# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 14:38:35 2021
#   Inital geometry file: a 110 line input string
#   Ligand name: [(2~{R},3~{S},5~{R})-5-[5-methyl-3-[2-(methylamino)-2-oxidanylidene-ethyl]-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphite
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)CN1C(=O)N(C=C(C)C1=O)[C@H]2C[C@H](O)[C@@H](COP(O)O)O2
#
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
 QCE  QCE  '[(2~{R},3~{S},5~{R})-5-[5-methyl-3-[2-(methylamino)-2-oxidanylidene-ethyl]-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphite'  ligand  45  25  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_QCE
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
 QCE  N    N  NH1   0  -0.625  -30.8151  30.8879  14.8943
 QCE  C4   C  CR6   0   0.598  -28.5973  33.8071  12.9266
 QCE  N3   N  NR6   0  -0.585  -29.2572  32.7910  12.2395
 QCE  C2   C  CR6   0   0.777  -28.8368  32.2361  11.0498
 QCE  O2   O  O     0  -0.493  -29.4150  31.3050  10.5213
 QCE  C5   C  CR6   0  -0.180  -27.4688  34.3955  12.2439
 QCE  C7   C  CH3   0  -0.708  -26.7541  35.5382  12.8889
 QCE  C6   C  CR16  0   0.036  -27.0930  33.8698  11.0653
 QCE  N1   N  NR6   0  -0.579  -27.7318  32.8155  10.4816
 QCE  C1'  C  CR15  0   0.197  -27.2964  32.2529   9.1804
 QCE  O4'  O  O     0  -0.498  -25.9638  32.6039   8.9546
 QCE  C2'  C  CH2   0  -0.543  -28.1028  32.8063   8.0082
 QCE  C3'  C  CR15  0   0.020  -27.2160  33.9412   7.5038
 QCE  O3'  O  OH1   0  -0.664  -27.3556  34.2582   6.1472
 QCE  C4'  C  CR15  0   0.017  -25.8317  33.3501   7.7479
 QCE  C5'  C  CH2   0  -0.192  -24.6806  34.3199   7.8444
 QCE  O5'  O  O2    0  -0.612  -24.9416  35.2867   8.8526
 QCE  P    P  P     0   0.954  -23.7958  36.2601   9.5170
 QCE  OP1  O  OH1   0  -0.776  -22.6280  35.1946   9.9476
 QCE  OP2  O  OH1   0  -0.774  -22.9693  36.7786   8.2010
 QCE  CA'  C  CH3   0  -0.512  -30.5645  29.9333  15.9491
 QCE  C1   C  C     0   0.548  -29.8956  31.2086  13.9804
 QCE  O21  O  O     0  -0.489  -28.7646  30.7497  13.9652
 QCE  C3   C  CH2   0  -0.457  -30.3796  32.1781  12.9110
 QCE  H1   H  HNH1  0   0.409  -31.7204  31.3259  14.8543
 QCE  H2   H  HCH3  0   0.247  -26.3431  35.2583  13.8598
 QCE  H3   H  HCH3  0   0.236  -25.9288  35.8823  12.2658
 QCE  H4   H  HCH3  0   0.247  -27.4205  36.3864  13.0513
 QCE  H5   H  HCR6  0   0.316  -26.2458  34.2610  10.5231
 QCE  H6   H  HCR5  0   0.276  -27.3841  31.1707   9.2712
 QCE  H7   H  HCH2  0   0.279  -29.1067  33.1195   8.2902
 QCE  H8   H  HCH2  0   0.264  -28.1891  32.0408   7.2333
 QCE  H9   H  HCR5  0   0.228  -27.3619  34.8292   8.1318
 QCE  H10  H  HOH1  0   0.461  -28.1543  34.7826   6.0381
 QCE  H11  H  HCR5  0   0.247  -25.5999  32.6664   6.9186
 QCE  H12  H  HCH2  0   0.244  -23.7581  33.7694   8.0477
 QCE  H13  H  HCH2  0   0.238  -24.5681  34.8015   6.8692
 QCE  H14  H  HOH1  0   0.482  -22.6787  34.9747  10.8848
 QCE  H15  H  HOH1  0   0.483  -23.3295  37.6047   7.8574
 QCE  H16  H  HCH3  0   0.252  -31.4621  29.8499  16.5545
 QCE  H17  H  HCH3  0   0.240  -30.3258  28.9469  15.5509
 QCE  H18  H  HCH3  0   0.240  -29.7445  30.2524  16.5927
 QCE  H19  H  HCH2  0   0.298  -31.0159  32.9513  13.3392
 QCE  H20  H  HCH2  0   0.317  -30.9777  31.6332  12.1831
 QCE  O4   O  O     0  -0.463  -28.9918  34.1531  14.0267

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
 QCE  O3'  C3'  single  1.400  0.020  1.400
 QCE  C3'  C4'  single  1.525  0.020  1.525
 QCE  C3'  C2'  single  1.526  0.020  1.526
 QCE  C4'  C5'  single  1.508  0.020  1.508
 QCE  C4'  O4'  single  1.425  0.020  1.425
 QCE  C5'  O5'  single  1.421  0.020  1.421
 QCE  C2'  C1'  single  1.527  0.020  1.527
 QCE  O4'  C1'  single  1.396  0.020  1.396
 QCE  C1'  N1   single  1.483  0.020  1.483
 QCE  O5'  P    single  1.644  0.020  1.644
 QCE  OP2  P    single  1.638  0.020  1.638
 QCE  P    OP1  single  1.638  0.020  1.638
 QCE  N1   C2   single  1.371  0.020  1.371
 QCE  N1   C6   single  1.364  0.020  1.364
 QCE  O2   C2   double  1.217  0.020  1.217
 QCE  C2   N3   single  1.378  0.020  1.378
 QCE  C6   C5   double  1.344  0.020  1.344
 QCE  C5   C7   single  1.494  0.020  1.494
 QCE  C5   C4   single  1.444  0.020  1.444
 QCE  N3   C4   single  1.393  0.020  1.393
 QCE  N3   C3   single  1.444  0.020  1.444
 QCE  C4   O4   double  1.219  0.020  1.219
 QCE  C3   C1   single  1.522  0.020  1.522
 QCE  O21  C1   double  1.221  0.020  1.221
 QCE  C1   N    single  1.335  0.020  1.335
 QCE  N    CA'  single  1.445  0.020  1.445
 QCE  N    H1   single  0.860  0.020  1.020
 QCE  C7   H2   single  0.970  0.020  1.090
 QCE  C7   H3   single  0.970  0.020  1.090
 QCE  C7   H4   single  0.970  0.020  1.090
 QCE  C6   H5   single  0.930  0.020  1.080
 QCE  C1'  H6   single  0.970  0.020  1.090
 QCE  C2'  H7   single  0.970  0.020  1.090
 QCE  C2'  H8   single  0.970  0.020  1.090
 QCE  C3'  H9   single  0.970  0.020  1.090
 QCE  O3'  H10  single  0.850  0.020  0.980
 QCE  C4'  H11  single  0.970  0.020  1.090
 QCE  C5'  H12  single  0.970  0.020  1.090
 QCE  C5'  H13  single  0.970  0.020  1.090
 QCE  OP1  H14  single  0.850  0.020  0.980
 QCE  OP2  H15  single  0.850  0.020  0.980
 QCE  CA'  H16  single  0.970  0.020  1.090
 QCE  CA'  H17  single  0.970  0.020  1.090
 QCE  CA'  H18  single  0.970  0.020  1.090
 QCE  C3   H19  single  0.970  0.020  1.090
 QCE  C3   H20  single  0.970  0.020  1.090

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
 QCE  H1   N    C1   119.19  3.000
 QCE  H1   N    CA'  118.20  3.000
 QCE  C1   N    CA'  122.61  3.000
 QCE  C5   C4   N3   115.73  3.000
 QCE  N3   C4   O4   119.93  3.000
 QCE  C5   C4   O4   124.33  3.000
 QCE  C3   N3   C2   117.87  3.000
 QCE  C3   N3   C4   116.64  3.000
 QCE  C2   N3   C4   125.10  3.000
 QCE  N1   C2   O2   121.76  3.000
 QCE  O2   C2   N3   122.54  3.000
 QCE  N1   C2   N3   115.68  3.000
 QCE  C6   C5   C7   122.94  3.000
 QCE  C7   C5   C4   118.77  3.000
 QCE  C6   C5   C4   118.27  3.000
 QCE  H4   C7   H3   107.59  3.000
 QCE  H4   C7   H2   107.30  3.000
 QCE  H3   C7   H2   107.73  3.000
 QCE  H4   C7   C5   111.51  3.000
 QCE  H3   C7   C5   110.91  3.000
 QCE  H2   C7   C5   111.60  3.000
 QCE  H5   C6   N1   115.65  3.000
 QCE  H5   C6   C5   121.22  3.000
 QCE  N1   C6   C5   123.13  3.000
 QCE  C1'  N1   C6   122.08  3.000
 QCE  C6   N1   C2   121.79  3.000
 QCE  C1'  N1   C2   116.10  3.000
 QCE  H6   C1'  C2'  112.43  3.000
 QCE  H6   C1'  O4'  109.87  3.000
 QCE  C2'  C1'  O4'  106.79  3.000
 QCE  H6   C1'  N1   106.26  3.000
 QCE  O4'  C1'  N1   109.07  3.000
 QCE  C2'  C1'  N1   112.40  3.000
 QCE  C4'  O4'  C1'  110.92  3.000
 QCE  H8   C2'  H7   108.20  3.000
 QCE  H8   C2'  C3'  109.42  3.000
 QCE  H7   C2'  C3'  114.05  3.000
 QCE  H8   C2'  C1'  109.41  3.000
 QCE  H7   C2'  C1'  113.11  3.000
 QCE  C3'  C2'  C1'  102.50  3.000
 QCE  H9   C3'  C4'  110.04  3.000
 QCE  H9   C3'  O3'  110.98  3.000
 QCE  C4'  C3'  O3'  109.48  3.000
 QCE  H9   C3'  C2'  109.60  3.000
 QCE  C4'  C3'  C2'  100.74  3.000
 QCE  O3'  C3'  C2'  115.51  3.000
 QCE  H10  O3'  C3'  108.43  3.000
 QCE  H11  C4'  C5'  106.69  3.000
 QCE  H11  C4'  C3'  108.16  3.000
 QCE  C5'  C4'  C3'  116.99  3.000
 QCE  H11  C4'  O4'  109.43  3.000
 QCE  C5'  C4'  O4'  110.69  3.000
 QCE  C3'  C4'  O4'  104.74  3.000
 QCE  H13  C5'  H12  107.50  3.000
 QCE  H13  C5'  O5'  110.61  3.000
 QCE  H12  C5'  O5'  111.45  3.000
 QCE  H13  C5'  C4'  107.74  3.000
 QCE  H12  C5'  C4'  109.39  3.000
 QCE  O5'  C5'  C4'  110.04  3.000
 QCE  P    O5'  C5'  124.17  3.000
 QCE  OP2  P    OP1   93.29  3.000
 QCE  OP1  P    O5'  102.59  3.000
 QCE  OP2  P    O5'  102.38  3.000
 QCE  H14  OP1  P    111.49  3.000
 QCE  H15  OP2  P    111.64  3.000
 QCE  H18  CA'  H17  108.41  3.000
 QCE  H18  CA'  H16  108.36  3.000
 QCE  H17  CA'  H16  108.38  3.000
 QCE  H18  CA'  N    111.60  3.000
 QCE  H17  CA'  N    111.67  3.000
 QCE  H16  CA'  N    108.33  3.000
 QCE  C3   C1   O21  121.68  3.000
 QCE  O21  C1   N    123.79  3.000
 QCE  C3   C1   N    114.50  3.000
 QCE  H20  C3   H19  107.30  3.000
 QCE  H20  C3   C1   109.01  3.000
 QCE  H19  C3   C1   111.20  3.000
 QCE  H20  C3   N3   109.18  3.000
 QCE  H19  C3   N3   109.61  3.000
 QCE  C1   C3   N3   110.47  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
 QCE  CONST_01  N1   C2   N3   C4     0.00   0.0  0
 QCE  CONST_02  C1'  N1   C2   N3   180.00   0.0  0
 QCE  CONST_03  C6   N1   C2   N3     0.00   0.0  0
 QCE  CONST_04  C5   C4   N3   C2     0.00   0.0  0
 QCE  CONST_05  C2   N3   C4   O4   180.00   0.0  0
 QCE  CONST_06  O2   C2   N3   C4   180.00   0.0  0
 QCE  CONST_07  C1'  N1   C2   O2     0.00   0.0  0
 QCE  CONST_08  C6   N1   C2   O2   180.00   0.0  0
 QCE  CONST_09  C3   N3   C4   C5   180.00   0.0  0
 QCE  CONST_10  C3   N3   C2   N1   180.00   0.0  0
 QCE  CONST_11  C3   N3   C4   O4     0.00   0.0  0
 QCE  CONST_12  C3   N3   C2   O2     0.00   0.0  0
 QCE  CONST_13  C3   C1   N    CA'  180.00   0.0  0
 QCE  CONST_14  O21  C1   N    CA'    0.00   0.0  0
 QCE  CONST_15  H1   N    C1   O21  180.00   0.0  0
 QCE  Var_01    C1   C3   N3   C4   -76.93  30.0  3
 QCE  Var_02    H2   C7   C5   C4    59.96  30.0  3
 QCE  Var_03    N3   C3   C1   N    161.84  30.0  1
 QCE  Var_04    OP2  P    O5'  C5'   45.37  30.0  3
 QCE  Var_05    H12  C5'  O5'  P     42.20  30.0  1
 QCE  Var_06    H16  CA'  N    C1   179.97  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
 QCE  chir_01  C1'  C2'  O4'  N1   negativ
 QCE  chir_02  C3'  O3'  C2'  C4'  negativ
 QCE  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
 QCE  plan-1  C4   0.020
 QCE  plan-1  N3   0.020
 QCE  plan-1  C2   0.020
 QCE  plan-1  O2   0.020
 QCE  plan-1  C5   0.020
 QCE  plan-1  C7   0.020
 QCE  plan-1  C6   0.020
 QCE  plan-1  N1   0.020
 QCE  plan-1  C1'  0.020
 QCE  plan-1  C3   0.020
 QCE  plan-1  H5   0.020
 QCE  plan-1  O4   0.020
 QCE  plan-2  N    0.020
 QCE  plan-2  CA'  0.020
 QCE  plan-2  C1   0.020
 QCE  plan-2  O21  0.020
 QCE  plan-2  C3   0.020
 QCE  plan-2  H1   0.020

