# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 12:33:30 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: 1-benzyl-1,4,5,6-tetrahydropyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)C1=CN(CCC1)Cc2ccccc2
#
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
 536  536  1-benzyl-1,4,5,6-tetrahydropyridine-3-carboxamide  ligand  32  16  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_536
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
 536  C1    C  CH2   0  -0.389   1.0384  -0.6691  -1.4853
 536  N2    N  NT    0  -0.424  -0.2209  -0.8286  -0.7978
 536  C3    C  C1    0   0.072  -1.2170   0.0645  -0.9323
 536  C4    C  C     0  -0.219  -2.3609   0.0740  -0.2007
 536  C5    C  CH2   0  -0.490  -2.5852  -0.9901   0.8422
 536  C6    C  CH2   0  -0.469  -1.7265  -2.2134   0.5335
 536  C7    C  CH2   0  -0.270  -0.2852  -1.8221   0.2565
 536  C8    C  C     0   0.465  -3.3256   1.1383  -0.4735
 536  O9    O  O     0  -0.529  -3.1924   1.9649  -1.3810
 536  N10   N  NH2   0  -0.835  -4.4135   1.1747   0.3334
 536  C11   C  CR6   0   0.124   2.1574  -0.2245  -0.5721
 536  C12   C  CR16  0  -0.312   3.3383  -0.9533  -0.4993
 536  C13   C  CR16  0  -0.241   4.3754  -0.5459   0.3320
 536  C14   C  CR16  0  -0.268   4.2342   0.5956   1.1075
 536  C15   C  CR16  0  -0.241   3.0531   1.3272   1.0455
 536  C16   C  CR16  0  -0.293   2.0225   0.9196   0.2118
 536  H1    H  HCH2  0   0.262   1.3136  -1.6157  -1.9597
 536  H11   H  HCH2  0   0.271   0.9003   0.0583  -2.2875
 536  H3    H  H     0   0.276  -1.0672   0.8122  -1.7026
 536  H5    H  HCH2  0   0.237  -2.3553  -0.6206   1.8482
 536  H51   H  HCH2  0   0.238  -3.6326  -1.3040   0.8638
 536  H6    H  HCH2  0   0.248  -1.7500  -2.9179   1.3653
 536  H61   H  HCH2  0   0.236  -2.1324  -2.7320  -0.3386
 536  H7    H  HCH2  0   0.249   0.2917  -2.6941  -0.0594
 536  H71   H  HCH2  0   0.236   0.1870  -1.4394   1.1686
 536  HN10  H  HNH2  0   0.403  -4.4822   0.6206   1.1685
 536  HN11  H  HNH2  0   0.389  -5.0566   1.9441   0.2509
 536  H12   H  HCR6  0   0.252   3.4485  -1.8511  -1.0968
 536  H13   H  HCR6  0   0.255   5.2890  -1.1249   0.3758
 536  H14   H  HCR6  0   0.256   5.0370   0.9139   1.7599
 536  H15   H  HCR6  0   0.256   2.9370   2.2185   1.6487
 536  H16   H  HCR6  0   0.257   1.1066   1.4988   0.1765

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
 536  C1   N2    single    1.444  0.020  1.444
 536  C1   C11   single    1.511  0.020  1.511
 536  N2   C3    single    1.345  0.020  1.345
 536  N2   C7    single    1.450  0.020  1.450
 536  C3   C4    double    1.358  0.020  1.358
 536  C4   C5    single    1.507  0.020  1.507
 536  C4   C8    single    1.462  0.020  1.462
 536  C5   C6    single    1.526  0.020  1.526
 536  C6   C7    single    1.519  0.020  1.519
 536  C8   O9    double    1.235  0.020  1.235
 536  C8   N10   single    1.355  0.020  1.355
 536  C11  C12   aromatic  1.390  0.020  1.390
 536  C11  C16   aromatic  1.393  0.020  1.393
 536  C12  C13   aromatic  1.390  0.020  1.390
 536  C13  C14   aromatic  1.387  0.020  1.387
 536  C14  C15   aromatic  1.391  0.020  1.391
 536  C15  C16   aromatic  1.387  0.020  1.387
 536  C1   H1    single    0.970  0.020  1.090
 536  C1   H11   single    0.970  0.020  1.090
 536  C3   H3    single    0.930  0.020  1.080
 536  C5   H5    single    0.970  0.020  1.090
 536  C5   H51   single    0.970  0.020  1.090
 536  C6   H6    single    0.970  0.020  1.090
 536  C6   H61   single    0.970  0.020  1.090
 536  C7   H7    single    0.970  0.020  1.090
 536  C7   H71   single    0.970  0.020  1.090
 536  N10  HN10  single    0.860  0.020  1.020
 536  N10  HN11  single    0.860  0.020  1.020
 536  C12  H12   single    0.930  0.020  1.080
 536  C13  H13   single    0.930  0.020  1.080
 536  C14  H14   single    0.930  0.020  1.080
 536  C15  H15   single    0.930  0.020  1.080
 536  C16  H16   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
 536  H11   C1   H1    106.84  3.000
 536  H11   C1   C11   109.98  3.000
 536  H1    C1   C11   109.29  3.000
 536  H11   C1   N2    108.26  3.000
 536  H1    C1   N2    109.29  3.000
 536  C11   C1   N2    112.99  3.000
 536  C7    N2   C3    119.67  3.000
 536  C7    N2   C1    117.43  3.000
 536  C3    N2   C1    121.68  3.000
 536  H3    C3   C4    119.64  3.000
 536  H3    C3   N2    115.27  3.000
 536  C4    C3   N2    125.09  3.000
 536  C8    C4   C5    123.03  3.000
 536  C8    C4   C3    117.41  3.000
 536  C5    C4   C3    119.56  3.000
 536  H51   C5   H5    106.23  3.000
 536  H51   C5   C6    108.23  3.000
 536  H5    C5   C6    109.75  3.000
 536  H51   C5   C4    111.03  3.000
 536  H5    C5   C4    111.46  3.000
 536  C6    C5   C4    110.02  3.000
 536  H61   C6   H6    107.11  3.000
 536  H61   C6   C7    109.22  3.000
 536  H6    C6   C7    109.03  3.000
 536  H61   C6   C5    109.44  3.000
 536  H6    C6   C5    110.58  3.000
 536  C7    C6   C5    111.36  3.000
 536  H71   C7   H7    106.97  3.000
 536  H71   C7   C6    110.31  3.000
 536  H7    C7   C6    110.38  3.000
 536  H71   C7   N2    110.29  3.000
 536  H7    C7   N2    108.25  3.000
 536  C6    C7   N2    110.56  3.000
 536  N10   C8   O9    120.42  3.000
 536  N10   C8   C4    115.99  3.000
 536  O9    C8   C4    123.59  3.000
 536  HN11  N10  HN10  116.51  3.000
 536  HN11  N10  C8    119.01  3.000
 536  HN10  N10  C8    122.35  3.000
 536  C16   C11  C12   118.91  3.000
 536  C16   C11  C1    120.65  3.000
 536  C12   C11  C1    120.44  3.000
 536  H12   C12  C13   119.77  3.000
 536  H12   C12  C11   119.46  3.000
 536  C13   C12  C11   120.77  3.000
 536  H13   C13  C14   120.23  3.000
 536  H13   C13  C12   119.80  3.000
 536  C14   C13  C12   119.97  3.000
 536  H14   C14  C15   120.13  3.000
 536  H14   C14  C13   120.23  3.000
 536  C15   C14  C13   119.63  3.000
 536  H15   C15  C16   119.82  3.000
 536  H15   C15  C14   119.96  3.000
 536  C16   C15  C14   120.22  3.000
 536  H16   C16  C15   119.36  3.000
 536  H16   C16  C11   120.14  3.000
 536  C15   C16  C11   120.50  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
 536  CONST_01  C14   C13  C12  C11    0.00   0.0  0
 536  CONST_02  C14   C15  C16  C11    0.00   0.0  0
 536  CONST_03  C15   C16  C11  C12    0.00   0.0  0
 536  CONST_04  C15   C14  C13  C12    0.00   0.0  0
 536  CONST_05  C16   C11  C12  C13    0.00   0.0  0
 536  CONST_06  C16   C15  C14  C13    0.00   0.0  0
 536  CONST_07  C13   C12  C11  C1   180.00   0.0  0
 536  CONST_08  C15   C16  C11  C1   180.00   0.0  0
 536  CONST_09  H13   C13  C12  C11  180.00   0.0  0
 536  CONST_10  H15   C15  C16  C11  180.00   0.0  0
 536  CONST_11  H16   C16  C11  C12  180.00   0.0  0
 536  CONST_12  H14   C14  C13  C12  180.00   0.0  0
 536  CONST_13  H12   C12  C13  C14  180.00   0.0  0
 536  CONST_14  HN10  N10  C8   C4     0.00   0.0  0
 536  CONST_15  HN11  N10  C8   C4   180.00   0.0  0
 536  Var_01    C5    C4   C3   N2    -0.89  30.0  1
 536  Var_02    C5    C6   C7   N2   -54.60  30.0  1
 536  Var_03    C6    C7   N2   C3    32.34  30.0  1
 536  Var_04    C6    C5   C4   C3   -22.06  30.0  1
 536  Var_05    C7    N2   C3   C4    -4.52  30.0  1
 536  Var_06    C7    C6   C5   C4    49.00  30.0  1
 536  Var_07    C12   C11  C1   N2   125.47  30.0  2
 536  Var_08    C11   C1   N2   C3   105.43  30.0  1
 536  Var_09    O9    C8   C4   C3     4.79  30.0  2

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
 536  plan-1  C1    0.020
 536  plan-1  C11   0.020
 536  plan-1  C12   0.020
 536  plan-1  C13   0.020
 536  plan-1  C14   0.020
 536  plan-1  C15   0.020
 536  plan-1  C16   0.020
 536  plan-1  H12   0.020
 536  plan-1  H13   0.020
 536  plan-1  H14   0.020
 536  plan-1  H15   0.020
 536  plan-1  H16   0.020
 536  plan-2  C4    0.020
 536  plan-2  C8    0.020
 536  plan-2  O9    0.020
 536  plan-2  N10   0.020
 536  plan-2  HN10  0.020
 536  plan-2  HN11  0.020
 536  plan-3  C1    0.020
 536  plan-3  N2    0.020
 536  plan-3  C3    0.020
 536  plan-3  C7    0.020

