# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 19:02:30 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: (1R)-3-{[(1R)-3-methoxy-1-methyl-3-oxopropyl]oxy}-1-methyl-3-oxopropyl (3R)-3-hydroxybutanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)C[C@@H](C)OC(=O)C[C@@H](C)OC(=O)C[C@@H](C)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
 RB3  RB3  '(1R)-3-{[(1R)-3-methoxy-1-methyl-3-oxopropyl]oxy}-1-methyl-3-oxopropyl (3R)-3-hydroxybutanoate'  ligand  42  20  .  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_RB3
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
 RB3  O1M   O  O2    0  -0.454  -0.5850   1.0611  -6.8172
 RB3  C1A   C  C     0   0.600  -1.0394   1.5940  -5.6888
 RB3  O1A   O  O     0  -0.439  -1.4648   2.7183  -5.6144
 RB3  C2A   C  CH2   0  -0.612  -0.9760   0.5935  -4.5628
 RB3  C3A   C  CH1   0   0.005  -1.0806   1.1711  -3.1572
 RB3  C4A   C  CH3   0  -0.679   0.0428   2.1251  -2.8055
 RB3  O3A   O  O2    0  -0.451  -2.3154   1.8841  -2.9741
 RB3  C1B   C  C     0   0.607  -3.4312   1.2023  -2.7721
 RB3  O1B   O  O     0  -0.454  -3.4892  -0.0011  -2.7099
 RB3  C2B   C  CH2   0  -0.589  -4.6229   2.1114  -2.6127
 RB3  C3B   C  CH1   0   0.023  -5.8434   1.5588  -3.3287
 RB3  C4B   C  CH3   0  -0.679  -7.0107   2.5234  -3.2660
 RB3  O3B   O  O2    0  -0.459  -5.4117   1.3588  -4.6874
 RB3  C1C   C  C     0   0.608  -6.0672   0.5145  -5.4697
 RB3  O1C   O  O     0  -0.456  -7.0461  -0.1002  -5.1244
 RB3  C2C   C  CH2   0  -0.592  -5.4147   0.3829  -6.8203
 RB3  C3C   C  CH1   0   0.021  -4.9956   1.7136  -7.4467
 RB3  C4C   C  CH3   0  -0.695  -4.4522   1.4929  -8.8497
 RB3  O3C   O  OH1   0  -0.660  -6.0640   2.6370  -7.4313
 RB3  C1    C  CH3   0  -0.431  -0.5958   1.8834  -7.9843
 RB3  H2A1  H  HCH2  0   0.293  -0.0418   0.0314  -4.6304
 RB3  H2A2  H  HCH2  0   0.300  -1.7659  -0.1456  -4.7283
 RB3  H3A   H  HCH1  0   0.266  -1.0532   0.3286  -2.4620
 RB3  H4A1  H  HCH3  0   0.240   0.0739   2.9940  -3.4613
 RB3  H4A2  H  HCH3  0   0.239   0.9960   1.6029  -2.8866
 RB3  H4A3  H  HCH3  0   0.248  -0.0544   2.4735  -1.7774
 RB3  H2B1  H  HCH2  0   0.271  -4.3925   3.1178  -2.9654
 RB3  H2B2  H  HCH2  0   0.295  -4.8487   2.1900  -1.5454
 RB3  H3B   H  HCH1  0   0.250  -6.1225   0.5972  -2.8937
 RB3  H4B1  H  HCH3  0   0.236  -6.7493   3.4812  -3.7173
 RB3  H4B2  H  HCH3  0   0.243  -7.2826   2.7027  -2.2257
 RB3  H4B3  H  HCH3  0   0.251  -7.8886   2.1268  -3.7725
 RB3  H2C1  H  HCH2  0   0.262  -6.1047  -0.1467  -7.4815
 RB3  H2C2  H  HCH2  0   0.275  -4.5371  -0.2628  -6.7089
 RB3  H1    H  HCH1  0   0.232  -4.2124   2.1645  -6.8325
 RB3  H4C1  H  HCH3  0   0.233  -5.2139   1.0588  -9.5021
 RB3  H4C2  H  HCH3  0   0.231  -3.6019   0.8096  -8.8388
 RB3  H4C3  H  HCH3  0   0.243  -4.1208   2.4334  -9.2907
 RB3  H3C   H  HOH1  0   0.443  -6.7465   2.3218  -8.0343
 RB3  H11   H  HCH3  0   0.254  -0.2124   1.2639  -8.7895
 RB3  H12   H  HCH3  0   0.243   0.0466   2.7549  -7.8613
 RB3  H13   H  HCH3  0   0.238  -1.6030   2.2163  -8.2343

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
 RB3  O1M  C1A   single  1.328  0.020  1.328
 RB3  O1M  C1    single  1.428  0.020  1.428
 RB3  C1A  O1A   double  1.204  0.020  1.204
 RB3  C1A  C2A   single  1.508  0.020  1.508
 RB3  C2A  C3A   single  1.523  0.020  1.523
 RB3  C2A  H2A1  single  0.970  0.020  1.090
 RB3  C2A  H2A2  single  0.970  0.020  1.090
 RB3  C3A  C4A   single  1.515  0.020  1.515
 RB3  C3A  O3A   single  1.438  0.020  1.438
 RB3  C3A  H3A   single  0.970  0.020  1.090
 RB3  C4A  H4A1  single  0.970  0.020  1.090
 RB3  C4A  H4A2  single  0.970  0.020  1.090
 RB3  C4A  H4A3  single  0.970  0.020  1.090
 RB3  O3A  C1B   single  1.323  0.020  1.323
 RB3  C1B  O1B   double  1.206  0.020  1.206
 RB3  C1B  C2B   single  1.507  0.020  1.507
 RB3  C2B  C3B   single  1.519  0.020  1.519
 RB3  C2B  H2B1  single  0.970  0.020  1.090
 RB3  C2B  H2B2  single  0.970  0.020  1.090
 RB3  C3B  C4B   single  1.516  0.020  1.516
 RB3  C3B  O3B   single  1.440  0.020  1.440
 RB3  C3B  H3B   single  0.970  0.020  1.090
 RB3  C4B  H4B1  single  0.970  0.020  1.090
 RB3  C4B  H4B2  single  0.970  0.020  1.090
 RB3  C4B  H4B3  single  0.970  0.020  1.090
 RB3  O3B  C1C   single  1.325  0.020  1.325
 RB3  C1C  O1C   double  1.206  0.020  1.206
 RB3  C1C  C2C   single  1.506  0.020  1.506
 RB3  C2C  C3C   single  1.529  0.020  1.529
 RB3  C2C  H2C1  single  0.970  0.020  1.090
 RB3  C2C  H2C2  single  0.970  0.020  1.090
 RB3  C3C  C4C   single  1.521  0.020  1.521
 RB3  C3C  O3C   single  1.412  0.020  1.412
 RB3  C3C  H1    single  0.970  0.020  1.090
 RB3  C4C  H4C1  single  0.970  0.020  1.090
 RB3  C4C  H4C2  single  0.970  0.020  1.090
 RB3  C4C  H4C3  single  0.970  0.020  1.090
 RB3  O3C  H3C   single  0.850  0.020  0.980
 RB3  C1   H11   single  0.970  0.020  1.090
 RB3  C1   H12   single  0.970  0.020  1.090
 RB3  C1   H13   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
 RB3  C1    O1M  C1A   117.44  3.000
 RB3  C2A   C1A  O1A   126.03  3.000
 RB3  C2A   C1A  O1M   110.72  3.000
 RB3  O1A   C1A  O1M   123.23  3.000
 RB3  H2A2  C2A  H2A1  105.10  3.000
 RB3  H2A2  C2A  C3A   110.25  3.000
 RB3  H2A1  C2A  C3A   108.12  3.000
 RB3  H2A2  C2A  C1A   107.75  3.000
 RB3  H2A1  C2A  C1A   109.35  3.000
 RB3  C3A   C2A  C1A   115.76  3.000
 RB3  H3A   C3A  O3A   108.84  3.000
 RB3  H3A   C3A  C4A   108.61  3.000
 RB3  O3A   C3A  C4A   107.16  3.000
 RB3  H3A   C3A  C2A   107.04  3.000
 RB3  O3A   C3A  C2A   111.38  3.000
 RB3  C4A   C3A  C2A   113.71  3.000
 RB3  H4A3  C4A  H4A2  107.54  3.000
 RB3  H4A3  C4A  H4A1  108.39  3.000
 RB3  H4A2  C4A  H4A1  108.21  3.000
 RB3  H4A3  C4A  C3A   110.74  3.000
 RB3  H4A2  C4A  C3A   109.24  3.000
 RB3  H4A1  C4A  C3A   112.56  3.000
 RB3  C1B   O3A  C3A   119.23  3.000
 RB3  C2B   C1B  O1B   123.92  3.000
 RB3  C2B   C1B  O3A   111.85  3.000
 RB3  O1B   C1B  O3A   124.23  3.000
 RB3  H2B2  C2B  H2B1  107.02  3.000
 RB3  H2B2  C2B  C3B   108.67  3.000
 RB3  H2B1  C2B  C3B   110.66  3.000
 RB3  H2B2  C2B  C1B   108.05  3.000
 RB3  H2B1  C2B  C1B   110.80  3.000
 RB3  C3B   C2B  C1B   111.47  3.000
 RB3  H3B   C3B  O3B   109.29  3.000
 RB3  H3B   C3B  C4B   110.31  3.000
 RB3  O3B   C3B  C4B   111.00  3.000
 RB3  H3B   C3B  C2B   109.75  3.000
 RB3  O3B   C3B  C2B   104.75  3.000
 RB3  C4B   C3B  C2B   111.58  3.000
 RB3  H4B3  C4B  H4B2  107.63  3.000
 RB3  H4B3  C4B  H4B1  108.71  3.000
 RB3  H4B2  C4B  H4B1  108.07  3.000
 RB3  H4B3  C4B  C3B   111.72  3.000
 RB3  H4B2  C4B  C3B   109.65  3.000
 RB3  H4B1  C4B  C3B   110.93  3.000
 RB3  C1C   O3B  C3B   119.84  3.000
 RB3  C2C   C1C  O1C   124.33  3.000
 RB3  C2C   C1C  O3B   111.77  3.000
 RB3  O1C   C1C  O3B   123.87  3.000
 RB3  H2C2  C2C  H2C1  106.37  3.000
 RB3  H2C2  C2C  C3C   109.58  3.000
 RB3  H2C1  C2C  C3C   110.30  3.000
 RB3  H2C2  C2C  C1C   107.91  3.000
 RB3  H2C1  C2C  C1C   108.15  3.000
 RB3  C3C   C2C  C1C   114.21  3.000
 RB3  H1    C3C  O3C   105.44  3.000
 RB3  H1    C3C  C4C   108.80  3.000
 RB3  O3C   C3C  C4C   112.05  3.000
 RB3  H1    C3C  C2C   108.98  3.000
 RB3  O3C   C3C  C2C   110.93  3.000
 RB3  C4C   C3C  C2C   110.46  3.000
 RB3  H4C3  C4C  H4C2  107.90  3.000
 RB3  H4C3  C4C  H4C1  108.24  3.000
 RB3  H4C2  C4C  H4C1  107.48  3.000
 RB3  H4C3  C4C  C3C   110.89  3.000
 RB3  H4C2  C4C  C3C   111.12  3.000
 RB3  H4C1  C4C  C3C   111.06  3.000
 RB3  H3C   O3C  C3C   108.36  3.000
 RB3  H13   C1   H12   109.06  3.000
 RB3  H13   C1   H11   109.29  3.000
 RB3  H12   C1   H11   109.38  3.000
 RB3  H13   C1   O1M   111.74  3.000
 RB3  H12   C1   O1M   111.34  3.000
 RB3  H11   C1   O1M   105.96  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
 RB3  Var_01  C3A  C2A  C1A  O1M   163.08  30.0  3
 RB3  Var_02  O1B  C1B  O3A  C3A     1.11  30.0  3
 RB3  Var_03  C3B  C2B  C1B  O3A   139.50  30.0  3
 RB3  Var_04  O1C  C1C  O3B  C3B     1.52  30.0  3
 RB3  Var_05  C3C  C2C  C1C  O3B   -44.84  30.0  3
 RB3  Var_06  H11  C1   O1M  C1A  -178.75  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
 RB3  chir_01  C3A  C2A  C4A  O3A  negativ
 RB3  chir_02  C3B  O3B  C2B  C4B  negativ
 RB3  chir_03  C3C  O3C  C2C  C4C  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
 RB3  plan-1  O1M  0.020
 RB3  plan-1  C1A  0.020
 RB3  plan-1  O1A  0.020
 RB3  plan-1  C2A  0.020
 RB3  plan-2  O3A  0.020
 RB3  plan-2  C1B  0.020
 RB3  plan-2  O1B  0.020
 RB3  plan-2  C2B  0.020
 RB3  plan-3  O3B  0.020
 RB3  plan-3  C1C  0.020
 RB3  plan-3  O1C  0.020
 RB3  plan-3  C2C  0.020

