# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 05:49:33 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: ~{N}-(2-methoxyethyl)-~{N}-[[(3~{S})-1-prop-2-ynylpiperidin-3-yl]methyl]naphthalene-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCN(C[C@H]1CCCN(CC#C)C1)C(=O)c2ccc3ccccc3c2
#
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
 6YC  6YC  ~{N}-(2-methoxyethyl)-~{N}-[[(3~{S})-1-prop-2-ynylpiperidin-3-yl]methyl]naphthalene-2-carboxamide  ligand  55  27  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6YC
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
 6YC  CAU  C  CR16  0  -0.341  -2.9539   0.0027  -0.9289
 6YC  CAV  C  CR66  0   0.128  -4.2215   0.4909  -0.5365
 6YC  CBA  C  CR16  0  -0.313  -5.4015   0.1480  -1.2375
 6YC  CAZ  C  CR16  0  -0.256  -6.6138   0.6454  -0.8440
 6YC  CAY  C  CR16  0  -0.255  -6.7039   1.5061   0.2708
 6YC  CAX  C  CR16  0  -0.309  -5.5794   1.8532   0.9689
 6YC  CAW  C  CR66  0   0.113  -4.3124   1.3564   0.5838
 6YC  CAT  C  CR16  0  -0.305  -3.1290   1.6984   1.2795
 6YC  CAS  C  CR16  0  -0.263  -1.9190   1.1985   0.8897
 6YC  CAR  C  CR6   0  -0.072  -1.8265   0.3348  -0.2274
 6YC  CAB  C  C     0   0.514  -0.4832  -0.1193  -0.7142
 6YC  OAA  O  O     0  -0.487  -0.0610   0.3044  -1.7827
 6YC  NAC  N  NT    0  -0.438   0.2161  -0.9627   0.0694
 6YC  CAD  C  CH2   0  -0.374  -0.3761  -1.6629   1.2008
 6YC  CAE  C  CH2   0  -0.118  -1.1559  -2.9000   0.8036
 6YC  OAF  O  O2    0  -0.477  -0.3019  -3.8130   0.1686
 6YC  CAG  C  CH3   0  -0.394  -0.9776  -4.9435  -0.3192
 6YC  CAH  C  CH2   0  -0.290   1.5681  -1.3278  -0.3383
 6YC  CAI  C  CH1   0  -0.267   2.6033  -0.2534  -0.0169
 6YC  CAQ  C  CH2   0  -0.308   3.9827  -0.7284  -0.4853
 6YC  CAJ  C  CH2   0  -0.427   2.6587   0.0758   1.4742
 6YC  CAK  C  CH2   0  -0.447   3.8034   1.0350   1.7874
 6YC  CAL  C  CH2   0  -0.325   5.1206   0.5007   1.2297
 6YC  NAM  N  NT    0  -0.410   5.0690   0.1916  -0.1927
 6YC  CAN  C  CH2   0  -0.430   5.0579   1.3660  -1.0473
 6YC  CAO  C  CSP   0   0.286   6.3362   2.0743  -1.0062
 6YC  CAP  C  CSP1  0  -0.551   7.3840   2.6627  -0.9787
 6YC  H1   H  HCR6  0   0.262  -2.8908  -0.6501  -1.7924
 6YC  H2   H  HCR6  0   0.258  -5.3322  -0.5152  -2.0912
 6YC  H3   H  HCR6  0   0.261  -7.5111   0.3819  -1.3886
 6YC  H4   H  HCR6  0   0.261  -7.6694   1.8918   0.5706
 6YC  H5   H  HCR6  0   0.258  -5.6467   2.5152   1.8239
 6YC  H6   H  HCR6  0   0.260  -3.1906   2.3681   2.1285
 6YC  H7   H  HCR6  0   0.268  -1.0226   1.4710   1.4346
 6YC  H8   H  HCH2  0   0.267   0.4264  -1.9300   1.8884
 6YC  H9   H  HCH2  0   0.275  -1.0406  -1.0056   1.7585
 6YC  H10  H  HCH2  0   0.212  -1.6042  -3.3343   1.7087
 6YC  H11  H  HCH2  0   0.200  -1.9888  -2.6175   0.1433
 6YC  H12  H  HCH3  0   0.205  -1.7377  -4.6780  -1.0642
 6YC  H13  H  HCH3  0   0.234  -0.2443  -5.5946  -0.7934
 6YC  H14  H  HCH3  0   0.205  -1.4738  -5.5055   0.4808
 6YC  H15  H  HCH2  0   0.248   1.8324  -2.2507   0.1785
 6YC  H16  H  HCH2  0   0.251   1.5815  -1.5548  -1.4064
 6YC  H17  H  HCH1  0   0.237   2.3396   0.6568  -0.5686
 6YC  H18  H  HCH2  0   0.232   4.2150  -1.6801   0.0082
 6YC  H19  H  HCH2  0   0.243   3.9717  -0.9288  -1.5605
 6YC  H20  H  HCH2  0   0.237   1.7080   0.4998   1.8087
 6YC  H21  H  HCH2  0   0.209   2.8003  -0.8537   2.0400
 6YC  H22  H  HCH2  0   0.221   3.5859   2.0227   1.3693
 6YC  H23  H  HCH2  0   0.236   3.8966   1.1750   2.8670
 6YC  H24  H  HCH2  0   0.244   5.9347   1.2063   1.4113
 6YC  H25  H  HCH2  0   0.230   5.3858  -0.4216   1.7578
 6YC  H27  H  HCH2  0   0.277   4.8811   1.0401  -2.0762
 6YC  H28  H  HCH2  0   0.244   4.2582   2.0875  -0.8231
 6YC  H29  H  H     0   0.279   8.3176   3.1764  -0.9568

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
 6YC  CAY  CAX  aromatic  1.368  0.020  1.368
 6YC  CAY  CAZ  aromatic  1.411  0.020  1.411
 6YC  CAX  CAW  aromatic  1.414  0.020  1.414
 6YC  CAZ  CBA  aromatic  1.368  0.020  1.368
 6YC  CAW  CAT  aromatic  1.415  0.020  1.415
 6YC  CAW  CAV  aromatic  1.419  0.020  1.419
 6YC  CBA  CAV  aromatic  1.415  0.020  1.415
 6YC  CAT  CAS  aromatic  1.366  0.020  1.366
 6YC  CAV  CAU  aromatic  1.414  0.020  1.414
 6YC  CAS  CAR  aromatic  1.415  0.020  1.415
 6YC  CAU  CAR  aromatic  1.369  0.020  1.369
 6YC  CAR  CAB  single    1.499  0.020  1.499
 6YC  CAD  CAE  single    1.515  0.020  1.515
 6YC  CAD  NAC  single    1.456  0.020  1.456
 6YC  OAF  CAE  single    1.402  0.020  1.402
 6YC  OAF  CAG  single    1.404  0.020  1.404
 6YC  CAB  NAC  single    1.347  0.020  1.347
 6YC  CAB  OAA  double    1.225  0.020  1.225
 6YC  NAC  CAH  single    1.459  0.020  1.459
 6YC  CAJ  CAK  single    1.526  0.020  1.526
 6YC  CAJ  CAI  single    1.528  0.020  1.528
 6YC  CAK  CAL  single    1.527  0.020  1.527
 6YC  CAH  CAI  single    1.526  0.020  1.526
 6YC  CAI  CAQ  single    1.532  0.020  1.532
 6YC  CAL  NAM  single    1.456  0.020  1.456
 6YC  CAQ  NAM  single    1.453  0.020  1.453
 6YC  NAM  CAN  single    1.453  0.020  1.453
 6YC  CAN  CAO  single    1.462  0.020  1.462
 6YC  CAO  CAP  triple    1.202  0.020  1.202
 6YC  CAU  H1   single    0.929  0.020  1.085
 6YC  CBA  H2   single    0.929  0.020  1.085
 6YC  CAZ  H3   single    0.929  0.020  1.085
 6YC  CAY  H4   single    0.929  0.020  1.085
 6YC  CAX  H5   single    0.929  0.020  1.085
 6YC  CAT  H6   single    0.929  0.020  1.085
 6YC  CAS  H7   single    0.929  0.020  1.085
 6YC  CAD  H8   single    0.939  0.020  1.096
 6YC  CAD  H9   single    0.939  0.020  1.096
 6YC  CAE  H10  single    0.939  0.020  1.096
 6YC  CAE  H11  single    0.939  0.020  1.096
 6YC  CAG  H12  single    0.939  0.020  1.096
 6YC  CAG  H13  single    0.939  0.020  1.096
 6YC  CAG  H14  single    0.939  0.020  1.096
 6YC  CAH  H15  single    0.939  0.020  1.096
 6YC  CAH  H16  single    0.939  0.020  1.096
 6YC  CAI  H17  single    0.939  0.020  1.096
 6YC  CAQ  H18  single    0.939  0.020  1.096
 6YC  CAQ  H19  single    0.939  0.020  1.096
 6YC  CAJ  H20  single    0.939  0.020  1.096
 6YC  CAJ  H21  single    0.939  0.020  1.096
 6YC  CAK  H22  single    0.939  0.020  1.096
 6YC  CAK  H23  single    0.939  0.020  1.096
 6YC  CAL  H24  single    0.939  0.020  1.096
 6YC  CAL  H25  single    0.939  0.020  1.096
 6YC  CAN  H27  single    0.939  0.020  1.096
 6YC  CAN  H28  single    0.939  0.020  1.096
 6YC  CAP  H29  single    0.913  0.020  1.066

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
 6YC  H1   CAU  CAR  120.42  3.000
 6YC  H1   CAU  CAV  118.75  3.000
 6YC  CAR  CAU  CAV  120.82  3.000
 6YC  CAW  CAV  CBA  119.06  3.000
 6YC  CBA  CAV  CAU  121.78  3.000
 6YC  CAW  CAV  CAU  119.16  3.000
 6YC  H2   CBA  CAZ  120.39  3.000
 6YC  H2   CBA  CAV  119.05  3.000
 6YC  CAZ  CBA  CAV  120.56  3.000
 6YC  H3   CAZ  CAY  119.54  3.000
 6YC  H3   CAZ  CBA  120.09  3.000
 6YC  CAY  CAZ  CBA  120.36  3.000
 6YC  H4   CAY  CAX  120.10  3.000
 6YC  H4   CAY  CAZ  119.56  3.000
 6YC  CAX  CAY  CAZ  120.35  3.000
 6YC  H5   CAX  CAW  119.02  3.000
 6YC  H5   CAX  CAY  120.44  3.000
 6YC  CAW  CAX  CAY  120.54  3.000
 6YC  CAT  CAW  CAX  122.04  3.000
 6YC  CAT  CAW  CAV  118.83  3.000
 6YC  CAX  CAW  CAV  119.12  3.000
 6YC  H6   CAT  CAS  120.02  3.000
 6YC  H6   CAT  CAW  119.17  3.000
 6YC  CAS  CAT  CAW  120.81  3.000
 6YC  H7   CAS  CAR  119.75  3.000
 6YC  H7   CAS  CAT  119.81  3.000
 6YC  CAR  CAS  CAT  120.43  3.000
 6YC  CAB  CAR  CAS  119.99  3.000
 6YC  CAB  CAR  CAU  119.87  3.000
 6YC  CAS  CAR  CAU  119.92  3.000
 6YC  NAC  CAB  OAA  123.04  3.000
 6YC  OAA  CAB  CAR  119.17  3.000
 6YC  NAC  CAB  CAR  117.77  3.000
 6YC  CAH  NAC  CAD  118.28  3.000
 6YC  CAH  NAC  CAB  118.39  3.000
 6YC  CAD  NAC  CAB  122.81  3.000
 6YC  H9   CAD  H8   105.92  3.000
 6YC  H9   CAD  CAE  108.25  3.000
 6YC  H8   CAD  CAE  110.13  3.000
 6YC  H9   CAD  NAC  110.86  3.000
 6YC  H8   CAD  NAC  107.96  3.000
 6YC  CAE  CAD  NAC  113.46  3.000
 6YC  H11  CAE  H10  106.67  3.000
 6YC  H11  CAE  OAF  110.89  3.000
 6YC  H10  CAE  OAF  111.34  3.000
 6YC  H11  CAE  CAD  109.72  3.000
 6YC  H10  CAE  CAD  108.45  3.000
 6YC  OAF  CAE  CAD  109.68  3.000
 6YC  CAG  OAF  CAE  112.85  3.000
 6YC  H14  CAG  H13  108.42  3.000
 6YC  H14  CAG  H12  107.82  3.000
 6YC  H13  CAG  H12  108.39  3.000
 6YC  H14  CAG  OAF  112.14  3.000
 6YC  H13  CAG  OAF  107.97  3.000
 6YC  H12  CAG  OAF  111.99  3.000
 6YC  H16  CAH  H15  106.54  3.000
 6YC  H16  CAH  CAI  110.12  3.000
 6YC  H15  CAH  CAI  109.37  3.000
 6YC  H16  CAH  NAC  109.68  3.000
 6YC  H15  CAH  NAC  107.70  3.000
 6YC  CAI  CAH  NAC  113.18  3.000
 6YC  H17  CAI  CAJ  108.71  3.000
 6YC  H17  CAI  CAQ  108.67  3.000
 6YC  CAJ  CAI  CAQ  109.42  3.000
 6YC  H17  CAI  CAH  108.38  3.000
 6YC  CAQ  CAI  CAH  109.15  3.000
 6YC  CAJ  CAI  CAH  112.44  3.000
 6YC  H19  CAQ  H18  106.58  3.000
 6YC  H19  CAQ  NAM  108.75  3.000
 6YC  H18  CAQ  NAM  107.47  3.000
 6YC  H19  CAQ  CAI  110.38  3.000
 6YC  H18  CAQ  CAI  108.79  3.000
 6YC  NAM  CAQ  CAI  114.53  3.000
 6YC  H21  CAJ  H20  106.44  3.000
 6YC  H21  CAJ  CAK  109.26  3.000
 6YC  H20  CAJ  CAK  110.23  3.000
 6YC  H21  CAJ  CAI  108.98  3.000
 6YC  H20  CAJ  CAI  110.52  3.000
 6YC  CAK  CAJ  CAI  111.28  3.000
 6YC  H23  CAK  H22  106.19  3.000
 6YC  H23  CAK  CAL  109.40  3.000
 6YC  H22  CAK  CAL  110.34  3.000
 6YC  H23  CAK  CAJ  110.33  3.000
 6YC  H22  CAK  CAJ  109.87  3.000
 6YC  CAL  CAK  CAJ  110.62  3.000
 6YC  H25  CAL  H24  106.45  3.000
 6YC  H25  CAL  NAM  107.50  3.000
 6YC  H24  CAL  NAM  109.02  3.000
 6YC  H25  CAL  CAK  109.11  3.000
 6YC  H24  CAL  CAK  110.86  3.000
 6YC  NAM  CAL  CAK  113.60  3.000
 6YC  CAN  NAM  CAL  113.78  3.000
 6YC  CAN  NAM  CAQ  112.81  3.000
 6YC  CAL  NAM  CAQ  110.95  3.000
 6YC  H28  CAN  H27  105.64  3.000
 6YC  H28  CAN  CAO  108.19  3.000
 6YC  H27  CAN  CAO  108.19  3.000
 6YC  H28  CAN  NAM  114.58  3.000
 6YC  H27  CAN  NAM  108.29  3.000
 6YC  CAO  CAN  NAM  111.62  3.000
 6YC  CAP  CAO  CAN  180.00  3.000
 6YC  H29  CAP  CAO  180.00  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
 6YC  CONST_01  CAX  CAW  CAV  CAU   180.00   0.0  0
 6YC  CONST_02  CAT  CAW  CAV  CAU     0.00   0.0  0
 6YC  CONST_03  CAZ  CBA  CAV  CAU   180.00   0.0  0
 6YC  CONST_04  CAT  CAS  CAR  CAU     0.00   0.0  0
 6YC  CONST_05  CAY  CAX  CAW  CAV     0.00   0.0  0
 6YC  CONST_06  CAS  CAT  CAW  CAV     0.00   0.0  0
 6YC  CONST_07  CAY  CAZ  CBA  CAV     0.00   0.0  0
 6YC  CONST_08  CAS  CAR  CAU  CAV     0.00   0.0  0
 6YC  CONST_09  CAX  CAY  CAZ  CBA     0.00   0.0  0
 6YC  CONST_10  CAX  CAW  CAV  CBA     0.00   0.0  0
 6YC  CONST_11  CAT  CAW  CAV  CBA   180.00   0.0  0
 6YC  CONST_12  CAR  CAU  CAV  CBA   180.00   0.0  0
 6YC  CONST_13  CAW  CAX  CAY  CAZ     0.00   0.0  0
 6YC  CONST_14  CAW  CAV  CBA  CAZ     0.00   0.0  0
 6YC  CONST_15  CAT  CAW  CAX  CAY   180.00   0.0  0
 6YC  CONST_16  CAS  CAT  CAW  CAX   180.00   0.0  0
 6YC  CONST_17  CAR  CAS  CAT  CAW     0.00   0.0  0
 6YC  CONST_18  CAR  CAU  CAV  CAW     0.00   0.0  0
 6YC  CONST_19  CAB  CAR  CAU  CAV   180.00   0.0  0
 6YC  CONST_20  CAB  CAR  CAS  CAT   180.00   0.0  0
 6YC  CONST_21  H2   CBA  CAV  CAU     0.00   0.0  0
 6YC  CONST_22  H7   CAS  CAR  CAU   180.00   0.0  0
 6YC  CONST_23  H5   CAX  CAW  CAV   180.00   0.0  0
 6YC  CONST_24  H6   CAT  CAW  CAV   180.00   0.0  0
 6YC  CONST_25  H3   CAZ  CBA  CAV   180.00   0.0  0
 6YC  CONST_26  H4   CAY  CAZ  CBA   180.00   0.0  0
 6YC  CONST_27  H1   CAU  CAV  CBA     0.00   0.0  0
 6YC  CONST_28  CAD  NAC  CAB  CAR     0.00   0.0  0
 6YC  CONST_29  CAH  NAC  CAB  CAR   180.00   0.0  0
 6YC  CONST_30  CAD  NAC  CAB  OAA   180.00   0.0  0
 6YC  CONST_31  CAH  NAC  CAB  OAA     0.00   0.0  0
 6YC  Var_01    CAL  CAK  CAJ  CAI   -52.71  30.0  1
 6YC  Var_02    CAL  NAM  CAQ  CAI    55.53  30.0  1
 6YC  Var_03    CAK  CAL  NAM  CAQ   -54.83  30.0  1
 6YC  Var_04    NAM  CAL  CAK  CAJ    54.21  30.0  1
 6YC  Var_05    NAC  CAB  CAR  CAU  -116.45  30.0  2
 6YC  Var_06    CAO  CAN  NAM  CAQ  -163.84  30.0  3
 6YC  Var_07    CAI  CAH  NAC  CAB    79.08  30.0  3
 6YC  Var_08    CAE  CAD  NAC  CAB    80.73  30.0  2
 6YC  Var_09    OAF  CAE  CAD  NAC    60.86  30.0  3
 6YC  Var_10    H12  CAG  OAF  CAE    60.75  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
 6YC  chir_01  CAI  CAJ  CAH  CAQ  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
 6YC  plan-1  CAU  0.020
 6YC  plan-1  CAV  0.020
 6YC  plan-1  CBA  0.020
 6YC  plan-1  CAZ  0.020
 6YC  plan-1  CAY  0.020
 6YC  plan-1  CAX  0.020
 6YC  plan-1  CAW  0.020
 6YC  plan-1  CAT  0.020
 6YC  plan-1  CAS  0.020
 6YC  plan-1  CAR  0.020
 6YC  plan-1  CAB  0.020
 6YC  plan-1  H1   0.020
 6YC  plan-1  H2   0.020
 6YC  plan-1  H3   0.020
 6YC  plan-1  H4   0.020
 6YC  plan-1  H5   0.020
 6YC  plan-1  H6   0.020
 6YC  plan-1  H7   0.020
 6YC  plan-2  CAR  0.020
 6YC  plan-2  CAB  0.020
 6YC  plan-2  OAA  0.020
 6YC  plan-2  NAC  0.020
 6YC  plan-2  CAD  0.020
 6YC  plan-2  CAH  0.020

