# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 03:38:18 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  38  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 PERFECT
;

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   0.556  -5.1493  -0.4235   0.4145
 64A  C3   C  CR6   0  -0.181  -4.7244   0.8866  -0.0297
 64A  C4   C  CH3   0  -0.706  -5.7316   1.9861  -0.1137
 64A  C5   C  CR16  0   0.052  -3.4285   1.0498  -0.3493
 64A  C12  C  CH1   0  -0.152   3.5642   0.0913  -0.2318
 64A  C10  C  CH1   0   0.044   1.2484   0.4806  -0.3809
 64A  C13  C  C     0   0.521   4.5175  -0.9983   0.2498
 64A  N21  N  NR16  0  -0.732  -4.1356  -1.3622   0.4567
 64A  N6   N  NR6   0  -0.552  -2.4760   0.0657  -0.2835
 64A  C22  C  CR6   0   0.736  -2.8111  -1.1994   0.1361
 64A  C7   C  CH1   0  -0.090  -1.1026   0.3918  -0.6738
 64A  C20  C  CH2   0  -0.478  -0.0361   0.2440   0.4064
 64A  C9   C  CH2   0  -0.492   0.9582   0.0084  -1.8296
 64A  C8   C  CH2   0  -0.441  -0.5302  -0.3696  -1.8688
 64A  O1   O  O     0  -0.459  -6.2868  -0.7219   0.7330
 64A  O11  O  O2    0  -0.482   2.3068  -0.2162   0.2532
 64A  O18  O  O     0  -0.417   3.7133   1.8961   1.3507
 64A  O17  O  OH1   0  -0.573   4.8429   2.0531  -0.5753
 64A  O14  O  OH1   0  -0.582   5.7700  -0.6904  -0.0345
 64A  O15  O  O     0  -0.407   4.1579  -2.0001   0.7994
 64A  O23  O  O     0  -0.483  -2.0193  -2.1167   0.2240
 64A  C16  C  C     0   0.511   4.0421   1.4528   0.2840
 64A  H1   H  HCH3  0   0.247  -6.5496   1.7246  -0.7861
 64A  H2   H  HCH3  0   0.247  -6.1713   2.1980   0.8620
 64A  H3   H  HCH3  0   0.246  -5.2772   2.9045  -0.4817
 64A  H4   H  HCR6  0   0.313  -3.0619   2.0094  -0.6867
 64A  H5   H  HCH1  0   0.304   3.6113   0.0910  -1.3315
 64A  H6   H  HCH1  0   0.236   1.4639   1.5564  -0.3912
 64A  H7   H  HNR6  0   0.423  -4.3903  -2.2928   0.7642
 64A  H8   H  HCH1  0   0.274  -1.1419   1.4469  -0.9518
 64A  H9   H  HCH2  0   0.258  -0.0343  -0.7686   0.8112
 64A  H10  H  HCH2  0   0.261  -0.1631   0.9498   1.2273
 64A  H11  H  HCH2  0   0.252   1.1734   0.8088  -2.5379
 64A  H12  H  HCH2  0   0.256   1.5856  -0.8410  -2.1059
 64A  H13  H  HCH2  0   0.252  -0.6564  -1.4424  -1.7354
 64A  H14  H  HCH2  0   0.252  -1.0128  -0.0865  -2.8041
 64A  H15  H  HOH1  0   0.490   5.1648   2.8929  -0.2121
 64A  H16  H  HOH1  0   0.495   6.3691  -1.3918   0.2646

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  double  1.201  0.020  1.201
 64A  O23  C22  double  1.215  0.020  1.215
 64A  C16  O17  single  1.319  0.020  1.319
 64A  C16  C12  single  1.532  0.020  1.532
 64A  C20  C10  single  1.525  0.020  1.525
 64A  C20  C7   single  1.525  0.020  1.525
 64A  C22  N21  single  1.373  0.020  1.373
 64A  C22  N6   single  1.374  0.020  1.374
 64A  C10  O11  single  1.417  0.020  1.417
 64A  C10  C9   single  1.551  0.020  1.551
 64A  C7   N6   single  1.464  0.020  1.464
 64A  C7   C8   single  1.528  0.020  1.528
 64A  N21  C2   single  1.382  0.020  1.382
 64A  N6   C5   single  1.371  0.020  1.371
 64A  O11  C12  single  1.382  0.020  1.382
 64A  C12  C13  single  1.526  0.020  1.526
 64A  C9   C8   single  1.536  0.020  1.536
 64A  C2   O1   double  1.218  0.020  1.218
 64A  C2   C3   single  1.447  0.020  1.447
 64A  C5   C3   double  1.345  0.020  1.345
 64A  C3   C4   single  1.493  0.020  1.493
 64A  C13  O15  double  1.198  0.020  1.198
 64A  C13  O14  single  1.321  0.020  1.321
 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
 64A  O17  H15  single  0.850  0.020  0.980
 64A  O14  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
 64A  O1   C2   N21  120.69  3.000
 64A  O1   C2   C3   125.18  3.000
 64A  N21  C2   C3   114.14  3.000
 64A  C5   C3   C4   123.18  3.000
 64A  C4   C3   C2   119.06  3.000
 64A  C5   C3   C2   117.76  3.000
 64A  H3   C4   H2   107.86  3.000
 64A  H3   C4   H1   107.87  3.000
 64A  H2   C4   H1   107.20  3.000
 64A  H3   C4   C3   111.01  3.000
 64A  H2   C4   C3   111.38  3.000
 64A  H1   C4   C3   111.34  3.000
 64A  H4   C5   N6   114.61  3.000
 64A  H4   C5   C3   120.57  3.000
 64A  N6   C5   C3   124.82  3.000
 64A  H5   C12  C16  108.86  3.000
 64A  H5   C12  O11  112.92  3.000
 64A  C16  C12  O11  111.30  3.000
 64A  H5   C12  C13  106.76  3.000
 64A  O11  C12  C13  107.38  3.000
 64A  C16  C12  C13  109.47  3.000
 64A  H6   C10  O11  109.86  3.000
 64A  H6   C10  C9   109.05  3.000
 64A  O11  C10  C9   114.08  3.000
 64A  H6   C10  C20  108.81  3.000
 64A  C9   C10  C20  106.10  3.000
 64A  O11  C10  C20  108.77  3.000
 64A  O15  C13  O14  125.34  3.000
 64A  O14  C13  C12  110.98  3.000
 64A  O15  C13  C12  123.67  3.000
 64A  H7   N21  C22  115.00  3.000
 64A  H7   N21  C2   116.68  3.000
 64A  C22  N21  C2   128.32  3.000
 64A  C7   N6   C22  120.99  3.000
 64A  C7   N6   C5   118.61  3.000
 64A  C22  N6   C5   120.39  3.000
 64A  O23  C22  N6   123.93  3.000
 64A  N6   C22  N21  114.57  3.000
 64A  O23  C22  N21  121.50  3.000
 64A  H8   C7   C8   107.21  3.000
 64A  H8   C7   C20  107.40  3.000
 64A  C8   C7   C20  104.10  3.000
 64A  H8   C7   N6   104.43  3.000
 64A  C8   C7   N6   116.66  3.000
 64A  C20  C7   N6   116.45  3.000
 64A  H10  C20  H9   108.78  3.000
 64A  H10  C20  C7   112.90  3.000
 64A  H9   C20  C7   110.73  3.000
 64A  H10  C20  C10  112.73  3.000
 64A  H9   C20  C10  109.53  3.000
 64A  C7   C20  C10  102.03  3.000
 64A  H12  C9   H11  107.06  3.000
 64A  H12  C9   C8   111.04  3.000
 64A  H11  C9   C8   110.81  3.000
 64A  H12  C9   C10  111.46  3.000
 64A  H11  C9   C10  110.27  3.000
 64A  C8   C9   C10  106.26  3.000
 64A  H14  C8   H13  108.05  3.000
 64A  H14  C8   C9   112.77  3.000
 64A  H13  C8   C9   110.60  3.000
 64A  H14  C8   C7   112.07  3.000
 64A  H13  C8   C7   110.60  3.000
 64A  C9   C8   C7   102.73  3.000
 64A  C10  O11  C12  114.39  3.000
 64A  H15  O17  C16  110.58  3.000
 64A  H16  O14  C13  110.54  3.000
 64A  O17  C16  O18  125.23  3.000
 64A  O17  C16  C12  111.98  3.000
 64A  O18  C16  C12  122.79  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  CONST_10  H15  O17  C16  C12  180.00   0.0  0
 64A  CONST_11  H16  O14  C13  C12  180.00   0.0  0
 64A  Var_01    C7   C8   C9   C10   21.09  30.0  1
 64A  Var_02    H1   C4   C3   C2   -58.55  30.0  3
 64A  Var_03    C16  C12  O11  C10   76.13  30.0  3
 64A  Var_04    O18  C16  C12  C13  -88.10  30.0  2
 64A  Var_05    O15  C13  C12  O11    8.38  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-2  H16  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
 64A  plan-3  H15  0.020

