# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 02:15:01 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: trans-4-[(1R)-1-aminoethyl]-N-pyridin-4-ylcyclohexanecarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](N)[C@H]1CC[C@@H](CC1)C(=O)Nc2ccncc2
#
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
 Y27  Y27  trans-4-[(1R)-1-aminoethyl]-N-pyridin-4-ylcyclohexanecarboxamide  ligand  39  18  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Y27
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
 Y27  O23   O  O     0  -0.453  -1.6420  -0.9085  -1.0930
 Y27  C22   C  C     0   0.582  -0.7043  -0.1959  -0.7934
 Y27  C31   C  CH1   0  -0.414  -0.3649   0.1717   0.6352
 Y27  C36   C  CH2   0  -0.411  -1.6029   0.2594   1.5208
 Y27  C35   C  CH2   0  -0.434  -1.2089   0.6305   2.9460
 Y27  C34   C  CH1   0  -0.218  -0.2156  -0.3632   3.5481
 Y27  C33   C  CH2   0  -0.438   1.0080  -0.4969   2.6417
 Y27  C32   C  CH2   0  -0.411   0.6265  -0.8519   1.2085
 Y27  C41   C  CH1   0  -0.093   0.1376  -0.0010   5.0053
 Y27  C42   C  CH3   0  -0.659   0.9736  -1.0834   5.6768
 Y27  N43   N  NH2   0  -0.795   0.7963   1.2880   5.1914
 Y27  N21   N  NH1   0  -0.746   0.1673   0.3247  -1.7096
 Y27  C14   C  CR6   0   0.466   0.2018   0.1598  -3.0845
 Y27  C15   C  CR16  0  -0.378  -0.6692  -0.6439  -3.8218
 Y27  C16   C  CR16  0  -0.069  -0.5007  -0.7019  -5.1966
 Y27  N11   N  N     0  -0.418   0.4313  -0.0462  -5.8765
 Y27  C12   C  CR16  0  -0.063   1.2559   0.7167  -5.1645
 Y27  C13   C  CR16  0  -0.420   1.1877   0.8532  -3.7926
 Y27  H31   H  HCH1  0   0.257   0.1290   1.1513   0.6370
 Y27  H361  H  HCH2  0   0.223  -2.1242  -0.7020   1.5219
 Y27  H362  H  HCH2  0   0.239  -2.3029   0.9970   1.1212
 Y27  H351  H  HCH2  0   0.232  -2.1035   0.6845   3.5731
 Y27  H352  H  HCH2  0   0.206  -0.7721   1.6357   2.9389
 Y27  H34   H  HCH1  0   0.208  -0.7127  -1.3428   3.5804
 Y27  H331  H  HCH2  0   0.208   1.5704   0.4440   2.6339
 Y27  H332  H  HCH2  0   0.240   1.6885  -1.2596   3.0264
 Y27  H321  H  HCH2  0   0.229   0.1679  -1.8456   1.1843
 Y27  H322  H  HCH2  0   0.242   1.5242  -0.9014   0.5874
 Y27  H41   H  HCH1  0   0.219  -0.8143   0.0573   5.5466
 Y27  H421  H  HCH3  0   0.217   1.9783  -1.1421   5.2528
 Y27  H422  H  HCH3  0   0.221   0.5113  -2.0654   5.5659
 Y27  H423  H  HCH3  0   0.230   1.0796  -0.8797   6.7428
 Y27  H431  H  HNH2  0   0.336   1.6600   1.3135   4.6619
 Y27  H432  H  HNH2  0   0.345   0.2220   2.0323   4.8160
 Y27  H21   H  HNH1  0   0.419   0.8932   0.9187  -1.3367
 Y27  H15   H  HCR6  0   0.289  -1.4581  -1.2123  -3.3599
 Y27  H16   H  HCR6  0   0.264  -1.1724  -1.3250  -5.7768
 Y27  H12   H  HCR6  0   0.266   2.0199   1.2545  -5.7147
 Y27  H13   H  HCR6  0   0.283   1.8947   1.4933  -3.2796

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
 Y27  O23  C22   double    1.215  0.020  1.215
 Y27  C22  C31   single    1.514  0.020  1.514
 Y27  C22  N21   single    1.367  0.020  1.367
 Y27  C31  C36   single    1.525  0.020  1.525
 Y27  C31  C32   single    1.536  0.020  1.536
 Y27  C31  H31   single    0.970  0.020  1.090
 Y27  C36  C35   single    1.524  0.020  1.524
 Y27  C36  H361  single    0.970  0.020  1.090
 Y27  C36  H362  single    0.970  0.020  1.090
 Y27  C35  C34   single    1.529  0.020  1.529
 Y27  C35  H351  single    0.970  0.020  1.090
 Y27  C35  H352  single    0.970  0.020  1.090
 Y27  C34  C33   single    1.529  0.020  1.529
 Y27  C34  C41   single    1.543  0.020  1.543
 Y27  C34  H34   single    0.970  0.020  1.090
 Y27  C33  C32   single    1.525  0.020  1.525
 Y27  C33  H331  single    0.970  0.020  1.090
 Y27  C33  H332  single    0.970  0.020  1.090
 Y27  C32  H321  single    0.970  0.020  1.090
 Y27  C32  H322  single    0.970  0.020  1.090
 Y27  C41  C42   single    1.524  0.020  1.524
 Y27  C41  N43   single    1.459  0.020  1.459
 Y27  C41  H41   single    0.970  0.020  1.090
 Y27  C42  H421  single    0.970  0.020  1.090
 Y27  C42  H422  single    0.970  0.020  1.090
 Y27  C42  H423  single    0.970  0.020  1.090
 Y27  N43  H431  single    0.890  0.020  1.040
 Y27  N43  H432  single    0.890  0.020  1.040
 Y27  N21  C14   single    1.385  0.020  1.385
 Y27  N21  H21   single    0.860  0.020  1.020
 Y27  C14  C15   aromatic  1.396  0.020  1.396
 Y27  C14  C13   aromatic  1.398  0.020  1.398
 Y27  C15  C16   aromatic  1.386  0.020  1.386
 Y27  C15  H15   single    0.930  0.020  1.080
 Y27  C16  N11   aromatic  1.327  0.020  1.327
 Y27  C16  H16   single    0.930  0.020  1.080
 Y27  N11  C12   aromatic  1.330  0.020  1.330
 Y27  C12  C13   aromatic  1.380  0.020  1.380
 Y27  C12  H12   single    0.930  0.020  1.080
 Y27  C13  H13   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
 Y27  N21   C22  C31   113.38  3.000
 Y27  N21   C22  O23   123.36  3.000
 Y27  C31   C22  O23   123.23  3.000
 Y27  H31   C31  C32   107.69  3.000
 Y27  H31   C31  C36   108.25  3.000
 Y27  C32   C31  C36   110.22  3.000
 Y27  H31   C31  C22   108.62  3.000
 Y27  C32   C31  C22   109.58  3.000
 Y27  C36   C31  C22   112.34  3.000
 Y27  H362  C36  H361  106.76  3.000
 Y27  H362  C36  C35   110.07  3.000
 Y27  H361  C36  C35   109.65  3.000
 Y27  H362  C36  C31   110.28  3.000
 Y27  H361  C36  C31   109.70  3.000
 Y27  C35   C36  C31   110.32  3.000
 Y27  H352  C35  H351  106.52  3.000
 Y27  H352  C35  C34   109.86  3.000
 Y27  H351  C35  C34   109.74  3.000
 Y27  H352  C35  C36   108.67  3.000
 Y27  H351  C35  C36   109.67  3.000
 Y27  C34   C35  C36   112.21  3.000
 Y27  H34   C34  C41   106.56  3.000
 Y27  H34   C34  C33   107.55  3.000
 Y27  C41   C34  C33   113.42  3.000
 Y27  H34   C34  C35   107.28  3.000
 Y27  C41   C34  C35   111.61  3.000
 Y27  C33   C34  C35   110.09  3.000
 Y27  H332  C33  H331  106.40  3.000
 Y27  H332  C33  C32   108.93  3.000
 Y27  H331  C33  C32   108.76  3.000
 Y27  H332  C33  C34   110.54  3.000
 Y27  H331  C33  C34   109.87  3.000
 Y27  C32   C33  C34   112.17  3.000
 Y27  H322  C32  H321  106.89  3.000
 Y27  H322  C32  C33   109.83  3.000
 Y27  H321  C32  C33   109.69  3.000
 Y27  H322  C32  C31   110.38  3.000
 Y27  H321  C32  C31   109.04  3.000
 Y27  C33   C32  C31   110.92  3.000
 Y27  H41   C41  N43   106.37  3.000
 Y27  H41   C41  C42   107.25  3.000
 Y27  N43   C41  C42   108.88  3.000
 Y27  H41   C41  C34   106.26  3.000
 Y27  N43   C41  C34   115.54  3.000
 Y27  C42   C41  C34   112.04  3.000
 Y27  H423  C42  H422  107.98  3.000
 Y27  H423  C42  H421  107.47  3.000
 Y27  H422  C42  H421  107.58  3.000
 Y27  H423  C42  C41   110.58  3.000
 Y27  H422  C42  C41   111.23  3.000
 Y27  H421  C42  C41   111.82  3.000
 Y27  H432  N43  H431  105.73  3.000
 Y27  H432  N43  C41   110.25  3.000
 Y27  H431  N43  C41   109.89  3.000
 Y27  H21   N21  C14   114.76  3.000
 Y27  H21   N21  C22   115.78  3.000
 Y27  C14   N21  C22   129.46  3.000
 Y27  C13   C14  C15   117.27  3.000
 Y27  C13   C14  N21   117.47  3.000
 Y27  C15   C14  N21   125.27  3.000
 Y27  H15   C15  C16   119.50  3.000
 Y27  H15   C15  C14   122.32  3.000
 Y27  C16   C15  C14   118.17  3.000
 Y27  H16   C16  N11   116.41  3.000
 Y27  H16   C16  C15   118.65  3.000
 Y27  N11   C16  C15   124.95  3.000
 Y27  C12   N11  C16   116.40  3.000
 Y27  H12   C12  C13   119.35  3.000
 Y27  H12   C12  N11   116.72  3.000
 Y27  C13   C12  N11   123.93  3.000
 Y27  H13   C13  C12   119.80  3.000
 Y27  H13   C13  C14   120.91  3.000
 Y27  C12   C13  C14   119.29  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
 Y27  CONST_01  N11  C16  C15  C14    0.00   0.0  0
 Y27  CONST_02  N11  C12  C13  C14    0.00   0.0  0
 Y27  CONST_03  C12  C13  C14  C15    0.00   0.0  0
 Y27  CONST_04  C12  N11  C16  C15    0.00   0.0  0
 Y27  CONST_05  C13  C14  C15  C16    0.00   0.0  0
 Y27  CONST_06  C13  C12  N11  C16    0.00   0.0  0
 Y27  CONST_07  C16  C15  C14  N21  180.00   0.0  0
 Y27  CONST_08  C12  C13  C14  N21  180.00   0.0  0
 Y27  CONST_09  H16  C16  C15  C14  180.00   0.0  0
 Y27  CONST_10  H12  C12  C13  C14  180.00   0.0  0
 Y27  CONST_11  H13  C13  C14  C15  180.00   0.0  0
 Y27  CONST_12  H15  C15  C16  N11  180.00   0.0  0
 Y27  CONST_13  C14  N21  C22  C31  180.00   0.0  0
 Y27  CONST_14  C15  C14  N21  C22    0.00   0.0  0
 Y27  CONST_15  C13  C14  N21  C22  180.00   0.0  0
 Y27  CONST_16  H21  N21  C14  C15  180.00   0.0  0
 Y27  CONST_17  C14  N21  C22  O23    0.00   0.0  0
 Y27  Var_01    C34  C35  C36  C31  -57.43  30.0  1
 Y27  Var_02    C34  C33  C32  C31   55.63  30.0  1

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
 Y27  chir_01  C31  C22  C36  C32  negativ
 Y27  chir_02  C34  C35  C33  C41  negativ
 Y27  chir_03  C41  N43  C34  C42  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
 Y27  plan-1  N21  0.020
 Y27  plan-1  C14  0.020
 Y27  plan-1  C15  0.020
 Y27  plan-1  C16  0.020
 Y27  plan-1  N11  0.020
 Y27  plan-1  C12  0.020
 Y27  plan-1  C13  0.020
 Y27  plan-1  H15  0.020
 Y27  plan-1  H16  0.020
 Y27  plan-1  H12  0.020
 Y27  plan-1  H13  0.020
 Y27  plan-2  O23  0.020
 Y27  plan-2  C22  0.020
 Y27  plan-2  C31  0.020
 Y27  plan-2  N21  0.020
 Y27  plan-2  C14  0.020
 Y27  plan-2  H21  0.020

