Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 39YJL

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 OptHSide
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
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2967692.966065
FMO2-HF: Nuclear repulsion 2874752.491085
FMO2-HF: Total energy -92940.47498
FMO2-MP2: Total energy -93206.494186


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.
0.8173.294-0.033-1.367-1.076-0.001
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 : -0.060 / q_NPA : -0.051
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].
3A16ILE0-0.036-0.0053.8070.3402.817-0.033-1.367-1.076-0.001
4A17ILE0-0.017-0.0196.5130.8030.8030.0000.0000.0000.000
5A18GLY00.0340.0208.851-0.181-0.1810.0000.0000.0000.000
6A19GLY00.0060.00612.545-0.054-0.0540.0000.0000.0000.000
7A20LYS10.8710.93614.125-0.319-0.3190.0000.0000.0000.000
8A21GLU-1-0.775-0.87315.7370.1180.1180.0000.0000.0000.000
9A22VAL0-0.061-0.01919.2200.0210.0210.0000.0000.0000.000
10A23SER00.0490.02221.679-0.007-0.0070.0000.0000.0000.000
11A24PRO00.0450.02724.189-0.011-0.0110.0000.0000.0000.000
12A25HIS00.0150.01627.180-0.003-0.0030.0000.0000.0000.000
13A26SER0-0.042-0.03125.497-0.004-0.0040.0000.0000.0000.000
14A27ARG10.8070.88722.114-0.147-0.1470.0000.0000.0000.000
15A28PRO00.0180.00128.342-0.007-0.0070.0000.0000.0000.000
16A29PHE00.0060.00527.161-0.004-0.0040.0000.0000.0000.000
17A30MET0-0.066-0.01727.099-0.008-0.0080.0000.0000.0000.000
18A31ALA0-0.0020.00630.7620.0000.0000.0000.0000.0000.000
19A32SER0-0.017-0.02331.303-0.003-0.0030.0000.0000.0000.000
20A33ILE0-0.006-0.02032.560-0.001-0.0010.0000.0000.0000.000
21A34GLN00.011-0.01833.102-0.003-0.0030.0000.0000.0000.000
22A35TYR00.0520.02836.019-0.001-0.0010.0000.0000.0000.000
23A37GLY00.0010.00537.650-0.001-0.0010.0000.0000.0000.000
24A38GLY00.0020.00837.7910.0010.0010.0000.0000.0000.000
25A39HIS00.0190.02133.4980.0020.0020.0000.0000.0000.000
26A40HIS0-0.0150.01127.8180.0010.0010.0000.0000.0000.000
27A41VAL0-0.035-0.02831.115-0.005-0.0050.0000.0000.0000.000
28A42CYS0-0.126-0.06029.632-0.010-0.0100.0000.0000.0000.000
29A43GLY00.0620.06328.7490.0070.0070.0000.0000.0000.000
30A44GLY00.0530.02029.729-0.008-0.0080.0000.0000.0000.000
31A45VAL0-0.037-0.00830.5350.0080.0080.0000.0000.0000.000
32A46LEU00.0050.02933.047-0.006-0.0060.0000.0000.0000.000
33A47ILE0-0.036-0.03435.6990.0040.0040.0000.0000.0000.000
34A48ASP-1-0.811-0.92537.9380.0160.0160.0000.0000.0000.000
35A49PRO00.0300.01541.1200.0000.0000.0000.0000.0000.000
36A50GLN00.0150.02543.141-0.001-0.0010.0000.0000.0000.000
37A51TRP00.0280.01341.084-0.004-0.0040.0000.0000.0000.000
38A52VAL00.0290.01035.3900.0040.0040.0000.0000.0000.000
39A53LEU0-0.061-0.02434.137-0.004-0.0040.0000.0000.0000.000
40A54THR00.030-0.00432.5730.0020.0020.0000.0000.0000.000
41A55ALA00.0370.02931.118-0.002-0.0020.0000.0000.0000.000
42A56ALA00.002-0.00833.2400.0020.0020.0000.0000.0000.000
43A57HIS00.016-0.00530.984-0.001-0.0010.0000.0000.0000.000
44A59GLN00.0200.02434.6980.0020.0020.0000.0000.0000.000
45A60TYR00.0280.00137.461-0.005-0.0050.0000.0000.0000.000
46A60ARG10.8490.90339.2780.0360.0360.0000.0000.0000.000
47A60PHE0-0.0030.01338.8310.0000.0000.0000.0000.0000.000
48A60THR00.0150.01142.3410.0010.0010.0000.0000.0000.000
49A60LYS10.9620.99244.8650.0150.0150.0000.0000.0000.000
50A61GLY00.017-0.00246.5290.0020.0020.0000.0000.0000.000
51A62GLN0-0.019-0.01741.090-0.001-0.0010.0000.0000.0000.000
52A63SER00.0150.00242.1050.0000.0000.0000.0000.0000.000
53A64PRO00.0120.02540.6600.0020.0020.0000.0000.0000.000
54A65THR0-0.021-0.02139.6010.0010.0010.0000.0000.0000.000
55A66VAL00.000-0.00436.219-0.001-0.0010.0000.0000.0000.000
56A67VAL0-0.0110.00834.7700.0010.0010.0000.0000.0000.000
57A68LEU00.008-0.01434.5560.0020.0020.0000.0000.0000.000
58A69GLY00.0370.01734.0090.0000.0000.0000.0000.0000.000
59A70ALA0-0.013-0.00231.9310.0010.0010.0000.0000.0000.000
60A71HIS0-0.083-0.05323.847-0.005-0.0050.0000.0000.0000.000
61A72SER0-0.044-0.03627.2900.0010.0010.0000.0000.0000.000
62A73LEU00.010-0.00627.753-0.006-0.0060.0000.0000.0000.000
63A74SER0-0.069-0.05429.519-0.003-0.0030.0000.0000.0000.000
64A75LYS10.8890.94627.963-0.070-0.0700.0000.0000.0000.000
65A76ASN00.0270.02333.062-0.002-0.0020.0000.0000.0000.000
66A77GLU-1-0.707-0.87830.9260.0750.0750.0000.0000.0000.000
67A78ALA00.0260.00935.774-0.004-0.0040.0000.0000.0000.000
68A79SER0-0.059-0.02734.654-0.002-0.0020.0000.0000.0000.000
69A80LYS10.8090.90732.835-0.047-0.0470.0000.0000.0000.000
70A81GLN0-0.049-0.03237.383-0.005-0.0050.0000.0000.0000.000
71A82THR00.0330.01338.9280.0010.0010.0000.0000.0000.000
72A83LEU0-0.039-0.00740.577-0.001-0.0010.0000.0000.0000.000
73A84GLU-1-0.811-0.89341.7610.0040.0040.0000.0000.0000.000
74A85ILE0-0.024-0.00639.1930.0010.0010.0000.0000.0000.000
75A86LYS10.8010.90343.726-0.007-0.0070.0000.0000.0000.000
76A87LYS10.9590.96745.2390.0030.0030.0000.0000.0000.000
77A88PHE00.0220.01039.1840.0010.0010.0000.0000.0000.000
78A89ILE0-0.023-0.01342.256-0.001-0.0010.0000.0000.0000.000
79A90PRO00.0640.01939.9240.0010.0010.0000.0000.0000.000
80A91PHE0-0.019-0.01639.5220.0010.0010.0000.0000.0000.000
81A92SER00.0290.00641.241-0.002-0.0020.0000.0000.0000.000
82A93ARG00.0220.03537.2550.0010.0010.0000.0000.0000.000
83A94VAL00.0200.01543.5410.0010.0010.0000.0000.0000.000
84A95THR00.010-0.00341.1670.0000.0000.0000.0000.0000.000
85A96SER0-0.115-0.08140.114-0.002-0.0020.0000.0000.0000.000
86A97ASP-1-0.808-0.90437.970-0.068-0.0680.0000.0000.0000.000
87A98PRO0-0.043-0.01632.9260.0030.0030.0000.0000.0000.000
88A99GLN00.004-0.00229.047-0.001-0.0010.0000.0000.0000.000
89A100SER00.0630.02632.8230.0010.0010.0000.0000.0000.000
90A101ASN0-0.030-0.00435.4440.0060.0060.0000.0000.0000.000
91A102ASP-1-0.703-0.84331.561-0.039-0.0390.0000.0000.0000.000
92A103ILE0-0.067-0.03233.1660.0030.0030.0000.0000.0000.000
93A104MET0-0.024-0.00835.493-0.002-0.0020.0000.0000.0000.000
94A105LEU0-0.0230.01337.2660.0030.0030.0000.0000.0000.000
95A106VAL0-0.001-0.01038.068-0.002-0.0020.0000.0000.0000.000
96A107LYS10.8580.94840.843-0.004-0.0040.0000.0000.0000.000
97A108LEU00.016-0.00240.139-0.001-0.0010.0000.0000.0000.000
98A109GLN0-0.025-0.02144.209-0.001-0.0010.0000.0000.0000.000
99A110THR00.0450.01246.1460.0000.0000.0000.0000.0000.000
100A111ALA0-0.033-0.02545.5270.0000.0000.0000.0000.0000.000
101A112ALA0-0.0060.00541.0500.0010.0010.0000.0000.0000.000
102A113LYS10.9410.97242.994-0.027-0.0270.0000.0000.0000.000
103A114LEU00.0370.02040.3350.0020.0020.0000.0000.0000.000
104A115ASN00.007-0.00738.4360.0030.0030.0000.0000.0000.000
105A116LYS10.9690.97235.842-0.061-0.0610.0000.0000.0000.000
106A117HIS00.0330.01933.0480.0000.0000.0000.0000.0000.000
107A118VAL0-0.0240.01434.4300.0000.0000.0000.0000.0000.000
108A119LYS10.9510.97534.430-0.059-0.0590.0000.0000.0000.000
109A120MET00.0200.02535.881-0.001-0.0010.0000.0000.0000.000
110A121LEU0-0.051-0.03230.1740.0050.0050.0000.0000.0000.000
111A122HIS00.0360.01334.639-0.004-0.0040.0000.0000.0000.000
112A123ILE00.0120.01334.1110.0020.0020.0000.0000.0000.000
113A124ARG10.8500.93130.9370.0080.0080.0000.0000.0000.000
114A125SER00.0340.01434.453-0.003-0.0030.0000.0000.0000.000
115A126LYS10.9750.96236.361-0.016-0.0160.0000.0000.0000.000
116A128THR0-0.0090.01430.811-0.003-0.0030.0000.0000.0000.000
117A129SER00.0340.02331.863-0.004-0.0040.0000.0000.0000.000
118A130LEU0-0.006-0.02024.7620.0070.0070.0000.0000.0000.000
119A131ARG10.9650.99624.161-0.004-0.0040.0000.0000.0000.000
120A132SER00.0560.03523.0030.0050.0050.0000.0000.0000.000
121A133GLY00.000-0.01119.5160.0040.0040.0000.0000.0000.000
122A134THR0-0.124-0.07519.4090.0200.0200.0000.0000.0000.000
123A135LYS10.9941.01015.986-0.253-0.2530.0000.0000.0000.000
124A136CYS0-0.044-0.03018.6790.0020.0020.0000.0000.0000.000
125A137LYN00.002-0.00317.0030.0240.0240.0000.0000.0000.000
126A138VAL00.0180.02219.718-0.017-0.0170.0000.0000.0000.000
127A139THR0-0.032-0.01720.6950.0240.0240.0000.0000.0000.000
128A140GLY00.0380.00123.111-0.018-0.0180.0000.0000.0000.000
129A141TRP00.0030.00223.2510.0120.0120.0000.0000.0000.000
130A142GLY0-0.0250.00522.243-0.006-0.0060.0000.0000.0000.000
131A143ALA0-0.022-0.01821.2500.0190.0190.0000.0000.0000.000
132A144THR0-0.010-0.03616.0570.0040.0040.0000.0000.0000.000
133A145ASP-1-0.889-0.91716.221-0.055-0.0550.0000.0000.0000.000
134A146PRO00.015-0.02816.9870.0200.0200.0000.0000.0000.000
135A147ASP-1-0.893-0.93119.995-0.182-0.1820.0000.0000.0000.000
136A148SER0-0.043-0.00621.9910.0150.0150.0000.0000.0000.000
137A148LEU00.022-0.00923.6140.0030.0030.0000.0000.0000.000
138A149ARG10.8130.89525.9000.0220.0220.0000.0000.0000.000
139A151PRO00.0120.00924.610-0.004-0.0040.0000.0000.0000.000
140A152SER00.0060.00821.2480.0080.0080.0000.0000.0000.000
141A153ASP-1-0.730-0.83423.1700.0600.0600.0000.0000.0000.000
142A154THR0-0.037-0.02822.182-0.008-0.0080.0000.0000.0000.000
143A155LEU0-0.0100.01023.0960.0010.0010.0000.0000.0000.000
144A156ARG10.9120.95216.470-0.154-0.1540.0000.0000.0000.000
145A157GLU-1-0.818-0.90118.1620.1950.1950.0000.0000.0000.000
146A158VAL00.0160.01615.6300.0520.0520.0000.0000.0000.000
147A159THR0-0.005-0.01013.083-0.026-0.0260.0000.0000.0000.000
148A160VAL00.0040.01114.536-0.009-0.0090.0000.0000.0000.000
149A161THR0-0.023-0.01714.8450.0350.0350.0000.0000.0000.000
150A162VAL0-0.042-0.01317.456-0.024-0.0240.0000.0000.0000.000
151A163LEU00.0740.03617.441-0.003-0.0030.0000.0000.0000.000
152A164SER0-0.016-0.01521.3260.0170.0170.0000.0000.0000.000
153A165ARG10.9050.92924.5030.0660.0660.0000.0000.0000.000
154A166LYS10.9490.97826.5530.1240.1240.0000.0000.0000.000
155A167LEU00.0040.01219.9480.0020.0020.0000.0000.0000.000
156A168CYS00.0280.05122.305-0.012-0.0120.0000.0000.0000.000
157A169ASN00.007-0.00324.510-0.002-0.0020.0000.0000.0000.000
158A170SER0-0.054-0.02524.341-0.002-0.0020.0000.0000.0000.000
159A170GLN00.0740.01926.645-0.014-0.0140.0000.0000.0000.000
160A170SER00.0070.01721.777-0.007-0.0070.0000.0000.0000.000
161A171TYR0-0.035-0.02017.903-0.025-0.0250.0000.0000.0000.000
162A172TYR00.061-0.00422.942-0.003-0.0030.0000.0000.0000.000
163A173ASN0-0.0100.00926.6960.0100.0100.0000.0000.0000.000
164A173GLY0-0.058-0.03229.2800.0070.0070.0000.0000.0000.000
165A173ASP-1-0.954-0.95130.676-0.096-0.0960.0000.0000.0000.000
166A174PRO00.0760.03228.426-0.008-0.0080.0000.0000.0000.000
167A175PHE0-0.0030.00429.763-0.003-0.0030.0000.0000.0000.000
168A176ILE00.015-0.00526.8840.0100.0100.0000.0000.0000.000
169A177THR00.0510.01930.3100.0040.0040.0000.0000.0000.000
170A178LYS10.9410.94831.7500.0410.0410.0000.0000.0000.000
171A179ASP-1-0.836-0.89433.123-0.031-0.0310.0000.0000.0000.000
172A180MET00.0030.02429.5170.0050.0050.0000.0000.0000.000
173A181VAL0-0.028-0.02124.5460.0000.0000.0000.0000.0000.000
174A183ALA0-0.013-0.01319.7210.0080.0080.0000.0000.0000.000
175A184GLY00.0630.03516.636-0.001-0.0010.0000.0000.0000.000
176A185ASP-1-0.778-0.87910.613-0.476-0.4760.0000.0000.0000.000
177A186ALA0-0.023-0.01310.056-0.002-0.0020.0000.0000.0000.000
178A187LYS10.9620.98910.4611.0511.0510.0000.0000.0000.000
179A188GLY00.005-0.00913.0950.0250.0250.0000.0000.0000.000
180A188GLN0-0.050-0.02811.815-0.039-0.0390.0000.0000.0000.000
181A188LYS10.7860.87615.5660.1410.1410.0000.0000.0000.000
182A189ASP-1-0.822-0.92312.887-0.174-0.1740.0000.0000.0000.000
183A190SER0-0.073-0.01415.7790.0260.0260.0000.0000.0000.000
184A191CYS00.0030.02218.221-0.036-0.0360.0000.0000.0000.000
185A192LYS10.9790.99021.1890.0610.0610.0000.0000.0000.000
186A193GLY00.0210.02024.7090.0120.0120.0000.0000.0000.000
187A194ASP-1-0.819-0.90522.893-0.036-0.0360.0000.0000.0000.000
188A195ALA00.0090.01024.9160.0060.0060.0000.0000.0000.000
189A196GLY00.019-0.01227.7510.0080.0080.0000.0000.0000.000
190A197GLY00.0140.02526.8910.0060.0060.0000.0000.0000.000
191A198PRO0-0.043-0.01826.455-0.008-0.0080.0000.0000.0000.000
192A199LEU0-0.0010.01322.3340.0090.0090.0000.0000.0000.000
193A200ILE0-0.021-0.03123.919-0.004-0.0040.0000.0000.0000.000
194A202LYS10.9360.96123.405-0.069-0.0690.0000.0000.0000.000
195A207GLY00.0400.01625.769-0.005-0.0050.0000.0000.0000.000
196A208VAL0-0.0240.00727.737-0.005-0.0050.0000.0000.0000.000
197A209PHE00.0480.01928.0080.0010.0010.0000.0000.0000.000
198A210HIS00.025-0.01427.275-0.012-0.0120.0000.0000.0000.000
199A211ALA0-0.0100.00027.230-0.007-0.0070.0000.0000.0000.000
200A212ILE00.0350.03828.2350.0090.0090.0000.0000.0000.000
201A213VAL0-0.0150.01324.270-0.008-0.0080.0000.0000.0000.000
202A214SER00.0130.00526.8800.0020.0020.0000.0000.0000.000
203A215GLY0-0.004-0.01827.057-0.004-0.0040.0000.0000.0000.000
204A216GLY0-0.039-0.01528.688-0.004-0.0040.0000.0000.0000.000
205A217HIS00.0010.00724.057-0.009-0.0090.0000.0000.0000.000
206A219GLU-1-0.897-0.94821.843-0.184-0.1840.0000.0000.0000.000
207A221GLY00.0450.01515.235-0.007-0.0070.0000.0000.0000.000
208A222VAL00.0390.03216.264-0.058-0.0580.0000.0000.0000.000
209A223ALA00.000-0.01414.7280.0150.0150.0000.0000.0000.000
210A223THR0-0.078-0.05316.3020.0300.0300.0000.0000.0000.000
211A224LYS10.9310.98618.6510.3390.3390.0000.0000.0000.000
212A225PRO0-0.0250.01718.7150.0130.0130.0000.0000.0000.000
213A226GLY00.0240.01919.6240.0150.0150.0000.0000.0000.000
214A227ILE00.016-0.00421.5370.0010.0010.0000.0000.0000.000
215A228TYR00.001-0.00320.9120.0090.0090.0000.0000.0000.000
216A229THR00.003-0.01626.865-0.007-0.0070.0000.0000.0000.000
217A230LEU0-0.039-0.01828.7800.0090.0090.0000.0000.0000.000
218A231LEU00.0770.03931.099-0.001-0.0010.0000.0000.0000.000
219A232THR0-0.070-0.03933.8770.0060.0060.0000.0000.0000.000
220A232LYS10.8720.91136.1510.0040.0040.0000.0000.0000.000
221A233LYS10.8640.95738.1980.0380.0380.0000.0000.0000.000
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