# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 22:23:27 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: {[(1S,3R)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)cyclopentyl]oxy}propanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN([C@@H]2CC[C@@H](C2)OC(C(O)=O)C(O)=O)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
 64A  64A  '{[(1S,3R)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)cyclopentyl]oxy}propanedioic acid'  ligand  36  22  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_64A
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
 64A  C2   C  CR6    0   0.555  -5.1333  -0.4470   0.4811
 64A  C3   C  CR6    0  -0.182  -4.7215   0.8555   0.0055
 64A  C4   C  CH3    0  -0.707  -5.7365   1.9466  -0.0933
 64A  C5   C  CR16   0   0.051  -3.4287   1.0205  -0.3275
 64A  C12  C  CH1    0  -0.160   3.5975   0.1831  -0.3613
 64A  C10  C  CH1    0   0.077   1.2604   0.4730  -0.4368
 64A  C13  C  C      0   0.351   4.6871  -0.7209   0.2543
 64A  N21  N  NR16   0  -0.732  -4.1132  -1.3778   0.5316
 64A  N6   N  NR6    0  -0.551  -2.4688   0.0457  -0.2511
 64A  C22  C  CR6    0   0.734  -2.7938  -1.2153   0.1870
 64A  C7   C  CH1    0  -0.086  -1.1010   0.3734  -0.6673
 64A  C20  C  CH2    0  -0.478  -0.0059   0.2198   0.3808
 64A  C9   C  CH2    0  -0.486   0.9315  -0.0224  -1.8746
 64A  C8   C  CH2    0  -0.443  -0.5631  -0.3808  -1.8827
 64A  O1   O  O      0  -0.461  -6.2658  -0.7464   0.8178
 64A  O11  O  O2     0  -0.498   2.3437  -0.1743   0.1691
 64A  O18  O  O      0  -0.617   3.6350   2.1027   1.0403
 64A  O17  O  OC    -1  -0.612   4.6093   2.2606  -0.9591
 64A  O14  O  OC    -1  -0.621   5.8239  -0.5924  -0.2421
 64A  O15  O  O      0  -0.602   4.3572  -1.4798   1.1813
 64A  O23  O  O      0  -0.483  -2.0003  -2.1314   0.2720
 64A  C16  C  C      0   0.360   3.9753   1.6568  -0.0730
 64A  H1   H  HCH3   0   0.246  -6.5658   1.6595  -0.7411
 64A  H2   H  HCH3   0   0.246  -6.1589   2.1880   0.8832
 64A  H3   H  HCH3   0   0.246  -5.2949   2.8551  -0.4997
 64A  H4   H  HCR6   0   0.312  -3.0715   1.9765  -0.6850
 64A  H5   H  HCH1   0   0.185   3.6130   0.0274  -1.4503
 64A  H6   H  HCH1   0   0.206   1.4324   1.5568  -0.4742
 64A  H7   H  HNR6   0   0.422  -4.3594  -2.3052   0.8552
 64A  H8   H  HCH1   0   0.267  -1.1467   1.4308  -0.9363
 64A  H9   H  HCH2   0   0.245   0.0118  -0.7958   0.7774
 64A  H10  H  HCH2   0   0.249  -0.1154   0.9178   1.2118
 64A  H11  H  HCH2   0   0.236   1.1471   0.7567  -2.6070
 64A  H12  H  HCH2   0   0.242   1.5429  -0.8864  -2.1402
 64A  H13  H  HCH2   0   0.246  -0.7015  -1.4533  -1.7555
 64A  H14  H  HCH2   0   0.244  -1.0682  -0.0853  -2.8028

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
 64A  O18  C16  deloc   1.247  0.020  1.247
 64A  O23  C22  double  1.215  0.020  1.215
 64A  C16  O17  deloc   1.246  0.020  1.246
 64A  C16  C12  single  1.548  0.020  1.548
 64A  C20  C10  single  1.528  0.020  1.528
 64A  C20  C7   single  1.524  0.020  1.524
 64A  C22  N21  single  1.373  0.020  1.373
 64A  C22  N6   single  1.374  0.020  1.374
 64A  C10  O11  single  1.400  0.020  1.400
 64A  C10  C9   single  1.556  0.020  1.556
 64A  C7   N6   single  1.467  0.020  1.467
 64A  C7   C8   single  1.528  0.020  1.528
 64A  N21  C2   single  1.382  0.020  1.382
 64A  N6   C5   single  1.370  0.020  1.370
 64A  O11  C12  single  1.408  0.020  1.408
 64A  C12  C13  single  1.544  0.020  1.544
 64A  C9   C8   single  1.537  0.020  1.537
 64A  C2   O1   double  1.219  0.020  1.219
 64A  C2   C3   single  1.446  0.020  1.446
 64A  C5   C3   double  1.345  0.020  1.345
 64A  C3   C4   single  1.493  0.020  1.493
 64A  C13  O15  deloc   1.243  0.020  1.243
 64A  C13  O14  deloc   1.247  0.020  1.247
 64A  C4   H1   single  0.970  0.020  1.090
 64A  C4   H2   single  0.970  0.020  1.090
 64A  C4   H3   single  0.970  0.020  1.090
 64A  C5   H4   single  0.930  0.020  1.080
 64A  C12  H5   single  0.970  0.020  1.090
 64A  C10  H6   single  0.970  0.020  1.090
 64A  N21  H7   single  0.860  0.020  1.020
 64A  C7   H8   single  0.970  0.020  1.090
 64A  C20  H9   single  0.970  0.020  1.090
 64A  C20  H10  single  0.970  0.020  1.090
 64A  C9   H11  single  0.970  0.020  1.090
 64A  C9   H12  single  0.970  0.020  1.090
 64A  C8   H13  single  0.970  0.020  1.090
 64A  C8   H14  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
 64A  O1   C2   N21  120.69  3.000
 64A  O1   C2   C3   125.20  3.000
 64A  N21  C2   C3   114.11  3.000
 64A  C5   C3   C4   123.17  3.000
 64A  C4   C3   C2   119.09  3.000
 64A  C5   C3   C2   117.74  3.000
 64A  H3   C4   H2   107.85  3.000
 64A  H3   C4   H1   107.84  3.000
 64A  H2   C4   H1   107.19  3.000
 64A  H3   C4   C3   111.02  3.000
 64A  H2   C4   C3   111.44  3.000
 64A  H1   C4   C3   111.33  3.000
 64A  H4   C5   N6   114.58  3.000
 64A  H4   C5   C3   120.51  3.000
 64A  N6   C5   C3   124.91  3.000
 64A  H5   C12  C16  108.40  3.000
 64A  H5   C12  O11  110.46  3.000
 64A  C16  C12  O11  112.88  3.000
 64A  H5   C12  C13  107.57  3.000
 64A  O11  C12  C13  109.25  3.000
 64A  C16  C12  C13  108.11  3.000
 64A  H6   C10  O11  110.49  3.000
 64A  H6   C10  C9   108.41  3.000
 64A  O11  C10  C9   114.60  3.000
 64A  H6   C10  C20  108.15  3.000
 64A  C9   C10  C20  105.45  3.000
 64A  O11  C10  C20  109.46  3.000
 64A  O15  C13  O14  127.00  3.000
 64A  O14  C13  C12  115.11  3.000
 64A  O15  C13  C12  117.89  3.000
 64A  H7   N21  C22  114.97  3.000
 64A  H7   N21  C2   116.68  3.000
 64A  C22  N21  C2   128.34  3.000
 64A  C7   N6   C22  121.08  3.000
 64A  C7   N6   C5   118.59  3.000
 64A  C22  N6   C5   120.33  3.000
 64A  O23  C22  N6   124.04  3.000
 64A  N6   C22  N21  114.58  3.000
 64A  O23  C22  N21  121.38  3.000
 64A  H8   C7   C8   107.26  3.000
 64A  H8   C7   C20  107.29  3.000
 64A  C8   C7   C20  104.15  3.000
 64A  H8   C7   N6   104.31  3.000
 64A  C8   C7   N6   116.33  3.000
 64A  C20  C7   N6   116.90  3.000
 64A  H10  C20  H9   108.69  3.000
 64A  H10  C20  C7   112.80  3.000
 64A  H9   C20  C7   110.84  3.000
 64A  H10  C20  C10  112.63  3.000
 64A  H9   C20  C10  109.59  3.000
 64A  C7   C20  C10  102.17  3.000
 64A  H12  C9   H11  106.94  3.000
 64A  H12  C9   C8   111.03  3.000
 64A  H11  C9   C8   110.81  3.000
 64A  H12  C9   C10  111.01  3.000
 64A  H11  C9   C10  110.57  3.000
 64A  C8   C9   C10  106.54  3.000
 64A  H14  C8   H13  107.86  3.000
 64A  H14  C8   C9   113.06  3.000
 64A  H13  C8   C9   110.65  3.000
 64A  H14  C8   C7   111.98  3.000
 64A  H13  C8   C7   110.39  3.000
 64A  C9   C8   C7   102.88  3.000
 64A  C10  O11  C12  114.13  3.000
 64A  O17  C16  O18  126.93  3.000
 64A  O17  C16  C12  116.94  3.000
 64A  O18  C16  C12  116.11  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
 64A  CONST_01  N6   C22  N21  C2     0.00   0.0  0
 64A  CONST_02  C22  N21  C2   C3     0.00   0.0  0
 64A  CONST_03  N21  C22  N6   C5     0.00   0.0  0
 64A  CONST_04  C7   N6   C22  N21  180.00   0.0  0
 64A  CONST_05  O23  C22  N21  C2   180.00   0.0  0
 64A  CONST_06  O23  C22  N6   C5   180.00   0.0  0
 64A  CONST_07  O1   C2   N21  C22  180.00   0.0  0
 64A  CONST_08  O23  C22  N6   C7     0.00   0.0  0
 64A  CONST_09  H7   N21  C2   C3   180.00   0.0  0
 64A  Var_01    C7   C8   C9   C10   19.45  30.0  1
 64A  Var_02    H1   C4   C3   C2   -57.70  30.0  3
 64A  Var_03    C16  C12  O11  C10   66.92  30.0  3
 64A  Var_04    O18  C16  C12  C13  -83.89  30.0  2
 64A  Var_05    O15  C13  C12  O11   -7.70  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
 64A  chir_01  C10  C20  O11  C9   negativ
 64A  chir_02  C7   N6   C8   C20  positiv

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
 64A  plan-1  C2   0.020
 64A  plan-1  C3   0.020
 64A  plan-1  C4   0.020
 64A  plan-1  C5   0.020
 64A  plan-1  N21  0.020
 64A  plan-1  N6   0.020
 64A  plan-1  C22  0.020
 64A  plan-1  C7   0.020
 64A  plan-1  O1   0.020
 64A  plan-1  O23  0.020
 64A  plan-1  H4   0.020
 64A  plan-1  H7   0.020
 64A  plan-2  C12  0.020
 64A  plan-2  C13  0.020
 64A  plan-2  O14  0.020
 64A  plan-2  O15  0.020
 64A  plan-3  C12  0.020
 64A  plan-3  O18  0.020
 64A  plan-3  O17  0.020
 64A  plan-3  C16  0.020

