# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 15:39:30 2022
#   Inital geometry file: a 131 line input string
#   Ligand name: 1-{2-[2-(2,4-diamino-5,7-dihydro-6H-pyrrolo[3,4-d]pyrimidin-6-yl)-2-oxoethoxy]phenyl}piperidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(N)c2CN(Cc2n1)C(=O)COc3ccccc3N4CCC(CC4)C(O)=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
 VY7  VY7  '1-{2-[2-(2,4-diamino-5,7-dihydro-6H-pyrrolo[3,4-d]pyrimidin-6-yl)-2-oxoethoxy]phenyl}piperidine-4-carboxylic acid'  ligand  53  30  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_VY7
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
 VY7  C11  C  CH2    0  -0.301  -2.8884  -2.6561  17.6300
 VY7  C13  C  CR6    0   0.349  -3.8959  -3.7451  19.4784
 VY7  C14  C  CR16   0  -0.379  -3.1244  -3.0551  20.4023
 VY7  C15  C  CR16   0  -0.263  -3.2871  -3.2870  21.7666
 VY7  C16  C  CR16   0  -0.270  -4.2177  -4.2095  22.2040
 VY7  C17  C  CR16   0  -0.328  -4.9765  -4.9173  21.2756
 VY7  C02  C  CR6    0   0.529   0.7962   1.0260  13.7612
 VY7  C04  C  CR56   0   0.219  -0.5835  -0.3208  14.8778
 VY7  C05  C  CR56   0  -0.129  -1.0878  -0.8540  13.7229
 VY7  C06  C  CH2    0  -0.279  -2.1328  -1.8825  13.9915
 VY7  C08  C  CH2    0  -0.311  -1.2416  -0.9423  16.0695
 VY7  C09  C  C      0   0.534  -2.9746  -2.7313  16.1127
 VY7  C18  C  CR6    0   0.237  -4.8371  -4.7094  19.9077
 VY7  C20  C  CH2    0  -0.302  -6.9051  -5.8773  19.3697
 VY7  C21  C  CH2    0  -0.411  -7.7772  -6.1720  18.1573
 VY7  C22  C  CH1    0  -0.392  -7.1053  -7.1521  17.1990
 VY7  C23  C  CH2    0  -0.417  -5.7041  -6.6566  16.8630
 VY7  C24  C  CH2    0  -0.296  -4.9067  -6.3432  18.1178
 VY7  C25  C  C      0   0.428  -7.9636  -7.4695  15.9509
 VY7  C28  C  CR6    0   0.477  -0.5549  -0.3494  12.5261
 VY7  N01  N  NH2    0  -0.825   1.7822   1.9511  13.7641
 VY7  N03  N  N      0  -0.506   0.3510   0.6137  14.9547
 VY7  N07  N  NR5    0  -0.506  -2.1622  -1.8904  15.4543
 VY7  N19  N  NT     0  -0.489  -5.6129  -5.3725  18.9475
 VY7  N30  N  N      0  -0.509   0.3878   0.5915  12.5675
 VY7  O10  O  O      0  -0.477  -3.7205  -3.5053  15.5377
 VY7  O12  O  O2     0  -0.460  -3.8328  -3.5479  18.1433
 VY7  O26  O  O      0  -0.603  -7.3518  -7.7414  14.8978
 VY7  O27  O  OC    -1  -0.607  -9.2028  -7.4588  16.1019
 VY7  H1   H  HCH2   0   0.261  -1.8691  -2.9137  17.9479
 VY7  H2   H  HCH2   0   0.259  -3.0780  -1.6280  17.9667
 VY7  H3   H  HCR6   0   0.276  -2.4063  -2.3122  20.0812
 VY7  H4   H  HCR6   0   0.250  -2.6844  -2.7323  22.4738
 VY7  H5   H  HCR6   0   0.246  -4.3547  -4.3940  23.2615
 VY7  H6   H  HCR6   0   0.260  -5.6919  -5.6481  21.6300
 VY7  H7   H  HCH2   0   0.256  -3.1121  -1.6177  13.5800
 VY7  H8   H  HCH2   0   0.256  -1.8745  -2.8717  13.6001
 VY7  H9   H  HCH2   0   0.274  -0.5067  -1.4346  16.7144
 VY7  H10  H  HCH2   0   0.275  -1.7605  -0.1892  16.6712
 VY7  H11  H  HCH2   0   0.238  -7.3891  -5.1278  19.9996
 VY7  H12  H  HCH2   0   0.191  -6.8123  -6.7946  19.9760
 VY7  H13  H  HCH2   0   0.204  -7.9917  -5.2314  17.6392
 VY7  H14  H  HCH2   0   0.220  -8.7334  -6.5699  18.4991
 VY7  H15  H  HCH1   0   0.211  -6.9908  -8.1038  17.7427
 VY7  H16  H  HCH2   0   0.217  -5.1624  -7.4005  16.2777
 VY7  H17  H  HCH2   0   0.201  -5.7604  -5.7499  16.2520
 VY7  H18  H  HCH2   0   0.195  -4.7303  -7.2717  18.6861
 VY7  H19  H  HCH2   0   0.244  -3.9283  -5.9512  17.8460
 VY7  H20  H  HNH2   0   0.389   1.9828   2.4372  12.9074
 VY7  H21  H  HNH2   0   0.389   1.9591   2.4525  14.6173
 VY7  H22  H  HNH2   0   0.396  -0.4907  -0.4558  10.4972
 VY7  H23  H  HNH2   0   0.409  -1.5778  -1.5637  11.2277
 VY7  N29  N  NH2    0  -0.829  -0.9771  -0.7636  11.3221

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
 VY7  N29  C28  single    1.341  0.020  1.341
 VY7  N30  C28  aromatic  1.333  0.020  1.333
 VY7  N30  C02  aromatic  1.334  0.020  1.334
 VY7  C28  C05  aromatic  1.404  0.020  1.404
 VY7  N01  C02  single    1.352  0.020  1.352
 VY7  C02  N03  aromatic  1.339  0.020  1.339
 VY7  C05  C06  single    1.491  0.020  1.491
 VY7  C05  C04  aromatic  1.368  0.020  1.368
 VY7  N03  C04  aromatic  1.324  0.020  1.324
 VY7  O26  C25  deloc     1.248  0.020  1.248
 VY7  C06  N07  single    1.463  0.020  1.463
 VY7  C04  C08  single    1.496  0.020  1.496
 VY7  O27  C25  deloc     1.248  0.020  1.248
 VY7  C25  C22  single    1.548  0.020  1.548
 VY7  N07  C08  single    1.458  0.020  1.458
 VY7  N07  C09  single    1.342  0.020  1.342
 VY7  C23  C22  single    1.524  0.020  1.524
 VY7  C23  C24  single    1.519  0.020  1.519
 VY7  C22  C21  single    1.527  0.020  1.527
 VY7  O10  C09  double    1.219  0.020  1.219
 VY7  C09  C11  single    1.522  0.020  1.522
 VY7  C24  N19  single    1.459  0.020  1.459
 VY7  C21  C20  single    1.522  0.020  1.522
 VY7  C11  O12  single    1.397  0.020  1.397
 VY7  O12  C13  single    1.351  0.020  1.351
 VY7  N19  C20  single    1.450  0.020  1.450
 VY7  N19  C18  single    1.401  0.020  1.401
 VY7  C13  C18  aromatic  1.414  0.020  1.414
 VY7  C13  C14  aromatic  1.387  0.020  1.387
 VY7  C18  C17  aromatic  1.391  0.020  1.391
 VY7  C14  C15  aromatic  1.393  0.020  1.393
 VY7  C17  C16  aromatic  1.392  0.020  1.392
 VY7  C15  C16  aromatic  1.381  0.020  1.381
 VY7  C11  H1   single    0.970  0.020  1.090
 VY7  C11  H2   single    0.970  0.020  1.090
 VY7  C14  H3   single    0.930  0.020  1.080
 VY7  C15  H4   single    0.930  0.020  1.080
 VY7  C16  H5   single    0.930  0.020  1.080
 VY7  C17  H6   single    0.930  0.020  1.080
 VY7  C06  H7   single    0.970  0.020  1.090
 VY7  C06  H8   single    0.970  0.020  1.090
 VY7  C08  H9   single    0.970  0.020  1.090
 VY7  C08  H10  single    0.970  0.020  1.090
 VY7  C20  H11  single    0.970  0.020  1.090
 VY7  C20  H12  single    0.970  0.020  1.090
 VY7  C21  H13  single    0.970  0.020  1.090
 VY7  C21  H14  single    0.970  0.020  1.090
 VY7  C22  H15  single    0.970  0.020  1.090
 VY7  C23  H16  single    0.970  0.020  1.090
 VY7  C23  H17  single    0.970  0.020  1.090
 VY7  C24  H18  single    0.970  0.020  1.090
 VY7  C24  H19  single    0.970  0.020  1.090
 VY7  N01  H20  single    0.890  0.020  1.040
 VY7  N01  H21  single    0.890  0.020  1.040
 VY7  N29  H22  single    0.860  0.020  1.020
 VY7  N29  H23  single    0.860  0.020  1.020

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
 VY7  H2   C11  H1   106.93  3.000
 VY7  H2   C11  O12  111.61  3.000
 VY7  H1   C11  O12  111.80  3.000
 VY7  H2   C11  C09  110.01  3.000
 VY7  H1   C11  C09  109.25  3.000
 VY7  O12  C11  C09  107.25  3.000
 VY7  O12  C13  C18  115.50  3.000
 VY7  C18  C13  C14  120.47  3.000
 VY7  O12  C13  C14  124.02  3.000
 VY7  H3   C14  C15  118.84  3.000
 VY7  H3   C14  C13  120.86  3.000
 VY7  C15  C14  C13  120.29  3.000
 VY7  H4   C15  C16  120.70  3.000
 VY7  H4   C15  C14  119.31  3.000
 VY7  C16  C15  C14  119.98  3.000
 VY7  H5   C16  C17  119.73  3.000
 VY7  H5   C16  C15  120.56  3.000
 VY7  C17  C16  C15  119.70  3.000
 VY7  H6   C17  C18  119.30  3.000
 VY7  H6   C17  C16  119.02  3.000
 VY7  C18  C17  C16  121.68  3.000
 VY7  N30  C02  N03  126.55  3.000
 VY7  N03  C02  N01  116.82  3.000
 VY7  N30  C02  N01  116.61  3.000
 VY7  N03  C04  C08  123.88  3.000
 VY7  C08  C04  C05  110.38  3.000
 VY7  N03  C04  C05  125.75  3.000
 VY7  C28  C05  C06  131.90  3.000
 VY7  C06  C05  C04  112.03  3.000
 VY7  C28  C05  C04  116.07  3.000
 VY7  H8   C06  H7   107.17  3.000
 VY7  H8   C06  N07  110.94  3.000
 VY7  H7   C06  N07  111.05  3.000
 VY7  H8   C06  C05  113.18  3.000
 VY7  H7   C06  C05  113.11  3.000
 VY7  N07  C06  C05  101.42  3.000
 VY7  H10  C08  H9   107.68  3.000
 VY7  H10  C08  N07  112.33  3.000
 VY7  H9   C08  N07  112.34  3.000
 VY7  H10  C08  C04  111.13  3.000
 VY7  H9   C08  C04  111.15  3.000
 VY7  N07  C08  C04  102.23  3.000
 VY7  O10  C09  N07  122.48  3.000
 VY7  O10  C09  C11  122.44  3.000
 VY7  N07  C09  C11  115.08  3.000
 VY7  N19  C18  C17  123.21  3.000
 VY7  C17  C18  C13  117.86  3.000
 VY7  N19  C18  C13  118.89  3.000
 VY7  H12  C20  H11  106.91  3.000
 VY7  H12  C20  N19  111.99  3.000
 VY7  H11  C20  N19  108.90  3.000
 VY7  H12  C20  C21  108.96  3.000
 VY7  H11  C20  C21  109.77  3.000
 VY7  N19  C20  C21  110.24  3.000
 VY7  H14  C21  H13  106.85  3.000
 VY7  H14  C21  C22  110.39  3.000
 VY7  H13  C21  C22  109.92  3.000
 VY7  H14  C21  C20  108.86  3.000
 VY7  H13  C21  C20  108.83  3.000
 VY7  C22  C21  C20  111.84  3.000
 VY7  H15  C22  C25  106.16  3.000
 VY7  H15  C22  C23  107.10  3.000
 VY7  C25  C22  C23  113.51  3.000
 VY7  H15  C22  C21  106.89  3.000
 VY7  C23  C22  C21  109.54  3.000
 VY7  C25  C22  C21  113.19  3.000
 VY7  H17  C23  H16  106.92  3.000
 VY7  H17  C23  C24  108.49  3.000
 VY7  H16  C23  C24  108.86  3.000
 VY7  H17  C23  C22  110.19  3.000
 VY7  H16  C23  C22  110.69  3.000
 VY7  C24  C23  C22  111.56  3.000
 VY7  H19  C24  H18  106.75  3.000
 VY7  H19  C24  N19  109.72  3.000
 VY7  H18  C24  N19  110.15  3.000
 VY7  H19  C24  C23  109.87  3.000
 VY7  H18  C24  C23  109.62  3.000
 VY7  N19  C24  C23  110.66  3.000
 VY7  O27  C25  O26  126.20  3.000
 VY7  O27  C25  C22  116.82  3.000
 VY7  O26  C25  C22  116.96  3.000
 VY7  N30  C28  N29  117.94  3.000
 VY7  N30  C28  C05  119.73  3.000
 VY7  N29  C28  C05  122.32  3.000
 VY7  H21  N01  H20  116.55  3.000
 VY7  H21  N01  C02  118.13  3.000
 VY7  H20  N01  C02  118.33  3.000
 VY7  C04  N03  C02  113.60  3.000
 VY7  C09  N07  C08  125.66  3.000
 VY7  C09  N07  C06  120.40  3.000
 VY7  C08  N07  C06  113.94  3.000
 VY7  C24  N19  C20  111.42  3.000
 VY7  C20  N19  C18  117.30  3.000
 VY7  C24  N19  C18  115.87  3.000
 VY7  C28  N30  C02  118.31  3.000
 VY7  C13  O12  C11  119.21  3.000
 VY7  H23  N29  H22  117.11  3.000
 VY7  H23  N29  C28  121.22  3.000
 VY7  H22  N29  C28  119.29  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
 VY7  CONST_01  C16  C17  C18  C13     0.00   0.0  0
 VY7  CONST_02  C16  C15  C14  C13     0.00   0.0  0
 VY7  CONST_03  C17  C18  C13  C14     0.00   0.0  0
 VY7  CONST_04  C17  C16  C15  C14     0.00   0.0  0
 VY7  CONST_05  C18  C13  C14  C15     0.00   0.0  0
 VY7  CONST_06  C18  C17  C16  C15     0.00   0.0  0
 VY7  CONST_07  C05  C28  N30  C02     0.00   0.0  0
 VY7  CONST_08  C05  C04  N03  C02     0.00   0.0  0
 VY7  CONST_09  N30  C28  C05  C04     0.00   0.0  0
 VY7  CONST_10  N30  C02  N03  C04     0.00   0.0  0
 VY7  CONST_11  N03  C02  N30  C28     0.00   0.0  0
 VY7  CONST_12  N03  C04  C05  C28     0.00   0.0  0
 VY7  CONST_13  N19  C18  C13  C14   180.00   0.0  0
 VY7  CONST_14  N19  C18  C17  C16   180.00   0.0  0
 VY7  CONST_15  O12  C13  C14  C15   180.00   0.0  0
 VY7  CONST_16  O12  C13  C18  C17   180.00   0.0  0
 VY7  CONST_17  N29  C28  N30  C02   180.00   0.0  0
 VY7  CONST_18  N29  C28  C05  C04   180.00   0.0  0
 VY7  CONST_19  N01  C02  N03  C04   180.00   0.0  0
 VY7  CONST_20  N29  C28  C05  C06     0.00   0.0  0
 VY7  CONST_21  N01  C02  N30  C28   180.00   0.0  0
 VY7  CONST_22  O12  C13  C18  N19     0.00   0.0  0
 VY7  CONST_23  H6   C17  C18  C13   180.00   0.0  0
 VY7  CONST_24  H4   C15  C14  C13   180.00   0.0  0
 VY7  CONST_25  H5   C16  C15  C14   180.00   0.0  0
 VY7  CONST_26  H3   C14  C15  C16   180.00   0.0  0
 VY7  CONST_27  C06  N07  C09  C11   180.00   0.0  0
 VY7  CONST_28  C08  N07  C09  C11     0.00   0.0  0
 VY7  CONST_29  O10  C09  N07  C06     0.00   0.0  0
 VY7  CONST_30  O10  C09  N07  C08   180.00   0.0  0
 VY7  CONST_31  H22  N29  C28  C05   180.00   0.0  0
 VY7  CONST_32  H23  N29  C28  C05     0.00   0.0  0
 VY7  CONST_33  H20  N01  C02  N03   180.00   0.0  0
 VY7  Var_01    C24  N19  C18  C13    71.35  30.0  2
 VY7  Var_02    N07  C06  C05  C04    -0.59  30.0  1
 VY7  Var_03    C06  N07  C08  C04    -0.87  30.0  1
 VY7  Var_04    C08  N07  C06  C05     0.91  30.0  1
 VY7  Var_05    N07  C08  C04  C05     0.45  30.0  1
 VY7  Var_06    C23  C24  N19  C18  -161.87  30.0  1
 VY7  Var_07    C21  C20  N19  C18   162.66  30.0  1
 VY7  Var_08    N19  C24  C23  C22   -56.22  30.0  1
 VY7  Var_09    N19  C20  C21  C22    56.54  30.0  1
 VY7  Var_10    C18  C13  O12  C11  -177.18  30.0  2
 VY7  Var_11    C09  C11  O12  C13   175.31  30.0  2
 VY7  Var_12    O12  C11  C09  N07   177.50  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
 VY7  chir_01  C22  C25  C23  C21  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
 VY7  plan-1  C13  0.020
 VY7  plan-1  C14  0.020
 VY7  plan-1  C15  0.020
 VY7  plan-1  C16  0.020
 VY7  plan-1  C17  0.020
 VY7  plan-1  C18  0.020
 VY7  plan-1  N19  0.020
 VY7  plan-1  O12  0.020
 VY7  plan-1  H3   0.020
 VY7  plan-1  H4   0.020
 VY7  plan-1  H5   0.020
 VY7  plan-1  H6   0.020
 VY7  plan-2  C11  0.020
 VY7  plan-2  C06  0.020
 VY7  plan-2  C08  0.020
 VY7  plan-2  C09  0.020
 VY7  plan-2  N07  0.020
 VY7  plan-2  O10  0.020
 VY7  plan-3  C02  0.020
 VY7  plan-3  N01  0.020
 VY7  plan-3  H20  0.020
 VY7  plan-3  H21  0.020
 VY7  plan-4  C02  0.020
 VY7  plan-4  C04  0.020
 VY7  plan-4  C05  0.020
 VY7  plan-4  C06  0.020
 VY7  plan-4  C08  0.020
 VY7  plan-4  C28  0.020
 VY7  plan-4  N01  0.020
 VY7  plan-4  N03  0.020
 VY7  plan-4  N30  0.020
 VY7  plan-4  N29  0.020
 VY7  plan-5  C28  0.020
 VY7  plan-5  H22  0.020
 VY7  plan-5  H23  0.020
 VY7  plan-5  N29  0.020
 VY7  plan-6  C22  0.020
 VY7  plan-6  C25  0.020
 VY7  plan-6  O26  0.020
 VY7  plan-6  O27  0.020

