# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 07:31:32 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 7-(cyclopropylmethylamino)-2-[(4-methoxyphenyl)amino]-5-methyl-pyrazolo[1,5-a]pyrimidine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(Nc2nn3c(NCC4CC4)cc(C)nc3c2C(N)=O)cc1
#
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
 KSC  KSC  7-(cyclopropylmethylamino)-2-[(4-methoxyphenyl)amino]-5-methyl-pyrazolo[1,5-a]pyrimidine-3-carboxamide  ligand  49  27  .  2022-07-25  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_KSC
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
 KSC  C1    C  CR5   0   0.587   0.1358   1.3504   0.2542
 KSC  N2    N  N     0  -0.393  -0.4272   0.1715   0.0585
 KSC  N3    N  N     0  -0.441  -1.7432   0.4456  -0.0649
 KSC  C4    C  CR56  0   0.618  -2.0425   1.7817   0.0246
 KSC  C5    C  CR5   0  -0.466  -0.8141   2.4128   0.2564
 KSC  C6    C  CR6   0   0.714  -2.6845  -0.5100  -0.2491
 KSC  C7    C  CR16  0  -0.488  -3.9942  -0.0473  -0.3444
 KSC  C8    C  CR6   0   0.245  -4.2394   1.3229  -0.2484
 KSC  N9    N  N     0  -0.477  -3.2878   2.2327  -0.0698
 KSC  C10   C  CH3   0  -0.724  -5.6436   1.8344  -0.3272
 KSC  N11   N  NH1   0  -0.673  -2.2757  -1.7711  -0.3252
 KSC  C12   C  CH2   0  -0.273  -3.1740  -2.9029  -0.4475
 KSC  C13   C  CH1   0  -0.291  -2.3797  -4.1583  -0.6591
 KSC  C14   C  CH2   0  -0.491  -2.9010  -5.4529  -0.1229
 KSC  C15   C  CH2   0  -0.484  -1.7082  -4.8085   0.5146
 KSC  N16   N  NH1   0  -0.795   1.4809   1.5003   0.3958
 KSC  C17   C  CR6   0   0.347   2.4723   0.5169   0.3831
 KSC  C18   C  CR16  0  -0.297   2.2485  -0.8291   0.6858
 KSC  C19   C  CR16  0  -0.336   3.2984  -1.7303   0.6865
 KSC  C20   C  CR6   0   0.361   4.6002  -1.3268   0.3966
 KSC  C21   C  CR16  0  -0.368   4.8317   0.0141   0.1052
 KSC  C22   C  CR16  0  -0.350   3.7762   0.9149   0.0972
 KSC  C23   C  C     0   0.443  -0.6316   3.8491   0.4356
 KSC  O24   O  O     0  -0.479  -1.4150   4.6717  -0.0196
 KSC  N25   N  NH2   0  -0.833   0.4891   4.2230   1.1156
 KSC  O26   O  O2    0  -0.475   5.5522  -2.2846   0.4232
 KSC  C27   C  CH3   0  -0.435   6.8807  -1.9159   0.1192
 KSC  H7    H  HCR6  0   0.288  -4.8073  -0.7441  -0.4791
 KSC  H10   H  HCH3  0   0.259  -5.9566   2.2206   0.6443
 KSC  H10A  H  HCH3  0   0.255  -5.7130   2.6567  -1.0390
 KSC  H10B  H  HCH3  0   0.247  -6.3440   1.0561  -0.6229
 KSC  HN11  H  HNH1  0   0.414  -1.2945  -1.9494  -0.1675
 KSC  H12   H  HCH2  0   0.246  -3.7936  -2.9928   0.4514
 KSC  H12A  H  HCH2  0   0.259  -3.8513  -2.7415  -1.2901
 KSC  H13   H  HCH1  0   0.273  -1.8495  -4.2038  -1.6050
 KSC  H14   H  HCH2  0   0.251  -3.8366  -5.4355   0.4229
 KSC  H14A  H  HCH2  0   0.258  -2.7492  -6.3446  -0.7165
 KSC  H15   H  HCH2  0   0.257  -0.7365  -5.2581   0.3577
 KSC  H15A  H  HCH2  0   0.252  -1.8392  -4.3562   1.4904
 KSC  HN16  H  HNH1  0   0.406   1.8171   2.4451   0.2883
 KSC  H18   H  HCR6  0   0.274   1.2585  -1.1836   0.9244
 KSC  H19   H  HCR6  0   0.262   3.1031  -2.7698   0.9201
 KSC  H21   H  HCR6  0   0.279   5.8219   0.3831  -0.1249
 KSC  H22   H  HCR6  0   0.268   3.9815   1.9532  -0.1361
 KSC  HN25  H  HNH2  0   0.399   0.8658   3.6122   1.8235
 KSC  HN2A  H  HNH2  0   0.398   0.5862   5.2052   1.3238
 KSC  H27   H  HCH3  0   0.225   7.2724  -1.1749   0.8214
 KSC  H27A  H  HCH3  0   0.258   7.4799  -2.8200   0.1979
 KSC  H27B  H  HCH3  0   0.225   6.9749  -1.5201  -0.8960

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
 KSC  N2   C1    aromatic  1.321  0.020  1.321
 KSC  C1   C5    aromatic  1.425  0.020  1.425
 KSC  C1   N16   single    1.361  0.020  1.361
 KSC  N3   N2    aromatic  1.350  0.020  1.350
 KSC  C6   N3    aromatic  1.354  0.020  1.354
 KSC  N3   C4    aromatic  1.372  0.020  1.372
 KSC  N9   C4    aromatic  1.328  0.020  1.328
 KSC  C4   C5    aromatic  1.400  0.020  1.400
 KSC  C5   C23   single    1.459  0.020  1.459
 KSC  N11  C6    single    1.328  0.020  1.328
 KSC  C7   C6    aromatic  1.392  0.020  1.392
 KSC  C7   C8    aromatic  1.395  0.020  1.395
 KSC  C7   H7    single    0.930  0.020  1.080
 KSC  C10  C8    single    1.496  0.020  1.496
 KSC  C8   N9    aromatic  1.329  0.020  1.329
 KSC  C10  H10   single    0.970  0.020  1.090
 KSC  C10  H10A  single    0.970  0.020  1.090
 KSC  C10  H10B  single    0.970  0.020  1.090
 KSC  N11  C12   single    1.450  0.020  1.450
 KSC  N11  HN11  single    0.860  0.020  1.020
 KSC  C12  C13   single    1.501  0.020  1.501
 KSC  C12  H12   single    0.970  0.020  1.090
 KSC  C12  H12A  single    0.970  0.020  1.090
 KSC  C13  C14   single    1.495  0.020  1.495
 KSC  C13  C15   single    1.500  0.020  1.500
 KSC  C13  H13   single    0.970  0.020  1.090
 KSC  C14  C15   single    1.498  0.020  1.498
 KSC  C14  H14   single    0.970  0.020  1.090
 KSC  C14  H14A  single    0.970  0.020  1.090
 KSC  C15  H15   single    0.970  0.020  1.090
 KSC  C15  H15A  single    0.970  0.020  1.090
 KSC  C17  N16   single    1.396  0.020  1.396
 KSC  N16  HN16  single    0.860  0.020  1.020
 KSC  C22  C17   aromatic  1.393  0.020  1.393
 KSC  C17  C18   aromatic  1.398  0.020  1.398
 KSC  C19  C18   aromatic  1.384  0.020  1.384
 KSC  C18  H18   single    0.930  0.020  1.080
 KSC  C20  C19   aromatic  1.393  0.020  1.393
 KSC  C19  H19   single    0.930  0.020  1.080
 KSC  O26  C20   single    1.351  0.020  1.351
 KSC  C21  C20   aromatic  1.392  0.020  1.392
 KSC  C21  C22   aromatic  1.388  0.020  1.388
 KSC  C21  H21   single    0.930  0.020  1.080
 KSC  C22  H22   single    0.930  0.020  1.080
 KSC  C23  N25   single    1.363  0.020  1.363
 KSC  C23  O24   double    1.224  0.020  1.224
 KSC  N25  HN25  single    0.890  0.020  1.040
 KSC  N25  HN2A  single    0.890  0.020  1.040
 KSC  O26  C27   single    1.412  0.020  1.412
 KSC  C27  H27   single    0.970  0.020  1.090
 KSC  C27  H27A  single    0.970  0.020  1.090
 KSC  C27  H27B  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
 KSC  N16   C1   C5    125.21  3.000
 KSC  N16   C1   N2    122.34  3.000
 KSC  C5    C1   N2    112.42  3.000
 KSC  N3    N2   C1    104.35  3.000
 KSC  C6    N3   C4    122.99  3.000
 KSC  C4    N3   N2    113.86  3.000
 KSC  C6    N3   N2    123.15  3.000
 KSC  N9    C4   C5    132.95  3.000
 KSC  C5    C4   N3    104.96  3.000
 KSC  N9    C4   N3    122.05  3.000
 KSC  C23   C5   C4    125.01  3.000
 KSC  C23   C5   C1    130.60  3.000
 KSC  C4    C5   C1    104.39  3.000
 KSC  N11   C6   C7    126.96  3.000
 KSC  C7    C6   N3    115.39  3.000
 KSC  N11   C6   N3    117.65  3.000
 KSC  H7    C7   C8    120.68  3.000
 KSC  H7    C7   C6    120.18  3.000
 KSC  C8    C7   C6    119.14  3.000
 KSC  C10   C8   N9    116.43  3.000
 KSC  N9    C8   C7    123.77  3.000
 KSC  C10   C8   C7    119.79  3.000
 KSC  C8    N9   C4    116.66  3.000
 KSC  H10B  C10  H10A  108.74  3.000
 KSC  H10B  C10  H10   108.08  3.000
 KSC  H10A  C10  H10   107.23  3.000
 KSC  H10B  C10  C8    111.96  3.000
 KSC  H10A  C10  C8    110.61  3.000
 KSC  H10   C10  C8    110.07  3.000
 KSC  HN11  N11  C12   118.51  3.000
 KSC  HN11  N11  C6    117.25  3.000
 KSC  C12   N11  C6    123.73  3.000
 KSC  H12A  C12  H12   107.12  3.000
 KSC  H12A  C12  C13   110.05  3.000
 KSC  H12   C12  C13   110.27  3.000
 KSC  H12A  C12  N11   109.49  3.000
 KSC  H12   C12  N11   110.19  3.000
 KSC  C13   C12  N11   109.69  3.000
 KSC  H13   C13  C15   116.42  3.000
 KSC  H13   C13  C14   116.53  3.000
 KSC  C15   C13  C14    60.02  3.000
 KSC  H13   C13  C12   114.62  3.000
 KSC  C15   C13  C12   119.28  3.000
 KSC  C14   C13  C12   119.29  3.000
 KSC  H14A  C14  H14   114.26  3.000
 KSC  H14A  C14  C15   118.44  3.000
 KSC  H14   C14  C15   117.80  3.000
 KSC  H14A  C14  C13   117.90  3.000
 KSC  H14   C14  C13   117.90  3.000
 KSC  C15   C14  C13    60.17  3.000
 KSC  H15A  C15  H15   114.36  3.000
 KSC  H15A  C15  C14   117.81  3.000
 KSC  H15   C15  C14   118.33  3.000
 KSC  H15A  C15  C13   118.01  3.000
 KSC  H15   C15  C13   117.94  3.000
 KSC  C14   C15  C13    59.82  3.000
 KSC  HN16  N16  C17   114.96  3.000
 KSC  HN16  N16  C1    114.94  3.000
 KSC  C17   N16  C1    128.55  3.000
 KSC  C22   C17  C18   118.00  3.000
 KSC  C18   C17  N16   124.23  3.000
 KSC  C22   C17  N16   117.72  3.000
 KSC  H18   C18  C19   118.84  3.000
 KSC  H18   C18  C17   120.77  3.000
 KSC  C19   C18  C17   120.39  3.000
 KSC  H19   C19  C20   119.42  3.000
 KSC  H19   C19  C18   119.24  3.000
 KSC  C20   C19  C18   121.34  3.000
 KSC  O26   C20  C21   124.76  3.000
 KSC  C21   C20  C19   118.56  3.000
 KSC  O26   C20  C19   116.68  3.000
 KSC  H21   C21  C22   118.27  3.000
 KSC  H21   C21  C20   121.72  3.000
 KSC  C22   C21  C20   120.01  3.000
 KSC  H22   C22  C21   118.62  3.000
 KSC  H22   C22  C17   119.69  3.000
 KSC  C21   C22  C17   121.69  3.000
 KSC  N25   C23  O24   121.83  3.000
 KSC  O24   C23  C5    122.41  3.000
 KSC  N25   C23  C5    115.73  3.000
 KSC  HN2A  N25  HN25  114.14  3.000
 KSC  HN2A  N25  C23   116.69  3.000
 KSC  HN25  N25  C23   119.43  3.000
 KSC  C27   O26  C20   118.28  3.000
 KSC  H27B  C27  H27A  108.70  3.000
 KSC  H27B  C27  H27   108.66  3.000
 KSC  H27A  C27  H27   108.63  3.000
 KSC  H27B  C27  O26   112.05  3.000
 KSC  H27A  C27  O26   106.61  3.000
 KSC  H27   C27  O26   112.07  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
 KSC  CONST_01  C6    N3   N2   C1    180.00   0.0  0
 KSC  CONST_02  C4    N3   N2   C1      0.00   0.0  0
 KSC  CONST_03  N3    C4   C5   C1      0.00   0.0  0
 KSC  CONST_04  N9    C4   C5   C1    180.00   0.0  0
 KSC  CONST_05  C4    C5   C1   N2      0.00   0.0  0
 KSC  CONST_06  C7    C6   N3   N2    180.00   0.0  0
 KSC  CONST_07  N9    C4   N3   N2    180.00   0.0  0
 KSC  CONST_08  C5    C4   N3   N2      0.00   0.0  0
 KSC  CONST_09  C5    C1   N2   N3      0.00   0.0  0
 KSC  CONST_10  C8    C7   C6   N3      0.00   0.0  0
 KSC  CONST_11  C8    N9   C4   N3      0.00   0.0  0
 KSC  CONST_12  C7    C6   N3   C4      0.00   0.0  0
 KSC  CONST_13  C7    C8   N9   C4      0.00   0.0  0
 KSC  CONST_14  C6    N3   C4   C5    180.00   0.0  0
 KSC  CONST_15  C8    N9   C4   C5    180.00   0.0  0
 KSC  CONST_16  N9    C4   N3   C6      0.00   0.0  0
 KSC  CONST_17  N9    C8   C7   C6      0.00   0.0  0
 KSC  CONST_18  C20   C21  C22  C17     0.00   0.0  0
 KSC  CONST_19  C20   C19  C18  C17     0.00   0.0  0
 KSC  CONST_20  C21   C22  C17  C18     0.00   0.0  0
 KSC  CONST_21  C21   C20  C19  C18     0.00   0.0  0
 KSC  CONST_22  C22   C17  C18  C19     0.00   0.0  0
 KSC  CONST_23  C22   C21  C20  C19     0.00   0.0  0
 KSC  CONST_24  C23   C5   C1   N2    180.00   0.0  0
 KSC  CONST_25  N11   C6   N3   N2      0.00   0.0  0
 KSC  CONST_26  N16   C1   N2   N3    180.00   0.0  0
 KSC  CONST_27  C23   C5   C4   N3    180.00   0.0  0
 KSC  CONST_28  N11   C6   N3   C4    180.00   0.0  0
 KSC  CONST_29  C10   C8   N9   C4    180.00   0.0  0
 KSC  CONST_30  N16   C1   C5   C4    180.00   0.0  0
 KSC  CONST_31  C10   C8   C7   C6    180.00   0.0  0
 KSC  CONST_32  N11   C6   C7   C8    180.00   0.0  0
 KSC  CONST_33  C23   C5   C4   N9      0.00   0.0  0
 KSC  CONST_34  C21   C22  C17  N16   180.00   0.0  0
 KSC  CONST_35  C19   C18  C17  N16   180.00   0.0  0
 KSC  CONST_36  O26   C20  C19  C18   180.00   0.0  0
 KSC  CONST_37  O26   C20  C21  C22   180.00   0.0  0
 KSC  CONST_38  H7    C7   C6   N3    180.00   0.0  0
 KSC  CONST_39  H21   C21  C22  C17   180.00   0.0  0
 KSC  CONST_40  H19   C19  C18  C17   180.00   0.0  0
 KSC  CONST_41  H22   C22  C17  C18   180.00   0.0  0
 KSC  CONST_42  H18   C18  C19  C20   180.00   0.0  0
 KSC  CONST_43  C12   N11  C6   N3    180.00   0.0  0
 KSC  CONST_44  C12   N11  C6   C7      0.00   0.0  0
 KSC  CONST_45  HN11  N11  C6   N3      0.00   0.0  0
 KSC  CONST_47  HN2A  N25  C23  C5    180.00   0.0  0
 KSC  Var_01    C22   C17  N16  C1    158.81  30.0  2
 KSC  Var_02    C17   N16  C1   N2     -0.86  30.0  2
 KSC  Var_03    C15   C14  C13  C12  -108.89  30.0  1
 KSC  Var_04    H15   C15  C14  C13  -107.59  30.0  1
 KSC  Var_05    N25   C23  C5   C1    -23.92  30.0  2
 KSC  Var_06    C13   C12  N11  C6    173.83  30.0  3
 KSC  Var_07    C14   C13  C12  N11   148.04  30.0  3
 KSC  Var_08    H10   C10  C8   C7    110.74  30.0  2
 KSC  Var_09    H27   C27  O26  C20    61.17  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
 KSC  chir_01  C13  C12  C14  C15  both

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
 KSC  plan-1  N16   0.020
 KSC  plan-1  C17   0.020
 KSC  plan-1  C18   0.020
 KSC  plan-1  C19   0.020
 KSC  plan-1  C20   0.020
 KSC  plan-1  C21   0.020
 KSC  plan-1  C22   0.020
 KSC  plan-1  O26   0.020
 KSC  plan-1  H18   0.020
 KSC  plan-1  H19   0.020
 KSC  plan-1  H21   0.020
 KSC  plan-1  H22   0.020
 KSC  plan-2  C1    0.020
 KSC  plan-2  N2    0.020
 KSC  plan-2  N3    0.020
 KSC  plan-2  C4    0.020
 KSC  plan-2  C5    0.020
 KSC  plan-2  C6    0.020
 KSC  plan-2  C7    0.020
 KSC  plan-2  C8    0.020
 KSC  plan-2  N9    0.020
 KSC  plan-2  C10   0.020
 KSC  plan-2  N11   0.020
 KSC  plan-2  N16   0.020
 KSC  plan-2  C23   0.020
 KSC  plan-2  H7    0.020
 KSC  plan-3  C6    0.020
 KSC  plan-3  N11   0.020
 KSC  plan-3  C12   0.020
 KSC  plan-3  HN11  0.020
 KSC  plan-4  C5    0.020
 KSC  plan-4  C23   0.020
 KSC  plan-4  O24   0.020
 KSC  plan-4  N25   0.020
 KSC  plan-4  HN25  0.020
 KSC  plan-4  HN2A  0.020

