# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 02:19:06 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: 8-[[(phenylmethyl)amino]methyl]-1~{H}-pyrido[3,4-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1N=CNc2c(CNCc3ccccc3)nccc12
#
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
 5V3  5V3  8-[[(phenylmethyl)amino]methyl]-1~{H}-pyrido[3,4-d]pyrimidin-4-one  ligand  34  20  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5V3
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
 5V3  C10  C  CR6   0   0.195  -1.1283  -1.0666  -0.6929
 5V3  C13  C  CR16  0  -0.349  -3.3282  -1.6152   0.8594
 5V3  C01  C  CH2   0  -0.330   2.4619  -0.3016  -1.3803
 5V3  C02  C  CR6   0   0.094   3.6007   0.0252  -0.4545
 5V3  C03  C  CR16  0  -0.286   3.9999  -0.8881   0.5210
 5V3  C04  C  CR16  0  -0.243   5.0464  -0.5909   1.3807
 5V3  C05  C  CR16  0  -0.269   5.7066   0.6296   1.2828
 5V3  C06  C  CR16  0  -0.241   5.3132   1.5468   0.3195
 5V3  C07  C  CR16  0  -0.313   4.2644   1.2438  -0.5420
 5V3  N08  N  NH1   0  -0.583   1.2325  -0.5111  -0.6326
 5V3  C09  C  CH2   0  -0.363   0.1127  -0.8180  -1.5055
 5V3  C11  C  CR66  0   0.343  -2.0396  -0.0393  -0.3894
 5V3  C12  C  CR66  0  -0.069  -3.1556  -0.3145   0.3970
 5V3  C14  C  CR16  0  -0.079  -2.3870  -2.5612   0.5165
 5V3  N15  N  N     0  -0.393  -1.3209  -2.2880  -0.2375
 5V3  C16  C  CR6   0   0.468  -4.1105   0.7687   0.7123
 5V3  N17  N  N     0  -0.473  -3.8380   2.0181   0.2056
 5V3  C18  C  CR16  0   0.157  -2.7806   2.1933  -0.5167
 5V3  N19  N  NR16  0  -0.690  -1.8845   1.2527  -0.8334
 5V3  O20  O  O     0  -0.442  -5.1003   0.5669   1.3924
 5V3  H1   H  HCR6  0   0.281  -4.1809  -1.8770   1.4699
 5V3  H2   H  HCH2  0   0.220   2.3674   0.4884  -2.1397
 5V3  H3   H  HCH2  0   0.243   2.6817  -1.2263  -1.9232
 5V3  H4   H  HCR6  0   0.248   3.4898  -1.8404   0.6029
 5V3  H5   H  HCR6  0   0.254   5.3511  -1.3125   2.1279
 5V3  H6   H  HCR6  0   0.255   6.5233   0.8607   1.9545
 5V3  H7   H  HCR6  0   0.254   5.8175   2.5012   0.2391
 5V3  H8   H  HCR6  0   0.250   3.9584   1.9659  -1.2902
 5V3  H9   H  HNH1  0   0.349   1.0318   0.3251  -0.0955
 5V3  H11  H  HCH2  0   0.270   0.3435  -1.7339  -2.0523
 5V3  H12  H  HCH2  0   0.216  -0.0620  -0.0493  -2.2748
 5V3  H13  H  HCR6  0   0.275  -2.4870  -3.5850   0.8552
 5V3  H14  H  HCR6  0   0.308  -2.5677   3.1768  -0.9182
 5V3  H15  H  HNR6  0   0.443  -1.1052   1.5106  -1.4205

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
 5V3  C14  C13  aromatic  1.378  0.020  1.378
 5V3  C14  N15  aromatic  1.334  0.020  1.334
 5V3  C13  C12  aromatic  1.391  0.020  1.391
 5V3  O20  C16  double    1.218  0.020  1.218
 5V3  N15  C10  aromatic  1.318  0.020  1.318
 5V3  C12  C16  single    1.478  0.020  1.478
 5V3  C12  C11  aromatic  1.393  0.020  1.393
 5V3  C16  N17  single    1.376  0.020  1.376
 5V3  C10  C11  aromatic  1.406  0.020  1.406
 5V3  C10  C09  single    1.504  0.020  1.504
 5V3  C11  N19  single    1.375  0.020  1.375
 5V3  N17  C18  double    1.292  0.020  1.292
 5V3  C09  N08  single    1.453  0.020  1.453
 5V3  N19  C18  single    1.337  0.020  1.337
 5V3  N08  C01  single    1.454  0.020  1.454
 5V3  C01  C02  single    1.504  0.020  1.504
 5V3  C02  C03  aromatic  1.395  0.020  1.395
 5V3  C02  C07  aromatic  1.390  0.020  1.390
 5V3  C03  C04  aromatic  1.387  0.020  1.387
 5V3  C07  C06  aromatic  1.391  0.020  1.391
 5V3  C04  C05  aromatic  1.391  0.020  1.391
 5V3  C06  C05  aromatic  1.387  0.020  1.387
 5V3  C13  H1   single    0.930  0.020  1.080
 5V3  C01  H2   single    0.970  0.020  1.090
 5V3  C01  H3   single    0.970  0.020  1.090
 5V3  C03  H4   single    0.930  0.020  1.080
 5V3  C04  H5   single    0.930  0.020  1.080
 5V3  C05  H6   single    0.930  0.020  1.080
 5V3  C06  H7   single    0.930  0.020  1.080
 5V3  C07  H8   single    0.930  0.020  1.080
 5V3  N08  H9   single    0.890  0.020  1.040
 5V3  C09  H11  single    0.970  0.020  1.090
 5V3  C09  H12  single    0.970  0.020  1.090
 5V3  C14  H13  single    0.930  0.020  1.080
 5V3  C18  H14  single    0.930  0.020  1.080
 5V3  N19  H15  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
 5V3  N15  C10  C11  120.51  3.000
 5V3  C11  C10  C09  122.04  3.000
 5V3  N15  C10  C09  117.42  3.000
 5V3  H1   C13  C14  120.87  3.000
 5V3  H1   C13  C12  120.80  3.000
 5V3  C14  C13  C12  118.32  3.000
 5V3  H3   C01  H2   106.35  3.000
 5V3  H3   C01  N08  107.65  3.000
 5V3  H2   C01  N08  112.70  3.000
 5V3  H3   C01  C02  109.69  3.000
 5V3  H2   C01  C02  109.51  3.000
 5V3  N08  C01  C02  110.80  3.000
 5V3  C07  C02  C03  118.77  3.000
 5V3  C07  C02  C01  120.89  3.000
 5V3  C03  C02  C01  120.34  3.000
 5V3  H4   C03  C04  119.80  3.000
 5V3  H4   C03  C02  119.58  3.000
 5V3  C04  C03  C02  120.62  3.000
 5V3  H5   C04  C05  119.99  3.000
 5V3  H5   C04  C03  119.84  3.000
 5V3  C05  C04  C03  120.18  3.000
 5V3  H6   C05  C06  120.26  3.000
 5V3  H6   C05  C04  120.12  3.000
 5V3  C06  C05  C04  119.63  3.000
 5V3  H7   C06  C07  119.83  3.000
 5V3  H7   C06  C05  120.16  3.000
 5V3  C07  C06  C05  120.01  3.000
 5V3  H8   C07  C06  119.69  3.000
 5V3  H8   C07  C02  119.51  3.000
 5V3  C06  C07  C02  120.79  3.000
 5V3  H9   N08  C09  109.88  3.000
 5V3  H9   N08  C01  108.72  3.000
 5V3  C09  N08  C01  111.92  3.000
 5V3  H12  C09  H11  105.62  3.000
 5V3  H12  C09  N08  113.24  3.000
 5V3  H11  C09  N08  108.38  3.000
 5V3  H12  C09  C10  111.21  3.000
 5V3  H11  C09  C10  107.84  3.000
 5V3  N08  C09  C10  110.27  3.000
 5V3  N19  C11  C12  117.28  3.000
 5V3  N19  C11  C10  122.93  3.000
 5V3  C12  C11  C10  119.79  3.000
 5V3  C16  C12  C11  119.56  3.000
 5V3  C11  C12  C13  118.15  3.000
 5V3  C16  C12  C13  122.28  3.000
 5V3  H13  C14  N15  116.37  3.000
 5V3  H13  C14  C13  120.54  3.000
 5V3  N15  C14  C13  123.09  3.000
 5V3  C14  N15  C10  120.13  3.000
 5V3  O20  C16  N17  121.15  3.000
 5V3  N17  C16  C12  117.33  3.000
 5V3  O20  C16  C12  121.52  3.000
 5V3  C18  N17  C16  119.41  3.000
 5V3  H14  C18  N19  114.77  3.000
 5V3  H14  C18  N17  119.41  3.000
 5V3  N19  C18  N17  125.82  3.000
 5V3  H15  N19  C18  118.39  3.000
 5V3  H15  N19  C11  121.01  3.000
 5V3  C18  N19  C11  120.59  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
 5V3  CONST_01  C13  C14  N15  C10    0.00   0.0  0
 5V3  CONST_02  C13  C12  C11  C10    0.00   0.0  0
 5V3  CONST_03  C05  C04  C03  C02    0.00   0.0  0
 5V3  CONST_04  C05  C06  C07  C02    0.00   0.0  0
 5V3  CONST_05  C06  C07  C02  C03    0.00   0.0  0
 5V3  CONST_06  C06  C05  C04  C03    0.00   0.0  0
 5V3  CONST_07  C07  C02  C03  C04    0.00   0.0  0
 5V3  CONST_08  C07  C06  C05  C04    0.00   0.0  0
 5V3  CONST_09  C14  C13  C12  C11    0.00   0.0  0
 5V3  CONST_10  C14  N15  C10  C11    0.00   0.0  0
 5V3  CONST_11  N15  C14  C13  C12    0.00   0.0  0
 5V3  CONST_12  N15  C10  C11  C12    0.00   0.0  0
 5V3  CONST_13  N17  C18  N19  C11    0.00   0.0  0
 5V3  CONST_14  N19  C18  N17  C16    0.00   0.0  0
 5V3  CONST_15  C04  C03  C02  C01  180.00   0.0  0
 5V3  CONST_16  C06  C07  C02  C01  180.00   0.0  0
 5V3  CONST_17  C14  N15  C10  C09  180.00   0.0  0
 5V3  CONST_18  C12  C11  C10  C09  180.00   0.0  0
 5V3  CONST_19  N19  C11  C10  C09    0.00   0.0  0
 5V3  CONST_20  H13  C14  N15  C10  180.00   0.0  0
 5V3  CONST_21  H5   C04  C03  C02  180.00   0.0  0
 5V3  CONST_22  H7   C06  C07  C02  180.00   0.0  0
 5V3  CONST_23  H8   C07  C02  C03  180.00   0.0  0
 5V3  CONST_24  H6   C05  C04  C03  180.00   0.0  0
 5V3  CONST_25  H4   C03  C04  C05  180.00   0.0  0
 5V3  CONST_26  H1   C13  C12  C11  180.00   0.0  0
 5V3  CONST_27  H14  C18  N19  C11  180.00   0.0  0
 5V3  CONST_28  H15  N19  C18  N17  180.00   0.0  0
 5V3  Var_01    N08  C01  C02  C03   60.99  30.0  2
 5V3  Var_02    N15  C10  C09  N08  -85.96  30.0  3
 5V3  Var_03    C01  N08  C09  C10  178.36  30.0  3
 5V3  Var_04    C09  N08  C01  C02  179.52  30.0  1

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
 5V3  plan-1  C01  0.020
 5V3  plan-1  C02  0.020
 5V3  plan-1  C03  0.020
 5V3  plan-1  C04  0.020
 5V3  plan-1  C05  0.020
 5V3  plan-1  C06  0.020
 5V3  plan-1  C07  0.020
 5V3  plan-1  H4   0.020
 5V3  plan-1  H5   0.020
 5V3  plan-1  H6   0.020
 5V3  plan-1  H7   0.020
 5V3  plan-1  H8   0.020
 5V3  plan-2  C10  0.020
 5V3  plan-2  C13  0.020
 5V3  plan-2  C09  0.020
 5V3  plan-2  C11  0.020
 5V3  plan-2  C12  0.020
 5V3  plan-2  C14  0.020
 5V3  plan-2  N15  0.020
 5V3  plan-2  C16  0.020
 5V3  plan-2  N17  0.020
 5V3  plan-2  C18  0.020
 5V3  plan-2  N19  0.020
 5V3  plan-2  O20  0.020
 5V3  plan-2  H1   0.020
 5V3  plan-2  H13  0.020
 5V3  plan-2  H14  0.020
 5V3  plan-2  H15  0.020

