# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Nov 22 17:29:38 2022
#   Inital geometry file: a 90 line input string
#   Ligand name: (3-{[(4-oxo-4,5-dihydro-3H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]amino}propyl)phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)CCCNCc1c[nH]c2C(=O)NC=Nc12
#
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
 WG7  WG7  "(3-{[(4-oxo-4,5-dihydro-3H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]amino}propyl)phosphonic acid"  ligand  34  19  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_WG7
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
 WG7  C10  C  CH2   0  -0.728  24.5763   1.2471  88.1460
 WG7  C15  C  CR15  0  -0.054  20.4208  -3.0648  88.5472
 WG7  C02  C  CR6   0   0.515  20.0715  -4.5031  91.8328
 WG7  C03  C  CR56  0   0.152  20.2233  -3.7387  90.6390
 WG7  C04  C  CR56  0   0.142  20.4032  -2.3589  90.6567
 WG7  C05  C  CR5   0  -0.042  20.5253  -1.9249  89.3127
 WG7  C06  C  CH2   0  -0.397  20.7882  -0.5285  88.8335
 WG7  C08  C  CH2   0  -0.281  23.2078  -0.7454  89.0441
 WG7  C09  C  CH2   0  -0.460  24.4853   0.0799  89.1322
 WG7  C18  C  CR16  0   0.121  20.3096  -2.3116  92.8893
 WG7  N07  N  NH1   0  -0.577  22.0322   0.0672  89.2910
 WG7  N16  N  NR15  0  -0.650  20.2343  -4.1471  89.3434
 WG7  N17  N  N     0  -0.445  20.4484  -1.6253  91.8106
 WG7  N19  N  NR16  0  -0.662  20.1310  -3.6602  92.9366
 WG7  O12  O  OH1   0  -0.752  25.7421  -0.3312  86.2423
 WG7  O13  O  OH1   0  -0.742  25.2061   2.0447  85.7052
 WG7  O14  O  O     0  -0.712  23.2505   0.3080  85.8607
 WG7  P11  P  P     0   1.355  24.5569   0.7551  86.4104
 WG7  H1   H  HCH2  0   0.281  25.4954   1.8079  88.3299
 WG7  H2   H  HCH2  0   0.275  23.7444   1.9373  88.2994
 WG7  H3   H  HCR5  0   0.288  20.4670  -3.1711  87.4746
 WG7  H4   H  HCH2  0   0.233  20.7862  -0.5252  87.7397
 WG7  H5   H  HCH2  0   0.241  19.9747   0.1326  89.1425
 WG7  H6   H  HCH2  0   0.224  23.1147  -1.1854  88.0482
 WG7  H7   H  HCH2  0   0.213  23.2942  -1.5960  89.7339
 WG7  H8   H  HCH2  0   0.237  25.3432  -0.5836  89.0026
 WG7  H9   H  HCH2  0   0.245  24.5755   0.4909  90.1412
 WG7  H10  H  HCR6  0   0.289  20.3307  -1.8202  93.8539
 WG7  H11  H  HNH1  0   0.342  21.9647   0.2685  90.2811
 WG7  H13  H  HNR5  0   0.417  20.1217  -5.0957  89.0237
 WG7  H14  H  HNR6  0   0.427  20.0346  -4.0910  93.8473
 WG7  H15  H  HOH1  0   0.487  25.4330  -1.2459  86.2594
 WG7  H16  H  HOH1  0   0.489  25.0966   2.0620  84.7445
 WG7  O01  O  O     0  -0.472  19.9128  -5.7092  91.9410

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
 WG7  O14  P11  double    1.486  0.020  1.486
 WG7  O13  P11  single    1.607  0.020  1.607
 WG7  P11  O12  single    1.617  0.020  1.617
 WG7  P11  C10  single    1.804  0.020  1.804
 WG7  C10  C09  single    1.531  0.020  1.531
 WG7  C09  C08  single    1.523  0.020  1.523
 WG7  C15  N16  aromatic  1.356  0.020  1.356
 WG7  C15  C05  aromatic  1.377  0.020  1.377
 WG7  C08  N07  single    1.450  0.020  1.450
 WG7  N16  C03  aromatic  1.358  0.020  1.358
 WG7  C06  C05  single    1.499  0.020  1.499
 WG7  C06  N07  single    1.453  0.020  1.453
 WG7  C05  C04  aromatic  1.418  0.020  1.418
 WG7  C03  C04  aromatic  1.392  0.020  1.392
 WG7  C03  C02  single    1.426  0.020  1.426
 WG7  C04  N17  single    1.368  0.020  1.368
 WG7  O01  C02  double    1.221  0.020  1.221
 WG7  C02  N19  single    1.390  0.020  1.390
 WG7  N17  C18  double    1.286  0.020  1.286
 WG7  N19  C18  single    1.361  0.020  1.361
 WG7  C10  H1   single    0.970  0.020  1.090
 WG7  C10  H2   single    0.970  0.020  1.090
 WG7  C15  H3   single    0.930  0.020  1.080
 WG7  C06  H4   single    0.970  0.020  1.090
 WG7  C06  H5   single    0.970  0.020  1.090
 WG7  C08  H6   single    0.970  0.020  1.090
 WG7  C08  H7   single    0.970  0.020  1.090
 WG7  C09  H8   single    0.970  0.020  1.090
 WG7  C09  H9   single    0.970  0.020  1.090
 WG7  C18  H10  single    0.930  0.020  1.080
 WG7  N07  H11  single    0.890  0.020  1.040
 WG7  N16  H13  single    0.860  0.020  1.020
 WG7  N19  H14  single    0.860  0.020  1.020
 WG7  O12  H15  single    0.850  0.020  0.980
 WG7  O13  H16  single    0.850  0.020  0.980

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
 WG7  H2   C10  H1   107.03  3.000
 WG7  H2   C10  P11  107.42  3.000
 WG7  H1   C10  P11  108.13  3.000
 WG7  H2   C10  C09  110.25  3.000
 WG7  H1   C10  C09  109.45  3.000
 WG7  P11  C10  C09  114.29  3.000
 WG7  H3   C15  N16  120.72  3.000
 WG7  H3   C15  C05  129.12  3.000
 WG7  N16  C15  C05  110.16  3.000
 WG7  O01  C02  N19  122.28  3.000
 WG7  N19  C02  C03  109.59  3.000
 WG7  O01  C02  C03  128.14  3.000
 WG7  N16  C03  C04  108.01  3.000
 WG7  C04  C03  C02  122.33  3.000
 WG7  N16  C03  C02  129.66  3.000
 WG7  N17  C04  C05  129.24  3.000
 WG7  N17  C04  C03  123.14  3.000
 WG7  C05  C04  C03  107.62  3.000
 WG7  C06  C05  C04  127.10  3.000
 WG7  C04  C05  C15  105.49  3.000
 WG7  C06  C05  C15  127.34  3.000
 WG7  H5   C06  H4   106.23  3.000
 WG7  H5   C06  N07  107.47  3.000
 WG7  H4   C06  N07  108.37  3.000
 WG7  H5   C06  C05  110.03  3.000
 WG7  H4   C06  C05  108.79  3.000
 WG7  N07  C06  C05  115.54  3.000
 WG7  H7   C08  H6   105.50  3.000
 WG7  H7   C08  N07  112.99  3.000
 WG7  H6   C08  N07  108.16  3.000
 WG7  H7   C08  C09  108.50  3.000
 WG7  H6   C08  C09  110.02  3.000
 WG7  N07  C08  C09  111.49  3.000
 WG7  H9   C09  H8   105.85  3.000
 WG7  H9   C09  C08  109.04  3.000
 WG7  H8   C09  C08  108.82  3.000
 WG7  H9   C09  C10  107.64  3.000
 WG7  H8   C09  C10  109.87  3.000
 WG7  C08  C09  C10  115.19  3.000
 WG7  H10  C18  N19  114.91  3.000
 WG7  H10  C18  N17  120.20  3.000
 WG7  N19  C18  N17  124.89  3.000
 WG7  H11  N07  C08  109.38  3.000
 WG7  H11  N07  C06  109.41  3.000
 WG7  C08  N07  C06  114.25  3.000
 WG7  H13  N16  C03  125.80  3.000
 WG7  H13  N16  C15  125.48  3.000
 WG7  C03  N16  C15  108.72  3.000
 WG7  C18  N17  C04  114.69  3.000
 WG7  H14  N19  C18  117.74  3.000
 WG7  H14  N19  C02  116.90  3.000
 WG7  C18  N19  C02  125.36  3.000
 WG7  H15  O12  P11  113.58  3.000
 WG7  H16  O13  P11  113.86  3.000
 WG7  O14  P11  O13  115.74  3.000
 WG7  O13  P11  O12  101.39  3.000
 WG7  O14  P11  O12  113.82  3.000
 WG7  O12  P11  C10  105.98  3.000
 WG7  O13  P11  C10  101.48  3.000
 WG7  O14  P11  C10  116.57  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
 WG7  CONST_01  C04  C03  N16  C15     0.00   0.0  0
 WG7  CONST_02  C03  C04  C05  C15     0.00   0.0  0
 WG7  CONST_03  C05  C15  N16  C03     0.00   0.0  0
 WG7  CONST_04  N16  C15  C05  C04     0.00   0.0  0
 WG7  CONST_05  N16  C03  C04  C05     0.00   0.0  0
 WG7  CONST_06  N17  C18  N19  C02     0.00   0.0  0
 WG7  CONST_07  C18  N19  C02  C03     0.00   0.0  0
 WG7  CONST_08  N19  C18  N17  C04     0.00   0.0  0
 WG7  CONST_09  C06  C05  C04  C03   180.00   0.0  0
 WG7  CONST_10  N16  C15  C05  C06   180.00   0.0  0
 WG7  CONST_11  N17  C04  C05  C06     0.00   0.0  0
 WG7  CONST_12  O01  C02  N19  C18   180.00   0.0  0
 WG7  CONST_13  H13  N16  C03  C02     0.00   0.0  0
 WG7  CONST_14  H3   C15  N16  C03   180.00   0.0  0
 WG7  CONST_15  H3   C15  C05  C04   180.00   0.0  0
 WG7  CONST_16  H13  N16  C03  C04   180.00   0.0  0
 WG7  CONST_17  H13  N16  C15  C05   180.00   0.0  0
 WG7  CONST_18  H10  C18  N19  C02   180.00   0.0  0
 WG7  CONST_19  H14  N19  C02  C03   180.00   0.0  0
 WG7  CONST_20  H10  C18  N17  C04   180.00   0.0  0
 WG7  CONST_21  H14  N19  C18  N17   180.00   0.0  0
 WG7  CONST_22  H14  N19  C02  O01     0.00   0.0  0
 WG7  CONST_23  H14  N19  C18  H10     0.00   0.0  0
 WG7  Var_01    N07  C06  C05  C15  -116.29  30.0  3
 WG7  Var_02    N07  C06  C05  C04    60.05  30.0  3
 WG7  Var_03    H4   C06  C05  C15     5.82  30.0  3
 WG7  Var_04    H5   C06  C05  C15   121.81  30.0  3
 WG7  Var_05    H4   C06  C05  C04  -177.84  30.0  3
 WG7  Var_06    H5   C06  C05  C04   -61.85  30.0  3
 WG7  Var_07    C08  N07  C06  C05    52.37  30.0  3
 WG7  Var_08    H11  N07  C06  C05   -70.63  30.0  3
 WG7  Var_09    N07  C08  C09  C10   -59.66  30.0  3
 WG7  Var_10    C09  C08  N07  C06   162.18  30.0  2
 WG7  Var_11    P11  C10  C09  C08   -61.98  30.0  1
 WG7  Var_12    O14  P11  C10  C09    73.81  30.0  1
 WG7  Var_13    O13  P11  C10  C09  -159.53  30.0  1
 WG7  Var_14    O12  P11  C10  C09   -54.00  30.0  1
 WG7  Var_15    H6   C08  C09  C10    60.33  30.0  3
 WG7  Var_16    H7   C08  C09  C10   175.28  30.0  3
 WG7  Var_17    H6   C08  N07  C06    41.10  30.0  2
 WG7  Var_18    H7   C08  N07  C06   -75.31  30.0  2
 WG7  Var_19    H1   C10  C09  C08   176.60  30.0  1
 WG7  Var_20    H2   C10  C09  C08    59.12  30.0  1
 WG7  Var_21    H4   C06  N07  C08   -69.96  30.0  1
 WG7  Var_22    H5   C06  N07  C08   175.62  30.0  1
 WG7  Var_23    H11  N07  C08  C09   -74.81  30.0  3
 WG7  Var_24    H8   C09  C08  N07   176.47  30.0  1
 WG7  Var_25    H9   C09  C08  N07    61.45  30.0  1
 WG7  Var_26    H1   C10  P11  O12    68.15  30.0  3
 WG7  Var_27    H2   C10  P11  O12  -176.65  30.0  3
 WG7  Var_28    H1   C10  P11  O13   -37.38  30.0  3
 WG7  Var_29    H2   C10  P11  O13    77.81  30.0  3
 WG7  Var_30    H1   C10  P11  O14  -164.04  30.0  3
 WG7  Var_31    H2   C10  P11  O14   -48.85  30.0  3
 WG7  Var_32    H8   C09  C10  P11    61.33  30.0  3
 WG7  Var_33    H9   C09  C10  P11   176.15  30.0  3

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
 WG7  plan-1  C15  0.020
 WG7  plan-1  C02  0.020
 WG7  plan-1  C03  0.020
 WG7  plan-1  C04  0.020
 WG7  plan-1  C05  0.020
 WG7  plan-1  C06  0.020
 WG7  plan-1  C18  0.020
 WG7  plan-1  N16  0.020
 WG7  plan-1  N17  0.020
 WG7  plan-1  N19  0.020
 WG7  plan-1  H3   0.020
 WG7  plan-1  H10  0.020
 WG7  plan-1  H13  0.020
 WG7  plan-1  H14  0.020
 WG7  plan-1  O01  0.020

