# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 13:49:37 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: [4-({4-[(5-cyclopropyl-1H-pyrazol-3-yl)amino]-6-(methylamino)pyrimidin-2-yl}amino)phenyl]acetonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1cc(Nc2cc([nH]n2)C3CC3)nc(Nc4ccc(CC#N)cc4)n1
#
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
 5CP  5CP  '[4-({4-[(5-cyclopropyl-1H-pyrazol-3-yl)amino]-6-(methylamino)pyrimidin-2-yl}amino)phenyl]acetonitrile'  ligand  47  27  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5CP
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
 5CP  C4    C  CR6   0   0.571  -1.6403  -1.7778   0.1465
 5CP  C5    C  CR16  0  -0.568  -1.1044  -3.0649   0.2542
 5CP  C6    C  CR6   0   0.560   0.2838  -3.1606   0.1794
 5CP  N1    N  N     0  -0.545   1.0601  -2.0716   0.0151
 5CP  N3    N  N     0  -0.552  -0.8805  -0.7009  -0.0200
 5CP  C1U   C  CH2   0  -0.475  -5.8165   3.7464   0.6160
 5CP  C1W   C  CH2   0  -0.477  -6.0140   3.5552  -0.8500
 5CP  C1T   C  CH1   0  -0.371  -4.7652   3.0319  -0.1921
 5CP  C1R   C  CR5   0   0.493  -4.5348   1.5899  -0.0351
 5CP  C1S   C  CR15  0  -0.550  -3.3471   0.8855  -0.0621
 5CP  N1Q   N  NR15  0  -0.524  -5.5022   0.6837   0.1750
 5CP  N1P   N  N     0  -0.333  -5.0404  -0.5674   0.2887
 5CP  C1H   C  CR5   0   0.452  -3.7328  -0.4553   0.1464
 5CP  N1G   N  NH1   0  -0.763  -2.9875  -1.6193   0.2162
 5CP  N1X   N  NH1   0  -0.650   0.9317  -4.3326   0.2636
 5CP  C1Y   C  CH3   0  -0.528   0.2845  -5.6021   0.4609
 5CP  C2    C  CR6   0   0.607   0.4361  -0.9161  -0.0748
 5CP  N1I   N  NH1   0  -0.772   1.1571   0.2347  -0.2446
 5CP  C1J   C  CR6   0   0.359   2.5193   0.4718  -0.3266
 5CP  C1O   C  CR16  0  -0.346   2.9118   1.8068  -0.4967
 5CP  C1N   C  CR16  0  -0.272   4.2461   2.1521  -0.5847
 5CP  C1K   C  CR16  0  -0.304   3.5158  -0.5056  -0.2535
 5CP  C1L   C  CR16  0  -0.277   4.8517  -0.1404  -0.3424
 5CP  C1M   C  CR6   0   0.087   5.2398   1.1812  -0.5081
 5CP  C1V   C  CH2   0  -0.630   6.6991   1.5598  -0.5838
 5CP  C1Z   C  CSP   0   0.138   7.2207   1.9263   0.7269
 5CP  N1A   N  NS    0  -0.278   7.6167   2.2117   1.7690
 5CP  H5    H  HCR6  0   0.275  -1.7405  -3.9281   0.3859
 5CP  H1UA  H  HCH2  0   0.256  -6.4184   3.1565   1.2965
 5CP  H1W   H  HCH2  0   0.256  -6.7536   2.8351  -1.1787
 5CP  H1WA  H  HCH2  0   0.266  -5.9112   4.4112  -1.5036
 5CP  H1T   H  HCH1  0   0.275  -3.8544   3.5852  -0.3842
 5CP  H1S   H  HCR5  0   0.270  -2.3595   1.2796  -0.2100
 5CP  HN1Q  H  HNR5  0   0.416  -6.4940   0.8424   0.2473
 5CP  HN1G  H  HNH1  0   0.405  -3.5313  -2.4565   0.3593
 5CP  HN1X  H  HNH1  0   0.392   1.9356  -4.3012   0.2147
 5CP  H1Y   H  HCH3  0   0.235  -0.2667  -5.6395   1.4038
 5CP  H1YA  H  HCH3  0   0.235  -0.4121  -5.8364  -0.3474
 5CP  H1YB  H  HCH3  0   0.265   1.0441  -6.3778   0.4840
 5CP  HN1I  H  HNH1  0   0.405   0.5716   1.0535  -0.3058
 5CP  H1O   H  HCR6  0   0.269   2.1581   2.5827  -0.5614
 5CP  H1N   H  HCR6  0   0.260   4.5118   3.1942  -0.7172
 5CP  H1K   H  HCR6  0   0.288   3.2512  -1.5421  -0.1279
 5CP  H1L   H  HCR6  0   0.257   5.6043  -0.9177  -0.2824
 5CP  H1V   H  HCH2  0   0.328   7.3038   0.7354  -0.9662
 5CP  H1VA  H  HCH2  0   0.328   6.8569   2.4050  -1.2566
 5CP  H1U   H  HCH2  0   0.265  -5.5736   4.7353   0.9816

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
 5CP  C4   C5    aromatic  1.398  0.020  1.398
 5CP  C4   N3    aromatic  1.328  0.020  1.328
 5CP  C4   N1G   single    1.358  0.020  1.358
 5CP  C5   C6    aromatic  1.393  0.020  1.393
 5CP  C6   N1    aromatic  1.347  0.020  1.347
 5CP  C6   N1X   single    1.342  0.020  1.342
 5CP  N1   C2    aromatic  1.316  0.020  1.316
 5CP  N3   C2    aromatic  1.335  0.020  1.335
 5CP  C1U  C1W   single    1.492  0.020  1.492
 5CP  C1U  C1T   single    1.506  0.020  1.506
 5CP  C1W  C1T   single    1.505  0.020  1.505
 5CP  C1T  C1R   single    1.469  0.020  1.469
 5CP  C1R  C1S   aromatic  1.381  0.020  1.381
 5CP  C1R  N1Q   aromatic  1.342  0.020  1.342
 5CP  C1S  C1H   aromatic  1.411  0.020  1.411
 5CP  N1Q  N1P   aromatic  1.338  0.020  1.338
 5CP  N1P  C1H   aromatic  1.320  0.020  1.320
 5CP  C1H  N1G   single    1.384  0.020  1.384
 5CP  N1X  C1Y   single    1.438  0.020  1.438
 5CP  C2   N1I   single    1.369  0.020  1.369
 5CP  N1I  C1J   single    1.385  0.020  1.385
 5CP  C1J  C1O   aromatic  1.402  0.020  1.402
 5CP  C1J  C1K   aromatic  1.398  0.020  1.398
 5CP  C1O  C1N   aromatic  1.381  0.020  1.381
 5CP  C1N  C1M   aromatic  1.391  0.020  1.391
 5CP  C1K  C1L   aromatic  1.388  0.020  1.388
 5CP  C1L  C1M   aromatic  1.387  0.020  1.387
 5CP  C1M  C1V   single    1.510  0.020  1.510
 5CP  C1V  C1Z   single    1.458  0.020  1.458
 5CP  C1Z  N1A   triple    1.151  0.020  1.151
 5CP  C5   H5    single    0.930  0.020  1.080
 5CP  C1U  H1U   single    0.970  0.020  1.090
 5CP  C1U  H1UA  single    0.970  0.020  1.090
 5CP  C1W  H1W   single    0.970  0.020  1.090
 5CP  C1W  H1WA  single    0.970  0.020  1.090
 5CP  C1T  H1T   single    0.970  0.020  1.090
 5CP  C1S  H1S   single    0.930  0.020  1.080
 5CP  N1Q  HN1Q  single    0.860  0.020  1.020
 5CP  N1G  HN1G  single    0.860  0.020  1.020
 5CP  N1X  HN1X  single    0.860  0.020  1.020
 5CP  C1Y  H1Y   single    0.970  0.020  1.090
 5CP  C1Y  H1YA  single    0.970  0.020  1.090
 5CP  C1Y  H1YB  single    0.970  0.020  1.090
 5CP  N1I  HN1I  single    0.860  0.020  1.020
 5CP  C1O  H1O   single    0.930  0.020  1.080
 5CP  C1N  H1N   single    0.930  0.020  1.080
 5CP  C1K  H1K   single    0.930  0.020  1.080
 5CP  C1L  H1L   single    0.930  0.020  1.080
 5CP  C1V  H1V   single    0.970  0.020  1.090
 5CP  C1V  H1VA  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
 5CP  N1G   C4   N3    118.63  3.000
 5CP  N1G   C4   C5    118.92  3.000
 5CP  N3    C4   C5    122.45  3.000
 5CP  H5    C5   C6    122.57  3.000
 5CP  H5    C5   C4    121.28  3.000
 5CP  C6    C5   C4    116.16  3.000
 5CP  N1X   C6   N1    115.81  3.000
 5CP  N1X   C6   C5    122.52  3.000
 5CP  N1    C6   C5    121.67  3.000
 5CP  C2    N1   C6    116.40  3.000
 5CP  C2    N3   C4    116.00  3.000
 5CP  H1UA  C1U  H1U   114.22  3.000
 5CP  H1UA  C1U  C1T   117.82  3.000
 5CP  H1U   C1U  C1T   117.26  3.000
 5CP  H1UA  C1U  C1W   118.30  3.000
 5CP  H1U   C1U  C1W   118.62  3.000
 5CP  C1T   C1U  C1W    60.28  3.000
 5CP  H1WA  C1W  H1W   114.05  3.000
 5CP  H1WA  C1W  C1T   117.40  3.000
 5CP  H1W   C1W  C1T   117.90  3.000
 5CP  H1WA  C1W  C1U   118.67  3.000
 5CP  H1W   C1W  C1U   118.28  3.000
 5CP  C1T   C1W  C1U    60.34  3.000
 5CP  H1T   C1T  C1R   112.88  3.000
 5CP  H1T   C1T  C1W   116.27  3.000
 5CP  C1R   C1T  C1W   121.21  3.000
 5CP  H1T   C1T  C1U   116.09  3.000
 5CP  C1R   C1T  C1U   121.19  3.000
 5CP  C1W   C1T  C1U    59.38  3.000
 5CP  N1Q   C1R  C1S   106.17  3.000
 5CP  N1Q   C1R  C1T   124.52  3.000
 5CP  C1S   C1R  C1T   129.31  3.000
 5CP  H1S   C1S  C1H   128.38  3.000
 5CP  H1S   C1S  C1R   127.34  3.000
 5CP  C1H   C1S  C1R   104.28  3.000
 5CP  HN1Q  N1Q  N1P   118.75  3.000
 5CP  HN1Q  N1Q  C1R   127.93  3.000
 5CP  N1P   N1Q  C1R   113.31  3.000
 5CP  C1H   N1P  N1Q   104.67  3.000
 5CP  N1G   C1H  N1P   117.16  3.000
 5CP  N1G   C1H  C1S   131.27  3.000
 5CP  N1P   C1H  C1S   111.56  3.000
 5CP  HN1G  N1G  C1H   114.52  3.000
 5CP  HN1G  N1G  C4    116.44  3.000
 5CP  C1H   N1G  C4    129.03  3.000
 5CP  HN1X  N1X  C1Y   118.91  3.000
 5CP  HN1X  N1X  C6    116.85  3.000
 5CP  C1Y   N1X  C6    124.21  3.000
 5CP  H1YB  C1Y  H1YA  107.97  3.000
 5CP  H1YB  C1Y  H1Y   108.06  3.000
 5CP  H1YA  C1Y  H1Y   108.02  3.000
 5CP  H1YB  C1Y  N1X   108.58  3.000
 5CP  H1YA  C1Y  N1X   112.01  3.000
 5CP  H1Y   C1Y  N1X   112.05  3.000
 5CP  N1I   C2   N3    112.89  3.000
 5CP  N1I   C2   N1    119.79  3.000
 5CP  N3    C2   N1    127.31  3.000
 5CP  HN1I  N1I  C1J   115.37  3.000
 5CP  HN1I  N1I  C2    112.60  3.000
 5CP  C1J   N1I  C2    132.02  3.000
 5CP  C1K   C1J  C1O   118.21  3.000
 5CP  C1K   C1J  N1I   125.33  3.000
 5CP  C1O   C1J  N1I   116.46  3.000
 5CP  H1O   C1O  C1N   119.29  3.000
 5CP  H1O   C1O  C1J   119.62  3.000
 5CP  C1N   C1O  C1J   121.09  3.000
 5CP  H1N   C1N  C1M   120.18  3.000
 5CP  H1N   C1N  C1O   119.02  3.000
 5CP  C1M   C1N  C1O   120.80  3.000
 5CP  H1K   C1K  C1L   119.81  3.000
 5CP  H1K   C1K  C1J   120.26  3.000
 5CP  C1L   C1K  C1J   119.93  3.000
 5CP  H1L   C1L  C1M   119.72  3.000
 5CP  H1L   C1L  C1K   118.44  3.000
 5CP  C1M   C1L  C1K   121.84  3.000
 5CP  C1V   C1M  C1L   121.02  3.000
 5CP  C1V   C1M  C1N   120.84  3.000
 5CP  C1L   C1M  C1N   118.14  3.000
 5CP  H1VA  C1V  H1V   106.79  3.000
 5CP  H1VA  C1V  C1Z   107.93  3.000
 5CP  H1V   C1V  C1Z   107.86  3.000
 5CP  H1VA  C1V  C1M   111.39  3.000
 5CP  H1V   C1V  C1M   111.33  3.000
 5CP  C1Z   C1V  C1M   111.34  3.000
 5CP  N1A   C1Z  C1V   180.00  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
 5CP  CONST_01  N1    C6   C5   C4      0.00   0.0  0
 5CP  CONST_02  N1    C2   N3   C4      0.00   0.0  0
 5CP  CONST_03  C2    N3   C4   C5      0.00   0.0  0
 5CP  CONST_04  C2    N1   C6   C5      0.00   0.0  0
 5CP  CONST_05  N3    C4   C5   C6      0.00   0.0  0
 5CP  CONST_06  N3    C2   N1   C6      0.00   0.0  0
 5CP  CONST_07  N1P   C1H  C1S  C1R     0.00   0.0  0
 5CP  CONST_08  C1H   N1P  N1Q  C1R     0.00   0.0  0
 5CP  CONST_09  N1P   N1Q  C1R  C1S     0.00   0.0  0
 5CP  CONST_10  N1Q   N1P  C1H  C1S     0.00   0.0  0
 5CP  CONST_11  C1H   C1S  C1R  N1Q     0.00   0.0  0
 5CP  CONST_12  C1M   C1N  C1O  C1J     0.00   0.0  0
 5CP  CONST_13  C1M   C1L  C1K  C1J     0.00   0.0  0
 5CP  CONST_14  C1L   C1K  C1J  C1O     0.00   0.0  0
 5CP  CONST_15  C1L   C1M  C1N  C1O     0.00   0.0  0
 5CP  CONST_16  C1K   C1J  C1O  C1N     0.00   0.0  0
 5CP  CONST_17  C1K   C1L  C1M  C1N     0.00   0.0  0
 5CP  CONST_18  C1H   C1S  C1R  C1T   180.00   0.0  0
 5CP  CONST_19  N1P   N1Q  C1R  C1T   180.00   0.0  0
 5CP  CONST_20  N1X   C6   C5   C4    180.00   0.0  0
 5CP  CONST_21  N1I   C2   N3   C4    180.00   0.0  0
 5CP  CONST_22  N1G   C4   C5   C6    180.00   0.0  0
 5CP  CONST_23  N1I   C2   N1   C6    180.00   0.0  0
 5CP  CONST_24  N1G   C1H  C1S  C1R   180.00   0.0  0
 5CP  CONST_25  N1G   C1H  N1P  N1Q   180.00   0.0  0
 5CP  CONST_26  C2    N3   C4   N1G   180.00   0.0  0
 5CP  CONST_27  C2    N1   C6   N1X   180.00   0.0  0
 5CP  CONST_28  C1N   C1O  C1J  N1I   180.00   0.0  0
 5CP  CONST_29  C1L   C1K  C1J  N1I   180.00   0.0  0
 5CP  CONST_30  C1V   C1M  C1N  C1O   180.00   0.0  0
 5CP  CONST_31  C1V   C1M  C1L  C1K   180.00   0.0  0
 5CP  CONST_32  H5    C5   C6   N1    180.00   0.0  0
 5CP  CONST_33  H1S   C1S  C1R  C1T     0.00   0.0  0
 5CP  CONST_34  HN1Q  N1Q  C1R  C1T     0.00   0.0  0
 5CP  CONST_35  H1N   C1N  C1O  C1J   180.00   0.0  0
 5CP  CONST_36  H1L   C1L  C1K  C1J   180.00   0.0  0
 5CP  CONST_37  H1K   C1K  C1J  C1O   180.00   0.0  0
 5CP  CONST_38  H1O   C1O  C1J  C1K   180.00   0.0  0
 5CP  CONST_39  C1Y   N1X  C6   C5      0.00   0.0  0
 5CP  CONST_40  C1Y   N1X  C6   N1    180.00   0.0  0
 5CP  CONST_41  HN1X  N1X  C6   C5    180.00   0.0  0
 5CP  Var_01    C1R   C1T  C1W  C1U   110.18  30.0  1
 5CP  Var_02    C1S   C1R  C1T  C1U  -142.42  30.0  2
 5CP  Var_03    C1S   C1H  N1G  C4      2.63  30.0  2
 5CP  Var_04    C1H   N1G  C4   C5    179.43  30.0  2
 5CP  Var_05    C1J   N1I  C2   N1     -1.41  30.0  2
 5CP  Var_06    C1O   C1J  N1I  C2   -179.57  30.0  2
 5CP  Var_07    C1Z   C1V  C1M  C1N    85.92  30.0  2
 5CP  Var_08    H1Y   C1Y  N1X  C6    -61.09  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
 5CP  chir_01  C1T  C1U  C1W  C1R  both

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
 5CP  plan-1  C1T   0.020
 5CP  plan-1  C1R   0.020
 5CP  plan-1  C1S   0.020
 5CP  plan-1  N1Q   0.020
 5CP  plan-1  N1P   0.020
 5CP  plan-1  C1H   0.020
 5CP  plan-1  N1G   0.020
 5CP  plan-1  H1S   0.020
 5CP  plan-1  HN1Q  0.020
 5CP  plan-2  C4    0.020
 5CP  plan-2  C5    0.020
 5CP  plan-2  C6    0.020
 5CP  plan-2  N1    0.020
 5CP  plan-2  N3    0.020
 5CP  plan-2  N1G   0.020
 5CP  plan-2  N1X   0.020
 5CP  plan-2  C2    0.020
 5CP  plan-2  N1I   0.020
 5CP  plan-2  H5    0.020
 5CP  plan-3  N1I   0.020
 5CP  plan-3  C1J   0.020
 5CP  plan-3  C1O   0.020
 5CP  plan-3  C1N   0.020
 5CP  plan-3  C1K   0.020
 5CP  plan-3  C1L   0.020
 5CP  plan-3  C1M   0.020
 5CP  plan-3  C1V   0.020
 5CP  plan-3  H1O   0.020
 5CP  plan-3  H1N   0.020
 5CP  plan-3  H1K   0.020
 5CP  plan-3  H1L   0.020
 5CP  plan-4  C6    0.020
 5CP  plan-4  N1X   0.020
 5CP  plan-4  C1Y   0.020
 5CP  plan-4  HN1X  0.020

