# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 11:05:21 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 3-oxo-3-[(3R)-3-(pyrrolo[2,3-b][1,2,3]triazolo[4,5-d]pyridin-1(6H)-yl)piperidin-1-yl]propanenitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(CC#N)N1CCC[C@H](C1)n2nnc3cnc4[nH]ccc4c23
#
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
 C5I  C5I  3-oxo-3-[(3R)-3-(pyrrolo[2,3-b][1,2,3]triazolo[4,5-d]pyridin-1(6H)-yl)piperidin-1-yl]propanenitrile  ligand  38  23  .  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_C5I
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
 C5I  C1    C  CR15  0  -0.442   1.6895  -2.1227  -0.8722
 C5I  C2    C  CR15  0  -0.004   2.6111  -3.1340  -0.9239
 C5I  N3    N  NR15  0  -0.649   3.7918  -2.7096  -0.3936
 C5I  C5    C  CR56  0   0.436   3.6711  -1.4194   0.0139
 C5I  C6    C  CR56  0   0.008   2.3509  -1.0165  -0.2746
 C5I  C7    C  CR56  0   0.442   2.0913   0.3097   0.0975
 C5I  C8    C  CR56  0  -0.004   3.0997   1.0725   0.6868
 C5I  C9    C  CR16  0  -0.114   4.3795   0.5293   0.9136
 C5I  N10   N  N     0  -0.422   4.6569  -0.7058   0.5783
 C5I  N11   N  N     0  -0.298   2.5951   2.3112   0.9483
 C5I  N12   N  N     0  -0.071   1.3818   2.3402   0.5623
 C5I  N13   N  NR5   0  -0.419   1.0427   1.1535   0.0442
 C5I  C14   C  CH1   0  -0.112  -0.2940   0.9329  -0.4748
 C5I  C16   C  CH2   0  -0.445  -0.6060   1.8643  -1.6423
 C5I  C17   C  CH2   0  -0.443  -2.0373   1.6430  -2.1173
 C5I  C18   C  CH2   0  -0.331  -3.0202   1.7609  -0.9610
 C5I  N19   N  NT    0  -0.464  -2.6515   0.8412   0.1062
 C5I  C20   C  CH2   0  -0.309  -1.3276   1.0808   0.6462
 C5I  C21   C  C     0   0.592  -3.3491  -0.2462   0.4808
 C5I  O22   O  O     0  -0.474  -2.9630  -1.0479   1.3138
 C5I  C23   C  CH2   0  -0.712  -4.7055  -0.4443  -0.1913
 C5I  C24   C  CSP   0   0.149  -5.3630  -1.6209   0.3465
 C5I  N25   N  NS    0  -0.261  -5.9180  -2.5437   0.7479
 C5I  H1    H  HCR5  0   0.258   0.6732  -2.1821  -1.2257
 C5I  H2    H  HCR5  0   0.294   2.5085  -4.1362  -1.3057
 C5I  HN3   H  HNR5  0   0.417   4.6289  -3.2650  -0.3168
 C5I  H9    H  HCR6  0   0.278   5.1632   1.1230   1.3699
 C5I  H14   H  HCH1  0   0.281  -0.3160  -0.1008  -0.8259
 C5I  H16   H  HCH2  0   0.246  -0.4791   2.9011  -1.3187
 C5I  H16A  H  HCH2  0   0.266   0.1009   1.6901  -2.4552
 C5I  H17   H  HCH2  0   0.260  -2.2926   2.3759  -2.8836
 C5I  H17A  H  HCH2  0   0.240  -2.1329   0.6534  -2.5730
 C5I  H18   H  HCH2  0   0.262  -3.0036   2.7761  -0.5540
 C5I  H18A  H  HCH2  0   0.289  -4.0351   1.5769  -1.3001
 C5I  H20   H  HCH2  0   0.289  -1.1216   0.3838   1.4543
 C5I  H20A  H  HCH2  0   0.269  -1.2908   2.0952   1.0535
 C5I  H23   H  HCH2  0   0.350  -5.3613   0.4158  -0.0382
 C5I  H23A  H  HCH2  0   0.347  -4.6004  -0.5745  -1.2712

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
 C5I  C1   C2    aromatic  1.369  0.020  1.369
 C5I  C1   C6    aromatic  1.421  0.020  1.421
 C5I  C2   N3    aromatic  1.362  0.020  1.362
 C5I  N3   C5    aromatic  1.358  0.020  1.358
 C5I  C5   C6    aromatic  1.410  0.020  1.410
 C5I  C5   N10   aromatic  1.342  0.020  1.342
 C5I  C6   C7    aromatic  1.402  0.020  1.402
 C5I  C7   C8    aromatic  1.395  0.020  1.395
 C5I  C7   N13   aromatic  1.347  0.020  1.347
 C5I  C8   C9    aromatic  1.409  0.020  1.409
 C5I  C8   N11   aromatic  1.363  0.020  1.363
 C5I  C9   N10   aromatic  1.310  0.020  1.310
 C5I  N11  N12   aromatic  1.274  0.020  1.274
 C5I  N12  N13   aromatic  1.339  0.020  1.339
 C5I  N13  C14   single    1.451  0.020  1.451
 C5I  C14  C16   single    1.526  0.020  1.526
 C5I  C14  C20   single    1.532  0.020  1.532
 C5I  C16  C17   single    1.524  0.020  1.524
 C5I  C17  C18   single    1.522  0.020  1.522
 C5I  C18  N19   single    1.456  0.020  1.456
 C5I  N19  C20   single    1.450  0.020  1.450
 C5I  N19  C21   single    1.345  0.020  1.345
 C5I  C21  O22   double    1.219  0.020  1.219
 C5I  C21  C23   single    1.527  0.020  1.527
 C5I  C23  C24   single    1.451  0.020  1.451
 C5I  C24  N25   triple    1.149  0.020  1.149
 C5I  C1   H1    single    0.930  0.020  1.080
 C5I  C2   H2    single    0.930  0.020  1.080
 C5I  N3   HN3   single    0.860  0.020  1.020
 C5I  C9   H9    single    0.930  0.020  1.080
 C5I  C14  H14   single    0.970  0.020  1.090
 C5I  C16  H16   single    0.970  0.020  1.090
 C5I  C16  H16A  single    0.970  0.020  1.090
 C5I  C17  H17   single    0.970  0.020  1.090
 C5I  C17  H17A  single    0.970  0.020  1.090
 C5I  C18  H18   single    0.970  0.020  1.090
 C5I  C18  H18A  single    0.970  0.020  1.090
 C5I  C20  H20   single    0.970  0.020  1.090
 C5I  C20  H20A  single    0.970  0.020  1.090
 C5I  C23  H23   single    0.970  0.020  1.090
 C5I  C23  H23A  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
 C5I  H1    C1   C6   128.31  3.000
 C5I  H1    C1   C2   125.57  3.000
 C5I  C6    C1   C2   106.12  3.000
 C5I  H2    C2   N3   120.69  3.000
 C5I  H2    C2   C1   129.52  3.000
 C5I  N3    C2   C1   109.79  3.000
 C5I  HN3   N3   C5   125.07  3.000
 C5I  HN3   N3   C2   125.32  3.000
 C5I  C5    N3   C2   109.61  3.000
 C5I  N10   C5   C6   128.47  3.000
 C5I  N10   C5   N3   124.48  3.000
 C5I  C6    C5   N3   107.05  3.000
 C5I  C7    C6   C5   112.92  3.000
 C5I  C7    C6   C1   139.66  3.000
 C5I  C5    C6   C1   107.42  3.000
 C5I  N13   C7   C8   103.70  3.000
 C5I  N13   C7   C6   136.58  3.000
 C5I  C8    C7   C6   119.71  3.000
 C5I  N11   C8   C9   130.99  3.000
 C5I  N11   C8   C7   108.09  3.000
 C5I  C9    C8   C7   120.92  3.000
 C5I  H9    C9   N10  118.11  3.000
 C5I  H9    C9   C8   120.90  3.000
 C5I  N10   C9   C8   120.99  3.000
 C5I  C9    N10  C5   116.99  3.000
 C5I  N12   N11  C8   108.38  3.000
 C5I  N13   N12  N11  109.79  3.000
 C5I  C14   N13  N12  120.45  3.000
 C5I  C14   N13  C7   129.50  3.000
 C5I  N12   N13  C7   110.05  3.000
 C5I  H14   C14  C20  108.24  3.000
 C5I  H14   C14  C16  109.13  3.000
 C5I  C20   C14  C16  111.29  3.000
 C5I  H14   C14  N13  106.11  3.000
 C5I  C20   C14  N13  110.19  3.000
 C5I  C16   C14  N13  111.67  3.000
 C5I  H16A  C16  H16  107.25  3.000
 C5I  H16A  C16  C17  110.67  3.000
 C5I  H16   C16  C17  109.81  3.000
 C5I  H16A  C16  C14  109.88  3.000
 C5I  H16   C16  C14  109.19  3.000
 C5I  C17   C16  C14  109.99  3.000
 C5I  H17A  C17  H17  107.15  3.000
 C5I  H17A  C17  C18  109.28  3.000
 C5I  H17   C17  C18  109.30  3.000
 C5I  H17A  C17  C16  110.08  3.000
 C5I  H17   C17  C16  109.95  3.000
 C5I  C18   C17  C16  111.00  3.000
 C5I  H18A  C18  H18  106.72  3.000
 C5I  H18A  C18  N19  111.01  3.000
 C5I  H18   C18  N19  108.04  3.000
 C5I  H18A  C18  C17  110.68  3.000
 C5I  H18   C18  C17  110.17  3.000
 C5I  N19   C18  C17  110.13  3.000
 C5I  C21   N19  C20  120.22  3.000
 C5I  C21   N19  C18  125.68  3.000
 C5I  C20   N19  C18  113.57  3.000
 C5I  H20A  C20  H20  108.15  3.000
 C5I  H20A  C20  N19  108.83  3.000
 C5I  H20   C20  N19  110.13  3.000
 C5I  H20A  C20  C14  109.84  3.000
 C5I  H20   C20  C14  110.75  3.000
 C5I  N19   C20  C14  109.12  3.000
 C5I  C23   C21  O22  119.80  3.000
 C5I  C23   C21  N19  116.30  3.000
 C5I  O22   C21  N19  123.90  3.000
 C5I  H23A  C23  H23  106.86  3.000
 C5I  H23A  C23  C24  108.24  3.000
 C5I  H23   C23  C24  108.32  3.000
 C5I  H23A  C23  C21  111.42  3.000
 C5I  H23   C23  C21  111.69  3.000
 C5I  C24   C23  C21  110.16  3.000
 C5I  N25   C24  C23  180.00  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
 C5I  CONST_01  C5   N3   C2   C1      0.00   0.0  0
 C5I  CONST_02  N3   C5   C6   C1      0.00   0.0  0
 C5I  CONST_03  N10  C5   C6   C1    180.00   0.0  0
 C5I  CONST_04  C8   C7   C6   C1    180.00   0.0  0
 C5I  CONST_05  N13  C7   C6   C1      0.00   0.0  0
 C5I  CONST_06  C5   C6   C1   C2      0.00   0.0  0
 C5I  CONST_07  C7   C6   C1   C2    180.00   0.0  0
 C5I  CONST_08  C6   C5   N3   C2      0.00   0.0  0
 C5I  CONST_09  N10  C5   N3   C2    180.00   0.0  0
 C5I  CONST_10  C6   C1   C2   N3      0.00   0.0  0
 C5I  CONST_11  C7   C6   C5   N3    180.00   0.0  0
 C5I  CONST_12  C9   N10  C5   N3    180.00   0.0  0
 C5I  CONST_13  C8   C7   C6   C5      0.00   0.0  0
 C5I  CONST_14  N13  C7   C6   C5    180.00   0.0  0
 C5I  CONST_15  C8   C9   N10  C5      0.00   0.0  0
 C5I  CONST_16  C9   N10  C5   C6      0.00   0.0  0
 C5I  CONST_17  C9   C8   C7   C6      0.00   0.0  0
 C5I  CONST_18  N11  C8   C7   C6    180.00   0.0  0
 C5I  CONST_19  N12  N13  C7   C6    180.00   0.0  0
 C5I  CONST_20  N10  C5   C6   C7      0.00   0.0  0
 C5I  CONST_21  N10  C9   C8   C7      0.00   0.0  0
 C5I  CONST_22  N12  N11  C8   C7      0.00   0.0  0
 C5I  CONST_23  N11  N12  N13  C7      0.00   0.0  0
 C5I  CONST_24  N12  N13  C7   C8      0.00   0.0  0
 C5I  CONST_25  N13  N12  N11  C8      0.00   0.0  0
 C5I  CONST_26  N13  C7   C8   C9    180.00   0.0  0
 C5I  CONST_27  N12  N11  C8   C9    180.00   0.0  0
 C5I  CONST_28  N11  C8   C9   N10   180.00   0.0  0
 C5I  CONST_29  N13  C7   C8   N11     0.00   0.0  0
 C5I  CONST_30  C14  N13  C7   C6      0.00   0.0  0
 C5I  CONST_31  C14  N13  C7   C8    180.00   0.0  0
 C5I  CONST_32  C14  N13  N12  N11   180.00   0.0  0
 C5I  CONST_33  HN3  N3   C2   C1    180.00   0.0  0
 C5I  CONST_34  H1   C1   C2   N3    180.00   0.0  0
 C5I  CONST_35  H2   C2   N3   C5    180.00   0.0  0
 C5I  CONST_36  H9   C9   N10  C5    180.00   0.0  0
 C5I  CONST_37  O22  C21  N19  C18   180.00   0.0  0
 C5I  CONST_38  C23  C21  N19  C18     0.00   0.0  0
 C5I  CONST_39  O22  C21  N19  C20     0.00   0.0  0
 C5I  CONST_40  C23  C21  N19  C20   180.00   0.0  0
 C5I  Var_01    C18  C17  C16  C14    53.29  30.0  1
 C5I  Var_02    C18  N19  C20  C14   -59.82  30.0  1
 C5I  Var_03    N19  C18  C17  C16   -55.39  30.0  1
 C5I  Var_04    C20  N19  C18  C17    59.91  30.0  1
 C5I  Var_05    C24  C23  C21  N19  -177.75  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
 C5I  chir_01  C14  N13  C16  C20  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
 C5I  plan-1  C1   0.020
 C5I  plan-1  C2   0.020
 C5I  plan-1  N3   0.020
 C5I  plan-1  C5   0.020
 C5I  plan-1  C6   0.020
 C5I  plan-1  C7   0.020
 C5I  plan-1  C8   0.020
 C5I  plan-1  C9   0.020
 C5I  plan-1  N10  0.020
 C5I  plan-1  N11  0.020
 C5I  plan-1  N12  0.020
 C5I  plan-1  N13  0.020
 C5I  plan-1  C14  0.020
 C5I  plan-1  H1   0.020
 C5I  plan-1  H2   0.020
 C5I  plan-1  HN3  0.020
 C5I  plan-1  H9   0.020
 C5I  plan-2  C18  0.020
 C5I  plan-2  N19  0.020
 C5I  plan-2  C20  0.020
 C5I  plan-2  C21  0.020
 C5I  plan-2  O22  0.020
 C5I  plan-2  C23  0.020

