# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 20:50:58 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: (5R)-5-(4-methoxy-3-propoxy-phenyl)-5-methyl-1,3-oxazolidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCOc1cc(ccc1OC)[C@]2(C)CNC(=O)O2
#
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
 5RM  5RM  (5R)-5-(4-methoxy-3-propoxy-phenyl)-5-methyl-1,3-oxazolidin-2-one  ligand  38  19  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5RM
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
 5RM  O19   O  O     0  -0.488  -3.9516  -2.3915   0.4390
 5RM  C4    C  CR5   0   0.671  -3.5651  -1.2659   0.2349
 5RM  O5    O  O     0  -0.482  -2.4240  -1.0129  -0.4312
 5RM  N3    N  NR15  0  -0.655  -4.1412  -0.0984   0.5764
 5RM  C2    C  CH2   0  -0.269  -3.2526   1.0161   0.3709
 5RM  C1    C  CR5   0   0.152  -2.2657   0.4001  -0.6453
 5RM  C18   C  CH3   0  -0.646  -2.6753   0.7091  -2.0800
 5RM  C6    C  CR6   0   0.081  -0.8329   0.7995  -0.3875
 5RM  C7    C  CR16  0  -0.311  -0.5149   2.1420  -0.2898
 5RM  C8    C  CR16  0  -0.370   0.7999   2.5485  -0.0779
 5RM  C9    C  CR6   0   0.290   1.8152   1.6142   0.0378
 5RM  O10   O  O2    0  -0.463   3.1139   1.9010   0.2453
 5RM  C11   C  CH3   0  -0.437   3.4856   3.2602   0.3457
 5RM  C12   C  CR6   0   0.345   1.4991   0.2448  -0.0629
 5RM  C17   C  CR16  0  -0.444   0.1865  -0.1476  -0.2765
 5RM  O13   O  O2    0  -0.471   2.5397  -0.5986   0.0644
 5RM  C14   C  CH2   0  -0.169   2.3074  -1.9944  -0.0350
 5RM  C15   C  CH2   0  -0.459   3.6228  -2.7138   0.1767
 5RM  C16   C  CH3   0  -0.673   3.4456  -4.2219   0.0659
 5RM  H2    H  HCH2  0   0.266  -3.7703   1.8822  -0.0413
 5RM  H181  H  HCH3  0   0.244  -3.7215   0.4500  -2.2526
 5RM  H182  H  HCH3  0   0.242  -2.5547   1.7724  -2.2837
 5RM  H183  H  HCH3  0   0.251  -2.0564   0.1559  -2.7864
 5RM  H7    H  HCR6  0   0.253  -1.2820   2.9025  -0.3707
 5RM  H8    H  HCR6  0   0.283   1.0085   3.6070  -0.0018
 5RM  H111  H  HCH3  0   0.259   4.5628   3.2764   0.4921
 5RM  H112  H  HCH3  0   0.227   3.2450   3.8178  -0.5634
 5RM  H113  H  HCH3  0   0.228   3.0079   3.7534   1.1966
 5RM  H17   H  HCR6  0   0.281  -0.0507  -1.1986  -0.3566
 5RM  H141  H  HCH2  0   0.219   1.5788  -2.3161   0.7188
 5RM  H142  H  HCH2  0   0.219   1.8916  -2.2411  -1.0196
 5RM  H151  H  HCH2  0   0.231   4.3516  -2.3704  -0.5616
 5RM  H152  H  HCH2  0   0.231   4.0211  -2.4586   1.1619
 5RM  H161  H  HCH3  0   0.239   4.3880  -4.7388   0.2441
 5RM  H162  H  HCH3  0   0.224   2.7235  -4.5924   0.7953
 5RM  H163  H  HCH3  0   0.225   3.0920  -4.5090  -0.9252
 5RM  H18   H  HNR5  0   0.415  -4.9006  -0.0738   1.2373
 5RM  H19   H  HCH2  0   0.261  -2.7571   1.3172   1.2976

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
 5RM  O19  C4    double    1.208  0.020  1.208
 5RM  C4   O5    single    1.345  0.020  1.345
 5RM  C4   N3    single    1.346  0.020  1.346
 5RM  O5   C1    single    1.438  0.020  1.438
 5RM  N3   C2    single    1.440  0.020  1.440
 5RM  C2   C1    single    1.545  0.020  1.545
 5RM  C2   H2    single    0.970  0.020  1.090
 5RM  C1   C18   single    1.524  0.020  1.524
 5RM  C1   C6    single    1.510  0.020  1.510
 5RM  C18  H181  single    0.970  0.020  1.090
 5RM  C18  H182  single    0.970  0.020  1.090
 5RM  C18  H183  single    0.970  0.020  1.090
 5RM  C6   C7    aromatic  1.383  0.020  1.383
 5RM  C6   C17   aromatic  1.396  0.020  1.396
 5RM  C7   C8    aromatic  1.392  0.020  1.392
 5RM  C7   H7    single    0.930  0.020  1.080
 5RM  C8   C9    aromatic  1.385  0.020  1.385
 5RM  C8   H8    single    0.930  0.020  1.080
 5RM  C9   O10   single    1.346  0.020  1.346
 5RM  C9   C12   aromatic  1.409  0.020  1.409
 5RM  O10  C11   single    1.413  0.020  1.413
 5RM  C11  H111  single    0.970  0.020  1.090
 5RM  C11  H112  single    0.970  0.020  1.090
 5RM  C11  H113  single    0.970  0.020  1.090
 5RM  C12  C17   aromatic  1.387  0.020  1.387
 5RM  C12  O13   single    1.345  0.020  1.345
 5RM  C17  H17   single    0.930  0.020  1.080
 5RM  O13  C14   single    1.418  0.020  1.418
 5RM  C14  C15   single    1.514  0.020  1.514
 5RM  C14  H141  single    0.970  0.020  1.090
 5RM  C14  H142  single    0.970  0.020  1.090
 5RM  C15  C16   single    1.523  0.020  1.523
 5RM  C15  H151  single    0.970  0.020  1.090
 5RM  C15  H152  single    0.970  0.020  1.090
 5RM  C16  H161  single    0.970  0.020  1.090
 5RM  C16  H162  single    0.970  0.020  1.090
 5RM  C16  H163  single    0.970  0.020  1.090
 5RM  N3   H18   single    0.890  0.020  1.040
 5RM  C2   H19   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
 5RM  N3    C4   O5    109.00  3.000
 5RM  N3    C4   O19   128.95  3.000
 5RM  O5    C4   O19   122.04  3.000
 5RM  C1    O5   C4    110.61  3.000
 5RM  H18   N3   C2    122.69  3.000
 5RM  H18   N3   C4    120.70  3.000
 5RM  C2    N3   C4    111.77  3.000
 5RM  H19   C2   H2    108.48  3.000
 5RM  H19   C2   C1    112.21  3.000
 5RM  H2    C2   C1    111.82  3.000
 5RM  H19   C2   N3    111.83  3.000
 5RM  H2    C2   N3    112.07  3.000
 5RM  C1    C2   N3    100.34  3.000
 5RM  C6    C1   C18   111.24  3.000
 5RM  C6    C1   C2    112.86  3.000
 5RM  C18   C1   C2    111.52  3.000
 5RM  C6    C1   O5    109.82  3.000
 5RM  C18   C1   O5    108.05  3.000
 5RM  C2    C1   O5    102.92  3.000
 5RM  H183  C18  H182  108.13  3.000
 5RM  H183  C18  H181  108.74  3.000
 5RM  H182  C18  H181  107.95  3.000
 5RM  H183  C18  C1    110.77  3.000
 5RM  H182  C18  C1    110.14  3.000
 5RM  H181  C18  C1    111.01  3.000
 5RM  C17   C6   C7    119.01  3.000
 5RM  C17   C6   C1    121.82  3.000
 5RM  C7    C6   C1    119.15  3.000
 5RM  H7    C7   C8    118.37  3.000
 5RM  H7    C7   C6    120.89  3.000
 5RM  C8    C7   C6    120.74  3.000
 5RM  H8    C8   C9    120.87  3.000
 5RM  H8    C8   C7    118.59  3.000
 5RM  C9    C8   C7    120.54  3.000
 5RM  C12   C9   O10   115.75  3.000
 5RM  C12   C9   C8    119.03  3.000
 5RM  O10   C9   C8    125.21  3.000
 5RM  C11   O10  C9    118.02  3.000
 5RM  H113  C11  H112  108.72  3.000
 5RM  H113  C11  H111  108.74  3.000
 5RM  H112  C11  H111  108.81  3.000
 5RM  H113  C11  O10   111.98  3.000
 5RM  H112  C11  O10   111.95  3.000
 5RM  H111  C11  O10   106.53  3.000
 5RM  O13   C12  C17   124.70  3.000
 5RM  O13   C12  C9    115.40  3.000
 5RM  C17   C12  C9    119.89  3.000
 5RM  H17   C17  C12   119.64  3.000
 5RM  H17   C17  C6    119.59  3.000
 5RM  C12   C17  C6    120.77  3.000
 5RM  C14   O13  C12   118.92  3.000
 5RM  H142  C14  H141  107.41  3.000
 5RM  H142  C14  C15   110.36  3.000
 5RM  H141  C14  C15   109.98  3.000
 5RM  H142  C14  O13   110.27  3.000
 5RM  H141  C14  O13   110.44  3.000
 5RM  C15   C14  O13   108.39  3.000
 5RM  H152  C15  H151  107.02  3.000
 5RM  H152  C15  C16   109.83  3.000
 5RM  H151  C15  C16   109.86  3.000
 5RM  H152  C15  C14   109.38  3.000
 5RM  H151  C15  C14   109.61  3.000
 5RM  C16   C15  C14   111.06  3.000
 5RM  H163  C16  H162  107.66  3.000
 5RM  H163  C16  H161  107.71  3.000
 5RM  H162  C16  H161  107.58  3.000
 5RM  H163  C16  C15   111.38  3.000
 5RM  H162  C16  C15   111.39  3.000
 5RM  H161  C16  C15   110.94  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
 5RM  CONST_01  C9    C8   C7   C6      0.00   0.0  0
 5RM  CONST_02  C9    C12  C17  C6      0.00   0.0  0
 5RM  CONST_03  C12   C17  C6   C7      0.00   0.0  0
 5RM  CONST_04  C12   C9   C8   C7      0.00   0.0  0
 5RM  CONST_05  C17   C6   C7   C8      0.00   0.0  0
 5RM  CONST_06  C17   C12  C9   C8      0.00   0.0  0
 5RM  CONST_07  C8    C7   C6   C1    180.00   0.0  0
 5RM  CONST_08  C12   C17  C6   C1    180.00   0.0  0
 5RM  CONST_09  O13   C12  C17  C6    180.00   0.0  0
 5RM  CONST_10  O10   C9   C8   C7    180.00   0.0  0
 5RM  CONST_11  O13   C12  C9   C8    180.00   0.0  0
 5RM  CONST_12  C17   C12  C9   O10   180.00   0.0  0
 5RM  CONST_13  H7    C7   C6   C1      0.00   0.0  0
 5RM  CONST_14  H17   C17  C6   C1      0.00   0.0  0
 5RM  CONST_15  H8    C8   C7   C6    180.00   0.0  0
 5RM  Var_01    C1    C2   N3   C4     21.00  30.0  1
 5RM  Var_02    C2    N3   C4   O5    -11.52  30.0  1
 5RM  Var_03    C12   C9   O10  C11   179.62  30.0  1
 5RM  Var_04    C15   C14  O13  C12  -178.61  30.0  3
 5RM  Var_05    H111  C11  O10  C9   -179.00  30.0  3
 5RM  Var_06    C16   C15  C14  O13  -179.33  30.0  3
 5RM  Var_07    H161  C16  C15  C14  -178.53  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
 5RM  chir_01  C1  C2  O5  C6  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
 5RM  plan-1  C1   0.020
 5RM  plan-1  C6   0.020
 5RM  plan-1  C7   0.020
 5RM  plan-1  C8   0.020
 5RM  plan-1  C9   0.020
 5RM  plan-1  O10  0.020
 5RM  plan-1  C12  0.020
 5RM  plan-1  C17  0.020
 5RM  plan-1  O13  0.020
 5RM  plan-1  H7   0.020
 5RM  plan-1  H8   0.020
 5RM  plan-1  H17  0.020
 5RM  plan-2  C4   0.020
 5RM  plan-2  N3   0.020
 5RM  plan-2  C2   0.020
 5RM  plan-2  H18  0.020
 5RM  plan-3  O19  0.020
 5RM  plan-3  C4   0.020
 5RM  plan-3  O5   0.020
 5RM  plan-3  N3   0.020

