# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 13:07:30 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: methyl {3-[2-(acetylamino)ethyl]-2-iodo-1H-indol-5-yl}carbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)Nc1ccc2[nH]c(I)c(CCNC(C)=O)c2c1
#
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
 52X  52X  'methyl {3-[2-(acetylamino)ethyl]-2-iodo-1H-indol-5-yl}carbamate'  ligand  37  21  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_52X
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
 52X  C1    C  CR56  0   0.336   0.4438   2.3506   0.3322
 52X  I1    I  I     0   0.108  -3.5459   1.2120  -0.2905
 52X  N1    N  NR15  0  -0.702  -0.9120   2.5214   0.3233
 52X  O1    O  O     0  -0.512  -0.7501  -4.3353   1.6800
 52X  C2    C  CR16  0  -0.284   1.4701   3.2167   0.6989
 52X  N2    N  NH1   0  -0.638  -0.8435  -3.3157  -0.3219
 52X  O2    O  O2    0  -0.480   6.3132   0.0233  -0.0902
 52X  C3    C  CR16  0  -0.367   2.7623   2.7523   0.5978
 52X  N3    N  NH1   0  -0.770   4.4200   1.1257   0.0761
 52X  O3    O  O     0  -0.496   4.3971  -1.1251  -0.3494
 52X  C4    C  CR6   0   0.372   3.0570   1.4487   0.1379
 52X  C5    C  CR16  0  -0.459   2.0335   0.5926  -0.2318
 52X  C6    C  CR56  0   0.077   0.7141   1.0518  -0.1327
 52X  C7    C  CR5   0   0.058  -0.5412   0.4319  -0.4366
 52X  C8    C  CR5   0  -0.040  -1.4881   1.3721  -0.1352
 52X  C11   C  CH2   0  -0.592  -0.7385  -0.9580  -0.9348
 52X  C12   C  CH2   0  -0.226  -0.6933  -1.9750   0.2012
 52X  C14   C  C     0   0.522  -0.8627  -4.4037   0.4620
 52X  C15   C  CH3   0  -0.776  -1.0372  -5.7217  -0.2502
 52X  C18   C  C     0   0.744   4.9843  -0.0867  -0.1396
 52X  C33   C  CH3   0  -0.416   7.0668  -1.1667  -0.3019
 52X  H2    H  HCR6  0   0.270   1.2692   4.2193   1.0527
 52X  HN2   H  HNH1  0   0.403  -0.9357  -3.4304  -1.3178
 52X  H3    H  HCR6  0   0.268   3.5784   3.4072   0.8797
 52X  HN3   H  HNH1  0   0.414   5.0562   1.8842   0.2706
 52X  H5    H  HCR6  0   0.268   2.2335  -0.4048  -0.5907
 52X  H11   H  HCH2  0   0.261  -1.6932  -1.0403  -1.4611
 52X  H11A  H  HCH2  0   0.260   0.0394  -1.1946  -1.6671
 52X  H12   H  HCH2  0   0.238  -1.4899  -1.7600   0.9184
 52X  H12A  H  HCH2  0   0.238   0.2530  -1.8863   0.7421
 52X  H15   H  HCH3  0   0.265  -1.9451  -6.2075   0.1079
 52X  H15A  H  HCH3  0   0.247  -1.1003  -5.6294  -1.3327
 52X  H15B  H  HCH3  0   0.264  -0.2022  -6.3790  -0.0082
 52X  H33   H  HCH3  0   0.237   6.8715  -1.9090   0.4719
 52X  H33A  H  HCH3  0   0.237   6.8637  -1.6044  -1.2790
 52X  H33B  H  HCH3  0   0.251   8.1099  -0.8677  -0.2542
 52X  HN1   H  HNR5  0   0.419  -1.4025   3.3539   0.6057

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
 52X  C6   C1    aromatic  1.406  0.020  1.406
 52X  C1   N1    aromatic  1.367  0.020  1.367
 52X  C1   C2    aromatic  1.392  0.020  1.392
 52X  I1   C8    single    2.070  0.020  2.070
 52X  C8   N1    aromatic  1.365  0.020  1.365
 52X  O1   C14   double    1.225  0.020  1.225
 52X  C3   C2    aromatic  1.377  0.020  1.377
 52X  C2   H2    single    0.930  0.020  1.080
 52X  C14  N2    single    1.341  0.020  1.341
 52X  N2   C12   single    1.447  0.020  1.447
 52X  N2   HN2   single    0.860  0.020  1.020
 52X  O2   C18   single    1.334  0.020  1.334
 52X  O2   C33   single    1.424  0.020  1.424
 52X  C4   C3    aromatic  1.413  0.020  1.413
 52X  C3   H3    single    0.930  0.020  1.080
 52X  N3   C18   single    1.355  0.020  1.355
 52X  N3   C4    single    1.402  0.020  1.402
 52X  N3   HN3   single    0.860  0.020  1.020
 52X  C18  O3    double    1.211  0.020  1.211
 52X  C5   C4    aromatic  1.385  0.020  1.385
 52X  C5   C6    aromatic  1.401  0.020  1.401
 52X  C5   H5    single    0.930  0.020  1.080
 52X  C7   C6    aromatic  1.433  0.020  1.433
 52X  C11  C7    single    1.490  0.020  1.490
 52X  C7   C8    aromatic  1.368  0.020  1.368
 52X  C11  C12   single    1.525  0.020  1.525
 52X  C11  H11   single    0.970  0.020  1.090
 52X  C11  H11A  single    0.970  0.020  1.090
 52X  C12  H12   single    0.970  0.020  1.090
 52X  C12  H12A  single    0.970  0.020  1.090
 52X  C14  C15   single    1.508  0.020  1.508
 52X  C15  H15   single    0.970  0.020  1.090
 52X  C15  H15A  single    0.970  0.020  1.090
 52X  C15  H15B  single    0.970  0.020  1.090
 52X  C33  H33   single    0.970  0.020  1.090
 52X  C33  H33A  single    0.970  0.020  1.090
 52X  C33  H33B  single    0.970  0.020  1.090
 52X  N1   HN1   single    0.860  0.020  1.020

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
 52X  C6    C1   C2    121.35  3.000
 52X  C2    C1   N1    130.95  3.000
 52X  C6    C1   N1    107.70  3.000
 52X  HN1   N1   C8    125.80  3.000
 52X  HN1   N1   C1    125.80  3.000
 52X  C8    N1   C1    108.40  3.000
 52X  H2    C2   C3    120.72  3.000
 52X  H2    C2   C1    121.72  3.000
 52X  C3    C2   C1    117.56  3.000
 52X  HN2   N2   C14   118.98  3.000
 52X  HN2   N2   C12   118.21  3.000
 52X  C14   N2   C12   122.81  3.000
 52X  C33   O2   C18   116.91  3.000
 52X  H3    C3   C4    119.01  3.000
 52X  H3    C3   C2    118.94  3.000
 52X  C4    C3   C2    122.05  3.000
 52X  HN3   N3   C18   116.16  3.000
 52X  HN3   N3   C4    115.55  3.000
 52X  C18   N3   C4    128.19  3.000
 52X  C5    C4   N3    124.36  3.000
 52X  C5    C4   C3    120.20  3.000
 52X  N3    C4   C3    115.44  3.000
 52X  H5    C5   C6    120.09  3.000
 52X  H5    C5   C4    121.57  3.000
 52X  C6    C5   C4    118.34  3.000
 52X  C7    C6   C5    131.96  3.000
 52X  C7    C6   C1    107.55  3.000
 52X  C5    C6   C1    120.49  3.000
 52X  C11   C7   C8    128.56  3.000
 52X  C8    C7   C6    105.21  3.000
 52X  C11   C7   C6    126.21  3.000
 52X  C7    C8   N1    111.14  3.000
 52X  C7    C8   I1    128.20  3.000
 52X  N1    C8   I1    120.66  3.000
 52X  H11A  C11  H11   106.39  3.000
 52X  H11A  C11  C12   109.46  3.000
 52X  H11   C11  C12   109.52  3.000
 52X  H11A  C11  C7    109.36  3.000
 52X  H11   C11  C7    110.29  3.000
 52X  C12   C11  C7    111.66  3.000
 52X  H12A  C12  H12   106.86  3.000
 52X  H12A  C12  C11   109.87  3.000
 52X  H12   C12  C11   109.63  3.000
 52X  H12A  C12  N2    110.11  3.000
 52X  H12   C12  N2    110.10  3.000
 52X  C11   C12  N2    110.21  3.000
 52X  C15   C14  N2    115.76  3.000
 52X  C15   C14  O1    121.93  3.000
 52X  N2    C14  O1    122.31  3.000
 52X  H15B  C15  H15A  108.45  3.000
 52X  H15B  C15  H15   107.24  3.000
 52X  H15A  C15  H15   108.44  3.000
 52X  H15B  C15  C14   109.48  3.000
 52X  H15A  C15  C14   113.72  3.000
 52X  H15   C15  C14   109.30  3.000
 52X  O3    C18  N3    126.37  3.000
 52X  O3    C18  O2    124.05  3.000
 52X  N3    C18  O2    109.59  3.000
 52X  H33B  C33  H33A  109.20  3.000
 52X  H33B  C33  H33   109.17  3.000
 52X  H33A  C33  H33   109.25  3.000
 52X  H33B  C33  O2    105.76  3.000
 52X  H33A  C33  O2    111.73  3.000
 52X  H33   C33  O2    111.64  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
 52X  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 52X  CONST_02  C8   C7   C6   C1      0.00   0.0  0
 52X  CONST_03  C7   C8   N1   C1      0.00   0.0  0
 52X  CONST_04  C4   C3   C2   C1      0.00   0.0  0
 52X  CONST_05  C5   C6   C1   N1    180.00   0.0  0
 52X  CONST_06  C7   C6   C1   N1      0.00   0.0  0
 52X  CONST_07  C3   C2   C1   N1    180.00   0.0  0
 52X  CONST_08  C6   C7   C8   N1      0.00   0.0  0
 52X  CONST_09  C5   C6   C1   C2      0.00   0.0  0
 52X  CONST_10  C7   C6   C1   C2    180.00   0.0  0
 52X  CONST_11  C8   N1   C1   C2    180.00   0.0  0
 52X  CONST_12  C5   C4   C3   C2      0.00   0.0  0
 52X  CONST_13  C6   C1   C2   C3      0.00   0.0  0
 52X  CONST_14  C6   C5   C4   C3      0.00   0.0  0
 52X  CONST_15  C7   C6   C5   C4    180.00   0.0  0
 52X  CONST_16  C8   C7   C6   C5    180.00   0.0  0
 52X  CONST_17  C8   N1   C1   C6      0.00   0.0  0
 52X  CONST_18  C11  C7   C6   C1    180.00   0.0  0
 52X  CONST_19  I1   C8   N1   C1    180.00   0.0  0
 52X  CONST_20  C6   C7   C8   I1    180.00   0.0  0
 52X  CONST_21  C11  C7   C8   N1    180.00   0.0  0
 52X  CONST_22  N3   C4   C3   C2    180.00   0.0  0
 52X  CONST_23  C6   C5   C4   N3    180.00   0.0  0
 52X  CONST_24  C11  C7   C6   C5      0.00   0.0  0
 52X  CONST_25  H5   C5   C6   C1    180.00   0.0  0
 52X  CONST_26  H3   C3   C2   C1    180.00   0.0  0
 52X  CONST_27  H2   C2   C1   N1      0.00   0.0  0
 52X  CONST_28  HN1  N1   C1   C2      0.00   0.0  0
 52X  CONST_29  C18  N3   C4   C3    180.00   0.0  0
 52X  CONST_30  C18  N3   C4   C5      0.00   0.0  0
 52X  CONST_31  HN3  N3   C4   C3      0.00   0.0  0
 52X  CONST_32  C4   N3   C18  O2    180.00   0.0  0
 52X  CONST_33  C4   N3   C18  O3      0.00   0.0  0
 52X  CONST_34  C12  N2   C14  O1      0.00   0.0  0
 52X  CONST_35  C15  C14  N2   C12   180.00   0.0  0
 52X  CONST_36  HN2  N2   C14  O1    180.00   0.0  0
 52X  Var_01    C12  C11  C7   C6     81.30  30.0  3
 52X  Var_02    C7   C11  C12  N2   -178.11  30.0  2
 52X  Var_03    C14  N2   C12  C11  -178.85  30.0  2
 52X  Var_04    H15  C15  C14  O1     60.04  30.0  3
 52X  Var_05    H33  C33  O2   C18   -63.09  30.0  3

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
 52X  plan-1  C1   0.020
 52X  plan-1  I1   0.020
 52X  plan-1  N1   0.020
 52X  plan-1  C2   0.020
 52X  plan-1  C3   0.020
 52X  plan-1  N3   0.020
 52X  plan-1  C4   0.020
 52X  plan-1  C5   0.020
 52X  plan-1  C6   0.020
 52X  plan-1  C7   0.020
 52X  plan-1  C8   0.020
 52X  plan-1  C11  0.020
 52X  plan-1  H2   0.020
 52X  plan-1  H3   0.020
 52X  plan-1  H5   0.020
 52X  plan-1  HN1  0.020
 52X  plan-2  O1   0.020
 52X  plan-2  N2   0.020
 52X  plan-2  C12  0.020
 52X  plan-2  C14  0.020
 52X  plan-2  C15  0.020
 52X  plan-2  HN2  0.020
 52X  plan-3  N3   0.020
 52X  plan-3  C4   0.020
 52X  plan-3  C18  0.020
 52X  plan-3  HN3  0.020
 52X  plan-4  O2   0.020
 52X  plan-4  N3   0.020
 52X  plan-4  O3   0.020
 52X  plan-4  C18  0.020

