5    C14  O3    123.56  3.000
 ABW  O5    C14  C1    112.47  3.000
 ABW  O3    C14  C1    123.96  3.000
 ABW  C16   O5   C14   117.34  3.000
 ABW  H163  C16  H162  109.34  3.000
 ABW  H163  C16  H161  109.37  3.000
 ABW  H162  C16  H161  109.19  3.000
 ABW  H163  C16  O5    105.97  3.000
 ABW  H162  C16  O5    111.51  3.000
 ABW  H161  C16  O5    111.38  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
 ABW  CONST_01  HO1   O1   C5  C3   180.00   0.0  0
 ABW  CONST_02  C8    N2   C6  C7   180.00   0.0  0
 ABW  CONST_03  C8    N2   C6  O4     0.00   0.0  0
 ABW  CONST_04  HN2   N2   C6  C7     0.00   0.0  0
 ABW  Var_01    C10   C9   C2  C8    60.47  30.0  3
 ABW  Var_02    H71   C7   C6  N2   -11.88  30.0  3
 ABW  Var_03    H101  C10  C9  C2   -63.81  30.0  3
 ABW  Var_04    H151  C15  C9  C2    57.80  30.0  3
 ABW  Var_05    H161  C16  O5  C14  -60.28  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
 ABW  chir_01  C1   C13  C4   C14  negativ
 ABW  chir_02  C13  O6   C8   C1   negativ
 ABW  chir_03  C3   O6   C4   C5   positiv
 ABW  chir_04  C8   N2   C13  C2   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
 ABW  plan-1  N2   0.020
 ABW  plan-1  C6   0.020
 ABW  plan-1  C7   0.020
 ABW  plan-1  O4   0.020
 ABW  plan-1  C8   0.020
 ABW  plan-1  HN2  0.020
 ABW  plan-2  C3   0.020
 ABW  plan-2  C5   0.020
 ABW  plan-2  O1   0.020
 ABW  plan-2  O2   0.020
 ABW  plan-2  HO1  0.020
 ABW  plan-3  C1   0.020
 ABW  plan-3  C14  0.020
 ABW  plan-3  O3   0.020
 ABW  plan-3  O5   0.020

