# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 00:23:36 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: (3'R)-1'-hydroxy-2',2',5',5'-tetramethyl-1,3'-bipyrrolidine-2,5-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)C[C@@H](N2C(=O)CCC2=O)C(C)(C)N1[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
 RCY  RCY  (3'R)-1'-hydroxy-2',2',5',5'-tetramethyl-1,3'-bipyrrolidine-2,5-dione  ligand  36  17  .  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_RCY
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
 RCY  C1C   C  CH3   0  -0.645  -0.3270  -0.4960   2.0955
 RCY  O1G   O  O     0  -0.433   1.5690   1.9536   1.2636
 RCY  O1H   O  O     0  -0.431   2.0705  -1.4705  -1.6921
 RCY  O1J   O  O     0  -0.452  -3.0304  -1.1061   0.8176
 RCY  C1L   C  CH2   0  -0.583   3.6097   0.9495   0.4365
 RCY  C1M   C  CH2   0  -0.479  -0.7843   1.2761  -0.5380
 RCY  C1P   C  CR5   0   0.574   2.1198   1.1276   0.5793
 RCY  C1Q   C  CR5   0   0.566   2.3892  -0.6078  -0.9123
 RCY  N1R   N  NR5   0  -0.573   1.4863   0.1840  -0.2135
 RCY  C1S   C  CH2   0  -0.589   3.7864  -0.2047  -0.5336
 RCY  C1U   C  CH1   0  -0.083   0.0584   0.0089  -0.4101
 RCY  C1V   C  CH3   0  -0.639  -0.4683  -2.3430   0.4191
 RCY  N1V   N  N     0  -0.016  -2.0525  -0.4652   0.3612
 RCY  C1W   C  CT    0   0.082  -2.2244   0.7574  -0.4450
 RCY  C1X   C  CT    0   0.088  -0.6626  -0.8511   0.6487
 RCY  C1Y   C  CH3   0  -0.638  -2.7983   0.3878  -1.8126
 RCY  C1Z   C  CH3   0  -0.643  -3.1434   1.7368   0.2734
 RCY  H1C   H  HCH3  0   0.243  -0.4713   0.5620   2.3080
 RCY  H1CA  H  HCH3  0   0.247  -0.9699  -1.0672   2.7657
 RCY  H1CB  H  HCH3  0   0.233   0.7045  -0.7589   2.3303
 RCY  H1L   H  HCH2  0   0.303   4.0426   1.8823   0.0743
 RCY  H1LA  H  HCH2  0   0.302   4.0387   0.7537   1.4195
 RCY  H1M   H  HCH2  0   0.270  -0.5907   1.9759   0.2720
 RCY  H1MA  H  HCH2  0   0.269  -0.5953   1.7911  -1.4798
 RCY  H1S   H  HCH2  0   0.303   4.3381   0.0674  -1.4336
 RCY  H1SA  H  HCH2  0   0.304   4.2934  -1.0631  -0.0912
 RCY  H1U   H  HCH1  0   0.282  -0.0178  -0.5326  -1.3555
 RCY  H1V   H  HCH3  0   0.243  -1.0983  -2.9222   1.0931
 RCY  H1VA  H  HCH3  0   0.236  -0.7080  -2.6253  -0.6065
 RCY  H1VB  H  HCH3  0   0.236   0.5670  -2.6218   0.6146
 RCY  H1Y   H  HCH3  0   0.237  -2.1406  -0.2898  -2.3588
 RCY  H1YA  H  HCH3  0   0.239  -3.7715  -0.0930  -1.7083
 RCY  H1YB  H  HCH3  0   0.235  -2.9299   1.2872  -2.4143
 RCY  H1Z   H  HCH3  0   0.236  -3.2264   2.6570  -0.3050
 RCY  H1ZA  H  HCH3  0   0.239  -4.1450   1.3245   0.3931
 RCY  H1ZB  H  HCH3  0   0.235  -2.7523   1.9925   1.2591

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
 RCY  C1C  C1X   single  1.527  0.020  1.527
 RCY  O1G  C1P   double  1.206  0.020  1.206
 RCY  O1H  C1Q   double  1.206  0.020  1.206
 RCY  O1J  N1V   single  1.255  0.020  1.255
 RCY  C1L  C1P   single  1.507  0.020  1.507
 RCY  C1L  C1S   single  1.518  0.020  1.518
 RCY  C1M  C1U   single  1.527  0.020  1.527
 RCY  C1M  C1W   single  1.533  0.020  1.533
 RCY  C1P  N1R   single  1.386  0.020  1.386
 RCY  C1Q  N1R   single  1.389  0.020  1.389
 RCY  C1Q  C1S   single  1.503  0.020  1.503
 RCY  N1R  C1U   single  1.452  0.020  1.452
 RCY  C1U  C1X   single  1.543  0.020  1.543
 RCY  C1V  C1X   single  1.522  0.020  1.522
 RCY  N1V  C1W   single  1.475  0.020  1.475
 RCY  N1V  C1X   single  1.471  0.020  1.471
 RCY  C1W  C1Y   single  1.528  0.020  1.528
 RCY  C1W  C1Z   single  1.523  0.020  1.523
 RCY  C1C  H1C   single  0.970  0.020  1.090
 RCY  C1C  H1CA  single  0.970  0.020  1.090
 RCY  C1C  H1CB  single  0.970  0.020  1.090
 RCY  C1L  H1L   single  0.970  0.020  1.090
 RCY  C1L  H1LA  single  0.970  0.020  1.090
 RCY  C1M  H1M   single  0.970  0.020  1.090
 RCY  C1M  H1MA  single  0.970  0.020  1.090
 RCY  C1S  H1S   single  0.970  0.020  1.090
 RCY  C1S  H1SA  single  0.970  0.020  1.090
 RCY  C1U  H1U   single  0.970  0.020  1.090
 RCY  C1V  H1V   single  0.970  0.020  1.090
 RCY  C1V  H1VA  single  0.970  0.020  1.090
 RCY  C1V  H1VB  single  0.970  0.020  1.090
 RCY  C1Y  H1Y   single  0.970  0.020  1.090
 RCY  C1Y  H1YA  single  0.970  0.020  1.090
 RCY  C1Y  H1YB  single  0.970  0.020  1.090
 RCY  C1Z  H1Z   single  0.970  0.020  1.090
 RCY  C1Z  H1ZA  single  0.970  0.020  1.090
 RCY  C1Z  H1ZB  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
 RCY  H1CB  C1C  H1CA  107.41  3.000
 RCY  H1CB  C1C  H1C   108.53  3.000
 RCY  H1CA  C1C  H1C   108.12  3.000
 RCY  H1CB  C1C  C1X   110.86  3.000
 RCY  H1CA  C1C  C1X   109.32  3.000
 RCY  H1C   C1C  C1X   112.44  3.000
 RCY  H1LA  C1L  H1L   107.28  3.000
 RCY  H1LA  C1L  C1S   113.19  3.000
 RCY  H1L   C1L  C1S   113.08  3.000
 RCY  H1LA  C1L  C1P   108.95  3.000
 RCY  H1L   C1L  C1P   108.84  3.000
 RCY  C1S   C1L  C1P   105.39  3.000
 RCY  H1MA  C1M  H1M   107.97  3.000
 RCY  H1MA  C1M  C1W   112.03  3.000
 RCY  H1M   C1M  C1W   109.85  3.000
 RCY  H1MA  C1M  C1U   111.63  3.000
 RCY  H1M   C1M  C1U   111.91  3.000
 RCY  C1W   C1M  C1U   103.44  3.000
 RCY  N1R   C1P  C1L   108.50  3.000
 RCY  N1R   C1P  O1G   125.61  3.000
 RCY  C1L   C1P  O1G   125.89  3.000
 RCY  C1S   C1Q  N1R   108.94  3.000
 RCY  C1S   C1Q  O1H   126.91  3.000
 RCY  N1R   C1Q  O1H   124.14  3.000
 RCY  C1U   N1R  C1Q   120.15  3.000
 RCY  C1U   N1R  C1P   127.53  3.000
 RCY  C1Q   N1R  C1P   112.25  3.000
 RCY  H1SA  C1S  H1S   107.23  3.000
 RCY  H1SA  C1S  C1Q   108.86  3.000
 RCY  H1S   C1S  C1Q   109.23  3.000
 RCY  H1SA  C1S  C1L   113.16  3.000
 RCY  H1S   C1S  C1L   113.37  3.000
 RCY  C1Q   C1S  C1L   104.88  3.000
 RCY  H1U   C1U  C1X   106.56  3.000
 RCY  H1U   C1U  N1R   104.22  3.000
 RCY  C1X   C1U  N1R   115.71  3.000
 RCY  H1U   C1U  C1M   107.48  3.000
 RCY  C1X   C1U  C1M   105.19  3.000
 RCY  N1R   C1U  C1M   117.00  3.000
 RCY  H1VB  C1V  H1VA  108.14  3.000
 RCY  H1VB  C1V  H1V   107.59  3.000
 RCY  H1VA  C1V  H1V   108.49  3.000
 RCY  H1VB  C1V  C1X   110.18  3.000
 RCY  H1VA  C1V  C1X   111.57  3.000
 RCY  H1V   C1V  C1X   110.74  3.000
 RCY  C1X   N1V  C1W   115.76  3.000
 RCY  C1X   N1V  O1J   122.09  3.000
 RCY  C1W   N1V  O1J   122.10  3.000
 RCY  C1Z   C1W  C1Y   110.54  3.000
 RCY  C1Z   C1W  N1V   110.22  3.000
 RCY  C1Y   C1W  N1V   109.42  3.000
 RCY  C1Z   C1W  C1M   112.19  3.000
 RCY  C1Y   C1W  C1M   112.34  3.000
 RCY  N1V   C1W  C1M   101.78  3.000
 RCY  N1V   C1X  C1V   110.39  3.000
 RCY  N1V   C1X  C1U    99.28  3.000
 RCY  C1V   C1X  C1U   112.53  3.000
 RCY  N1V   C1X  C1C   109.38  3.000
 RCY  C1V   C1X  C1C   110.05  3.000
 RCY  C1U   C1X  C1C   114.70  3.000
 RCY  H1YB  C1Y  H1YA  107.99  3.000
 RCY  H1YB  C1Y  H1Y   107.99  3.000
 RCY  H1YA  C1Y  H1Y   108.17  3.000
 RCY  H1YB  C1Y  C1W   109.86  3.000
 RCY  H1YA  C1Y  C1W   110.87  3.000
 RCY  H1Y   C1Y  C1W   111.83  3.000
 RCY  H1ZB  C1Z  H1ZA  108.60  3.000
 RCY  H1ZB  C1Z  H1Z   107.99  3.000
 RCY  H1ZA  C1Z  H1Z   107.92  3.000
 RCY  H1ZB  C1Z  C1W   111.13  3.000
 RCY  H1ZA  C1Z  C1W   111.29  3.000
 RCY  H1Z   C1Z  C1W   109.79  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
 RCY  CONST_01  C1Q  N1R  C1P  C1L     0.00   0.0  0
 RCY  CONST_02  C1U  N1R  C1P  C1L   180.00   0.0  0
 RCY  CONST_03  C1Q  N1R  C1P  O1G   180.00   0.0  0
 RCY  CONST_04  C1U  N1R  C1P  O1G     0.00   0.0  0
 RCY  Var_01    N1R  C1Q  C1S  C1L    -1.82  30.0  1
 RCY  Var_02    C1X  N1V  C1W  C1M    -6.77  30.0  1
 RCY  Var_03    C1Q  C1S  C1L  C1P     1.00  30.0  1
 RCY  Var_04    C1S  C1Q  N1R  C1P     2.03  30.0  1
 RCY  Var_05    C1S  C1L  C1P  N1R     0.12  30.0  1
 RCY  Var_06    N1V  C1W  C1M  C1U    27.37  30.0  1
 RCY  Var_07    C1W  N1V  C1X  C1U   -16.35  30.0  1
 RCY  Var_08    H1Y  C1Y  C1W  C1M    52.08  30.0  3
 RCY  Var_09    H1Z  C1Z  C1W  C1M    64.57  30.0  3
 RCY  Var_10    H1C  C1C  C1X  C1U    53.01  30.0  3
 RCY  Var_11    H1V  C1V  C1X  C1U  -172.06  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
 RCY  chir_01  C1U  C1M  N1R  C1X  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
 RCY  plan-1  O1H  0.020
 RCY  plan-1  C1Q  0.020
 RCY  plan-1  N1R  0.020
 RCY  plan-1  C1S  0.020
 RCY  plan-2  O1G  0.020
 RCY  plan-2  C1L  0.020
 RCY  plan-2  C1P  0.020
 RCY  plan-2  C1Q  0.020
 RCY  plan-2  N1R  0.020
 RCY  plan-2  C1U  0.020

