# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 06:08:22 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: 1-butyl-1,4,5,6-tetrahydropyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCN1CCCC(=C1)C(N)=O
#
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
 XEN  XEN  1-butyl-1,4,5,6-tetrahydropyridine-3-carboxamide  ligand  31  13  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XEN
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
 XEN  C1    C  CH3   0  -0.661  -4.8650   1.1141  -0.9318
 XEN  C2    C  CH2   0  -0.424  -4.0760   0.5129   0.2230
 XEN  C3    C  CH2   0  -0.423  -2.6500   0.1462  -0.1699
 XEN  C4    C  CH2   0  -0.303  -1.8480  -0.3917   1.0109
 XEN  N5    N  NT    0  -0.433  -0.4836  -0.7488   0.6810
 XEN  C6    C  C1    0   0.067   0.4612   0.2068   0.6132
 XEN  C7    C  C     0  -0.211   1.7062   0.0450   0.0953
 XEN  C8    C  CH2   0  -0.491   2.1284  -1.3012  -0.4347
 XEN  C9    C  CH2   0  -0.468   1.2253  -2.3953   0.1282
 XEN  C10   C  CH2   0  -0.278  -0.2412  -2.0142   0.0156
 XEN  C11   C  C     0   0.463   2.5872   1.2122   0.0776
 XEN  O12   O  O     0  -0.529   2.2959   2.2972   0.5898
 XEN  N13   N  NH2   0  -0.835   3.7818   1.0440  -0.5410
 XEN  H13   H  HCH3  0   0.218  -4.3887   2.0250  -1.2985
 XEN  H11   H  HCH3  0   0.218  -4.9345   0.4182  -1.7697
 XEN  H12   H  HCH3  0   0.228  -5.8810   1.3706  -0.6300
 XEN  H22   H  HCH2  0   0.216  -4.0511   1.2227   1.0555
 XEN  H21   H  HCH2  0   0.217  -4.5913  -0.3770   0.5967
 XEN  H32   H  HCH2  0   0.224  -2.6727  -0.5944  -0.9757
 XEN  H31   H  HCH2  0   0.220  -2.1411   1.0290  -0.5714
 XEN  H42   H  HCH2  0   0.246  -1.8246   0.3543   1.8095
 XEN  H41   H  HCH2  0   0.241  -2.3391  -1.2756   1.4262
 XEN  H61   H  H     0   0.270   0.1718   1.1690   1.0202
 XEN  H81   H  HCH2  0   0.236   2.1057  -1.3281  -1.5304
 XEN  H91   H  HCH2  0   0.246   1.3926  -3.3362  -0.3973
 XEN  H101  H  HCH2  0   0.247  -0.8682  -2.7754   0.4832
 XEN  H132  H  HNH2  0   0.389   4.3650   1.8497  -0.6937
 XEN  H131  H  HNH2  0   0.403   3.9793   0.2388  -1.1088
 XEN  H1    H  HCH2  0   0.239   3.1596  -1.5260  -0.1471
 XEN  H2    H  HCH2  0   0.235   1.4691  -2.5666   1.1795
 XEN  H3    H  HCH2  0   0.230  -0.5334  -1.9589  -1.0401

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
 XEN  N13  C11   single  1.356  0.020  1.356
 XEN  C11  O12   double  1.235  0.020  1.235
 XEN  C11  C7    single  1.462  0.020  1.462
 XEN  C8   C7    single  1.507  0.020  1.507
 XEN  C8   C9    single  1.526  0.020  1.526
 XEN  C7   C6    double  1.358  0.020  1.358
 XEN  C9   C10   single  1.519  0.020  1.519
 XEN  C6   N5    single  1.346  0.020  1.346
 XEN  C10  N5    single  1.450  0.020  1.450
 XEN  N5   C4    single  1.448  0.020  1.448
 XEN  C1   C2    single  1.522  0.020  1.522
 XEN  C4   C3    single  1.525  0.020  1.525
 XEN  C2   C3    single  1.524  0.020  1.524
 XEN  C1   H13   single  0.970  0.020  1.090
 XEN  C1   H11   single  0.970  0.020  1.090
 XEN  C1   H12   single  0.970  0.020  1.090
 XEN  C2   H22   single  0.970  0.020  1.090
 XEN  C2   H21   single  0.970  0.020  1.090
 XEN  C3   H32   single  0.970  0.020  1.090
 XEN  C3   H31   single  0.970  0.020  1.090
 XEN  C4   H42   single  0.970  0.020  1.090
 XEN  C4   H41   single  0.970  0.020  1.090
 XEN  C6   H61   single  0.930  0.020  1.080
 XEN  C8   H81   single  0.970  0.020  1.090
 XEN  C9   H91   single  0.970  0.020  1.090
 XEN  C10  H101  single  0.970  0.020  1.090
 XEN  N13  H132  single  0.860  0.020  1.020
 XEN  N13  H131  single  0.860  0.020  1.020
 XEN  C8   H1    single  0.970  0.020  1.090
 XEN  C9   H2    single  0.970  0.020  1.090
 XEN  C10  H3    single  0.970  0.020  1.090

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
 XEN  H12   C1   H11   107.65  3.000
 XEN  H12   C1   H13   107.66  3.000
 XEN  H11   C1   H13   107.58  3.000
 XEN  H12   C1   C2    111.45  3.000
 XEN  H11   C1   C2    111.31  3.000
 XEN  H13   C1   C2    110.99  3.000
 XEN  H21   C2   H22   106.17  3.000
 XEN  H21   C2   C3    109.45  3.000
 XEN  H22   C2   C3    109.33  3.000
 XEN  H21   C2   C1    109.65  3.000
 XEN  H22   C2   C1    109.44  3.000
 XEN  C3    C2   C1    112.61  3.000
 XEN  H31   C3   H32   106.57  3.000
 XEN  H31   C3   C4    108.89  3.000
 XEN  H32   C3   C4    110.01  3.000
 XEN  H31   C3   C2    109.59  3.000
 XEN  H32   C3   C2    109.47  3.000
 XEN  C4    C3   C2    112.16  3.000
 XEN  H41   C4   H42   106.50  3.000
 XEN  H41   C4   N5    108.08  3.000
 XEN  H42   C4   N5    108.33  3.000
 XEN  H41   C4   C3    110.06  3.000
 XEN  H42   C4   C3    109.64  3.000
 XEN  N5    C4   C3    113.95  3.000
 XEN  C10   N5   C6    118.63  3.000
 XEN  C10   N5   C4    118.50  3.000
 XEN  C6    N5   C4    119.86  3.000
 XEN  H61   C6   C7    119.58  3.000
 XEN  H61   C6   N5    115.08  3.000
 XEN  C7    C6   N5    125.33  3.000
 XEN  C11   C7   C8    122.67  3.000
 XEN  C8    C7   C6    119.83  3.000
 XEN  C11   C7   C6    117.50  3.000
 XEN  H1    C8   H81   106.10  3.000
 XEN  H1    C8   C9    108.26  3.000
 XEN  H81   C8   C9    109.80  3.000
 XEN  H1    C8   C7    110.81  3.000
 XEN  H81   C8   C7    111.58  3.000
 XEN  C9    C8   C7    110.17  3.000
 XEN  H2    C9   H91   107.10  3.000
 XEN  H2    C9   C10   109.02  3.000
 XEN  H91   C9   C10   109.19  3.000
 XEN  H2    C9   C8    109.59  3.000
 XEN  H91   C9   C8    110.49  3.000
 XEN  C10   C9   C8    111.35  3.000
 XEN  H3    C10  H101  107.13  3.000
 XEN  H3    C10  C9    109.94  3.000
 XEN  H101  C10  C9    110.36  3.000
 XEN  H3    C10  N5    110.68  3.000
 XEN  H101  C10  N5    108.42  3.000
 XEN  C9    C10  N5    110.25  3.000
 XEN  N13   C11  O12   120.41  3.000
 XEN  O12   C11  C7    123.66  3.000
 XEN  N13   C11  C7    115.93  3.000
 XEN  H131  N13  H132  116.23  3.000
 XEN  H131  N13  C11   122.04  3.000
 XEN  H132  N13  C11   118.72  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
 XEN  CONST_01  H132  N13  C11  C7   180.00   0.0  0
 XEN  CONST_02  H131  N13  C11  C7     0.00   0.0  0
 XEN  Var_01    C8    C7   C6   N5    -1.38  30.0  1
 XEN  Var_02    C8    C9   C10  N5   -56.41  30.0  1
 XEN  Var_03    C9    C8   C7   C6   -19.18  30.0  1
 XEN  Var_04    C9    C10  N5   C6    36.51  30.0  1
 XEN  Var_05    C10   C9   C8   C7    47.21  30.0  1
 XEN  Var_06    C10   N5   C6   C7    -7.83  30.0  1
 XEN  Var_07    C6    N5   C4   C3    81.12  30.0  2
 XEN  Var_08    N13   C11  C7   C6  -174.97  30.0  2
 XEN  Var_09    N5    C4   C3   C2  -179.81  30.0  1
 XEN  Var_10    C4    C3   C2   C1   177.21  30.0  3
 XEN  Var_11    H13   C1   C2   C3   -59.93  30.0  3

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
 XEN  plan-1  C7    0.020
 XEN  plan-1  C11   0.020
 XEN  plan-1  O12   0.020
 XEN  plan-1  N13   0.020
 XEN  plan-1  H132  0.020
 XEN  plan-1  H131  0.020
 XEN  plan-2  C4    0.020
 XEN  plan-2  N5    0.020
 XEN  plan-2  C6    0.020
 XEN  plan-2  C10   0.020

