# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 19:09:14 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 2-cyclopropyl-N-[(2S)-3-hydroxy-3-methylbutan-2-yl]-5H-pyrrolo[2,3-b]pyrazine-7-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](NC(=O)c1c[nH]c2ncc(nc12)C3CC3)C(C)(C)O
#
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
 19Q  19Q  2-cyclopropyl-N-[(2S)-3-hydroxy-3-methylbutan-2-yl]-5H-pyrrolo[2,3-b]pyrazine-7-carboxamide  ligand  41  21  .  2022-09-22  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_19Q
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
 19Q  C1   C  CR5   0  -0.203   0.0052  -0.7149  -0.1510
 19Q  C2   C  CR15  0  -0.009  -0.1630  -2.0555  -0.4153
 19Q  N3   N  NR15  0  -0.661   1.0363  -2.6811  -0.4853
 19Q  C4   C  CR56  0   0.124   1.4176  -0.5158  -0.0446
 19Q  C5   C  CR56  0   0.474   2.0239  -1.7683  -0.2667
 19Q  N6   N  N     0  -0.377   3.3252  -1.9728  -0.2590
 19Q  C7   C  CR16  0  -0.152   4.0419  -0.8873  -0.0252
 19Q  C8   C  CR6   0   0.252   3.4714   0.3859   0.1908
 19Q  N9   N  N     0  -0.416   2.1575   0.5666   0.1792
 19Q  C10  C  C     0   0.513  -1.0400   0.2999   0.0520
 19Q  N11  N  NH1   0  -0.671  -2.2325   0.0281  -0.5225
 19Q  O12  O  O     0  -0.487  -0.8229   1.3083   0.7110
 19Q  C13  C  CH1   0  -0.075  -3.3900   0.9039  -0.4552
 19Q  C14  C  CH3   0  -0.679  -3.8950   1.1655  -1.8692
 19Q  C15  C  CT    0   0.216  -4.4643   0.3178   0.4947
 19Q  C16  C  CH3   0  -0.680  -3.8973   0.1696   1.9054
 19Q  C17  C  CH3   0  -0.675  -5.6842   1.2297   0.5350
 19Q  O18  O  OH1   0  -0.676  -4.9141  -0.9390   0.0127
 19Q  C19  C  CH1   0  -0.369   4.3070   1.5820   0.4354
 19Q  C20  C  CH2   0  -0.479   5.6094   1.4922   1.1860
 19Q  C21  C  CH2   0  -0.479   5.6213   1.7743  -0.2761
 19Q  H1   H  HCR5  0   0.311  -1.0721  -2.6227  -0.5401
 19Q  H2   H  HNR5  0   0.425   1.1699  -3.6682  -0.6404
 19Q  H3   H  HCR6  0   0.265   5.1176  -1.0168  -0.0080
 19Q  H4   H  HNH1  0   0.398  -2.2670  -0.7164  -1.2010
 19Q  H5   H  HCH1  0   0.245  -3.0533   1.8489  -0.0254
 19Q  H6   H  HCH3  0   0.242  -4.6824   1.9166  -1.8804
 19Q  H7   H  HCH3  0   0.242  -3.0816   1.5358  -2.4933
 19Q  H8   H  HCH3  0   0.227  -4.2900   0.2583  -2.3286
 19Q  H9   H  HCH3  0   0.229  -3.5442   1.1263   2.2914
 19Q  H10  H  HCH3  0   0.237  -4.6672  -0.2043   2.5823
 19Q  H11  H  HCH3  0   0.230  -3.0584  -0.5281   1.9384
 19Q  H12  H  HCH3  0   0.238  -6.2144   1.2480  -0.4173
 19Q  H13  H  HCH3  0   0.237  -6.3875   0.8956   1.2993
 19Q  H14  H  HCH3  0   0.229  -5.3913   2.2524   0.7767
 19Q  H15  H  HOH1  0   0.439  -4.2192  -1.5895   0.1595
 19Q  H16  H  HCH1  0   0.270   3.7191   2.4763   0.6032
 19Q  H17  H  HCH2  0   0.267   5.8398   2.2983   1.8704
 19Q  H18  H  HCH2  0   0.257   5.9342   0.5164   1.5249
 19Q  H19  H  HCH2  0   0.257   5.9508   0.9916  -0.9483
 19Q  H20  H  HCH2  0   0.266   5.8618   2.7756  -0.6086

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
 19Q  C17  C15  single    1.524  0.020  1.524
 19Q  O18  C15  single    1.419  0.020  1.419
 19Q  C16  C15  single    1.528  0.020  1.528
 19Q  C15  C13  single    1.549  0.020  1.549
 19Q  C13  N11  single    1.453  0.020  1.453
 19Q  C13  C14  single    1.524  0.020  1.524
 19Q  N11  C10  single    1.351  0.020  1.351
 19Q  C20  C19  single    1.506  0.020  1.506
 19Q  C20  C21  single    1.489  0.020  1.489
 19Q  O12  C10  double    1.224  0.020  1.224
 19Q  C10  C1   single    1.471  0.020  1.471
 19Q  C1   C2   aromatic  1.377  0.020  1.377
 19Q  C1   C4   aromatic  1.430  0.020  1.430
 19Q  C2   N3   aromatic  1.354  0.020  1.354
 19Q  N9   C4   aromatic  1.330  0.020  1.330
 19Q  N9   C8   aromatic  1.326  0.020  1.326
 19Q  C4   C5   aromatic  1.409  0.020  1.409
 19Q  C19  C21  single    1.507  0.020  1.507
 19Q  C19  C8   single    1.479  0.020  1.479
 19Q  C8   C7   aromatic  1.412  0.020  1.412
 19Q  N3   C5   aromatic  1.363  0.020  1.363
 19Q  C5   N6   aromatic  1.317  0.020  1.317
 19Q  C7   N6   aromatic  1.322  0.020  1.322
 19Q  C2   H1   single    0.930  0.020  1.080
 19Q  N3   H2   single    0.860  0.020  1.020
 19Q  C7   H3   single    0.930  0.020  1.080
 19Q  N11  H4   single    0.860  0.020  1.020
 19Q  C13  H5   single    0.970  0.020  1.090
 19Q  C14  H6   single    0.970  0.020  1.090
 19Q  C14  H7   single    0.970  0.020  1.090
 19Q  C14  H8   single    0.970  0.020  1.090
 19Q  C16  H9   single    0.970  0.020  1.090
 19Q  C16  H10  single    0.970  0.020  1.090
 19Q  C16  H11  single    0.970  0.020  1.090
 19Q  C17  H12  single    0.970  0.020  1.090
 19Q  C17  H13  single    0.970  0.020  1.090
 19Q  C17  H14  single    0.970  0.020  1.090
 19Q  O18  H15  single    0.850  0.020  0.980
 19Q  C19  H16  single    0.970  0.020  1.090
 19Q  C20  H17  single    0.970  0.020  1.090
 19Q  C20  H18  single    0.970  0.020  1.090
 19Q  C21  H19  single    0.970  0.020  1.090
 19Q  C21  H20  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
 19Q  C10  C1   C4   126.54  3.000
 19Q  C4   C1   C2   105.69  3.000
 19Q  C10  C1   C2   127.70  3.000
 19Q  H1   C2   N3   119.83  3.000
 19Q  H1   C2   C1   129.58  3.000
 19Q  N3   C2   C1   110.58  3.000
 19Q  H2   N3   C5   125.78  3.000
 19Q  H2   N3   C2   125.28  3.000
 19Q  C5   N3   C2   108.91  3.000
 19Q  N9   C4   C5   120.70  3.000
 19Q  C5   C4   C1   106.83  3.000
 19Q  N9   C4   C1   132.46  3.000
 19Q  N6   C5   C4   124.20  3.000
 19Q  N6   C5   N3   127.81  3.000
 19Q  C4   C5   N3   107.99  3.000
 19Q  C7   N6   C5   114.16  3.000
 19Q  H3   C7   C8   120.43  3.000
 19Q  H3   C7   N6   116.30  3.000
 19Q  C8   C7   N6   123.27  3.000
 19Q  C19  C8   N9   116.80  3.000
 19Q  C19  C8   C7   121.75  3.000
 19Q  N9   C8   C7   121.45  3.000
 19Q  C8   N9   C4   116.21  3.000
 19Q  O12  C10  N11  123.45  3.000
 19Q  O12  C10  C1   121.11  3.000
 19Q  N11  C10  C1   115.44  3.000
 19Q  H4   N11  C13  116.68  3.000
 19Q  H4   N11  C10  117.71  3.000
 19Q  C13  N11  C10  124.20  3.000
 19Q  H5   C13  C15  107.46  3.000
 19Q  H5   C13  C14  108.60  3.000
 19Q  C15  C13  C14  113.83  3.000
 19Q  H5   C13  N11  107.11  3.000
 19Q  C14  C13  N11  108.93  3.000
 19Q  C15  C13  N11  110.66  3.000
 19Q  H8   C14  H7   108.16  3.000
 19Q  H8   C14  H6   107.91  3.000
 19Q  H7   C14  H6   107.43  3.000
 19Q  H8   C14  C13  111.59  3.000
 19Q  H7   C14  C13  110.01  3.000
 19Q  H6   C14  C13  111.58  3.000
 19Q  O18  C15  C17  106.58  3.000
 19Q  O18  C15  C16  110.20  3.000
 19Q  C17  C15  C16  109.32  3.000
 19Q  C16  C15  C13  110.22  3.000
 19Q  O18  C15  C13  110.28  3.000
 19Q  C17  C15  C13  110.19  3.000
 19Q  H11  C16  H10  107.73  3.000
 19Q  H11  C16  H9   107.53  3.000
 19Q  H10  C16  H9   108.02  3.000
 19Q  H11  C16  C15  112.04  3.000
 19Q  H10  C16  C15  110.13  3.000
 19Q  H9   C16  C15  111.22  3.000
 19Q  H14  C17  H13  107.76  3.000
 19Q  H14  C17  H12  107.96  3.000
 19Q  H13  C17  H12  107.67  3.000
 19Q  H14  C17  C15  110.61  3.000
 19Q  H13  C17  C15  110.57  3.000
 19Q  H12  C17  C15  112.10  3.000
 19Q  H15  O18  C15  108.52  3.000
 19Q  H16  C19  C21  116.17  3.000
 19Q  H16  C19  C20  116.19  3.000
 19Q  C21  C19  C20   59.24  3.000
 19Q  H16  C19  C8   112.74  3.000
 19Q  C21  C19  C8   121.18  3.000
 19Q  C20  C19  C8   121.52  3.000
 19Q  H18  C20  H17  114.17  3.000
 19Q  H18  C20  C21  118.40  3.000
 19Q  H17  C20  C21  118.56  3.000
 19Q  H18  C20  C19  117.98  3.000
 19Q  H17  C20  C19  117.06  3.000
 19Q  C21  C20  C19   60.41  3.000
 19Q  H20  C21  H19  114.24  3.000
 19Q  H20  C21  C20  118.60  3.000
 19Q  H19  C21  C20  118.35  3.000
 19Q  H20  C21  C19  117.19  3.000
 19Q  H19  C21  C19  117.78  3.000
 19Q  C20  C21  C19   60.34  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
 19Q  CONST_01  C5   N3   C2   C1     0.00   0.0  0
 19Q  CONST_02  C8   N9   C4   C1   180.00   0.0  0
 19Q  CONST_03  N3   C5   C4   C1     0.00   0.0  0
 19Q  CONST_04  N6   C5   C4   C1   180.00   0.0  0
 19Q  CONST_05  N9   C4   C1   C2   180.00   0.0  0
 19Q  CONST_06  C5   C4   C1   C2     0.00   0.0  0
 19Q  CONST_07  C4   C5   N3   C2     0.00   0.0  0
 19Q  CONST_08  N6   C5   N3   C2   180.00   0.0  0
 19Q  CONST_09  C4   C1   C2   N3     0.00   0.0  0
 19Q  CONST_10  N9   C4   C5   N3   180.00   0.0  0
 19Q  CONST_11  C7   N6   C5   N3   180.00   0.0  0
 19Q  CONST_12  C7   C8   N9   C4     0.00   0.0  0
 19Q  CONST_13  C7   N6   C5   C4     0.00   0.0  0
 19Q  CONST_14  C8   N9   C4   C5     0.00   0.0  0
 19Q  CONST_15  C8   C7   N6   C5     0.00   0.0  0
 19Q  CONST_16  N9   C4   C5   N6     0.00   0.0  0
 19Q  CONST_17  N9   C8   C7   N6     0.00   0.0  0
 19Q  CONST_18  C19  C8   N9   C4   180.00   0.0  0
 19Q  CONST_19  C19  C8   C7   N6   180.00   0.0  0
 19Q  CONST_20  C10  C1   C2   N3   180.00   0.0  0
 19Q  CONST_21  C10  C1   C4   C5   180.00   0.0  0
 19Q  CONST_22  C10  C1   C4   N9     0.00   0.0  0
 19Q  CONST_23  H2   N3   C2   C1   180.00   0.0  0
 19Q  CONST_24  H1   C2   C1   C4   180.00   0.0  0
 19Q  CONST_25  H3   C7   N6   C5   180.00   0.0  0
 19Q  CONST_26  C13  N11  C10  C1   180.00   0.0  0
 19Q  CONST_27  H4   N11  C10  C1     0.00   0.0  0
 19Q  CONST_28  C13  N11  C10  O12    0.00   0.0  0
 19Q  Var_01    C20  C19  C8   C7   -33.86  30.0  3
 19Q  Var_02    C21  C20  C19  C8   109.99  30.0  1
 19Q  Var_03    N11  C10  C1   C2   -24.90  30.0  2
 19Q  Var_04    H12  C17  C15  C13   67.37  30.0  3
 19Q  Var_05    H9   C16  C15  C13   57.93  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
 19Q  chir_01  C13  C15  N11  C14  negativ
 19Q  chir_02  C19  C20  C21  C8   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
 19Q  plan-1  C1   0.020
 19Q  plan-1  C2   0.020
 19Q  plan-1  N3   0.020
 19Q  plan-1  C4   0.020
 19Q  plan-1  C5   0.020
 19Q  plan-1  N6   0.020
 19Q  plan-1  C7   0.020
 19Q  plan-1  C8   0.020
 19Q  plan-1  N9   0.020
 19Q  plan-1  C10  0.020
 19Q  plan-1  C19  0.020
 19Q  plan-1  H1   0.020
 19Q  plan-1  H2   0.020
 19Q  plan-1  H3   0.020
 19Q  plan-2  C1   0.020
 19Q  plan-2  C10  0.020
 19Q  plan-2  N11  0.020
 19Q  plan-2  O12  0.020
 19Q  plan-2  C13  0.020
 19Q  plan-2  H4   0.020

