# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 18:08:05 2022
#   Inital geometry file: a 83 line input string
#   Ligand name: N-[(3,5-dimethyl-1H-pyrazol-4-yl)methyl]cyclohexanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1[nH]nc(C)c1CNC2CCCCC2
#
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
 8C2  8C2  "N-[(3,5-dimethyl-1H-pyrazol-4-yl)methyl]cyclohexanamine"
  ligand  36  15  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_8C2
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
 8C2  C10  C  CH1   0  -0.061  -0.6973  4.1119   -8.6506
 8C2  C13  C  CH2   0  -0.427  -0.8530  4.2405   -5.6918
 8C2  C15  C  CH2   0  -0.426  -1.2097  2.9370   -7.8219
 8C2  C02  C  CR5   0   0.388   1.0867  3.4276  -12.0751
 8C2  N03  N  NR15  0  -0.490   2.4290  3.4387  -12.1279
 8C2  N04  N  N     0  -0.308   2.9787  4.4637  -11.4779
 8C2  C05  C  CR5   0   0.235   1.9559  5.1399  -10.9810
 8C2  C06  C  CH3   0  -0.749   2.1674  6.3677  -10.1614
 8C2  C07  C  CR5   0  -0.168   0.7293  4.5348  -11.3298
 8C2  C08  C  CH2   0  -0.400  -0.6574  4.9522  -10.9639
 8C2  N09  N  NH1   0  -0.596  -1.2627  4.0495   -9.9907
 8C2  C11  C  CH2   0  -0.444  -0.9581  5.4265   -7.9087
 8C2  C12  C  CH2   0  -0.431  -0.3417  5.4186   -6.5128
 8C2  C14  C  CH2   0  -0.433  -0.6069  2.9239   -6.4201
 8C2  H1   H  HCH1  0   0.214   0.3886  3.9917   -8.7579
 8C2  H2   H  HCH2  0   0.207  -1.9274  4.3630   -5.5163
 8C2  H3   H  HCH2  0   0.223  -0.3765  4.2250   -4.7085
 8C2  H4   H  HCH2  0   0.204  -2.3021  3.0035   -7.7461
 8C2  H5   H  HCH2  0   0.223  -0.9865  2.0023   -8.3423
 8C2  H6   H  HCH3  0   0.252  -0.3198  1.8270  -11.9828
 8C2  H7   H  HCH3  0   0.253  -0.4674  2.8364  -13.4107
 8C2  H8   H  HCH3  0   0.253   0.8554  1.6774  -13.2911
 8C2  H9   H  HNR5  0   0.406   3.0189  2.7728  -12.6017
 8C2  H10  H  HCH3  0   0.245   3.2217  6.6391  -10.1361
 8C2  H11  H  HCH3  0   0.240   1.6103  7.2172  -10.5588
 8C2  H12  H  HCH3  0   0.245   1.8362  6.2224   -9.1311
 8C2  H13  H  HCH2  0   0.209  -0.6374  6.0013  -10.6363
 8C2  H14  H  HCH2  0   0.238  -1.2920  4.9309  -11.8544
 8C2  H15  H  HNH1  0   0.336  -2.2559  4.2472   -9.9369
 8C2  H17  H  HCH2  0   0.228  -0.5695  6.2735   -8.4798
 8C2  H18  H  HCH2  0   0.205  -2.0423  5.5740   -7.8284
 8C2  H19  H  HCH2  0   0.209   0.7486  5.3531   -6.6021
 8C2  H20  H  HCH2  0   0.224  -0.5538  6.3614   -6.0030
 8C2  H21  H  HCH2  0   0.225  -1.0138  2.0884   -5.8453
 8C2  H22  H  HCH2  0   0.208   0.4722  2.7512   -6.4947
 8C2  C01  C  CH3   0  -0.737   0.2508  2.3849  -12.7252

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
 8C2  C01  C02  single    1.486  0.020  1.486
 8C2  C02  N03  aromatic  1.343  0.020  1.343
 8C2  C02  C07  aromatic  1.382  0.020  1.382
 8C2  N03  N04  aromatic  1.332  0.020  1.332
 8C2  C07  C08  single    1.494  0.020  1.494
 8C2  C07  C05  aromatic  1.412  0.020  1.412
 8C2  C08  N09  single    1.459  0.020  1.459
 8C2  N04  C05  aromatic  1.323  0.020  1.323
 8C2  C05  C06  single    1.491  0.020  1.491
 8C2  N09  C10  single    1.456  0.020  1.456
 8C2  C10  C15  single    1.526  0.020  1.526
 8C2  C10  C11  single    1.532  0.020  1.532
 8C2  C15  C14  single    1.526  0.020  1.526
 8C2  C11  C12  single    1.526  0.020  1.526
 8C2  C14  C13  single    1.525  0.020  1.525
 8C2  C12  C13  single    1.524  0.020  1.524
 8C2  C10  H1   single    0.970  0.020  1.090
 8C2  C13  H2   single    0.970  0.020  1.090
 8C2  C13  H3   single    0.970  0.020  1.090
 8C2  C15  H4   single    0.970  0.020  1.090
 8C2  C15  H5   single    0.970  0.020  1.090
 8C2  C01  H6   single    0.970  0.020  1.090
 8C2  C01  H7   single    0.970  0.020  1.090
 8C2  C01  H8   single    0.970  0.020  1.090
 8C2  N03  H9   single    0.860  0.020  1.020
 8C2  C06  H10  single    0.970  0.020  1.090
 8C2  C06  H11  single    0.970  0.020  1.090
 8C2  C06  H12  single    0.970  0.020  1.090
 8C2  C08  H13  single    0.970  0.020  1.090
 8C2  C08  H14  single    0.970  0.020  1.090
 8C2  N09  H15  single    0.890  0.020  1.040
 8C2  C11  H17  single    0.970  0.020  1.090
 8C2  C11  H18  single    0.970  0.020  1.090
 8C2  C12  H19  single    0.970  0.020  1.090
 8C2  C12  H20  single    0.970  0.020  1.090
 8C2  C14  H21  single    0.970  0.020  1.090
 8C2  C14  H22  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
 8C2  H1   C10  C11  108.04  3.000
 8C2  H1   C10  N09  106.83  3.000
 8C2  C11  C10  N09  114.61  3.000
 8C2  H1   C10  C15  107.51  3.000
 8C2  C11  C10  C15  109.91  3.000
 8C2  N09  C10  C15  109.66  3.000
 8C2  H3   C13  H2   106.56  3.000
 8C2  H3   C13  C14  110.32  3.000
 8C2  H2   C13  C14  109.35  3.000
 8C2  H3   C13  C12  110.45  3.000
 8C2  H2   C13  C12  109.20  3.000
 8C2  C14  C13  C12  110.85  3.000
 8C2  H5   C15  H4   106.74  3.000
 8C2  H5   C15  C14  110.45  3.000
 8C2  H4   C15  C14  109.29  3.000
 8C2  H5   C15  C10  109.35  3.000
 8C2  H4   C15  C10  108.98  3.000
 8C2  C14  C15  C10  111.89  3.000
 8C2  C07  C02  N03  105.85  3.000
 8C2  C07  C02  C01  130.75  3.000
 8C2  N03  C02  C01  123.41  3.000
 8C2  H9   N03  N04  119.74  3.000
 8C2  H9   N03  C02  126.72  3.000
 8C2  N04  N03  C02  113.54  3.000
 8C2  C05  N04  N03  104.92  3.000
 8C2  C07  C05  C06  127.73  3.000
 8C2  C06  C05  N04  121.17  3.000
 8C2  C07  C05  N04  111.10  3.000
 8C2  H12  C06  H11  107.01  3.000
 8C2  H12  C06  H10  107.75  3.000
 8C2  H11  C06  H10  107.99  3.000
 8C2  H12  C06  C05  111.47  3.000
 8C2  H11  C06  C05  111.62  3.000
 8C2  H10  C06  C05  110.81  3.000
 8C2  C08  C07  C05  128.79  3.000
 8C2  C05  C07  C02  104.59  3.000
 8C2  C08  C07  C02  126.60  3.000
 8C2  H14  C08  H13  105.77  3.000
 8C2  H14  C08  N09  106.88  3.000
 8C2  H13  C08  N09  113.54  3.000
 8C2  H14  C08  C07  109.50  3.000
 8C2  H13  C08  C07  108.84  3.000
 8C2  N09  C08  C07  112.06  3.000
 8C2  H15  N09  C08  108.73  3.000
 8C2  H15  N09  C10  108.86  3.000
 8C2  C08  N09  C10  115.24  3.000
 8C2  H18  C11  H17  106.58  3.000
 8C2  H18  C11  C12  109.45  3.000
 8C2  H17  C11  C12  109.78  3.000
 8C2  H18  C11  C10  108.60  3.000
 8C2  H17  C11  C10  110.58  3.000
 8C2  C12  C11  C10  111.70  3.000
 8C2  H20  C12  H19  106.43  3.000
 8C2  H20  C12  C11  110.12  3.000
 8C2  H19  C12  C11  109.13  3.000
 8C2  H20  C12  C13  110.51  3.000
 8C2  H19  C12  C13  109.35  3.000
 8C2  C11  C12  C13  111.18  3.000
 8C2  H22  C14  H21  106.38  3.000
 8C2  H22  C14  C15  109.14  3.000
 8C2  H21  C14  C15  110.04  3.000
 8C2  H22  C14  C13  109.13  3.000
 8C2  H21  C14  C13  110.42  3.000
 8C2  C15  C14  C13  111.57  3.000
 8C2  H8   C01  H7   107.93  3.000
 8C2  H8   C01  H6   108.18  3.000
 8C2  H7   C01  H6   107.17  3.000
 8C2  H8   C01  C02  111.77  3.000
 8C2  H7   C01  C02  110.79  3.000
 8C2  H6   C01  C02  110.83  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
 8C2  CONST_01  C05  N04  N03  C02     0.00   0.0  0
 8C2  CONST_02  N04  C05  C07  C02     0.00   0.0  0
 8C2  CONST_03  C05  C07  C02  N03     0.00   0.0  0
 8C2  CONST_04  C07  C05  N04  N03     0.00   0.0  0
 8C2  CONST_05  C07  C02  N03  N04     0.00   0.0  0
 8C2  CONST_06  N04  N03  C02  C01   180.00   0.0  0
 8C2  CONST_07  C05  C07  C02  C01   180.00   0.0  0
 8C2  CONST_08  C06  C05  C07  C02   180.00   0.0  0
 8C2  CONST_09  C08  C07  C02  N03   180.00   0.0  0
 8C2  CONST_10  C06  C05  N04  N03   180.00   0.0  0
 8C2  CONST_11  C08  C07  C05  N04   180.00   0.0  0
 8C2  CONST_12  H9   N03  N04  C05   180.00   0.0  0
 8C2  CONST_13  H9   N03  C02  C07   180.00   0.0  0
 8C2  Var_01    C13  C14  C15  C10    55.54  30.0  1
 8C2  Var_02    C13  C12  C11  C10   -56.44  30.0  1
 8C2  Var_03    C12  C13  C14  C15   -54.89  30.0  1
 8C2  Var_04    C14  C13  C12  C11    55.31  30.0  1
 8C2  Var_05    H21  C14  C15  C10   178.47  30.0  1
 8C2  Var_06    H22  C14  C15  C10   -65.14  30.0  1
 8C2  Var_07    H19  C12  C11  C10    64.25  30.0  1
 8C2  Var_08    H20  C12  C11  C10  -179.27  30.0  1
 8C2  Var_09    H4   C15  C14  C13   -65.25  30.0  1
 8C2  Var_10    H5   C15  C14  C13   177.61  30.0  1
 8C2  Var_11    H17  C11  C12  C13  -179.48  30.0  1
 8C2  Var_12    H18  C11  C12  C13    63.87  30.0  1
 8C2  Var_13    H2   C13  C14  C15    65.56  30.0  1
 8C2  Var_14    H3   C13  C14  C15  -177.56  30.0  1
 8C2  Var_15    H2   C13  C12  C11   -65.23  30.0  1
 8C2  Var_16    H3   C13  C12  C11   177.90  30.0  1
 8C2  Var_17    H21  C14  C13  C12  -177.60  30.0  1
 8C2  Var_18    H22  C14  C13  C12    65.80  30.0  1
 8C2  Var_19    H19  C12  C13  C14   -65.26  30.0  1
 8C2  Var_20    H20  C12  C13  C14   177.91  30.0  1
 8C2  Var_21    C07  C08  N09  C10    70.25  30.0  1
 8C2  Var_22    N09  C08  C07  C02    70.15  30.0  2
 8C2  Var_23    N09  C08  C07  C05  -108.21  30.0  2
 8C2  Var_24    H13  C08  C07  C02  -163.44  30.0  2
 8C2  Var_25    H14  C08  C07  C02   -48.27  30.0  2
 8C2  Var_26    H6   C01  C02  N03   117.34  30.0  2
 8C2  Var_27    H7   C01  C02  N03  -123.82  30.0  2
 8C2  Var_28    H8   C01  C02  N03    -3.41  30.0  2
 8C2  Var_29    H10  C06  C05  N04     5.40  30.0  2
 8C2  Var_30    H11  C06  C05  N04   125.80  30.0  2
 8C2  Var_31    H12  C06  C05  N04  -114.59  30.0  2
 8C2  Var_32    H13  C08  C07  C05    18.20  30.0  2
 8C2  Var_33    H14  C08  C07  C05   133.38  30.0  2
 8C2  Var_34    H6   C01  C02  C07   -62.70  30.0  2
 8C2  Var_35    H7   C01  C02  C07    56.14  30.0  2
 8C2  Var_36    H8   C01  C02  C07   176.55  30.0  2
 8C2  Var_37    H10  C06  C05  C07  -175.04  30.0  2
 8C2  Var_38    H11  C06  C05  C07   -54.65  30.0  2
 8C2  Var_39    H12  C06  C05  C07    64.96  30.0  2
 8C2  Var_40    H13  C08  N09  C10   -53.56  30.0  1
 8C2  Var_41    H14  C08  N09  C10  -169.79  30.0  1
 8C2  Var_42    H15  N09  C08  C07  -167.27  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
 8C2  chir_01  C10  N09  C15  C11  positiv

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
 8C2  plan-1  C02  0.020
 8C2  plan-1  N03  0.020
 8C2  plan-1  N04  0.020
 8C2  plan-1  C05  0.020
 8C2  plan-1  C06  0.020
 8C2  plan-1  C07  0.020
 8C2  plan-1  C08  0.020
 8C2  plan-1  H9   0.020
 8C2  plan-1  C01  0.020

