# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 23:33:11 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 7-(cyclopropylamino)-5-[3-(6-oxo-1,6-dihydropyridin-3-yl)thiophen-2-yl]pyrazolo[1,5-a]pyrimidine-3-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NC=C(C=C1)c2ccsc2c3cc(NC4CC4)n5ncc(C#N)c5n3
#
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
 75E  75E  7-(cyclopropylamino)-5-[3-(6-oxo-1,6-dihydropyridin-3-yl)thiophen-2-yl]pyrazolo[1,5-a]pyrimidine-3-carbonitrile  ligand  41  27  .  2022-09-16  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_75E
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
 75E  C1   C  CR16  0  -0.460   3.3555   0.2656   1.4557
 75E  C2   C  CR6   0   0.534   4.5741   0.2495   0.6889
 75E  C3   C  CR16  0   0.017   3.4849  -1.3979  -0.7233
 75E  C7   C  CR15  0  -0.449   0.1952  -4.2348  -1.0033
 75E  C8   C  CR5   0  -0.317  -0.1303  -1.8470  -0.4576
 75E  C9   C  CR6   0   0.225  -0.7154  -0.5199  -0.2855
 75E  C10  C  CR16  0  -0.468  -2.0538  -0.3831   0.1109
 75E  C11  C  CR6   0   0.723  -2.6012   0.8863   0.2361
 75E  C12  C  CR56  0   0.672  -0.4383   1.7097  -0.3629
 75E  C13  C  CR5   0  -0.342   0.0938   2.9990  -0.4905
 75E  C14  C  CR15  0   0.037  -0.9737   3.8660  -0.1894
 75E  C15  C  CSP   0  -0.004   1.4156   3.3192  -0.8367
 75E  C16  C  CH1   0  -0.113  -4.8277   0.1913   0.8782
 75E  N4   N  NS    0  -0.264   2.5023   3.5853  -1.1219
 75E  N3   N  N     0  -0.302  -2.0773   3.2190   0.1022
 75E  N1   N  N     0  -0.457  -1.7455   1.9186  -0.0023
 75E  N5   N  NH1   0  -0.667  -3.8536   1.1849   0.5648
 75E  C18  C  CH2   0  -0.503  -6.2032   0.3811   0.3310
 75E  C17  C  CH2   0  -0.488  -5.3277  -0.6996  -0.2188
 75E  N2   N  N     0  -0.464   0.0842   0.5091  -0.5324
 75E  S    S  S2    0   0.249  -1.1380  -3.1786  -0.8937
 75E  C6   C  CR15  0  -0.216   1.3635  -3.6016  -0.7138
 75E  C5   C  CR5   0   0.205   1.1949  -2.2232  -0.3973
 75E  C4   C  CR6   0  -0.079   2.3245  -1.3677  -0.0146
 75E  C    C  CR16  0  -0.119   2.2908  -0.5012   1.1143
 75E  N    N  NR16  0  -0.660   4.5393  -0.6264  -0.3788
 75E  O    O  O     0  -0.511   5.5787   0.9174   0.9183
 75E  H1   H  HCR6  0   0.271   3.3172   0.9121   2.3218
 75E  H2   H  HCR6  0   0.307   3.6251  -2.0178  -1.5977
 75E  H3   H  HCR5  0   0.306   0.0506  -5.2714  -1.2652
 75E  H4   H  HCR6  0   0.295  -2.6639  -1.2422   0.3446
 75E  H5   H  HCR5  0   0.298  -0.9545   4.9448  -0.1799
 75E  H6   H  HCH1  0   0.286  -4.7369  -0.2405   1.8703
 75E  H7   H  HNH1  0   0.422  -4.0822   2.1581   0.7098
 75E  H8   H  HCH2  0   0.268  -7.0341   0.1077   0.9673
 75E  H9   H  HCH2  0   0.266  -6.3762   1.2501  -0.2911
 75E  H10  H  HCH2  0   0.268  -4.9149  -0.5567  -1.2092
 75E  H11  H  HCH2  0   0.268  -5.5485  -1.7276   0.0365
 75E  H12  H  HCR5  0   0.274   2.3222  -4.1006  -0.7021
 75E  H14  H  HCR6  0   0.269   1.4017  -0.4739   1.7307
 75E  H13  H  HNR6  0   0.423   5.3741  -0.6829  -0.9467

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
 75E  O    C2   double    1.228  0.020  1.228
 75E  N4   C15  triple    1.155  0.020  1.155
 75E  C15  C13  single    1.403  0.020  1.403
 75E  C2   C1   single    1.440  0.020  1.440
 75E  C2   N    single    1.381  0.020  1.381
 75E  C1   C    double    1.356  0.020  1.356
 75E  N    C3   single    1.351  0.020  1.351
 75E  C13  C14  aromatic  1.408  0.020  1.408
 75E  C13  C12  aromatic  1.401  0.020  1.401
 75E  C14  N3   aromatic  1.312  0.020  1.312
 75E  C    C4   single    1.423  0.020  1.423
 75E  C3   C4   double    1.360  0.020  1.360
 75E  C12  N2   aromatic  1.320  0.020  1.320
 75E  C12  N1   aromatic  1.372  0.020  1.372
 75E  N3   N1   aromatic  1.346  0.020  1.346
 75E  C4   C5   single    1.468  0.020  1.468
 75E  N2   C9   aromatic  1.326  0.020  1.326
 75E  N1   C11  aromatic  1.362  0.020  1.362
 75E  C5   C8   aromatic  1.379  0.020  1.379
 75E  C5   C6   aromatic  1.424  0.020  1.424
 75E  C9   C8   single    1.461  0.020  1.461
 75E  C9   C10  aromatic  1.403  0.020  1.403
 75E  C11  C10  aromatic  1.388  0.020  1.388
 75E  C11  N5   single    1.329  0.020  1.329
 75E  C8   S    aromatic  1.726  0.020  1.726
 75E  C6   C7   aromatic  1.360  0.020  1.360
 75E  N5   C16  single    1.426  0.020  1.426
 75E  C7   S    aromatic  1.704  0.020  1.704
 75E  C16  C18  single    1.492  0.020  1.492
 75E  C16  C17  single    1.499  0.020  1.499
 75E  C18  C17  single    1.496  0.020  1.496
 75E  C1   H1   single    0.930  0.020  1.080
 75E  C3   H2   single    0.930  0.020  1.080
 75E  C7   H3   single    0.930  0.020  1.080
 75E  C10  H4   single    0.930  0.020  1.080
 75E  C14  H5   single    0.930  0.020  1.080
 75E  C16  H6   single    0.970  0.020  1.090
 75E  N5   H7   single    0.860  0.020  1.020
 75E  C18  H8   single    0.970  0.020  1.090
 75E  C18  H9   single    0.970  0.020  1.090
 75E  C17  H10  single    0.970  0.020  1.090
 75E  C17  H11  single    0.970  0.020  1.090
 75E  C6   H12  single    0.930  0.020  1.080
 75E  C    H14  single    0.930  0.020  1.080
 75E  N    H13  single    0.860  0.020  1.020

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
 75E  H1   C1   C    120.79  3.000
 75E  H1   C1   C2   117.59  3.000
 75E  C    C1   C2   121.61  3.000
 75E  O    C2   N    120.65  3.000
 75E  N    C2   C1   113.41  3.000
 75E  O    C2   C1   125.93  3.000
 75E  H2   C3   N    115.63  3.000
 75E  H2   C3   C4   123.01  3.000
 75E  N    C3   C4   121.35  3.000
 75E  H3   C7   C6   127.89  3.000
 75E  H3   C7   S    120.41  3.000
 75E  C6   C7   S    111.70  3.000
 75E  C5   C8   S    111.20  3.000
 75E  S    C8   C9   119.80  3.000
 75E  C5   C8   C9   128.89  3.000
 75E  N2   C9   C10  123.52  3.000
 75E  C10  C9   C8   120.28  3.000
 75E  N2   C9   C8   116.20  3.000
 75E  H4   C10  C11  119.04  3.000
 75E  H4   C10  C9   121.53  3.000
 75E  C11  C10  C9   119.41  3.000
 75E  N5   C11  N1   117.72  3.000
 75E  N5   C11  C10  126.84  3.000
 75E  N1   C11  C10  115.44  3.000
 75E  N2   C12  N1   123.31  3.000
 75E  N1   C12  C13  104.23  3.000
 75E  N2   C12  C13  132.45  3.000
 75E  C15  C13  C14  128.79  3.000
 75E  C14  C13  C12  105.03  3.000
 75E  C15  C13  C12  126.18  3.000
 75E  H5   C14  N3   120.40  3.000
 75E  H5   C14  C13  127.16  3.000
 75E  N3   C14  C13  112.44  3.000
 75E  N4   C15  C13  180.00  3.000
 75E  H6   C16  C17  117.41  3.000
 75E  H6   C16  C18  117.56  3.000
 75E  C17  C16  C18   59.99  3.000
 75E  H6   C16  N5   114.87  3.000
 75E  C17  C16  N5   118.75  3.000
 75E  C18  C16  N5   117.40  3.000
 75E  N1   N3   C14  104.58  3.000
 75E  N3   N1   C12  113.72  3.000
 75E  N3   N1   C11  124.32  3.000
 75E  C12  N1   C11  121.96  3.000
 75E  H7   N5   C16  119.01  3.000
 75E  H7   N5   C11  117.73  3.000
 75E  C16  N5   C11  122.78  3.000
 75E  H9   C18  H8   114.72  3.000
 75E  H9   C18  C17  117.54  3.000
 75E  H8   C18  C17  118.90  3.000
 75E  H9   C18  C16  117.39  3.000
 75E  H8   C18  C16  117.39  3.000
 75E  C17  C18  C16   60.22  3.000
 75E  H11  C17  H10  114.78  3.000
 75E  H11  C17  C18  118.71  3.000
 75E  H10  C17  C18  117.66  3.000
 75E  H11  C17  C16  117.39  3.000
 75E  H10  C17  C16  117.64  3.000
 75E  C18  C17  C16   59.79  3.000
 75E  C12  N2   C9   116.30  3.000
 75E  C8   S    C7    92.16  3.000
 75E  H12  C6   C5   123.32  3.000
 75E  H12  C6   C7   123.32  3.000
 75E  C5   C6   C7   113.34  3.000
 75E  C4   C5   C6   122.07  3.000
 75E  C6   C5   C8   111.59  3.000
 75E  C4   C5   C8   126.30  3.000
 75E  C    C4   C5   122.91  3.000
 75E  C5   C4   C3   120.52  3.000
 75E  C    C4   C3   116.55  3.000
 75E  H14  C    C4   119.11  3.000
 75E  H14  C    C1   119.17  3.000
 75E  C4   C    C1   121.70  3.000
 75E  H13  N    C3   117.97  3.000
 75E  H13  N    C2   116.66  3.000
 75E  C3   N    C2   125.36  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
 75E  CONST_01  C8   C5   C6   C7      0.00   0.0  0
 75E  CONST_02  C5   C8   S    C7      0.00   0.0  0
 75E  CONST_03  C9   C8   S    C7    180.00   0.0  0
 75E  CONST_04  C12  N2   C9   C8    180.00   0.0  0
 75E  CONST_05  C11  C10  C9   C8    180.00   0.0  0
 75E  CONST_06  C6   C7   S    C8      0.00   0.0  0
 75E  CONST_07  C13  C12  N2   C9    180.00   0.0  0
 75E  CONST_08  N1   C12  N2   C9      0.00   0.0  0
 75E  CONST_09  C6   C5   C8   C9    180.00   0.0  0
 75E  CONST_10  N1   C11  C10  C9      0.00   0.0  0
 75E  CONST_11  C12  N2   C9   C10     0.00   0.0  0
 75E  CONST_14  C12  N1   C11  C10     0.00   0.0  0
 75E  CONST_15  N3   N1   C11  C10   180.00   0.0  0
 75E  CONST_16  C13  C12  N1   C11   180.00   0.0  0
 75E  CONST_17  N2   C12  N1   C11     0.00   0.0  0
 75E  CONST_18  C14  N3   N1   C11   180.00   0.0  0
 75E  CONST_19  N2   C9   C10  C11     0.00   0.0  0
 75E  CONST_20  N3   C14  C13  C12     0.00   0.0  0
 75E  CONST_21  C14  N3   N1   C12     0.00   0.0  0
 75E  CONST_22  N1   N3   C14  C13     0.00   0.0  0
 75E  CONST_23  N3   N1   C12  C13     0.00   0.0  0
 75E  CONST_24  N2   C12  C13  C14   180.00   0.0  0
 75E  CONST_25  N1   C12  C13  C14     0.00   0.0  0
 75E  CONST_26  N2   C12  N1   N3    180.00   0.0  0
 75E  CONST_29  C6   C5   C8   S       0.00   0.0  0
 75E  CONST_30  C5   C6   C7   S       0.00   0.0  0
 75E  CONST_31  C4   C5   C6   C7    180.00   0.0  0
 75E  CONST_32  C4   C5   C8   C9      0.00   0.0  0
 75E  CONST_33  C4   C5   C8   S     180.00   0.0  0
 75E  CONST_34  C3   N    C2   C1      0.00   0.0  0
 75E  CONST_35  N5   C11  C10  C9    180.00   0.0  0
 75E  CONST_36  N5   C11  N1   C12   180.00   0.0  0
 75E  CONST_37  N3   C14  C13  C15   180.00   0.0  0
 75E  CONST_38  N2   C12  C13  C15     0.00   0.0  0
 75E  CONST_39  N1   C12  C13  C15   180.00   0.0  0
 75E  CONST_40  N5   C11  N1   N3      0.00   0.0  0
 75E  CONST_41  C16  N5   C11  C10     0.00   0.0  0
 75E  CONST_42  N1   C11  N5   C16   180.00   0.0  0
 75E  CONST_43  O    C2   N    C3    180.00   0.0  0
 75E  CONST_44  H12  C6   C5   C8    180.00   0.0  0
 75E  CONST_45  H4   C10  C9   C8      0.00   0.0  0
 75E  CONST_46  H3   C7   S    C8    180.00   0.0  0
 75E  CONST_47  H5   C14  C13  C12   180.00   0.0  0
 75E  CONST_48  H13  N    C2   C1    180.00   0.0  0
 75E  CONST_49  H7   N5   C11  C10   180.00   0.0  0
 75E  Var_01    C8   C5   C4   C3   -136.38  30.0  2
 75E  Var_02    C18  C16  N5   C11  -138.30  30.0  3
 75E  Var_03    C17  C18  C16  N5    109.04  30.0  1
 75E  Var_04    H10  C17  C18  C16  -107.51  30.0  1

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
 75E  chir_01  C16  N5  C18  C17  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
 75E  plan-1  C7   0.020
 75E  plan-1  C8   0.020
 75E  plan-1  C9   0.020
 75E  plan-1  S    0.020
 75E  plan-1  C6   0.020
 75E  plan-1  C5   0.020
 75E  plan-1  C4   0.020
 75E  plan-1  H3   0.020
 75E  plan-1  H12  0.020
 75E  plan-2  C1   0.020
 75E  plan-2  C2   0.020
 75E  plan-2  C3   0.020
 75E  plan-2  C5   0.020
 75E  plan-2  C4   0.020
 75E  plan-2  C    0.020
 75E  plan-2  N    0.020
 75E  plan-2  O    0.020
 75E  plan-2  H1   0.020
 75E  plan-2  H2   0.020
 75E  plan-2  H14  0.020
 75E  plan-2  H13  0.020
 75E  plan-3  C8   0.020
 75E  plan-3  C9   0.020
 75E  plan-3  C10  0.020
 75E  plan-3  C11  0.020
 75E  plan-3  C12  0.020
 75E  plan-3  C13  0.020
 75E  plan-3  C14  0.020
 75E  plan-3  C15  0.020
 75E  plan-3  N4   0.020
 75E  plan-3  N3   0.020
 75E  plan-3  N1   0.020
 75E  plan-3  N5   0.020
 75E  plan-3  N2   0.020
 75E  plan-3  H4   0.020
 75E  plan-3  H5   0.020
 75E  plan-4  C11  0.020
 75E  plan-4  C16  0.020
 75E  plan-4  N5   0.020
 75E  plan-4  H7   0.020

