# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 09:26:30 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: N-methyl-1-[4-(1H-pyrazol-1-ylmethyl)phenyl]methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNCc1ccc(Cn2cccn2)cc1
#
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
 3VR  3VR  N-methyl-1-[4-(1H-pyrazol-1-ylmethyl)phenyl]methanamine  ligand  30  15  .  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_3VR
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
 3VR  CAA  C  CH3   0  -0.520   5.3873   1.3755  -0.5031
 3VR  NAL  N  NH1   0  -0.584   3.9700   1.1368  -0.3216
 3VR  CAI  C  CH2   0  -0.323   3.6842  -0.2381   0.0386
 3VR  CAM  C  CR6   0   0.082   2.2060  -0.4752   0.1885
 3VR  CAE  C  CR16  0  -0.273   1.3215  -0.1082  -0.8257
 3VR  CAG  C  CR16  0  -0.272  -0.0383  -0.3381  -0.7022
 3VR  CAD  C  CR16  0  -0.301   1.6853  -1.0638   1.3337
 3VR  CAF  C  CR16  0  -0.292   0.3196  -1.2896   1.4625
 3VR  CAN  C  CR6   0   0.095  -0.5559  -0.9350   0.4457
 3VR  CAJ  C  CH2   0  -0.354  -2.0267  -1.2342   0.5808
 3VR  NAO  N  NR5   0  -0.262  -2.8669  -0.1734   0.0769
 3VR  NAK  N  N     0  -0.283  -2.9139   0.9972   0.7047
 3VR  CAC  C  CR15  0  -0.050  -3.7171   1.7506  -0.0243
 3VR  CAB  C  CR15  0  -0.516  -4.1941   1.0561  -1.1479
 3VR  CAH  C  CR15  0   0.044  -3.6148  -0.1870  -1.0428
 3VR  H1   H  HCH3  0   0.234   5.5598   2.4294  -0.7202
 3VR  H2   H  HCH3  0   0.195   6.0058   1.1030   0.3635
 3VR  H3   H  HCH3  0   0.223   5.7515   0.7980  -1.3551
 3VR  H4   H  HNH1  0   0.345   3.6206   1.7453   0.4084
 3VR  H6   H  HCH2  0   0.236   4.0735  -0.8783  -0.7608
 3VR  H7   H  HCH2  0   0.211   4.1990  -0.5588   0.9577
 3VR  H8   H  HCR6  0   0.247   1.7045   0.3623  -1.7226
 3VR  H9   H  HCR6  0   0.247  -0.6987  -0.0470  -1.5109
 3VR  H10  H  HCR6  0   0.249   2.3497  -1.3440   2.1427
 3VR  H11  H  HCR6  0   0.252  -0.0632  -1.7413   2.3702
 3VR  H12  H  HCH2  0   0.280  -2.2852  -2.1376   0.0260
 3VR  H13  H  HCH2  0   0.279  -2.2810  -1.4201   1.6249
 3VR  H14  H  HCR5  0   0.259  -3.9335   2.7646   0.2764
 3VR  H15  H  HCR5  0   0.261  -4.8606   1.4079  -1.9172
 3VR  H16  H  HCR5  0   0.292  -3.6793  -1.0631  -1.6676

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
 3VR  CAC  NAK  aromatic  1.321  0.020  1.321
 3VR  CAC  CAB  aromatic  1.404  0.020  1.404
 3VR  NAK  NAO  aromatic  1.329  0.020  1.329
 3VR  CAB  CAH  aromatic  1.375  0.020  1.375
 3VR  NAO  CAH  aromatic  1.346  0.020  1.346
 3VR  NAO  CAJ  single    1.444  0.020  1.444
 3VR  CAJ  CAN  single    1.507  0.020  1.507
 3VR  CAA  NAL  single    1.449  0.020  1.449
 3VR  CAF  CAN  aromatic  1.388  0.020  1.388
 3VR  CAF  CAD  aromatic  1.390  0.020  1.390
 3VR  CAN  CAG  aromatic  1.393  0.020  1.393
 3VR  CAD  CAM  aromatic  1.389  0.020  1.389
 3VR  CAG  CAE  aromatic  1.385  0.020  1.385
 3VR  NAL  CAI  single    1.450  0.020  1.450
 3VR  CAM  CAE  aromatic  1.395  0.020  1.395
 3VR  CAM  CAI  single    1.505  0.020  1.505
 3VR  CAA  H1   single    0.970  0.020  1.090
 3VR  CAA  H2   single    0.970  0.020  1.090
 3VR  CAA  H3   single    0.970  0.020  1.090
 3VR  NAL  H4   single    0.890  0.020  1.040
 3VR  CAI  H6   single    0.970  0.020  1.090
 3VR  CAI  H7   single    0.970  0.020  1.090
 3VR  CAE  H8   single    0.930  0.020  1.080
 3VR  CAG  H9   single    0.930  0.020  1.080
 3VR  CAD  H10  single    0.930  0.020  1.080
 3VR  CAF  H11  single    0.930  0.020  1.080
 3VR  CAJ  H12  single    0.970  0.020  1.090
 3VR  CAJ  H13  single    0.970  0.020  1.090
 3VR  CAC  H14  single    0.930  0.020  1.080
 3VR  CAB  H15  single    0.930  0.020  1.080
 3VR  CAH  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
 3VR  H3   CAA  H2   107.24  3.000
 3VR  H3   CAA  H1   107.65  3.000
 3VR  H2   CAA  H1   107.93  3.000
 3VR  H3   CAA  NAL  109.69  3.000
 3VR  H2   CAA  NAL  114.27  3.000
 3VR  H1   CAA  NAL  109.83  3.000
 3VR  H4   NAL  CAI  108.83  3.000
 3VR  H4   NAL  CAA  109.20  3.000
 3VR  CAI  NAL  CAA  112.35  3.000
 3VR  H7   CAI  H6   105.82  3.000
 3VR  H7   CAI  CAM  109.28  3.000
 3VR  H6   CAI  CAM  109.25  3.000
 3VR  H7   CAI  NAL  113.05  3.000
 3VR  H6   CAI  NAL  107.63  3.000
 3VR  CAM  CAI  NAL  111.59  3.000
 3VR  CAD  CAM  CAE  118.25  3.000
 3VR  CAE  CAM  CAI  120.60  3.000
 3VR  CAD  CAM  CAI  121.15  3.000
 3VR  H8   CAE  CAG  119.57  3.000
 3VR  H8   CAE  CAM  119.49  3.000
 3VR  CAG  CAE  CAM  120.94  3.000
 3VR  H9   CAG  CAN  120.22  3.000
 3VR  H9   CAG  CAE  119.16  3.000
 3VR  CAN  CAG  CAE  120.62  3.000
 3VR  H10  CAD  CAF  119.41  3.000
 3VR  H10  CAD  CAM  119.69  3.000
 3VR  CAF  CAD  CAM  120.90  3.000
 3VR  H11  CAF  CAN  119.82  3.000
 3VR  H11  CAF  CAD  119.49  3.000
 3VR  CAN  CAF  CAD  120.68  3.000
 3VR  CAJ  CAN  CAF  119.95  3.000
 3VR  CAF  CAN  CAG  118.60  3.000
 3VR  CAJ  CAN  CAG  121.43  3.000
 3VR  H13  CAJ  H12  106.88  3.000
 3VR  H13  CAJ  NAO  108.88  3.000
 3VR  H12  CAJ  NAO  107.03  3.000
 3VR  H13  CAJ  CAN  110.32  3.000
 3VR  H12  CAJ  CAN  110.49  3.000
 3VR  NAO  CAJ  CAN  113.00  3.000
 3VR  CAH  NAO  NAK  112.46  3.000
 3VR  CAH  NAO  CAJ  127.30  3.000
 3VR  NAK  NAO  CAJ  120.18  3.000
 3VR  CAC  NAK  NAO  105.26  3.000
 3VR  H14  CAC  CAB  128.26  3.000
 3VR  H14  CAC  NAK  120.26  3.000
 3VR  CAB  CAC  NAK  111.47  3.000
 3VR  H15  CAB  CAH  127.63  3.000
 3VR  H15  CAB  CAC  128.32  3.000
 3VR  CAH  CAB  CAC  104.05  3.000
 3VR  H16  CAH  CAB  131.68  3.000
 3VR  H16  CAH  NAO  121.56  3.000
 3VR  CAB  CAH  NAO  106.76  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
 3VR  CONST_01  CAN  CAF  CAD  CAM     0.00   0.0  0
 3VR  CONST_02  CAN  CAG  CAE  CAM     0.00   0.0  0
 3VR  CONST_03  CAF  CAN  CAG  CAE     0.00   0.0  0
 3VR  CONST_04  CAF  CAD  CAM  CAE     0.00   0.0  0
 3VR  CONST_05  CAD  CAF  CAN  CAG     0.00   0.0  0
 3VR  CONST_06  CAD  CAM  CAE  CAG     0.00   0.0  0
 3VR  CONST_07  CAB  CAC  NAK  NAO     0.00   0.0  0
 3VR  CONST_08  CAC  CAB  CAH  NAO     0.00   0.0  0
 3VR  CONST_09  CAH  CAB  CAC  NAK     0.00   0.0  0
 3VR  CONST_10  CAB  CAH  NAO  NAK     0.00   0.0  0
 3VR  CONST_11  CAH  NAO  NAK  CAC     0.00   0.0  0
 3VR  CONST_12  CAF  CAD  CAM  CAI   180.00   0.0  0
 3VR  CONST_13  CAG  CAE  CAM  CAI   180.00   0.0  0
 3VR  CONST_14  CAJ  CAN  CAG  CAE   180.00   0.0  0
 3VR  CONST_15  CAJ  CAN  CAF  CAD   180.00   0.0  0
 3VR  CONST_16  CAC  NAK  NAO  CAJ   180.00   0.0  0
 3VR  CONST_17  CAB  CAH  NAO  CAJ   180.00   0.0  0
 3VR  CONST_18  H11  CAF  CAD  CAM   180.00   0.0  0
 3VR  CONST_19  H9   CAG  CAE  CAM   180.00   0.0  0
 3VR  CONST_20  H10  CAD  CAM  CAE   180.00   0.0  0
 3VR  CONST_21  H8   CAE  CAM  CAD   180.00   0.0  0
 3VR  CONST_22  H14  CAC  NAK  NAO   180.00   0.0  0
 3VR  CONST_23  H15  CAB  CAH  NAO   180.00   0.0  0
 3VR  CONST_24  H16  CAH  NAO  NAK   180.00   0.0  0
 3VR  Var_01    NAO  CAJ  CAN  CAG   -41.34  30.0  2
 3VR  Var_02    NAK  NAO  CAJ  CAN   -68.28  30.0  1
 3VR  Var_03    CAD  CAM  CAI  NAL  -128.04  30.0  2
 3VR  Var_04    CAM  CAI  NAL  CAA  -178.55  30.0  3
 3VR  Var_05    H1   CAA  NAL  CAI  -177.03  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
 3VR  plan-1  CAJ  0.020
 3VR  plan-1  NAO  0.020
 3VR  plan-1  NAK  0.020
 3VR  plan-1  CAC  0.020
 3VR  plan-1  CAB  0.020
 3VR  plan-1  CAH  0.020
 3VR  plan-1  H14  0.020
 3VR  plan-1  H15  0.020
 3VR  plan-1  H16  0.020
 3VR  plan-2  CAI  0.020
 3VR  plan-2  CAM  0.020
 3VR  plan-2  CAE  0.020
 3VR  plan-2  CAG  0.020
 3VR  plan-2  CAD  0.020
 3VR  plan-2  CAF  0.020
 3VR  plan-2  CAN  0.020
 3VR  plan-2  CAJ  0.020
 3VR  plan-2  H8   0.020
 3VR  plan-2  H9   0.020
 3VR  plan-2  H10  0.020
 3VR  plan-2  H11  0.020

