# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 10:02:50 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: (3~{S})-3-[2-[(dimethylamino)methyl]-1~{H}-indol-3-yl]-5-oxidanyl-2,3-dihydroisoindol-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)Cc1[nH]c2ccccc2c1[C@H]3NC(=O)c4ccc(O)cc34
#
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
 EZZ  EZZ  (3~{S})-3-[2-[(dimethylamino)methyl]-1~{H}-indol-3-yl]-5-oxidanyl-2,3-dihydroisoindol-1-one  ligand  43  24  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_EZZ
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
 EZZ  C4   C  CR16  0  -0.467  -1.8350   0.8604   0.7199
 EZZ  C5   C  CR56  0   0.162  -1.5316  -0.0606  -0.2615
 EZZ  C6   C  CR56  0  -0.129  -2.2903  -1.2016  -0.4480
 EZZ  C7   C  CR15  0  -0.227  -0.4086  -0.0292  -1.2669
 EZZ  C15  C  CR56  0   0.046   1.6202  -1.0124   0.0817
 EZZ  C17  C  CR16  0  -0.309   3.8009  -1.2247   1.1994
 EZZ  C24  C  CH3   0  -0.544   0.9609   3.4794   0.8380
 EZZ  C1   C  CR16  0  -0.285  -3.3843  -1.4674   0.3629
 EZZ  C11  C  CR5   0   0.040   0.9536   0.0189  -0.6558
 EZZ  C12  C  CR5   0   0.303   1.7951   1.0992  -0.6815
 EZZ  C14  C  CR56  0   0.334   2.8748  -0.4870   0.4645
 EZZ  C16  C  CR16  0  -0.376   1.2925  -2.3199   0.4639
 EZZ  C18  C  CR16  0  -0.286   3.4492  -2.5113   1.5595
 EZZ  C19  C  CR16  0  -0.265   2.2053  -3.0525   1.1970
 EZZ  C2   C  CR16  0  -0.346  -3.7012  -0.5635   1.3596
 EZZ  C23  C  CH3   0  -0.519   0.1286   4.3753  -1.2158
 EZZ  C3   C  CR6   0   0.381  -2.9341   0.5978   1.5369
 EZZ  C9   C  CR5   0   0.501  -1.7324  -1.9672  -1.5783
 EZZ  N13  N  NR15  0  -0.735   2.9448   0.7899  -0.0116
 EZZ  N21  N  NT    0  -0.391   0.5397   3.1792  -0.5136
 EZZ  N8   N  NR15  0  -0.657  -0.6633  -1.2548  -2.0045
 EZZ  O10  O  O     0  -0.480  -2.1379  -3.0219  -2.0412
 EZZ  O22  O  OH1   0  -0.623  -3.3122   1.4333   2.5186
 EZZ  H1   H  HCR6  0   0.298  -1.2395   1.7601   0.8272
 EZZ  H2   H  HCR5  0   0.288  -0.5368   0.8370  -1.9254
 EZZ  H3   H  HCR6  0   0.259   4.7579  -0.8048   1.4822
 EZZ  H4   H  HCH2  0   0.229   2.5140   3.0093  -1.2999
 EZZ  H5   H  HCH2  0   0.264   1.2169   2.3536  -2.2880
 EZZ  H6   H  HCH3  0   0.209   1.8483   4.1308   0.8775
 EZZ  H7   H  HCH3  0   0.238   0.1542   3.9817   1.3731
 EZZ  H8   H  HCH3  0   0.244   1.1929   2.5623   1.3811
 EZZ  H9   H  HCR6  0   0.263  -3.9834  -2.3587   0.2266
 EZZ  H10  H  HCR6  0   0.240   0.3390  -2.7575   0.1991
 EZZ  H11  H  HCR6  0   0.250   4.1428  -3.1110   2.1343
 EZZ  H12  H  HCR6  0   0.247   1.9604  -4.0624   1.4996
 EZZ  H13  H  HCR6  0   0.271  -4.5477  -0.7389   2.0113
 EZZ  H14  H  HCH3  0   0.234  -0.2262   4.1189  -2.2148
 EZZ  H15  H  HCH3  0   0.236  -0.6942   4.8521  -0.6815
 EZZ  H16  H  HCH3  0   0.194   0.9328   5.1197  -1.3237
 EZZ  H17  H  HNR5  0   0.406   3.7196   1.4201   0.1169
 EZZ  H19  H  HNR5  0   0.398  -0.0752  -1.5548  -2.7658
 EZZ  H20  H  HOH1  0   0.476  -2.7272   2.1984   2.5590
 EZZ  C20  C  CH2   0  -0.373   1.5595   2.4575  -1.2548

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
 EZZ  O22  C3   single    1.343  0.020  1.343
 EZZ  C2   C3   aromatic  1.403  0.020  1.403
 EZZ  C2   C1   aromatic  1.382  0.020  1.382
 EZZ  C3   C4   aromatic  1.394  0.020  1.394
 EZZ  C18  C19  aromatic  1.404  0.020  1.404
 EZZ  C18  C17  aromatic  1.382  0.020  1.382
 EZZ  C19  C16  aromatic  1.381  0.020  1.381
 EZZ  C17  C14  aromatic  1.393  0.020  1.393
 EZZ  C1   C6   aromatic  1.387  0.020  1.387
 EZZ  C4   C5   aromatic  1.380  0.020  1.380
 EZZ  C16  C15  aromatic  1.401  0.020  1.401
 EZZ  C14  C15  aromatic  1.413  0.020  1.413
 EZZ  C14  N13  aromatic  1.365  0.020  1.365
 EZZ  C15  C11  aromatic  1.432  0.020  1.432
 EZZ  C6   C5   aromatic  1.383  0.020  1.383
 EZZ  C6   C9   single    1.475  0.020  1.475
 EZZ  C5   C7   single    1.508  0.020  1.508
 EZZ  N13  C12  aromatic  1.366  0.020  1.366
 EZZ  C11  C12  aromatic  1.370  0.020  1.370
 EZZ  C11  C7   single    1.494  0.020  1.494
 EZZ  C12  C20  single    1.493  0.020  1.493
 EZZ  C9   O10  double    1.221  0.020  1.221
 EZZ  C9   N8   single    1.354  0.020  1.354
 EZZ  C7   N8   single    1.453  0.020  1.453
 EZZ  C20  N21  single    1.453  0.020  1.453
 EZZ  N21  C23  single    1.447  0.020  1.447
 EZZ  N21  C24  single    1.447  0.020  1.447
 EZZ  C4   H1   single    0.930  0.020  1.080
 EZZ  C7   H2   single    0.970  0.020  1.090
 EZZ  C17  H3   single    0.930  0.020  1.080
 EZZ  C20  H4   single    0.970  0.020  1.090
 EZZ  C20  H5   single    0.970  0.020  1.090
 EZZ  C24  H6   single    0.970  0.020  1.090
 EZZ  C24  H7   single    0.970  0.020  1.090
 EZZ  C24  H8   single    0.970  0.020  1.090
 EZZ  C1   H9   single    0.930  0.020  1.080
 EZZ  C16  H10  single    0.930  0.020  1.080
 EZZ  C18  H11  single    0.930  0.020  1.080
 EZZ  C19  H12  single    0.930  0.020  1.080
 EZZ  C2   H13  single    0.930  0.020  1.080
 EZZ  C23  H14  single    0.970  0.020  1.090
 EZZ  C23  H15  single    0.970  0.020  1.090
 EZZ  C23  H16  single    0.970  0.020  1.090
 EZZ  N13  H17  single    0.860  0.020  1.020
 EZZ  N8   H19  single    0.860  0.020  1.020
 EZZ  O22  H20  single    0.850  0.020  0.980

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
 EZZ  H1   C4   C3   122.08  3.000
 EZZ  H1   C4   C5   120.24  3.000
 EZZ  C3   C4   C5   117.67  3.000
 EZZ  C7   C5   C6   109.63  3.000
 EZZ  C7   C5   C4   128.63  3.000
 EZZ  C6   C5   C4   121.74  3.000
 EZZ  C9   C6   C1   130.30  3.000
 EZZ  C9   C6   C5   108.92  3.000
 EZZ  C1   C6   C5   120.78  3.000
 EZZ  H2   C7   N8   109.95  3.000
 EZZ  H2   C7   C11  109.10  3.000
 EZZ  N8   C7   C11  113.25  3.000
 EZZ  H2   C7   C5   109.28  3.000
 EZZ  N8   C7   C5   100.98  3.000
 EZZ  C11  C7   C5   114.03  3.000
 EZZ  C16  C15  C14  118.73  3.000
 EZZ  C14  C15  C11  106.56  3.000
 EZZ  C16  C15  C11  134.71  3.000
 EZZ  H3   C17  C18  121.20  3.000
 EZZ  H3   C17  C14  121.33  3.000
 EZZ  C18  C17  C14  117.47  3.000
 EZZ  H8   C24  H7   107.47  3.000
 EZZ  H8   C24  H6   107.94  3.000
 EZZ  H7   C24  H6   107.81  3.000
 EZZ  H8   C24  N21  110.64  3.000
 EZZ  H7   C24  N21  109.78  3.000
 EZZ  H6   C24  N21  112.99  3.000
 EZZ  H9   C1   C2   120.15  3.000
 EZZ  H9   C1   C6   121.36  3.000
 EZZ  C2   C1   C6   118.48  3.000
 EZZ  C12  C11  C15  106.95  3.000
 EZZ  C12  C11  C7   125.31  3.000
 EZZ  C15  C11  C7   127.72  3.000
 EZZ  N13  C12  C11  109.22  3.000
 EZZ  C11  C12  C20  128.89  3.000
 EZZ  N13  C12  C20  121.81  3.000
 EZZ  N13  C14  C17  130.18  3.000
 EZZ  N13  C14  C15  107.39  3.000
 EZZ  C17  C14  C15  122.42  3.000
 EZZ  H10  C16  C19  119.86  3.000
 EZZ  H10  C16  C15  121.12  3.000
 EZZ  C19  C16  C15  119.03  3.000
 EZZ  H11  C18  C19  119.43  3.000
 EZZ  H11  C18  C17  119.43  3.000
 EZZ  C19  C18  C17  121.14  3.000
 EZZ  H12  C19  C18  119.20  3.000
 EZZ  H12  C19  C16  119.59  3.000
 EZZ  C18  C19  C16  121.21  3.000
 EZZ  H13  C2   C3   119.05  3.000
 EZZ  H13  C2   C1   120.48  3.000
 EZZ  C3   C2   C1   120.47  3.000
 EZZ  H16  C23  H15  107.66  3.000
 EZZ  H16  C23  H14  107.86  3.000
 EZZ  H15  C23  H14  107.82  3.000
 EZZ  H16  C23  N21  113.52  3.000
 EZZ  H15  C23  N21  109.76  3.000
 EZZ  H14  C23  N21  110.04  3.000
 EZZ  O22  C3   C2   116.95  3.000
 EZZ  C2   C3   C4   120.85  3.000
 EZZ  O22  C3   C4   122.20  3.000
 EZZ  O10  C9   N8   126.69  3.000
 EZZ  N8   C9   C6   105.48  3.000
 EZZ  O10  C9   C6   127.83  3.000
 EZZ  H17  N13  C14  125.49  3.000
 EZZ  H17  N13  C12  124.64  3.000
 EZZ  C14  N13  C12  109.87  3.000
 EZZ  C23  N21  C24  111.38  3.000
 EZZ  C24  N21  C20  112.04  3.000
 EZZ  C23  N21  C20  111.26  3.000
 EZZ  H19  N8   C9   122.83  3.000
 EZZ  H19  N8   C7   122.17  3.000
 EZZ  C9   N8   C7   115.00  3.000
 EZZ  H20  O22  C3   110.69  3.000
 EZZ  H5   C20  H4   106.26  3.000
 EZZ  H5   C20  N21  108.03  3.000
 EZZ  H4   C20  N21  112.31  3.000
 EZZ  H5   C20  C12  109.01  3.000
 EZZ  H4   C20  C12  109.52  3.000
 EZZ  N21  C20  C12  111.52  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
 EZZ  CONST_01  C1   C2   C3   C4     0.00   0.0  0
 EZZ  CONST_02  C1   C6   C5   C4     0.00   0.0  0
 EZZ  CONST_03  C2   C3   C4   C5     0.00   0.0  0
 EZZ  CONST_04  C2   C1   C6   C5     0.00   0.0  0
 EZZ  CONST_05  C3   C2   C1   C6     0.00   0.0  0
 EZZ  CONST_06  C3   C4   C5   C6     0.00   0.0  0
 EZZ  CONST_07  C18  C19  C16  C15    0.00   0.0  0
 EZZ  CONST_08  C18  C17  C14  C15    0.00   0.0  0
 EZZ  CONST_09  C12  N13  C14  C15    0.00   0.0  0
 EZZ  CONST_10  N13  C12  C11  C15    0.00   0.0  0
 EZZ  CONST_11  C16  C19  C18  C17    0.00   0.0  0
 EZZ  CONST_12  C16  C15  C14  C17    0.00   0.0  0
 EZZ  CONST_13  C11  C15  C14  C17  180.00   0.0  0
 EZZ  CONST_14  C12  N13  C14  C17  180.00   0.0  0
 EZZ  CONST_15  C19  C16  C15  C11  180.00   0.0  0
 EZZ  CONST_16  N13  C14  C15  C11    0.00   0.0  0
 EZZ  CONST_17  C14  N13  C12  C11    0.00   0.0  0
 EZZ  CONST_18  C16  C15  C11  C12  180.00   0.0  0
 EZZ  CONST_19  C14  C15  C11  C12    0.00   0.0  0
 EZZ  CONST_20  C19  C18  C17  C14    0.00   0.0  0
 EZZ  CONST_21  C19  C16  C15  C14    0.00   0.0  0
 EZZ  CONST_22  N13  C14  C15  C16  180.00   0.0  0
 EZZ  CONST_23  N13  C14  C17  C18  180.00   0.0  0
 EZZ  CONST_24  C16  C15  C11  C7     0.00   0.0  0
 EZZ  CONST_25  C14  C15  C11  C7   180.00   0.0  0
 EZZ  CONST_26  N13  C12  C11  C7   180.00   0.0  0
 EZZ  CONST_27  C7   N8   C9   C6     0.00   0.0  0
 EZZ  CONST_28  O22  C3   C4   C5   180.00   0.0  0
 EZZ  CONST_29  C20  C12  C11  C7     0.00   0.0  0
 EZZ  CONST_30  C20  C12  C11  C15  180.00   0.0  0
 EZZ  CONST_31  C14  N13  C12  C20  180.00   0.0  0
 EZZ  CONST_32  O22  C3   C2   C1   180.00   0.0  0
 EZZ  CONST_33  O10  C9   N8   C7   180.00   0.0  0
 EZZ  CONST_34  H13  C2   C3   C4   180.00   0.0  0
 EZZ  CONST_35  H9   C1   C6   C5   180.00   0.0  0
 EZZ  CONST_36  H1   C4   C5   C6   180.00   0.0  0
 EZZ  CONST_37  H12  C19  C16  C15  180.00   0.0  0
 EZZ  CONST_38  H3   C17  C14  C15  180.00   0.0  0
 EZZ  CONST_39  H17  N13  C14  C15  180.00   0.0  0
 EZZ  CONST_40  H10  C16  C15  C11    0.00   0.0  0
 EZZ  CONST_41  H11  C18  C17  C14  180.00   0.0  0
 EZZ  CONST_42  H19  N8   C9   C6   180.00   0.0  0
 EZZ  Var_01    N21  C20  C12  C11   67.31  30.0  2
 EZZ  Var_02    C12  C20  N21  C24   65.80  30.0  2
 EZZ  Var_03    H14  C23  N21  C20   56.75  30.0  3
 EZZ  Var_04    H6   C24  N21  C20   62.04  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
 EZZ  chir_01  C7  C5  C11  N8  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
 EZZ  plan-1  C7   0.020
 EZZ  plan-1  C15  0.020
 EZZ  plan-1  C17  0.020
 EZZ  plan-1  C11  0.020
 EZZ  plan-1  C12  0.020
 EZZ  plan-1  C14  0.020
 EZZ  plan-1  C16  0.020
 EZZ  plan-1  C18  0.020
 EZZ  plan-1  C19  0.020
 EZZ  plan-1  N13  0.020
 EZZ  plan-1  H3   0.020
 EZZ  plan-1  H10  0.020
 EZZ  plan-1  H11  0.020
 EZZ  plan-1  H12  0.020
 EZZ  plan-1  H17  0.020
 EZZ  plan-1  C20  0.020
 EZZ  plan-2  C4   0.020
 EZZ  plan-2  C5   0.020
 EZZ  plan-2  C6   0.020
 EZZ  plan-2  C7   0.020
 EZZ  plan-2  C1   0.020
 EZZ  plan-2  C2   0.020
 EZZ  plan-2  C3   0.020
 EZZ  plan-2  C9   0.020
 EZZ  plan-2  N8   0.020
 EZZ  plan-2  O10  0.020
 EZZ  plan-2  O22  0.020
 EZZ  plan-2  H1   0.020
 EZZ  plan-2  H9   0.020
 EZZ  plan-2  H13  0.020
 EZZ  plan-2  H19  0.020

