# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 18:06:39 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: (2R)-2-amino-1-[2-(propan-2-yl)pyrazolo[1,5-a]pyridin-3-yl]propan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)c1nn2ccccc2c1C(=O)[C@@H](C)N
#
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
 AVR  AVR  (2R)-2-amino-1-[2-(propan-2-yl)pyrazolo[1,5-a]pyridin-3-yl]propan-1-one  ligand  34  17  .  2022-07-24  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_AVR
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
 AVR  C     C  C     0   0.326  -0.9549  -1.4771   0.4084
 AVR  N     N  NH2   0  -0.783  -3.2632  -2.2438   0.4251
 AVR  O     O  O     0  -0.428  -0.6185  -2.5037   0.9767
 AVR  N1    N  N     0  -0.326   0.9548   1.6591   0.0091
 AVR  C2    C  CR5   0   0.372  -0.2025   1.0265   0.0549
 AVR  C3    C  CR5   0  -0.370  -0.0245  -0.3641   0.2774
 AVR  C4    C  CR56  0   0.589   1.3702  -0.5256   0.3792
 AVR  N5    N  N     0  -0.395   1.8944   0.7227   0.1870
 AVR  C6    C  CR16  0   0.034   3.2228   0.9905   0.1815
 AVR  C7    C  CR16  0  -0.384   4.0979  -0.0304   0.3773
 AVR  C8    C  CR16  0  -0.139   3.6096  -1.3405   0.5807
 AVR  C9    C  CR16  0  -0.400   2.2655  -1.5925   0.5847
 AVR  CA    C  CH1   0  -0.236  -2.3025  -1.4268  -0.2901
 AVR  CB    C  CH3   0  -0.675  -2.0679  -1.8481  -1.7496
 AVR  C11   C  CH3   0  -0.642  -1.3158   3.2100   0.5765
 AVR  C12   C  CH3   0  -0.653  -1.8449   1.9971  -1.5590
 AVR  HN    H  HNH2  0   0.351  -4.1433  -2.2220  -0.0749
 AVR  HNA   H  HNH2  0   0.341  -2.9621  -3.2107   0.4125
 AVR  H6    H  HCR6  0   0.317   3.5021   2.0202   0.0166
 AVR  H7    H  HCR6  0   0.285   5.1580   0.1740   0.3749
 AVR  H8    H  HCR6  0   0.281   4.3092  -2.1497   0.7380
 AVR  H9    H  HCR6  0   0.280   1.8820  -2.5870   0.7480
 AVR  HA    H  HCH1  0   0.252  -2.6801  -0.4049  -0.2949
 AVR  HB    H  HCH3  0   0.234  -1.7305  -2.8851  -1.7992
 AVR  HBA   H  HCH3  0   0.245  -2.9974  -1.7661  -2.3141
 AVR  HBB   H  HCH3  0   0.231  -1.3207  -1.2274  -2.2466
 AVR  H10   H  HCH1  0   0.254  -2.2641   1.3161   0.4317
 AVR  H11   H  HCH3  0   0.233  -1.0447   3.1197   1.6285
 AVR  H11A  H  HCH3  0   0.226  -0.5558   3.8158   0.0836
 AVR  H11B  H  HCH3  0   0.232  -2.2629   3.7474   0.5192
 AVR  H12   H  HCH3  0   0.239  -1.9984   1.0367  -2.0515
 AVR  H12A  H  HCH3  0   0.237  -2.7706   2.5672  -1.6473
 AVR  H12B  H  HCH3  0   0.230  -1.0669   2.5316  -2.1060
 AVR  C10   C  CH1   0  -0.359  -1.4587   1.8411  -0.0859

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
 AVR  C    O     double    1.221  0.020  1.221
 AVR  C    C3    single    1.457  0.020  1.457
 AVR  C    CA    single    1.519  0.020  1.519
 AVR  N    CA    single    1.450  0.020  1.450
 AVR  N1   C2    aromatic  1.320  0.020  1.320
 AVR  N1   N5    aromatic  1.338  0.020  1.338
 AVR  C2   C3    aromatic  1.420  0.020  1.420
 AVR  C2   C10   single    1.504  0.020  1.504
 AVR  C3   C4    aromatic  1.408  0.020  1.408
 AVR  C4   N5    aromatic  1.367  0.020  1.367
 AVR  C4   C9    aromatic  1.408  0.020  1.408
 AVR  N5   C6    aromatic  1.355  0.020  1.355
 AVR  C6   C7    aromatic  1.359  0.020  1.359
 AVR  C7   C8    aromatic  1.413  0.020  1.413
 AVR  C8   C9    aromatic  1.368  0.020  1.368
 AVR  CA   CB    single    1.537  0.020  1.537
 AVR  C10  C11   single    1.527  0.020  1.527
 AVR  C10  C12   single    1.531  0.020  1.531
 AVR  N    HN    single    0.890  0.020  1.040
 AVR  N    HNA   single    0.890  0.020  1.040
 AVR  C6   H6    single    0.930  0.020  1.080
 AVR  C7   H7    single    0.930  0.020  1.080
 AVR  C8   H8    single    0.930  0.020  1.080
 AVR  C9   H9    single    0.930  0.020  1.080
 AVR  CA   HA    single    0.970  0.020  1.090
 AVR  CB   HB    single    0.970  0.020  1.090
 AVR  CB   HBA   single    0.970  0.020  1.090
 AVR  CB   HBB   single    0.970  0.020  1.090
 AVR  C10  H10   single    0.970  0.020  1.090
 AVR  C11  H11   single    0.970  0.020  1.090
 AVR  C11  H11A  single    0.970  0.020  1.090
 AVR  C11  H11B  single    0.970  0.020  1.090
 AVR  C12  H12   single    0.970  0.020  1.090
 AVR  C12  H12A  single    0.970  0.020  1.090
 AVR  C12  H12B  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
 AVR  CA    C    C3    120.01  3.000
 AVR  CA    C    O     119.11  3.000
 AVR  C3    C    O     120.56  3.000
 AVR  HNA   N    HN    105.83  3.000
 AVR  HNA   N    CA    109.57  3.000
 AVR  HN    N    CA    108.68  3.000
 AVR  N5    N1   C2    106.00  3.000
 AVR  C10   C2   C3    130.55  3.000
 AVR  C10   C2   N1    118.01  3.000
 AVR  C3    C2   N1    111.41  3.000
 AVR  C4    C3   C2    104.35  3.000
 AVR  C4    C3   C     122.60  3.000
 AVR  C2    C3   C     133.04  3.000
 AVR  C9    C4   N5    117.94  3.000
 AVR  C9    C4   C3    136.68  3.000
 AVR  N5    C4   C3    105.36  3.000
 AVR  C6    N5   C4    123.83  3.000
 AVR  C6    N5   N1    123.33  3.000
 AVR  C4    N5   N1    112.84  3.000
 AVR  H6    C6   C7    124.89  3.000
 AVR  H6    C6   N5    116.28  3.000
 AVR  C7    C6   N5    118.83  3.000
 AVR  H7    C7   C8    121.02  3.000
 AVR  H7    C7   C6    119.32  3.000
 AVR  C8    C7   C6    119.66  3.000
 AVR  H8    C8   C9    119.84  3.000
 AVR  H8    C8   C7    119.43  3.000
 AVR  C9    C8   C7    120.73  3.000
 AVR  H9    C9   C8    121.33  3.000
 AVR  H9    C9   C4    119.66  3.000
 AVR  C8    C9   C4    119.01  3.000
 AVR  HA    CA   CB    107.81  3.000
 AVR  HA    CA   N     107.52  3.000
 AVR  CB    CA   N     114.52  3.000
 AVR  HA    CA   C     109.91  3.000
 AVR  CB    CA   C     106.99  3.000
 AVR  N     CA   C     110.03  3.000
 AVR  HBB   CB   HBA   107.77  3.000
 AVR  HBB   CB   HB    107.94  3.000
 AVR  HBA   CB   HB    108.14  3.000
 AVR  HBB   CB   CA    112.40  3.000
 AVR  HBA   CB   CA    109.92  3.000
 AVR  HB    CB   CA    110.52  3.000
 AVR  H11B  C11  H11A  107.93  3.000
 AVR  H11B  C11  H11   107.91  3.000
 AVR  H11A  C11  H11   108.00  3.000
 AVR  H11B  C11  C10   109.74  3.000
 AVR  H11A  C11  C10   111.56  3.000
 AVR  H11   C11  C10   111.56  3.000
 AVR  H12B  C12  H12A  107.97  3.000
 AVR  H12B  C12  H12   107.79  3.000
 AVR  H12A  C12  H12   107.73  3.000
 AVR  H12B  C12  C10   110.63  3.000
 AVR  H12A  C12  C10   110.20  3.000
 AVR  H12   C12  C10   112.36  3.000
 AVR  H10   C10  C12   108.61  3.000
 AVR  H10   C10  C11   107.12  3.000
 AVR  C12   C10  C11   110.46  3.000
 AVR  H10   C10  C2    108.14  3.000
 AVR  C12   C10  C2    110.86  3.000
 AVR  C11   C10  C2    111.52  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
 AVR  CONST_01  C4   C3   C2   N1     0.00   0.0  0
 AVR  CONST_02  C3   C4   N5   N1     0.00   0.0  0
 AVR  CONST_03  C9   C4   N5   N1   180.00   0.0  0
 AVR  CONST_04  C7   C6   N5   N1   180.00   0.0  0
 AVR  CONST_05  C4   N5   N1   C2     0.00   0.0  0
 AVR  CONST_06  C6   N5   N1   C2   180.00   0.0  0
 AVR  CONST_07  N5   C4   C3   C2     0.00   0.0  0
 AVR  CONST_08  C9   C4   C3   C2   180.00   0.0  0
 AVR  CONST_09  N5   N1   C2   C3     0.00   0.0  0
 AVR  CONST_10  C6   N5   C4   C3   180.00   0.0  0
 AVR  CONST_11  C8   C9   C4   C3   180.00   0.0  0
 AVR  CONST_12  C7   C6   N5   C4     0.00   0.0  0
 AVR  CONST_13  C7   C8   C9   C4     0.00   0.0  0
 AVR  CONST_14  C8   C9   C4   N5     0.00   0.0  0
 AVR  CONST_15  C8   C7   C6   N5     0.00   0.0  0
 AVR  CONST_16  C9   C4   N5   C6     0.00   0.0  0
 AVR  CONST_17  C9   C8   C7   C6     0.00   0.0  0
 AVR  CONST_18  N1   C2   C3   C    180.00   0.0  0
 AVR  CONST_19  N5   C4   C3   C    180.00   0.0  0
 AVR  CONST_20  C9   C4   C3   C      0.00   0.0  0
 AVR  CONST_21  C10  C2   C3   C4   180.00   0.0  0
 AVR  CONST_22  C10  C2   N1   N5   180.00   0.0  0
 AVR  CONST_23  H6   C6   N5   N1     0.00   0.0  0
 AVR  CONST_24  H9   C9   C4   C3     0.00   0.0  0
 AVR  CONST_25  H8   C8   C9   C4   180.00   0.0  0
 AVR  CONST_26  H7   C7   C6   N5   180.00   0.0  0
 AVR  Var_01    C2   C3   C    O   -158.22  30.0  2
 AVR  Var_02    C11  C10  C2   N1   -35.48  30.0  2
 AVR  Var_03    H11  C11  C10  C2   -56.48  30.0  3
 AVR  Var_04    H12  C12  C10  C2    58.40  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
 AVR  chir_01  CA  C  N  CB  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
 AVR  plan-1  C    0.020
 AVR  plan-1  N1   0.020
 AVR  plan-1  C2   0.020
 AVR  plan-1  C3   0.020
 AVR  plan-1  C4   0.020
 AVR  plan-1  N5   0.020
 AVR  plan-1  C6   0.020
 AVR  plan-1  C7   0.020
 AVR  plan-1  C8   0.020
 AVR  plan-1  C9   0.020
 AVR  plan-1  H6   0.020
 AVR  plan-1  H7   0.020
 AVR  plan-1  H8   0.020
 AVR  plan-1  H9   0.020
 AVR  plan-1  C10  0.020
 AVR  plan-2  C    0.020
 AVR  plan-2  O    0.020
 AVR  plan-2  C3   0.020
 AVR  plan-2  CA   0.020

