# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 18:14:25 2021
#   Inital geometry file: a 84 line input string
#   Ligand name: 4-(1,4-oxazonan-4-yl)-7H-pyrrolo[2,3-d]pyrimidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CCOCCN(CC1)c2ncnc3[nH]ccc23
#
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
 W5D  W5D  4-(1,4-oxazonan-4-yl)-7H-pyrrolo[2,3-d]pyrimidine  ligand  36  18  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_W5D
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
 W5D  C10   C  CR6   0   0.458  -45.4640  -29.8550   4.0482
 W5D  C17   C  CR15  0  -0.417  -47.5257  -28.1914   4.4730
 W5D  C01   C  CH2   0  -0.267  -46.6475  -31.2363   0.3537
 W5D  C03   C  CH2   0  -0.369  -47.2348  -29.2000   1.4467
 W5D  C04   C  CH2   0  -1.214  -45.8485  -28.7318   1.9155
 W5D  C05   C  CH2   0  -0.716  -45.2484  -31.2029  -0.2674
 W5D  C06   C  CH2   0  -0.413  -44.2269  -32.0915   0.4314
 W5D  C07   C  CH2   0  -0.492  -44.0266  -31.7865   1.9177
 W5D  C08   C  CH2   0  -0.365  -43.8896  -30.2969   2.2682
 W5D  C12   C  CR16  0   0.032  -45.0088  -30.9908   6.0085
 W5D  C14   C  CR56  0   0.451  -46.6809  -29.5622   6.0746
 W5D  C16   C  CR15  0  -0.006  -48.2200  -28.0247   5.6325
 W5D  C18   C  CR56  0  -0.208  -46.5203  -29.1851   4.7267
 W5D  N09   N  NT    0  -0.530  -45.1124  -29.6588   2.7571
 W5D  N11   N  N     0  -0.469  -44.7355  -30.7456   4.7338
 W5D  N13   N  N     0  -0.447  -45.9543  -30.4554   6.7499
 W5D  N15   N  NR15  0  -0.570  -47.7076  -28.8524   6.5937
 W5D  O02   O  O2    0  -0.538  -47.2855  -29.9751   0.2770
 W5D  H171  H  HCR5  0   0.262  -47.7348  -27.6484   3.5681
 W5D  H012  H  HCH2  0   0.260  -46.6111  -31.5817   1.3934
 W5D  H031  H  HCH2  0   0.257  -47.7387  -29.7199   2.2719
 W5D  H032  H  HCH2  0   0.293  -47.8223  -28.3051   1.2273
 W5D  H041  H  HCH2  0  -0.143  -44.8849  -30.1735  -0.2621
 W5D  H1    H  HCH2  0   0.332  -45.9716  -27.7858   2.4464
 W5D  H2    H  HCH2  0   0.268  -45.3070  -31.4787  -1.3231
 W5D  H051  H  HCH2  0   1.949  -45.2324  -28.4849   1.0513
 W5D  H061  H  HCH2  0   0.214  -44.5050  -33.1441   0.3237
 W5D  H062  H  HCH2  0   0.216  -43.2726  -31.9803  -0.0909
 W5D  H071  H  HCH2  0   0.258  -44.8364  -32.2135   2.5100
 W5D  H072  H  HCH2  0   0.260  -43.1248  -32.3045   2.2518
 W5D  H081  H  HCH2  0   0.280  -43.1188  -30.1753   3.0279
 W5D  H082  H  HCH2  0   0.276  -43.5567  -29.7245   1.4017
 W5D  H121  H  HCR6  0   0.255  -44.3720  -31.7254   6.4915
 W5D  H161  H  HCR5  0   0.288  -49.0498  -27.3728   5.8495
 W5D  H151  H  HNR5  0   0.428  -48.0337  -28.9213   7.5441
 W5D  H011  H  HCH2  0   0.132  -47.2755  -31.9516  -0.1839

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
 W5D  C10  C18   aromatic  1.423  0.020  1.423
 W5D  C10  N09   single    1.352  0.020  1.352
 W5D  C10  N11   aromatic  1.339  0.020  1.339
 W5D  C17  C16   aromatic  1.362  0.020  1.362
 W5D  C17  C18   aromatic  1.436  0.020  1.436
 W5D  C01  C05   single    1.531  0.020  1.531
 W5D  C01  O02   single    1.415  0.020  1.415
 W5D  C03  C04   single    1.537  0.020  1.537
 W5D  C03  O02   single    1.404  0.020  1.404
 W5D  C04  N09   single    1.452  0.020  1.452
 W5D  C05  C06   single    1.524  0.020  1.524
 W5D  C06  C07   single    1.530  0.020  1.530
 W5D  C07  C08   single    1.536  0.020  1.536
 W5D  C08  N09   single    1.463  0.020  1.463
 W5D  C12  N11   aromatic  1.326  0.020  1.326
 W5D  C12  N13   aromatic  1.315  0.020  1.315
 W5D  C14  C18   aromatic  1.409  0.020  1.409
 W5D  C14  N13   aromatic  1.335  0.020  1.335
 W5D  C14  N15   aromatic  1.352  0.020  1.352
 W5D  C16  N15   aromatic  1.368  0.020  1.368
 W5D  C17  H171  single    0.930  0.020  1.080
 W5D  C01  H011  single    0.970  0.020  1.090
 W5D  C01  H012  single    0.970  0.020  1.090
 W5D  C03  H031  single    0.970  0.020  1.090
 W5D  C03  H032  single    0.970  0.020  1.090
 W5D  C04  H041  single    0.970  0.020  1.090
 W5D  C04  H1    single    0.970  0.020  1.090
 W5D  C05  H2    single    0.970  0.020  1.090
 W5D  C05  H051  single    0.970  0.020  1.090
 W5D  C06  H061  single    0.970  0.020  1.090
 W5D  C06  H062  single    0.970  0.020  1.090
 W5D  C07  H071  single    0.970  0.020  1.090
 W5D  C07  H072  single    0.970  0.020  1.090
 W5D  C08  H081  single    0.970  0.020  1.090
 W5D  C08  H082  single    0.970  0.020  1.090
 W5D  C12  H121  single    0.930  0.020  1.080
 W5D  C16  H161  single    0.930  0.020  1.080
 W5D  N15  H151  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
 W5D  N11   C10  N09   116.34  3.000
 W5D  N11   C10  C18   118.21  3.000
 W5D  N09   C10  C18   125.44  3.000
 W5D  H171  C17  C18   129.33  3.000
 W5D  H171  C17  C16   123.74  3.000
 W5D  C18   C17  C16   106.93  3.000
 W5D  H012  C01  H011  106.23  3.000
 W5D  H012  C01  O02   110.31  3.000
 W5D  H011  C01  O02   107.30  3.000
 W5D  H012  C01  C05   111.18  3.000
 W5D  H011  C01  C05   109.85  3.000
 W5D  O02   C01  C05   111.74  3.000
 W5D  H032  C03  H031  106.98  3.000
 W5D  H032  C03  O02   105.39  3.000
 W5D  H031  C03  O02   110.38  3.000
 W5D  H032  C03  C04   107.26  3.000
 W5D  H031  C03  C04   109.21  3.000
 W5D  O02   C03  C04   117.06  3.000
 W5D  H1    C04  H041  150.25  3.000
 W5D  H1    C04  N09   109.17  3.000
 W5D  H041  C04  N09    86.98  3.000
 W5D  H1    C04  C03   108.10  3.000
 W5D  H041  C04  C03    85.17  3.000
 W5D  N09   C04  C03   116.07  3.000
 W5D  H051  C05  H2    130.47  3.000
 W5D  H051  C05  C06   108.72  3.000
 W5D  H2    C05  C06   109.38  3.000
 W5D  H051  C05  C01    81.22  3.000
 W5D  H2    C05  C01   109.72  3.000
 W5D  C06   C05  C01   114.45  3.000
 W5D  H062  C06  H061  105.82  3.000
 W5D  H062  C06  C07   109.23  3.000
 W5D  H061  C06  C07   108.69  3.000
 W5D  H062  C06  C05   107.86  3.000
 W5D  H061  C06  C05   110.21  3.000
 W5D  C07   C06  C05   114.64  3.000
 W5D  H072  C07  H071  105.15  3.000
 W5D  H072  C07  C08   108.44  3.000
 W5D  H071  C07  C08   108.78  3.000
 W5D  H072  C07  C06   108.09  3.000
 W5D  H071  C07  C06   110.63  3.000
 W5D  C08   C07  C06   115.24  3.000
 W5D  H082  C08  H081  106.23  3.000
 W5D  H082  C08  N09   106.96  3.000
 W5D  H081  C08  N09   108.04  3.000
 W5D  H082  C08  C07   110.78  3.000
 W5D  H081  C08  C07   109.30  3.000
 W5D  N09   C08  C07   115.11  3.000
 W5D  H121  C12  N13   116.51  3.000
 W5D  H121  C12  N11   115.58  3.000
 W5D  N13   C12  N11   127.91  3.000
 W5D  N15   C14  N13   124.79  3.000
 W5D  N15   C14  C18   108.27  3.000
 W5D  N13   C14  C18   126.94  3.000
 W5D  H161  C16  N15   120.87  3.000
 W5D  H161  C16  C17   129.66  3.000
 W5D  N15   C16  C17   109.47  3.000
 W5D  C14   C18  C17   105.92  3.000
 W5D  C14   C18  C10   114.51  3.000
 W5D  C17   C18  C10   139.57  3.000
 W5D  C08   N09  C04   120.54  3.000
 W5D  C08   N09  C10   118.23  3.000
 W5D  C04   N09  C10   120.93  3.000
 W5D  C12   N11  C10   120.18  3.000
 W5D  C14   N13  C12   112.24  3.000
 W5D  H151  N15  C16   125.67  3.000
 W5D  H151  N15  C14   124.92  3.000
 W5D  C16   N15  C14   109.41  3.000
 W5D  C03   O02  C01   115.49  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
 W5D  CONST_01  C16   C17  C18  C10  180.00  0.0  0
 W5D  CONST_02  N13   C14  C18  C10    0.00  0.0  0
 W5D  CONST_03  N15   C14  C18  C10  180.00  0.0  0
 W5D  CONST_04  N13   C12  N11  C10    0.00  0.0  0
 W5D  CONST_05  C14   N15  C16  C17    0.00  0.0  0
 W5D  CONST_06  N11   C10  C18  C17  180.00  0.0  0
 W5D  CONST_07  N13   C14  C18  C17  180.00  0.0  0
 W5D  CONST_08  N15   C14  C18  C17    0.00  0.0  0
 W5D  CONST_09  C18   C10  N11  C12    0.00  0.0  0
 W5D  CONST_10  C18   C14  N13  C12    0.00  0.0  0
 W5D  CONST_11  N15   C14  N13  C12  180.00  0.0  0
 W5D  CONST_12  N11   C10  C18  C14    0.00  0.0  0
 W5D  CONST_13  C16   C17  C18  C14    0.00  0.0  0
 W5D  CONST_14  N11   C12  N13  C14    0.00  0.0  0
 W5D  CONST_15  C18   C14  N15  C16    0.00  0.0  0
 W5D  CONST_16  N13   C14  N15  C16  180.00  0.0  0
 W5D  CONST_17  N15   C16  C17  C18    0.00  0.0  0
 W5D  CONST_18  N09   C10  C18  C17    0.00  0.0  0
 W5D  CONST_19  N09   C10  N11  C12  180.00  0.0  0
 W5D  CONST_20  N09   C10  C18  C14  180.00  0.0  0
 W5D  CONST_21  H171  C17  C18  C10    0.00  0.0  0
 W5D  CONST_22  H121  C12  N11  C10  180.00  0.0  0
 W5D  CONST_23  H151  N15  C16  C17  180.00  0.0  0
 W5D  CONST_24  H161  C16  N15  C14  180.00  0.0  0

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
 W5D  plan-1  C10   0.020
 W5D  plan-1  C17   0.020
 W5D  plan-1  C12   0.020
 W5D  plan-1  C14   0.020
 W5D  plan-1  C16   0.020
 W5D  plan-1  C18   0.020
 W5D  plan-1  N09   0.020
 W5D  plan-1  N11   0.020
 W5D  plan-1  N13   0.020
 W5D  plan-1  N15   0.020
 W5D  plan-1  H171  0.020
 W5D  plan-1  H121  0.020
 W5D  plan-1  H161  0.020
 W5D  plan-1  H151  0.020

