# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 16:32:26 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: 2-[(3,5-dimethoxyphenyl)amino]-5-ethyl-7-[(2R)-2-(hydroxymethyl)pyrrolidin-1-yl]pyrazolo[1,5-a]pyrimidine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1cc(N2CCC[C@@H]2CO)n3nc(Nc4cc(OC)cc(OC)c4)c(C(N)=O)c3n1
#
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
 KSH  KSH  2-[(3,5-dimethoxyphenyl)amino]-5-ethyl-7-[(2R)-2-(hydroxymethyl)pyrrolidin-1-yl]pyrazolo[1,5-a]pyrimidine-3-carboxamide  ligand  60  32  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_KSH
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
 KSH  N1    N  N     0  -0.442   1.5015   0.2329  -0.3389
 KSH  C2    C  CR6   0   0.730   2.3651  -0.8178  -0.4110
 KSH  C3    C  CR16  0  -0.515   3.7166  -0.4543  -0.4606
 KSH  C4    C  CR6   0   0.290   4.0942   0.8835  -0.4576
 KSH  N5    N  N     0  -0.516   3.2204   1.8809  -0.4034
 KSH  C6    C  CR56  0   0.660   1.9397   1.5394  -0.3386
 KSH  C7    C  CR5   0  -0.509   0.7923   2.3239  -0.2285
 KSH  C8    C  CR5   0   0.607  -0.2683   1.3832  -0.1476
 KSH  N9    N  N     0  -0.388   0.1557   0.1362  -0.2038
 KSH  C10   C  C     0   0.495   0.6867   3.7732  -0.1807
 KSH  O11   O  O     0  -0.522  -0.4121   4.3334  -0.0837
 KSH  N12   N  NH2   0  -0.839   1.8410   4.4539  -0.2461
 KSH  N16   N  NH1   0  -0.803  -1.5739   1.7387  -0.0193
 KSH  C17   C  CR6   0   0.410  -2.7105   0.9537   0.0503
 KSH  C18   C  CR16  0  -0.489  -2.6904  -0.4390   0.0170
 KSH  C19   C  CR6   0   0.447  -3.8931  -1.1377   0.0924
 KSH  C20   C  CR16  0  -0.561  -5.1167  -0.4821   0.2030
 KSH  C21   C  CR6   0   0.433  -5.1155   0.9139   0.2370
 KSH  C22   C  CR16  0  -0.505  -3.9295   1.6299   0.1605
 KSH  O26   O  O2    0  -0.477  -6.2382   1.6495   0.3457
 KSH  C27   C  CH3   0  -0.437  -7.4826   0.9870   0.4477
 KSH  O31   O  O2    0  -0.474  -3.7766  -2.4788   0.0510
 KSH  C32   C  CH3   0  -0.439  -4.9415  -3.2715   0.1543
 KSH  C37   C  CH2   0  -0.499   5.5452   1.2601  -0.4778
 KSH  C38   C  CH3   0  -0.663   6.0182   1.7043   0.9060
 KSH  N42   N  NT    0  -0.514   1.9250  -2.0771  -0.4193
 KSH  C43   C  CH2   0  -0.280   0.6178  -2.5459  -0.8955
 KSH  C44   C  CH2   0  -0.466   0.9426  -3.9232  -1.4493
 KSH  C45   C  CH2   0  -0.473   1.9925  -4.4363  -0.4783
 KSH  C46   C  CH1   0  -0.103   2.8405  -3.2015  -0.1641
 KSH  C53   C  CH2   0  -0.168   3.3925  -3.1967   1.2515
 KSH  O55   O  OH1   0  -0.662   2.3231  -3.1453   2.1613
 KSH  H3    H  HCR6  0   0.288   4.4773  -1.2136  -0.5380
 KSH  HN12  H  HNH2  0   0.411   2.7262   3.9709  -0.3142
 KSH  HN1A  H  HNH2  0   0.397   1.8348   5.4596  -0.2172
 KSH  HN16  H  HNH1  0   0.414  -1.7024   2.7426   0.0145
 KSH  H18   H  HCR6  0   0.306  -1.7655  -0.9864  -0.0664
 KSH  H20   H  HCR6  0   0.297  -6.0397  -1.0397   0.2605
 KSH  H22   H  HCR6  0   0.262  -3.9573   2.7128   0.1865
 KSH  H27   H  HCH3  0   0.228  -7.5314   0.3404   1.3275
 KSH  H27A  H  HCH3  0   0.261  -8.2377   1.7632   0.5434
 KSH  H27B  H  HCH3  0   0.228  -7.7037   0.3908  -0.4414
 KSH  H32   H  HCH3  0   0.228  -5.4626  -3.1130   1.1022
 KSH  H32A  H  HCH3  0   0.228  -5.6401  -3.0852  -0.6655
 KSH  H32B  H  HCH3  0   0.260  -4.6141  -4.3072   0.1048
 KSH  H37   H  HCH2  0   0.246   6.1446   0.4159  -0.8212
 KSH  H37A  H  HCH2  0   0.251   5.6899   2.0729  -1.1923
 KSH  H38   H  HCH3  0   0.231   5.4448   2.5619   1.2569
 KSH  H38A  H  HCH3  0   0.229   5.9077   0.9013   1.6353
 KSH  H38B  H  HCH3  0   0.238   7.0693   1.9902   0.8774
 KSH  H43   H  HCH2  0   0.244  -0.0926  -2.6162  -0.0692
 KSH  H43A  H  HCH2  0   0.263   0.2047  -1.8787  -1.6460
 KSH  H44   H  HCH2  0   0.254   0.0585  -4.5575  -1.5011
 KSH  H44A  H  HCH2  0   0.240   1.3554  -3.8353  -2.4566
 KSH  H45   H  HCH2  0   0.246   1.5135  -4.8105   0.4277
 KSH  H45A  H  HCH2  0   0.258   2.6057  -5.2371  -0.8889
 KSH  H46   H  HCH1  0   0.269   3.6872  -3.1614  -0.8585
 KSH  H53   H  HCH2  0   0.216   3.9949  -4.1082   1.3635
 KSH  H53A  H  HCH2  0   0.217   4.0788  -2.3527   1.3915
 KSH  HO55  H  HOH1  0   0.459   2.6871  -3.1708   3.0505

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
 KSH  N1   C2    aromatic  1.362  0.020  1.362
 KSH  N1   C6    aromatic  1.378  0.020  1.378
 KSH  N1   N9    aromatic  1.356  0.020  1.356
 KSH  C2   C3    aromatic  1.400  0.020  1.400
 KSH  C2   N42   single    1.334  0.020  1.334
 KSH  C3   C4    aromatic  1.390  0.020  1.390
 KSH  C4   N5    aromatic  1.327  0.020  1.327
 KSH  C4   C37   single    1.499  0.020  1.499
 KSH  N5   C6    aromatic  1.327  0.020  1.327
 KSH  C6   C7    aromatic  1.394  0.020  1.394
 KSH  C7   C8    aromatic  1.420  0.020  1.420
 KSH  C7   C10   single    1.454  0.020  1.454
 KSH  C8   N9    aromatic  1.318  0.020  1.318
 KSH  C8   N16   single    1.359  0.020  1.359
 KSH  C10  O11   double    1.237  0.020  1.237
 KSH  C10  N12   single    1.342  0.020  1.342
 KSH  N16  C17   single    1.383  0.020  1.383
 KSH  C17  C18   aromatic  1.393  0.020  1.393
 KSH  C17  C22   aromatic  1.398  0.020  1.398
 KSH  C18  C19   aromatic  1.393  0.020  1.393
 KSH  C19  C20   aromatic  1.393  0.020  1.393
 KSH  C19  O31   single    1.347  0.020  1.347
 KSH  C20  C21   aromatic  1.396  0.020  1.396
 KSH  C21  C22   aromatic  1.388  0.020  1.388
 KSH  C21  O26   single    1.347  0.020  1.347
 KSH  O26  C27   single    1.413  0.020  1.413
 KSH  O31  C32   single    1.413  0.020  1.413
 KSH  C37  C38   single    1.528  0.020  1.528
 KSH  N42  C43   single    1.468  0.020  1.468
 KSH  N42  C46   single    1.472  0.020  1.472
 KSH  C43  C44   single    1.520  0.020  1.520
 KSH  C44  C45   single    1.519  0.020  1.519
 KSH  C45  C46   single    1.530  0.020  1.530
 KSH  C46  C53   single    1.520  0.020  1.520
 KSH  C53  O55   single    1.405  0.020  1.405
 KSH  C3   H3    single    0.930  0.020  1.080
 KSH  N12  HN12  single    0.860  0.020  1.020
 KSH  N12  HN1A  single    0.860  0.020  1.020
 KSH  N16  HN16  single    0.860  0.020  1.020
 KSH  C18  H18   single    0.930  0.020  1.080
 KSH  C20  H20   single    0.930  0.020  1.080
 KSH  C22  H22   single    0.930  0.020  1.080
 KSH  C27  H27   single    0.970  0.020  1.090
 KSH  C27  H27A  single    0.970  0.020  1.090
 KSH  C27  H27B  single    0.970  0.020  1.090
 KSH  C32  H32   single    0.970  0.020  1.090
 KSH  C32  H32A  single    0.970  0.020  1.090
 KSH  C32  H32B  single    0.970  0.020  1.090
 KSH  C37  H37   single    0.970  0.020  1.090
 KSH  C37  H37A  single    0.970  0.020  1.090
 KSH  C38  H38   single    0.970  0.020  1.090
 KSH  C38  H38A  single    0.970  0.020  1.090
 KSH  C38  H38B  single    0.970  0.020  1.090
 KSH  C43  H43   single    0.970  0.020  1.090
 KSH  C43  H43A  single    0.970  0.020  1.090
 KSH  C44  H44   single    0.970  0.020  1.090
 KSH  C44  H44A  single    0.970  0.020  1.090
 KSH  C45  H45   single    0.970  0.020  1.090
 KSH  C45  H45A  single    0.970  0.020  1.090
 KSH  C46  H46   single    0.970  0.020  1.090
 KSH  C53  H53   single    0.970  0.020  1.090
 KSH  C53  H53A  single    0.970  0.020  1.090
 KSH  O55  HO55  single    0.850  0.020  0.980

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
 KSH  N9    N1   C6    112.53  3.000
 KSH  N9    N1   C2    125.42  3.000
 KSH  C6    N1   C2    121.99  3.000
 KSH  N42   C2   C3    124.28  3.000
 KSH  N42   C2   N1    121.29  3.000
 KSH  C3    C2   N1    114.43  3.000
 KSH  H3    C3   C4    119.11  3.000
 KSH  H3    C3   C2    120.06  3.000
 KSH  C4    C3   C2    120.79  3.000
 KSH  C37   C4   N5    116.68  3.000
 KSH  C37   C4   C3    120.31  3.000
 KSH  N5    C4   C3    122.99  3.000
 KSH  C6    N5   C4    116.36  3.000
 KSH  C7    C6   N5    130.78  3.000
 KSH  C7    C6   N1    105.77  3.000
 KSH  N5    C6   N1    123.43  3.000
 KSH  C10   C7   C8    127.17  3.000
 KSH  C10   C7   C6    128.55  3.000
 KSH  C8    C7   C6    104.27  3.000
 KSH  N16   C8   N9    124.08  3.000
 KSH  N16   C8   C7    123.34  3.000
 KSH  N9    C8   C7    112.58  3.000
 KSH  C8    N9   N1    104.83  3.000
 KSH  N12   C10  O11   122.56  3.000
 KSH  N12   C10  C7    116.21  3.000
 KSH  O11   C10  C7    121.23  3.000
 KSH  HN1A  N12  HN12  119.01  3.000
 KSH  HN1A  N12  C10   120.03  3.000
 KSH  HN12  N12  C10   120.95  3.000
 KSH  HN16  N16  C17   117.17  3.000
 KSH  HN16  N16  C8    112.60  3.000
 KSH  C17   N16  C8    130.22  3.000
 KSH  C22   C17  C18   119.86  3.000
 KSH  C22   C17  N16   116.48  3.000
 KSH  C18   C17  N16   123.66  3.000
 KSH  H18   C18  C19   119.36  3.000
 KSH  H18   C18  C17   121.45  3.000
 KSH  C19   C18  C17   119.18  3.000
 KSH  O31   C19  C20   123.18  3.000
 KSH  O31   C19  C18   115.03  3.000
 KSH  C20   C19  C18   121.79  3.000
 KSH  H20   C20  C21   121.03  3.000
 KSH  H20   C20  C19   120.81  3.000
 KSH  C21   C20  C19   118.16  3.000
 KSH  O26   C21  C22   115.80  3.000
 KSH  O26   C21  C20   123.19  3.000
 KSH  C22   C21  C20   121.01  3.000
 KSH  H22   C22  C21   119.50  3.000
 KSH  H22   C22  C17   120.50  3.000
 KSH  C21   C22  C17   120.00  3.000
 KSH  C27   O26  C21   118.93  3.000
 KSH  H27B  C27  H27A  108.70  3.000
 KSH  H27B  C27  H27   108.85  3.000
 KSH  H27A  C27  H27   108.69  3.000
 KSH  H27B  C27  O26   112.03  3.000
 KSH  H27A  C27  O26   106.46  3.000
 KSH  H27   C27  O26   112.00  3.000
 KSH  C32   O31  C19   119.02  3.000
 KSH  H32B  C32  H32A  108.70  3.000
 KSH  H32B  C32  H32   108.73  3.000
 KSH  H32A  C32  H32   108.73  3.000
 KSH  H32B  C32  O31   106.43  3.000
 KSH  H32A  C32  O31   112.11  3.000
 KSH  H32   C32  O31   112.03  3.000
 KSH  H37A  C37  H37   107.30  3.000
 KSH  H37A  C37  C38   109.58  3.000
 KSH  H37   C37  C38   109.87  3.000
 KSH  H37A  C37  C4    108.91  3.000
 KSH  H37   C37  C4    109.97  3.000
 KSH  C38   C37  C4    111.12  3.000
 KSH  H38B  C38  H38A  107.97  3.000
 KSH  H38B  C38  H38   108.03  3.000
 KSH  H38A  C38  H38   108.11  3.000
 KSH  H38B  C38  C37   110.55  3.000
 KSH  H38A  C38  C37   111.12  3.000
 KSH  H38   C38  C37   110.94  3.000
 KSH  C46   N42  C43   111.47  3.000
 KSH  C46   N42  C2    120.98  3.000
 KSH  C43   N42  C2    126.67  3.000
 KSH  H43A  C43  H43   108.37  3.000
 KSH  H43A  C43  C44   112.73  3.000
 KSH  H43   C43  C44   110.88  3.000
 KSH  H43A  C43  N42   111.52  3.000
 KSH  H43   C43  N42   110.76  3.000
 KSH  C44   C43  N42   102.55  3.000
 KSH  H44A  C44  H44   108.04  3.000
 KSH  H44A  C44  C45   110.82  3.000
 KSH  H44   C44  C45   113.24  3.000
 KSH  H44A  C44  C43   110.12  3.000
 KSH  H44   C44  C43   111.81  3.000
 KSH  C45   C44  C43   102.76  3.000
 KSH  H45A  C45  H45   107.95  3.000
 KSH  H45A  C45  C46   111.02  3.000
 KSH  H45   C45  C46   110.46  3.000
 KSH  H45A  C45  C44   113.36  3.000
 KSH  H45   C45  C44   110.07  3.000
 KSH  C46   C45  C44   103.98  3.000
 KSH  H46   C46  C53   108.03  3.000
 KSH  H46   C46  C45   109.12  3.000
 KSH  C53   C46  C45   113.27  3.000
 KSH  H46   C46  N42   110.04  3.000
 KSH  C53   C46  N42   112.64  3.000
 KSH  C45   C46  N42   103.66  3.000
 KSH  H53A  C53  H53   106.41  3.000
 KSH  H53A  C53  O55   111.44  3.000
 KSH  H53   C53  O55   112.45  3.000
 KSH  H53A  C53  C46   110.41  3.000
 KSH  H53   C53  C46   106.96  3.000
 KSH  O55   C53  C46   109.08  3.000
 KSH  HO55  O55  C53   108.05  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
 KSH  CONST_01  C4    C3   C2   N1      0.00   0.0  0
 KSH  CONST_02  C4    N5   C6   N1      0.00   0.0  0
 KSH  CONST_03  C8    C7   C6   N1      0.00   0.0  0
 KSH  CONST_04  C7    C8   N9   N1      0.00   0.0  0
 KSH  CONST_05  N5    C6   N1   C2      0.00   0.0  0
 KSH  CONST_06  C7    C6   N1   C2    180.00   0.0  0
 KSH  CONST_07  C8    N9   N1   C2    180.00   0.0  0
 KSH  CONST_08  N5    C4   C3   C2      0.00   0.0  0
 KSH  CONST_09  C6    N1   C2   C3      0.00   0.0  0
 KSH  CONST_10  N9    N1   C2   C3    180.00   0.0  0
 KSH  CONST_11  C6    N5   C4   C3      0.00   0.0  0
 KSH  CONST_12  C7    C6   N5   C4    180.00   0.0  0
 KSH  CONST_13  N9    N1   C6   N5    180.00   0.0  0
 KSH  CONST_14  C8    C7   C6   N5    180.00   0.0  0
 KSH  CONST_15  C8    N9   N1   C6      0.00   0.0  0
 KSH  CONST_16  N9    C8   C7   C6      0.00   0.0  0
 KSH  CONST_17  N9    N1   C6   C7      0.00   0.0  0
 KSH  CONST_18  C20   C19  C18  C17     0.00   0.0  0
 KSH  CONST_19  C20   C21  C22  C17     0.00   0.0  0
 KSH  CONST_20  C21   C22  C17  C18     0.00   0.0  0
 KSH  CONST_21  C21   C20  C19  C18     0.00   0.0  0
 KSH  CONST_22  C22   C17  C18  C19     0.00   0.0  0
 KSH  CONST_23  C22   C21  C20  C19     0.00   0.0  0
 KSH  CONST_24  N42   C2   C3   C4    180.00   0.0  0
 KSH  CONST_25  N42   C2   N1   C6    180.00   0.0  0
 KSH  CONST_26  N42   C2   N1   N9      0.00   0.0  0
 KSH  CONST_27  C10   C7   C6   N1    180.00   0.0  0
 KSH  CONST_28  N16   C8   N9   N1    180.00   0.0  0
 KSH  CONST_29  C37   C4   C3   C2    180.00   0.0  0
 KSH  CONST_30  C10   C7   C6   N5      0.00   0.0  0
 KSH  CONST_31  C37   C4   N5   C6    180.00   0.0  0
 KSH  CONST_32  N16   C8   C7   C6    180.00   0.0  0
 KSH  CONST_33  C10   C7   C8   N9    180.00   0.0  0
 KSH  CONST_34  C19   C18  C17  N16   180.00   0.0  0
 KSH  CONST_35  C21   C22  C17  N16   180.00   0.0  0
 KSH  CONST_36  O31   C19  C18  C17   180.00   0.0  0
 KSH  CONST_37  O26   C21  C22  C17   180.00   0.0  0
 KSH  CONST_38  O26   C21  C20  C19   180.00   0.0  0
 KSH  CONST_39  O31   C19  C20  C21   180.00   0.0  0
 KSH  CONST_40  H3    C3   C2   N1    180.00   0.0  0
 KSH  CONST_41  H22   C22  C17  C18   180.00   0.0  0
 KSH  CONST_42  H20   C20  C19  C18   180.00   0.0  0
 KSH  CONST_43  H18   C18  C19  C20   180.00   0.0  0
 KSH  CONST_44  HN12  N12  C10  C7      0.00   0.0  0
 KSH  CONST_45  HN1A  N12  C10  C7    180.00   0.0  0
 KSH  Var_01    C43   N42  C2   N1     26.90  30.0  2
 KSH  Var_02    C44   C43  N42  C2    147.13  30.0  1
 KSH  Var_03    C45   C44  C43  N42    36.75  30.0  1
 KSH  Var_04    C46   C45  C44  C43   -38.47  30.0  1
 KSH  Var_05    C17   N16  C8   C7    178.84  30.0  2
 KSH  Var_06    C18   C17  N16  C8      1.09  30.0  2
 KSH  Var_07    C38   C37  C4   C3   -103.20  30.0  2
 KSH  Var_08    O11   C10  C7   C6    179.82  30.0  2
 KSH  Var_09    H38   C38  C37  C4    -59.31  30.0  3
 KSH  Var_10    H32   C32  O31  C19   -60.89  30.0  3
 KSH  Var_11    H27   C27  O26  C21    60.28  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
 KSH  chir_01  C46  N42  C45  C53  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
 KSH  plan-1  N16   0.020
 KSH  plan-1  C17   0.020
 KSH  plan-1  C18   0.020
 KSH  plan-1  C19   0.020
 KSH  plan-1  C20   0.020
 KSH  plan-1  C21   0.020
 KSH  plan-1  C22   0.020
 KSH  plan-1  O26   0.020
 KSH  plan-1  O31   0.020
 KSH  plan-1  H18   0.020
 KSH  plan-1  H20   0.020
 KSH  plan-1  H22   0.020
 KSH  plan-2  N1    0.020
 KSH  plan-2  C2    0.020
 KSH  plan-2  C3    0.020
 KSH  plan-2  C4    0.020
 KSH  plan-2  N5    0.020
 KSH  plan-2  C6    0.020
 KSH  plan-2  C7    0.020
 KSH  plan-2  C8    0.020
 KSH  plan-2  N9    0.020
 KSH  plan-2  C10   0.020
 KSH  plan-2  N16   0.020
 KSH  plan-2  C37   0.020
 KSH  plan-2  N42   0.020
 KSH  plan-2  H3    0.020
 KSH  plan-3  C7    0.020
 KSH  plan-3  C10   0.020
 KSH  plan-3  O11   0.020
 KSH  plan-3  N12   0.020
 KSH  plan-3  HN12  0.020
 KSH  plan-3  HN1A  0.020

