# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 04:42:14 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: (3R)-1-[5-chloro-6-ethyl-2-(pyrido[2,3-b]pyrazin-7-ylsulfanyl)-7H-pyrrolo[2,3-d]pyrimidin-4-yl]pyrrolidin-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1[nH]c2nc(Sc3cnc4nccnc4c3)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
 1A0  1A0  (3R)-1-[5-chloro-6-ethyl-2-(pyrido[2,3-b]pyrazin-7-ylsulfanyl)-7H-pyrrolo[2,3-d]pyrimidin-4-yl]pyrrolidin-3-amine  ligand  48  29  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1A0
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
 1A0  CL1  CL  CL    0  -0.152   4.1992   2.3500   0.2359
 1A0  C4   C   CR5   0  -0.314   2.5434   1.9512   0.0021
 1A0  C5   C   CR5   0   0.427   1.6320   2.9156  -0.3219
 1A0  C6   C   CH2   0  -0.512   1.8272   4.3587  -0.6258
 1A0  C7   C   CH3   0  -0.654   2.1112   4.6118  -2.1070
 1A0  N1   N   NR15  0  -0.709   0.3994   2.3202  -0.3751
 1A0  C3   C   CR56  0   0.061   1.8558   0.6969   0.1553
 1A0  C8   C   CR6   0   0.495   2.0874  -0.6749   0.4727
 1A0  N13  N   NT    0  -0.494   3.2729  -1.2784   0.6272
 1A0  C17  C   CH2   0  -0.278   4.5698  -0.7846   0.1799
 1A0  C16  C   CH1   0  -0.142   5.3731  -2.0569  -0.0742
 1A0  N18  N   NH2   0  -0.788   5.1620  -2.5292  -1.4336
 1A0  C15  C   CH2   0  -0.489   4.8394  -2.9731   1.0303
 1A0  C14  C   CH2   0  -0.276   3.3444  -2.6862   1.0273
 1A0  N9   N   N     0  -0.503   1.0224  -1.4738   0.6378
 1A0  C10  C   CR6   0   0.213  -0.1927  -1.0056   0.4255
 1A0  N11  N   N     0  -0.437  -0.5490   0.1935   0.0470
 1A0  C2   C   CR56  0   0.466   0.4996   1.0121  -0.0678
 1A0  S19  S   S2    0   0.091  -1.4326  -2.2444   0.6997
 1A0  C20  C   CR6   0  -0.207  -2.9136  -1.3547   0.3563
 1A0  C25  C   CR16  0  -0.012  -3.2017  -0.9222  -0.9647
 1A0  N24  N   N     0  -0.406  -4.2981  -0.3085  -1.3049
 1A0  C23  C   CR66  0   0.350  -5.2235  -0.0804  -0.3501
 1A0  N26  N   N     0  -0.357  -6.3520   0.5505  -0.7308
 1A0  C27  C   CR16  0  -0.090  -7.2447   0.7680   0.1943
 1A0  C28  C   CR16  0  -0.117  -7.0569   0.3679   1.5397
 1A0  N29  N   N     0  -0.372  -5.9771  -0.2466   1.9327
 1A0  C22  C   CR66  0   0.149  -5.0396  -0.4825   0.9907
 1A0  C21  C   CR16  0  -0.167  -3.8366  -1.1340   1.3372
 1A0  H1   H   HCH2  0   0.260   0.9392   4.9151  -0.3181
 1A0  H2   H   HCH2  0   0.254   2.6527   4.7400  -0.0237
 1A0  H3   H   HCH3  0   0.229   3.0166   4.0943  -2.4238
 1A0  H4   H   HCH3  0   0.230   1.2888   4.2648  -2.7325
 1A0  H5   H   HCH3  0   0.239   2.2483   5.6770  -2.2921
 1A0  H6   H   HNR5  0   0.417  -0.4690   2.7981  -0.5607
 1A0  H7   H   HCH2  0   0.252   4.4785  -0.1861  -0.7255
 1A0  H8   H   HCH2  0   0.249   5.0509  -0.1815   0.9513
 1A0  H9   H   HCH1  0   0.254   6.4388  -1.8581   0.0527
 1A0  H10  H   HNH2  0   0.350   5.6299  -3.4181  -1.5606
 1A0  H11  H   HNH2  0   0.344   4.1785  -2.7097  -1.6010
 1A0  H13  H   HCH2  0   0.255   5.0577  -4.0264   0.8535
 1A0  H14  H   HCH2  0   0.241   5.2801  -2.6962   1.9911
 1A0  H15  H   HCH2  0   0.255   2.8792  -2.8431   2.0005
 1A0  H16  H   HCH2  0   0.237   2.8130  -3.3189   0.3116
 1A0  H17  H   HCR6  0   0.284  -2.4782  -1.1103  -1.7503
 1A0  H18  H   HCR6  0   0.290  -8.1589   1.2750  -0.0915
 1A0  H19  H   HCR6  0   0.287  -7.8250   0.5712   2.2762
 1A0  H20  H   HCR6  0   0.300  -3.6710  -1.4379   2.3629

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
 1A0  C27  N26  aromatic  1.304  0.020  1.304
 1A0  C27  C28  aromatic  1.416  0.020  1.416
 1A0  N26  C23  aromatic  1.348  0.020  1.348
 1A0  C28  N29  aromatic  1.303  0.020  1.303
 1A0  C23  N24  aromatic  1.349  0.020  1.349
 1A0  C23  C22  aromatic  1.412  0.020  1.412
 1A0  N24  C25  aromatic  1.302  0.020  1.302
 1A0  N29  C22  aromatic  1.350  0.020  1.350
 1A0  C22  C21  aromatic  1.411  0.020  1.411
 1A0  C25  C20  aromatic  1.420  0.020  1.420
 1A0  C21  C20  aromatic  1.365  0.020  1.365
 1A0  C20  S19  single    1.762  0.020  1.762
 1A0  N18  C16  single    1.454  0.020  1.454
 1A0  S19  C10  single    1.774  0.020  1.774
 1A0  C15  C14  single    1.522  0.020  1.522
 1A0  C15  C16  single    1.531  0.020  1.531
 1A0  C14  N13  single    1.465  0.020  1.465
 1A0  C16  C17  single    1.526  0.020  1.526
 1A0  C10  N9   aromatic  1.319  0.020  1.319
 1A0  C10  N11  aromatic  1.307  0.020  1.307
 1A0  N9   C8   aromatic  1.341  0.020  1.341
 1A0  N13  C8   single    1.339  0.020  1.339
 1A0  N13  C17  single    1.458  0.020  1.458
 1A0  N11  C2   aromatic  1.335  0.020  1.335
 1A0  C8   C3   aromatic  1.427  0.020  1.427
 1A0  C2   C3   aromatic  1.410  0.020  1.410
 1A0  C2   N1   aromatic  1.347  0.020  1.347
 1A0  C3   C4   aromatic  1.439  0.020  1.439
 1A0  N1   C5   aromatic  1.370  0.020  1.370
 1A0  C4   C5   aromatic  1.366  0.020  1.366
 1A0  C4   CL1  single    1.719  0.020  1.719
 1A0  C5   C6   single    1.488  0.020  1.488
 1A0  C6   C7   single    1.529  0.020  1.529
 1A0  C6   H1   single    0.970  0.020  1.090
 1A0  C6   H2   single    0.970  0.020  1.090
 1A0  C7   H3   single    0.970  0.020  1.090
 1A0  C7   H4   single    0.970  0.020  1.090
 1A0  C7   H5   single    0.970  0.020  1.090
 1A0  N1   H6   single    0.860  0.020  1.020
 1A0  C17  H7   single    0.970  0.020  1.090
 1A0  C17  H8   single    0.970  0.020  1.090
 1A0  C16  H9   single    0.970  0.020  1.090
 1A0  N18  H10  single    0.890  0.020  1.040
 1A0  N18  H11  single    0.890  0.020  1.040
 1A0  C15  H13  single    0.970  0.020  1.090
 1A0  C15  H14  single    0.970  0.020  1.090
 1A0  C14  H15  single    0.970  0.020  1.090
 1A0  C14  H16  single    0.970  0.020  1.090
 1A0  C25  H17  single    0.930  0.020  1.080
 1A0  C27  H18  single    0.930  0.020  1.080
 1A0  C28  H19  single    0.930  0.020  1.080
 1A0  C21  H20  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
 1A0  C3   C4   C5   108.78  3.000
 1A0  C5   C4   CL1  120.74  3.000
 1A0  C3   C4   CL1  130.41  3.000
 1A0  N1   C5   C6   122.12  3.000
 1A0  C6   C5   C4   130.23  3.000
 1A0  N1   C5   C4   107.62  3.000
 1A0  H2   C6   H1   106.37  3.000
 1A0  H2   C6   C7   109.65  3.000
 1A0  H1   C6   C7   109.85  3.000
 1A0  H2   C6   C5   109.01  3.000
 1A0  H1   C6   C5   109.27  3.000
 1A0  C7   C6   C5   112.51  3.000
 1A0  H5   C7   H4   107.97  3.000
 1A0  H5   C7   H3   108.07  3.000
 1A0  H4   C7   H3   107.99  3.000
 1A0  H5   C7   C6   110.46  3.000
 1A0  H4   C7   C6   111.29  3.000
 1A0  H3   C7   C6   110.93  3.000
 1A0  H6   N1   C2   124.48  3.000
 1A0  H6   N1   C5   125.17  3.000
 1A0  C2   N1   C5   110.25  3.000
 1A0  C2   C3   C8   113.96  3.000
 1A0  C2   C3   C4   104.36  3.000
 1A0  C8   C3   C4   141.66  3.000
 1A0  N9   C8   N13  114.85  3.000
 1A0  N13  C8   C3   127.05  3.000
 1A0  N9   C8   C3   118.10  3.000
 1A0  C14  N13  C17  111.45  3.000
 1A0  C17  N13  C8   126.83  3.000
 1A0  C14  N13  C8   120.51  3.000
 1A0  H8   C17  H7   108.72  3.000
 1A0  H8   C17  C16  110.28  3.000
 1A0  H7   C17  C16  111.33  3.000
 1A0  H8   C17  N13  111.26  3.000
 1A0  H7   C17  N13  111.50  3.000
 1A0  C16  C17  N13  103.71  3.000
 1A0  H9   C16  C15  111.44  3.000
 1A0  H9   C16  N18  108.03  3.000
 1A0  C15  C16  N18  115.42  3.000
 1A0  H9   C16  C17  110.04  3.000
 1A0  C15  C16  C17  101.26  3.000
 1A0  N18  C16  C17  110.48  3.000
 1A0  H11  N18  H10  105.74  3.000
 1A0  H11  N18  C16  110.67  3.000
 1A0  H10  N18  C16  109.59  3.000
 1A0  H14  C15  H13  107.86  3.000
 1A0  H14  C15  C14  110.49  3.000
 1A0  H13  C15  C14  112.24  3.000
 1A0  H14  C15  C16  110.00  3.000
 1A0  H13  C15  C16  113.04  3.000
 1A0  C14  C15  C16  103.19  3.000
 1A0  H16  C14  H15  107.08  3.000
 1A0  H16  C14  C15  111.69  3.000
 1A0  H15  C14  C15  112.97  3.000
 1A0  H16  C14  N13  110.70  3.000
 1A0  H15  C14  N13  111.18  3.000
 1A0  C15  C14  N13  103.28  3.000
 1A0  C10  N9   C8   120.00  3.000
 1A0  S19  C10  N11  119.66  3.000
 1A0  N11  C10  N9   128.56  3.000
 1A0  S19  C10  N9   111.78  3.000
 1A0  C2   N11  C10  111.92  3.000
 1A0  N11  C2   C3   127.20  3.000
 1A0  C3   C2   N1   108.94  3.000
 1A0  N11  C2   N1   123.81  3.000
 1A0  C20  S19  C10  101.82  3.000
 1A0  C21  C20  C25  118.83  3.000
 1A0  C21  C20  S19  120.68  3.000
 1A0  C25  C20  S19  120.39  3.000
 1A0  H17  C25  N24  117.02  3.000
 1A0  H17  C25  C20  119.07  3.000
 1A0  N24  C25  C20  123.90  3.000
 1A0  C23  N24  C25  118.19  3.000
 1A0  C22  C23  N26  120.71  3.000
 1A0  C22  C23  N24  122.32  3.000
 1A0  N26  C23  N24  116.97  3.000
 1A0  C27  N26  C23  116.80  3.000
 1A0  H18  C27  C28  119.64  3.000
 1A0  H18  C27  N26  117.94  3.000
 1A0  C28  C27  N26  122.43  3.000
 1A0  H19  C28  N29  118.10  3.000
 1A0  H19  C28  C27  119.92  3.000
 1A0  N29  C28  C27  121.98  3.000
 1A0  C22  N29  C28  116.59  3.000
 1A0  C21  C22  N29  120.09  3.000
 1A0  C21  C22  C23  118.41  3.000
 1A0  N29  C22  C23  121.50  3.000
 1A0  H20  C21  C22  119.52  3.000
 1A0  H20  C21  C20  122.14  3.000
 1A0  C22  C21  C20  118.34  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
 1A0  CONST_01  N9   C8   C3   C4    180.00   0.0  0
 1A0  CONST_02  N11  C2   C3   C4    180.00   0.0  0
 1A0  CONST_03  N1   C2   C3   C4      0.00   0.0  0
 1A0  CONST_04  C2   N1   C5   C4      0.00   0.0  0
 1A0  CONST_05  N11  C2   N1   C5    180.00   0.0  0
 1A0  CONST_06  C3   C2   N1   C5      0.00   0.0  0
 1A0  CONST_07  C8   C3   C4   C5    180.00   0.0  0
 1A0  CONST_08  C2   C3   C4   C5      0.00   0.0  0
 1A0  CONST_09  C10  N11  C2   N1    180.00   0.0  0
 1A0  CONST_10  C8   C3   C2   N1    180.00   0.0  0
 1A0  CONST_11  C3   C4   C5   N1      0.00   0.0  0
 1A0  CONST_12  C10  N9   C8   C3      0.00   0.0  0
 1A0  CONST_13  C10  N11  C2   C3      0.00   0.0  0
 1A0  CONST_14  N11  C10  N9   C8      0.00   0.0  0
 1A0  CONST_15  N11  C2   C3   C8      0.00   0.0  0
 1A0  CONST_16  C2   N11  C10  N9      0.00   0.0  0
 1A0  CONST_17  C2   C3   C8   N9      0.00   0.0  0
 1A0  CONST_18  C23  N24  C25  C20     0.00   0.0  0
 1A0  CONST_19  C23  C22  C21  C20     0.00   0.0  0
 1A0  CONST_20  N29  C22  C21  C20   180.00   0.0  0
 1A0  CONST_21  N26  C23  N24  C25   180.00   0.0  0
 1A0  CONST_22  C22  C23  N24  C25     0.00   0.0  0
 1A0  CONST_23  C22  C21  C20  C25     0.00   0.0  0
 1A0  CONST_24  C27  N26  C23  N24   180.00   0.0  0
 1A0  CONST_25  N29  C22  C23  N24   180.00   0.0  0
 1A0  CONST_26  C21  C22  C23  N24     0.00   0.0  0
 1A0  CONST_27  C21  C20  C25  N24     0.00   0.0  0
 1A0  CONST_28  C28  C27  N26  C23     0.00   0.0  0
 1A0  CONST_29  C28  N29  C22  C23     0.00   0.0  0
 1A0  CONST_30  N29  C28  C27  N26     0.00   0.0  0
 1A0  CONST_31  N29  C22  C23  N26     0.00   0.0  0
 1A0  CONST_32  C21  C22  C23  N26   180.00   0.0  0
 1A0  CONST_33  C22  C23  N26  C27     0.00   0.0  0
 1A0  CONST_34  C22  N29  C28  C27     0.00   0.0  0
 1A0  CONST_35  C21  C22  N29  C28   180.00   0.0  0
 1A0  CONST_36  N13  C8   C3   C4      0.00   0.0  0
 1A0  CONST_37  C10  N9   C8   N13   180.00   0.0  0
 1A0  CONST_38  C2   C3   C8   N13   180.00   0.0  0
 1A0  CONST_39  C8   C3   C4   CL1     0.00   0.0  0
 1A0  CONST_40  C2   C3   C4   CL1   180.00   0.0  0
 1A0  CONST_41  N1   C5   C4   CL1   180.00   0.0  0
 1A0  CONST_42  C2   N1   C5   C6    180.00   0.0  0
 1A0  CONST_43  C3   C4   C5   C6    180.00   0.0  0
 1A0  CONST_44  S19  C10  N9   C8    180.00   0.0  0
 1A0  CONST_45  S19  C10  N11  C2    180.00   0.0  0
 1A0  CONST_46  N24  C25  C20  S19   180.00   0.0  0
 1A0  CONST_47  C22  C21  C20  S19   180.00   0.0  0
 1A0  CONST_48  H6   N1   C5   C4    180.00   0.0  0
 1A0  CONST_49  H20  C21  C20  C25   180.00   0.0  0
 1A0  CONST_50  H18  C27  N26  C23   180.00   0.0  0
 1A0  CONST_51  H17  C25  N24  C23   180.00   0.0  0
 1A0  CONST_52  H19  C28  C27  N26   180.00   0.0  0
 1A0  Var_01    C14  N13  C8   C3    176.60  30.0  1
 1A0  Var_02    C15  C14  N13  C8    177.89  30.0  1
 1A0  Var_03    C16  C17  N13  C8   -151.05  30.0  1
 1A0  Var_04    C16  C15  C14  N13   -31.58  30.0  1
 1A0  Var_05    C25  C20  S19  C10    67.85  30.0  2
 1A0  Var_06    C7   C6   C5   C4     88.00  30.0  2
 1A0  Var_07    H3   C7   C6   C5    -60.19  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
 1A0  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
 1A0  plan-1  CL1  0.020
 1A0  plan-1  C4   0.020
 1A0  plan-1  C5   0.020
 1A0  plan-1  C6   0.020
 1A0  plan-1  N1   0.020
 1A0  plan-1  C3   0.020
 1A0  plan-1  C8   0.020
 1A0  plan-1  N13  0.020
 1A0  plan-1  N9   0.020
 1A0  plan-1  C10  0.020
 1A0  plan-1  N11  0.020
 1A0  plan-1  C2   0.020
 1A0  plan-1  S19  0.020
 1A0  plan-1  H6   0.020
 1A0  plan-2  S19  0.020
 1A0  plan-2  C20  0.020
 1A0  plan-2  C25  0.020
 1A0  plan-2  N24  0.020
 1A0  plan-2  C23  0.020
 1A0  plan-2  N26  0.020
 1A0  plan-2  C27  0.020
 1A0  plan-2  C28  0.020
 1A0  plan-2  N29  0.020
 1A0  plan-2  C22  0.020
 1A0  plan-2  C21  0.020
 1A0  plan-2  H17  0.020
 1A0  plan-2  H18  0.020
 1A0  plan-2  H19  0.020
 1A0  plan-2  H20  0.020

