# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 13:28:21 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: 2-[2-(oxan-4-ylamino)pyrimidin-4-yl]-5-(phenylmethyl)-6,7-dihydro-1~{H}-pyrrolo[3,2-c]pyridin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1N(CCc2[nH]c(cc12)c3ccnc(NC4CCOCC4)n3)Cc5ccccc5
#
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
 8X5  8X5  2-[2-(oxan-4-ylamino)pyrimidin-4-yl]-5-(phenylmethyl)-6,7-dihydro-1~{H}-pyrrolo[3,2-c]pyridin-4-one  ligand  55  30  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8X5
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
 8X5  C1   C  CR16  0  -0.241  -8.6467  -0.7982   0.1674
 8X5  C2   C  CR16  0  -0.312  -7.6285  -0.6558  -0.7665
 8X5  C3   C  CR6   0   0.096  -6.2946  -0.7775  -0.3895
 8X5  C7   C  CH2   0  -0.293  -4.1273   1.4218  -0.7086
 8X5  C8   C  CH2   0  -0.530  -3.2451   1.9265   0.4256
 8X5  C9   C  CR5   0   0.372  -1.9008   1.3396   0.2218
 8X5  C10  C  CR5   0  -0.146  -1.6996   0.1449  -0.4385
 8X5  C11  C  CR15  0  -0.383  -0.3175  -0.1371  -0.4006
 8X5  C12  C  CR5   0   0.309   0.2823   0.9017   0.2754
 8X5  C13  C  CR6   0   0.250   1.6853   1.1109   0.5782
 8X5  C14  C  CR16  0  -0.401   2.1509   2.2360   1.2655
 8X5  C15  C  CR16  0  -0.015   3.5144   2.2948   1.4782
 8X5  C16  C  CR6   0   0.593   3.8192   0.3213   0.4313
 8X5  C19  C  CH2   0  -0.186   8.2516   0.0843  -0.8755
 8X5  C20  C  CH2   0  -0.183   8.1470  -2.0355   0.1069
 8X5  C21  C  CH2   0  -0.471   6.6263  -2.0643   0.0686
 8X5  C22  C  C     0   0.525  -2.8102  -0.6504  -0.9564
 8X5  O1   O  O     0  -0.495  -2.6628  -1.8027  -1.3481
 8X5  N    N  NT    0  -0.499  -4.0163  -0.0184  -0.9253
 8X5  C6   C  CH2   0  -0.355  -5.2043  -0.6708  -1.4284
 8X5  C4   C  CR16  0  -0.289  -5.9956  -1.0327   0.9465
 8X5  C5   C  CR16  0  -0.239  -7.0108  -1.1698   1.8832
 8X5  C    C  CR16  0  -0.270  -8.3403  -1.0558   1.4967
 8X5  N1   N  NR15  0  -0.719  -0.7102   1.7844   0.6476
 8X5  N3   N  N     0  -0.503   2.5192   0.1637   0.1652
 8X5  N2   N  N     0  -0.470   4.3625   1.3628   1.0736
 8X5  N4   N  NH1   0  -0.671   4.6356  -0.6694   0.0252
 8X5  C17  C  CH1   0  -0.058   6.0768  -0.6434   0.1232
 8X5  O    O  O2    0  -0.483   8.6905  -1.2560  -0.9351
 8X5  C18  C  CH2   0  -0.456   6.7373   0.1930  -0.9729
 8X5  H1   H  HCR6  0   0.255  -9.6791  -0.6992  -0.1428
 8X5  H2   H  HCR6  0   0.251  -7.8751  -0.4432  -1.8004
 8X5  H3   H  HCH2  0   0.266  -5.1688   1.6450  -0.4819
 8X5  H4   H  HCH2  0   0.256  -3.8741   1.9531  -1.6324
 8X5  H5   H  HCH2  0   0.278  -3.2290   3.0170   0.4116
 8X5  H6   H  HCH2  0   0.271  -3.6495   1.6207   1.3958
 8X5  H7   H  HCR5  0   0.256   0.1902  -0.9896  -0.8213
 8X5  H8   H  HCR6  0   0.258   1.5104   3.0305   1.6180
 8X5  H9   H  HCR6  0   0.268   3.9449   3.1429   2.0002
 8X5  H11  H  HCH2  0   0.238   8.7289   0.6135  -1.7017
 8X5  H12  H  HCH2  0   0.199   8.4784  -1.6520   1.0833
 8X5  H13  H  HCH2  0   0.239   8.5500  -3.0436  -0.0028
 8X5  H14  H  HCH2  0   0.231   6.2910  -2.5569  -0.8506
 8X5  H15  H  HCH2  0   0.248   6.2538  -2.6524   0.9106
 8X5  H16  H  HCH2  0   0.281  -4.9289  -1.6648  -1.7792
 8X5  H17  H  HCH2  0   0.259  -5.5799  -0.1255  -2.3006
 8X5  H18  H  HCR6  0   0.247  -4.9630  -1.1203   1.2622
 8X5  H19  H  HCR6  0   0.255  -6.7624  -1.3657   2.9185
 8X5  H20  H  HCR6  0   0.255  -9.1313  -1.1613   2.2278
 8X5  H21  H  HNR5  0   0.421  -0.5754   2.6369   1.1683
 8X5  H22  H  HNH1  0   0.386   4.2088  -1.3927  -0.5316
 8X5  H23  H  HCH1  0   0.240   6.3398  -0.2100   1.0926
 8X5  H24  H  HCH2  0   0.242   6.4429   1.2409  -0.8814
 8X5  H25  H  HCH2  0   0.225   6.4002  -0.1606  -1.9522
 8X5  H10  H  HCH2  0   0.198   8.5950   0.5553   0.0580

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
 8X5  C    C1   aromatic  1.388  0.020  1.388
 8X5  C    C5   aromatic  1.389  0.020  1.389
 8X5  C1   C2   aromatic  1.389  0.020  1.389
 8X5  C5   C4   aromatic  1.388  0.020  1.388
 8X5  C2   C3   aromatic  1.392  0.020  1.392
 8X5  C4   C3   aromatic  1.393  0.020  1.393
 8X5  C3   C6   single    1.510  0.020  1.510
 8X5  O1   C22  double    1.226  0.020  1.226
 8X5  C6   N    single    1.446  0.020  1.446
 8X5  C22  N    single    1.362  0.020  1.362
 8X5  C22  C10  single    1.461  0.020  1.461
 8X5  N    C7   single    1.461  0.020  1.461
 8X5  C11  C10  aromatic  1.411  0.020  1.411
 8X5  C11  C12  aromatic  1.377  0.020  1.377
 8X5  C10  C9   aromatic  1.380  0.020  1.380
 8X5  C14  C15  aromatic  1.381  0.020  1.381
 8X5  C14  C13  aromatic  1.398  0.020  1.398
 8X5  C12  C13  single    1.450  0.020  1.450
 8X5  C12  N1   aromatic  1.379  0.020  1.379
 8X5  C15  N2   aromatic  1.323  0.020  1.323
 8X5  C9   C8   single    1.481  0.020  1.481
 8X5  C9   N1   aromatic  1.340  0.020  1.340
 8X5  C13  N3   aromatic  1.328  0.020  1.328
 8X5  C7   C8   single    1.523  0.020  1.523
 8X5  N2   C16  aromatic  1.339  0.020  1.339
 8X5  N3   C16  aromatic  1.336  0.020  1.336
 8X5  C16  N4   single    1.346  0.020  1.346
 8X5  N4   C17  single    1.445  0.020  1.445
 8X5  C17  C21  single    1.524  0.020  1.524
 8X5  C17  C18  single    1.529  0.020  1.529
 8X5  C21  C20  single    1.521  0.020  1.521
 8X5  C20  O    single    1.410  0.020  1.410
 8X5  C18  C19  single    1.521  0.020  1.521
 8X5  C19  O    single    1.412  0.020  1.412
 8X5  C1   H1   single    0.930  0.020  1.080
 8X5  C2   H2   single    0.930  0.020  1.080
 8X5  C7   H3   single    0.970  0.020  1.090
 8X5  C7   H4   single    0.970  0.020  1.090
 8X5  C8   H5   single    0.970  0.020  1.090
 8X5  C8   H6   single    0.970  0.020  1.090
 8X5  C11  H7   single    0.930  0.020  1.080
 8X5  C14  H8   single    0.930  0.020  1.080
 8X5  C15  H9   single    0.930  0.020  1.080
 8X5  C19  H10  single    0.970  0.020  1.090
 8X5  C19  H11  single    0.970  0.020  1.090
 8X5  C20  H12  single    0.970  0.020  1.090
 8X5  C20  H13  single    0.970  0.020  1.090
 8X5  C21  H14  single    0.970  0.020  1.090
 8X5  C21  H15  single    0.970  0.020  1.090
 8X5  C6   H16  single    0.970  0.020  1.090
 8X5  C6   H17  single    0.970  0.020  1.090
 8X5  C4   H18  single    0.930  0.020  1.080
 8X5  C5   H19  single    0.930  0.020  1.080
 8X5  C    H20  single    0.930  0.020  1.080
 8X5  N1   H21  single    0.860  0.020  1.020
 8X5  N4   H22  single    0.860  0.020  1.020
 8X5  C17  H23  single    0.970  0.020  1.090
 8X5  C18  H24  single    0.970  0.020  1.090
 8X5  C18  H25  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
 8X5  H1   C1   C    120.12  3.000
 8X5  H1   C1   C2   119.80  3.000
 8X5  C    C1   C2   120.07  3.000
 8X5  H2   C2   C3   119.58  3.000
 8X5  H2   C2   C1   119.65  3.000
 8X5  C3   C2   C1   120.77  3.000
 8X5  C4   C3   C6   121.20  3.000
 8X5  C6   C3   C2   119.98  3.000
 8X5  C4   C3   C2   118.80  3.000
 8X5  H4   C7   H3   107.29  3.000
 8X5  H4   C7   N    109.60  3.000
 8X5  H3   C7   N    107.79  3.000
 8X5  H4   C7   C8   109.48  3.000
 8X5  H3   C7   C8   109.34  3.000
 8X5  N    C7   C8   113.16  3.000
 8X5  H6   C8   H5   107.23  3.000
 8X5  H6   C8   C9   110.27  3.000
 8X5  H5   C8   C9   112.40  3.000
 8X5  H6   C8   C7   110.70  3.000
 8X5  H5   C8   C7   109.29  3.000
 8X5  C9   C8   C7   106.98  3.000
 8X5  N1   C9   C10  108.05  3.000
 8X5  N1   C9   C8   129.13  3.000
 8X5  C10  C9   C8   122.78  3.000
 8X5  C22  C10  C11  130.19  3.000
 8X5  C11  C10  C9   107.64  3.000
 8X5  C22  C10  C9   122.02  3.000
 8X5  H7   C11  C12  125.68  3.000
 8X5  H7   C11  C10  127.52  3.000
 8X5  C12  C11  C10  106.80  3.000
 8X5  N1   C12  C13  123.18  3.000
 8X5  N1   C12  C11  107.57  3.000
 8X5  C13  C12  C11  129.25  3.000
 8X5  N3   C13  C14  121.18  3.000
 8X5  N3   C13  C12  116.08  3.000
 8X5  C14  C13  C12  122.74  3.000
 8X5  H8   C14  C15  120.27  3.000
 8X5  H8   C14  C13  123.71  3.000
 8X5  C15  C14  C13  116.02  3.000
 8X5  H9   C15  N2   116.32  3.000
 8X5  H9   C15  C14  119.94  3.000
 8X5  N2   C15  C14  123.74  3.000
 8X5  N4   C16  N2   118.10  3.000
 8X5  N4   C16  N3   116.30  3.000
 8X5  N2   C16  N3   125.59  3.000
 8X5  H11  C19  H10  107.35  3.000
 8X5  H11  C19  C18  110.63  3.000
 8X5  H10  C19  C18  109.53  3.000
 8X5  H11  C19  O    107.01  3.000
 8X5  H10  C19  O    110.19  3.000
 8X5  C18  C19  O    111.99  3.000
 8X5  H13  C20  H12  107.46  3.000
 8X5  H13  C20  O    107.10  3.000
 8X5  H12  C20  O    110.30  3.000
 8X5  H13  C20  C21  110.43  3.000
 8X5  H12  C20  C21  109.27  3.000
 8X5  O    C20  C21  112.15  3.000
 8X5  H15  C21  H14  107.47  3.000
 8X5  H15  C21  C17  110.56  3.000
 8X5  H14  C21  C17  109.81  3.000
 8X5  H15  C21  C20  109.36  3.000
 8X5  H14  C21  C20  109.61  3.000
 8X5  C17  C21  C20  109.99  3.000
 8X5  N    C22  O1   123.35  3.000
 8X5  N    C22  C10  114.37  3.000
 8X5  O1   C22  C10  122.25  3.000
 8X5  C6   N    C22  120.69  3.000
 8X5  C22  N    C7   121.88  3.000
 8X5  C6   N    C7   115.73  3.000
 8X5  H17  C6   H16  106.54  3.000
 8X5  H17  C6   N    109.53  3.000
 8X5  H16  C6   N    108.42  3.000
 8X5  H17  C6   C3   109.61  3.000
 8X5  H16  C6   C3   109.86  3.000
 8X5  N    C6   C3   112.70  3.000
 8X5  H18  C4   C5   119.50  3.000
 8X5  H18  C4   C3   119.94  3.000
 8X5  C5   C4   C3   120.56  3.000
 8X5  H19  C5   C    120.03  3.000
 8X5  H19  C5   C4   119.70  3.000
 8X5  C    C5   C4   120.27  3.000
 8X5  H20  C    C5   120.23  3.000
 8X5  H20  C    C1   120.24  3.000
 8X5  C5   C    C1   119.53  3.000
 8X5  H21  N1   C12  125.76  3.000
 8X5  H21  N1   C9   124.30  3.000
 8X5  C12  N1   C9   109.94  3.000
 8X5  C16  N3   C13  117.71  3.000
 8X5  C16  N2   C15  115.75  3.000
 8X5  H22  N4   C17  118.23  3.000
 8X5  H22  N4   C16  115.97  3.000
 8X5  C17  N4   C16  124.83  3.000
 8X5  H23  C17  C18  108.35  3.000
 8X5  H23  C17  N4   107.88  3.000
 8X5  C18  C17  N4   113.09  3.000
 8X5  H23  C17  C21  108.32  3.000
 8X5  C18  C17  C21  109.18  3.000
 8X5  N4   C17  C21  109.90  3.000
 8X5  C20  O    C19  111.95  3.000
 8X5  H25  C18  H24  107.57  3.000
 8X5  H25  C18  C17  109.38  3.000
 8X5  H24  C18  C17  110.38  3.000
 8X5  H25  C18  C19  109.93  3.000
 8X5  H24  C18  C19  109.35  3.000
 8X5  C17  C18  C19  110.19  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
 8X5  CONST_01  C4   C5   C    C1     0.00   0.0  0
 8X5  CONST_02  C4   C3   C2   C1     0.00   0.0  0
 8X5  CONST_03  C5   C    C1   C2     0.00   0.0  0
 8X5  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 8X5  CONST_05  C    C1   C2   C3     0.00   0.0  0
 8X5  CONST_06  C    C5   C4   C3     0.00   0.0  0
 8X5  CONST_07  C12  C11  C10  C9     0.00   0.0  0
 8X5  CONST_08  C11  C12  N1   C9     0.00   0.0  0
 8X5  CONST_09  C13  C12  N1   C9   180.00   0.0  0
 8X5  CONST_10  C13  C12  C11  C10  180.00   0.0  0
 8X5  CONST_11  N1   C12  C11  C10    0.00   0.0  0
 8X5  CONST_12  C12  N1   C9   C10    0.00   0.0  0
 8X5  CONST_13  N1   C9   C10  C11    0.00   0.0  0
 8X5  CONST_14  C14  C13  C12  C11  180.00   0.0  0
 8X5  CONST_15  N3   C13  C12  C11    0.00   0.0  0
 8X5  CONST_16  C15  C14  C13  C12  180.00   0.0  0
 8X5  CONST_17  C16  N3   C13  C12  180.00   0.0  0
 8X5  CONST_18  N2   C15  C14  C13    0.00   0.0  0
 8X5  CONST_19  N2   C16  N3   C13    0.00   0.0  0
 8X5  CONST_20  C16  N2   C15  C14    0.00   0.0  0
 8X5  CONST_21  N1   C12  C13  C14    0.00   0.0  0
 8X5  CONST_22  C16  N3   C13  C14    0.00   0.0  0
 8X5  CONST_23  N3   C13  C14  C15    0.00   0.0  0
 8X5  CONST_24  N3   C16  N2   C15    0.00   0.0  0
 8X5  CONST_25  N3   C13  C12  N1   180.00   0.0  0
 8X5  CONST_26  C10  C22  N    C7     0.00   0.0  0
 8X5  CONST_27  C6   C3   C2   C1   180.00   0.0  0
 8X5  CONST_28  N4   C16  N3   C13  180.00   0.0  0
 8X5  CONST_29  N4   C16  N2   C15  180.00   0.0  0
 8X5  CONST_30  C5   C4   C3   C6   180.00   0.0  0
 8X5  CONST_31  C17  N4   C16  N3   180.00   0.0  0
 8X5  CONST_32  C17  N4   C16  N2     0.00   0.0  0
 8X5  CONST_33  O1   C22  N    C7   180.00   0.0  0
 8X5  CONST_34  C6   N    C22  C10  180.00   0.0  0
 8X5  CONST_35  H19  C5   C    C1   180.00   0.0  0
 8X5  CONST_36  H20  C    C1   C2   180.00   0.0  0
 8X5  CONST_37  H18  C4   C3   C2   180.00   0.0  0
 8X5  CONST_38  H1   C1   C2   C3   180.00   0.0  0
 8X5  CONST_39  H21  N1   C9   C8     0.00   0.0  0
 8X5  CONST_40  H7   C11  C10  C9   180.00   0.0  0
 8X5  CONST_41  H8   C14  C13  C12    0.00   0.0  0
 8X5  CONST_42  H9   C15  C14  C13  180.00   0.0  0
 8X5  CONST_43  H2   C2   C3   C4   180.00   0.0  0
 8X5  CONST_44  C6   N    C22  O1     0.00   0.0  0
 8X5  CONST_45  H22  N4   C16  N3     0.00   0.0  0
 8X5  Var_01    C10  C9   C8   C7   -26.93  30.0  1
 8X5  Var_02    C22  N    C7   C8   -45.22  30.0  1
 8X5  Var_03    N    C22  C10  C9    10.06  30.0  1
 8X5  Var_04    N    C7   C8   C9    47.42  30.0  1
 8X5  Var_05    C21  C20  O    C19   59.76  30.0  1
 8X5  Var_06    C18  C19  O    C20  -59.47  30.0  1
 8X5  Var_07    O    C20  C21  C17  -56.63  30.0  1
 8X5  Var_08    O    C19  C18  C17   56.20  30.0  1
 8X5  Var_09    N    C6   C3   C2   144.40  30.0  2

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
 8X5  chir_01  C17  N4  C21  C18  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
 8X5  plan-1  C12  0.020
 8X5  plan-1  C13  0.020
 8X5  plan-1  C14  0.020
 8X5  plan-1  C15  0.020
 8X5  plan-1  C16  0.020
 8X5  plan-1  N3   0.020
 8X5  plan-1  N2   0.020
 8X5  plan-1  N4   0.020
 8X5  plan-1  H8   0.020
 8X5  plan-1  H9   0.020
 8X5  plan-2  C1   0.020
 8X5  plan-2  C2   0.020
 8X5  plan-2  C3   0.020
 8X5  plan-2  C6   0.020
 8X5  plan-2  C4   0.020
 8X5  plan-2  C5   0.020
 8X5  plan-2  C    0.020
 8X5  plan-2  H1   0.020
 8X5  plan-2  H2   0.020
 8X5  plan-2  H18  0.020
 8X5  plan-2  H19  0.020
 8X5  plan-2  H20  0.020
 8X5  plan-3  C8   0.020
 8X5  plan-3  C9   0.020
 8X5  plan-3  C10  0.020
 8X5  plan-3  C11  0.020
 8X5  plan-3  C12  0.020
 8X5  plan-3  C13  0.020
 8X5  plan-3  C22  0.020
 8X5  plan-3  N1   0.020
 8X5  plan-3  H7   0.020
 8X5  plan-3  H21  0.020
 8X5  plan-4  C16  0.020
 8X5  plan-4  N4   0.020
 8X5  plan-4  C17  0.020
 8X5  plan-4  H22  0.020
 8X5  plan-5  C7   0.020
 8X5  plan-5  C10  0.020
 8X5  plan-5  C22  0.020
 8X5  plan-5  O1   0.020
 8X5  plan-5  N    0.020
 8X5  plan-5  C6   0.020

