# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 09:11:36 2022
#   Inital geometry file: a 110 line input string
#   Ligand name: 3-(hydroxymethyl)-1-methyl-5-[(2R)-2-methylaziridin-1-yl]-2-phenyl-1H-indole-4,7-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1CN1C2=CC(=O)c3n(C)c(c4ccccc4)c(CO)c3C2=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
 ARH  ARH  3-(hydroxymethyl)-1-methyl-5-[(2R)-2-methylaziridin-1-yl]-2-phenyl-1H-indole-4,7-dione  ligand  42  24  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_ARH
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
 ARH  C1    C  CR16  0  -0.507   1.3963  -0.2395   2.6822
 ARH  C2    C  CR6   0   0.379   1.9969  -0.1509   1.3537
 ARH  C3    C  CR56  0   0.256   1.0399  -0.0816   0.2521
 ARH  C4    C  CR56  0  -0.095  -0.3308  -0.1172   0.4263
 ARH  C5    C  CR6   0   0.293  -0.9215  -0.2156   1.7472
 ARH  C6    C  CR6   0   0.237   0.0622  -0.2732   2.8946
 ARH  N7    N  NR5   0  -0.528   1.2991   0.0285  -1.0729
 ARH  C8    C  CR5   0   0.305   0.1110   0.0592  -1.7544
 ARH  C9    C  CR5   0  -0.011  -0.9303  -0.0230  -0.8489
 ARH  O10   O  O     0  -0.367  -2.1143  -0.2398   1.9632
 ARH  O11   O  O     0  -0.420   3.2083  -0.1326   1.1942
 ARH  N12   N  NT    0  -0.415  -0.4978  -0.4500   4.1240
 ARH  C13   C  CH2   0  -0.348  -1.3757   0.4885   4.7793
 ARH  C14   C  CH1   0  -0.124  -0.0333   0.1707   5.3374
 ARH  C17   C  CH3   0  -0.673   0.1505  -0.7005   6.5453
 ARH  C25   C  CH3   0  -0.529   2.6149   0.1757  -1.6696
 ARH  C32   C  CR6   0   0.004   0.0380   0.1418  -3.2199
 ARH  C33   C  CH2   0  -0.265  -2.3834  -0.0862  -1.1722
 ARH  O34   O  OH1   0  -0.667  -2.8435  -1.4021  -0.9422
 ARH  C38   C  CR16  0  -0.278   0.5342  -0.8913  -4.0159
 ARH  C39   C  CR16  0  -0.242   0.4457  -0.8177  -5.3978
 ARH  C40   C  CR16  0  -0.255  -0.1454   0.2859  -6.0004
 ARH  C41   C  CR16  0  -0.244  -0.6455   1.3156  -5.2153
 ARH  C42   C  CR16  0  -0.283  -0.5522   1.2461  -3.8320
 ARH  HC1   H  HCR6  0   0.276   2.0848  -0.2892   3.5175
 ARH  H131  H  HCH2  0   0.258  -2.2638   0.0655   5.2340
 ARH  H132  H  HCH2  0   0.266  -1.5148   1.4609   4.3199
 ARH  HC41  H  HCH1  0   0.273   0.7199   0.9449   5.2051
 ARH  H171  H  HCH3  0   0.239   0.1347  -0.0949   7.4512
 ARH  H172  H  HCH3  0   0.235  -0.6395  -1.4475   6.6215
 ARH  H173  H  HCH3  0   0.241   1.1085  -1.2202   6.5070
 ARH  H251  H  HCH3  0   0.265   3.1969  -0.7356  -1.5570
 ARH  H252  H  HCH3  0   0.268   2.5017   0.3909  -2.7264
 ARH  H253  H  HCH3  0   0.270   3.1491   0.9986  -1.2040
 ARH  H331  H  HCH2  0   0.213  -2.9224   0.6388  -0.5537
 ARH  H332  H  HCH2  0   0.207  -2.5364   0.2118  -2.2157
 ARH  HO43  H  HOH1  0   0.455  -3.8048  -1.3830  -0.9681
 ARH  HC83  H  HCR6  0   0.263   0.9818  -1.7608  -3.5508
 ARH  HC93  H  HCR6  0   0.262   0.8334  -1.6263  -6.0034
 ARH  HC04  H  HCR6  0   0.262  -0.2165   0.3420  -7.0788
 ARH  HC14  H  HCR6  0   0.262  -1.1045   2.1789  -5.6786
 ARH  HC24  H  HCR6  0   0.262  -0.9326   2.0580  -3.2250

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
 ARH  C1   C2    single    1.461  0.020  1.461
 ARH  C1   C6    double    1.351  0.020  1.351
 ARH  C1   HC1   single    0.930  0.020  1.080
 ARH  C2   C3    single    1.461  0.020  1.461
 ARH  C2   O11   double    1.222  0.020  1.222
 ARH  C3   C4    aromatic  1.382  0.020  1.382
 ARH  C3   N7    aromatic  1.355  0.020  1.355
 ARH  C4   C5    single    1.450  0.020  1.450
 ARH  C4   C9    aromatic  1.412  0.020  1.412
 ARH  C5   C6    single    1.512  0.020  1.512
 ARH  C5   O10   double    1.212  0.020  1.212
 ARH  C6   N12   single    1.362  0.020  1.362
 ARH  N7   C8    aromatic  1.370  0.020  1.370
 ARH  N7   C25   single    1.452  0.020  1.452
 ARH  C8   C9    aromatic  1.382  0.020  1.382
 ARH  C8   C32   single    1.470  0.020  1.470
 ARH  C9   C33   single    1.490  0.020  1.490
 ARH  N12  C13   single    1.443  0.020  1.443
 ARH  N12  C14   single    1.440  0.020  1.440
 ARH  C13  C14   single    1.488  0.020  1.488
 ARH  C13  H131  single    0.970  0.020  1.090
 ARH  C13  H132  single    0.970  0.020  1.090
 ARH  C14  C17   single    1.501  0.020  1.501
 ARH  C14  HC41  single    0.970  0.020  1.090
 ARH  C17  H171  single    0.970  0.020  1.090
 ARH  C17  H172  single    0.970  0.020  1.090
 ARH  C17  H173  single    0.970  0.020  1.090
 ARH  C25  H251  single    0.970  0.020  1.090
 ARH  C25  H252  single    0.970  0.020  1.090
 ARH  C25  H253  single    0.970  0.020  1.090
 ARH  C32  C38   aromatic  1.395  0.020  1.395
 ARH  C32  C42   aromatic  1.394  0.020  1.394
 ARH  C33  O34   single    1.413  0.020  1.413
 ARH  C33  H331  single    0.970  0.020  1.090
 ARH  C33  H332  single    0.970  0.020  1.090
 ARH  O34  HO43  single    0.850  0.020  0.980
 ARH  C38  C39   aromatic  1.387  0.020  1.387
 ARH  C38  HC83  single    0.930  0.020  1.080
 ARH  C39  C40   aromatic  1.389  0.020  1.389
 ARH  C39  HC93  single    0.930  0.020  1.080
 ARH  C40  C41   aromatic  1.388  0.020  1.388
 ARH  C40  HC04  single    0.930  0.020  1.080
 ARH  C41  C42   aromatic  1.388  0.020  1.388
 ARH  C41  HC14  single    0.930  0.020  1.080
 ARH  C42  HC24  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
 ARH  HC1   C1   C6    120.33  3.000
 ARH  HC1   C1   C2    116.28  3.000
 ARH  C6    C1   C2    123.39  3.000
 ARH  O11   C2   C3    123.39  3.000
 ARH  O11   C2   C1    121.82  3.000
 ARH  C3    C2   C1    114.79  3.000
 ARH  N7    C3   C4    108.37  3.000
 ARH  N7    C3   C2    128.03  3.000
 ARH  C4    C3   C2    123.60  3.000
 ARH  C9    C4   C5    130.85  3.000
 ARH  C9    C4   C3    107.79  3.000
 ARH  C5    C4   C3    121.36  3.000
 ARH  O10   C5   C6    120.26  3.000
 ARH  O10   C5   C4    124.35  3.000
 ARH  C6    C5   C4    115.38  3.000
 ARH  N12   C6   C5    114.97  3.000
 ARH  N12   C6   C1    123.42  3.000
 ARH  C5    C6   C1    121.46  3.000
 ARH  C25   N7   C8    125.38  3.000
 ARH  C25   N7   C3    125.70  3.000
 ARH  C8    N7   C3    108.81  3.000
 ARH  C32   C8   C9    128.25  3.000
 ARH  C32   C8   N7    122.72  3.000
 ARH  C9    C8   N7    109.03  3.000
 ARH  C33   C9   C8    126.51  3.000
 ARH  C33   C9   C4    127.38  3.000
 ARH  C8    C9   C4    106.00  3.000
 ARH  C14   N12  C13    62.16  3.000
 ARH  C14   N12  C6    124.88  3.000
 ARH  C13   N12  C6    125.14  3.000
 ARH  H132  C13  H131  115.00  3.000
 ARH  H132  C13  C14   117.78  3.000
 ARH  H131  C13  C14   119.91  3.000
 ARH  H132  C13  N12   117.97  3.000
 ARH  H131  C13  N12   115.81  3.000
 ARH  C14   C13  N12    58.83  3.000
 ARH  HC41  C14  C17   115.22  3.000
 ARH  HC41  C14  C13   115.27  3.000
 ARH  C17   C14  C13   122.44  3.000
 ARH  HC41  C14  N12   115.31  3.000
 ARH  C17   C14  N12   117.87  3.000
 ARH  C13   C14  N12    59.01  3.000
 ARH  H173  C17  H172  108.22  3.000
 ARH  H173  C17  H171  107.86  3.000
 ARH  H172  C17  H171  108.19  3.000
 ARH  H173  C17  C14   110.86  3.000
 ARH  H172  C17  C14   111.43  3.000
 ARH  H171  C17  C14   110.16  3.000
 ARH  H253  C25  H252  108.59  3.000
 ARH  H253  C25  H251  109.11  3.000
 ARH  H252  C25  H251  108.86  3.000
 ARH  H253  C25  N7    110.26  3.000
 ARH  H252  C25  N7    109.03  3.000
 ARH  H251  C25  N7    110.95  3.000
 ARH  C42   C32  C38   119.12  3.000
 ARH  C42   C32  C8    120.23  3.000
 ARH  C38   C32  C8    120.63  3.000
 ARH  H332  C33  H331  106.80  3.000
 ARH  H332  C33  O34   111.27  3.000
 ARH  H331  C33  O34   111.38  3.000
 ARH  H332  C33  C9    109.34  3.000
 ARH  H331  C33  C9    109.24  3.000
 ARH  O34   C33  C9    108.77  3.000
 ARH  HO43  O34  C33   107.61  3.000
 ARH  HC83  C38  C39   119.80  3.000
 ARH  HC83  C38  C32   119.76  3.000
 ARH  C39   C38  C32   120.43  3.000
 ARH  HC93  C39  C40   120.21  3.000
 ARH  HC93  C39  C38   119.68  3.000
 ARH  C40   C39  C38   120.10  3.000
 ARH  HC04  C40  C41   120.10  3.000
 ARH  HC04  C40  C39   120.09  3.000
 ARH  C41   C40  C39   119.81  3.000
 ARH  HC14  C41  C42   119.68  3.000
 ARH  HC14  C41  C40   120.16  3.000
 ARH  C42   C41  C40   120.15  3.000
 ARH  HC24  C42  C41   119.84  3.000
 ARH  HC24  C42  C32   119.78  3.000
 ARH  C41   C42  C32   120.38  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
 ARH  CONST_01  C8    C9   C4   C3      0.00   0.0  0
 ARH  CONST_02  C9    C8   N7   C3      0.00   0.0  0
 ARH  CONST_03  C32   C8   N7   C3    180.00   0.0  0
 ARH  CONST_04  C8    N7   C3   C4      0.00   0.0  0
 ARH  CONST_05  N7    C8   C9   C4      0.00   0.0  0
 ARH  CONST_06  C32   C8   C9   C4    180.00   0.0  0
 ARH  CONST_07  C9    C4   C3   N7      0.00   0.0  0
 ARH  CONST_10  C39   C38  C32  C8    180.00   0.0  0
 ARH  CONST_11  C41   C42  C32  C8    180.00   0.0  0
 ARH  CONST_14  C40   C39  C38  C32     0.00   0.0  0
 ARH  CONST_15  C40   C41  C42  C32     0.00   0.0  0
 ARH  CONST_16  C41   C42  C32  C38     0.00   0.0  0
 ARH  CONST_17  C41   C40  C39  C38     0.00   0.0  0
 ARH  CONST_18  C42   C32  C38  C39     0.00   0.0  0
 ARH  CONST_19  C42   C41  C40  C39     0.00   0.0  0
 ARH  CONST_21  C25   N7   C3   C2      0.00   0.0  0
 ARH  CONST_22  C33   C9   C4   C3    180.00   0.0  0
 ARH  CONST_23  C25   N7   C3   C4    180.00   0.0  0
 ARH  CONST_24  C33   C9   C4   C5      0.00   0.0  0
 ARH  CONST_25  C33   C9   C8   N7    180.00   0.0  0
 ARH  CONST_26  C25   N7   C8   C9    180.00   0.0  0
 ARH  CONST_27  C32   C8   N7   C25     0.00   0.0  0
 ARH  CONST_28  C33   C9   C8   C32     0.00   0.0  0
 ARH  CONST_29  HC83  C38  C32  C8      0.00   0.0  0
 ARH  CONST_30  HC24  C42  C32  C8      0.00   0.0  0
 ARH  CONST_31  HC93  C39  C38  C32   180.00   0.0  0
 ARH  CONST_32  HC14  C41  C42  C32   180.00   0.0  0
 ARH  CONST_33  HC04  C40  C39  C38   180.00   0.0  0
 ARH  Var_01    C13   N12  C6   C1    119.78  30.0  2
 ARH  Var_02    C17   C14  N12  C6   -131.86  30.0  1
 ARH  Var_03    H131  C13  N12  C6    134.44  30.0  1
 ARH  Var_04    O34   C33  C9   C4    -69.28  30.0  2
 ARH  Var_05    H251  C25  N7   C3     68.68  30.0  2
 ARH  Var_06    H171  C17  C14  N12  -158.91  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
 ARH  chir_01  C14  N12  C13  C17  both

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
 ARH  plan-1  C8    0.020
 ARH  plan-1  C32   0.020
 ARH  plan-1  C38   0.020
 ARH  plan-1  C39   0.020
 ARH  plan-1  C40   0.020
 ARH  plan-1  C41   0.020
 ARH  plan-1  C42   0.020
 ARH  plan-1  HC83  0.020
 ARH  plan-1  HC93  0.020
 ARH  plan-1  HC04  0.020
 ARH  plan-1  HC14  0.020
 ARH  plan-1  HC24  0.020
 ARH  plan-2  C1    0.020
 ARH  plan-2  C2    0.020
 ARH  plan-2  C3    0.020
 ARH  plan-2  C4    0.020
 ARH  plan-2  C5    0.020
 ARH  plan-2  C6    0.020
 ARH  plan-2  N7    0.020
 ARH  plan-2  C8    0.020
 ARH  plan-2  C9    0.020
 ARH  plan-2  O10   0.020
 ARH  plan-2  O11   0.020
 ARH  plan-2  N12   0.020
 ARH  plan-2  C25   0.020
 ARH  plan-2  C32   0.020
 ARH  plan-2  C33   0.020
 ARH  plan-2  HC1   0.020
 ARH  plan-3  C6    0.020
 ARH  plan-3  N12   0.020
 ARH  plan-3  C13   0.020
 ARH  plan-3  C14   0.020

