# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 04:49:58 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: [(2~{S},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methylselanylphosphonous acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN([C@H]2C[C@H](O)[C@@H](C[Se]P(O)O)O2)C(=O)NC1=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
 XCI  XCI  '[(2~{S},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methylselanylphosphonous acid'  ligand  35  20  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XCI
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
 XCI  SE1   SE  SE    0  -0.177   2.2574  -0.7447  -0.5348
 XCI  C1'   C   CH1   0   0.221  -1.7424   1.2800  -0.7877
 XCI  C2    C   CR6   0   0.741  -2.7596   0.0243   1.0597
 XCI  C2'   C   CH2   0  -0.564  -1.5902   2.6378  -0.0926
 XCI  C3'   C   CH1   0   0.043  -0.2064   2.5932   0.5598
 XCI  C4    C   CR6   0   0.559  -4.7645  -1.3640   0.6281
 XCI  C4'   C   CH1   0   0.055   0.5045   1.5045  -0.2502
 XCI  C5    C   CR6   0  -0.184  -4.7193  -0.9326  -0.7543
 XCI  C5'   C   CH2   0  -0.615   1.5184   0.7233   0.5526
 XCI  C6    C   CR16  0   0.059  -3.7380  -0.0895  -1.1174
 XCI  N1    N   NR6   0  -0.568  -2.7826   0.3997  -0.2638
 XCI  N3    N   NR16  0  -0.734  -3.7621  -0.8373   1.4223
 XCI  O2    O   O     0  -0.472  -1.9318   0.4170   1.8547
 XCI  O3'   O   OH1   0  -0.668   0.5335   3.7824   0.4594
 XCI  O4    O   O     0  -0.454  -5.5909  -2.1256   1.0963
 XCI  O4'   O   O2    0  -0.490  -0.5071   0.6255  -0.7047
 XCI  P     P   P     0   0.741   4.1513  -1.0249   0.6806
 XCI  H1'   H   HCH1  0   0.258  -2.0161   1.4313  -1.8345
 XCI  H2''  H   HCH2  0   0.269  -1.6028   3.4200  -0.8533
 XCI  H2'   H   HCH2  0   0.277  -2.3939   2.8469   0.6114
 XCI  H3'   H   HCH1  0   0.233  -0.2973   2.2777   1.6028
 XCI  H4'   H   HCH1  0   0.236   0.9971   1.9821  -1.1098
 XCI  H5'   H   HCH2  0   0.276   1.0587   0.3143   1.4534
 XCI  H5''  H   HCH2  0   0.278   2.3315   1.3908   0.8427
 XCI  H6    H   HCR6  0   0.317  -3.6578   0.2592  -2.1383
 XCI  H72   H   HCH3  0   0.247  -5.7396  -2.5336  -1.7545
 XCI  H73   H   HCH3  0   0.247  -6.7548  -1.1442  -1.4034
 XCI  H71   H   HCH3  0   0.247  -5.5759  -1.0626  -2.7102
 XCI  H3    H   HNR6  0   0.425  -3.7555  -1.1199   2.3948
 XCI  H1    H   HOH1  0   0.458   0.1897   4.4074   1.1043
 XCI  H2    H   HOH1  0   0.488   5.2724  -2.8039   0.1040
 XCI  H4    H   HOH1  0   0.486   5.4291   0.7049   1.0032
 XCI  C7    C   CH3   0  -0.706  -5.7505  -1.4441  -1.7055
 XCI  OP1   O   OH1   0  -0.769   4.7779  -2.1236  -0.3695
 XCI  OP2   O   OH1   0  -0.761   4.9419   0.3503   0.2486

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
 XCI  OP1  P     single  1.644  0.020  1.644
 XCI  OP2  P     single  1.644  0.020  1.644
 XCI  P    SE1   single  2.268  0.020  2.268
 XCI  SE1  C5'   single  1.971  0.020  1.971
 XCI  C7   C5    single  1.493  0.020  1.493
 XCI  C5'  C4'   single  1.511  0.020  1.511
 XCI  C5   C6    double  1.344  0.020  1.344
 XCI  C5   C4    single  1.449  0.020  1.449
 XCI  O3'  C3'   single  1.404  0.020  1.404
 XCI  C6   N1    single  1.371  0.020  1.371
 XCI  C3'  C4'   single  1.532  0.020  1.532
 XCI  C3'  C2'   single  1.530  0.020  1.530
 XCI  C4'  O4'   single  1.415  0.020  1.415
 XCI  O4   C4    double  1.217  0.020  1.217
 XCI  C4   N3    single  1.383  0.020  1.383
 XCI  O4'  C1'   single  1.400  0.020  1.400
 XCI  N1   C1'   single  1.460  0.020  1.460
 XCI  N1   C2    single  1.376  0.020  1.376
 XCI  C2'  C1'   single  1.533  0.020  1.533
 XCI  N3   C2    single  1.371  0.020  1.371
 XCI  C2   O2    double  1.213  0.020  1.213
 XCI  C1'  H1'   single  0.970  0.020  1.090
 XCI  C2'  H2''  single  0.970  0.020  1.090
 XCI  C2'  H2'   single  0.970  0.020  1.090
 XCI  C3'  H3'   single  0.970  0.020  1.090
 XCI  C4'  H4'   single  0.970  0.020  1.090
 XCI  C5'  H5'   single  0.970  0.020  1.090
 XCI  C5'  H5''  single  0.970  0.020  1.090
 XCI  C6   H6    single  0.930  0.020  1.080
 XCI  C7   H72   single  0.970  0.020  1.090
 XCI  C7   H73   single  0.970  0.020  1.090
 XCI  C7   H71   single  0.970  0.020  1.090
 XCI  N3   H3    single  0.860  0.020  1.020
 XCI  O3'  H1    single  0.850  0.020  0.980
 XCI  OP1  H2    single  0.850  0.020  0.980
 XCI  OP2  H4    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
 XCI  P     SE1  C5'    96.29  3.000
 XCI  H1'   C1'  O4'   110.03  3.000
 XCI  H1'   C1'  N1    104.40  3.000
 XCI  O4'   C1'  N1    108.99  3.000
 XCI  H1'   C1'  C2'   109.67  3.000
 XCI  N1    C1'  C2'   116.24  3.000
 XCI  O4'   C1'  C2'   107.43  3.000
 XCI  O2    C2   N3    121.95  3.000
 XCI  O2    C2   N1    123.61  3.000
 XCI  N3    C2   N1    114.44  3.000
 XCI  H2'   C2'  H2''  107.73  3.000
 XCI  H2'   C2'  C3'   113.41  3.000
 XCI  H2''  C2'  C3'   109.18  3.000
 XCI  H2'   C2'  C1'   112.96  3.000
 XCI  H2''  C2'  C1'   108.52  3.000
 XCI  C3'   C2'  C1'   104.91  3.000
 XCI  H3'   C3'  O3'   110.87  3.000
 XCI  H3'   C3'  C4'   109.74  3.000
 XCI  O3'   C3'  C4'   108.63  3.000
 XCI  H3'   C3'  C2'   109.87  3.000
 XCI  C4'   C3'  C2'   102.41  3.000
 XCI  O3'   C3'  C2'   114.92  3.000
 XCI  O4    C4   N3    120.62  3.000
 XCI  N3    C4   C5    114.32  3.000
 XCI  O4    C4   C5    125.06  3.000
 XCI  H4'   C4'  O4'   109.81  3.000
 XCI  H4'   C4'  C5'   109.83  3.000
 XCI  O4'   C4'  C5'   109.22  3.000
 XCI  H4'   C4'  C3'   108.21  3.000
 XCI  O4'   C4'  C3'   106.23  3.000
 XCI  C5'   C4'  C3'   113.45  3.000
 XCI  C7    C5   C6    123.16  3.000
 XCI  C6    C5   C4    117.87  3.000
 XCI  C7    C5   C4    118.96  3.000
 XCI  H5''  C5'  H5'   108.90  3.000
 XCI  H5''  C5'  C4'   108.97  3.000
 XCI  H5'   C5'  C4'   110.47  3.000
 XCI  H5''  C5'  SE1   108.84  3.000
 XCI  H5'   C5'  SE1   109.53  3.000
 XCI  C4'   C5'  SE1   110.09  3.000
 XCI  H6    C6   N1    114.88  3.000
 XCI  H6    C6   C5    120.76  3.000
 XCI  N1    C6   C5    124.36  3.000
 XCI  C6    N1   C2    120.86  3.000
 XCI  C2    N1   C1'   119.85  3.000
 XCI  C6    N1   C1'   119.22  3.000
 XCI  H3    N3   C4    116.73  3.000
 XCI  H3    N3   C2    115.13  3.000
 XCI  C4    N3   C2    128.14  3.000
 XCI  H1    O3'  C3'   108.30  3.000
 XCI  C4'   O4'  C1'   111.06  3.000
 XCI  OP2   P    OP1   102.00  3.000
 XCI  OP2   P    SE1    99.06  3.000
 XCI  OP1   P    SE1    93.36  3.000
 XCI  H71   C7   H73   107.88  3.000
 XCI  H71   C7   H72   107.87  3.000
 XCI  H73   C7   H72   107.23  3.000
 XCI  H71   C7   C5    110.92  3.000
 XCI  H73   C7   C5    111.42  3.000
 XCI  H72   C7   C5    111.34  3.000
 XCI  H2    OP1  P     110.67  3.000
 XCI  H4    OP2  P     110.15  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
 XCI  CONST_01  N3   C2   N1   C1'   180.00   0.0  0
 XCI  CONST_02  C5   C4   N3   C2      0.00   0.0  0
 XCI  CONST_03  N1   C2   N3   C4      0.00   0.0  0
 XCI  CONST_04  N3   C2   N1   C6      0.00   0.0  0
 XCI  CONST_05  O2   C2   N1   C1'     0.00   0.0  0
 XCI  CONST_06  O4   C4   N3   C2    180.00   0.0  0
 XCI  CONST_07  O2   C2   N3   C4    180.00   0.0  0
 XCI  CONST_08  O2   C2   N1   C6    180.00   0.0  0
 XCI  CONST_09  H3   N3   C4   C5    180.00   0.0  0
 XCI  Var_01    H72  C7   C5   C4    -58.11  30.0  3
 XCI  Var_02    OP1  P    SE1  C5'  -174.00  30.0  1
 XCI  Var_03    H5'  C5'  SE1  P     -79.33  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
 XCI  chir_01  C1'  O4'  N1   C2'  negativ
 XCI  chir_02  C3'  O3'  C4'  C2'  positiv
 XCI  chir_03  C4'  O4'  C3'  C5'  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
 XCI  plan-1  C1'  0.020
 XCI  plan-1  C2   0.020
 XCI  plan-1  C4   0.020
 XCI  plan-1  C5   0.020
 XCI  plan-1  C6   0.020
 XCI  plan-1  N1   0.020
 XCI  plan-1  N3   0.020
 XCI  plan-1  O2   0.020
 XCI  plan-1  O4   0.020
 XCI  plan-1  H6   0.020
 XCI  plan-1  H3   0.020
 XCI  plan-1  C7   0.020

