# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 14:49:21 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 2-[[(2R)-2-[[(1R,2S,3R,4R,5R)-4-acetamido-2-oxidanyl-6,8-dioxabicyclo[3.2.1]octan-3-yl]oxy]propanoyl]amino]propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](NC(=O)[C@@H](C)O[C@H]1[C@H](O)[C@H]2CO[C@H](O2)[C@@H]1NC(C)=O)C(N)=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
 89A  89A  2-[[(2R)-2-[[(1R,2S,3R,4R,5R)-4-acetamido-2-oxidanyl-6,8-dioxabicyclo[3.2.1]octan-3-yl]oxy]propanoyl]amino]propanamide  ligand  47  24  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_89A
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
 89A  CAD   C  CH3   0  -0.676  -1.4960   2.7625   0.9515
 89A  CBB   C  C     0   0.518  -5.0023  -0.8243  -0.9011
 89A  CBC   C  CH1   0  -0.190  -4.0320  -0.7539   0.2746
 89A  CBD   C  CH3   0  -0.652  -4.8031  -0.4491   1.5619
 89A  CBE   C  C     0   0.532  -1.8472   0.3098   0.5828
 89A  CBF   C  CH1   0  -0.084  -1.0108   1.5358   0.1934
 89A  NBK   N  NH1   0  -0.644  -3.0424   0.2520  -0.0216
 89A  OBM   O  O     0  -0.484  -5.1555   0.1211  -1.6608
 89A  OBN   O  O     0  -0.482  -1.4534  -0.5157   1.3904
 89A  C1    C  CH1   0   0.259   3.3746   0.6230   0.5802
 89A  C2    C  CH1   0  -0.139   2.1170  -0.2529   0.4867
 89A  N2    N  NH1   0  -0.633   2.4619  -1.5212  -0.1125
 89A  C3    C  CH1   0  -0.009   1.0246   0.4508  -0.3364
 89A  O3    O  O2    0  -0.482   0.3331   1.3277   0.5210
 89A  C4    C  CH1   0   0.062   1.6155   1.2144  -1.5374
 89A  O4    O  OH1   0  -0.666   1.7818   0.2594  -2.5608
 89A  C5    C  CH1   0  -0.148   2.9502   1.8672  -1.1752
 89A  O5    O  O2    0  -0.480   3.8498   0.8714  -0.7115
 89A  C6    C  CH2   0  -0.174   2.8727   2.7813   0.0456
 89A  O6    O  O2    0  -0.502   3.0824   1.8828   1.1302
 89A  C7    C  C     0   0.523   2.7427  -2.6285   0.6002
 89A  O7    O  O     0  -0.504   2.6951  -2.6646   1.8221
 89A  C8    C  CH3   0  -0.780   3.1385  -3.8313  -0.2186
 89A  HAD1  H  HCH3  0   0.252  -0.9186   3.6384   0.6564
 89A  HAD2  H  HCH3  0   0.239  -2.5440   2.9627   0.7334
 89A  HAD3  H  HCH3  0   0.241  -1.3919   2.6243   2.0282
 89A  HBF   H  HCH1  0   0.244  -1.1344   1.7178  -0.8846
 89A  HBC   H  HCH1  0   0.278  -3.5301  -1.7188   0.3807
 89A  HBJ1  H  HNH2  0   0.413  -5.5089  -2.7436  -0.3737
 89A  HBJ2  H  HNH2  0   0.407  -6.3904  -2.0917  -1.6988
 89A  HBD1  H  HCH3  0   0.240  -5.5375  -1.2260   1.7740
 89A  HBD2  H  HCH3  0   0.252  -4.1174  -0.3986   2.4060
 89A  HBD3  H  HCH3  0   0.237  -5.3248   0.5052   1.4839
 89A  HBK   H  HNH1  0   0.399  -3.3064   0.9700  -0.6812
 89A  H1    H  HCH1  0   0.257   4.1550   0.1285   1.1650
 89A  H2    H  HCH1  0   0.279   1.7198  -0.4456   1.4838
 89A  HA    H  HNH1  0   0.399   2.5779  -1.5476  -1.1138
 89A  H3    H  HCH1  0   0.257   0.3526  -0.3215  -0.7316
 89A  H4    H  HCH1  0   0.239   0.9166   2.0070  -1.8434
 89A  HB    H  HOH1  0   0.459   2.2373   0.6661  -3.3055
 89A  H5    H  HCH1  0   0.277   3.3880   2.3638  -2.0438
 89A  H61C  H  HCH2  0   0.239   3.6690   3.5296   0.0236
 89A  H62C  H  HCH2  0   0.240   1.9168   3.2955   0.1467
 89A  H81C  H  HCH3  0   0.269   4.2054  -4.0179  -0.0880
 89A  H82C  H  HCH3  0   0.264   2.6071  -4.7105   0.1419
 89A  H83C  H  HCH3  0   0.250   2.9418  -3.7145  -1.2826
 89A  NBJ   N  NH2   0  -0.797  -5.6829  -1.9698  -0.9921

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
 89A  CAD  CBF   single  1.522  0.020  1.522
 89A  CBB  CBC   single  1.526  0.020  1.526
 89A  CBB  NBJ   single  1.336  0.020  1.336
 89A  CBB  OBM   double  1.222  0.020  1.222
 89A  CBC  CBD   single  1.531  0.020  1.531
 89A  CBC  NBK   single  1.442  0.020  1.442
 89A  CBE  CBF   single  1.534  0.020  1.534
 89A  CBE  NBK   single  1.341  0.020  1.341
 89A  CBE  OBN   double  1.220  0.020  1.220
 89A  CBF  O3    single  1.399  0.020  1.399
 89A  C1   C2    single  1.535  0.020  1.535
 89A  C1   O5    single  1.399  0.020  1.399
 89A  C1   O6    single  1.405  0.020  1.405
 89A  C2   N2    single  1.444  0.020  1.444
 89A  C2   C3    single  1.538  0.020  1.538
 89A  N2   C7    single  1.346  0.020  1.346
 89A  C3   O3    single  1.408  0.020  1.408
 89A  C3   C4    single  1.541  0.020  1.541
 89A  C4   O4    single  1.410  0.020  1.410
 89A  C4   C5    single  1.529  0.020  1.529
 89A  C5   O5    single  1.420  0.020  1.420
 89A  C5   C6    single  1.527  0.020  1.527
 89A  C6   O6    single  1.424  0.020  1.424
 89A  C7   O7    double  1.223  0.020  1.223
 89A  C7   C8    single  1.508  0.020  1.508
 89A  CAD  HAD1  single  0.970  0.020  1.090
 89A  CAD  HAD2  single  0.970  0.020  1.090
 89A  CAD  HAD3  single  0.970  0.020  1.090
 89A  CBF  HBF   single  0.970  0.020  1.090
 89A  CBC  HBC   single  0.970  0.020  1.090
 89A  NBJ  HBJ1  single  0.860  0.020  1.020
 89A  NBJ  HBJ2  single  0.860  0.020  1.020
 89A  CBD  HBD1  single  0.970  0.020  1.090
 89A  CBD  HBD2  single  0.970  0.020  1.090
 89A  CBD  HBD3  single  0.970  0.020  1.090
 89A  NBK  HBK   single  0.860  0.020  1.020
 89A  C1   H1    single  0.970  0.020  1.090
 89A  C2   H2    single  0.970  0.020  1.090
 89A  N2   HA    single  0.860  0.020  1.020
 89A  C3   H3    single  0.970  0.020  1.090
 89A  C4   H4    single  0.970  0.020  1.090
 89A  O4   HB    single  0.850  0.020  0.980
 89A  C5   H5    single  0.970  0.020  1.090
 89A  C6   H61C  single  0.970  0.020  1.090
 89A  C6   H62C  single  0.970  0.020  1.090
 89A  C8   H81C  single  0.970  0.020  1.090
 89A  C8   H82C  single  0.970  0.020  1.090
 89A  C8   H83C  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
 89A  HAD3  CAD  HAD2  108.24  3.000
 89A  HAD3  CAD  HAD1  108.58  3.000
 89A  HAD2  CAD  HAD1  107.93  3.000
 89A  HAD3  CAD  CBF   111.06  3.000
 89A  HAD2  CAD  CBF   110.81  3.000
 89A  HAD1  CAD  CBF   110.13  3.000
 89A  OBM   CBB  NBJ   123.86  3.000
 89A  OBM   CBB  CBC   121.52  3.000
 89A  NBJ   CBB  CBC   114.59  3.000
 89A  HBC   CBC  NBK   108.71  3.000
 89A  HBC   CBC  CBD   108.99  3.000
 89A  NBK   CBC  CBD   112.30  3.000
 89A  HBC   CBC  CBB   109.03  3.000
 89A  NBK   CBC  CBB   108.08  3.000
 89A  CBD   CBC  CBB   109.67  3.000
 89A  HBD3  CBD  HBD2  108.43  3.000
 89A  HBD3  CBD  HBD1  108.39  3.000
 89A  HBD2  CBD  HBD1  107.85  3.000
 89A  HBD3  CBD  CBC   110.80  3.000
 89A  HBD2  CBD  CBC   110.11  3.000
 89A  HBD1  CBD  CBC   111.16  3.000
 89A  OBN   CBE  NBK   123.85  3.000
 89A  OBN   CBE  CBF   122.18  3.000
 89A  NBK   CBE  CBF   113.96  3.000
 89A  HBF   CBF  O3    111.22  3.000
 89A  HBF   CBF  CBE   108.64  3.000
 89A  O3    CBF  CBE   110.21  3.000
 89A  HBF   CBF  CAD   108.60  3.000
 89A  O3    CBF  CAD   108.03  3.000
 89A  CBE   CBF  CAD   110.11  3.000
 89A  HBK   NBK  CBE   119.78  3.000
 89A  HBK   NBK  CBC   116.79  3.000
 89A  CBE   NBK  CBC   123.32  3.000
 89A  H1    C1   O6    110.15  3.000
 89A  H1    C1   O5    109.37  3.000
 89A  O6    C1   O5    105.84  3.000
 89A  H1    C1   C2    111.05  3.000
 89A  O6    C1   C2    111.40  3.000
 89A  O5    C1   C2    108.87  3.000
 89A  H2    C2   C3    108.15  3.000
 89A  H2    C2   N2    108.13  3.000
 89A  C3    C2   N2    110.44  3.000
 89A  H2    C2   C1    110.09  3.000
 89A  C3    C2   C1    110.69  3.000
 89A  N2    C2   C1    109.31  3.000
 89A  HA    N2   C7    118.69  3.000
 89A  HA    N2   C2    117.54  3.000
 89A  C7    N2   C2    123.53  3.000
 89A  H3    C3   C4    107.63  3.000
 89A  H3    C3   O3    110.90  3.000
 89A  C4    C3   O3    110.75  3.000
 89A  H3    C3   C2    107.80  3.000
 89A  C4    C3   C2    111.80  3.000
 89A  O3    C3   C2    107.93  3.000
 89A  C3    O3   CBF   114.95  3.000
 89A  H4    C4   C5    108.23  3.000
 89A  H4    C4   O4    111.17  3.000
 89A  C5    C4   O4    110.99  3.000
 89A  H4    C4   C3    109.28  3.000
 89A  C5    C4   C3    111.20  3.000
 89A  O4    C4   C3    105.98  3.000
 89A  HB    O4   C4    109.33  3.000
 89A  H5    C5   C6    112.58  3.000
 89A  H5    C5   O5    108.95  3.000
 89A  C6    C5   O5    101.01  3.000
 89A  H5    C5   C4    110.83  3.000
 89A  C6    C5   C4    113.61  3.000
 89A  O5    C5   C4    109.32  3.000
 89A  C5    O5   C1    102.17  3.000
 89A  H62C  C6   H61C  108.53  3.000
 89A  H62C  C6   O6    110.86  3.000
 89A  H61C  C6   O6    109.88  3.000
 89A  H62C  C6   C5    113.64  3.000
 89A  H61C  C6   C5    110.90  3.000
 89A  O6    C6   C5    102.93  3.000
 89A  C6    O6   C1    107.34  3.000
 89A  C8    C7   O7    121.94  3.000
 89A  C8    C7   N2    115.04  3.000
 89A  O7    C7   N2    123.01  3.000
 89A  H83C  C8   H82C  108.79  3.000
 89A  H83C  C8   H81C  108.20  3.000
 89A  H82C  C8   H81C  107.43  3.000
 89A  H83C  C8   C7    113.44  3.000
 89A  H82C  C8   C7    109.65  3.000
 89A  H81C  C8   C7    109.16  3.000
 89A  HBJ2  NBJ  HBJ1  117.37  3.000
 89A  HBJ2  NBJ  CBB   120.63  3.000
 89A  HBJ1  NBJ  CBB   121.99  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
 89A  CONST_01  O7    C7   N2   C2     0.00   0.0  0
 89A  CONST_02  C8    C7   N2   C2   180.00   0.0  0
 89A  CONST_03  CBF   CBE  NBK  CBC  180.00   0.0  0
 89A  CONST_04  OBN   CBE  NBK  CBC    0.00   0.0  0
 89A  CONST_05  HBJ1  NBJ  CBB  CBC    0.00   0.0  0
 89A  CONST_06  HBJ2  NBJ  CBB  CBC  180.00   0.0  0
 89A  CONST_07  HBK   NBK  CBE  CBF    0.00   0.0  0
 89A  CONST_08  HA    N2   C7   O7   180.00   0.0  0
 89A  Var_01    C5    C6   O6   C1     5.02  30.0  3
 89A  Var_02    H81C  C8   C7   N2   108.33  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
 89A  chir_01  CBC  CBB  CBD  NBK  positiv
 89A  chir_02  CBF  O3   CAD  CBE  positiv
 89A  chir_03  C1   O5   O6   C2   negativ
 89A  chir_04  C2   N2   C3   C1   positiv
 89A  chir_05  C3   O3   C4   C2   negativ
 89A  chir_06  C4   O4   C3   C5   negativ
 89A  chir_07  C5   O5   C4   C6   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
 89A  plan-1  CBB   0.020
 89A  plan-1  CBC   0.020
 89A  plan-1  OBM   0.020
 89A  plan-1  HBJ1  0.020
 89A  plan-1  HBJ2  0.020
 89A  plan-1  NBJ   0.020
 89A  plan-2  CBC   0.020
 89A  plan-2  CBE   0.020
 89A  plan-2  CBF   0.020
 89A  plan-2  NBK   0.020
 89A  plan-2  OBN   0.020
 89A  plan-2  HBK   0.020
 89A  plan-3  C2    0.020
 89A  plan-3  N2    0.020
 89A  plan-3  C7    0.020
 89A  plan-3  O7    0.020
 89A  plan-3  C8    0.020
 89A  plan-3  HA    0.020

