# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 15:49:25 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: 2-[4-(1,3-benzodioxol-5-ylmethyl)piperazin-1-yl]-N-[(1S,2S,5S)-2,5-dimethoxycyclohexyl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H]1CC[C@H](OC)[C@H](C1)NC(=O)CN2CCN(CC2)Cc3ccc4OCOc4c3
#
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
 1KV  1KV  2-[4-(1,3-benzodioxol-5-ylmethyl)piperazin-1-yl]-N-[(1S,2S,5S)-2,5-dimethoxycyclohexyl]acetamide  ligand  63  30  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1KV
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
 1KV  CAB  C  CH3   0  -0.400   4.1879  -1.6949   3.2919
 1KV  OAS  O  O2    0  -0.498   3.9089  -1.3862   1.9489
 1KV  CBB  C  CH1   0   0.089   4.9433  -0.7119   1.2760
 1KV  CAH  C  CH2   0  -0.532   6.1397  -1.6097   0.9707
 1KV  CAG  C  CH2   0  -0.539   7.2081  -0.8724   0.1691
 1KV  CAZ  C  CH1   0   0.057   6.6226  -0.3338  -1.1316
 1KV  OAR  O  O2    0  -0.523   7.5486   0.4192  -1.8835
 1KV  CAA  C  CH3   0  -0.517   8.5119  -0.3520  -2.5571
 1KV  CAO  C  CH2   0  -0.540   5.4346   0.5684  -0.8357
 1KV  CBA  C  CH1   0  -0.117   4.3606  -0.1550  -0.0205
 1KV  NAQ  N  NH1   0  -0.647   3.2482   0.7235   0.2666
 1KV  C    C  C     0   0.504   2.1792   0.8662  -0.5324
 1KV  O    O  O     0  -0.514   1.9906   0.1923  -1.5334
 1KV  CA   C  CH2   0  -0.441   1.2363   1.9853  -0.1083
 1KV  N    N  NT    0  -0.416  -0.1027   1.7789  -0.5846
 1KV  CAK  C  CH2   0  -0.290  -0.8954   2.9922  -0.5538
 1KV  CAM  C  CH2   0  -0.273  -2.2514   2.7438  -1.1837
 1KV  CAJ  C  CH2   0  -0.272  -0.7927   0.7180   0.1234
 1KV  CAL  C  CH2   0  -0.275  -2.1512   0.4654  -0.4994
 1KV  NBD  N  NT    0  -0.413  -2.9518   1.6756  -0.4958
 1KV  CAP  C  CH2   0  -0.302  -4.2652   1.4605  -1.0624
 1KV  CAW  C  CR6   0   0.072  -5.1421   0.5707  -0.2174
 1KV  CAF  C  CR16  0  -0.384  -5.9772  -0.3627  -0.8480
 1KV  CAY  C  CR56  0   0.316  -6.8034  -1.1163  -0.0509
 1KV  OAU  O  O     0  -0.486  -7.7068  -2.0581  -0.4215
 1KV  CAI  C  CH2   0   0.092  -8.1578  -2.6659   0.7819
 1KV  OAT  O  O     0  -0.486  -7.7365  -1.8324   1.8526
 1KV  CAX  C  CR56  0   0.286  -6.8195  -0.9802   1.3260
 1KV  CAE  C  CR16  0  -0.313  -6.0049  -0.0801   1.9682
 1KV  CAD  C  CR16  0  -0.291  -5.1632   0.6990   1.1659
 1KV  H1   H  HCH3  0   0.195   4.5398  -0.8176   3.8475
 1KV  H2   H  HCH3  0   0.227   3.2621  -2.0407   3.7506
 1KV  H3   H  HCH3  0   0.203   4.9357  -2.4867   3.4046
 1KV  H4   H  HCH1  0   0.180   5.2970   0.1359   1.8903
 1KV  H5   H  HCH2  0   0.262   6.5782  -1.9810   1.8989
 1KV  H6   H  HCH2  0   0.268   5.7940  -2.4873   0.4136
 1KV  H7   H  HCH2  0   0.256   7.6050  -0.0365   0.7551
 1KV  H8   H  HCH2  0   0.284   8.0422  -1.5503  -0.0240
 1KV  H9   H  HCH1  0   0.262   6.2703  -1.1894  -1.7320
 1KV  H10  H  HCH3  0   0.243   9.1195   0.3254  -3.1563
 1KV  H11  H  HCH3  0   0.256   9.1791  -0.8928  -1.8780
 1KV  H12  H  HCH3  0   0.263   8.0494  -1.0854  -3.2286
 1KV  H13  H  HCH2  0   0.282   5.7739   1.4509  -0.2823
 1KV  H14  H  HCH2  0   0.277   4.9920   0.9219  -1.7700
 1KV  H15  H  HCH1  0   0.307   3.9765  -0.9944  -0.6072
 1KV  H16  H  HNH1  0   0.435   3.3390   1.3476   1.0537
 1KV  H17  H  HCH2  0   0.294   1.2911   2.1344   0.9832
 1KV  H18  H  HCH2  0   0.269   1.6310   2.9039  -0.5566
 1KV  H20  H  HCH2  0   0.212  -1.0362   3.3693   0.4736
 1KV  H21  H  HCH2  0   0.232  -0.3791   3.7727  -1.1171
 1KV  H22  H  HCH2  0   0.217  -2.8483   3.6573  -1.1245
 1KV  H23  H  HCH2  0   0.183  -2.1109   2.5162  -2.2544
 1KV  H24  H  HCH2  0   0.223  -0.2076  -0.2020   0.0720
 1KV  H25  H  HCH2  0   0.194  -0.9207   0.9640   1.1917
 1KV  H26  H  HCH2  0   0.187  -2.0114   0.0802  -1.5245
 1KV  H27  H  HCH2  0   0.233  -2.6658  -0.3102   0.0704
 1KV  H29  H  HCH2  0   0.239  -4.7486   2.4378  -1.1632
 1KV  H30  H  HCH2  0   0.197  -4.2080   1.0468  -2.0838
 1KV  H31  H  HCR6  0   0.240  -5.9678  -0.4831  -1.9242
 1KV  H32  H  HCH2  0   0.227  -9.2455  -2.7364   0.7744
 1KV  H33  H  HCH2  0   0.217  -7.7108  -3.6609   0.8859
 1KV  H34  H  HCR6  0   0.248  -6.0131   0.0294   3.0444
 1KV  H35  H  HCR6  0   0.242  -4.4989   1.4121   1.6366

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
 1KV  CAP  CAW  single    1.508  0.020  1.508
 1KV  CAP  NBD  single    1.447  0.020  1.447
 1KV  CAF  CAW  aromatic  1.402  0.020  1.402
 1KV  CAF  CAY  aromatic  1.373  0.020  1.373
 1KV  CAW  CAD  aromatic  1.389  0.020  1.389
 1KV  OAU  CAY  single    1.357  0.020  1.357
 1KV  OAU  CAI  single    1.422  0.020  1.422
 1KV  CAY  CAX  aromatic  1.384  0.020  1.384
 1KV  NBD  CAM  single    1.451  0.020  1.451
 1KV  NBD  CAL  single    1.451  0.020  1.451
 1KV  CAD  CAE  aromatic  1.400  0.020  1.400
 1KV  CAI  OAT  single    1.421  0.020  1.421
 1KV  CAX  CAE  aromatic  1.373  0.020  1.373
 1KV  CAX  OAT  single    1.358  0.020  1.358
 1KV  CAM  CAK  single    1.516  0.020  1.516
 1KV  CAL  CAJ  single    1.516  0.020  1.516
 1KV  CAK  N    single    1.450  0.020  1.450
 1KV  CAJ  N    single    1.450  0.020  1.450
 1KV  N    CA   single    1.436  0.020  1.436
 1KV  CA   C    single    1.524  0.020  1.524
 1KV  CAB  OAS  single    1.406  0.020  1.406
 1KV  C    NAQ  single    1.342  0.020  1.342
 1KV  C    O    double    1.221  0.020  1.221
 1KV  OAS  CBB  single    1.406  0.020  1.406
 1KV  NAQ  CBA  single    1.446  0.020  1.446
 1KV  CBB  CBA  single    1.527  0.020  1.527
 1KV  CBB  CAH  single    1.527  0.020  1.527
 1KV  CBA  CAO  single    1.530  0.020  1.530
 1KV  CAH  CAG  single    1.526  0.020  1.526
 1KV  CAO  CAZ  single    1.521  0.020  1.521
 1KV  CAG  CAZ  single    1.525  0.020  1.525
 1KV  CAZ  OAR  single    1.411  0.020  1.411
 1KV  OAR  CAA  single    1.406  0.020  1.406
 1KV  CAB  H1   single    0.970  0.020  1.090
 1KV  CAB  H2   single    0.970  0.020  1.090
 1KV  CAB  H3   single    0.970  0.020  1.090
 1KV  CBB  H4   single    0.970  0.020  1.090
 1KV  CAH  H5   single    0.970  0.020  1.090
 1KV  CAH  H6   single    0.970  0.020  1.090
 1KV  CAG  H7   single    0.970  0.020  1.090
 1KV  CAG  H8   single    0.970  0.020  1.090
 1KV  CAZ  H9   single    0.970  0.020  1.090
 1KV  CAA  H10  single    0.970  0.020  1.090
 1KV  CAA  H11  single    0.970  0.020  1.090
 1KV  CAA  H12  single    0.970  0.020  1.090
 1KV  CAO  H13  single    0.970  0.020  1.090
 1KV  CAO  H14  single    0.970  0.020  1.090
 1KV  CBA  H15  single    0.970  0.020  1.090
 1KV  NAQ  H16  single    0.860  0.020  1.020
 1KV  CA   H17  single    0.970  0.020  1.090
 1KV  CA   H18  single    0.970  0.020  1.090
 1KV  CAK  H20  single    0.970  0.020  1.090
 1KV  CAK  H21  single    0.970  0.020  1.090
 1KV  CAM  H22  single    0.970  0.020  1.090
 1KV  CAM  H23  single    0.970  0.020  1.090
 1KV  CAJ  H24  single    0.970  0.020  1.090
 1KV  CAJ  H25  single    0.970  0.020  1.090
 1KV  CAL  H26  single    0.970  0.020  1.090
 1KV  CAL  H27  single    0.970  0.020  1.090
 1KV  CAP  H29  single    0.970  0.020  1.090
 1KV  CAP  H30  single    0.970  0.020  1.090
 1KV  CAF  H31  single    0.930  0.020  1.080
 1KV  CAI  H32  single    0.970  0.020  1.090
 1KV  CAI  H33  single    0.970  0.020  1.090
 1KV  CAE  H34  single    0.930  0.020  1.080
 1KV  CAD  H35  single    0.930  0.020  1.080

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
 1KV  H3   CAB  H2   107.91  3.000
 1KV  H3   CAB  H1   107.89  3.000
 1KV  H2   CAB  H1   108.26  3.000
 1KV  H3   CAB  OAS  113.12  3.000
 1KV  H2   CAB  OAS  107.65  3.000
 1KV  H1   CAB  OAS  111.84  3.000
 1KV  CBB  OAS  CAB  114.60  3.000
 1KV  H4   CBB  CBA  108.32  3.000
 1KV  H4   CBB  CAH  108.15  3.000
 1KV  CBA  CBB  CAH  110.11  3.000
 1KV  H4   CBB  OAS  109.72  3.000
 1KV  CAH  CBB  OAS  112.97  3.000
 1KV  CBA  CBB  OAS  107.49  3.000
 1KV  H6   CAH  H5   106.66  3.000
 1KV  H6   CAH  CAG  109.94  3.000
 1KV  H5   CAH  CAG  109.26  3.000
 1KV  H6   CAH  CBB  109.00  3.000
 1KV  H5   CAH  CBB  110.17  3.000
 1KV  CAG  CAH  CBB  111.70  3.000
 1KV  H8   CAG  H7   106.95  3.000
 1KV  H8   CAG  CAZ  111.21  3.000
 1KV  H7   CAG  CAZ  109.02  3.000
 1KV  H8   CAG  CAH  109.14  3.000
 1KV  H7   CAG  CAH  109.97  3.000
 1KV  CAZ  CAG  CAH  110.49  3.000
 1KV  H9   CAZ  CAO  108.46  3.000
 1KV  H9   CAZ  OAR  109.48  3.000
 1KV  CAO  CAZ  OAR  107.45  3.000
 1KV  H9   CAZ  CAG  108.24  3.000
 1KV  OAR  CAZ  CAG  113.03  3.000
 1KV  CAO  CAZ  CAG  110.10  3.000
 1KV  CAA  OAR  CAZ  114.36  3.000
 1KV  H12  CAA  H11  107.84  3.000
 1KV  H12  CAA  H10  108.32  3.000
 1KV  H11  CAA  H10  107.96  3.000
 1KV  H12  CAA  OAR  111.79  3.000
 1KV  H11  CAA  OAR  113.03  3.000
 1KV  H10  CAA  OAR  107.74  3.000
 1KV  H14  CAO  H13  107.26  3.000
 1KV  H14  CAO  CBA  108.92  3.000
 1KV  H13  CAO  CBA  109.21  3.000
 1KV  H14  CAO  CAZ  110.00  3.000
 1KV  H13  CAO  CAZ  109.52  3.000
 1KV  CBA  CAO  CAZ  111.81  3.000
 1KV  H15  CBA  NAQ  107.61  3.000
 1KV  H15  CBA  CAO  108.87  3.000
 1KV  NAQ  CBA  CAO  111.01  3.000
 1KV  H15  CBA  CBB  108.03  3.000
 1KV  CAO  CBA  CBB  110.92  3.000
 1KV  NAQ  CBA  CBB  110.28  3.000
 1KV  H16  NAQ  C    118.07  3.000
 1KV  H16  NAQ  CBA  117.49  3.000
 1KV  C    NAQ  CBA  123.99  3.000
 1KV  CA   C    O    122.54  3.000
 1KV  O    C    NAQ  123.52  3.000
 1KV  CA   C    NAQ  113.91  3.000
 1KV  H18  CA   H17  105.88  3.000
 1KV  H18  CA   N    108.70  3.000
 1KV  H17  CA   N    113.20  3.000
 1KV  H18  CA   C    106.20  3.000
 1KV  H17  CA   C    110.12  3.000
 1KV  N    CA   C    112.28  3.000
 1KV  CAJ  N    CAK  109.98  3.000
 1KV  CAJ  N    CA   112.76  3.000
 1KV  CAK  N    CA   112.49  3.000
 1KV  H21  CAK  H20  107.23  3.000
 1KV  H21  CAK  CAM  109.01  3.000
 1KV  H20  CAK  CAM  109.19  3.000
 1KV  H21  CAK  N    109.19  3.000
 1KV  H20  CAK  N    112.06  3.000
 1KV  CAM  CAK  N    110.08  3.000
 1KV  H23  CAM  H22  107.13  3.000
 1KV  H23  CAM  NBD  111.70  3.000
 1KV  H22  CAM  NBD  109.03  3.000
 1KV  H23  CAM  CAK  108.85  3.000
 1KV  H22  CAM  CAK  109.21  3.000
 1KV  NBD  CAM  CAK  110.82  3.000
 1KV  H25  CAJ  H24  107.19  3.000
 1KV  H25  CAJ  CAL  109.33  3.000
 1KV  H24  CAJ  CAL  108.71  3.000
 1KV  H25  CAJ  N    111.38  3.000
 1KV  H24  CAJ  N    109.79  3.000
 1KV  CAL  CAJ  N    110.35  3.000
 1KV  H27  CAL  H26  107.25  3.000
 1KV  H27  CAL  NBD  109.34  3.000
 1KV  H26  CAL  NBD  111.30  3.000
 1KV  H27  CAL  CAJ  109.06  3.000
 1KV  H26  CAL  CAJ  109.04  3.000
 1KV  NBD  CAL  CAJ  110.76  3.000
 1KV  CAP  NBD  CAL  112.08  3.000
 1KV  CAL  NBD  CAM  110.27  3.000
 1KV  CAP  NBD  CAM  111.23  3.000
 1KV  H30  CAP  H29  105.80  3.000
 1KV  H30  CAP  CAW  109.12  3.000
 1KV  H29  CAP  CAW  108.75  3.000
 1KV  H30  CAP  NBD  111.79  3.000
 1KV  H29  CAP  NBD  107.71  3.000
 1KV  CAW  CAP  NBD  113.34  3.000
 1KV  CAD  CAW  CAF  120.01  3.000
 1KV  CAD  CAW  CAP  120.81  3.000
 1KV  CAF  CAW  CAP  119.15  3.000
 1KV  H31  CAF  CAY  121.40  3.000
 1KV  H31  CAF  CAW  121.05  3.000
 1KV  CAY  CAF  CAW  117.55  3.000
 1KV  CAX  CAY  OAU  109.41  3.000
 1KV  CAX  CAY  CAF  122.04  3.000
 1KV  OAU  CAY  CAF  128.54  3.000
 1KV  CAI  OAU  CAY  106.07  3.000
 1KV  H33  CAI  H32  110.43  3.000
 1KV  H33  CAI  OAT  109.89  3.000
 1KV  H32  CAI  OAT  109.82  3.000
 1KV  H33  CAI  OAU  109.82  3.000
 1KV  H32  CAI  OAU  109.78  3.000
 1KV  OAT  CAI  OAU  107.04  3.000
 1KV  CAX  OAT  CAI  106.03  3.000
 1KV  CAE  CAX  OAT  129.08  3.000
 1KV  OAT  CAX  CAY  109.39  3.000
 1KV  CAE  CAX  CAY  121.52  3.000
 1KV  H34  CAE  CAD  121.23  3.000
 1KV  H34  CAE  CAX  121.80  3.000
 1KV  CAD  CAE  CAX  116.97  3.000
 1KV  H35  CAD  CAE  119.11  3.000
 1KV  H35  CAD  CAW  118.98  3.000
 1KV  CAE  CAD  CAW  121.90  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
 1KV  CONST_01  CAX  CAY  CAF  CAW     0.00   0.0  0
 1KV  CONST_02  CAX  CAE  CAD  CAW     0.00   0.0  0
 1KV  CONST_03  CAE  CAD  CAW  CAF     0.00   0.0  0
 1KV  CONST_04  CAE  CAX  CAY  CAF     0.00   0.0  0
 1KV  CONST_05  CAD  CAW  CAF  CAY     0.00   0.0  0
 1KV  CONST_06  CAD  CAE  CAX  CAY     0.00   0.0  0
 1KV  CONST_07  CAY  CAF  CAW  CAP   180.00   0.0  0
 1KV  CONST_08  CAE  CAD  CAW  CAP   180.00   0.0  0
 1KV  CONST_09  H34  CAE  CAD  CAW   180.00   0.0  0
 1KV  CONST_10  H35  CAD  CAW  CAF   180.00   0.0  0
 1KV  CONST_11  H31  CAF  CAY  OAU     0.00   0.0  0
 1KV  CONST_12  CA   C    NAQ  CBA   180.00   0.0  0
 1KV  CONST_13  O    C    NAQ  CBA     0.00   0.0  0
 1KV  CONST_14  H16  NAQ  C    O     180.00   0.0  0
 1KV  Var_01    CAZ  CAG  CAH  CBB   -57.51  30.0  1
 1KV  Var_02    NBD  CAM  CAK  N      58.08  30.0  1
 1KV  Var_03    NBD  CAL  CAJ  N     -57.60  30.0  1
 1KV  Var_04    CAL  NBD  CAM  CAK   -56.88  30.0  1
 1KV  Var_05    CAL  CAJ  N    CAK    58.46  30.0  1
 1KV  Var_06    CAJ  CAL  NBD  CAM    56.56  30.0  1
 1KV  Var_07    CAJ  N    CAK  CAM   -58.59  30.0  1
 1KV  Var_08    OAT  CAI  OAU  CAY    13.93  30.0  1
 1KV  Var_09    CAX  CAY  OAU  CAI    -8.65  30.0  1
 1KV  Var_10    CAE  CAX  OAT  CAI  -171.93  30.0  1
 1KV  Var_11    CAW  CAP  NBD  CAM  -168.04  30.0  1
 1KV  Var_12    CAF  CAW  CAP  NBD  -140.97  30.0  2
 1KV  Var_13    CAK  N    CA   C    -162.20  30.0  2
 1KV  Var_14    N    CA   C    NAQ  -155.71  30.0  1
 1KV  Var_15    H1   CAB  OAS  CBB    50.91  30.0  3
 1KV  Var_16    H10  CAA  OAR  CAZ   175.91  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
 1KV  chir_01  CBB  OAS  CBA  CAH  positiv
 1KV  chir_02  CAZ  OAR  CAO  CAG  positiv
 1KV  chir_03  CBA  NAQ  CBB  CAO  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
 1KV  plan-1  CBA  0.020
 1KV  plan-1  NAQ  0.020
 1KV  plan-1  C    0.020
 1KV  plan-1  O    0.020
 1KV  plan-1  CA   0.020
 1KV  plan-1  H16  0.020
 1KV  plan-2  CAP  0.020
 1KV  plan-2  CAW  0.020
 1KV  plan-2  CAF  0.020
 1KV  plan-2  CAY  0.020
 1KV  plan-2  OAU  0.020
 1KV  plan-2  OAT  0.020
 1KV  plan-2  CAX  0.020
 1KV  plan-2  CAE  0.020
 1KV  plan-2  CAD  0.020
 1KV  plan-2  H31  0.020
 1KV  plan-2  H34  0.020
 1KV  plan-2  H35  0.020

