# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 11:49:00 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: 6-[(cyclohexylacetyl)(2-hydroxyethyl)amino]-6-deoxy-D-allitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCN(C[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)CO)C(=O)CC1CCCCC1
#
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
 CHK  CHK  6-[(cyclohexylacetyl)(2-hydroxyethyl)amino]-6-deoxy-D-allitol  ligand  55  24  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_CHK
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
 CHK  OX1   O  O     0  -0.522  -1.0537   0.5800   1.2712
 CHK  CX1   C  C     0   0.583  -0.1063  -0.1238   1.6152
 CHK  CX2   C  CH2   0  -0.580  -0.1474  -0.8665   2.9347
 CHK  CX3   C  CH1   0  -0.220  -1.0224  -0.2016   3.9930
 CHK  CX4   C  CH2   0  -0.415  -0.4435   1.1427   4.4374
 CHK  CX5   C  CH2   0  -0.431  -1.2599   1.7758   5.5602
 CHK  CX6   C  CH2   0  -0.429  -1.3978   0.8334   6.7506
 CHK  CX7   C  CH2   0  -0.432  -1.9863  -0.5052   6.3179
 CHK  CX8   C  CH2   0  -0.415  -1.1677  -1.1352   5.1962
 CHK  NX1   N  NT    0  -0.446   0.9694  -0.2850   0.8121
 CHK  CX9   C  CH2   0  -0.372   2.1027  -1.1466   1.0997
 CHK  CXA   C  CH2   0  -0.141   3.3096  -0.4016   1.6371
 CHK  OX2   O  OH1   0  -0.657   2.9792   0.2117   2.8589
 CHK  CXB   C  CH2   0  -0.352   1.0077   0.3997  -0.4674
 CHK  CXC   C  CH1   0  -0.008   0.4362  -0.4551  -1.6010
 CHK  OX3   O  OH1   0  -0.671  -0.8475  -0.9615  -1.2735
 CHK  CXD   C  CH1   0  -0.015   0.3598   0.3492  -2.9105
 CHK  OX4   O  OH1   0  -0.659   1.5579   1.0465  -3.1639
 CHK  CXE   C  CH1   0  -0.007  -0.0374  -0.5135  -4.1383
 CHK  OX5   O  OH1   0  -0.686  -0.7101  -1.7103  -3.8229
 CHK  CXF   C  CH1   0  -0.017  -0.8746   0.2998  -5.1420
 CHK  OX6   O  OH1   0  -0.661  -0.3387   1.5813  -5.3788
 CHK  CXG   C  CH2   0  -0.160  -1.0661  -0.4743  -6.4368
 CHK  OX7   O  OH1   0  -0.673  -1.9387   0.2471  -7.2759
 CHK  HX21  H  HCH2  0   0.270  -0.5323  -1.8712   2.7181
 CHK  HX22  H  HCH2  0   0.257   0.8479  -1.0087   3.3522
 CHK  H1    H  HCH1  0   0.213  -2.0213  -0.0279   3.5768
 CHK  HX41  H  HCH2  0   0.204   0.5876   0.9883   4.7778
 CHK  HX42  H  HCH2  0   0.228  -0.3899   1.8296   3.5900
 CHK  HX51  H  HCH2  0   0.207  -2.2569   2.0301   5.1838
 CHK  HX52  H  HCH2  0   0.224  -0.7988   2.7170   5.8701
 CHK  HX61  H  HCH2  0   0.224  -2.0183   1.2880   7.5270
 CHK  HX62  H  HCH2  0   0.206  -0.4106   0.6677   7.1969
 CHK  HX71  H  HCH2  0   0.207  -3.0148  -0.3535   5.9719
 CHK  HX72  H  HCH2  0   0.225  -2.0437  -1.1893   7.1681
 CHK  HX81  H  HCH2  0   0.224  -1.6256  -2.0779   4.8818
 CHK  HX82  H  HCH2  0   0.204  -0.1702  -1.3887   5.5755
 CHK  HX91  H  HCH2  0   0.266   2.4027  -1.6431   0.1738
 CHK  HX92  H  HCH2  0   0.273   1.8139  -1.9481   1.7769
 CHK  HXA1  H  HCH2  0   0.201   3.6441   0.3344   0.8950
 CHK  HXA2  H  HCH2  0   0.206   4.1246  -1.1288   1.7464
 CHK  HX2   H  HOH1  0   0.458   3.7153   0.7696   3.1250
 CHK  HXB1  H  HCH2  0   0.261   0.4658   1.3433  -0.3932
 CHK  HXB2  H  HCH2  0   0.265   2.0431   0.6531  -0.6938
 CHK  HXC   H  HCH1  0   0.244   1.0792  -1.3329  -1.7376
 CHK  HX3   H  HOH1  0   0.455  -1.3663  -0.2569  -0.8649
 CHK  HXD   H  HCH1  0   0.243  -0.4001   1.1242  -2.7550
 CHK  HX4   H  HOH1  0   0.447   2.2571   0.4053  -3.3351
 CHK  HXE   H  HCH1  0   0.215   0.9003  -0.8123  -4.6319
 CHK  HX5   H  HOH1  0   0.451  -1.1824  -1.5820  -2.9865
 CHK  HXF   H  HCH1  0   0.227  -1.8578   0.4712  -4.6857
 CHK  HX6   H  HOH1  0   0.439   0.5888   1.4902  -5.6211
 CHK  HXG1  H  HCH2  0   0.186  -0.0825  -0.6241  -6.9089
 CHK  HXG2  H  HCH2  0   0.203  -1.4617  -1.4686  -6.2043
 CHK  HX7   H  HOH1  0   0.454  -2.0964  -0.2818  -8.0625

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
 CHK  OX1  CX1   double  1.229  0.020  1.229
 CHK  CX1  CX2   single  1.515  0.020  1.515
 CHK  CX1  NX1   single  1.352  0.020  1.352
 CHK  CX2  CX3   single  1.526  0.020  1.526
 CHK  CX2  HX21  single  0.970  0.020  1.090
 CHK  CX2  HX22  single  0.970  0.020  1.090
 CHK  CX3  CX4   single  1.530  0.020  1.530
 CHK  CX3  CX8   single  1.530  0.020  1.530
 CHK  CX3  H1    single  0.970  0.020  1.090
 CHK  CX4  CX5   single  1.526  0.020  1.526
 CHK  CX4  HX41  single  0.970  0.020  1.090
 CHK  CX4  HX42  single  0.970  0.020  1.090
 CHK  CX5  CX6   single  1.524  0.020  1.524
 CHK  CX5  HX51  single  0.970  0.020  1.090
 CHK  CX5  HX52  single  0.970  0.020  1.090
 CHK  CX6  CX7   single  1.525  0.020  1.525
 CHK  CX6  HX61  single  0.970  0.020  1.090
 CHK  CX6  HX62  single  0.970  0.020  1.090
 CHK  CX7  CX8   single  1.525  0.020  1.525
 CHK  CX7  HX71  single  0.970  0.020  1.090
 CHK  CX7  HX72  single  0.970  0.020  1.090
 CHK  CX8  HX81  single  0.970  0.020  1.090
 CHK  CX8  HX82  single  0.970  0.020  1.090
 CHK  NX1  CX9   single  1.452  0.020  1.452
 CHK  NX1  CXB   single  1.452  0.020  1.452
 CHK  CX9  CXA   single  1.517  0.020  1.517
 CHK  CX9  HX91  single  0.970  0.020  1.090
 CHK  CX9  HX92  single  0.970  0.020  1.090
 CHK  CXA  OX2   single  1.406  0.020  1.406
 CHK  CXA  HXA1  single  0.970  0.020  1.090
 CHK  CXA  HXA2  single  0.970  0.020  1.090
 CHK  OX2  HX2   single  0.850  0.020  0.980
 CHK  CXB  CXC   single  1.530  0.020  1.530
 CHK  CXB  HXB1  single  0.970  0.020  1.090
 CHK  CXB  HXB2  single  0.970  0.020  1.090
 CHK  CXC  OX3   single  1.418  0.020  1.418
 CHK  CXC  CXD   single  1.539  0.020  1.539
 CHK  CXC  HXC   single  0.970  0.020  1.090
 CHK  OX3  HX3   single  0.850  0.020  0.980
 CHK  CXD  OX4   single  1.409  0.020  1.409
 CHK  CXD  CXE   single  1.552  0.020  1.552
 CHK  CXD  HXD   single  0.970  0.020  1.090
 CHK  OX4  HX4   single  0.850  0.020  0.980
 CHK  CXE  OX5   single  1.409  0.020  1.409
 CHK  CXE  CXF   single  1.539  0.020  1.539
 CHK  CXE  HXE   single  0.970  0.020  1.090
 CHK  OX5  HX5   single  0.850  0.020  0.980
 CHK  CXF  OX6   single  1.409  0.020  1.409
 CHK  CXF  CXG   single  1.521  0.020  1.521
 CHK  CXF  HXF   single  0.970  0.020  1.090
 CHK  OX6  HX6   single  0.850  0.020  0.980
 CHK  CXG  OX7   single  1.409  0.020  1.409
 CHK  CXG  HXG1  single  0.970  0.020  1.090
 CHK  CXG  HXG2  single  0.970  0.020  1.090
 CHK  OX7  HX7   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
 CHK  NX1   CX1  CX2   118.72  3.000
 CHK  NX1   CX1  OX1   121.01  3.000
 CHK  CX2   CX1  OX1   120.24  3.000
 CHK  HX22  CX2  HX21  106.07  3.000
 CHK  HX22  CX2  CX3   108.37  3.000
 CHK  HX21  CX2  CX3   109.56  3.000
 CHK  HX22  CX2  CX1   111.92  3.000
 CHK  HX21  CX2  CX1   106.65  3.000
 CHK  CX3   CX2  CX1   113.96  3.000
 CHK  H1    CX3  CX8   107.99  3.000
 CHK  H1    CX3  CX4   108.42  3.000
 CHK  CX8   CX3  CX4   110.11  3.000
 CHK  H1    CX3  CX2   109.17  3.000
 CHK  CX8   CX3  CX2   109.52  3.000
 CHK  CX4   CX3  CX2   111.56  3.000
 CHK  HX42  CX4  HX41  106.45  3.000
 CHK  HX42  CX4  CX5   109.65  3.000
 CHK  HX41  CX4  CX5   109.45  3.000
 CHK  HX42  CX4  CX3   110.24  3.000
 CHK  HX41  CX4  CX3   108.80  3.000
 CHK  CX5   CX4  CX3   112.08  3.000
 CHK  HX52  CX5  HX51  106.35  3.000
 CHK  HX52  CX5  CX6   110.44  3.000
 CHK  HX51  CX5  CX6   109.23  3.000
 CHK  HX52  CX5  CX4   109.88  3.000
 CHK  HX51  CX5  CX4   109.29  3.000
 CHK  CX6   CX5  CX4   111.50  3.000
 CHK  HX62  CX6  HX61  106.55  3.000
 CHK  HX62  CX6  CX7   109.30  3.000
 CHK  HX61  CX6  CX7   110.34  3.000
 CHK  HX62  CX6  CX5   109.26  3.000
 CHK  HX61  CX6  CX5   110.42  3.000
 CHK  CX7   CX6  CX5   110.86  3.000
 CHK  HX72  CX7  HX71  106.45  3.000
 CHK  HX72  CX7  CX8   109.99  3.000
 CHK  HX71  CX7  CX8   109.20  3.000
 CHK  HX72  CX7  CX6   110.43  3.000
 CHK  HX71  CX7  CX6   109.29  3.000
 CHK  CX8   CX7  CX6   111.36  3.000
 CHK  HX82  CX8  HX81  106.31  3.000
 CHK  HX82  CX8  CX7   109.23  3.000
 CHK  HX81  CX8  CX7   110.03  3.000
 CHK  HX82  CX8  CX3   109.06  3.000
 CHK  HX81  CX8  CX3   109.85  3.000
 CHK  CX7   CX8  CX3   112.17  3.000
 CHK  CXB   NX1  CX9   115.70  3.000
 CHK  CXB   NX1  CX1   119.23  3.000
 CHK  CX9   NX1  CX1   125.03  3.000
 CHK  HX92  CX9  HX91  105.40  3.000
 CHK  HX92  CX9  CXA   110.63  3.000
 CHK  HX91  CX9  CXA   107.76  3.000
 CHK  HX92  CX9  NX1   110.67  3.000
 CHK  HX91  CX9  NX1   108.43  3.000
 CHK  CXA   CX9  NX1   113.56  3.000
 CHK  HXA2  CXA  HXA1  106.58  3.000
 CHK  HXA2  CXA  OX2   112.14  3.000
 CHK  HXA1  CXA  OX2   111.50  3.000
 CHK  HXA2  CXA  CX9   107.50  3.000
 CHK  HXA1  CXA  CX9   109.41  3.000
 CHK  OX2   CXA  CX9   109.58  3.000
 CHK  HX2   OX2  CXA   108.29  3.000
 CHK  HXB2  CXB  HXB1  106.56  3.000
 CHK  HXB2  CXB  CXC   109.32  3.000
 CHK  HXB1  CXB  CXC   110.36  3.000
 CHK  HXB2  CXB  NX1   108.54  3.000
 CHK  HXB1  CXB  NX1   109.57  3.000
 CHK  CXC   CXB  NX1   112.31  3.000
 CHK  HXC   CXC  CXD   109.97  3.000
 CHK  HXC   CXC  OX3   105.88  3.000
 CHK  CXD   CXC  OX3   109.77  3.000
 CHK  HXC   CXC  CXB   108.68  3.000
 CHK  CXD   CXC  CXB   110.91  3.000
 CHK  OX3   CXC  CXB   111.50  3.000
 CHK  HX3   OX3  CXC   108.87  3.000
 CHK  HXD   CXD  CXE   109.12  3.000
 CHK  HXD   CXD  OX4   105.37  3.000
 CHK  CXE   CXD  OX4   110.51  3.000
 CHK  HXD   CXD  CXC   106.45  3.000
 CHK  CXE   CXD  CXC   113.29  3.000
 CHK  OX4   CXD  CXC   111.68  3.000
 CHK  HX4   OX4  CXD   108.63  3.000
 CHK  HXE   CXE  CXF   108.31  3.000
 CHK  HXE   CXE  OX5   106.06  3.000
 CHK  CXF   CXE  OX5   109.58  3.000
 CHK  HXE   CXE  CXD   106.71  3.000
 CHK  CXF   CXE  CXD   111.18  3.000
 CHK  OX5   CXE  CXD   114.66  3.000
 CHK  HX5   OX5  CXE   108.27  3.000
 CHK  HXF   CXF  CXG   108.71  3.000
 CHK  HXF   CXF  OX6   105.58  3.000
 CHK  CXG   CXF  OX6   111.58  3.000
 CHK  HXF   CXF  CXE   107.38  3.000
 CHK  CXG   CXF  CXE   110.77  3.000
 CHK  OX6   CXF  CXE   112.53  3.000
 CHK  HX6   OX6  CXF   108.82  3.000
 CHK  HXG2  CXG  HXG1  106.87  3.000
 CHK  HXG2  CXG  OX7   111.56  3.000
 CHK  HXG1  CXG  OX7   111.56  3.000
 CHK  HXG2  CXG  CXF   109.08  3.000
 CHK  HXG1  CXG  CXF   108.78  3.000
 CHK  OX7   CXG  CXF   108.93  3.000
 CHK  HX7   OX7  CXG   107.89  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
 CHK  CONST_01  CX9  NX1  CX1  OX1   180.00   0.0  0
 CHK  CONST_02  CXB  NX1  CX1  OX1     0.00   0.0  0
 CHK  CONST_03  CX9  NX1  CX1  CX2     0.00   0.0  0
 CHK  CONST_04  CXB  NX1  CX1  CX2   180.00   0.0  0
 CHK  Var_01    CX6  CX5  CX4  CX3    55.49  30.0  1
 CHK  Var_02    CX6  CX7  CX8  CX3   -55.65  30.0  1
 CHK  Var_03    CX7  CX6  CX5  CX4   -55.14  30.0  1
 CHK  Var_04    CX8  CX7  CX6  CX5    55.16  30.0  1
 CHK  Var_05    CX3  CX2  CX1  OX1   -27.25  30.0  3
 CHK  Var_06    CXA  CX9  NX1  CX1  -100.33  30.0  3
 CHK  Var_07    CXC  CXB  NX1  CX1   -91.71  30.0  3
 CHK  Var_08    OX2  CXA  CX9  NX1    62.11  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
 CHK  chir_01  CX3  CX2  CX4  CX8  positiv
 CHK  chir_02  CXC  OX3  CXB  CXD  positiv
 CHK  chir_03  CXD  OX4  CXC  CXE  positiv
 CHK  chir_04  CXE  OX5  CXF  CXD  negativ
 CHK  chir_05  CXF  OX6  CXE  CXG  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
 CHK  plan-1  OX1  0.020
 CHK  plan-1  CX1  0.020
 CHK  plan-1  CX2  0.020
 CHK  plan-1  NX1  0.020
 CHK  plan-1  CX9  0.020
 CHK  plan-1  CXB  0.020

