FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: JLJQ9

Calculation Name: 1MZA-A-Xray372

Preferred Name: Granzyme K

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1MZA

Chain ID: A

ChEMBL ID: CHEMBL4930

UniProt ID: P49863

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 236
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2967273.131658
FMO2-HF: Nuclear repulsion 2874334.125879
FMO2-HF: Total energy -92939.005779
FMO2-MP2: Total energy -93205.171329


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:14:MET)


Summations of interaction energy for fragment #1(A:14:MET)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
0.6342.927-0.032-1.256-1.005-0.001
Interaction energy analysis for fragmet #1(A:14:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.061 / q_NPA : -0.053
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A16ILE00.0000.0213.8070.5292.822-0.032-1.256-1.005-0.001
4A17ILE0-0.030-0.0246.4390.8230.8230.0000.0000.0000.000
5A18GLY00.0560.0318.851-0.178-0.1780.0000.0000.0000.000
6A19GLY00.0020.00512.560-0.060-0.0600.0000.0000.0000.000
7A20LYS10.9360.97513.120-0.595-0.5950.0000.0000.0000.000
8A21GLU-1-0.848-0.92515.7370.1650.1650.0000.0000.0000.000
9A22VAL0-0.031-0.00519.2200.0240.0240.0000.0000.0000.000
10A23SER00.0290.01621.679-0.013-0.0130.0000.0000.0000.000
11A24PRO00.0870.09624.189-0.014-0.0140.0000.0000.0000.000
12A25HIS00.0250.01827.180-0.003-0.0030.0000.0000.0000.000
13A26SER0-0.078-0.10325.655-0.004-0.0040.0000.0000.0000.000
14A27ARG10.8530.92722.322-0.176-0.1760.0000.0000.0000.000
15A28PRO00.0180.00128.342-0.008-0.0080.0000.0000.0000.000
16A29PHE00.0140.00827.201-0.005-0.0050.0000.0000.0000.000
17A30MET0-0.066-0.02127.342-0.009-0.0090.0000.0000.0000.000
18A31ALA00.0060.01030.7650.0000.0000.0000.0000.0000.000
19A32SER0-0.016-0.00131.268-0.003-0.0030.0000.0000.0000.000
20A33ILE0-0.010-0.01732.560-0.002-0.0020.0000.0000.0000.000
21A34GLN00.003-0.01832.948-0.004-0.0040.0000.0000.0000.000
22A35TYR00.0360.02536.000-0.002-0.0020.0000.0000.0000.000
23A37GLY00.0080.00837.573-0.001-0.0010.0000.0000.0000.000
24A38GLY00.0030.01037.7160.0010.0010.0000.0000.0000.000
25A39HIS00.0110.01033.3570.0040.0040.0000.0000.0000.000
26A40HIS0-0.017-0.01827.6530.0000.0000.0000.0000.0000.000
27A41VAL0-0.049-0.04031.038-0.005-0.0050.0000.0000.0000.000
28A42CYS0-0.137-0.06929.645-0.010-0.0100.0000.0000.0000.000
29A43GLY00.0660.06728.7720.0080.0080.0000.0000.0000.000
30A44GLY00.0540.00929.752-0.009-0.0090.0000.0000.0000.000
31A45VAL0-0.040-0.01030.4640.0090.0090.0000.0000.0000.000
32A46LEU00.0040.03133.072-0.007-0.0070.0000.0000.0000.000
33A47ILE0-0.055-0.04235.7420.0040.0040.0000.0000.0000.000
34A48ASP-1-0.844-0.94137.9630.0230.0230.0000.0000.0000.000
35A49PRO00.0260.01541.1480.0000.0000.0000.0000.0000.000
36A50GLN0-0.0030.00043.170-0.001-0.0010.0000.0000.0000.000
37A51TRP00.0310.01241.110-0.004-0.0040.0000.0000.0000.000
38A52VAL00.0460.02235.4100.0040.0040.0000.0000.0000.000
39A53LEU0-0.065-0.02734.067-0.005-0.0050.0000.0000.0000.000
40A54THR00.0350.01332.5820.0030.0030.0000.0000.0000.000
41A55ALA00.0270.01831.155-0.002-0.0020.0000.0000.0000.000
42A56ALA0-0.007-0.00833.2540.0020.0020.0000.0000.0000.000
43A57HIS00.000-0.01330.942-0.001-0.0010.0000.0000.0000.000
44A59GLN00.0240.02134.7140.0030.0030.0000.0000.0000.000
45A60TYR00.017-0.00437.659-0.003-0.0030.0000.0000.0000.000
46A60ARG10.8670.90339.2920.0340.0340.0000.0000.0000.000
47A60PHE0-0.0040.01338.8890.0000.0000.0000.0000.0000.000
48A60THR00.0270.00942.3980.0010.0010.0000.0000.0000.000
49A60LYS10.9590.99144.8790.0120.0120.0000.0000.0000.000
50A61GLY00.016-0.00346.4690.0020.0020.0000.0000.0000.000
51A62GLN0-0.023-0.01240.4170.0010.0010.0000.0000.0000.000
52A63SER00.0160.00342.0280.0000.0000.0000.0000.0000.000
53A64PRO00.0060.02240.6360.0020.0020.0000.0000.0000.000
54A65THR0-0.028-0.02339.5310.0030.0030.0000.0000.0000.000
55A66VAL00.012-0.00236.470-0.001-0.0010.0000.0000.0000.000
56A67VAL0-0.0020.01534.7260.0010.0010.0000.0000.0000.000
57A68LEU00.006-0.02334.5560.0030.0030.0000.0000.0000.000
58A69GLY00.0340.02034.0070.0000.0000.0000.0000.0000.000
59A70ALA00.0020.00531.9640.0010.0010.0000.0000.0000.000
60A71HIS0-0.089-0.04723.916-0.007-0.0070.0000.0000.0000.000
61A72SER0-0.034-0.03227.2770.0010.0010.0000.0000.0000.000
62A73LEU0-0.007-0.00827.614-0.007-0.0070.0000.0000.0000.000
63A74SER0-0.062-0.02629.541-0.005-0.0050.0000.0000.0000.000
64A75LYS10.9791.00028.438-0.093-0.0930.0000.0000.0000.000
65A76ASN00.0410.02932.999-0.002-0.0020.0000.0000.0000.000
66A77GLU-1-0.735-0.88930.9090.0940.0940.0000.0000.0000.000
67A78ALA00.0200.00835.720-0.004-0.0040.0000.0000.0000.000
68A79SER0-0.076-0.04334.830-0.002-0.0020.0000.0000.0000.000
69A80LYS10.8040.89932.717-0.061-0.0610.0000.0000.0000.000
70A81GLN0-0.045-0.02637.383-0.007-0.0070.0000.0000.0000.000
71A82THR00.0390.02038.9280.0000.0000.0000.0000.0000.000
72A83LEU0-0.039-0.01340.578-0.001-0.0010.0000.0000.0000.000
73A84GLU-1-0.868-0.93241.7610.0110.0110.0000.0000.0000.000
74A85ILE0-0.025-0.00539.2540.0010.0010.0000.0000.0000.000
75A86LYS10.8600.93943.750-0.011-0.0110.0000.0000.0000.000
76A87LYS10.9340.95345.252-0.003-0.0030.0000.0000.0000.000
77A88PHE00.0330.01539.2390.0020.0020.0000.0000.0000.000
78A89ILE0-0.020-0.01142.273-0.001-0.0010.0000.0000.0000.000
79A90PRO00.0700.02240.0380.0020.0020.0000.0000.0000.000
80A91PHE0-0.009-0.01439.4650.0000.0000.0000.0000.0000.000
81A92SER00.0260.00341.251-0.002-0.0020.0000.0000.0000.000
82A93ARG0-0.019-0.01436.9560.0000.0000.0000.0000.0000.000
83A94VAL00.0240.02243.5450.0010.0010.0000.0000.0000.000
84A95THR00.002-0.01341.0590.0000.0000.0000.0000.0000.000
85A96SER0-0.088-0.04540.180-0.001-0.0010.0000.0000.0000.000
86A97ASP-1-0.830-0.91937.482-0.070-0.0700.0000.0000.0000.000
87A98PRO0-0.039-0.01132.9300.0040.0040.0000.0000.0000.000
88A99GLN00.0250.00129.1320.0000.0000.0000.0000.0000.000
89A100SER00.0670.02432.8240.0010.0010.0000.0000.0000.000
90A101ASN0-0.0230.03735.4430.0060.0060.0000.0000.0000.000
91A102ASP-1-0.696-0.84131.703-0.034-0.0340.0000.0000.0000.000
92A103ILE0-0.061-0.03033.1770.0030.0030.0000.0000.0000.000
93A104MET0-0.019-0.01235.505-0.003-0.0030.0000.0000.0000.000
94A105LEU0-0.0200.00937.2840.0040.0040.0000.0000.0000.000
95A106VAL00.009-0.00238.202-0.003-0.0030.0000.0000.0000.000
96A107LYS10.8890.97340.864-0.007-0.0070.0000.0000.0000.000
97A108LEU00.016-0.00440.209-0.001-0.0010.0000.0000.0000.000
98A109GLN00.011-0.00244.235-0.001-0.0010.0000.0000.0000.000
99A110THR0-0.017-0.00546.2120.0000.0000.0000.0000.0000.000
100A111ALA00.005-0.01245.5270.0000.0000.0000.0000.0000.000
101A112ALA00.0070.01241.0690.0010.0010.0000.0000.0000.000
102A113LYS10.9340.96342.930-0.036-0.0360.0000.0000.0000.000
103A114LEU00.0380.02140.4330.0030.0030.0000.0000.0000.000
104A115ASN00.020-0.00438.4550.0030.0030.0000.0000.0000.000
105A116LYS10.9630.96735.847-0.075-0.0750.0000.0000.0000.000
106A117HIS00.0210.01633.2950.0000.0000.0000.0000.0000.000
107A118VAL0-0.0100.02834.4300.0000.0000.0000.0000.0000.000
108A119LYS10.9470.97133.926-0.075-0.0750.0000.0000.0000.000
109A120MET00.0130.01935.912-0.001-0.0010.0000.0000.0000.000
110A121LEU0-0.045-0.02230.2390.0050.0050.0000.0000.0000.000
111A122HIS00.0390.01434.666-0.005-0.0050.0000.0000.0000.000
112A123ILE00.0100.00734.1330.0020.0020.0000.0000.0000.000
113A124ARG10.8480.93031.2130.0010.0010.0000.0000.0000.000
114A125SER00.0260.00834.471-0.004-0.0040.0000.0000.0000.000
115A126LYS10.9670.95436.398-0.021-0.0210.0000.0000.0000.000
116A128THR0-0.0140.01430.618-0.003-0.0030.0000.0000.0000.000
117A129SER00.0210.01531.894-0.004-0.0040.0000.0000.0000.000
118A130LEU00.002-0.01324.8880.0080.0080.0000.0000.0000.000
119A131ARG10.9811.00025.211-0.013-0.0130.0000.0000.0000.000
120A132SER00.0360.03123.0450.0050.0050.0000.0000.0000.000
121A133GLY00.002-0.01219.5170.0030.0030.0000.0000.0000.000
122A134THR0-0.110-0.07419.4140.0220.0220.0000.0000.0000.000
123A135LYS11.0091.01816.313-0.291-0.2910.0000.0000.0000.000
124A136CYS0-0.061-0.04118.6960.0010.0010.0000.0000.0000.000
125A137LYN00.0170.01116.7700.0290.0290.0000.0000.0000.000
126A138VAL00.0050.02019.741-0.022-0.0220.0000.0000.0000.000
127A139THR0-0.024-0.01020.7210.0270.0270.0000.0000.0000.000
128A140GLY00.022-0.00423.108-0.020-0.0200.0000.0000.0000.000
129A141TRP00.0060.00323.2510.0130.0130.0000.0000.0000.000
130A142GLY0-0.0300.00222.259-0.007-0.0070.0000.0000.0000.000
131A143ALA0-0.019-0.01721.2090.0210.0210.0000.0000.0000.000
132A144THR0-0.003-0.02915.8830.0050.0050.0000.0000.0000.000
133A145ASP-1-0.895-0.92316.143-0.041-0.0410.0000.0000.0000.000
134A146PRO00.014-0.04416.9810.0190.0190.0000.0000.0000.000
135A147ASP-1-0.888-0.92419.918-0.177-0.1770.0000.0000.0000.000
136A148SER0-0.051-0.01021.9250.0150.0150.0000.0000.0000.000
137A148LEU00.0410.00123.5390.0030.0030.0000.0000.0000.000
138A149ARG10.8140.90025.8170.0130.0130.0000.0000.0000.000
139A151PRO00.0060.00724.534-0.003-0.0030.0000.0000.0000.000
140A152SER00.0140.02021.2040.0090.0090.0000.0000.0000.000
141A153ASP-1-0.770-0.88623.0960.0780.0780.0000.0000.0000.000
142A154THR0-0.0070.00122.275-0.006-0.0060.0000.0000.0000.000
143A155LEU0-0.0070.00623.0710.0010.0010.0000.0000.0000.000
144A156ARG10.9050.94416.160-0.185-0.1850.0000.0000.0000.000
145A157GLU-1-0.917-0.97018.0800.2290.2290.0000.0000.0000.000
146A158VAL00.0100.01115.7770.0570.0570.0000.0000.0000.000
147A159THR0-0.003-0.02013.077-0.034-0.0340.0000.0000.0000.000
148A160VAL0-0.0210.00414.554-0.008-0.0080.0000.0000.0000.000
149A161THR0-0.019-0.01814.9350.0350.0350.0000.0000.0000.000
150A162VAL0-0.033-0.00717.463-0.028-0.0280.0000.0000.0000.000
151A163LEU00.0660.03017.486-0.005-0.0050.0000.0000.0000.000
152A164SER0-0.016-0.01221.3220.0170.0170.0000.0000.0000.000
153A165ARG10.8750.90324.4960.0680.0680.0000.0000.0000.000
154A166LYS10.9380.97526.3340.1310.1310.0000.0000.0000.000
155A167LEU00.0170.01819.9360.0020.0020.0000.0000.0000.000
156A168CYS00.0280.05622.342-0.013-0.0130.0000.0000.0000.000
157A169ASN00.006-0.00124.499-0.002-0.0020.0000.0000.0000.000
158A170SER0-0.054-0.03924.364-0.003-0.0030.0000.0000.0000.000
159A170GLN00.0550.01126.701-0.018-0.0180.0000.0000.0000.000
160A170SER0-0.0120.00421.799-0.010-0.0100.0000.0000.0000.000
161A171TYR0-0.013-0.01817.889-0.019-0.0190.0000.0000.0000.000
162A172TYR00.041-0.01822.912-0.003-0.0030.0000.0000.0000.000
163A173ASN00.0020.01826.6820.0140.0140.0000.0000.0000.000
164A173GLY0-0.069-0.03629.2630.0070.0070.0000.0000.0000.000
165A173ASP-1-0.962-0.95830.672-0.100-0.1000.0000.0000.0000.000
166A174PRO00.0740.03728.357-0.007-0.0070.0000.0000.0000.000
167A175PHE00.0060.00029.754-0.004-0.0040.0000.0000.0000.000
168A176ILE00.0500.01426.9240.0110.0110.0000.0000.0000.000
169A177THR00.0670.03830.3050.0030.0030.0000.0000.0000.000
170A178LYS10.9350.94731.7490.0430.0430.0000.0000.0000.000
171A179ASP-1-0.904-0.94133.126-0.029-0.0290.0000.0000.0000.000
172A180MET0-0.0030.01729.5130.0040.0040.0000.0000.0000.000
173A181VAL0-0.041-0.02724.6190.0000.0000.0000.0000.0000.000
174A183ALA0-0.005-0.00819.7320.0080.0080.0000.0000.0000.000
175A184GLY00.0550.03216.639-0.001-0.0010.0000.0000.0000.000
176A185ASP-1-0.758-0.85510.916-0.412-0.4120.0000.0000.0000.000
177A186ALA0-0.022-0.02310.062-0.011-0.0110.0000.0000.0000.000
178A187LYS10.9380.97711.0970.9270.9270.0000.0000.0000.000
179A188GLY00.025-0.00213.0790.0230.0230.0000.0000.0000.000
180A188GLN0-0.027-0.01812.050-0.038-0.0380.0000.0000.0000.000
181A188LYS10.8360.90815.5630.1300.1300.0000.0000.0000.000
182A189ASP-1-0.833-0.93112.708-0.120-0.1200.0000.0000.0000.000
183A190SER0-0.104-0.02915.7910.0290.0290.0000.0000.0000.000
184A191CYS0-0.0170.01618.170-0.038-0.0380.0000.0000.0000.000
185A192LYS11.0020.99421.2030.0500.0500.0000.0000.0000.000
186A193GLY00.0030.01424.6430.0130.0130.0000.0000.0000.000
187A194ASP-1-0.804-0.88622.932-0.023-0.0230.0000.0000.0000.000
188A195ALA00.0110.01024.9350.0060.0060.0000.0000.0000.000
189A196GLY00.015-0.01427.7670.0080.0080.0000.0000.0000.000
190A197GLY00.0110.02426.9130.0060.0060.0000.0000.0000.000
191A198PRO0-0.050-0.02526.361-0.009-0.0090.0000.0000.0000.000
192A199LEU00.0070.02022.2010.0110.0110.0000.0000.0000.000
193A200ILE0-0.014-0.03023.942-0.006-0.0060.0000.0000.0000.000
194A202LYS10.9230.95823.446-0.080-0.0800.0000.0000.0000.000
195A207GLY00.0440.01925.790-0.007-0.0070.0000.0000.0000.000
196A208VAL0-0.0270.00727.765-0.006-0.0060.0000.0000.0000.000
197A209PHE00.0470.02528.0290.0020.0020.0000.0000.0000.000
198A210HIS00.026-0.01627.275-0.014-0.0140.0000.0000.0000.000
199A211ALA0-0.015-0.00627.297-0.009-0.0090.0000.0000.0000.000
200A212ILE00.0360.04528.2520.0100.0100.0000.0000.0000.000
201A213VAL0-0.0140.01624.152-0.009-0.0090.0000.0000.0000.000
202A214SER00.0220.00626.8940.0040.0040.0000.0000.0000.000
203A215GLY0-0.007-0.02327.066-0.003-0.0030.0000.0000.0000.000
204A216GLY0-0.041-0.01728.704-0.004-0.0040.0000.0000.0000.000
205A217HIS0-0.0060.01024.139-0.011-0.0110.0000.0000.0000.000
206A219GLU-1-0.907-0.95022.109-0.180-0.1800.0000.0000.0000.000
207A221GLY00.0470.01215.236-0.009-0.0090.0000.0000.0000.000
208A222VAL00.0420.03716.264-0.061-0.0610.0000.0000.0000.000
209A223ALA00.006-0.01114.6090.0140.0140.0000.0000.0000.000
210A223THR0-0.107-0.05816.2870.0440.0440.0000.0000.0000.000
211A224LYS10.9711.00918.6380.3340.3340.0000.0000.0000.000
212A225PRO0-0.0250.01518.6970.0160.0160.0000.0000.0000.000
213A226GLY00.0270.01919.6370.0150.0150.0000.0000.0000.000
214A227ILE00.0410.01221.5410.0010.0010.0000.0000.0000.000
215A228TYR0-0.040-0.02420.8560.0090.0090.0000.0000.0000.000
216A229THR00.017-0.00426.873-0.009-0.0090.0000.0000.0000.000
217A230LEU0-0.028-0.01828.6650.0100.0100.0000.0000.0000.000
218A231LEU00.0770.04431.108-0.002-0.0020.0000.0000.0000.000
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