# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:08:28 2022
#   Inital geometry file: a 109 line input string
#   Ligand name: (1R)-2-[(5-chloro-2,4-dihydroxyphenyl)carbonyl]-N-ethyl-2,3-dihydro-1H-isoindole-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCNC(=O)[C@@H]1N(Cc2ccccc12)C(=O)c3cc(Cl)c(O)cc3O
#
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
 1RC  1RC  (1R)-2-[(5-chloro-2,4-dihydroxyphenyl)carbonyl]-N-ethyl-2,3-dihydro-1H-isoindole-1-carboxamide  ligand  42  25  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1RC
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
 1RC  N1    N   NR5   0  -0.508   0.5592  -0.1399  -0.3198
 1RC  C4    C   CR16  0  -0.308   3.8752  -1.6395  -0.7736
 1RC  C5    C   CR56  0   0.107   2.5606  -1.2653  -0.5494
 1RC  C6    C   CR56  0   0.062   1.5734  -2.2110  -0.3432
 1RC  C7    C   CH2   0  -0.329   0.2562  -1.5510  -0.0920
 1RC  C8    C   CR15  0  -0.254   1.9813   0.1178  -0.4892
 1RC  C10   C   CR6   0  -0.210  -1.7505   0.7432  -0.3701
 1RC  C13   C   CR6   0   0.449  -4.5673   0.5855  -0.2954
 1RC  C15   C   CR6   0   0.379  -2.5537   1.6996  -1.0400
 1RC  C17   C   CH2   0  -0.263   4.3790   2.3419   1.4411
 1RC  C1    C   CR16  0  -0.252   4.1822  -2.9943  -0.7905
 1RC  C2    C   CR16  0  -0.254   3.1888  -3.9480  -0.5851
 1RC  C3    C   CR16  0  -0.310   1.8730  -3.5633  -0.3576
 1RC  C9    C   C     0   0.619  -0.2823   0.8928  -0.4687
 1RC  C11   C   CR16  0  -0.212  -2.4018  -0.2358   0.3805
 1RC  C12   C   CR6   0  -0.197  -3.7742  -0.3180   0.4231
 1RC  C14   C   CR16  0  -0.444  -3.9395   1.5882  -1.0171
 1RC  O1    O   OH1   0  -0.627  -2.0355   2.7200  -1.7163
 1RC  O2    O   OH1   0  -0.601  -5.8986   0.5418  -0.3070
 1RC  CL1   CL  CL    0  -0.112  -4.5470  -1.5455   1.3746
 1RC  O3    O   O     0  -0.546   0.1891   2.0077  -0.7530
 1RC  C16   C   C     0   0.570   2.5475   0.8847   0.7078
 1RC  N2    N   NH1   0  -0.629   3.6315   1.6150   0.4318
 1RC  C18   C   CH3   0  -0.698   5.7300   2.7660   0.8983
 1RC  O4    O   O     0  -0.482   2.0673   0.7608   1.8216
 1RC  H4    H   HCR6  0   0.254   4.6500  -0.8999  -0.9329
 1RC  H7    H   HCH2  0   0.282  -0.0618  -1.7389   0.9362
 1RC  H7A   H   HCH2  0   0.285  -0.5309  -1.9030  -0.7621
 1RC  H8    H   HCR5  0   0.312   2.1700   0.6655  -1.4175
 1RC  H17   H   HCH2  0   0.238   3.8147   3.2184   1.7710
 1RC  H17A  H   HCH2  0   0.242   4.5084   1.7002   2.3132
 1RC  H1    H   HCR6  0   0.262   5.2017  -3.3104  -0.9677
 1RC  H2    H   HCR6  0   0.262   3.4431  -4.9996  -0.6047
 1RC  H3    H   HCR6  0   0.258   1.1024  -4.3068  -0.1975
 1RC  H11   H   HCR6  0   0.291  -1.8447  -0.9384   0.9792
 1RC  H14   H   HCR6  0   0.287  -4.5395   2.3134  -1.5528
 1RC  HO1   H   HOH1  0   0.479  -1.0693   2.7376  -1.5058
 1RC  HO2   H   HOH1  0   0.475  -6.2341  -0.1920   0.2254
 1RC  HN2   H   HNH1  0   0.405   3.8966   1.7457  -0.5319
 1RC  H18   H   HCH3  0   0.235   6.3192   1.9038   0.5838
 1RC  H18A  H   HCH3  0   0.235   5.6249   3.4386   0.0460
 1RC  H18B  H   HCH3  0   0.247   6.2906   3.2931   1.6686

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
 1RC  N1   C7    single    1.461  0.020  1.461
 1RC  N1   C8    single    1.455  0.020  1.455
 1RC  N1   C9    single    1.340  0.020  1.340
 1RC  C4   C5    aromatic  1.385  0.020  1.385
 1RC  C4   C1    aromatic  1.389  0.020  1.389
 1RC  C5   C6    aromatic  1.382  0.020  1.382
 1RC  C5   C8    single    1.501  0.020  1.501
 1RC  C6   C7    single    1.495  0.020  1.495
 1RC  C6   C3    aromatic  1.385  0.020  1.385
 1RC  C8   C16   single    1.530  0.020  1.530
 1RC  C10  C15   aromatic  1.417  0.020  1.417
 1RC  C10  C9    single    1.479  0.020  1.479
 1RC  C10  C11   aromatic  1.395  0.020  1.395
 1RC  C13  C12   aromatic  1.401  0.020  1.401
 1RC  C13  C14   aromatic  1.386  0.020  1.386
 1RC  C13  O2    single    1.332  0.020  1.332
 1RC  C15  C14   aromatic  1.390  0.020  1.390
 1RC  C15  O1    single    1.329  0.020  1.329
 1RC  C17  N2    single    1.451  0.020  1.451
 1RC  C17  C18   single    1.516  0.020  1.516
 1RC  C1   C2    aromatic  1.392  0.020  1.392
 1RC  C2   C3    aromatic  1.390  0.020  1.390
 1RC  C9   O3    double    1.243  0.020  1.243
 1RC  C11  C12   aromatic  1.375  0.020  1.375
 1RC  C12  CL1   single    1.735  0.020  1.735
 1RC  C16  N2    single    1.336  0.020  1.336
 1RC  C16  O4    double    1.219  0.020  1.219
 1RC  C4   H4    single    0.930  0.020  1.080
 1RC  C7   H7    single    0.970  0.020  1.090
 1RC  C7   H7A   single    0.970  0.020  1.090
 1RC  C8   H8    single    0.970  0.020  1.090
 1RC  C17  H17   single    0.970  0.020  1.090
 1RC  C17  H17A  single    0.970  0.020  1.090
 1RC  C1   H1    single    0.930  0.020  1.080
 1RC  C2   H2    single    0.930  0.020  1.080
 1RC  C3   H3    single    0.930  0.020  1.080
 1RC  C11  H11   single    0.930  0.020  1.080
 1RC  C14  H14   single    0.930  0.020  1.080
 1RC  O1   HO1   single    0.850  0.020  0.980
 1RC  O2   HO2   single    0.850  0.020  0.980
 1RC  N2   HN2   single    0.860  0.020  1.020
 1RC  C18  H18   single    0.970  0.020  1.090
 1RC  C18  H18A  single    0.970  0.020  1.090
 1RC  C18  H18B  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
 1RC  C9    N1   C8    117.66  3.000
 1RC  C9    N1   C7    129.14  3.000
 1RC  C8    N1   C7    113.07  3.000
 1RC  H4    C4   C1    120.40  3.000
 1RC  H4    C4   C5    121.23  3.000
 1RC  C1    C4   C5    118.37  3.000
 1RC  C8    C5   C6    110.42  3.000
 1RC  C8    C5   C4    128.45  3.000
 1RC  C6    C5   C4    121.14  3.000
 1RC  C3    C6   C7    128.57  3.000
 1RC  C3    C6   C5    120.79  3.000
 1RC  C7    C6   C5    110.63  3.000
 1RC  H7A   C7   H7    108.20  3.000
 1RC  H7A   C7   C6    112.93  3.000
 1RC  H7    C7   C6    109.80  3.000
 1RC  H7A   C7   N1    111.41  3.000
 1RC  H7    C7   N1    111.92  3.000
 1RC  C6    C7   N1    102.56  3.000
 1RC  H8    C8   C16   110.42  3.000
 1RC  H8    C8   C5    111.15  3.000
 1RC  C16   C8   C5    110.52  3.000
 1RC  H8    C8   N1    110.84  3.000
 1RC  C16   C8   N1    111.06  3.000
 1RC  C5    C8   N1    102.63  3.000
 1RC  C11   C10  C9    124.77  3.000
 1RC  C11   C10  C15   117.60  3.000
 1RC  C9    C10  C15   117.57  3.000
 1RC  O2    C13  C14   118.17  3.000
 1RC  O2    C13  C12   123.32  3.000
 1RC  C14   C13  C12   118.51  3.000
 1RC  O1    C15  C14   117.29  3.000
 1RC  O1    C15  C10   122.51  3.000
 1RC  C14   C15  C10   120.20  3.000
 1RC  H17A  C17  H17   106.96  3.000
 1RC  H17A  C17  C18   110.19  3.000
 1RC  H17   C17  C18   110.09  3.000
 1RC  H17A  C17  N2    108.82  3.000
 1RC  H17   C17  N2    110.22  3.000
 1RC  C18   C17  N2    110.49  3.000
 1RC  H1    C1   C2    119.75  3.000
 1RC  H1    C1   C4    119.68  3.000
 1RC  C2    C1   C4    120.57  3.000
 1RC  H2    C2   C3    119.64  3.000
 1RC  H2    C2   C1    119.69  3.000
 1RC  C3    C2   C1    120.67  3.000
 1RC  H3    C3   C2    120.53  3.000
 1RC  H3    C3   C6    121.00  3.000
 1RC  C2    C3   C6    118.47  3.000
 1RC  O3    C9   C10   118.84  3.000
 1RC  O3    C9   N1    118.57  3.000
 1RC  C10   C9   N1    122.54  3.000
 1RC  H11   C11  C12   117.35  3.000
 1RC  H11   C11  C10   120.99  3.000
 1RC  C12   C11  C10   121.62  3.000
 1RC  CL1   C12  C11   120.24  3.000
 1RC  CL1   C12  C13   119.05  3.000
 1RC  C11   C12  C13   120.71  3.000
 1RC  H14   C14  C15   119.36  3.000
 1RC  H14   C14  C13   119.41  3.000
 1RC  C15   C14  C13   121.20  3.000
 1RC  HO1   O1   C15   106.64  3.000
 1RC  HO2   O2   C13   111.53  3.000
 1RC  O4    C16  N2    124.32  3.000
 1RC  O4    C16  C8    121.20  3.000
 1RC  N2    C16  C8    114.37  3.000
 1RC  HN2   N2   C16   118.80  3.000
 1RC  HN2   N2   C17   117.68  3.000
 1RC  C16   N2   C17   123.24  3.000
 1RC  H18B  C18  H18A  107.69  3.000
 1RC  H18B  C18  H18   107.97  3.000
 1RC  H18A  C18  H18   108.31  3.000
 1RC  H18B  C18  C17   109.93  3.000
 1RC  H18A  C18  C17   111.49  3.000
 1RC  H18   C18  C17   111.31  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
 1RC  CONST_01  C3   C6   C5   C4      0.00   0.0  0
 1RC  CONST_02  C3   C2   C1   C4      0.00   0.0  0
 1RC  CONST_03  C2   C1   C4   C5      0.00   0.0  0
 1RC  CONST_04  C2   C3   C6   C5      0.00   0.0  0
 1RC  CONST_05  C1   C4   C5   C6      0.00   0.0  0
 1RC  CONST_06  C1   C2   C3   C6      0.00   0.0  0
 1RC  CONST_07  C13  C14  C15  C10     0.00   0.0  0
 1RC  CONST_08  C13  C12  C11  C10     0.00   0.0  0
 1RC  CONST_09  C12  C11  C10  C15     0.00   0.0  0
 1RC  CONST_10  C12  C13  C14  C15     0.00   0.0  0
 1RC  CONST_11  C14  C15  C10  C11     0.00   0.0  0
 1RC  CONST_12  C14  C13  C12  C11     0.00   0.0  0
 1RC  CONST_13  CL1  C12  C11  C10   180.00   0.0  0
 1RC  CONST_14  O1   C15  C14  C13   180.00   0.0  0
 1RC  CONST_15  O2   C13  C14  C15   180.00   0.0  0
 1RC  CONST_16  C14  C15  C10  C9    180.00   0.0  0
 1RC  CONST_17  C12  C11  C10  C9    180.00   0.0  0
 1RC  CONST_18  O1   C15  C10  C11   180.00   0.0  0
 1RC  CONST_19  O2   C13  C12  C11   180.00   0.0  0
 1RC  CONST_20  CL1  C12  C13  C14   180.00   0.0  0
 1RC  CONST_21  C10  C9   N1   C7      0.00   0.0  0
 1RC  CONST_22  C10  C9   N1   C8    180.00   0.0  0
 1RC  CONST_23  H2   C2   C1   C4    180.00   0.0  0
 1RC  CONST_24  H1   C1   C4   C5    180.00   0.0  0
 1RC  CONST_25  H3   C3   C6   C5    180.00   0.0  0
 1RC  CONST_26  H4   C4   C5   C6    180.00   0.0  0
 1RC  CONST_27  H14  C14  C15  C10   180.00   0.0  0
 1RC  CONST_28  H11  C11  C12  C13   180.00   0.0  0
 1RC  CONST_29  O3   C9   N1   C7    180.00   0.0  0
 1RC  CONST_30  O3   C9   N1   C8      0.00   0.0  0
 1RC  CONST_31  C17  N2   C16  C8    180.00   0.0  0
 1RC  CONST_32  HN2  N2   C16  C8      0.00   0.0  0
 1RC  CONST_33  O4   C16  N2   C17     0.00   0.0  0
 1RC  Var_01    C5   C6   C7   N1      5.95  30.0  1
 1RC  Var_02    C8   N1   C7   C6     -8.61  30.0  1
 1RC  Var_03    C15  C10  C9   N1   -155.36  30.0  2
 1RC  Var_04    C18  C17  N2   C16   165.31  30.0  2
 1RC  Var_05    H18  C18  C17  N2    -59.31  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
 1RC  chir_01  C8  N1  C5  C16  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
 1RC  plan-1  C10  0.020
 1RC  plan-1  C13  0.020
 1RC  plan-1  C15  0.020
 1RC  plan-1  C9   0.020
 1RC  plan-1  C11  0.020
 1RC  plan-1  C12  0.020
 1RC  plan-1  C14  0.020
 1RC  plan-1  O1   0.020
 1RC  plan-1  O2   0.020
 1RC  plan-1  CL1  0.020
 1RC  plan-1  H11  0.020
 1RC  plan-1  H14  0.020
 1RC  plan-2  C4   0.020
 1RC  plan-2  C5   0.020
 1RC  plan-2  C6   0.020
 1RC  plan-2  C7   0.020
 1RC  plan-2  C8   0.020
 1RC  plan-2  C1   0.020
 1RC  plan-2  C2   0.020
 1RC  plan-2  C3   0.020
 1RC  plan-2  H4   0.020
 1RC  plan-2  H1   0.020
 1RC  plan-2  H2   0.020
 1RC  plan-2  H3   0.020
 1RC  plan-3  N1   0.020
 1RC  plan-3  C7   0.020
 1RC  plan-3  C8   0.020
 1RC  plan-3  C10  0.020
 1RC  plan-3  C9   0.020
 1RC  plan-3  O3   0.020
 1RC  plan-4  C8   0.020
 1RC  plan-4  C17  0.020
 1RC  plan-4  C16  0.020
 1RC  plan-4  N2   0.020
 1RC  plan-4  O4   0.020
 1RC  plan-4  HN2  0.020

