# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 07:04:35 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: 6-ethyl-5-{3-[3-(pyrimidin-5-yl)phenyl]prop-1-yn-1-yl}pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1nc(N)nc(N)c1C#CCc2cccc(c2)c3cncnc3
#
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
 25U  25U  6-ethyl-5-{3-[3-(pyrimidin-5-yl)phenyl]prop-1-yn-1-yl}pyrimidine-2,4-diamine  ligand  43  25  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_25U
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
 25U  CAA  C  CH3   0  -0.663   5.1352   2.3103  -0.9612
 25U  CAO  C  CH2   0  -0.517   4.4897   1.1535  -1.7236
 25U  C4   C  CR6   0   0.270   4.1046   0.0415  -0.7960
 25U  N3   N  N     0  -0.499   5.0421  -0.8580  -0.5238
 25U  C2   C  CR6   0   0.537   4.7146  -1.8293   0.3352
 25U  NAD  N  NH2   0  -0.820   5.6557  -2.7560   0.5893
 25U  N1   N  N     0  -0.504   3.5383  -1.9844   0.9415
 25U  C6   C  CR6   0   0.465   2.5983  -1.0874   0.6732
 25U  NAE  N  NH2   0  -0.822   1.4157  -1.2192   1.2881
 25U  C5   C  CR6   0  -0.321   2.8369  -0.0086  -0.2213
 25U  CAF  C  CSP   0   0.149   1.8162   0.9388  -0.4800
 25U  CAG  C  CSP   0   0.028   0.8987   1.7052  -0.6491
 25U  CBB  C  CH2   0  -0.679  -0.2352   2.6057  -0.8226
 25U  CAY  C  CR6   0   0.129  -1.3991   2.1611   0.0337
 25U  CAN  C  CR16  0  -0.355  -2.2081   1.1116  -0.3855
 25U  CAM  C  CR16  0  -0.307  -1.6503   2.7627   1.2603
 25U  CAV  C  CR16  0  -0.224  -2.7015   2.3210   2.0526
 25U  CAL  C  CR16  0  -0.321  -3.5072   1.2771   1.6281
 25U  CAX  C  CR6   0   0.108  -3.2667   0.6602   0.3996
 25U  CAW  C  CR6   0  -0.045  -4.1160  -0.4476  -0.0629
 25U  CAJ  C  CR16  0  -0.047  -4.4859  -0.5994  -1.3964
 25U  NAO  N  N     0  -0.387  -5.2460  -1.5983  -1.8199
 25U  CAI  C  CR16  0   0.050  -5.6556  -2.4633  -0.9047
 25U  NAP  N  N     0  -0.386  -5.3735  -2.4233   0.3884
 25U  CAK  C  CR16  0  -0.047  -4.6071  -1.4237   0.7997
 25U  H1   H  HCH3  0   0.237   5.4371   3.0994  -1.6498
 25U  H2   H  HCH3  0   0.229   4.4421   2.7446  -0.2400
 25U  H3   H  HCH3  0   0.229   6.0219   1.9788  -0.4204
 25U  H4   H  HCH2  0   0.243   3.6133   1.5153  -2.2629
 25U  H5   H  HCH2  0   0.249   5.1917   0.7627  -2.4619
 25U  H6   H  HNH2  0   0.395   6.5968  -2.6006   0.2746
 25U  H7   H  HNH2  0   0.395   5.5133  -3.4167   1.3322
 25U  H8   H  HNH2  0   0.398   1.2280  -2.0474   1.8262
 25U  H9   H  HNH2  0   0.398   0.6345  -0.6417   1.0299
 25U  H10  H  HCH2  0   0.287   0.0558   3.6254  -0.5585
 25U  H11  H  HCH2  0   0.289  -0.5309   2.6301  -1.8750
 25U  H12  H  HCR6  0   0.257  -1.9948   0.6289  -1.3327
 25U  H13  H  HCR6  0   0.258  -1.0255   3.5803   1.5992
 25U  H14  H  HCR6  0   0.263  -2.8988   2.7983   3.0034
 25U  H15  H  HCR6  0   0.260  -4.3374   0.9563   2.2445
 25U  H16  H  HCR6  0   0.277  -4.1677   0.1205  -2.1440
 25U  H17  H  HCR6  0   0.268  -6.2805  -3.2810  -1.2459
 25U  H18  H  HCR6  0   0.277  -4.3590  -1.4029   1.8561

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
 25U  NAD  C2   single    1.345  0.020  1.345
 25U  C2   N3   aromatic  1.337  0.020  1.337
 25U  C2   N1   aromatic  1.332  0.020  1.332
 25U  N3   C4   aromatic  1.328  0.020  1.328
 25U  CAA  CAO  single    1.528  0.020  1.528
 25U  N1   C6   aromatic  1.327  0.020  1.327
 25U  C4   CAO  single    1.498  0.020  1.498
 25U  C4   C5   aromatic  1.393  0.020  1.393
 25U  C6   C5   aromatic  1.422  0.020  1.422
 25U  C6   NAE  single    1.339  0.020  1.339
 25U  C5   CAF  single    1.416  0.020  1.416
 25U  CAF  CAG  triple    1.207  0.020  1.207
 25U  CAG  CBB  single    1.458  0.020  1.458
 25U  CBB  CAY  single    1.512  0.020  1.512
 25U  NAO  CAJ  aromatic  1.325  0.020  1.325
 25U  NAO  CAI  aromatic  1.324  0.020  1.324
 25U  CAN  CAY  aromatic  1.390  0.020  1.390
 25U  CAN  CAX  aromatic  1.393  0.020  1.393
 25U  CAJ  CAW  aromatic  1.392  0.020  1.392
 25U  CAI  NAP  aromatic  1.324  0.020  1.324
 25U  CAY  CAM  aromatic  1.389  0.020  1.389
 25U  CAW  CAX  single    1.470  0.020  1.470
 25U  CAW  CAK  aromatic  1.392  0.020  1.392
 25U  NAP  CAK  aromatic  1.325  0.020  1.325
 25U  CAX  CAL  aromatic  1.396  0.020  1.396
 25U  CAM  CAV  aromatic  1.389  0.020  1.389
 25U  CAL  CAV  aromatic  1.385  0.020  1.385
 25U  CAA  H1   single    0.970  0.020  1.090
 25U  CAA  H2   single    0.970  0.020  1.090
 25U  CAA  H3   single    0.970  0.020  1.090
 25U  CAO  H4   single    0.970  0.020  1.090
 25U  CAO  H5   single    0.970  0.020  1.090
 25U  NAD  H6   single    0.890  0.020  1.040
 25U  NAD  H7   single    0.890  0.020  1.040
 25U  NAE  H8   single    0.860  0.020  1.020
 25U  NAE  H9   single    0.860  0.020  1.020
 25U  CBB  H10  single    0.970  0.020  1.090
 25U  CBB  H11  single    0.970  0.020  1.090
 25U  CAN  H12  single    0.930  0.020  1.080
 25U  CAM  H13  single    0.930  0.020  1.080
 25U  CAV  H14  single    0.930  0.020  1.080
 25U  CAL  H15  single    0.930  0.020  1.080
 25U  CAJ  H16  single    0.930  0.020  1.080
 25U  CAI  H17  single    0.930  0.020  1.080
 25U  CAK  H18  single    0.930  0.020  1.080

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
 25U  H3   CAA  H2   108.06  3.000
 25U  H3   CAA  H1   107.96  3.000
 25U  H2   CAA  H1   107.79  3.000
 25U  H3   CAA  CAO  111.15  3.000
 25U  H2   CAA  CAO  111.28  3.000
 25U  H1   CAA  CAO  110.47  3.000
 25U  H5   CAO  H4   107.52  3.000
 25U  H5   CAO  C4   108.57  3.000
 25U  H4   CAO  C4   110.23  3.000
 25U  H5   CAO  CAA  109.69  3.000
 25U  H4   CAO  CAA  109.56  3.000
 25U  C4   CAO  CAA  111.19  3.000
 25U  C5   C4   N3   122.26  3.000
 25U  C5   C4   CAO  121.07  3.000
 25U  N3   C4   CAO  116.63  3.000
 25U  C2   N3   C4   116.80  3.000
 25U  N1   C2   NAD  116.84  3.000
 25U  N1   C2   N3   126.38  3.000
 25U  NAD  C2   N3   116.77  3.000
 25U  H7   NAD  H6   117.80  3.000
 25U  H7   NAD  C2   119.59  3.000
 25U  H6   NAD  C2   119.33  3.000
 25U  C6   N1   C2   117.05  3.000
 25U  C5   C6   NAE  120.78  3.000
 25U  NAE  C6   N1   117.79  3.000
 25U  C5   C6   N1   121.42  3.000
 25U  H9   NAE  H8   117.75  3.000
 25U  H9   NAE  C6   120.78  3.000
 25U  H8   NAE  C6   119.46  3.000
 25U  CAF  C5   C6   120.10  3.000
 25U  CAF  C5   C4   123.81  3.000
 25U  C6   C5   C4   116.09  3.000
 25U  CAG  CAF  C5   180.00  3.000
 25U  CBB  CAG  CAF  180.00  3.000
 25U  H11  CBB  H10  106.49  3.000
 25U  H11  CBB  CAY  110.09  3.000
 25U  H10  CBB  CAY  110.03  3.000
 25U  H11  CBB  CAG  109.79  3.000
 25U  H10  CBB  CAG  109.90  3.000
 25U  CAY  CBB  CAG  110.46  3.000
 25U  CAM  CAY  CAN  119.22  3.000
 25U  CAM  CAY  CBB  120.79  3.000
 25U  CAN  CAY  CBB  119.96  3.000
 25U  H12  CAN  CAX  119.84  3.000
 25U  H12  CAN  CAY  119.02  3.000
 25U  CAX  CAN  CAY  121.13  3.000
 25U  H13  CAM  CAV  119.88  3.000
 25U  H13  CAM  CAY  119.92  3.000
 25U  CAV  CAM  CAY  120.20  3.000
 25U  H14  CAV  CAL  119.72  3.000
 25U  H14  CAV  CAM  119.94  3.000
 25U  CAL  CAV  CAM  120.34  3.000
 25U  H15  CAL  CAX  120.15  3.000
 25U  H15  CAL  CAV  119.65  3.000
 25U  CAX  CAL  CAV  120.18  3.000
 25U  CAW  CAX  CAL  120.69  3.000
 25U  CAL  CAX  CAN  118.93  3.000
 25U  CAW  CAX  CAN  120.38  3.000
 25U  CAK  CAW  CAJ  115.05  3.000
 25U  CAK  CAW  CAX  122.48  3.000
 25U  CAJ  CAW  CAX  122.47  3.000
 25U  H16  CAJ  NAO  116.62  3.000
 25U  H16  CAJ  CAW  120.63  3.000
 25U  NAO  CAJ  CAW  122.74  3.000
 25U  CAI  NAO  CAJ  116.69  3.000
 25U  H17  CAI  NAP  116.93  3.000
 25U  H17  CAI  NAO  116.96  3.000
 25U  NAP  CAI  NAO  126.11  3.000
 25U  CAK  NAP  CAI  116.69  3.000
 25U  H18  CAK  NAP  116.67  3.000
 25U  H18  CAK  CAW  120.60  3.000
 25U  NAP  CAK  CAW  122.72  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
 25U  CONST_01  N1   C2   N3   C4     0.00   0.0  0
 25U  CONST_02  N1   C6   C5   C4     0.00   0.0  0
 25U  CONST_03  C6   N1   C2   N3     0.00   0.0  0
 25U  CONST_04  C6   C5   C4   N3     0.00   0.0  0
 25U  CONST_05  C5   C4   N3   C2     0.00   0.0  0
 25U  CONST_06  C5   C6   N1   C2     0.00   0.0  0
 25U  CONST_07  CAW  CAX  CAN  CAY  180.00   0.0  0
 25U  CONST_08  CAL  CAX  CAN  CAY    0.00   0.0  0
 25U  CONST_09  CAL  CAV  CAM  CAY    0.00   0.0  0
 25U  CONST_10  CAV  CAM  CAY  CAN    0.00   0.0  0
 25U  CONST_13  CAV  CAL  CAX  CAN    0.00   0.0  0
 25U  CONST_14  CAX  CAN  CAY  CAM    0.00   0.0  0
 25U  CONST_15  CAX  CAL  CAV  CAM    0.00   0.0  0
 25U  CONST_16  CAW  CAX  CAL  CAV  180.00   0.0  0
 25U  CONST_19  NAO  CAJ  CAW  CAX  180.00   0.0  0
 25U  CONST_20  NAP  CAK  CAW  CAX  180.00   0.0  0
 25U  CONST_21  CAI  NAO  CAJ  CAW    0.00   0.0  0
 25U  CONST_22  CAI  NAP  CAK  CAW    0.00   0.0  0
 25U  CONST_23  NAP  CAI  NAO  CAJ    0.00   0.0  0
 25U  CONST_24  NAP  CAK  CAW  CAJ    0.00   0.0  0
 25U  CONST_25  CAK  CAW  CAJ  NAO    0.00   0.0  0
 25U  CONST_26  CAK  NAP  CAI  NAO    0.00   0.0  0
 25U  CONST_27  C2   N3   C4   CAO  180.00   0.0  0
 25U  CONST_28  C6   C5   C4   CAO  180.00   0.0  0
 25U  CONST_29  NAD  C2   N3   C4   180.00   0.0  0
 25U  CONST_30  NAE  C6   C5   C4   180.00   0.0  0
 25U  CONST_31  CAF  C5   C4   N3   180.00   0.0  0
 25U  CONST_32  NAE  C6   N1   C2   180.00   0.0  0
 25U  CONST_33  C6   N1   C2   NAD  180.00   0.0  0
 25U  CONST_34  CAF  C5   C6   N1   180.00   0.0  0
 25U  CONST_35  CAX  CAN  CAY  CBB  180.00   0.0  0
 25U  CONST_36  CAV  CAM  CAY  CBB  180.00   0.0  0
 25U  CONST_37  H14  CAV  CAM  CAY  180.00   0.0  0
 25U  CONST_38  H13  CAM  CAY  CAN  180.00   0.0  0
 25U  CONST_39  H15  CAL  CAX  CAN  180.00   0.0  0
 25U  CONST_40  H12  CAN  CAY  CAM  180.00   0.0  0
 25U  CONST_41  H16  CAJ  CAW  CAX    0.00   0.0  0
 25U  CONST_42  H18  CAK  CAW  CAX    0.00   0.0  0
 25U  CONST_43  H17  CAI  NAO  CAJ  180.00   0.0  0
 25U  CONST_44  H6   NAD  C2   N3     0.00   0.0  0
 25U  CONST_45  H7   NAD  C2   N3   180.00   0.0  0
 25U  CONST_46  H8   NAE  C6   N1     0.00   0.0  0
 25U  CONST_47  H9   NAE  C6   N1   180.00   0.0  0
 25U  Var_01    N3   C4   CAO  CAA  -86.59  30.0  1
 25U  Var_02    CAN  CAY  CBB  CAG  -79.18  30.0  2
 25U  Var_03    CAY  CBB  CAG  CAF   -0.21  30.0  3
 25U  Var_04    H1   CAA  CAO  C4   178.34  30.0  3

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
 25U  plan-1  CAO  0.020
 25U  plan-1  C4   0.020
 25U  plan-1  N3   0.020
 25U  plan-1  C2   0.020
 25U  plan-1  NAD  0.020
 25U  plan-1  N1   0.020
 25U  plan-1  C6   0.020
 25U  plan-1  NAE  0.020
 25U  plan-1  C5   0.020
 25U  plan-1  CAF  0.020
 25U  plan-1  CAG  0.020
 25U  plan-2  CBB  0.020
 25U  plan-2  CAY  0.020
 25U  plan-2  CAN  0.020
 25U  plan-2  CAM  0.020
 25U  plan-2  CAV  0.020
 25U  plan-2  CAL  0.020
 25U  plan-2  CAX  0.020
 25U  plan-2  CAW  0.020
 25U  plan-2  H12  0.020
 25U  plan-2  H13  0.020
 25U  plan-2  H14  0.020
 25U  plan-2  H15  0.020
 25U  plan-3  CAX  0.020
 25U  plan-3  CAW  0.020
 25U  plan-3  CAJ  0.020
 25U  plan-3  NAO  0.020
 25U  plan-3  CAI  0.020
 25U  plan-3  NAP  0.020
 25U  plan-3  CAK  0.020
 25U  plan-3  H16  0.020
 25U  plan-3  H17  0.020
 25U  plan-3  H18  0.020
 25U  plan-4  C2   0.020
 25U  plan-4  NAD  0.020
 25U  plan-4  H6   0.020
 25U  plan-4  H7   0.020
 25U  plan-5  C6   0.020
 25U  plan-5  NAE  0.020
 25U  plan-5  H8   0.020
 25U  plan-5  H9   0.020

