# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 21:02:35 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: (2R)-3-[4-amino-5-(4-chlorophenyl)-7-(2-methoxyethyl)-7H-pyrrolo[2,3-d]pyrimidin-6-yl]-2-cyano-N-(propan-2-yl)propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCn1c(C[C@H](C#N)C(=O)NC(C)C)c(c2ccc(Cl)cc2)c3c(N)ncnc13
#
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
 71D  71D  (2R)-3-[4-amino-5-(4-chlorophenyl)-7-(2-methoxyethyl)-7H-pyrrolo[2,3-d]pyrimidin-6-yl]-2-cyano-N-(propan-2-yl)propanamide  ligand  56  31  .  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_71D
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
 71D  C1   C   CR16  0   0.039   3.3560   3.3444   1.5444
 71D  C2   C   CR56  0   0.488   1.6217   2.1691   0.8551
 71D  C3   C   CR56  0  -0.071   2.4154   1.0708   0.5174
 71D  C4   C   CR5   0  -0.041   1.5453   0.0696  -0.0218
 71D  C5   C   CR6   0  -0.006   1.9116  -1.2756  -0.4849
 71D  C6   C   CR16  0  -0.321   1.6162  -1.6985  -1.7800
 71D  C13  C   CH1   0  -0.513  -1.7679  -0.5977   0.8837
 71D  C14  C   CSP   0   0.177  -1.0088  -1.6721   1.5065
 71D  C15  C   C     0   0.591  -3.1267  -1.1382   0.4246
 71D  C16  C   CH1   0  -0.100  -5.4974  -0.5225   0.1247
 71D  C17  C   CH3   0  -0.647  -6.3127  -1.1096   1.2704
 71D  C18  C   CH3   0  -0.664  -6.1031   0.7638  -0.4162
 71D  C20  C   CH2   0  -0.124  -0.9253   3.5835  -0.6610
 71D  O    O   O     0  -0.471  -3.2154  -2.2493  -0.0671
 71D  N4   N   NH1   0  -0.622  -4.1265  -0.2627   0.5459
 71D  N3   N   NS    0  -0.251  -0.4075  -2.5131   2.0086
 71D  C11  C   CR5   0   0.363   0.2820   0.6027   0.0128
 71D  N5   N   NR5   0  -0.572   0.3315   1.8729   0.5565
 71D  O1   O   O2    0  -0.482  -2.0423   4.4162  -0.5288
 71D  C21  C   CH3   0  -0.397  -2.3002   5.1673  -1.6891
 71D  N2   N   N     0  -0.465   2.0503   3.3228   1.3681
 71D  N1   N   N     0  -0.474   4.2384   2.3921   1.2551
 71D  C    C   CR6   0   0.403   3.8003   1.2457   0.7262
 71D  N    N   NH2   0  -0.824   4.7129   0.3096   0.4310
 71D  C10  C   CR16  0  -0.313   2.5670  -2.1632   0.3692
 71D  C9   C   CR16  0  -0.194   2.9199  -3.4349  -0.0517
 71D  C8   C   CR6   0  -0.052   2.6030  -3.8308  -1.3419
 71D  CL   CL  CL    0  -0.129   3.0346  -5.4228  -1.8744
 71D  C7   C   CR16  0  -0.198   1.9504  -2.9730  -2.2125
 71D  H1   H   HCR6  0   0.248   3.7696   4.2522   1.9710
 71D  H2   H   HCR6  0   0.267   1.1309  -1.0212  -2.4713
 71D  H3   H   HCH1  0   0.346  -1.8933   0.1832   1.6392
 71D  H4   H   HCH1  0   0.253  -5.4472  -1.2518  -0.6847
 71D  H5   H   HCH3  0   0.234  -7.3271  -1.3334   0.9391
 71D  H6   H   HCH3  0   0.238  -5.8659  -2.0348   1.6348
 71D  H7   H   HCH3  0   0.225  -6.3767  -0.4077   2.1039
 71D  H8   H   HCH3  0   0.228  -6.1348   1.5412   0.3503
 71D  H9   H   HCH3  0   0.242  -5.5307   1.1413  -1.2634
 71D  H10  H   HCH3  0   0.242  -7.1249   0.5872  -0.7506
 71D  H11  H   HCH2  0   0.287  -0.5618   3.4975   1.4658
 71D  H12  H   HCH2  0   0.254  -1.6828   2.2825   0.8859
 71D  H13  H   HCH2  0   0.215  -0.0117   4.1603  -0.8631
 71D  H14  H   HCH2  0   0.208  -1.0505   2.8807  -1.4980
 71D  H15  H   HNH1  0   0.403  -3.9629   0.5871   1.0641
 71D  H16  H   HCH2  0   0.307  -0.8504  -0.8358  -1.0597
 71D  H17  H   HCH2  0   0.297  -1.6762   0.6842  -0.8432
 71D  H18  H   HCH3  0   0.208  -1.4766   5.8502  -1.9278
 71D  H19  H   HCH3  0   0.208  -2.4705   4.5257  -2.5617
 71D  H20  H   HCH3  0   0.237  -3.1986   5.7575  -1.5140
 71D  H21  H   HNH2  0   0.411   4.4724  -0.5028  -0.1092
 71D  H22  H   HNH2  0   0.400   5.6883   0.5482   0.4928
 71D  H23  H   HCR6  0   0.267   2.7930  -1.8650   1.3849
 71D  H24  H   HCR6  0   0.283   3.4275  -4.1104   0.6233
 71D  H25  H   HCR6  0   0.282   1.7134  -3.2849  -3.2205
 71D  C19  C   CH2   0  -0.372  -0.7622   2.8139   0.6417
 71D  C12  C   CH2   0  -0.549  -1.0150  -0.0301  -0.3457

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
 71D  C21  O1   single    1.406  0.020  1.406
 71D  O1   C20  single    1.399  0.020  1.399
 71D  N3   C14  triple    1.149  0.020  1.149
 71D  C20  C19  single    1.522  0.020  1.522
 71D  C19  N5   single    1.445  0.020  1.445
 71D  C14  C13  single    1.455  0.020  1.455
 71D  N2   C1   aromatic  1.318  0.020  1.318
 71D  N2   C2   aromatic  1.333  0.020  1.333
 71D  N5   C2   aromatic  1.357  0.020  1.357
 71D  N5   C11  aromatic  1.383  0.020  1.383
 71D  O    C15  double    1.218  0.020  1.218
 71D  C18  C16  single    1.521  0.020  1.521
 71D  C1   N1   aromatic  1.330  0.020  1.330
 71D  C2   C3   aromatic  1.397  0.020  1.397
 71D  C15  C13  single    1.533  0.020  1.533
 71D  C15  N4   single    1.334  0.020  1.334
 71D  C13  C12  single    1.549  0.020  1.549
 71D  N4   C16  single    1.457  0.020  1.457
 71D  C11  C12  single    1.487  0.020  1.487
 71D  C11  C4   aromatic  1.372  0.020  1.372
 71D  N1   C    aromatic  1.336  0.020  1.336
 71D  C3   C    aromatic  1.411  0.020  1.411
 71D  C3   C4   aromatic  1.432  0.020  1.432
 71D  C16  C17  single    1.524  0.020  1.524
 71D  C    N    single    1.340  0.020  1.340
 71D  C4   C5   single    1.469  0.020  1.469
 71D  C6   C5   aromatic  1.394  0.020  1.394
 71D  C6   C7   aromatic  1.387  0.020  1.387
 71D  C5   C10  aromatic  1.395  0.020  1.395
 71D  C7   C8   aromatic  1.385  0.020  1.385
 71D  C10  C9   aromatic  1.385  0.020  1.385
 71D  C8   C9   aromatic  1.386  0.020  1.386
 71D  C8   CL   single    1.733  0.020  1.733
 71D  C1   H1   single    0.930  0.020  1.080
 71D  C6   H2   single    0.930  0.020  1.080
 71D  C13  H3   single    0.970  0.020  1.090
 71D  C16  H4   single    0.970  0.020  1.090
 71D  C17  H5   single    0.970  0.020  1.090
 71D  C17  H6   single    0.970  0.020  1.090
 71D  C17  H7   single    0.970  0.020  1.090
 71D  C18  H8   single    0.970  0.020  1.090
 71D  C18  H9   single    0.970  0.020  1.090
 71D  C18  H10  single    0.970  0.020  1.090
 71D  C19  H11  single    0.970  0.020  1.090
 71D  C19  H12  single    0.970  0.020  1.090
 71D  C20  H13  single    0.970  0.020  1.090
 71D  C20  H14  single    0.970  0.020  1.090
 71D  N4   H15  single    0.860  0.020  1.020
 71D  C12  H16  single    0.970  0.020  1.090
 71D  C12  H17  single    0.970  0.020  1.090
 71D  C21  H18  single    0.970  0.020  1.090
 71D  C21  H19  single    0.970  0.020  1.090
 71D  C21  H20  single    0.970  0.020  1.090
 71D  N    H21  single    0.860  0.020  1.020
 71D  N    H22  single    0.860  0.020  1.020
 71D  C10  H23  single    0.930  0.020  1.080
 71D  C9   H24  single    0.930  0.020  1.080
 71D  C7   H25  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
 71D  H1   C1   N1   115.58  3.000
 71D  H1   C1   N2   116.36  3.000
 71D  N1   C1   N2   128.06  3.000
 71D  N2   C2   N5   125.39  3.000
 71D  N5   C2   C3   108.39  3.000
 71D  N2   C2   C3   126.21  3.000
 71D  C    C3   C4   137.61  3.000
 71D  C4   C3   C2   107.20  3.000
 71D  C    C3   C2   115.11  3.000
 71D  C11  C4   C5   126.40  3.000
 71D  C5   C4   C3   127.41  3.000
 71D  C11  C4   C3   106.17  3.000
 71D  C10  C5   C6   118.37  3.000
 71D  C10  C5   C4   120.44  3.000
 71D  C6   C5   C4   121.19  3.000
 71D  H2   C6   C7   118.94  3.000
 71D  H2   C6   C5   119.89  3.000
 71D  C7   C6   C5   121.16  3.000
 71D  H3   C13  C12  110.01  3.000
 71D  H3   C13  C15  110.92  3.000
 71D  C12  C13  C15  108.80  3.000
 71D  H3   C13  C14  106.93  3.000
 71D  C12  C13  C14  110.89  3.000
 71D  C15  C13  C14  109.28  3.000
 71D  N3   C14  C13  180.00  3.000
 71D  N4   C15  O    125.49  3.000
 71D  N4   C15  C13  113.93  3.000
 71D  O    C15  C13  120.47  3.000
 71D  H4   C16  N4   106.88  3.000
 71D  H4   C16  C18  108.65  3.000
 71D  N4   C16  C18  109.06  3.000
 71D  H4   C16  C17  108.96  3.000
 71D  N4   C16  C17  110.77  3.000
 71D  C18  C16  C17  112.34  3.000
 71D  H7   C17  H6   108.33  3.000
 71D  H7   C17  H5   108.03  3.000
 71D  H6   C17  H5   107.98  3.000
 71D  H7   C17  C16  110.96  3.000
 71D  H6   C17  C16  111.04  3.000
 71D  H5   C17  C16  110.39  3.000
 71D  H10  C18  H9   108.06  3.000
 71D  H10  C18  H8   107.67  3.000
 71D  H9   C18  H8   108.31  3.000
 71D  H10  C18  C16  110.21  3.000
 71D  H9   C18  C16  111.11  3.000
 71D  H8   C18  C16  111.34  3.000
 71D  H14  C20  H13  106.85  3.000
 71D  H14  C20  O1   111.17  3.000
 71D  H13  C20  O1   111.63  3.000
 71D  H14  C20  C19  109.90  3.000
 71D  H13  C20  C19  109.49  3.000
 71D  O1   C20  C19  107.79  3.000
 71D  H15  N4   C16  116.82  3.000
 71D  H15  N4   C15  118.55  3.000
 71D  C16  N4   C15  124.16  3.000
 71D  N5   C11  C12  121.13  3.000
 71D  C12  C11  C4   129.19  3.000
 71D  N5   C11  C4   109.51  3.000
 71D  C11  N5   C19  126.46  3.000
 71D  C11  N5   C2   108.73  3.000
 71D  C19  N5   C2   124.36  3.000
 71D  C21  O1   C20  112.72  3.000
 71D  H20  C21  H19  108.48  3.000
 71D  H20  C21  H18  108.49  3.000
 71D  H19  C21  H18  107.94  3.000
 71D  H20  C21  O1   107.94  3.000
 71D  H19  C21  O1   111.88  3.000
 71D  H18  C21  O1   112.01  3.000
 71D  C2   N2   C1   112.59  3.000
 71D  C    N1   C1   118.86  3.000
 71D  N    C    N1   117.58  3.000
 71D  N    C    C3   123.30  3.000
 71D  N1   C    C3   119.12  3.000
 71D  H22  N    H21  117.19  3.000
 71D  H22  N    C    118.74  3.000
 71D  H21  N    C    121.34  3.000
 71D  H23  C10  C9   119.00  3.000
 71D  H23  C10  C5   119.82  3.000
 71D  C9   C10  C5   121.18  3.000
 71D  H24  C9   C8   120.65  3.000
 71D  H24  C9   C10  120.22  3.000
 71D  C8   C9   C10  119.12  3.000
 71D  C7   C8   CL   119.53  3.000
 71D  CL   C8   C9   119.42  3.000
 71D  C7   C8   C9   121.04  3.000
 71D  H25  C7   C8   120.69  3.000
 71D  H25  C7   C6   120.19  3.000
 71D  C8   C7   C6   119.12  3.000
 71D  H12  C19  H11  106.96  3.000
 71D  H12  C19  N5   109.55  3.000
 71D  H11  C19  N5   108.29  3.000
 71D  H12  C19  C20  110.34  3.000
 71D  H11  C19  C20  110.49  3.000
 71D  N5   C19  C20  111.10  3.000
 71D  H17  C12  H16  106.05  3.000
 71D  H17  C12  C11  111.06  3.000
 71D  H16  C12  C11  109.94  3.000
 71D  H17  C12  C13  107.85  3.000
 71D  H16  C12  C13  108.82  3.000
 71D  C11  C12  C13  112.86  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
 71D  CONST_01  N5   C2   N2   C1    180.00   0.0  0
 71D  CONST_02  C3   C2   N2   C1      0.00   0.0  0
 71D  CONST_03  C3   C    N1   C1      0.00   0.0  0
 71D  CONST_04  N1   C1   N2   C2      0.00   0.0  0
 71D  CONST_05  C4   C11  N5   C2      0.00   0.0  0
 71D  CONST_06  N1   C    C3   C2      0.00   0.0  0
 71D  CONST_07  C11  C4   C3   C2      0.00   0.0  0
 71D  CONST_08  C5   C4   C3   C2    180.00   0.0  0
 71D  CONST_09  C11  N5   C2   C3      0.00   0.0  0
 71D  CONST_10  N5   C11  C4   C3      0.00   0.0  0
 71D  CONST_13  N2   C2   C3   C4    180.00   0.0  0
 71D  CONST_14  N5   C2   C3   C4      0.00   0.0  0
 71D  CONST_15  N1   C    C3   C4    180.00   0.0  0
 71D  CONST_16  C7   C6   C5   C4    180.00   0.0  0
 71D  CONST_17  C9   C10  C5   C4    180.00   0.0  0
 71D  CONST_18  N5   C11  C4   C5    180.00   0.0  0
 71D  CONST_19  C    C3   C4   C5      0.00   0.0  0
 71D  CONST_20  C8   C7   C6   C5      0.00   0.0  0
 71D  CONST_21  C8   C9   C10  C5      0.00   0.0  0
 71D  CONST_23  C9   C10  C5   C6      0.00   0.0  0
 71D  CONST_24  C9   C8   C7   C6      0.00   0.0  0
 71D  CONST_25  N2   C2   N5   C11   180.00   0.0  0
 71D  CONST_26  C    C3   C4   C11   180.00   0.0  0
 71D  CONST_28  C    C3   C2   N5    180.00   0.0  0
 71D  CONST_29  C    N1   C1   N2      0.00   0.0  0
 71D  CONST_30  C    C3   C2   N2      0.00   0.0  0
 71D  CONST_31  C7   C6   C5   C10     0.00   0.0  0
 71D  CONST_32  C7   C8   C9   C10     0.00   0.0  0
 71D  CONST_33  N    C    N1   C1    180.00   0.0  0
 71D  CONST_34  C12  C11  N5   C2    180.00   0.0  0
 71D  CONST_35  N    C    C3   C2    180.00   0.0  0
 71D  CONST_36  C19  N5   C2   C3    180.00   0.0  0
 71D  CONST_37  C12  C11  C4   C3    180.00   0.0  0
 71D  CONST_38  C19  N5   C11  C4    180.00   0.0  0
 71D  CONST_39  N    C    C3   C4      0.00   0.0  0
 71D  CONST_40  C12  C11  C4   C5      0.00   0.0  0
 71D  CONST_41  CL   C8   C7   C6    180.00   0.0  0
 71D  CONST_42  N2   C2   N5   C19     0.00   0.0  0
 71D  CONST_43  CL   C8   C9   C10   180.00   0.0  0
 71D  CONST_44  H1   C1   N2   C2    180.00   0.0  0
 71D  CONST_45  H2   C6   C5   C4      0.00   0.0  0
 71D  CONST_46  H23  C10  C5   C4      0.00   0.0  0
 71D  CONST_47  H25  C7   C6   C5    180.00   0.0  0
 71D  CONST_48  H24  C9   C10  C5    180.00   0.0  0
 71D  CONST_49  H21  N    C    C3      0.00   0.0  0
 71D  CONST_50  H22  N    C    C3    180.00   0.0  0
 71D  CONST_51  C16  N4   C15  C13   180.00   0.0  0
 71D  CONST_52  O    C15  N4   C16     0.00   0.0  0
 71D  CONST_53  H15  N4   C15  C13     0.00   0.0  0
 71D  Var_01    C20  C19  N5   C2     88.27  30.0  2
 71D  Var_02    C13  C12  C11  C4     96.41  30.0  2
 71D  Var_03    O1   C20  C19  N5    176.78  30.0  2
 71D  Var_04    C18  C16  N4   C15  -144.59  30.0  3
 71D  Var_05    H8   C18  C16  C17    61.79  30.0  3
 71D  Var_06    H5   C17  C16  C18    59.71  30.0  3
 71D  Var_07    H18  C21  O1   C20   -62.54  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
 71D  chir_01  C13  C14  C15  C12  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
 71D  plan-1  C4   0.020
 71D  plan-1  C5   0.020
 71D  plan-1  C6   0.020
 71D  plan-1  C10  0.020
 71D  plan-1  C9   0.020
 71D  plan-1  C8   0.020
 71D  plan-1  CL   0.020
 71D  plan-1  C7   0.020
 71D  plan-1  H2   0.020
 71D  plan-1  H23  0.020
 71D  plan-1  H24  0.020
 71D  plan-1  H25  0.020
 71D  plan-2  C1   0.020
 71D  plan-2  C2   0.020
 71D  plan-2  C3   0.020
 71D  plan-2  C4   0.020
 71D  plan-2  C5   0.020
 71D  plan-2  C11  0.020
 71D  plan-2  N5   0.020
 71D  plan-2  N2   0.020
 71D  plan-2  N1   0.020
 71D  plan-2  C    0.020
 71D  plan-2  N    0.020
 71D  plan-2  H1   0.020
 71D  plan-2  C19  0.020
 71D  plan-2  C12  0.020
 71D  plan-3  C13  0.020
 71D  plan-3  C15  0.020
 71D  plan-3  C16  0.020
 71D  plan-3  O    0.020
 71D  plan-3  N4   0.020
 71D  plan-3  H15  0.020
 71D  plan-4  C    0.020
 71D  plan-4  N    0.020
 71D  plan-4  H21  0.020
 71D  plan-4  H22  0.020

