# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 01:19:58 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 6-{[(4R,5R)-4-(hydroxymethyl)-5-methyl-2,6-dioxohexahydropyrimidin-5-yl]methyl}-5-methylpyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=C(C[C@]2(C)[C@H](CO)NC(=O)NC2=O)NC(=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
 RCA  RCA  6-{[(4R,5R)-4-(hydroxymethyl)-5-methyl-2,6-dioxohexahydropyrimidin-5-yl]methyl}-5-methylpyrimidine-2,4(1H,3H)-dione  ligand  37  21  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RCA
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
 RCA  O2    O  OC    0  -0.466   1.8519  -0.6460   4.6120
 RCA  C3    C  CR6   0  -0.207   1.3875   0.0205   2.3810
 RCA  C4    C  CH3   0  -0.752   2.8266  -0.0618   1.9647
 RCA  C5    C  CR6   0   0.435   0.3866   0.4085   1.5549
 RCA  C1    C  CR6   0   0.655  -1.3145   0.1714   3.2545
 RCA  N1    N  NR16  0  -0.727  -0.9083   0.4755   1.9906
 RCA  C2    C  CR6   0   0.565   1.0516  -0.3008   3.7588
 RCA  N2    N  NR16  0  -0.714  -0.2889  -0.1925   4.0846
 RCA  C11   C  CH1   0  -0.115   0.9871   0.0738  -2.2378
 RCA  N4    N  NH1   0  -0.630   0.4533  -0.7464  -3.3060
 RCA  C10   C  C     0   0.657  -0.8590  -0.8166  -3.5780
 RCA  C12   C  CH2   0  -0.129   1.0862   1.5377  -2.6706
 RCA  O5    O  OH1   0  -0.666   1.8369   1.5690  -3.8581
 RCA  C7    C  CT    0  -0.252   0.1440  -0.1509  -0.9683
 RCA  N3    N  NH1   0  -0.693  -1.6847  -0.3034  -2.5751
 RCA  C9    C  C     0   0.630  -1.3189   0.0694  -1.3180
 RCA  C6    C  CH2   0  -0.573   0.6106   0.8324   0.1331
 RCA  C8    C  CH3   0  -0.653   0.2912  -1.6097  -0.5047
 RCA  H43   H  HCH3  0   0.265   3.4156  -0.5603   2.7304
 RCA  H42   H  HCH3  0   0.244   2.9579  -0.6243   1.0408
 RCA  H41   H  HCH3  0   0.253   3.2647   0.9262   1.8109
 RCA  H1    H  HNR6  0   0.437  -1.6239   0.6872   1.2983
 RCA  H2    H  HNR6  0   0.423  -0.5452  -0.4178   5.0378
 RCA  H11   H  HCH1  0   0.293   1.9964  -0.2912  -2.0313
 RCA  H4    H  HNH1  0   0.415   1.0745  -1.0238  -4.0499
 RCA  H122  H  HCH2  0   0.203   0.0808   1.9577  -2.8161
 RCA  H121  H  HCH2  0   0.226   1.5670   2.1232  -1.8803
 RCA  H5    H  HOH1  0   0.462   1.9169   2.4846  -4.1398
 RCA  H3    H  HNH1  0   0.425  -2.6727  -0.2736  -2.7957
 RCA  H62   H  HCH2  0   0.308   0.1387   1.8079  -0.0109
 RCA  H61   H  HCH2  0   0.305   1.6783   0.9994   0.0036
 RCA  H83   H  HCH3  0   0.260  -0.3680  -1.8338   0.3326
 RCA  H82   H  HCH3  0   0.266   0.0625  -2.3161  -1.3004
 RCA  H81   H  HCH3  0   0.261   1.3180  -1.7949  -0.1867
 RCA  O1    O  OC    0  -0.485  -2.4748   0.2207   3.6144
 RCA  O4    O  O     0  -0.482  -1.3432  -1.2901  -4.5872
 RCA  O3    O  O     0  -0.445  -2.1446   0.5100  -0.5401

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
 RCA  O2   C2    double    1.220  0.020  1.220
 RCA  C3   C4    single    1.500  0.020  1.500
 RCA  C3   C5    aromatic  1.354  0.020  1.354
 RCA  C3   C2    aromatic  1.454  0.020  1.454
 RCA  C4   H43   single    0.970  0.020  1.090
 RCA  C4   H42   single    0.970  0.020  1.090
 RCA  C4   H41   single    0.970  0.020  1.090
 RCA  C5   N1    aromatic  1.368  0.020  1.368
 RCA  C5   C6    single    1.500  0.020  1.500
 RCA  C1   N1    aromatic  1.362  0.020  1.362
 RCA  C1   N2    aromatic  1.369  0.020  1.369
 RCA  C1   O1    double    1.216  0.020  1.216
 RCA  N1   H1    single    0.860  0.020  1.020
 RCA  C2   N2    aromatic  1.384  0.020  1.384
 RCA  N2   H2    single    0.860  0.020  1.020
 RCA  C11  N4    single    1.449  0.020  1.449
 RCA  C11  C12   single    1.530  0.020  1.530
 RCA  C11  C7    single    1.540  0.020  1.540
 RCA  C11  H11   single    0.970  0.020  1.090
 RCA  O4   C10   double    1.215  0.020  1.215
 RCA  O3   C9    double    1.217  0.020  1.217
 RCA  N4   C10   single    1.342  0.020  1.342
 RCA  N4   H4    single    0.890  0.020  1.040
 RCA  C10  N3    single    1.397  0.020  1.397
 RCA  C12  O5    single    1.405  0.020  1.405
 RCA  C12  H122  single    0.970  0.020  1.090
 RCA  C12  H121  single    0.970  0.020  1.090
 RCA  O5   H5    single    0.850  0.020  0.980
 RCA  C7   C9    single    1.520  0.020  1.520
 RCA  C7   C6    single    1.548  0.020  1.548
 RCA  C7   C8    single    1.538  0.020  1.538
 RCA  N3   C9    single    1.361  0.020  1.361
 RCA  N3   H3    single    0.860  0.020  1.020
 RCA  C6   H62   single    0.970  0.020  1.090
 RCA  C6   H61   single    0.970  0.020  1.090
 RCA  C8   H83   single    0.970  0.020  1.090
 RCA  C8   H82   single    0.970  0.020  1.090
 RCA  C8   H81   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
 RCA  C2    C3   C5    118.06  3.000
 RCA  C2    C3   C4    118.19  3.000
 RCA  C5    C3   C4    123.73  3.000
 RCA  H41   C4   H42   107.42  3.000
 RCA  H41   C4   H43   107.27  3.000
 RCA  H42   C4   H43   107.18  3.000
 RCA  H41   C4   C3    111.98  3.000
 RCA  H42   C4   C3    112.28  3.000
 RCA  H43   C4   C3    110.45  3.000
 RCA  C6    C5   N1    115.42  3.000
 RCA  C6    C5   C3    123.27  3.000
 RCA  N1    C5   C3    121.29  3.000
 RCA  O1    C1   N2    123.12  3.000
 RCA  O1    C1   N1    123.39  3.000
 RCA  N2    C1   N1    113.49  3.000
 RCA  H1    N1   C1    117.90  3.000
 RCA  H1    N1   C5    117.32  3.000
 RCA  C1    N1   C5    124.54  3.000
 RCA  N2    C2   C3    115.44  3.000
 RCA  N2    C2   O2    119.55  3.000
 RCA  C3    C2   O2    125.01  3.000
 RCA  H2    N2   C2    116.71  3.000
 RCA  H2    N2   C1    116.13  3.000
 RCA  C2    N2   C1    127.16  3.000
 RCA  H11   C11  C7    107.52  3.000
 RCA  H11   C11  C12   108.25  3.000
 RCA  C7    C11  C12   114.09  3.000
 RCA  H11   C11  N4    106.89  3.000
 RCA  C7    C11  N4    108.87  3.000
 RCA  C12   C11  N4    110.92  3.000
 RCA  H4    N4   C10   116.01  3.000
 RCA  H4    N4   C11   118.22  3.000
 RCA  C10   N4   C11   122.64  3.000
 RCA  N3    C10  N4    114.41  3.000
 RCA  N3    C10  O4    120.25  3.000
 RCA  N4    C10  O4    125.33  3.000
 RCA  H121  C12  H122  107.03  3.000
 RCA  H121  C12  O5    111.31  3.000
 RCA  H122  C12  O5    111.61  3.000
 RCA  H121  C12  C11   109.64  3.000
 RCA  H122  C12  C11   110.12  3.000
 RCA  O5    C12  C11   107.16  3.000
 RCA  H5    O5   C12   108.26  3.000
 RCA  C8    C7   C6    111.04  3.000
 RCA  C8    C7   C9    107.39  3.000
 RCA  C6    C7   C9    111.20  3.000
 RCA  C8    C7   C11   109.54  3.000
 RCA  C6    C7   C11   109.19  3.000
 RCA  C9    C7   C11   108.42  3.000
 RCA  H3    N3   C9    117.08  3.000
 RCA  H3    N3   C10   115.53  3.000
 RCA  C9    N3   C10   127.22  3.000
 RCA  N3    C9   C7    115.55  3.000
 RCA  N3    C9   O3    120.47  3.000
 RCA  C7    C9   O3    123.94  3.000
 RCA  H61   C6   H62   105.71  3.000
 RCA  H61   C6   C7    107.96  3.000
 RCA  H62   C6   C7    110.05  3.000
 RCA  H61   C6   C5    107.61  3.000
 RCA  H62   C6   C5    108.21  3.000
 RCA  C7    C6   C5    116.73  3.000
 RCA  H81   C8   H82   107.50  3.000
 RCA  H81   C8   H83   108.10  3.000
 RCA  H82   C8   H83   107.53  3.000
 RCA  H81   C8   C7    109.83  3.000
 RCA  H82   C8   C7    112.04  3.000
 RCA  H83   C8   C7    111.66  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
 RCA  CONST_01  C1   N1   C5   C3      0.00   0.0  0
 RCA  CONST_02  C1   N2   C2   C3      0.00   0.0  0
 RCA  CONST_03  N2   C2   C3   C5      0.00   0.0  0
 RCA  CONST_04  N2   C1   N1   C5      0.00   0.0  0
 RCA  CONST_05  C2   C3   C5   N1      0.00   0.0  0
 RCA  CONST_06  C2   N2   C1   N1      0.00   0.0  0
 RCA  CONST_07  N3   C10  N4   C11     0.00   0.0  0
 RCA  CONST_08  C9   N3   C10  N4      0.00   0.0  0
 RCA  CONST_09  C7   C9   N3   C10     0.00   0.0  0
 RCA  CONST_10  C5   C3   C2   O2    180.00   0.0  0
 RCA  CONST_11  C1   N2   C2   O2    180.00   0.0  0
 RCA  CONST_12  N1   C5   C3   C4    180.00   0.0  0
 RCA  CONST_13  N2   C2   C3   C4    180.00   0.0  0
 RCA  CONST_14  O1   C1   N1   C5    180.00   0.0  0
 RCA  CONST_15  C6   C5   N1   C1    180.00   0.0  0
 RCA  CONST_16  C6   C5   C3   C2    180.00   0.0  0
 RCA  CONST_17  O1   C1   N2   C2    180.00   0.0  0
 RCA  CONST_18  O4   C10  N4   C11   180.00   0.0  0
 RCA  CONST_19  C9   N3   C10  O4    180.00   0.0  0
 RCA  CONST_20  C10  N3   C9   O3    180.00   0.0  0
 RCA  CONST_21  H1   N1   C5   C3    180.00   0.0  0
 RCA  CONST_22  H2   N2   C2   C3    180.00   0.0  0
 RCA  CONST_23  H3   N3   C10  N4    180.00   0.0  0
 RCA  CONST_24  H4   N4   C10  N3    180.00   0.0  0
 RCA  Var_01    C7   C6   C5   C3    107.77  30.0  2
 RCA  Var_02    H43  C4   C3   C5   -169.94  30.0  2

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
 RCA  chir_01  C11  N4  C12  C7   negativ
 RCA  chir_02  C7   C6  C9   C11  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
 RCA  plan-1  O2   0.020
 RCA  plan-1  C3   0.020
 RCA  plan-1  C4   0.020
 RCA  plan-1  C5   0.020
 RCA  plan-1  C1   0.020
 RCA  plan-1  N1   0.020
 RCA  plan-1  C2   0.020
 RCA  plan-1  N2   0.020
 RCA  plan-1  C6   0.020
 RCA  plan-1  H1   0.020
 RCA  plan-1  H2   0.020
 RCA  plan-1  O1   0.020
 RCA  plan-2  C11  0.020
 RCA  plan-2  N4   0.020
 RCA  plan-2  C10  0.020
 RCA  plan-2  C7   0.020
 RCA  plan-2  N3   0.020
 RCA  plan-2  C9   0.020
 RCA  plan-2  H4   0.020
 RCA  plan-2  H3   0.020
 RCA  plan-2  O4   0.020
 RCA  plan-2  O3   0.020

