# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 12:29:40 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 5-[[5-chloranyl-2-(pyridin-3-ylmethylamino)pyrimidin-4-yl]amino]-1,3-dihydroindol-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cnc(NCc2cccnc2)nc1Nc3ccc4NC(=O)Cc4c3
#
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
 7Z6  7Z6  5-[[5-chloranyl-2-(pyridin-3-ylmethylamino)pyrimidin-4-yl]amino]-1,3-dihydroindol-2-one  ligand  41  26  .  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_7Z6
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
 7Z6  C4   C   CR16  0  -0.323   1.6589   0.9060  -0.3066
 7Z6  C5   C   CR16  0  -0.441   3.6685  -0.3639   0.1269
 7Z6  C6   C   CR16  0  -0.066  -6.1697   3.2656  -0.3444
 7Z6  C7   C   CR16  0  -0.083  -5.3926   1.3094  -1.2024
 7Z6  C8   C   CR16  0   0.019  -1.4519  -3.4474   0.3164
 7Z6  C10  C   CR6   0  -0.045  -4.9268   0.8723   0.0327
 7Z6  C13  C   CR6   0  -0.262  -0.1059  -3.2004   0.2414
 7Z6  C15  C   CR6   0   0.625  -1.9018  -1.2485   0.1427
 7Z6  C17  C   CH2   0  -0.621   5.8682   1.0501   0.1913
 7Z6  C1   C   CR16  0  -0.320  -5.7438   2.9337   0.9334
 7Z6  C2   C   CR16  0  -0.168  -5.1109   1.7158   1.1218
 7Z6  C3   C   CR16  0  -0.296   2.4066   2.0800  -0.3852
 7Z6  C9   C   CR56  0   0.023   4.4027   0.7936   0.0454
 7Z6  C11  C   CR56  0   0.401   3.7708   2.0101  -0.2060
 7Z6  C12  C   CR6   0   0.372   2.2756  -0.3178  -0.0475
 7Z6  C14  C   CR6   0   0.636   0.3009  -1.8489   0.1112
 7Z6  C16  C   CR5   0   0.512   5.9826   2.5557  -0.0038
 7Z6  C18  C   CH2   0  -0.310  -4.2250  -0.4473   0.1698
 7Z6  N19  N   N     0  -0.401  -6.0006   2.4726  -1.3959
 7Z6  N20  N   N     0  -0.495  -2.3716  -2.4891   0.2704
 7Z6  N21  N   N     0  -0.529  -0.6130  -0.8973   0.0624
 7Z6  N22  N   NR15  0  -0.740   4.7242   3.0230  -0.2306
 7Z6  N23  N   NH1   0  -0.779   1.6152  -1.5489   0.0411
 7Z6  O25  O   O     0  -0.460   6.9925   3.2274   0.0339
 7Z6  CL1  CL  CL    0  -0.121   1.0432  -4.4915   0.3094
 7Z6  H1   H   HCR6  0   0.291   0.5922   0.9573  -0.4432
 7Z6  H2   H   HCR6  0   0.271   4.1609  -1.3082   0.3301
 7Z6  H4   H   HCR6  0   0.262  -5.2676   0.6783  -2.0774
 7Z6  H5   H   HCR6  0   0.284  -1.8086  -4.4666   0.4204
 7Z6  H6   H   HCH2  0   0.304   6.2609   0.7707   1.1719
 7Z6  H7   H   HCH2  0   0.304   6.4756   0.5307  -0.5540
 7Z6  H8   H   HCR6  0   0.274  -5.9095   3.6128   1.7581
 7Z6  H9   H   HCR6  0   0.274  -4.7694   1.4200   2.1064
 7Z6  H10  H   HCR6  0   0.268   1.9084   3.0193  -0.5859
 7Z6  H11  H   HCH2  0   0.253  -4.4910  -0.9103   1.1239
 7Z6  H12  H   HCH2  0   0.253  -4.5577  -1.1310  -0.6152
 7Z6  H13  H   HNR5  0   0.411   4.5166   3.9982  -0.3823
 7Z6  H14  H   HNH1  0   0.409   2.2360  -2.3398   0.1221
 7Z6  N24  N   NH1   0  -0.655  -2.7945  -0.2458   0.0872
 7Z6  H3   H   HCR6  0   0.267  -6.6703   4.2103  -0.5247
 7Z6  H15  H   HNH1  0   0.401  -2.4345   0.6883  -0.0154

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
 7Z6  O25  C16  double    1.213  0.020  1.213
 7Z6  C16  C17  single    1.522  0.020  1.522
 7Z6  C16  N22  single    1.361  0.020  1.361
 7Z6  C17  C9   single    1.495  0.020  1.495
 7Z6  N22  C11  single    1.391  0.020  1.391
 7Z6  C9   C11  aromatic  1.394  0.020  1.394
 7Z6  C9   C5   aromatic  1.373  0.020  1.373
 7Z6  C11  C3   aromatic  1.378  0.020  1.378
 7Z6  C5   C12  aromatic  1.404  0.020  1.404
 7Z6  C3   C4   aromatic  1.394  0.020  1.394
 7Z6  C12  C4   aromatic  1.395  0.020  1.395
 7Z6  C12  N23  single    1.400  0.020  1.400
 7Z6  N23  C14  single    1.350  0.020  1.350
 7Z6  N19  C6   aromatic  1.328  0.020  1.328
 7Z6  N19  C7   aromatic  1.327  0.020  1.327
 7Z6  C6   C1   aromatic  1.387  0.020  1.387
 7Z6  C14  N21  aromatic  1.320  0.020  1.320
 7Z6  C14  C13  aromatic  1.417  0.020  1.417
 7Z6  C7   C10  aromatic  1.391  0.020  1.391
 7Z6  CL1  C13  single    1.730  0.020  1.730
 7Z6  N21  C15  aromatic  1.338  0.020  1.338
 7Z6  C13  C8   aromatic  1.370  0.020  1.370
 7Z6  C1   C2   aromatic  1.385  0.020  1.385
 7Z6  C10  C2   aromatic  1.390  0.020  1.390
 7Z6  C10  C18  single    1.501  0.020  1.501
 7Z6  C18  N24  single    1.447  0.020  1.447
 7Z6  C15  N24  single    1.344  0.020  1.344
 7Z6  C15  N20  aromatic  1.333  0.020  1.333
 7Z6  C8   N20  aromatic  1.329  0.020  1.329
 7Z6  C4   H1   single    0.930  0.020  1.080
 7Z6  C5   H2   single    0.930  0.020  1.080
 7Z6  C6   H3   single    0.930  0.020  1.080
 7Z6  C7   H4   single    0.930  0.020  1.080
 7Z6  C8   H5   single    0.930  0.020  1.080
 7Z6  C17  H6   single    0.970  0.020  1.090
 7Z6  C17  H7   single    0.970  0.020  1.090
 7Z6  C1   H8   single    0.930  0.020  1.080
 7Z6  C2   H9   single    0.930  0.020  1.080
 7Z6  C3   H10  single    0.930  0.020  1.080
 7Z6  C18  H11  single    0.970  0.020  1.090
 7Z6  C18  H12  single    0.970  0.020  1.090
 7Z6  N22  H13  single    0.860  0.020  1.020
 7Z6  N23  H14  single    0.860  0.020  1.020
 7Z6  N24  H15  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
 7Z6  H1   C4   C12  120.23  3.000
 7Z6  H1   C4   C3   118.95  3.000
 7Z6  C12  C4   C3   120.82  3.000
 7Z6  H2   C5   C12  120.15  3.000
 7Z6  H2   C5   C9   120.16  3.000
 7Z6  C12  C5   C9   119.69  3.000
 7Z6  H3   C6   N19  116.59  3.000
 7Z6  H3   C6   C1   120.22  3.000
 7Z6  N19  C6   C1   123.20  3.000
 7Z6  H4   C7   N19  116.41  3.000
 7Z6  H4   C7   C10  119.63  3.000
 7Z6  N19  C7   C10  123.96  3.000
 7Z6  H5   C8   N20  116.95  3.000
 7Z6  H5   C8   C13  119.84  3.000
 7Z6  N20  C8   C13  123.21  3.000
 7Z6  C18  C10  C2   121.60  3.000
 7Z6  C18  C10  C7   120.94  3.000
 7Z6  C2   C10  C7   117.45  3.000
 7Z6  CL1  C13  C14  121.64  3.000
 7Z6  CL1  C13  C8   121.05  3.000
 7Z6  C14  C13  C8   117.31  3.000
 7Z6  N24  C15  N21  116.20  3.000
 7Z6  N24  C15  N20  117.68  3.000
 7Z6  N21  C15  N20  126.12  3.000
 7Z6  H7   C17  H6   106.91  3.000
 7Z6  H7   C17  C16  109.93  3.000
 7Z6  H6   C17  C16  109.93  3.000
 7Z6  H7   C17  C9   113.38  3.000
 7Z6  H6   C17  C9   113.33  3.000
 7Z6  C16  C17  C9   103.34  3.000
 7Z6  H8   C1   C2   121.23  3.000
 7Z6  H8   C1   C6   120.35  3.000
 7Z6  C2   C1   C6   118.41  3.000
 7Z6  H9   C2   C1   120.51  3.000
 7Z6  H9   C2   C10  120.31  3.000
 7Z6  C1   C2   C10  119.18  3.000
 7Z6  H10  C3   C11  121.60  3.000
 7Z6  H10  C3   C4   119.65  3.000
 7Z6  C11  C3   C4   118.75  3.000
 7Z6  C11  C9   C17  108.20  3.000
 7Z6  C11  C9   C5   120.27  3.000
 7Z6  C17  C9   C5   131.53  3.000
 7Z6  N22  C11  C9   109.15  3.000
 7Z6  C9   C11  C3   121.11  3.000
 7Z6  N22  C11  C3   129.74  3.000
 7Z6  N23  C12  C5   115.54  3.000
 7Z6  N23  C12  C4   125.09  3.000
 7Z6  C5   C12  C4   119.37  3.000
 7Z6  N23  C14  N21  120.79  3.000
 7Z6  N21  C14  C13  119.47  3.000
 7Z6  N23  C14  C13  119.75  3.000
 7Z6  O25  C16  N22  125.76  3.000
 7Z6  N22  C16  C17  106.94  3.000
 7Z6  O25  C16  C17  127.30  3.000
 7Z6  H12  C18  H11  106.73  3.000
 7Z6  H12  C18  N24  110.31  3.000
 7Z6  H11  C18  N24  110.45  3.000
 7Z6  H12  C18  C10  110.00  3.000
 7Z6  H11  C18  C10  109.77  3.000
 7Z6  N24  C18  C10  109.55  3.000
 7Z6  C7   N19  C6   117.81  3.000
 7Z6  C15  N20  C8   115.51  3.000
 7Z6  C14  N21  C15  118.38  3.000
 7Z6  H13  N22  C16  123.17  3.000
 7Z6  H13  N22  C11  124.44  3.000
 7Z6  C16  N22  C11  112.37  3.000
 7Z6  H14  N23  C14  114.89  3.000
 7Z6  H14  N23  C12  113.84  3.000
 7Z6  C14  N23  C12  131.15  3.000
 7Z6  H15  N24  C18  119.26  3.000
 7Z6  H15  N24  C15  117.34  3.000
 7Z6  C18  N24  C15  123.40  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
 7Z6  CONST_01  C9   C11  C3   C4      0.00   0.0  0
 7Z6  CONST_02  C9   C5   C12  C4      0.00   0.0  0
 7Z6  CONST_03  C3   C11  C9   C5      0.00   0.0  0
 7Z6  CONST_04  C3   C4   C12  C5      0.00   0.0  0
 7Z6  CONST_05  C10  C7   N19  C6      0.00   0.0  0
 7Z6  CONST_06  C10  C2   C1   C6      0.00   0.0  0
 7Z6  CONST_07  C1   C6   N19  C7      0.00   0.0  0
 7Z6  CONST_08  C1   C2   C10  C7      0.00   0.0  0
 7Z6  CONST_09  N21  C14  C13  C8      0.00   0.0  0
 7Z6  CONST_10  N21  C15  N20  C8      0.00   0.0  0
 7Z6  CONST_11  C15  N21  C14  C13     0.00   0.0  0
 7Z6  CONST_12  C15  N20  C8   C13     0.00   0.0  0
 7Z6  CONST_13  N19  C6   C1   C2      0.00   0.0  0
 7Z6  CONST_14  N19  C7   C10  C2      0.00   0.0  0
 7Z6  CONST_15  C12  C5   C9   C11     0.00   0.0  0
 7Z6  CONST_16  C12  C4   C3   C11     0.00   0.0  0
 7Z6  CONST_17  N20  C15  N21  C14     0.00   0.0  0
 7Z6  CONST_18  N20  C8   C13  C14     0.00   0.0  0
 7Z6  CONST_19  C11  N22  C16  C17     0.00   0.0  0
 7Z6  CONST_20  N23  C14  C13  C8    180.00   0.0  0
 7Z6  CONST_21  N24  C15  N20  C8    180.00   0.0  0
 7Z6  CONST_22  N23  C14  N21  C15   180.00   0.0  0
 7Z6  CONST_23  C18  C10  C2   C1    180.00   0.0  0
 7Z6  CONST_24  N23  C12  C4   C3    180.00   0.0  0
 7Z6  CONST_25  N23  C12  C5   C9    180.00   0.0  0
 7Z6  CONST_26  N24  C15  N21  C14   180.00   0.0  0
 7Z6  CONST_27  N19  C7   C10  C18   180.00   0.0  0
 7Z6  CONST_28  CL1  C13  C8   N20   180.00   0.0  0
 7Z6  CONST_29  CL1  C13  C14  N21   180.00   0.0  0
 7Z6  CONST_30  O25  C16  N22  C11   180.00   0.0  0
 7Z6  CONST_31  H2   C5   C12  C4    180.00   0.0  0
 7Z6  CONST_32  H1   C4   C12  C5    180.00   0.0  0
 7Z6  CONST_33  H4   C7   N19  C6    180.00   0.0  0
 7Z6  CONST_34  H9   C2   C1   C6    180.00   0.0  0
 7Z6  CONST_35  H3   C6   N19  C7    180.00   0.0  0
 7Z6  CONST_36  H8   C1   C2   C10   180.00   0.0  0
 7Z6  CONST_37  H5   C8   N20  C15   180.00   0.0  0
 7Z6  CONST_38  H10  C3   C11  C9    180.00   0.0  0
 7Z6  CONST_39  H13  N22  C16  C17   180.00   0.0  0
 7Z6  CONST_40  N21  C15  N24  C18   180.00   0.0  0
 7Z6  CONST_41  N20  C15  N24  C18     0.00   0.0  0
 7Z6  CONST_42  H15  N24  C15  N20   180.00   0.0  0
 7Z6  Var_01    C14  N23  C12  C4    -11.32  30.0  2
 7Z6  Var_02    C12  N23  C14  C13  -177.85  30.0  2
 7Z6  Var_03    H6   C17  C9   C5    -60.44  30.0  1
 7Z6  Var_04    N24  C18  C10  C7     94.58  30.0  2
 7Z6  Var_05    C15  N24  C18  C10  -178.26  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
 7Z6  plan-1  C8   0.020
 7Z6  plan-1  C13  0.020
 7Z6  plan-1  C15  0.020
 7Z6  plan-1  C14  0.020
 7Z6  plan-1  N20  0.020
 7Z6  plan-1  N21  0.020
 7Z6  plan-1  N23  0.020
 7Z6  plan-1  CL1  0.020
 7Z6  plan-1  H5   0.020
 7Z6  plan-1  N24  0.020
 7Z6  plan-2  C6   0.020
 7Z6  plan-2  C7   0.020
 7Z6  plan-2  C10  0.020
 7Z6  plan-2  C1   0.020
 7Z6  plan-2  C2   0.020
 7Z6  plan-2  C18  0.020
 7Z6  plan-2  N19  0.020
 7Z6  plan-2  H4   0.020
 7Z6  plan-2  H8   0.020
 7Z6  plan-2  H9   0.020
 7Z6  plan-2  H3   0.020
 7Z6  plan-3  C15  0.020
 7Z6  plan-3  C18  0.020
 7Z6  plan-3  N24  0.020
 7Z6  plan-3  H15  0.020
 7Z6  plan-4  C4   0.020
 7Z6  plan-4  C5   0.020
 7Z6  plan-4  C17  0.020
 7Z6  plan-4  C3   0.020
 7Z6  plan-4  C9   0.020
 7Z6  plan-4  C11  0.020
 7Z6  plan-4  C12  0.020
 7Z6  plan-4  C16  0.020
 7Z6  plan-4  N22  0.020
 7Z6  plan-4  N23  0.020
 7Z6  plan-4  O25  0.020
 7Z6  plan-4  H1   0.020
 7Z6  plan-4  H2   0.020
 7Z6  plan-4  H10  0.020
 7Z6  plan-4  H13  0.020

