# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 18:59:02 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: N-(1-methylpiperidin-4-yl)-4-[3-(propan-2-yl)-1H-pyrazol-4-yl]pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)c1n[nH]cc1c2ccnc(NC3CCN(C)CC3)n2
#
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
 3NU  3NU  N-(1-methylpiperidin-4-yl)-4-[3-(propan-2-yl)-1H-pyrazol-4-yl]pyrimidin-2-amine  ligand  46  22  .  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_3NU
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
 3NU  C1    C  CR5   0  -0.190  -3.1766  -0.6699   0.2214
 3NU  N1    N  NR15  0  -0.431  -5.3205  -0.7093   0.5940
 3NU  C2    C  CR15  0   0.013  -4.2702  -1.5019   0.3937
 3NU  N2    N  N     0  -0.287  -5.0129   0.5854   0.5644
 3NU  C3    C  CR5   0   0.307  -3.7138   0.6430   0.3436
 3NU  N3    N  N     0  -0.474   0.7640  -1.9013  -0.5391
 3NU  C4    C  CR6   0   0.593   0.4177  -0.6619  -0.1804
 3NU  N4    N  N     0  -0.498  -0.8282  -0.2444   0.0810
 3NU  C5    C  CR6   0   0.245  -1.8168  -1.1171  -0.0524
 3NU  N5    N  NH1   0  -0.672   1.3859   0.2684  -0.0786
 3NU  C6    C  CR16  0  -0.417  -1.5586  -2.4357  -0.4517
 3NU  N6    N  NT    0  -0.408   5.5862   0.5142   0.4084
 3NU  C7    C  CR16  0  -0.019  -0.2373  -2.7613  -0.6701
 3NU  C8    C  CH1   0  -0.328  -3.0320   1.9720   0.1877
 3NU  C9    C  CH3   0  -0.648  -3.1131   2.4212  -1.2736
 3NU  C10   C  CH3   0  -0.646  -3.6217   3.0258   1.1206
 3NU  C11   C  CH1   0  -0.056   2.7992   0.0130  -0.2326
 3NU  C12   C  CH2   0  -0.449   3.5161   1.2822  -0.6754
 3NU  C13   C  CH2   0  -0.279   5.0070   1.0203  -0.8217
 3NU  C14   C  CH2   0  -0.282   4.9441  -0.7175   0.8299
 3NU  C15   C  CH2   0  -0.434   3.4512  -0.5208   1.0406
 3NU  H2    H  HCR5  0   0.298  -4.3634  -2.5757   0.3894
 3NU  HN5   H  HNH1  0   0.385   1.0978   1.1702   0.2668
 3NU  H6    H  HCR6  0   0.260  -2.3400  -3.1694  -0.5814
 3NU  H7    H  HCR6  0   0.264   0.0331  -3.7683  -0.9704
 3NU  H8    H  HCH1  0   0.255  -1.9807   1.8264   0.4311
 3NU  H9    H  HCH3  0   0.225  -2.6372   3.3940  -1.4086
 3NU  H9A   H  HCH3  0   0.229  -2.6114   1.7125  -1.9342
 3NU  H9B   H  HCH3  0   0.218  -4.1516   2.5060  -1.5997
 3NU  H10   H  HCH3  0   0.226  -3.5299   2.7302   2.1665
 3NU  H10A  H  HCH3  0   0.224  -3.0963   3.9740   0.9967
 3NU  H10B  H  HCH3  0   0.218  -4.6781   3.1983   0.9122
 3NU  H11   H  HCH1  0   0.234   2.9212  -0.7355  -1.0203
 3NU  H12   H  HCH2  0   0.243   3.1150   1.6267  -1.6311
 3NU  H12A  H  HCH2  0   0.224   3.3531   2.0788   0.0582
 3NU  H13   H  HCH2  0   0.237   5.5158   1.9491  -1.0902
 3NU  H13A  H  HCH2  0   0.186   5.1661   0.3175  -1.6602
 3NU  H14   H  HCH2  0   0.186   5.1043  -1.5277   0.0944
 3NU  H14A  H  HCH2  0   0.236   5.4064  -1.0484   1.7630
 3NU  H15   H  HCH2  0   0.217   3.2858   0.1891   1.8569
 3NU  H15A  H  HCH2  0   0.238   2.9936  -1.4697   1.3279
 3NU  H16   H  HCH3  0   0.231   7.4862   1.2840  -0.0001
 3NU  H16A  H  HCH3  0   0.232   7.4454   0.0207   1.2278
 3NU  H16B  H  HCH3  0   0.190   7.2922  -0.4080  -0.4827
 3NU  HN1   H  HNR5  0   0.424  -6.2693  -0.9961   0.7747
 3NU  C16   C  CH3   0  -0.518   7.0145   0.3398   0.2773

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
 3NU  C1   C2    aromatic  1.385  0.020  1.385
 3NU  C5   C1    single    1.457  0.020  1.457
 3NU  C1   C3    aromatic  1.424  0.020  1.424
 3NU  N1   C2    aromatic  1.331  0.020  1.331
 3NU  N2   N1    aromatic  1.331  0.020  1.331
 3NU  C2   H2    single    0.930  0.020  1.080
 3NU  C3   N2    aromatic  1.319  0.020  1.319
 3NU  C8   C3    single    1.502  0.020  1.502
 3NU  N3   C4    aromatic  1.336  0.020  1.336
 3NU  N3   C7    aromatic  1.326  0.020  1.326
 3NU  N5   C4    single    1.346  0.020  1.346
 3NU  C4   N4    aromatic  1.340  0.020  1.340
 3NU  N4   C5    aromatic  1.325  0.020  1.325
 3NU  C5   C6    aromatic  1.402  0.020  1.402
 3NU  C11  N5    single    1.444  0.020  1.444
 3NU  N5   HN5   single    0.860  0.020  1.020
 3NU  C7   C6    aromatic  1.378  0.020  1.378
 3NU  C6   H6    single    0.930  0.020  1.080
 3NU  C16  N6    single    1.445  0.020  1.445
 3NU  C13  N6    single    1.451  0.020  1.451
 3NU  C14  N6    single    1.452  0.020  1.452
 3NU  C7   H7    single    0.930  0.020  1.080
 3NU  C10  C8    single    1.526  0.020  1.526
 3NU  C8   C9    single    1.531  0.020  1.531
 3NU  C8   H8    single    0.970  0.020  1.090
 3NU  C9   H9    single    0.970  0.020  1.090
 3NU  C9   H9A   single    0.970  0.020  1.090
 3NU  C9   H9B   single    0.970  0.020  1.090
 3NU  C10  H10   single    0.970  0.020  1.090
 3NU  C10  H10A  single    0.970  0.020  1.090
 3NU  C10  H10B  single    0.970  0.020  1.090
 3NU  C11  C12   single    1.523  0.020  1.523
 3NU  C11  C15   single    1.527  0.020  1.527
 3NU  C11  H11   single    0.970  0.020  1.090
 3NU  C13  C12   single    1.521  0.020  1.521
 3NU  C12  H12   single    0.970  0.020  1.090
 3NU  C12  H12A  single    0.970  0.020  1.090
 3NU  C13  H13   single    0.970  0.020  1.090
 3NU  C13  H13A  single    0.970  0.020  1.090
 3NU  C14  C15   single    1.520  0.020  1.520
 3NU  C14  H14   single    0.970  0.020  1.090
 3NU  C14  H14A  single    0.970  0.020  1.090
 3NU  C15  H15   single    0.970  0.020  1.090
 3NU  C15  H15A  single    0.970  0.020  1.090
 3NU  C16  H16   single    0.970  0.020  1.090
 3NU  C16  H16A  single    0.970  0.020  1.090
 3NU  C16  H16B  single    0.970  0.020  1.090
 3NU  N1   HN1   single    0.860  0.020  1.020

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
 3NU  C5    C1   C3    130.62  3.000
 3NU  C3    C1   C2    104.20  3.000
 3NU  C5    C1   C2    125.16  3.000
 3NU  HN1   N1   N2    119.90  3.000
 3NU  HN1   N1   C2    126.91  3.000
 3NU  N2    N1   C2    113.18  3.000
 3NU  H2    C2   N1    121.71  3.000
 3NU  H2    C2   C1    131.78  3.000
 3NU  N1    C2   C1    106.50  3.000
 3NU  C3    N2   N1    105.89  3.000
 3NU  C8    C3   N2    120.21  3.000
 3NU  C8    C3   C1    129.48  3.000
 3NU  N2    C3   C1    110.23  3.000
 3NU  C7    N3   C4    115.61  3.000
 3NU  N5    C4   N4    116.02  3.000
 3NU  N4    C4   N3    125.63  3.000
 3NU  N5    C4   N3    118.35  3.000
 3NU  C5    N4   C4    117.96  3.000
 3NU  C6    C5   N4    120.71  3.000
 3NU  C6    C5   C1    120.93  3.000
 3NU  N4    C5   C1    118.36  3.000
 3NU  HN5   N5   C11   118.32  3.000
 3NU  HN5   N5   C4    116.02  3.000
 3NU  C11   N5   C4    124.98  3.000
 3NU  H6    C6   C7    120.95  3.000
 3NU  H6    C6   C5    122.70  3.000
 3NU  C7    C6   C5    116.35  3.000
 3NU  C16   N6   C14   111.17  3.000
 3NU  C14   N6   C13   111.44  3.000
 3NU  C16   N6   C13   111.09  3.000
 3NU  H7    C7   C6    120.13  3.000
 3NU  H7    C7   N3    116.16  3.000
 3NU  C6    C7   N3    123.71  3.000
 3NU  H8    C8   C10   109.20  3.000
 3NU  H8    C8   C9    107.69  3.000
 3NU  C10   C8   C9    111.12  3.000
 3NU  H8    C8   C3    107.27  3.000
 3NU  C9    C8   C3    109.55  3.000
 3NU  C10   C8   C3    111.85  3.000
 3NU  H9B   C9   H9A   107.88  3.000
 3NU  H9B   C9   H9    107.98  3.000
 3NU  H9A   C9   H9    107.67  3.000
 3NU  H9B   C9   C8    111.00  3.000
 3NU  H9A   C9   C8    111.28  3.000
 3NU  H9    C9   C8    110.88  3.000
 3NU  H10B  C10  H10A  107.89  3.000
 3NU  H10B  C10  H10   107.91  3.000
 3NU  H10A  C10  H10   107.69  3.000
 3NU  H10B  C10  C8    111.52  3.000
 3NU  H10A  C10  C8    110.16  3.000
 3NU  H10   C10  C8    111.51  3.000
 3NU  H11   C11  C15   108.28  3.000
 3NU  H11   C11  C12   107.96  3.000
 3NU  C15   C11  C12   109.43  3.000
 3NU  H11   C11  N5    107.88  3.000
 3NU  C15   C11  N5    113.00  3.000
 3NU  C12   C11  N5    110.13  3.000
 3NU  H12A  C12  H12   107.58  3.000
 3NU  H12A  C12  C13   109.61  3.000
 3NU  H12   C12  C13   109.28  3.000
 3NU  H12A  C12  C11   109.95  3.000
 3NU  H12   C12  C11   110.14  3.000
 3NU  C13   C12  C11   110.23  3.000
 3NU  H13A  C13  H13   106.68  3.000
 3NU  H13A  C13  C12   108.88  3.000
 3NU  H13   C13  C12   109.50  3.000
 3NU  H13A  C13  N6    111.34  3.000
 3NU  H13   C13  N6    108.60  3.000
 3NU  C12   C13  N6    111.71  3.000
 3NU  H14A  C14  H14   106.55  3.000
 3NU  H14A  C14  C15   109.65  3.000
 3NU  H14   C14  C15   109.22  3.000
 3NU  H14A  C14  N6    108.53  3.000
 3NU  H14   C14  N6    111.37  3.000
 3NU  C15   C14  N6    111.40  3.000
 3NU  H15A  C15  H15   107.71  3.000
 3NU  H15A  C15  C14   109.60  3.000
 3NU  H15   C15  C14   109.61  3.000
 3NU  H15A  C15  C11   110.14  3.000
 3NU  H15   C15  C11   109.31  3.000
 3NU  C14   C15  C11   110.42  3.000
 3NU  H16B  C16  H16A  107.62  3.000
 3NU  H16B  C16  H16   107.64  3.000
 3NU  H16A  C16  H16   107.67  3.000
 3NU  H16B  C16  N6    113.19  3.000
 3NU  H16A  C16  N6    110.28  3.000
 3NU  H16   C16  N6    110.24  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
 3NU  CONST_01  N2   N1   C2   C1      0.00   0.0  0
 3NU  CONST_02  C4   N4   C5   C1    180.00   0.0  0
 3NU  CONST_03  C7   C6   C5   C1    180.00   0.0  0
 3NU  CONST_04  N1   N2   C3   C1      0.00   0.0  0
 3NU  CONST_05  C5   C1   C2   N1    180.00   0.0  0
 3NU  CONST_06  C3   C1   C2   N1      0.00   0.0  0
 3NU  CONST_07  N4   C5   C1   C2    180.00   0.0  0
 3NU  CONST_08  C6   C5   C1   C2      0.00   0.0  0
 3NU  CONST_09  N2   C3   C1   C2      0.00   0.0  0
 3NU  CONST_10  C3   N2   N1   C2      0.00   0.0  0
 3NU  CONST_11  C5   C1   C3   N2    180.00   0.0  0
 3NU  CONST_14  C5   N4   C4   N3      0.00   0.0  0
 3NU  CONST_15  C5   C6   C7   N3      0.00   0.0  0
 3NU  CONST_16  C6   C7   N3   C4      0.00   0.0  0
 3NU  CONST_17  C6   C5   N4   C4      0.00   0.0  0
 3NU  CONST_18  C7   N3   C4   N4      0.00   0.0  0
 3NU  CONST_19  C7   C6   C5   N4      0.00   0.0  0
 3NU  CONST_20  C8   C3   N2   N1    180.00   0.0  0
 3NU  CONST_21  C8   C3   C1   C2    180.00   0.0  0
 3NU  CONST_22  C8   C3   C1   C5      0.00   0.0  0
 3NU  CONST_23  N5   C4   N4   C5    180.00   0.0  0
 3NU  CONST_24  C7   N3   C4   N5    180.00   0.0  0
 3NU  CONST_25  C11  N5   C4   N3      0.00   0.0  0
 3NU  CONST_26  C11  N5   C4   N4    180.00   0.0  0
 3NU  CONST_27  HN1  N1   C2   C1    180.00   0.0  0
 3NU  CONST_28  H6   C6   C5   C1      0.00   0.0  0
 3NU  CONST_29  H2   C2   N1   N2    180.00   0.0  0
 3NU  CONST_30  H7   C7   N3   C4    180.00   0.0  0
 3NU  CONST_31  HN5  N5   C4   N3    180.00   0.0  0
 3NU  Var_01    C11  C12  C13  N6    -56.82  30.0  1
 3NU  Var_02    C11  C15  C14  N6     56.84  30.0  1
 3NU  Var_03    C14  N6   C13  C12    58.59  30.0  1
 3NU  Var_04    C15  C14  N6   C13   -58.49  30.0  1
 3NU  Var_05    C10  C8   C3   C1   -146.65  30.0  2
 3NU  Var_06    H16  C16  N6   C13    57.59  30.0  3
 3NU  Var_07    H10  C10  C8   C3     59.56  30.0  3
 3NU  Var_08    H9   C9   C8   C3    179.10  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
 3NU  chir_01  C11  N5  C12  C15  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
 3NU  plan-1  C1   0.020
 3NU  plan-1  N1   0.020
 3NU  plan-1  C2   0.020
 3NU  plan-1  N2   0.020
 3NU  plan-1  C3   0.020
 3NU  plan-1  C5   0.020
 3NU  plan-1  C8   0.020
 3NU  plan-1  H2   0.020
 3NU  plan-1  HN1  0.020
 3NU  plan-2  C1   0.020
 3NU  plan-2  N3   0.020
 3NU  plan-2  C4   0.020
 3NU  plan-2  N4   0.020
 3NU  plan-2  C5   0.020
 3NU  plan-2  N5   0.020
 3NU  plan-2  C6   0.020
 3NU  plan-2  C7   0.020
 3NU  plan-2  H6   0.020
 3NU  plan-2  H7   0.020
 3NU  plan-3  C4   0.020
 3NU  plan-3  N5   0.020
 3NU  plan-3  C11  0.020
 3NU  plan-3  HN5  0.020

