# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 14:21:10 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: N-(cyclohexylmethyl)-5-pyridin-4-yl-1H-pyrazol-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CCC(CC1)CNc2cc([nH]n2)c3ccncc3
#
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
 6NF  6NF  N-(cyclohexylmethyl)-5-pyridin-4-yl-1H-pyrazol-3-amine  ligand  39  19  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6NF
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
 6NF  C1    C  CR16  0  -0.369  -4.7296  -0.6798  -0.0035
 6NF  C2    C  CR16  0  -0.058  -5.9514  -0.0306  -0.0734
 6NF  N3    N  N     0  -0.408  -6.0841   1.2872  -0.1646
 6NF  C4    C  CR16  0  -0.056  -4.9672   2.0070  -0.1868
 6NF  C5    C  CR16  0  -0.400  -3.6981   1.4600  -0.1181
 6NF  C6    C  CR6   0   0.167  -3.5581   0.0759  -0.0229
 6NF  C7    C  CR5   0   0.459  -2.2337  -0.5264   0.0453
 6NF  C8    C  CR15  0  -0.574  -0.9878   0.0386  -0.1565
 6NF  C9    C  CR5   0   0.446  -0.0805  -1.0244   0.0296
 6NF  N10   N  N     0  -0.316  -0.7191  -2.1458   0.3305
 6NF  N11   N  NR15  0  -0.528  -2.0139  -1.8223   0.3240
 6NF  N12   N  NH1   0  -0.684   1.2892  -1.0046  -0.1107
 6NF  C13   C  CH2   0  -0.257   1.9721   0.2641   0.0522
 6NF  C14   C  CH1   0  -0.254   3.4543   0.1748  -0.2885
 6NF  C15   C  CH2   0  -0.418   4.0726   1.5733  -0.2408
 6NF  C16   C  CH2   0  -0.431   5.5643   1.5561  -0.5542
 6NF  C17   C  CH2   0  -0.429   6.3169   0.6150   0.3797
 6NF  C18   C  CH2   0  -0.428   5.7155  -0.7853   0.3344
 6NF  C19   C  CH2   0  -0.429   4.2208  -0.7671   0.6425
 6NF  H1    H  HCR6  0   0.262  -4.7177  -1.7599   0.0533
 6NF  H2    H  HCR6  0   0.269  -6.8666  -0.6119  -0.0578
 6NF  H4    H  HCR6  0   0.269  -5.0841   3.0824  -0.2609
 6NF  H5    H  HCR6  0   0.271  -2.8363   2.1129  -0.1318
 6NF  H8    H  HCR5  0   0.276  -0.7704   1.0627  -0.4086
 6NF  H11   H  HNR5  0   0.419  -2.6904  -2.5267   0.5689
 6NF  H12   H  HNH1  0   0.369   1.7298  -1.7692   0.3800
 6NF  H131  H  HCH2  0   0.236   1.5079   0.9900  -0.6201
 6NF  H132  H  HCH2  0   0.205   1.8562   0.6641   1.0710
 6NF  H14   H  HCH1  0   0.217   3.5395  -0.2043  -1.3153
 6NF  H151  H  HCH2  0   0.227   3.5504   2.2337  -0.9391
 6NF  H152  H  HCH2  0   0.208   3.9166   1.9938   0.7599
 6NF  H191  H  HCH2  0   0.210   4.0677  -0.4402   1.6785
 6NF  H192  H  HCH2  0   0.224   3.8349  -1.7884   0.5764
 6NF  H161  H  HCH2  0   0.209   5.7115   1.2291  -1.5893
 6NF  H162  H  HCH2  0   0.226   5.9707   2.5682  -0.4874
 6NF  H171  H  HCH2  0   0.226   7.3756   0.5794   0.1109
 6NF  H172  H  HCH2  0   0.208   6.2692   1.0000   1.4042
 6NF  H181  H  HCH2  0   0.209   5.8745  -1.2100  -0.6628
 6NF  H182  H  HCH2  0   0.227   6.2302  -1.4451   1.0370

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
 6NF  C1   C2    aromatic  1.385  0.020  1.385
 6NF  C1   C6    aromatic  1.394  0.020  1.394
 6NF  C2   N3    aromatic  1.328  0.020  1.328
 6NF  N3   C4    aromatic  1.329  0.020  1.329
 6NF  C4   C5    aromatic  1.384  0.020  1.384
 6NF  C5   C6    aromatic  1.394  0.020  1.394
 6NF  C6   C7    single    1.457  0.020  1.457
 6NF  C7   C8    aromatic  1.383  0.020  1.383
 6NF  C7   N11   aromatic  1.344  0.020  1.344
 6NF  C8   C9    aromatic  1.410  0.020  1.410
 6NF  C9   N10   aromatic  1.325  0.020  1.325
 6NF  C9   N12   single    1.377  0.020  1.377
 6NF  N10  N11   aromatic  1.335  0.020  1.335
 6NF  N12  C13   single    1.450  0.020  1.450
 6NF  C13  C14   single    1.524  0.020  1.524
 6NF  C14  C15   single    1.530  0.020  1.530
 6NF  C14  C19   single    1.530  0.020  1.530
 6NF  C15  C16   single    1.524  0.020  1.524
 6NF  C16  C17   single    1.525  0.020  1.525
 6NF  C17  C18   single    1.525  0.020  1.525
 6NF  C18  C19   single    1.526  0.020  1.526
 6NF  C1   H1    single    0.930  0.020  1.080
 6NF  C2   H2    single    0.930  0.020  1.080
 6NF  C4   H4    single    0.930  0.020  1.080
 6NF  C5   H5    single    0.930  0.020  1.080
 6NF  C8   H8    single    0.930  0.020  1.080
 6NF  N11  H11   single    0.860  0.020  1.020
 6NF  N12  H12   single    0.890  0.020  1.040
 6NF  C13  H131  single    0.970  0.020  1.090
 6NF  C13  H132  single    0.970  0.020  1.090
 6NF  C14  H14   single    0.970  0.020  1.090
 6NF  C15  H151  single    0.970  0.020  1.090
 6NF  C15  H152  single    0.970  0.020  1.090
 6NF  C19  H191  single    0.970  0.020  1.090
 6NF  C19  H192  single    0.970  0.020  1.090
 6NF  C16  H161  single    0.970  0.020  1.090
 6NF  C16  H162  single    0.970  0.020  1.090
 6NF  C17  H171  single    0.970  0.020  1.090
 6NF  C17  H172  single    0.970  0.020  1.090
 6NF  C18  H181  single    0.970  0.020  1.090
 6NF  C18  H182  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
 6NF  H1    C1   C6    122.19  3.000
 6NF  H1    C1   C2    118.70  3.000
 6NF  C6    C1   C2    119.10  3.000
 6NF  H2    C2   N3    116.67  3.000
 6NF  H2    C2   C1    119.50  3.000
 6NF  N3    C2   C1    123.83  3.000
 6NF  C4    N3   C2    117.05  3.000
 6NF  H4    C4   C5    119.63  3.000
 6NF  H4    C4   N3    116.60  3.000
 6NF  C5    C4   N3    123.77  3.000
 6NF  H5    C5   C6    121.35  3.000
 6NF  H5    C5   C4    119.45  3.000
 6NF  C6    C5   C4    119.20  3.000
 6NF  C7    C6   C5    120.33  3.000
 6NF  C7    C6   C1    122.63  3.000
 6NF  C5    C6   C1    117.04  3.000
 6NF  N11   C7   C8    106.08  3.000
 6NF  N11   C7   C6    123.87  3.000
 6NF  C8    C7   C6    130.05  3.000
 6NF  H8    C8   C9    128.17  3.000
 6NF  H8    C8   C7    127.20  3.000
 6NF  C9    C8   C7    104.62  3.000
 6NF  N12   C9   N10   120.98  3.000
 6NF  N12   C9   C8    128.01  3.000
 6NF  N10   C9   C8    110.97  3.000
 6NF  N11   N10  C9    105.15  3.000
 6NF  H11   N11  N10   118.76  3.000
 6NF  H11   N11  C7    127.97  3.000
 6NF  N10   N11  C7    113.17  3.000
 6NF  H12   N12  C13   113.73  3.000
 6NF  H12   N12  C9    111.94  3.000
 6NF  C13   N12  C9    118.01  3.000
 6NF  H132  C13  H131  106.46  3.000
 6NF  H132  C13  C14   109.31  3.000
 6NF  H131  C13  C14   108.33  3.000
 6NF  H132  C13  N12   111.87  3.000
 6NF  H131  C13  N12   108.18  3.000
 6NF  C14   C13  N12   112.44  3.000
 6NF  H14   C14  C19   108.52  3.000
 6NF  H14   C14  C15   108.27  3.000
 6NF  C19   C14  C15   109.96  3.000
 6NF  H14   C14  C13   107.75  3.000
 6NF  C19   C14  C13   112.79  3.000
 6NF  C15   C14  C13   109.43  3.000
 6NF  H152  C15  H151  106.45  3.000
 6NF  H152  C15  C16   109.33  3.000
 6NF  H151  C15  C16   110.05  3.000
 6NF  H152  C15  C14   108.75  3.000
 6NF  H151  C15  C14   109.82  3.000
 6NF  C16   C15  C14   112.26  3.000
 6NF  H162  C16  H161  106.51  3.000
 6NF  H162  C16  C17   110.54  3.000
 6NF  H161  C16  C17   109.16  3.000
 6NF  H162  C16  C15   109.93  3.000
 6NF  H161  C16  C15   109.21  3.000
 6NF  C17   C16  C15   111.35  3.000
 6NF  H172  C17  H171  106.48  3.000
 6NF  H172  C17  C18   109.48  3.000
 6NF  H171  C17  C18   110.17  3.000
 6NF  H172  C17  C16   109.54  3.000
 6NF  H171  C17  C16   110.34  3.000
 6NF  C18   C17  C16   110.74  3.000
 6NF  H182  C18  H181  106.43  3.000
 6NF  H182  C18  C19   109.79  3.000
 6NF  H181  C18  C19   109.30  3.000
 6NF  H182  C18  C17   110.47  3.000
 6NF  H181  C18  C17   109.02  3.000
 6NF  C19   C18  C17   111.68  3.000
 6NF  H192  C19  H191  106.62  3.000
 6NF  H192  C19  C18   108.80  3.000
 6NF  H191  C19  C18   109.32  3.000
 6NF  H192  C19  C14   111.18  3.000
 6NF  H191  C19  C14   108.74  3.000
 6NF  C18   C19  C14   112.03  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
 6NF  CONST_01  C4   N3   C2   C1      0.00   0.0  0
 6NF  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 6NF  CONST_03  C8   C7   C6   C1    180.00   0.0  0
 6NF  CONST_04  N11  C7   C6   C1      0.00   0.0  0
 6NF  CONST_05  C5   C6   C1   C2      0.00   0.0  0
 6NF  CONST_06  C7   C6   C1   C2    180.00   0.0  0
 6NF  CONST_07  C5   C4   N3   C2      0.00   0.0  0
 6NF  CONST_08  C6   C1   C2   N3      0.00   0.0  0
 6NF  CONST_09  C6   C5   C4   N3      0.00   0.0  0
 6NF  CONST_10  C7   C6   C5   C4    180.00   0.0  0
 6NF  CONST_11  C8   C7   C6   C5      0.00   0.0  0
 6NF  CONST_12  N11  C7   C6   C5    180.00   0.0  0
 6NF  CONST_13  C9   C8   C7   C6    180.00   0.0  0
 6NF  CONST_14  N10  N11  C7   C6    180.00   0.0  0
 6NF  CONST_15  N10  C9   C8   C7      0.00   0.0  0
 6NF  CONST_16  C9   N10  N11  C7      0.00   0.0  0
 6NF  CONST_17  N10  N11  C7   C8      0.00   0.0  0
 6NF  CONST_18  N11  N10  C9   C8      0.00   0.0  0
 6NF  CONST_19  N11  C7   C8   C9      0.00   0.0  0
 6NF  CONST_20  N12  C9   C8   C7    180.00   0.0  0
 6NF  CONST_21  N12  C9   N10  N11   180.00   0.0  0
 6NF  CONST_22  H5   C5   C6   C1    180.00   0.0  0
 6NF  CONST_23  H4   C4   N3   C2    180.00   0.0  0
 6NF  CONST_24  H1   C1   C2   N3    180.00   0.0  0
 6NF  CONST_25  H2   C2   N3   C4    180.00   0.0  0
 6NF  CONST_26  H8   C8   C7   C6      0.00   0.0  0
 6NF  CONST_27  H11  N11  C7   C6      0.00   0.0  0
 6NF  Var_01    C17  C16  C15  C14   -55.87  30.0  1
 6NF  Var_02    C17  C18  C19  C14    55.48  30.0  1
 6NF  Var_03    C18  C17  C16  C15    55.10  30.0  1
 6NF  Var_04    C19  C18  C17  C16   -55.05  30.0  1
 6NF  Var_05    C14  C13  N12  C9   -173.28  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
 6NF  chir_01  C14  C13  C15  C19  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
 6NF  plan-1  C6   0.020
 6NF  plan-1  C7   0.020
 6NF  plan-1  C8   0.020
 6NF  plan-1  C9   0.020
 6NF  plan-1  N10  0.020
 6NF  plan-1  N11  0.020
 6NF  plan-1  N12  0.020
 6NF  plan-1  H8   0.020
 6NF  plan-1  H11  0.020
 6NF  plan-2  C1   0.020
 6NF  plan-2  C2   0.020
 6NF  plan-2  N3   0.020
 6NF  plan-2  C4   0.020
 6NF  plan-2  C5   0.020
 6NF  plan-2  C6   0.020
 6NF  plan-2  C7   0.020
 6NF  plan-2  H1   0.020
 6NF  plan-2  H2   0.020
 6NF  plan-2  H4   0.020
 6NF  plan-2  H5   0.020
 6NF  plan-3  C9   0.020
 6NF  plan-3  N12  0.020
 6NF  plan-3  C13  0.020
 6NF  plan-3  H12  0.020

