# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 10:12:38 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: 5-[(5-chloranylpyrimidin-4-yl)amino]-1,3-dihydroindol-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cncnc1Nc2ccc3NC(=O)Cc3c2
#
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
 7ZO  7ZO  5-[(5-chloranylpyrimidin-4-yl)amino]-1,3-dihydroindol-2-one  ligand  27  18  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7ZO
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
 7ZO  C4   C   CR16  0  -0.000   4.2057   1.0955  -0.1507
 7ZO  C5   C   CR16  0   0.063   2.4186   2.3362  -0.7016
 7ZO  C6   C   CR56  0   0.003  -2.3991   0.2111   0.3422
 7ZO  C7   C   CR56  0   0.406  -3.0040  -0.8861  -0.2706
 7ZO  C8   C   CR6   0   0.334  -0.2600  -0.7884  -0.0051
 7ZO  C10  C   CR6   0   0.608   1.9997   0.1884  -0.0789
 7ZO  C1   C   CR16  0  -0.301  -2.2599  -1.9455  -0.7487
 7ZO  C2   C   CR16  0  -0.328  -0.8766  -1.8763  -0.6156
 7ZO  C3   C   CR16  0  -0.347  -1.0322   0.2676   0.4904
 7ZO  C9   C   CR6   0  -0.200   3.3901   0.0229   0.1041
 7ZO  C11  C   CR5   0   0.515  -4.7513   0.4741   0.2987
 7ZO  C12  C   CH2   0  -0.621  -3.4745   1.1640   0.7556
 7ZO  N13  N   N     0  -0.423   3.7296   2.2742  -0.5570
 7ZO  N14  N   N     0  -0.451   1.5442   1.3692  -0.4893
 7ZO  N15  N   NR15  0  -0.740  -4.3806  -0.7014  -0.2826
 7ZO  N16  N   NH1   0  -0.761   1.1389  -0.8215   0.1504
 7ZO  O17  O   O     0  -0.458  -5.8891   0.8766   0.4214
 7ZO  CL1  CL  CL    0  -0.102   4.0448  -1.4828   0.6320
 7ZO  H1   H   HCR6  0   0.294   5.2785   1.0051  -0.0222
 7ZO  H2   H   HCR6  0   0.264   2.0079   3.2834  -1.0339
 7ZO  H3   H   HCR6  0   0.272  -2.7234  -2.8018  -1.2198
 7ZO  H4   H   HCR6  0   0.273  -0.2695  -2.6887  -0.9956
 7ZO  H5   H   HCR6  0   0.268  -0.5694   1.1077   0.9876
 7ZO  H6   H   HCH2  0   0.304  -3.5098   1.3336   1.8345
 7ZO  H7   H   HCH2  0   0.305  -3.3886   2.1452   0.2826
 7ZO  H8   H   HNR5  0   0.412  -5.0411  -1.3600  -0.6674
 7ZO  H9   H   HNH1  0   0.409   1.5401  -1.7290   0.3314

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
 7ZO  O17  C11  double    1.213  0.020  1.213
 7ZO  C11  C12  single    1.521  0.020  1.521
 7ZO  C11  N15  single    1.363  0.020  1.363
 7ZO  C12  C6   single    1.495  0.020  1.495
 7ZO  N15  C7   single    1.389  0.020  1.389
 7ZO  C6   C7   aromatic  1.395  0.020  1.395
 7ZO  C6   C3   aromatic  1.376  0.020  1.376
 7ZO  C7   C1   aromatic  1.380  0.020  1.380
 7ZO  C3   C8   aromatic  1.399  0.020  1.399
 7ZO  C1   C2   aromatic  1.391  0.020  1.391
 7ZO  C8   C2   aromatic  1.392  0.020  1.392
 7ZO  C8   N16  single    1.408  0.020  1.408
 7ZO  N16  C10  single    1.347  0.020  1.347
 7ZO  C10  N14  aromatic  1.330  0.020  1.330
 7ZO  C10  C9   aromatic  1.412  0.020  1.412
 7ZO  CL1  C9   single    1.725  0.020  1.725
 7ZO  N14  C5   aromatic  1.321  0.020  1.321
 7ZO  C9   C4   aromatic  1.371  0.020  1.371
 7ZO  C5   N13  aromatic  1.320  0.020  1.320
 7ZO  C4   N13  aromatic  1.335  0.020  1.335
 7ZO  C4   H1   single    0.930  0.020  1.080
 7ZO  C5   H2   single    0.930  0.020  1.080
 7ZO  C1   H3   single    0.930  0.020  1.080
 7ZO  C2   H4   single    0.930  0.020  1.080
 7ZO  C3   H5   single    0.930  0.020  1.080
 7ZO  C12  H6   single    0.970  0.020  1.090
 7ZO  C12  H7   single    0.970  0.020  1.090
 7ZO  N15  H8   single    0.860  0.020  1.020
 7ZO  N16  H9   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
 7ZO  H1   C4   N13  117.57  3.000
 7ZO  H1   C4   C9   120.08  3.000
 7ZO  N13  C4   C9   122.35  3.000
 7ZO  H2   C5   N14  115.98  3.000
 7ZO  H2   C5   N13  116.78  3.000
 7ZO  N14  C5   N13  127.24  3.000
 7ZO  C12  C6   C3   131.19  3.000
 7ZO  C3   C6   C7   120.69  3.000
 7ZO  C12  C6   C7   108.11  3.000
 7ZO  N15  C7   C1   129.30  3.000
 7ZO  C1   C7   C6   121.49  3.000
 7ZO  N15  C7   C6   109.21  3.000
 7ZO  N16  C8   C3   121.81  3.000
 7ZO  N16  C8   C2   118.06  3.000
 7ZO  C3   C8   C2   120.06  3.000
 7ZO  N16  C10  N14  119.95  3.000
 7ZO  N14  C10  C9   118.75  3.000
 7ZO  N16  C10  C9   121.30  3.000
 7ZO  H3   C1   C2   120.47  3.000
 7ZO  H3   C1   C7   121.84  3.000
 7ZO  C2   C1   C7   117.69  3.000
 7ZO  H4   C2   C1   119.10  3.000
 7ZO  H4   C2   C8   119.47  3.000
 7ZO  C1   C2   C8   121.43  3.000
 7ZO  H5   C3   C8   120.90  3.000
 7ZO  H5   C3   C6   120.46  3.000
 7ZO  C8   C3   C6   118.64  3.000
 7ZO  CL1  C9   C10  121.05  3.000
 7ZO  CL1  C9   C4   120.93  3.000
 7ZO  C10  C9   C4   118.02  3.000
 7ZO  O17  C11  N15  125.76  3.000
 7ZO  N15  C11  C12  106.91  3.000
 7ZO  O17  C11  C12  127.33  3.000
 7ZO  H7   C12  H6   106.89  3.000
 7ZO  H7   C12  C11  110.07  3.000
 7ZO  H6   C12  C11  109.86  3.000
 7ZO  H7   C12  C6   113.33  3.000
 7ZO  H6   C12  C6   113.27  3.000
 7ZO  C11  C12  C6   103.39  3.000
 7ZO  C5   N13  C4   115.41  3.000
 7ZO  C10  N14  C5   118.21  3.000
 7ZO  H8   N15  C11  123.21  3.000
 7ZO  H8   N15  C7   124.42  3.000
 7ZO  C11  N15  C7   112.37  3.000
 7ZO  H9   N16  C10  116.81  3.000
 7ZO  H9   N16  C8   115.86  3.000
 7ZO  C10  N16  C8   126.78  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
 7ZO  CONST_01  N14  C10  C9   C4     0.00   0.0  0
 7ZO  CONST_02  N14  C5   N13  C4     0.00   0.0  0
 7ZO  CONST_03  C9   C10  N14  C5     0.00   0.0  0
 7ZO  CONST_04  C9   C4   N13  C5     0.00   0.0  0
 7ZO  CONST_05  C2   C1   C7   C6     0.00   0.0  0
 7ZO  CONST_06  C2   C8   C3   C6     0.00   0.0  0
 7ZO  CONST_07  C8   C3   C6   C7     0.00   0.0  0
 7ZO  CONST_08  C8   C2   C1   C7     0.00   0.0  0
 7ZO  CONST_09  N13  C5   N14  C10    0.00   0.0  0
 7ZO  CONST_10  N13  C4   C9   C10    0.00   0.0  0
 7ZO  CONST_11  C3   C6   C7   C1     0.00   0.0  0
 7ZO  CONST_12  C3   C8   C2   C1     0.00   0.0  0
 7ZO  CONST_13  C12  C11  N15  C7     0.00   0.0  0
 7ZO  CONST_14  N16  C10  C9   C4   180.00   0.0  0
 7ZO  CONST_15  N16  C10  N14  C5   180.00   0.0  0
 7ZO  CONST_16  N16  C8   C3   C6   180.00   0.0  0
 7ZO  CONST_17  N16  C8   C2   C1   180.00   0.0  0
 7ZO  CONST_18  CL1  C9   C4   N13  180.00   0.0  0
 7ZO  CONST_19  CL1  C9   C10  N14  180.00   0.0  0
 7ZO  CONST_20  O17  C11  N15  C7   180.00   0.0  0
 7ZO  CONST_21  H2   C5   N13  C4   180.00   0.0  0
 7ZO  CONST_22  H1   C4   N13  C5   180.00   0.0  0
 7ZO  CONST_23  H3   C1   C7   C6   180.00   0.0  0
 7ZO  CONST_24  H5   C3   C6   C7   180.00   0.0  0
 7ZO  CONST_25  H4   C2   C1   C7   180.00   0.0  0
 7ZO  CONST_26  H8   N15  C11  C12  180.00   0.0  0
 7ZO  Var_01    N14  C10  N16  C8     0.44  30.0  2
 7ZO  Var_02    C3   C8   N16  C10  -46.50  30.0  2
 7ZO  Var_03    H6   C12  C6   C7   118.68  30.0  1

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
 7ZO  plan-1  C4   0.020
 7ZO  plan-1  C5   0.020
 7ZO  plan-1  C10  0.020
 7ZO  plan-1  C9   0.020
 7ZO  plan-1  N13  0.020
 7ZO  plan-1  N14  0.020
 7ZO  plan-1  N16  0.020
 7ZO  plan-1  CL1  0.020
 7ZO  plan-1  H1   0.020
 7ZO  plan-1  H2   0.020
 7ZO  plan-2  C6   0.020
 7ZO  plan-2  C7   0.020
 7ZO  plan-2  C8   0.020
 7ZO  plan-2  C1   0.020
 7ZO  plan-2  C2   0.020
 7ZO  plan-2  C3   0.020
 7ZO  plan-2  C11  0.020
 7ZO  plan-2  C12  0.020
 7ZO  plan-2  N15  0.020
 7ZO  plan-2  N16  0.020
 7ZO  plan-2  O17  0.020
 7ZO  plan-2  H3   0.020
 7ZO  plan-2  H4   0.020
 7ZO  plan-2  H5   0.020
 7ZO  plan-2  H8   0.020

