# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 02:33:56 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: (1S)-cyclohex-3-en-1-yl-N-methyl-N-[(1E)-prop-2-en-1-ylidene]methanaminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C\[N+](C[C@H]1CCC=CC1)=C/C=C
#
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
 NYP  NYP  (1S)-cyclohex-3-en-1-yl-N-methyl-N-[(1E)-prop-2-en-1-ylidene]methanaminium  ligand  30  12  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_NYP
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
 NYP  C8N   C  CH3   0  -0.573   1.5860  -1.2791  -1.4884
 NYP  N8    N  N     1  -0.323   1.4183  -0.7850  -0.1227
 NYP  C9    C  C1    0   0.120   2.2813  -0.0182   0.4432
 NYP  C10   C  C1    0  -0.267   3.4935   0.4561  -0.1592
 NYP  C11   C  C2    0  -0.442   4.3041   1.2403   0.5596
 NYP  C7    C  CH2   0  -0.334   0.1789  -1.1570   0.5628
 NYP  C1    C  CH1   0  -0.273  -1.0406  -0.4760  -0.0498
 NYP  C2    C  CH2   0  -0.433  -2.2902  -0.9127   0.7121
 NYP  C3    C  CH2   0  -0.476  -3.5489  -0.3530   0.0603
 NYP  C4    C  C1    0  -0.223  -3.3946   1.0894  -0.3123
 NYP  C5    C  C1    0  -0.224  -2.2223   1.7173  -0.3366
 NYP  C6    C  CH2   0  -0.467  -0.9157   1.0460  -0.0349
 NYP  H8N1  H  HCH3  0   0.300   0.8311  -2.0330  -1.6824
 NYP  H8N2  H  HCH3  0   0.294   1.4699  -0.4662  -2.2026
 NYP  H8N3  H  HCH3  0   0.300   2.5668  -1.7318  -1.6066
 NYP  H9    H  H     0   0.343   2.0623   0.2915   1.4587
 NYP  H10   H  H     0   0.316   3.7367   0.1894  -1.1782
 NYP  H11   H  H     0   0.294   4.0713   1.5217   1.5786
 NYP  H111  H  H     0   0.298   5.2242   1.6231   0.1422
 NYP  HC71  H  HCH2  0   0.303   0.0875  -2.2424   0.5008
 NYP  HC72  H  HCH2  0   0.285   0.2795  -0.8856   1.6139
 NYP  H1    H  HCH1  0   0.258  -1.1498  -0.8068  -1.0893
 NYP  H2    H  HCH2  0   0.231  -2.2194  -0.5569   1.7451
 NYP  H21   H  HCH2  0   0.244  -2.3476  -2.0027   0.7578
 NYP  H3    H  HCH2  0   0.245  -4.3982  -0.4675   0.7391
 NYP  H31   H  HCH2  0   0.240  -3.8073  -0.9360  -0.8308
 NYP  H4    H  H     0   0.239  -4.2962   1.6352  -0.5699
 NYP  H5    H  H     0   0.240  -2.1831   2.7699  -0.5949
 NYP  H6    H  HCH2  0   0.246  -0.1707   1.3797  -0.7637
 NYP  H61   H  HCH2  0   0.240  -0.5463   1.3866   0.9416

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
 NYP  C8N  N8    single  1.462  0.020  1.462
 NYP  C8N  H8N1  single  0.970  0.020  1.090
 NYP  C8N  H8N2  single  0.970  0.020  1.090
 NYP  C8N  H8N3  single  0.970  0.020  1.090
 NYP  N8   C9    double  1.286  0.020  1.286
 NYP  N8   C7    single  1.464  0.020  1.464
 NYP  C9   C10   single  1.434  0.020  1.434
 NYP  C9   H9    single  0.930  0.020  1.080
 NYP  C10  C11   double  1.337  0.020  1.337
 NYP  C10  H10   single  0.930  0.020  1.080
 NYP  C11  H11   single  0.930  0.020  1.080
 NYP  C11  H111  single  0.930  0.020  1.080
 NYP  C7   C1    single  1.525  0.020  1.525
 NYP  C7   HC71  single  0.970  0.020  1.090
 NYP  C7   HC72  single  0.970  0.020  1.090
 NYP  C1   C2    single  1.527  0.020  1.527
 NYP  C1   C6    single  1.527  0.020  1.527
 NYP  C1   H1    single  0.970  0.020  1.090
 NYP  C2   C3    single  1.524  0.020  1.524
 NYP  C2   H2    single  0.970  0.020  1.090
 NYP  C2   H21   single  0.970  0.020  1.090
 NYP  C3   C4    single  1.498  0.020  1.498
 NYP  C3   H3    single  0.970  0.020  1.090
 NYP  C3   H31   single  0.970  0.020  1.090
 NYP  C4   C5    double  1.330  0.020  1.330
 NYP  C4   H4    single  0.930  0.020  1.080
 NYP  C5   C6    single  1.500  0.020  1.500
 NYP  C5   H5    single  0.930  0.020  1.080
 NYP  C6   H6    single  0.970  0.020  1.090
 NYP  C6   H61   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
 NYP  H8N3  C8N  H8N2  109.64  3.000
 NYP  H8N3  C8N  H8N1  108.61  3.000
 NYP  H8N2  C8N  H8N1  109.12  3.000
 NYP  H8N3  C8N  N8    110.24  3.000
 NYP  H8N2  C8N  N8    110.39  3.000
 NYP  H8N1  C8N  N8    108.80  3.000
 NYP  C7    N8   C9    120.91  3.000
 NYP  C7    N8   C8N   116.65  3.000
 NYP  C9    N8   C8N   122.39  3.000
 NYP  H9    C9   C10   118.02  3.000
 NYP  H9    C9   N8    116.55  3.000
 NYP  C10   C9   N8    125.43  3.000
 NYP  H10   C10  C11   120.99  3.000
 NYP  H10   C10  C9    120.29  3.000
 NYP  C11   C10  C9    118.71  3.000
 NYP  H111  C11  H11   117.04  3.000
 NYP  H111  C11  C10   121.08  3.000
 NYP  H11   C11  C10   121.87  3.000
 NYP  HC72  C7   HC71  108.07  3.000
 NYP  HC72  C7   C1    110.48  3.000
 NYP  HC71  C7   C1    110.76  3.000
 NYP  HC72  C7   N8    108.05  3.000
 NYP  HC71  C7   N8    107.28  3.000
 NYP  C1    C7   N8    112.04  3.000
 NYP  H1    C1   C6    108.55  3.000
 NYP  H1    C1   C2    107.77  3.000
 NYP  C6    C1   C2    110.30  3.000
 NYP  H1    C1   C7    109.01  3.000
 NYP  C6    C1   C7    112.07  3.000
 NYP  C2    C1   C7    109.03  3.000
 NYP  H21   C2   H2    106.75  3.000
 NYP  H21   C2   C3    109.93  3.000
 NYP  H2    C2   C3    109.73  3.000
 NYP  H21   C2   C1    110.43  3.000
 NYP  H2    C2   C1    108.96  3.000
 NYP  C3    C2   C1    110.94  3.000
 NYP  H31   C3   H3    105.43  3.000
 NYP  H31   C3   C4    109.53  3.000
 NYP  H3    C3   C4    109.59  3.000
 NYP  H31   C3   C2    110.32  3.000
 NYP  H3    C3   C2    109.73  3.000
 NYP  C4    C3   C2    112.03  3.000
 NYP  H4    C4   C5    119.37  3.000
 NYP  H4    C4   C3    117.26  3.000
 NYP  C5    C4   C3    123.36  3.000
 NYP  H5    C5   C6    116.80  3.000
 NYP  H5    C5   C4    119.63  3.000
 NYP  C6    C5   C4    123.57  3.000
 NYP  H61   C6   H6    105.58  3.000
 NYP  H61   C6   C5    109.46  3.000
 NYP  H6    C6   C5    108.82  3.000
 NYP  H61   C6   C1    110.20  3.000
 NYP  H6    C6   C1    110.67  3.000
 NYP  C5    C6   C1    111.89  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
 NYP  Var_01  C4    C3   C2   C1    -44.48  30.0  1
 NYP  Var_02  C4    C5   C6   C1     14.49  30.0  1
 NYP  Var_03  C5    C4   C3   C2     13.44  30.0  1
 NYP  Var_04  C6    C5   C4   C3      1.92  30.0  1
 NYP  Var_05  C1    C7   N8   C8N   -68.70  30.0  3
 NYP  Var_06  C10   C9   N8   C8N     0.24   0.0  2
 NYP  Var_07  C11   C10  C9   N8   -179.34  30.0  2
 NYP  Var_08  H11   C11  C10  C9      0.18   0.0  2
 NYP  Var_09  H8N1  C8N  N8   C9    170.36  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
 NYP  chir_01  C1  C7  C2  C6  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
 NYP  plan-1  C8N   0.020
 NYP  plan-1  N8    0.020
 NYP  plan-1  C9    0.020
 NYP  plan-1  C10   0.020
 NYP  plan-1  C7    0.020
 NYP  plan-1  H9    0.020
 NYP  plan-2  C9    0.020
 NYP  plan-2  C10   0.020
 NYP  plan-2  C11   0.020
 NYP  plan-2  H10   0.020
 NYP  plan-2  H11   0.020
 NYP  plan-2  H111  0.020

