# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 20:32:12 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: (5R)-5-[(7-chloro-1H-indol-3-yl)methyl]-3-methylimidazolidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)N[C@H](Cc2c[nH]c3c(Cl)cccc23)C1=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
 RCM  RCM  (5R)-5-[(7-chloro-1H-indol-3-yl)methyl]-3-methylimidazolidine-2,4-dione  ligand  31  19  .  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_RCM
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
 RCM  O2   O   O     0  -0.483  -3.9819  -2.0671  -1.2009
 RCM  C14  C   CR5   0   0.708  -3.4630  -1.0700  -0.7491
 RCM  N3   N   NR5   0  -0.541  -4.1653   0.0158  -0.2148
 RCM  C17  C   CH3   0  -0.527  -5.6064   0.0628  -0.1477
 RCM  C12  C   CR5   0   0.556  -3.3257   1.0049   0.1961
 RCM  O1   O   O     0  -0.443  -3.6435   2.0612   0.6913
 RCM  N2   N   NR15  0  -0.668  -2.1555  -0.7705  -0.6527
 RCM  C11  C   CR15  0  -0.178  -1.9130   0.5184  -0.0653
 RCM  C10  C   CH2   0  -0.544  -1.0817   0.4573   1.2223
 RCM  C7   C   CR5   0   0.006   0.2763  -0.1038   0.9740
 RCM  C2   C   CR56  0   0.035   1.3803   0.5689   0.3559
 RCM  C8   C   CR15  0  -0.077   0.7030  -1.3744   1.2393
 RCM  N1   N   NR15  0  -0.683   1.9981  -1.5316   0.8335
 RCM  C3   C   CR56  0   0.467   2.4372  -0.3647   0.2916
 RCM  C4   C   CR6   0  -0.119   3.6689  -0.0161  -0.2535
 RCM  CL1  CL  CL    0  -0.124   4.9374  -1.1934  -0.3076
 RCM  C5   C   CR16  0  -0.266   3.8506   1.2615  -0.7371
 RCM  C6   C   CR16  0  -0.275   2.8029   2.1940  -0.6754
 RCM  C1   C   CR16  0  -0.371   1.5756   1.8637  -0.1367
 RCM  H1   H   HCH3  0   0.259  -6.0371   0.3353  -1.1102
 RCM  H2   H   HCH3  0   0.262  -5.9957  -0.9061   0.1535
 RCM  H3   H   HCH3  0   0.264  -5.9010   0.8021   0.5916
 RCM  H4   H   HNR5  0   0.415  -1.4309  -1.3847  -0.9863
 RCM  H5   H   HCR5  0   0.307  -1.4354   1.1949  -0.7819
 RCM  H6   H   HCH2  0   0.266  -1.0123   1.4687   1.6300
 RCM  H7   H   HCH2  0   0.270  -1.6110  -0.1503   1.9595
 RCM  H8   H   HCR5  0   0.291   0.1722  -2.1919   1.7015
 RCM  H9   H   HNR5  0   0.412   2.5361  -2.3764   0.9341
 RCM  H10  H   HCR6  0   0.274   4.8029   1.5464  -1.1634
 RCM  H11  H   HCR6  0   0.259   2.9735   3.1906  -1.0605
 RCM  H12  H   HCR6  0   0.248   0.7815   2.5985  -0.0945

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
 RCM  C17  N3   single    1.443  0.020  1.443
 RCM  CL1  C4   single    1.732  0.020  1.732
 RCM  N3   C12  single    1.361  0.020  1.361
 RCM  N3   C14  single    1.399  0.020  1.399
 RCM  N1   C8   aromatic  1.366  0.020  1.366
 RCM  N1   C3   aromatic  1.359  0.020  1.359
 RCM  O1   C12  double    1.209  0.020  1.209
 RCM  C8   C7   aromatic  1.366  0.020  1.366
 RCM  O2   C14  double    1.211  0.020  1.211
 RCM  C12  C11  single    1.517  0.020  1.517
 RCM  C4   C3   aromatic  1.391  0.020  1.391
 RCM  C4   C5   aromatic  1.378  0.020  1.378
 RCM  C3   C2   aromatic  1.412  0.020  1.412
 RCM  C14  N2   single    1.345  0.020  1.345
 RCM  C7   C2   aromatic  1.433  0.020  1.433
 RCM  C7   C10  single    1.490  0.020  1.490
 RCM  C5   C6   aromatic  1.404  0.020  1.404
 RCM  C2   C1   aromatic  1.399  0.020  1.399
 RCM  C11  N2   single    1.437  0.020  1.437
 RCM  C11  C10  single    1.534  0.020  1.534
 RCM  C6   C1   aromatic  1.380  0.020  1.380
 RCM  C17  H1   single    0.970  0.020  1.090
 RCM  C17  H2   single    0.970  0.020  1.090
 RCM  C17  H3   single    0.970  0.020  1.090
 RCM  N2   H4   single    0.860  0.020  1.020
 RCM  C11  H5   single    0.970  0.020  1.090
 RCM  C10  H6   single    0.970  0.020  1.090
 RCM  C10  H7   single    0.970  0.020  1.090
 RCM  C8   H8   single    0.930  0.020  1.080
 RCM  N1   H9   single    0.860  0.020  1.020
 RCM  C5   H10  single    0.930  0.020  1.080
 RCM  C6   H11  single    0.930  0.020  1.080
 RCM  C1   H12  single    0.930  0.020  1.080

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
 RCM  N2   C14  N3   106.73  3.000
 RCM  N2   C14  O2   128.79  3.000
 RCM  N3   C14  O2   124.49  3.000
 RCM  C12  N3   C17  125.32  3.000
 RCM  C12  N3   C14  111.70  3.000
 RCM  C17  N3   C14  122.97  3.000
 RCM  H3   C17  H2   108.73  3.000
 RCM  H3   C17  H1   108.90  3.000
 RCM  H2   C17  H1   109.04  3.000
 RCM  H3   C17  N3   108.94  3.000
 RCM  H2   C17  N3   109.97  3.000
 RCM  H1   C17  N3   111.22  3.000
 RCM  C11  C12  O1   126.56  3.000
 RCM  C11  C12  N3   106.82  3.000
 RCM  O1   C12  N3   126.62  3.000
 RCM  H4   N2   C11  124.14  3.000
 RCM  H4   N2   C14  122.69  3.000
 RCM  C11  N2   C14  113.15  3.000
 RCM  H5   C11  C10  109.73  3.000
 RCM  H5   C11  N2   111.11  3.000
 RCM  C10  C11  N2   113.51  3.000
 RCM  H5   C11  C12  108.71  3.000
 RCM  C10  C11  C12  111.89  3.000
 RCM  N2   C11  C12  101.59  3.000
 RCM  H7   C10  H6   107.09  3.000
 RCM  H7   C10  C7   110.16  3.000
 RCM  H6   C10  C7   110.66  3.000
 RCM  H7   C10  C11  109.03  3.000
 RCM  H6   C10  C11  108.10  3.000
 RCM  C7   C10  C11  111.66  3.000
 RCM  C8   C7   C2   106.24  3.000
 RCM  C2   C7   C10  126.67  3.000
 RCM  C8   C7   C10  127.04  3.000
 RCM  C1   C2   C3   119.44  3.000
 RCM  C1   C2   C7   133.94  3.000
 RCM  C3   C2   C7   106.62  3.000
 RCM  H8   C8   N1   120.44  3.000
 RCM  H8   C8   C7   129.36  3.000
 RCM  N1   C8   C7   110.20  3.000
 RCM  H9   N1   C3   125.99  3.000
 RCM  H9   N1   C8   124.99  3.000
 RCM  C3   N1   C8   109.02  3.000
 RCM  C4   C3   N1   131.09  3.000
 RCM  C4   C3   C2   120.99  3.000
 RCM  N1   C3   C2   107.92  3.000
 RCM  C5   C4   CL1  121.52  3.000
 RCM  C5   C4   C3   119.11  3.000
 RCM  CL1  C4   C3   119.37  3.000
 RCM  H10  C5   C6   119.96  3.000
 RCM  H10  C5   C4   119.91  3.000
 RCM  C6   C5   C4   120.13  3.000
 RCM  H11  C6   C1   119.96  3.000
 RCM  H11  C6   C5   118.59  3.000
 RCM  C1   C6   C5   121.44  3.000
 RCM  H12  C1   C6   120.32  3.000
 RCM  H12  C1   C2   120.80  3.000
 RCM  C6   C1   C2   118.88  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
 RCM  CONST_01  C3   N1   C8   C7      0.00   0.0  0
 RCM  CONST_02  N1   C3   C2   C7      0.00   0.0  0
 RCM  CONST_03  C4   C3   C2   C7    180.00   0.0  0
 RCM  CONST_04  C6   C1   C2   C7    180.00   0.0  0
 RCM  CONST_05  C8   N1   C3   C2      0.00   0.0  0
 RCM  CONST_06  C5   C4   C3   C2      0.00   0.0  0
 RCM  CONST_07  N1   C8   C7   C2      0.00   0.0  0
 RCM  CONST_08  C5   C6   C1   C2      0.00   0.0  0
 RCM  CONST_09  C4   C3   N1   C8    180.00   0.0  0
 RCM  CONST_10  C3   C2   C7   C8      0.00   0.0  0
 RCM  CONST_11  C1   C2   C7   C8    180.00   0.0  0
 RCM  CONST_12  C5   C4   C3   N1    180.00   0.0  0
 RCM  CONST_13  C1   C2   C3   N1    180.00   0.0  0
 RCM  CONST_14  C6   C5   C4   C3      0.00   0.0  0
 RCM  CONST_15  C6   C1   C2   C3      0.00   0.0  0
 RCM  CONST_16  C1   C2   C3   C4      0.00   0.0  0
 RCM  CONST_17  C1   C6   C5   C4      0.00   0.0  0
 RCM  CONST_18  C11  C12  N3   C14     0.00   0.0  0
 RCM  CONST_19  C11  N2   C14  N3      0.00   0.0  0
 RCM  CONST_20  N2   C14  N3   C12     0.00   0.0  0
 RCM  CONST_21  N1   C8   C7   C10   180.00   0.0  0
 RCM  CONST_22  C3   C2   C7   C10   180.00   0.0  0
 RCM  CONST_23  C1   C2   C7   C10     0.00   0.0  0
 RCM  CONST_24  CL1  C4   C3   C2    180.00   0.0  0
 RCM  CONST_25  CL1  C4   C3   N1      0.00   0.0  0
 RCM  CONST_26  C6   C5   C4   CL1   180.00   0.0  0
 RCM  CONST_27  C12  N3   C14  O2    180.00   0.0  0
 RCM  CONST_28  C11  N2   C14  O2    180.00   0.0  0
 RCM  CONST_29  C11  C12  N3   C17   180.00   0.0  0
 RCM  CONST_30  N2   C14  N3   C17   180.00   0.0  0
 RCM  CONST_31  H9   N1   C8   C7    180.00   0.0  0
 RCM  CONST_32  H12  C1   C2   C7      0.00   0.0  0
 RCM  CONST_33  H8   C8   C7   C2    180.00   0.0  0
 RCM  CONST_34  H11  C6   C1   C2    180.00   0.0  0
 RCM  CONST_35  H10  C5   C4   C3    180.00   0.0  0
 RCM  CONST_36  H4   N2   C14  N3    180.00   0.0  0
 RCM  CONST_37  C17  N3   C14  O2      0.00   0.0  0
 RCM  Var_01    C8   C7   C10  C11  -101.43  30.0  2
 RCM  Var_02    H1   C17  N3   C14   -79.56  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
 RCM  chir_01  C11  C12  N2  C10  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
 RCM  plan-1  C10  0.020
 RCM  plan-1  C7   0.020
 RCM  plan-1  C2   0.020
 RCM  plan-1  C8   0.020
 RCM  plan-1  N1   0.020
 RCM  plan-1  C3   0.020
 RCM  plan-1  C4   0.020
 RCM  plan-1  CL1  0.020
 RCM  plan-1  C5   0.020
 RCM  plan-1  C6   0.020
 RCM  plan-1  C1   0.020
 RCM  plan-1  H8   0.020
 RCM  plan-1  H9   0.020
 RCM  plan-1  H10  0.020
 RCM  plan-1  H11  0.020
 RCM  plan-1  H12  0.020
 RCM  plan-2  O2   0.020
 RCM  plan-2  C14  0.020
 RCM  plan-2  N3   0.020
 RCM  plan-2  C17  0.020
 RCM  plan-2  C12  0.020
 RCM  plan-2  O1   0.020
 RCM  plan-2  N2   0.020
 RCM  plan-2  C11  0.020
 RCM  plan-2  H4   0.020

