# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 17:56:12 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 7-({4-[(3R)-3-aminopyrrolidin-1-yl]-5-chloro-6-ethyl-7H-pyrrolo[2,3-d]pyrimidin-2-yl}sulfanyl)pyrido[2,3-b]pyrazin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1[nH]c2nc(Sc3cnc4N=CC(=O)Nc4c3)nc(N5CC[C@@H](N)C5)c2c1Cl
#
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
 CJC  CJC  7-({4-[(3R)-3-aminopyrrolidin-1-yl]-5-chloro-6-ethyl-7H-pyrrolo[2,3-d]pyrimidin-2-yl}sulfanyl)pyrido[2,3-b]pyrazin-2(1H)-one  ligand  49  30  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CJC
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
 CJC  O47  O   O     0  -0.455  -7.7724   0.2255   1.9159
 CJC  C28  C   CR6   0   0.480  -6.8792   0.1626   1.0908
 CJC  C27  C   CR16  0  -0.177  -6.9437  -0.6955  -0.1076
 CJC  N29  N   NR16  0  -0.718  -5.7215   0.8757   1.1809
 CJC  C22  C   CR66  0   0.317  -4.7171   0.8004   0.2548
 CJC  C23  C   CR66  0   0.320  -4.8828  -0.0466  -0.8460
 CJC  N26  N   N     0  -0.331  -6.0285  -0.7892  -0.9960
 CJC  N24  N   N     0  -0.398  -3.9542  -0.1714  -1.7948
 CJC  C25  C   CR16  0  -0.035  -2.8467   0.5209  -1.6905
 CJC  C20  C   CR6   0  -0.202  -2.5826   1.3788  -0.6097
 CJC  C21  C   CR16  0  -0.194  -3.5303   1.5241   0.3773
 CJC  S19  S   S2    0   0.095  -1.0919   2.3168  -0.5542
 CJC  C10  C   CR6   0   0.206   0.1337   1.0417  -0.4031
 CJC  N9   N   N     0  -0.502   1.3585   1.5279  -0.4726
 CJC  C8   C   CR6   0   0.495   2.4116   0.7055  -0.3505
 CJC  N13  N   NT    0  -0.494   3.6045   1.3133  -0.3120
 CJC  C14  C   CH2   0  -0.276   3.7086   2.7654  -0.4804
 CJC  C15  C   CH2   0  -0.490   5.1902   3.0381  -0.2628
 CJC  C16  C   CH1   0  -0.141   5.6037   1.9520   0.7345
 CJC  N18  N   NH2   0  -0.788   5.2304   2.2003   2.1181
 CJC  C17  C   CH2   0  -0.280   4.8524   0.7442   0.1833
 CJC  C3   C   CR56  0   0.061   2.1635  -0.6973  -0.2756
 CJC  C2   C   CR56  0   0.464   0.7978  -1.0330  -0.1861
 CJC  N11  N   N     0  -0.432  -0.2420  -0.1968  -0.2216
 CJC  N1   N   NR15  0  -0.709   0.6816  -2.3729  -0.1032
 CJC  C5   C   CR5   0   0.429   1.9162  -2.9620  -0.1863
 CJC  C4   C   CR5   0  -0.317   2.8436  -1.9647  -0.2942
 CJC  CL1  CL  CL    0  -0.152   4.5125  -2.3231  -0.4994
 CJC  C6   C   CH2   0  -0.509   2.0862  -4.4376  -0.1171
 CJC  C7   C   CH3   0  -0.655   2.1510  -4.9508   1.3220
 CJC  H1   H   HCR6  0   0.296  -7.8479  -1.2841  -0.2258
 CJC  H2   H   HNR6  0   0.433  -5.6063   1.4890   1.9793
 CJC  H3   H   HCR6  0   0.282  -2.1160   0.4107  -2.4829
 CJC  H4   H   HCR6  0   0.311  -3.3641   2.1740   1.2272
 CJC  H5   H   HCH2  0   0.255   3.3585   3.0714  -1.4663
 CJC  H6   H   HCH2  0   0.238   3.0893   3.2845   0.2550
 CJC  H7   H   HCH2  0   0.241   5.7441   2.9198  -1.1972
 CJC  H8   H   HCH2  0   0.255   5.3756   4.0470   0.1064
 CJC  H9   H   HCH1  0   0.254   6.6793   1.7694   0.7032
 CJC  H10  H   HNH2  0   0.350   5.6781   3.0497   2.4402
 CJC  H11  H   HNH2  0   0.344   4.2336   2.3688   2.1964
 CJC  H13  H   HCH2  0   0.253   4.6691  -0.0022   0.9552
 CJC  H14  H   HCH2  0   0.249   5.4248   0.2811  -0.6214
 CJC  H15  H   HNR5  0   0.417  -0.1955  -2.8676  -0.0454
 CJC  H16  H   HCH2  0   0.259   1.2612  -4.9206  -0.6459
 CJC  H17  H   HCH2  0   0.253   2.9974  -4.7171  -0.6465
 CJC  H18  H   HCH3  0   0.230   2.9974  -4.5146   1.8525
 CJC  H19  H   HCH3  0   0.230   1.2439  -4.7035   1.8732
 CJC  H20  H   HCH3  0   0.239   2.2669  -6.0344   1.3357

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
 CJC  O47  C28  double    1.218  0.020  1.218
 CJC  C27  C28  single    1.475  0.020  1.475
 CJC  C27  N26  double    1.279  0.020  1.279
 CJC  C28  N29  single    1.363  0.020  1.363
 CJC  N26  C23  single    1.374  0.020  1.374
 CJC  N29  C22  single    1.368  0.020  1.368
 CJC  C23  C22  aromatic  1.399  0.020  1.399
 CJC  C23  N24  aromatic  1.333  0.020  1.333
 CJC  C22  C21  aromatic  1.395  0.020  1.395
 CJC  N24  C25  aromatic  1.310  0.020  1.310
 CJC  C21  C20  aromatic  1.376  0.020  1.376
 CJC  C25  C20  aromatic  1.405  0.020  1.405
 CJC  C20  S19  single    1.762  0.020  1.762
 CJC  N18  C16  single    1.454  0.020  1.454
 CJC  S19  C10  single    1.775  0.020  1.775
 CJC  C15  C14  single    1.522  0.020  1.522
 CJC  C15  C16  single    1.531  0.020  1.531
 CJC  C14  N13  single    1.466  0.020  1.466
 CJC  C16  C17  single    1.525  0.020  1.525
 CJC  C10  N9   aromatic  1.320  0.020  1.320
 CJC  C10  N11  aromatic  1.307  0.020  1.307
 CJC  N9   C8   aromatic  1.342  0.020  1.342
 CJC  N13  C8   single    1.339  0.020  1.339
 CJC  N13  C17  single    1.458  0.020  1.458
 CJC  N11  C2   aromatic  1.335  0.020  1.335
 CJC  C8   C3   aromatic  1.427  0.020  1.427
 CJC  C2   C3   aromatic  1.409  0.020  1.409
 CJC  C2   N1   aromatic  1.347  0.020  1.347
 CJC  C3   C4   aromatic  1.438  0.020  1.438
 CJC  N1   C5   aromatic  1.370  0.020  1.370
 CJC  C4   C5   aromatic  1.366  0.020  1.366
 CJC  C4   CL1  single    1.719  0.020  1.719
 CJC  C5   C6   single    1.487  0.020  1.487
 CJC  C6   C7   single    1.529  0.020  1.529
 CJC  C27  H1   single    0.930  0.020  1.080
 CJC  N29  H2   single    0.860  0.020  1.020
 CJC  C25  H3   single    0.930  0.020  1.080
 CJC  C21  H4   single    0.930  0.020  1.080
 CJC  C14  H5   single    0.970  0.020  1.090
 CJC  C14  H6   single    0.970  0.020  1.090
 CJC  C15  H7   single    0.970  0.020  1.090
 CJC  C15  H8   single    0.970  0.020  1.090
 CJC  C16  H9   single    0.970  0.020  1.090
 CJC  N18  H10  single    0.890  0.020  1.040
 CJC  N18  H11  single    0.890  0.020  1.040
 CJC  C17  H13  single    0.970  0.020  1.090
 CJC  C17  H14  single    0.970  0.020  1.090
 CJC  N1   H15  single    0.860  0.020  1.020
 CJC  C6   H16  single    0.970  0.020  1.090
 CJC  C6   H17  single    0.970  0.020  1.090
 CJC  C7   H18  single    0.970  0.020  1.090
 CJC  C7   H19  single    0.970  0.020  1.090
 CJC  C7   H20  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
 CJC  N29  C28  C27  113.28  3.000
 CJC  N29  C28  O47  123.46  3.000
 CJC  C27  C28  O47  123.26  3.000
 CJC  H1   C27  N26  118.73  3.000
 CJC  H1   C27  C28  116.12  3.000
 CJC  N26  C27  C28  125.14  3.000
 CJC  H2   N29  C22  118.89  3.000
 CJC  H2   N29  C28  117.74  3.000
 CJC  C22  N29  C28  123.37  3.000
 CJC  C21  C22  C23  118.94  3.000
 CJC  C21  C22  N29  122.43  3.000
 CJC  C23  C22  N29  118.62  3.000
 CJC  N24  C23  N26  116.91  3.000
 CJC  N24  C23  C22  122.28  3.000
 CJC  N26  C23  C22  120.81  3.000
 CJC  C23  N26  C27  118.78  3.000
 CJC  C25  N24  C23  118.85  3.000
 CJC  H3   C25  C20  119.87  3.000
 CJC  H3   C25  N24  117.26  3.000
 CJC  C20  C25  N24  122.87  3.000
 CJC  S19  C20  C21  120.25  3.000
 CJC  S19  C20  C25  120.55  3.000
 CJC  C21  C20  C25  119.13  3.000
 CJC  H4   C21  C20  121.38  3.000
 CJC  H4   C21  C22  120.72  3.000
 CJC  C20  C21  C22  117.90  3.000
 CJC  C10  S19  C20  101.79  3.000
 CJC  N11  C10  N9   128.56  3.000
 CJC  N11  C10  S19  119.61  3.000
 CJC  N9   C10  S19  111.82  3.000
 CJC  C8   N9   C10  119.86  3.000
 CJC  C3   C8   N13  126.85  3.000
 CJC  C3   C8   N9   118.10  3.000
 CJC  N13  C8   N9   115.06  3.000
 CJC  C17  N13  C14  111.40  3.000
 CJC  C17  N13  C8   126.50  3.000
 CJC  C14  N13  C8   120.63  3.000
 CJC  H6   C14  H5   107.06  3.000
 CJC  H6   C14  C15  111.74  3.000
 CJC  H5   C14  C15  113.05  3.000
 CJC  H6   C14  N13  110.69  3.000
 CJC  H5   C14  N13  111.05  3.000
 CJC  C15  C14  N13  103.31  3.000
 CJC  H8   C15  H7   107.67  3.000
 CJC  H8   C15  C16  112.95  3.000
 CJC  H7   C15  C16  110.07  3.000
 CJC  H8   C15  C14  112.32  3.000
 CJC  H7   C15  C14  110.60  3.000
 CJC  C16  C15  C14  103.23  3.000
 CJC  H9   C16  C17  110.03  3.000
 CJC  H9   C16  N18  107.99  3.000
 CJC  C17  C16  N18  110.64  3.000
 CJC  H9   C16  C15  111.47  3.000
 CJC  C17  C16  C15  101.14  3.000
 CJC  N18  C16  C15  115.41  3.000
 CJC  H11  N18  H10  105.70  3.000
 CJC  H11  N18  C16  110.74  3.000
 CJC  H10  N18  C16  109.41  3.000
 CJC  H14  C17  H13  108.67  3.000
 CJC  H14  C17  C16  110.14  3.000
 CJC  H13  C17  C16  111.68  3.000
 CJC  H14  C17  N13  111.35  3.000
 CJC  H13  C17  N13  111.35  3.000
 CJC  C16  C17  N13  103.61  3.000
 CJC  C4   C3   C2   104.43  3.000
 CJC  C4   C3   C8   141.58  3.000
 CJC  C2   C3   C8   113.96  3.000
 CJC  N1   C2   N11  123.88  3.000
 CJC  N1   C2   C3   108.92  3.000
 CJC  N11  C2   C3   127.16  3.000
 CJC  C2   N11  C10  111.92  3.000
 CJC  H15  N1   C5   125.17  3.000
 CJC  H15  N1   C2   124.49  3.000
 CJC  C5   N1   C2   110.25  3.000
 CJC  C6   C5   C4   130.58  3.000
 CJC  C6   C5   N1   121.78  3.000
 CJC  C4   C5   N1   107.61  3.000
 CJC  CL1  C4   C5   121.07  3.000
 CJC  CL1  C4   C3   130.11  3.000
 CJC  C5   C4   C3   108.74  3.000
 CJC  H17  C6   H16  106.43  3.000
 CJC  H17  C6   C7   109.60  3.000
 CJC  H16  C6   C7   109.82  3.000
 CJC  H17  C6   C5   109.10  3.000
 CJC  H16  C6   C5   109.27  3.000
 CJC  C7   C6   C5   112.44  3.000
 CJC  H20  C7   H19  107.92  3.000
 CJC  H20  C7   H18  108.01  3.000
 CJC  H19  C7   H18  108.01  3.000
 CJC  H20  C7   C6   110.49  3.000
 CJC  H19  C7   C6   111.38  3.000
 CJC  H18  C7   C6   110.90  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
 CJC  CONST_01  C25  N24  C23  C22     0.00   0.0  0
 CJC  CONST_02  C25  C20  C21  C22     0.00   0.0  0
 CJC  CONST_03  C20  C21  C22  C23     0.00   0.0  0
 CJC  CONST_04  C20  C25  N24  C23     0.00   0.0  0
 CJC  CONST_05  C21  C22  C23  N24     0.00   0.0  0
 CJC  CONST_06  C21  C20  C25  N24     0.00   0.0  0
 CJC  CONST_07  C3   C8   N9   C10     0.00   0.0  0
 CJC  CONST_08  C3   C2   N11  C10     0.00   0.0  0
 CJC  CONST_09  N1   C2   N11  C10   180.00   0.0  0
 CJC  CONST_10  C2   N11  C10  N9      0.00   0.0  0
 CJC  CONST_11  C2   C3   C8   N9      0.00   0.0  0
 CJC  CONST_12  C4   C3   C8   N9    180.00   0.0  0
 CJC  CONST_13  N11  C10  N9   C8      0.00   0.0  0
 CJC  CONST_14  N11  C2   C3   C8      0.00   0.0  0
 CJC  CONST_15  N1   C2   C3   C8    180.00   0.0  0
 CJC  CONST_16  C5   C4   C3   C8    180.00   0.0  0
 CJC  CONST_17  C5   N1   C2   C3      0.00   0.0  0
 CJC  CONST_18  N1   C5   C4   C3      0.00   0.0  0
 CJC  CONST_19  C5   C4   C3   C2      0.00   0.0  0
 CJC  CONST_20  C4   C5   N1   C2      0.00   0.0  0
 CJC  CONST_21  C4   C3   C2   N11   180.00   0.0  0
 CJC  CONST_22  C5   N1   C2   N11   180.00   0.0  0
 CJC  CONST_23  C4   C3   C2   N1      0.00   0.0  0
 CJC  CONST_24  N13  C8   N9   C10   180.00   0.0  0
 CJC  CONST_25  C2   C3   C8   N13   180.00   0.0  0
 CJC  CONST_26  C4   C3   C8   N13     0.00   0.0  0
 CJC  CONST_27  C22  N29  C28  C27     0.00   0.0  0
 CJC  CONST_28  S19  C20  C21  C22   180.00   0.0  0
 CJC  CONST_29  S19  C20  C25  N24   180.00   0.0  0
 CJC  CONST_30  C8   N9   C10  S19   180.00   0.0  0
 CJC  CONST_31  C2   N11  C10  S19   180.00   0.0  0
 CJC  CONST_32  CL1  C4   C3   C8      0.00   0.0  0
 CJC  CONST_33  C6   C5   C4   C3    180.00   0.0  0
 CJC  CONST_34  CL1  C4   C3   C2    180.00   0.0  0
 CJC  CONST_35  C6   C5   N1   C2    180.00   0.0  0
 CJC  CONST_36  CL1  C4   C5   N1    180.00   0.0  0
 CJC  CONST_37  C22  N29  C28  O47   180.00   0.0  0
 CJC  CONST_38  H4   C21  C22  N29     0.00   0.0  0
 CJC  CONST_39  H3   C25  N24  C23   180.00   0.0  0
 CJC  CONST_40  H15  N1   C2   C3    180.00   0.0  0
 CJC  CONST_41  H2   N29  C28  C27   180.00   0.0  0
 CJC  Var_01    C14  N13  C8   N9     -3.66  30.0  1
 CJC  Var_02    C15  C14  N13  C8    175.77  30.0  1
 CJC  Var_03    C16  C17  N13  C8   -148.82  30.0  1
 CJC  Var_04    C16  C15  C14  N13   -31.11  30.0  1
 CJC  Var_05    N9   C10  S19  C20   173.94  30.0  2
 CJC  Var_06    C7   C6   C5   N1    -84.48  30.0  2
 CJC  Var_07    H18  C7   C6   C5    -60.75  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
 CJC  chir_01  C16  N18  C15  C17  positiv

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
 CJC  plan-1  S19  0.020
 CJC  plan-1  C10  0.020
 CJC  plan-1  N9   0.020
 CJC  plan-1  C8   0.020
 CJC  plan-1  N13  0.020
 CJC  plan-1  C3   0.020
 CJC  plan-1  C2   0.020
 CJC  plan-1  N11  0.020
 CJC  plan-1  N1   0.020
 CJC  plan-1  C5   0.020
 CJC  plan-1  C4   0.020
 CJC  plan-1  CL1  0.020
 CJC  plan-1  C6   0.020
 CJC  plan-1  H15  0.020
 CJC  plan-2  O47  0.020
 CJC  plan-2  C28  0.020
 CJC  plan-2  C27  0.020
 CJC  plan-2  N29  0.020
 CJC  plan-2  C22  0.020
 CJC  plan-2  C23  0.020
 CJC  plan-2  N26  0.020
 CJC  plan-2  N24  0.020
 CJC  plan-2  C25  0.020
 CJC  plan-2  C20  0.020
 CJC  plan-2  C21  0.020
 CJC  plan-2  S19  0.020
 CJC  plan-2  H1   0.020
 CJC  plan-2  H2   0.020
 CJC  plan-2  H3   0.020
 CJC  plan-2  H4   0.020

