# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 05:57:34 2022
#   Inital geometry file: a 65 line input string
#   Ligand name: N-methyl-1-(1-methyl-1H-indazol-3-yl)methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNCc1nn(C)c2ccccc12
#
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
 R2J  R2J  "N-methyl-1-(1-methyl-1H-indazol-3-yl)methanamine"
  ligand  26  13  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_R2J
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
 R2J  CAI  C  CR16  0  -0.310   -9.4966  1.3902  29.0884
 R2J  CAH  C  CR56  0   0.455  -10.3488  2.4374  28.7190
 R2J  CAD  C  CR5   0   0.229  -11.1210  4.2507  27.6678
 R2J  CAC  C  CH2   0  -0.346  -11.3108  5.4450  26.7966
 R2J  CAA  C  CH3   0  -0.518  -11.3011  6.2532  24.5303
 R2J  CAJ  C  CR16  0  -0.264   -8.2960  1.3032  28.4195
 R2J  CAK  C  CR16  0  -0.271   -7.9377  2.2214  27.4108
 R2J  CAL  C  CR16  0  -0.334   -8.7827  3.2466  27.0494
 R2J  CAM  C  CR56  0  -0.113  -10.0088  3.3620  27.7170
 R2J  NAB  N  NH1   0  -0.587  -11.1444  5.1026  25.3966
 R2J  NAE  N  N     0  -0.267  -12.0272  3.8860  28.5410
 R2J  NAF  N  NR5   0  -0.390  -11.5727  2.7976  29.1732
 R2J  H1   H  HCR6  0   0.269   -9.7620  0.6809  29.8614
 R2J  H2   H  HCH2  0   0.235  -10.5572  6.1995  27.0473
 R2J  H3   H  HCH2  0   0.215  -12.2876  5.8972  27.0249
 R2J  H4   H  HCH3  0   0.234  -11.2341  5.9406  23.4886
 R2J  H5   H  HCH3  0   0.195  -12.2506  6.7903  24.6622
 R2J  H6   H  HCH3  0   0.223  -10.4949  6.9665  24.7131
 R2J  H7   H  HCR6  0   0.256   -7.6062  0.5088  28.6737
 R2J  H8   H  HCR6  0   0.251   -6.9827  2.1101  26.9139
 R2J  H9   H  HCH3  0   0.268  -13.3201  2.6232  30.2486
 R2J  H10  H  HCH3  0   0.252  -12.4301  1.1082  30.0538
 R2J  H11  H  HCH3  0   0.251  -11.8553  2.3318  31.1995
 R2J  H12  H  HCR6  0   0.247   -8.5117  3.9443  26.2681
 R2J  H13  H  HNH1  0   0.346  -11.8331  4.4035  25.1471
 R2J  CAG  C  CH3   0  -0.525  -12.3297  2.1786  30.2298

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
 R2J  CAA  NAB  single    1.449  0.020  1.449
 R2J  NAB  CAC  single    1.451  0.020  1.451
 R2J  CAC  CAD  single    1.490  0.020  1.490
 R2J  CAL  CAK  aromatic  1.377  0.020  1.377
 R2J  CAL  CAM  aromatic  1.401  0.020  1.401
 R2J  CAK  CAJ  aromatic  1.410  0.020  1.410
 R2J  CAD  CAM  aromatic  1.424  0.020  1.424
 R2J  CAD  NAE  aromatic  1.310  0.020  1.310
 R2J  CAM  CAH  aromatic  1.405  0.020  1.405
 R2J  CAJ  CAI  aromatic  1.377  0.020  1.377
 R2J  NAE  NAF  aromatic  1.338  0.020  1.338
 R2J  CAH  CAI  aromatic  1.400  0.020  1.400
 R2J  CAH  NAF  aromatic  1.354  0.020  1.354
 R2J  NAF  CAG  single    1.440  0.020  1.440
 R2J  CAI  H1   single    0.930  0.020  1.080
 R2J  CAC  H2   single    0.970  0.020  1.090
 R2J  CAC  H3   single    0.970  0.020  1.090
 R2J  CAA  H4   single    0.970  0.020  1.090
 R2J  CAA  H5   single    0.970  0.020  1.090
 R2J  CAA  H6   single    0.970  0.020  1.090
 R2J  CAJ  H7   single    0.930  0.020  1.080
 R2J  CAK  H8   single    0.930  0.020  1.080
 R2J  CAG  H9   single    0.970  0.020  1.090
 R2J  CAG  H10  single    0.970  0.020  1.090
 R2J  CAG  H11  single    0.970  0.020  1.090
 R2J  CAL  H12  single    0.930  0.020  1.080
 R2J  NAB  H13  single    0.890  0.020  1.040

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
 R2J  H1   CAI  CAJ  121.29  3.000
 R2J  H1   CAI  CAH  121.98  3.000
 R2J  CAJ  CAI  CAH  116.73  3.000
 R2J  NAF  CAH  CAM  106.43  3.000
 R2J  NAF  CAH  CAI  131.35  3.000
 R2J  CAM  CAH  CAI  122.22  3.000
 R2J  NAE  CAD  CAM  110.08  3.000
 R2J  NAE  CAD  CAC  121.64  3.000
 R2J  CAM  CAD  CAC  128.28  3.000
 R2J  H3   CAC  H2   106.27  3.000
 R2J  H3   CAC  NAB  113.52  3.000
 R2J  H2   CAC  NAB  107.73  3.000
 R2J  H3   CAC  CAD  108.73  3.000
 R2J  H2   CAC  CAD  109.30  3.000
 R2J  NAB  CAC  CAD  111.12  3.000
 R2J  H6   CAA  H5   107.38  3.000
 R2J  H6   CAA  H4   107.58  3.000
 R2J  H5   CAA  H4   107.94  3.000
 R2J  H6   CAA  NAB  109.81  3.000
 R2J  H5   CAA  NAB  114.19  3.000
 R2J  H4   CAA  NAB  109.70  3.000
 R2J  H7   CAJ  CAK  118.94  3.000
 R2J  H7   CAJ  CAI  119.20  3.000
 R2J  CAK  CAJ  CAI  121.86  3.000
 R2J  H8   CAK  CAL  119.84  3.000
 R2J  H8   CAK  CAJ  119.06  3.000
 R2J  CAL  CAK  CAJ  121.10  3.000
 R2J  H12  CAL  CAM  120.68  3.000
 R2J  H12  CAL  CAK  121.06  3.000
 R2J  CAM  CAL  CAK  118.26  3.000
 R2J  CAL  CAM  CAD  135.92  3.000
 R2J  CAD  CAM  CAH  104.25  3.000
 R2J  CAL  CAM  CAH  119.83  3.000
 R2J  H13  NAB  CAA  109.12  3.000
 R2J  H13  NAB  CAC  108.83  3.000
 R2J  CAA  NAB  CAC  112.16  3.000
 R2J  NAF  NAE  CAD  107.84  3.000
 R2J  NAE  NAF  CAG  121.18  3.000
 R2J  CAG  NAF  CAH  127.38  3.000
 R2J  NAE  NAF  CAH  111.40  3.000
 R2J  H11  CAG  H10  108.77  3.000
 R2J  H11  CAG  H9   108.90  3.000
 R2J  H10  CAG  H9   108.73  3.000
 R2J  H11  CAG  NAF  111.32  3.000
 R2J  H10  CAG  NAF  110.63  3.000
 R2J  H9   CAG  NAF  108.44  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
 R2J  CONST_01  CAL  CAK  CAJ  CAI     0.00   0.0  0
 R2J  CONST_02  CAL  CAM  CAH  CAI     0.00   0.0  0
 R2J  CONST_03  CAD  CAM  CAH  CAI   180.00   0.0  0
 R2J  CONST_04  NAE  NAF  CAH  CAI   180.00   0.0  0
 R2J  CONST_05  CAK  CAL  CAM  CAH     0.00   0.0  0
 R2J  CONST_06  NAE  CAD  CAM  CAH     0.00   0.0  0
 R2J  CONST_07  CAK  CAJ  CAI  CAH     0.00   0.0  0
 R2J  CONST_08  CAD  NAE  NAF  CAH     0.00   0.0  0
 R2J  CONST_09  CAK  CAL  CAM  CAD   180.00   0.0  0
 R2J  CONST_10  NAF  CAH  CAM  CAD     0.00   0.0  0
 R2J  CONST_11  CAM  CAL  CAK  CAJ     0.00   0.0  0
 R2J  CONST_12  CAM  CAH  CAI  CAJ     0.00   0.0  0
 R2J  CONST_13  NAF  CAH  CAI  CAJ   180.00   0.0  0
 R2J  CONST_14  NAE  CAD  CAM  CAL   180.00   0.0  0
 R2J  CONST_15  NAF  CAH  CAM  CAL   180.00   0.0  0
 R2J  CONST_16  NAF  NAE  CAD  CAM     0.00   0.0  0
 R2J  CONST_17  NAE  NAF  CAH  CAM     0.00   0.0  0
 R2J  CONST_18  CAG  NAF  CAH  CAI     0.00   0.0  0
 R2J  CONST_19  CAC  CAD  CAM  CAH   180.00   0.0  0
 R2J  CONST_20  CAG  NAF  NAE  CAD   180.00   0.0  0
 R2J  CONST_21  CAL  CAM  CAD  CAC     0.00   0.0  0
 R2J  CONST_22  NAF  NAE  CAD  CAC   180.00   0.0  0
 R2J  CONST_23  CAM  CAH  NAF  CAG   180.00   0.0  0
 R2J  CONST_24  H8   CAK  CAJ  CAI   180.00   0.0  0
 R2J  CONST_25  H12  CAL  CAM  CAH   180.00   0.0  0
 R2J  CONST_26  H7   CAJ  CAI  CAH   180.00   0.0  0
 R2J  CONST_27  H12  CAL  CAM  CAD     0.00   0.0  0
 R2J  CONST_28  H12  CAL  CAK  CAJ   180.00   0.0  0
 R2J  CONST_29  H1   CAI  CAJ  CAK   180.00   0.0  0
 R2J  CONST_30  H7   CAJ  CAK  CAL   180.00   0.0  0
 R2J  CONST_31  H8   CAK  CAL  CAM   180.00   0.0  0
 R2J  CONST_32  H1   CAI  CAH  CAM   180.00   0.0  0
 R2J  CONST_33  H1   CAI  CAH  NAF     0.00   0.0  0
 R2J  Var_01    NAB  CAC  CAD  CAM    54.36  30.0  3
 R2J  Var_02    NAE  CAD  CAC  NAB  -126.07  30.0  2
 R2J  Var_03    H9   CAG  NAF  CAH  -172.30  30.0  2
 R2J  Var_04    H10  CAG  NAF  CAH   -53.14  30.0  2
 R2J  Var_05    H11  CAG  NAF  CAH    67.92  30.0  2
 R2J  Var_06    H2   CAC  CAD  CAM   -64.41  30.0  3
 R2J  Var_07    H3   CAC  CAD  CAM   179.99  30.0  3
 R2J  Var_08    H2   CAC  CAD  NAE   115.16  30.0  3
 R2J  Var_09    H3   CAC  CAD  NAE    -0.44  30.0  3
 R2J  Var_10    H9   CAG  NAF  NAE    10.32  30.0  2
 R2J  Var_11    H10  CAG  NAF  NAE   129.48  30.0  2
 R2J  Var_12    H11  CAG  NAF  NAE  -109.46  30.0  2
 R2J  Var_13    CAA  NAB  CAC  CAD  -178.98  30.0  1
 R2J  Var_14    H13  NAB  CAC  CAD    60.19  30.0  1
 R2J  Var_15    H4   CAA  NAB  CAC  -176.28  30.0  3
 R2J  Var_16    H5   CAA  NAB  CAC   -54.98  30.0  3
 R2J  Var_17    H6   CAA  NAB  CAC    65.68  30.0  3
 R2J  Var_18    H2   CAC  NAB  CAA   -59.28  30.0  3
 R2J  Var_19    H3   CAC  NAB  CAA    58.10  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
 R2J  plan-1  CAI  0.020
 R2J  plan-1  CAH  0.020
 R2J  plan-1  CAD  0.020
 R2J  plan-1  CAC  0.020
 R2J  plan-1  CAJ  0.020
 R2J  plan-1  CAK  0.020
 R2J  plan-1  CAL  0.020
 R2J  plan-1  CAM  0.020
 R2J  plan-1  NAE  0.020
 R2J  plan-1  NAF  0.020
 R2J  plan-1  H1   0.020
 R2J  plan-1  H7   0.020
 R2J  plan-1  H8   0.020
 R2J  plan-1  H12  0.020
 R2J  plan-1  CAG  0.020

