# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 08:22:32 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 4-(4-{[(3R)-2-oxo-2,3-dihydro-1H-indol-3-yl]methyl}phenyl)piperazine-1-carbaldehyde
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=CN1CCN(CC1)c2ccc(C[C@H]3C(=O)Nc4ccccc34)cc2
#
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
 SU2  SU2  4-(4-{[(3R)-2-oxo-2,3-dihydro-1H-indol-3-yl]methyl}phenyl)piperazine-1-carbaldehyde  ligand  46  25  .  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_SU2
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
 SU2  N1    N  NR15  0  -0.738   1.7715  -0.3910   4.4373
 SU2  C2    C  CR5   0   0.548   1.3268  -0.5872   3.1630
 SU2  O2    O  O     0  -0.446   2.0260  -0.8431   2.2064
 SU2  C3    C  CR15  0  -0.449  -0.1901  -0.4072   3.1797
 SU2  C4    C  CR16  0  -0.330  -1.6606   0.0380   5.3059
 SU2  C5    C  CR16  0  -0.265  -1.6262   0.2581   6.6837
 SU2  C6    C  CR16  0  -0.267  -0.4137   0.2701   7.3608
 SU2  C7    C  CR16  0  -0.308   0.7913   0.0640   6.6915
 SU2  C8    C  CR56  0   0.379   0.7332  -0.1539   5.3278
 SU2  C9    C  CR56  0   0.065  -0.4752  -0.1695   4.6328
 SU2  C10   C  CH2   0  -0.514  -0.6437   0.7656   2.2868
 SU2  C1'   C  CR6   0   0.130  -0.4663   0.5275   0.8146
 SU2  C2'   C  CR16  0  -0.298  -1.3307  -0.3206   0.1229
 SU2  C3'   C  CR16  0  -0.306  -1.1849  -0.5556  -1.2312
 SU2  C4'   C  CR6   0   0.340  -0.1658   0.0661  -1.9662
 SU2  C5'   C  CR16  0  -0.344   0.6963   0.9215  -1.2764
 SU2  C6'   C  CR16  0  -0.287   0.5484   1.1335   0.0891
 SU2  N1'   N  NT    0  -0.411   0.1495  -0.2957  -6.1404
 SU2  C11   C  C1    0   0.256   0.1767   0.2701  -7.3543
 SU2  O3    O  O     0  -0.496  -0.7888   0.4614  -8.0746
 SU2  C2B   C  CH2   0  -0.300   1.3364  -0.4487  -5.3299
 SU2  C3B   C  CH2   0  -0.304   1.1696   0.2601  -3.9957
 SU2  N4'   N  NT    0  -0.522  -0.0313  -0.2072  -3.3331
 SU2  C5B   C  CH2   0  -0.302  -1.2191  -0.0090  -4.1545
 SU2  C6B   C  CH2   0  -0.309  -1.0723  -0.7173  -5.4894
 SU2  HN1   H  HNR5  0   0.409   2.7451  -0.4477   4.6962
 SU2  H3    H  HCR5  0   0.310  -0.6601  -1.3300   2.8237
 SU2  H4    H  HCR6  0   0.254  -2.6065   0.0265   4.7777
 SU2  H5    H  HCR6  0   0.254  -2.5477   0.4205   7.2265
 SU2  H6    H  HCR6  0   0.259  -0.3989   0.4398   8.4296
 SU2  H7    H  HCR6  0   0.266   1.7328   0.0751   7.2248
 SU2  H101  H  HCH2  0   0.261  -0.1161   1.6721   2.5928
 SU2  H102  H  HCH2  0   0.267  -1.7008   0.9399   2.5016
 SU2  H2'   H  HCR6  0   0.244  -2.1343  -0.8168   0.6559
 SU2  H3'   H  HCR6  0   0.257  -1.8635  -1.2440  -1.7192
 SU2  H5'   H  HCR6  0   0.264   1.4914   1.4426  -1.7924
 SU2  H6'   H  HCR6  0   0.241   1.2387   1.8028   0.5892
 SU2  H11   H  H     0   0.193   1.1976   0.5538  -7.6543
 SU2  H2'1  H  HCH2  0   0.247   1.5243  -1.5120  -5.1555
 SU2  H2'2  H  HCH2  0   0.266   2.1975  -0.0398  -5.8583
 SU2  H3'1  H  HCH2  0   0.261   2.0398   0.0271  -3.3809
 SU2  H3'2  H  HCH2  0   0.220   1.1591   1.3488  -4.1580
 SU2  H5'1  H  HCH2  0   0.263  -2.0963  -0.4090  -3.6502
 SU2  H5'2  H  HCH2  0   0.225  -1.4004   1.0619  -4.3284
 SU2  H6'1  H  HCH2  0   0.268  -1.9228  -0.4919  -6.1286
 SU2  H6'2  H  HCH2  0   0.251  -1.0420  -1.7997  -5.3325

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
 SU2  N1   C2    single    1.364  0.020  1.364
 SU2  N1   C8    single    1.388  0.020  1.388
 SU2  N1   HN1   single    0.860  0.020  1.020
 SU2  C2   O2    double    1.212  0.020  1.212
 SU2  C2   C3    single    1.528  0.020  1.528
 SU2  C3   C9    single    1.500  0.020  1.500
 SU2  C3   C10   single    1.542  0.020  1.542
 SU2  C3   H3    single    0.970  0.020  1.090
 SU2  C4   C5    aromatic  1.396  0.020  1.396
 SU2  C4   C9    aromatic  1.379  0.020  1.379
 SU2  C4   H4    single    0.930  0.020  1.080
 SU2  C5   C6    aromatic  1.389  0.020  1.389
 SU2  C5   H5    single    0.930  0.020  1.080
 SU2  C6   C7    aromatic  1.394  0.020  1.394
 SU2  C6   H6    single    0.930  0.020  1.080
 SU2  C7   C8    aromatic  1.382  0.020  1.382
 SU2  C7   H7    single    0.930  0.020  1.080
 SU2  C8   C9    aromatic  1.394  0.020  1.394
 SU2  C10  C1'   single    1.502  0.020  1.502
 SU2  C10  H101  single    0.970  0.020  1.090
 SU2  C10  H102  single    0.970  0.020  1.090
 SU2  C1'  C2'   aromatic  1.394  0.020  1.394
 SU2  C1'  C6'   aromatic  1.387  0.020  1.387
 SU2  C2'  C3'   aromatic  1.382  0.020  1.382
 SU2  C2'  H2'   single    0.930  0.020  1.080
 SU2  C3'  C4'   aromatic  1.402  0.020  1.402
 SU2  C3'  H3'   single    0.930  0.020  1.080
 SU2  C4'  C5'   aromatic  1.397  0.020  1.397
 SU2  C4'  N4'   single    1.400  0.020  1.400
 SU2  C5'  C6'   aromatic  1.390  0.020  1.390
 SU2  C5'  H5'   single    0.930  0.020  1.080
 SU2  C6'  H6'   single    0.930  0.020  1.080
 SU2  N1'  C11   single    1.340  0.020  1.340
 SU2  N1'  C2B   single    1.445  0.020  1.445
 SU2  N1'  C6B   single    1.447  0.020  1.447
 SU2  C11  O3    double    1.220  0.020  1.220
 SU2  C11  H11   single    0.930  0.020  1.080
 SU2  C2B  C3B   single    1.520  0.020  1.520
 SU2  C2B  H2'1  single    0.970  0.020  1.090
 SU2  C2B  H2'2  single    0.970  0.020  1.090
 SU2  C3B  N4'   single    1.449  0.020  1.449
 SU2  C3B  H3'1  single    0.970  0.020  1.090
 SU2  C3B  H3'2  single    0.970  0.020  1.090
 SU2  N4'  C5B   single    1.458  0.020  1.458
 SU2  C5B  C6B   single    1.518  0.020  1.518
 SU2  C5B  H5'1  single    0.970  0.020  1.090
 SU2  C5B  H5'2  single    0.970  0.020  1.090
 SU2  C6B  H6'1  single    0.970  0.020  1.090
 SU2  C6B  H6'2  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
 SU2  HN1   N1   C8    124.52  3.000
 SU2  HN1   N1   C2    123.12  3.000
 SU2  C8    N1   C2    112.33  3.000
 SU2  C3    C2   O2    127.32  3.000
 SU2  C3    C2   N1    107.25  3.000
 SU2  O2    C2   N1    125.42  3.000
 SU2  H3    C3   C10   109.05  3.000
 SU2  H3    C3   C9    111.53  3.000
 SU2  C10   C3   C9    112.62  3.000
 SU2  H3    C3   C2    108.86  3.000
 SU2  C10   C3   C2    112.04  3.000
 SU2  C9    C3   C2    102.59  3.000
 SU2  H4    C4   C9    120.73  3.000
 SU2  H4    C4   C5    120.30  3.000
 SU2  C9    C4   C5    118.97  3.000
 SU2  H5    C5   C6    119.85  3.000
 SU2  H5    C5   C4    119.87  3.000
 SU2  C6    C5   C4    120.28  3.000
 SU2  H6    C6   C7    119.06  3.000
 SU2  H6    C6   C5    119.66  3.000
 SU2  C7    C6   C5    121.29  3.000
 SU2  H7    C7   C8    121.63  3.000
 SU2  H7    C7   C6    120.93  3.000
 SU2  C8    C7   C6    117.44  3.000
 SU2  C9    C8   C7    122.01  3.000
 SU2  C9    C8   N1    109.06  3.000
 SU2  C7    C8   N1    128.93  3.000
 SU2  C8    C9   C4    120.01  3.000
 SU2  C8    C9   C3    108.66  3.000
 SU2  C4    C9   C3    131.32  3.000
 SU2  H102  C10  H101  106.25  3.000
 SU2  H102  C10  C1'   109.41  3.000
 SU2  H101  C10  C1'   110.43  3.000
 SU2  H102  C10  C3    106.98  3.000
 SU2  H101  C10  C3    109.07  3.000
 SU2  C1'   C10  C3    114.35  3.000
 SU2  C6'   C1'  C2'   117.37  3.000
 SU2  C6'   C1'  C10   122.00  3.000
 SU2  C2'   C1'  C10   120.62  3.000
 SU2  H2'   C2'  C3'   118.80  3.000
 SU2  H2'   C2'  C1'   119.59  3.000
 SU2  C3'   C2'  C1'   121.60  3.000
 SU2  H3'   C3'  C4'   120.08  3.000
 SU2  H3'   C3'  C2'   118.92  3.000
 SU2  C4'   C3'  C2'   121.00  3.000
 SU2  N4'   C4'  C5'   122.84  3.000
 SU2  N4'   C4'  C3'   119.67  3.000
 SU2  C5'   C4'  C3'   117.48  3.000
 SU2  H5'   C5'  C6'   118.26  3.000
 SU2  H5'   C5'  C4'   120.88  3.000
 SU2  C6'   C5'  C4'   120.86  3.000
 SU2  H6'   C6'  C5'   118.67  3.000
 SU2  H6'   C6'  C1'   119.64  3.000
 SU2  C5'   C6'  C1'   121.69  3.000
 SU2  C6B   N1'  C2B   114.21  3.000
 SU2  C6B   N1'  C11   123.21  3.000
 SU2  C2B   N1'  C11   122.43  3.000
 SU2  H11   C11  O3    122.18  3.000
 SU2  H11   C11  N1'   111.99  3.000
 SU2  O3    C11  N1'   125.83  3.000
 SU2  H2'2  C2B  H2'1  107.83  3.000
 SU2  H2'2  C2B  C3B   109.71  3.000
 SU2  H2'1  C2B  C3B   109.40  3.000
 SU2  H2'2  C2B  N1'   109.71  3.000
 SU2  H2'1  C2B  N1'   109.48  3.000
 SU2  C3B   C2B  N1'   110.66  3.000
 SU2  H3'2  C3B  H3'1  107.58  3.000
 SU2  H3'2  C3B  N4'   112.24  3.000
 SU2  H3'1  C3B  N4'   109.55  3.000
 SU2  H3'2  C3B  C2B   109.44  3.000
 SU2  H3'1  C3B  C2B   107.92  3.000
 SU2  N4'   C3B  C2B   109.99  3.000
 SU2  C5B   N4'  C3B   111.95  3.000
 SU2  C5B   N4'  C4'   116.44  3.000
 SU2  C3B   N4'  C4'   117.58  3.000
 SU2  H5'2  C5B  H5'1  107.36  3.000
 SU2  H5'2  C5B  C6B   109.34  3.000
 SU2  H5'1  C5B  C6B   108.30  3.000
 SU2  H5'2  C5B  N4'   110.84  3.000
 SU2  H5'1  C5B  N4'   110.23  3.000
 SU2  C6B   C5B  N4'   110.69  3.000
 SU2  H6'2  C6B  H6'1  108.12  3.000
 SU2  H6'2  C6B  C5B   109.76  3.000
 SU2  H6'1  C6B  C5B   110.15  3.000
 SU2  H6'2  C6B  N1'   109.23  3.000
 SU2  H6'1  C6B  N1'   109.61  3.000
 SU2  C5B   C6B  N1'   109.95  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
 SU2  CONST_01  C7   C6   C5   C4      0.00   0.0  0
 SU2  CONST_02  C7   C8   C9   C4      0.00   0.0  0
 SU2  CONST_03  C8   C9   C4   C5      0.00   0.0  0
 SU2  CONST_04  C8   C7   C6   C5      0.00   0.0  0
 SU2  CONST_05  C9   C4   C5   C6      0.00   0.0  0
 SU2  CONST_06  C9   C8   C7   C6      0.00   0.0  0
 SU2  CONST_07  C4'  C3'  C2'  C1'     0.00   0.0  0
 SU2  CONST_08  C4'  C5'  C6'  C1'     0.00   0.0  0
 SU2  CONST_09  C5'  C6'  C1'  C2'     0.00   0.0  0
 SU2  CONST_10  C5'  C4'  C3'  C2'     0.00   0.0  0
 SU2  CONST_11  C6'  C1'  C2'  C3'     0.00   0.0  0
 SU2  CONST_12  C6'  C5'  C4'  C3'     0.00   0.0  0
 SU2  CONST_13  N4'  C4'  C3'  C2'   180.00   0.0  0
 SU2  CONST_14  N4'  C4'  C5'  C6'   180.00   0.0  0
 SU2  CONST_15  C8   N1   C2   C3      0.00   0.0  0
 SU2  CONST_16  C3'  C2'  C1'  C10   180.00   0.0  0
 SU2  CONST_17  C5'  C6'  C1'  C10   180.00   0.0  0
 SU2  CONST_18  C8   N1   C2   O2    180.00   0.0  0
 SU2  CONST_19  H7   C7   C8   N1      0.00   0.0  0
 SU2  CONST_20  H4   C4   C9   C3      0.00   0.0  0
 SU2  CONST_21  H6   C6   C5   C4    180.00   0.0  0
 SU2  CONST_22  H5   C5   C6   C7    180.00   0.0  0
 SU2  CONST_23  H3'  C3'  C2'  C1'   180.00   0.0  0
 SU2  CONST_24  H5'  C5'  C6'  C1'   180.00   0.0  0
 SU2  CONST_25  H6'  C6'  C1'  C2'   180.00   0.0  0
 SU2  CONST_26  H2'  C2'  C3'  C4'   180.00   0.0  0
 SU2  CONST_27  HN1  N1   C2   C3    180.00   0.0  0
 SU2  CONST_28  C2B  N1'  C11  O3    180.00   0.0  0
 SU2  CONST_29  C6B  N1'  C11  O3      0.00   0.0  0
 SU2  Var_01    C3B  N4'  C4'  C3'  -169.02  30.0  2
 SU2  Var_02    C2B  C3B  N4'  C4'   163.83  30.0  1
 SU2  Var_03    C6B  C5B  N4'  C4'  -163.03  30.0  1
 SU2  Var_04    N4'  C3B  C2B  N1'    54.50  30.0  1
 SU2  Var_05    N4'  C5B  C6B  N1'   -54.12  30.0  1
 SU2  Var_06    C5B  C6B  N1'  C2B    53.97  30.0  1
 SU2  Var_07    C6B  N1'  C2B  C3B   -54.44  30.0  1
 SU2  Var_08    C2'  C1'  C10  C3     75.00  30.0  2

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
 SU2  chir_01  C3  C2  C9  C10  negativ

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
 SU2  plan-1  C10  0.020
 SU2  plan-1  C1'  0.020
 SU2  plan-1  C2'  0.020
 SU2  plan-1  C3'  0.020
 SU2  plan-1  C4'  0.020
 SU2  plan-1  C5'  0.020
 SU2  plan-1  C6'  0.020
 SU2  plan-1  N4'  0.020
 SU2  plan-1  H2'  0.020
 SU2  plan-1  H3'  0.020
 SU2  plan-1  H5'  0.020
 SU2  plan-1  H6'  0.020
 SU2  plan-2  N1'  0.020
 SU2  plan-2  C11  0.020
 SU2  plan-2  O3   0.020
 SU2  plan-2  C2B  0.020
 SU2  plan-2  C6B  0.020
 SU2  plan-2  H11  0.020
 SU2  plan-3  N1   0.020
 SU2  plan-3  C2   0.020
 SU2  plan-3  O2   0.020
 SU2  plan-3  C3   0.020
 SU2  plan-3  C4   0.020
 SU2  plan-3  C5   0.020
 SU2  plan-3  C6   0.020
 SU2  plan-3  C7   0.020
 SU2  plan-3  C8   0.020
 SU2  plan-3  C9   0.020
 SU2  plan-3  HN1  0.020
 SU2  plan-3  H4   0.020
 SU2  plan-3  H5   0.020
 SU2  plan-3  H6   0.020
 SU2  plan-3  H7   0.020

