# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 20:28:01 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: (3~{S})-3-phenyl-4-(2~{H}-pyrazolo[3,4-b]pyridin-4-yl)morpholine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CN([C@H](CO1)c2ccccc2)c3ccnc4n[nH]cc34
#
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
 C9B  C9B  (3~{S})-3-phenyl-4-(2~{H}-pyrazolo[3,4-b]pyridin-4-yl)morpholine  ligand  37  21  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C9B
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
 C9B  C1   C  CR56  0   0.339  -2.9431  -0.9171  -0.1461
 C9B  C2   C  CR56  0  -0.184  -1.8962   0.0057   0.1499
 C9B  C3   C  CR6   0   0.440  -0.8922   0.2512  -0.8327
 C9B  C7   C  CR6   0   0.170   1.7017  -0.1801   0.7463
 C9B  C8   C  CR16  0  -0.321   2.9497  -0.3470   0.1445
 C9B  C9   C  CR16  0  -0.238   3.6306  -1.5530   0.2500
 C9B  C10  C  CR16  0  -0.268   3.0821  -2.6129   0.9592
 C9B  C11  C  CR16  0  -0.242   1.8477  -2.4551   1.5736
 C9B  C12  C  CR16  0  -0.300   1.1693  -1.2491   1.4666
 C9B  C13  C  CH2   0  -0.183   1.6569   2.3918   0.8060
 C9B  C14  C  CH2   0  -0.188   1.6669   2.8302  -1.4646
 C9B  C15  C  CH2   0  -0.345   0.9313   1.5417  -1.7768
 C9B  C16  C  CR15  0  -0.019  -2.2280   0.4856   1.4140
 C9B  N1   N  N     0  -0.442  -3.0770  -1.6022  -1.3006
 C9B  C4   C  CR16  0  -0.464  -1.0704  -0.4438  -2.0169
 C9B  N2   N  NT    0  -0.504   0.1303   1.1460  -0.6309
 C9B  N3   N  NR15  0  -0.401  -3.3477  -0.1501   1.7567
 C9B  C5   C  CR16  0  -0.080  -2.1520  -1.3352  -2.1849
 C9B  C6   C  CH1   0  -0.262   0.8804   1.0902   0.6331
 C9B  N4   N  N     0  -0.308  -3.8149  -1.0013   0.8567
 C9B  O1   O  O2    0  -0.472   2.4578   2.7118  -0.3044
 C9B  H1   H  HCR6  0   0.255   3.4088   0.4643  -0.4016
 C9B  H2   H  HCR6  0   0.255   4.5976  -1.6623  -0.2241
 C9B  H3   H  HCR6  0   0.256   3.6155  -3.5515   1.0367
 C9B  H4   H  HCR6  0   0.255   1.4119  -3.2679   2.1403
 C9B  H5   H  HCR6  0   0.252   0.2106  -1.1351   1.9584
 C9B  H6   H  HCH2  0   0.229   0.9325   3.1973   0.9931
 C9B  H7   H  HCH2  0   0.252   2.3093   2.3147   1.6764
 C9B  H8   H  HCH2  0   0.249   2.3289   3.0836  -2.2929
 C9B  H9   H  HCH2  0   0.213   0.9377   3.6432  -1.3459
 C9B  H10  H  HCH2  0   0.272   0.2718   1.7305  -2.6248
 C9B  H11  H  HCH2  0   0.236   1.6388   0.7601  -2.0819
 C9B  H12  H  HCR5  0   0.302  -1.7884   1.2194   2.0679
 C9B  H13  H  HCR6  0   0.276  -0.3712  -0.3528  -2.8352
 C9B  H14  H  HNR5  0   0.434  -3.8471  -0.0278   2.6251
 C9B  H15  H  HCR6  0   0.257  -2.2214  -1.8640  -3.1306
 C9B  H16  H  HCH1  0   0.280   0.1665   1.0779   1.4543

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
 C9B  C14  O1   single    1.409  0.020  1.409
 C9B  C14  C15  single    1.516  0.020  1.516
 C9B  O1   C13  single    1.406  0.020  1.406
 C9B  C13  C6   single    1.525  0.020  1.525
 C9B  C15  N2   single    1.453  0.020  1.453
 C9B  C4   C5   aromatic  1.412  0.020  1.412
 C9B  C4   C3   aromatic  1.385  0.020  1.385
 C9B  N2   C6   single    1.471  0.020  1.471
 C9B  N2   C3   single    1.374  0.020  1.374
 C9B  C5   N1   aromatic  1.307  0.020  1.307
 C9B  C6   C7   single    1.517  0.020  1.517
 C9B  C3   C2   aromatic  1.426  0.020  1.426
 C9B  N1   C1   aromatic  1.349  0.020  1.349
 C9B  C2   C1   aromatic  1.427  0.020  1.427
 C9B  C2   C16  aromatic  1.392  0.020  1.392
 C9B  C7   C8   aromatic  1.396  0.020  1.396
 C9B  C7   C12  aromatic  1.395  0.020  1.395
 C9B  C1   N4   aromatic  1.331  0.020  1.331
 C9B  C8   C9   aromatic  1.389  0.020  1.389
 C9B  C12  C11  aromatic  1.388  0.020  1.388
 C9B  C16  N3   aromatic  1.332  0.020  1.332
 C9B  N4   N3   aromatic  1.324  0.020  1.324
 C9B  C9   C10  aromatic  1.388  0.020  1.388
 C9B  C11  C10  aromatic  1.388  0.020  1.388
 C9B  C8   H1   single    0.930  0.020  1.080
 C9B  C9   H2   single    0.930  0.020  1.080
 C9B  C10  H3   single    0.930  0.020  1.080
 C9B  C11  H4   single    0.930  0.020  1.080
 C9B  C12  H5   single    0.930  0.020  1.080
 C9B  C13  H6   single    0.970  0.020  1.090
 C9B  C13  H7   single    0.970  0.020  1.090
 C9B  C14  H8   single    0.970  0.020  1.090
 C9B  C14  H9   single    0.970  0.020  1.090
 C9B  C15  H10  single    0.970  0.020  1.090
 C9B  C15  H11  single    0.970  0.020  1.090
 C9B  C16  H12  single    0.930  0.020  1.080
 C9B  C4   H13  single    0.930  0.020  1.080
 C9B  N3   H14  single    0.860  0.020  1.020
 C9B  C5   H15  single    0.930  0.020  1.080
 C9B  C6   H16  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
 C9B  N4   C1   N1   123.19  3.000
 C9B  N4   C1   C2   111.41  3.000
 C9B  N1   C1   C2   125.37  3.000
 C9B  C16  C2   C3   137.22  3.000
 C9B  C16  C2   C1   103.68  3.000
 C9B  C3   C2   C1   119.02  3.000
 C9B  N2   C3   C4   123.25  3.000
 C9B  N2   C3   C2   122.35  3.000
 C9B  C4   C3   C2   114.35  3.000
 C9B  C6   C7   C12  118.27  3.000
 C9B  C12  C7   C8   118.20  3.000
 C9B  C6   C7   C8   123.52  3.000
 C9B  H1   C8   C9   118.82  3.000
 C9B  H1   C8   C7   120.54  3.000
 C9B  C9   C8   C7   120.63  3.000
 C9B  H2   C9   C10  119.98  3.000
 C9B  H2   C9   C8   119.50  3.000
 C9B  C10  C9   C8   120.53  3.000
 C9B  H3   C10  C11  120.34  3.000
 C9B  H3   C10  C9   120.26  3.000
 C9B  C11  C10  C9   119.40  3.000
 C9B  H4   C11  C12  119.74  3.000
 C9B  H4   C11  C10  120.30  3.000
 C9B  C12  C11  C10  119.96  3.000
 C9B  H5   C12  C11  119.27  3.000
 C9B  H5   C12  C7   119.45  3.000
 C9B  C11  C12  C7   121.28  3.000
 C9B  H7   C13  H6   108.07  3.000
 C9B  H7   C13  O1   107.80  3.000
 C9B  H6   C13  O1   110.06  3.000
 C9B  H7   C13  C6   109.55  3.000
 C9B  H6   C13  C6   108.00  3.000
 C9B  O1   C13  C6   113.24  3.000
 C9B  H9   C14  H8   108.25  3.000
 C9B  H9   C14  O1   110.23  3.000
 C9B  H8   C14  O1   107.71  3.000
 C9B  H9   C14  C15  109.22  3.000
 C9B  H8   C14  C15  109.61  3.000
 C9B  O1   C14  C15  111.75  3.000
 C9B  H11  C15  H10  107.27  3.000
 C9B  H11  C15  N2   112.37  3.000
 C9B  H10  C15  N2   109.08  3.000
 C9B  H11  C15  C14  110.47  3.000
 C9B  H10  C15  C14  107.84  3.000
 C9B  N2   C15  C14  109.66  3.000
 C9B  H12  C16  N3   120.80  3.000
 C9B  H12  C16  C2   133.56  3.000
 C9B  N3   C16  C2   105.63  3.000
 C9B  C5   N1   C1   113.88  3.000
 C9B  H13  C4   C5   117.32  3.000
 C9B  H13  C4   C3   121.49  3.000
 C9B  C5   C4   C3   121.15  3.000
 C9B  C6   N2   C15  114.01  3.000
 C9B  C6   N2   C3   118.76  3.000
 C9B  C15  N2   C3   118.16  3.000
 C9B  H14  N3   N4   119.22  3.000
 C9B  H14  N3   C16  125.41  3.000
 C9B  N4   N3   C16  115.37  3.000
 C9B  H15  C5   C4   117.40  3.000
 C9B  H15  C5   N1   116.39  3.000
 C9B  C4   C5   N1   126.20  3.000
 C9B  H16  C6   N2   108.33  3.000
 C9B  H16  C6   C13  104.95  3.000
 C9B  N2   C6   C13  108.94  3.000
 C9B  H16  C6   C7   106.82  3.000
 C9B  N2   C6   C7   111.84  3.000
 C9B  C13  C6   C7   115.50  3.000
 C9B  N3   N4   C1   103.91  3.000
 C9B  C14  O1   C13  110.47  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
 C9B  CONST_01  C4   C5   N1   C1      0.00   0.0  0
 C9B  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 C9B  CONST_03  N3   C16  C2   C1      0.00   0.0  0
 C9B  CONST_04  C16  N3   N4   C1      0.00   0.0  0
 C9B  CONST_05  C5   C4   C3   C2      0.00   0.0  0
 C9B  CONST_06  C5   N1   C1   C2      0.00   0.0  0
 C9B  CONST_07  N3   N4   C1   C2      0.00   0.0  0
 C9B  CONST_08  N4   N3   C16  C2      0.00   0.0  0
 C9B  CONST_09  N1   C5   C4   C3      0.00   0.0  0
 C9B  CONST_10  N1   C1   C2   C3      0.00   0.0  0
 C9B  CONST_11  N4   C1   C2   C3    180.00   0.0  0
 C9B  CONST_12  N3   C16  C2   C3    180.00   0.0  0
 C9B  CONST_13  C10  C9   C8   C7      0.00   0.0  0
 C9B  CONST_14  C10  C11  C12  C7      0.00   0.0  0
 C9B  CONST_15  C11  C12  C7   C8      0.00   0.0  0
 C9B  CONST_16  C11  C10  C9   C8      0.00   0.0  0
 C9B  CONST_17  C12  C7   C8   C9      0.00   0.0  0
 C9B  CONST_18  C12  C11  C10  C9      0.00   0.0  0
 C9B  CONST_19  C4   C3   C2   C16   180.00   0.0  0
 C9B  CONST_20  N1   C1   C2   C16   180.00   0.0  0
 C9B  CONST_21  N4   C1   C2   C16     0.00   0.0  0
 C9B  CONST_22  N3   N4   C1   N1    180.00   0.0  0
 C9B  CONST_23  N4   C1   N1   C5    180.00   0.0  0
 C9B  CONST_24  N2   C3   C2   C1    180.00   0.0  0
 C9B  CONST_25  C6   C7   C8   C9    180.00   0.0  0
 C9B  CONST_26  C6   C7   C12  C11   180.00   0.0  0
 C9B  CONST_27  N2   C3   C2   C16     0.00   0.0  0
 C9B  CONST_28  C5   C4   C3   N2    180.00   0.0  0
 C9B  CONST_29  H15  C5   N1   C1    180.00   0.0  0
 C9B  CONST_30  H12  C16  C2   C1    180.00   0.0  0
 C9B  CONST_31  H14  N3   N4   C1    180.00   0.0  0
 C9B  CONST_32  H13  C4   C3   C2    180.00   0.0  0
 C9B  CONST_33  H2   C9   C8   C7    180.00   0.0  0
 C9B  CONST_34  H4   C11  C12  C7    180.00   0.0  0
 C9B  CONST_35  H5   C12  C7   C8    180.00   0.0  0
 C9B  CONST_36  H3   C10  C9   C8    180.00   0.0  0
 C9B  CONST_37  H1   C8   C9   C10   180.00   0.0  0
 C9B  Var_01    C15  N2   C3   C2   -167.04  30.0  1
 C9B  Var_02    C14  C15  N2   C3    161.25  30.0  1
 C9B  Var_03    C15  C14  O1   C13   -59.88  30.0  1
 C9B  Var_04    C6   C13  O1   C14    58.84  30.0  1
 C9B  Var_05    O1   C14  C15  N2     56.13  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
 C9B  chir_01  C6  C13  N2  C7  negativ

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
 C9B  plan-1  C7   0.020
 C9B  plan-1  C8   0.020
 C9B  plan-1  C9   0.020
 C9B  plan-1  C10  0.020
 C9B  plan-1  C11  0.020
 C9B  plan-1  C12  0.020
 C9B  plan-1  C6   0.020
 C9B  plan-1  H1   0.020
 C9B  plan-1  H2   0.020
 C9B  plan-1  H3   0.020
 C9B  plan-1  H4   0.020
 C9B  plan-1  H5   0.020
 C9B  plan-2  C1   0.020
 C9B  plan-2  C2   0.020
 C9B  plan-2  C3   0.020
 C9B  plan-2  C16  0.020
 C9B  plan-2  N1   0.020
 C9B  plan-2  C4   0.020
 C9B  plan-2  N2   0.020
 C9B  plan-2  N3   0.020
 C9B  plan-2  C5   0.020
 C9B  plan-2  N4   0.020
 C9B  plan-2  H12  0.020
 C9B  plan-2  H13  0.020
 C9B  plan-2  H14  0.020
 C9B  plan-2  H15  0.020

