# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 15:12:15 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: N~2~-[(trans-4-aminocyclohexyl)methyl]-N~4~-(3-cyclopropyl-1H-pyrazol-5-yl)pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1CC[C@@H](CC1)CNc2nccc(Nc3[nH]nc(c3)C4CC4)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
 4T5  4T5  N~2~-[(trans-4-aminocyclohexyl)methyl]-N~4~-(3-cyclopropyl-1H-pyrazol-5-yl)pyrimidine-2,4-diamine  ligand  49  24  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_4T5
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
 4T5  N3   N  N     0  -0.521   1.2450   1.2683   0.0261
 4T5  C4   C  CR6   0   0.611   0.0727   1.9185   0.0946
 4T5  C6   C  CR16  0  -0.016   1.0027   3.9375  -0.2793
 4T5  C8   C  CH2   0  -0.215  -2.3485   1.6743   0.4771
 4T5  C13  C  CR16  0  -0.074  -5.8654  -0.6960  -0.6140
 4T5  C15  C  C     0  -0.428  -5.8565   0.0667   0.7062
 4T5  C24  C  CR15  0  -0.570   2.9967  -1.0884   0.0403
 4T5  C26  C  CH2   0  -0.480   2.5158  -4.0303   1.1609
 4T5  C1   C  CR16  0  -0.469   2.2572   3.3888  -0.3749
 4T5  C2   C  CR6   0   0.561   2.3212   1.9928  -0.2057
 4T5  N5   N  N     0  -0.497  -0.1033   3.2333  -0.0439
 4T5  N7   N  NH1   0  -0.666  -1.0109   1.1556   0.3160
 4T5  C9   C  CR16  0  -0.291  -3.3835   0.5575   0.4562
 4T5  C11  C  C     0  -0.418  -3.3916  -0.2067  -0.8678
 4T5  C12  C  C     0  -0.439  -4.4776  -1.2766  -0.8892
 4T5  C16  C  C     0  -0.421  -4.7700   1.1351   0.7372
 4T5  N17  N  NH2   0  -0.793  -6.9369  -1.6837  -0.6076
 4T5  N18  N  NH1   0  -0.774   3.5314   1.3718  -0.2852
 4T5  C19  C  CR5   0   0.629   3.7869   0.0247  -0.1693
 4T5  N20  N  NR15  0  -0.523   5.0545  -0.4209  -0.2680
 4T5  N22  N  N     0  -0.321   5.1491  -1.7514  -0.1357
 4T5  C23  C  CR5   0   0.334   3.9115  -2.1644   0.0514
 4T5  C25  C  CH1   0  -0.352   3.6222  -3.5957   0.2390
 4T5  C27  C  CH2   0  -0.479   2.3570  -4.1923  -0.3140
 4T5  H1   H  HCR6  0   0.264   0.8720   5.0082  -0.3961
 4T5  H2   H  HCH2  0   0.227  -2.4343   2.2386   1.4134
 4T5  H3   H  HCH2  0   0.224  -2.5608   2.3795  -0.3307
 4T5  H4   H  HCR6  0   0.208  -6.0925   0.0222  -1.4121
 4T5  H6   H  H     0   0.208  -5.6930  -0.6442   1.5257
 4T5  H7   H  HCR5  0   0.270   1.9304  -1.1140   0.1643
 4T5  H8   H  HCH2  0   0.258   2.6824  -4.9153   1.7611
 4T5  H9   H  HCH2  0   0.251   1.9426  -3.2571   1.6572
 4T5  H10  H  HCR6  0   0.273   3.1340   3.9909  -0.5650
 4T5  H11  H  HNH1  0   0.391  -0.8430   0.1818   0.5093
 4T5  H12  H  HCR6  0   0.223  -3.1478  -0.1518   1.2621
 4T5  H13  H  H     0   0.210  -3.5598   0.5060  -1.6842
 4T5  H14  H  H     0   0.230  -2.4177  -0.6642  -1.0578
 4T5  H15  H  H     0   0.205  -4.2596  -2.0369  -0.1287
 4T5  H16  H  H     0   0.226  -4.4780  -1.7924  -1.8543
 4T5  H17  H  H     0   0.212  -4.9942   1.9013  -0.0145
 4T5  H18  H  H     0   0.232  -4.7729   1.6431   1.7055
 4T5  H19  H  HNH2  0   0.340  -6.9329  -2.1888  -1.4864
 4T5  H21  H  HNH2  0   0.331  -6.7348  -2.3812   0.1011
 4T5  H22  H  HNH1  0   0.420   4.3257   1.9675  -0.4620
 4T5  H23  H  HNR5  0   0.416   5.8859   0.1269  -0.4232
 4T5  H24  H  HCH1  0   0.259   4.5025  -4.2274   0.2131
 4T5  H25  H  HCH2  0   0.258   2.4144  -5.1896  -0.7312
 4T5  H26  H  HCH2  0   0.251   1.6740  -3.5314  -0.8331
 4T5  H5   H  H     0   0.229  -6.8364   0.5198   0.8756

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
 4T5  N20  C19  aromatic  1.347  0.020  1.347
 4T5  N20  N22  aromatic  1.340  0.020  1.340
 4T5  C1   C6   aromatic  1.373  0.020  1.373
 4T5  C1   C2   aromatic  1.408  0.020  1.408
 4T5  N18  C19  single    1.376  0.020  1.376
 4T5  N18  C2   single    1.363  0.020  1.363
 4T5  C19  C24  aromatic  1.381  0.020  1.381
 4T5  C6   N5   aromatic  1.332  0.020  1.332
 4T5  C2   N3   aromatic  1.318  0.020  1.318
 4T5  N22  C23  aromatic  1.318  0.020  1.318
 4T5  C24  C23  aromatic  1.412  0.020  1.412
 4T5  N5   C4   aromatic  1.334  0.020  1.334
 4T5  C23  C25  single    1.472  0.020  1.472
 4T5  N3   C4   aromatic  1.342  0.020  1.342
 4T5  C4   N7   single    1.344  0.020  1.344
 4T5  C25  C27  single    1.504  0.020  1.504
 4T5  C25  C26  single    1.504  0.020  1.504
 4T5  N7   C8   single    1.444  0.020  1.444
 4T5  C27  C26  single    1.492  0.020  1.492
 4T5  C11  C12  single    1.525  0.020  1.525
 4T5  C11  C9   single    1.529  0.020  1.529
 4T5  C8   C9   single    1.523  0.020  1.523
 4T5  C12  C13  single    1.529  0.020  1.529
 4T5  C9   C16  single    1.528  0.020  1.528
 4T5  C13  N17  single    1.457  0.020  1.457
 4T5  C13  C15  single    1.525  0.020  1.525
 4T5  C16  C15  single    1.524  0.020  1.524
 4T5  C6   H1   single    0.930  0.020  1.080
 4T5  C8   H2   single    0.970  0.020  1.090
 4T5  C8   H3   single    0.970  0.020  1.090
 4T5  C13  H4   single    0.970  0.020  1.090
 4T5  C15  H5   single    0.970  0.020  1.090
 4T5  C15  H6   single    0.970  0.020  1.090
 4T5  C24  H7   single    0.930  0.020  1.080
 4T5  C26  H8   single    0.970  0.020  1.090
 4T5  C26  H9   single    0.970  0.020  1.090
 4T5  C1   H10  single    0.930  0.020  1.080
 4T5  N7   H11  single    0.860  0.020  1.020
 4T5  C9   H12  single    0.970  0.020  1.090
 4T5  C11  H13  single    0.970  0.020  1.090
 4T5  C11  H14  single    0.970  0.020  1.090
 4T5  C12  H15  single    0.970  0.020  1.090
 4T5  C12  H16  single    0.970  0.020  1.090
 4T5  C16  H17  single    0.970  0.020  1.090
 4T5  C16  H18  single    0.970  0.020  1.090
 4T5  N17  H19  single    0.890  0.020  1.040
 4T5  N17  H21  single    0.890  0.020  1.040
 4T5  N18  H22  single    0.860  0.020  1.020
 4T5  N20  H23  single    0.860  0.020  1.020
 4T5  C25  H24  single    0.970  0.020  1.090
 4T5  C27  H25  single    0.970  0.020  1.090
 4T5  C27  H26  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
 4T5  C2   N3   C4   117.12  3.000
 4T5  N7   C4   N5   118.06  3.000
 4T5  N7   C4   N3   115.95  3.000
 4T5  N5   C4   N3   125.98  3.000
 4T5  H1   C6   N5   116.15  3.000
 4T5  H1   C6   C1   119.81  3.000
 4T5  N5   C6   C1   124.04  3.000
 4T5  H3   C8   H2   106.48  3.000
 4T5  H3   C8   C9   109.33  3.000
 4T5  H2   C8   C9   109.62  3.000
 4T5  H3   C8   N7   109.23  3.000
 4T5  H2   C8   N7   110.65  3.000
 4T5  C9   C8   N7   111.39  3.000
 4T5  H4   C13  N17  107.14  3.000
 4T5  H4   C13  C12  107.78  3.000
 4T5  N17  C13  C12  114.25  3.000
 4T5  H4   C13  C15  107.67  3.000
 4T5  N17  C13  C15  109.85  3.000
 4T5  C12  C13  C15  109.91  3.000
 4T5  H6   C15  H5   106.65  3.000
 4T5  H6   C15  C16  109.44  3.000
 4T5  H5   C15  C16  110.21  3.000
 4T5  H6   C15  C13  108.87  3.000
 4T5  H5   C15  C13  109.66  3.000
 4T5  C16  C15  C13  111.87  3.000
 4T5  H7   C24  C23  128.62  3.000
 4T5  H7   C24  C19  127.22  3.000
 4T5  C23  C24  C19  104.16  3.000
 4T5  H9   C26  H8   114.28  3.000
 4T5  H9   C26  C27  118.31  3.000
 4T5  H8   C26  C27  118.41  3.000
 4T5  H9   C26  C25  117.64  3.000
 4T5  H8   C26  C25  117.58  3.000
 4T5  C27  C26  C25   60.26  3.000
 4T5  H10  C1   C2   122.47  3.000
 4T5  H10  C1   C6   122.09  3.000
 4T5  C2   C1   C6   115.45  3.000
 4T5  N18  C2   C1   119.04  3.000
 4T5  N18  C2   N3   119.01  3.000
 4T5  C1   C2   N3   121.95  3.000
 4T5  C6   N5   C4   115.46  3.000
 4T5  H11  N7   C8   118.72  3.000
 4T5  H11  N7   C4   116.51  3.000
 4T5  C8   N7   C4   124.17  3.000
 4T5  H12  C9   C16  107.68  3.000
 4T5  H12  C9   C11  108.27  3.000
 4T5  C16  C9   C11  110.08  3.000
 4T5  H12  C9   C8   108.51  3.000
 4T5  C16  C9   C8   109.69  3.000
 4T5  C11  C9   C8   112.46  3.000
 4T5  H14  C11  H13  106.22  3.000
 4T5  H14  C11  C12  109.79  3.000
 4T5  H13  C11  C12  109.65  3.000
 4T5  H14  C11  C9   110.80  3.000
 4T5  H13  C11  C9   108.71  3.000
 4T5  C12  C11  C9   111.52  3.000
 4T5  H16  C12  H15  106.55  3.000
 4T5  H16  C12  C11  110.09  3.000
 4T5  H15  C12  C11  109.57  3.000
 4T5  H16  C12  C13  109.72  3.000
 4T5  H15  C12  C13  108.58  3.000
 4T5  C11  C12  C13  112.17  3.000
 4T5  H18  C16  H17  106.38  3.000
 4T5  H18  C16  C9   109.93  3.000
 4T5  H17  C16  C9   108.88  3.000
 4T5  H18  C16  C15  109.98  3.000
 4T5  H17  C16  C15  109.27  3.000
 4T5  C9   C16  C15  112.22  3.000
 4T5  H21  N17  H19  105.21  3.000
 4T5  H21  N17  C13  108.82  3.000
 4T5  H19  N17  C13  109.33  3.000
 4T5  H22  N18  C19  116.53  3.000
 4T5  H22  N18  C2   116.14  3.000
 4T5  C19  N18  C2   127.32  3.000
 4T5  N20  C19  N18  119.49  3.000
 4T5  N18  C19  C24  134.07  3.000
 4T5  N20  C19  C24  106.44  3.000
 4T5  H23  N20  N22  119.77  3.000
 4T5  H23  N20  C19  127.44  3.000
 4T5  N22  N20  C19  112.79  3.000
 4T5  C23  N22  N20  105.00  3.000
 4T5  C25  C23  N22  120.48  3.000
 4T5  C25  C23  C24  127.91  3.000
 4T5  N22  C23  C24  111.61  3.000
 4T5  H24  C25  C27  116.31  3.000
 4T5  H24  C25  C23  113.83  3.000
 4T5  C27  C25  C23  120.27  3.000
 4T5  H24  C25  C26  116.33  3.000
 4T5  C27  C25  C26   59.48  3.000
 4T5  C23  C25  C26  120.23  3.000
 4T5  H26  C27  H25  114.26  3.000
 4T5  H26  C27  C25  117.69  3.000
 4T5  H25  C27  C25  117.55  3.000
 4T5  H26  C27  C26  118.34  3.000
 4T5  H25  C27  C26  118.38  3.000
 4T5  C25  C27  C26   60.27  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
 4T5  CONST_01  C6   C1   C2   N3      0.00   0.0  0
 4T5  CONST_02  C6   N5   C4   N3      0.00   0.0  0
 4T5  CONST_03  C1   C6   N5   C4      0.00   0.0  0
 4T5  CONST_04  C1   C2   N3   C4      0.00   0.0  0
 4T5  CONST_05  N22  N20  C19  C24     0.00   0.0  0
 4T5  CONST_06  N20  N22  C23  C24     0.00   0.0  0
 4T5  CONST_07  N5   C6   C1   C2      0.00   0.0  0
 4T5  CONST_08  N5   C4   N3   C2      0.00   0.0  0
 4T5  CONST_09  C23  N22  N20  C19     0.00   0.0  0
 4T5  CONST_10  N22  C23  C24  C19     0.00   0.0  0
 4T5  CONST_11  C23  C24  C19  N20     0.00   0.0  0
 4T5  CONST_12  C25  C23  C24  C19   180.00   0.0  0
 4T5  CONST_13  C25  C23  N22  N20   180.00   0.0  0
 4T5  CONST_14  N18  C2   N3   C4    180.00   0.0  0
 4T5  CONST_15  N18  C2   C1   C6    180.00   0.0  0
 4T5  CONST_16  N7   C4   N5   C6    180.00   0.0  0
 4T5  CONST_17  N7   C4   N3   C2    180.00   0.0  0
 4T5  CONST_18  N22  N20  C19  N18   180.00   0.0  0
 4T5  CONST_19  C23  C24  C19  N18   180.00   0.0  0
 4T5  CONST_20  H10  C1   C2   N3    180.00   0.0  0
 4T5  CONST_21  H1   C6   N5   C4    180.00   0.0  0
 4T5  CONST_22  H23  N20  C19  C24   180.00   0.0  0
 4T5  CONST_23  H7   C24  C19  N20   180.00   0.0  0
 4T5  CONST_24  C8   N7   C4   N3    180.00   0.0  0
 4T5  CONST_25  N5   C4   N7   C8      0.00   0.0  0
 4T5  CONST_26  H11  N7   C4   N3      0.00   0.0  0
 4T5  Var_01    C9   C11  C12  C13    56.20  30.0  1
 4T5  Var_02    C9   C16  C15  C13   -55.73  30.0  1
 4T5  Var_03    C27  C25  C23  C24    35.44  30.0  2
 4T5  Var_04    C23  C25  C27  C26  -109.43  30.0  1
 4T5  Var_05    C19  N18  C2   N3      1.07  30.0  1
 4T5  Var_06    C2   N18  C19  C24     0.46  30.0  1
 4T5  Var_07    C9   C8   N7   C4    169.50  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
 4T5  chir_01  C13  C12  N17  C15  negativ
 4T5  chir_02  C9   C16  C8   C11  positiv
 4T5  chir_03  C25  C23  C27  C26  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
 4T5  plan-1  C24  0.020
 4T5  plan-1  N18  0.020
 4T5  plan-1  C19  0.020
 4T5  plan-1  N20  0.020
 4T5  plan-1  N22  0.020
 4T5  plan-1  C23  0.020
 4T5  plan-1  C25  0.020
 4T5  plan-1  H7   0.020
 4T5  plan-1  H23  0.020
 4T5  plan-2  N3   0.020
 4T5  plan-2  C4   0.020
 4T5  plan-2  C6   0.020
 4T5  plan-2  C1   0.020
 4T5  plan-2  C2   0.020
 4T5  plan-2  N5   0.020
 4T5  plan-2  N7   0.020
 4T5  plan-2  N18  0.020
 4T5  plan-2  H1   0.020
 4T5  plan-2  H10  0.020
 4T5  plan-3  C4   0.020
 4T5  plan-3  C8   0.020
 4T5  plan-3  N7   0.020
 4T5  plan-3  H11  0.020

