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: LZ8N9

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 OptAll
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 -2969396.704321
FMO2-HF: Nuclear repulsion 2876455.176366
FMO2-HF: Total energy -92941.527955
FMO2-MP2: Total energy -93207.504585


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.
1.7323.632-0.007-1.072-0.820.002
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 : 0.009 / q_NPA : -0.008
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].
3A16ILE0-0.034-0.0133.807-0.9490.951-0.007-1.072-0.8200.002
4A17ILE0-0.019-0.0105.7740.2660.2660.0000.0000.0000.000
5A18GLY00.0320.0147.4920.1180.1180.0000.0000.0000.000
6A19GLY00.0170.02111.3280.0560.0560.0000.0000.0000.000
7A20LYS10.8740.93613.4200.2370.2370.0000.0000.0000.000
8A21GLU-1-0.705-0.82714.654-0.191-0.1910.0000.0000.0000.000
9A22VAL0-0.073-0.02917.9270.0210.0210.0000.0000.0000.000
10A23SER00.0590.02220.5540.0160.0160.0000.0000.0000.000
11A24PRO00.0580.03723.010-0.011-0.0110.0000.0000.0000.000
12A25HIS0-0.009-0.00425.9630.0090.0090.0000.0000.0000.000
13A26SER0-0.079-0.04524.2950.0010.0010.0000.0000.0000.000
14A27ARG10.8020.87521.0280.1420.1420.0000.0000.0000.000
15A28PRO00.0410.01927.396-0.008-0.0080.0000.0000.0000.000
16A29PHE00.0090.01826.5000.0050.0050.0000.0000.0000.000
17A30MET0-0.056-0.01326.195-0.007-0.0070.0000.0000.0000.000
18A31ALA0-0.018-0.00329.7440.0110.0110.0000.0000.0000.000
19A32SER0-0.003-0.01730.000-0.011-0.0110.0000.0000.0000.000
20A33ILE00.007-0.00631.2250.0140.0140.0000.0000.0000.000
21A34GLN0-0.011-0.02932.008-0.006-0.0060.0000.0000.0000.000
22A35TYR00.0410.02134.8630.0050.0050.0000.0000.0000.000
23A37GLY0-0.0030.00436.733-0.004-0.0040.0000.0000.0000.000
24A38GLY00.0030.01236.5370.0020.0020.0000.0000.0000.000
25A39HIS00.0160.02332.698-0.015-0.0150.0000.0000.0000.000
26A40HIS0-0.0200.01026.7990.0160.0160.0000.0000.0000.000
27A41VAL0-0.018-0.01830.039-0.010-0.0100.0000.0000.0000.000
28A42CYS0-0.109-0.03428.553-0.021-0.0210.0000.0000.0000.000
29A43GLY00.0490.04427.5670.0120.0120.0000.0000.0000.000
30A44GLY00.0560.02228.5030.0030.0030.0000.0000.0000.000
31A45VAL0-0.050-0.02529.882-0.001-0.0010.0000.0000.0000.000
32A46LEU00.0110.01632.2860.0040.0040.0000.0000.0000.000
33A47ILE0-0.032-0.03435.3830.0000.0000.0000.0000.0000.000
34A48ASP-1-0.789-0.90837.515-0.070-0.0700.0000.0000.0000.000
35A49PRO00.0150.00140.475-0.004-0.0040.0000.0000.0000.000
36A50GLN0-0.0090.00142.2650.0000.0000.0000.0000.0000.000
37A51TRP00.0240.01740.725-0.004-0.0040.0000.0000.0000.000
38A52VAL00.0120.00634.6050.0000.0000.0000.0000.0000.000
39A53LEU0-0.041-0.01733.8170.0020.0020.0000.0000.0000.000
40A54THR00.021-0.00331.631-0.008-0.0080.0000.0000.0000.000
41A55ALA00.0480.02630.6450.0040.0040.0000.0000.0000.000
42A56ALA0-0.025-0.01832.7560.0070.0070.0000.0000.0000.000
43A57HIS00.036-0.00130.0410.0080.0080.0000.0000.0000.000
44A59GLN00.0150.02033.8800.0050.0050.0000.0000.0000.000
45A60TYR00.0600.02336.334-0.006-0.0060.0000.0000.0000.000
46A60ARG10.8040.86738.1720.1500.1500.0000.0000.0000.000
47A60PHE00.0000.01737.9630.0050.0050.0000.0000.0000.000
48A60THR0-0.015-0.02141.3870.0050.0050.0000.0000.0000.000
49A60LYS10.9560.98043.7320.0850.0850.0000.0000.0000.000
50A61GLY00.0310.00744.9250.0050.0050.0000.0000.0000.000
51A62GLN00.0160.02140.102-0.005-0.0050.0000.0000.0000.000
52A63SER00.0380.01140.890-0.004-0.0040.0000.0000.0000.000
53A64PRO00.0120.03039.581-0.003-0.0030.0000.0000.0000.000
54A65THR0-0.015-0.02338.2870.0050.0050.0000.0000.0000.000
55A66VAL00.001-0.00434.824-0.009-0.0090.0000.0000.0000.000
56A67VAL0-0.0200.00233.4280.0090.0090.0000.0000.0000.000
57A68LEU00.0210.00333.325-0.008-0.0080.0000.0000.0000.000
58A69GLY00.0360.01533.2760.0040.0040.0000.0000.0000.000
59A70ALA0-0.0130.00030.7710.0070.0070.0000.0000.0000.000
60A71HIS0-0.061-0.03822.6370.0000.0000.0000.0000.0000.000
61A72SER0-0.022-0.02826.090-0.014-0.0140.0000.0000.0000.000
62A73LEU0-0.011-0.00326.8030.0110.0110.0000.0000.0000.000
63A74SER0-0.046-0.05828.6530.0140.0140.0000.0000.0000.000
64A75LYS10.8720.93227.1650.1280.1280.0000.0000.0000.000
65A76ASN00.0290.01732.202-0.007-0.0070.0000.0000.0000.000
66A77GLU-1-0.693-0.86329.867-0.099-0.0990.0000.0000.0000.000
67A78ALA00.0080.00134.455-0.002-0.0020.0000.0000.0000.000
68A79SER0-0.031-0.01633.5790.0030.0030.0000.0000.0000.000
69A80LYS10.7750.88731.8230.1020.1020.0000.0000.0000.000
70A81GLN00.0250.00736.3310.0070.0070.0000.0000.0000.000
71A82THR00.0310.01837.785-0.007-0.0070.0000.0000.0000.000
72A83LEU0-0.049-0.01739.0910.0060.0060.0000.0000.0000.000
73A84GLU-1-0.816-0.89740.416-0.082-0.0820.0000.0000.0000.000
74A85ILE0-0.040-0.01338.2330.0010.0010.0000.0000.0000.000
75A86LYS10.8140.90942.7760.0710.0710.0000.0000.0000.000
76A87LYS10.9570.97344.5680.0840.0840.0000.0000.0000.000
77A88PHE00.0310.01237.953-0.001-0.0010.0000.0000.0000.000
78A89ILE0-0.027-0.01841.3200.0050.0050.0000.0000.0000.000
79A90PRO00.0600.02739.370-0.004-0.0040.0000.0000.0000.000
80A91PHE00.006-0.00739.2650.0070.0070.0000.0000.0000.000
81A92SER00.008-0.00141.003-0.002-0.0020.0000.0000.0000.000
82A93ARG0-0.0190.03037.3200.0030.0030.0000.0000.0000.000
83A94VAL00.0370.01943.2690.0020.0020.0000.0000.0000.000
84A95THR00.0180.01341.2530.0030.0030.0000.0000.0000.000
85A96SER0-0.075-0.05040.258-0.005-0.0050.0000.0000.0000.000
86A97ASP-1-0.799-0.90837.777-0.165-0.1650.0000.0000.0000.000
87A98PRO00.0150.00332.734-0.001-0.0010.0000.0000.0000.000
88A99GLN0-0.013-0.01429.4190.0090.0090.0000.0000.0000.000
89A100SER0-0.0140.01332.6120.0030.0030.0000.0000.0000.000
90A101ASN0-0.041-0.04035.7030.0070.0070.0000.0000.0000.000
91A102ASP-1-0.682-0.83331.423-0.199-0.1990.0000.0000.0000.000
92A103ILE0-0.074-0.01932.913-0.009-0.0090.0000.0000.0000.000
93A104MET0-0.030-0.00935.2020.0100.0100.0000.0000.0000.000
94A105LEU0-0.0190.01036.576-0.003-0.0030.0000.0000.0000.000
95A106VAL00.006-0.00537.0630.0000.0000.0000.0000.0000.000
96A107LYS10.8420.94340.0810.0800.0800.0000.0000.0000.000
97A108LEU00.0350.00739.0340.0000.0000.0000.0000.0000.000
98A109GLN0-0.001-0.00843.1300.0050.0050.0000.0000.0000.000
99A110THR00.0310.01444.7790.0040.0040.0000.0000.0000.000
100A111ALA00.005-0.00144.507-0.004-0.0040.0000.0000.0000.000
101A112ALA0-0.008-0.00339.7990.0020.0020.0000.0000.0000.000
102A113LYS10.8660.93041.8820.0630.0630.0000.0000.0000.000
103A114LEU00.0340.00839.524-0.002-0.0020.0000.0000.0000.000
104A115ASN00.007-0.00537.1890.0050.0050.0000.0000.0000.000
105A116LYS10.9690.97134.8580.0270.0270.0000.0000.0000.000
106A117HIS00.0370.02031.771-0.003-0.0030.0000.0000.0000.000
107A118VAL0-0.0210.00533.413-0.009-0.0090.0000.0000.0000.000
108A119LYS10.9100.96133.8380.0850.0850.0000.0000.0000.000
109A120MET00.0050.01934.502-0.005-0.0050.0000.0000.0000.000
110A121LEU0-0.041-0.02529.5680.0050.0050.0000.0000.0000.000
111A122HIS00.0430.01833.978-0.009-0.0090.0000.0000.0000.000
112A123ILE00.0260.01933.935-0.006-0.0060.0000.0000.0000.000
113A124ARG10.8400.91930.8790.1580.1580.0000.0000.0000.000
114A125SER00.0360.02034.558-0.001-0.0010.0000.0000.0000.000
115A126LYS10.9700.96336.6100.0700.0700.0000.0000.0000.000
116A128THR0-0.0030.01430.9540.0020.0020.0000.0000.0000.000
117A129SER00.0370.02432.176-0.009-0.0090.0000.0000.0000.000
118A130LEU0-0.012-0.01724.9020.0020.0020.0000.0000.0000.000
119A131ARG10.9630.99324.0500.1570.1570.0000.0000.0000.000
120A132SER00.0800.03922.950-0.007-0.0070.0000.0000.0000.000
121A133GLY00.0010.00319.5710.0230.0230.0000.0000.0000.000
122A134THR0-0.113-0.07519.8290.0210.0210.0000.0000.0000.000
123A135LYS10.9931.00815.6650.1940.1940.0000.0000.0000.000
124A136CYS0-0.069-0.03618.7730.0310.0310.0000.0000.0000.000
125A137LYN0-0.005-0.00316.931-0.022-0.0220.0000.0000.0000.000
126A138VAL00.0040.00219.3860.0230.0230.0000.0000.0000.000
127A139THR0-0.009-0.00319.915-0.015-0.0150.0000.0000.0000.000
128A140GLY00.037-0.00122.1350.0120.0120.0000.0000.0000.000
129A141TRP0-0.023-0.01122.079-0.016-0.0160.0000.0000.0000.000
130A142GLY0-0.0260.00021.2180.0030.0030.0000.0000.0000.000
131A143ALA0-0.011-0.01620.023-0.007-0.0070.0000.0000.0000.000
132A144THR0-0.026-0.04714.8900.0010.0010.0000.0000.0000.000
133A145ASP-1-0.868-0.89815.127-0.637-0.6370.0000.0000.0000.000
134A146PRO00.017-0.02616.4550.0580.0580.0000.0000.0000.000
135A147ASP-1-0.900-0.94319.469-0.426-0.4260.0000.0000.0000.000
136A148SER0-0.026-0.00121.2150.0550.0550.0000.0000.0000.000
137A148LEU00.023-0.00722.9850.0080.0080.0000.0000.0000.000
138A149ARG10.7830.86824.9690.2210.2210.0000.0000.0000.000
139A151PRO00.0190.01623.771-0.025-0.0250.0000.0000.0000.000
140A152SER00.0060.00620.4200.0000.0000.0000.0000.0000.000
141A153ASP-1-0.723-0.81322.335-0.128-0.1280.0000.0000.0000.000
142A154THR0-0.028-0.02621.2410.0110.0110.0000.0000.0000.000
143A155LEU0-0.0230.02122.269-0.030-0.0300.0000.0000.0000.000
144A156ARG10.8510.90316.1280.3360.3360.0000.0000.0000.000
145A157GLU-1-0.818-0.89317.145-0.176-0.1760.0000.0000.0000.000
146A158VAL00.0220.02215.039-0.041-0.0410.0000.0000.0000.000
147A159THR0-0.062-0.03913.0070.0950.0950.0000.0000.0000.000
148A160VAL00.0430.03114.564-0.077-0.0770.0000.0000.0000.000
149A161THR0-0.010-0.00814.9580.0940.0940.0000.0000.0000.000
150A162VAL0-0.029-0.01817.576-0.019-0.0190.0000.0000.0000.000
151A163LEU00.0690.03617.3140.0210.0210.0000.0000.0000.000
152A164SER0-0.025-0.02321.2510.0370.0370.0000.0000.0000.000
153A165ARG10.8980.92424.5780.1820.1820.0000.0000.0000.000
154A166LYS10.9620.99126.9210.2260.2260.0000.0000.0000.000
155A167LEU00.0050.01820.0470.0110.0110.0000.0000.0000.000
156A168CYS00.0180.03522.414-0.014-0.0140.0000.0000.0000.000
157A169ASN00.0390.00624.479-0.002-0.0020.0000.0000.0000.000
158A170SER0-0.045-0.01924.3940.0090.0090.0000.0000.0000.000
159A170GLN00.0650.02026.397-0.025-0.0250.0000.0000.0000.000
160A170SER00.0120.02021.6660.0010.0010.0000.0000.0000.000
161A171TYR0-0.030-0.00617.851-0.067-0.0670.0000.0000.0000.000
162A172TYR00.048-0.00523.0580.0020.0020.0000.0000.0000.000
163A173ASN0-0.030-0.00626.6200.0210.0210.0000.0000.0000.000
164A173GLY0-0.043-0.01929.2070.0170.0170.0000.0000.0000.000
165A173ASP-1-0.958-0.95930.461-0.201-0.2010.0000.0000.0000.000
166A174PRO00.0620.01828.595-0.015-0.0150.0000.0000.0000.000
167A175PHE0-0.0030.00830.027-0.007-0.0070.0000.0000.0000.000
168A176ILE0-0.006-0.00927.0580.0070.0070.0000.0000.0000.000
169A177THR00.0720.00630.4410.0120.0120.0000.0000.0000.000
170A178LYS10.9380.95132.0890.1240.1240.0000.0000.0000.000
171A179ASP-1-0.841-0.88833.413-0.140-0.1400.0000.0000.0000.000
172A180MET00.0150.04829.6210.0040.0040.0000.0000.0000.000
173A181VAL0-0.041-0.02424.7960.0060.0060.0000.0000.0000.000
174A183ALA0-0.039-0.02619.7610.0180.0180.0000.0000.0000.000
175A184GLY00.0930.04516.5390.0030.0030.0000.0000.0000.000
176A185ASP-1-0.774-0.87910.576-1.261-1.2610.0000.0000.0000.000
177A186ALA0-0.031-0.01910.4970.1190.1190.0000.0000.0000.000
178A187LYS10.9200.9698.4332.4022.4020.0000.0000.0000.000
179A188GLY00.0070.00312.9040.0950.0950.0000.0000.0000.000
180A188GLN0-0.057-0.03811.4480.0990.0990.0000.0000.0000.000
181A188LYS10.7930.88115.4590.4890.4890.0000.0000.0000.000
182A189ASP-1-0.839-0.92112.473-1.132-1.1320.0000.0000.0000.000
183A190SER0-0.049-0.01915.0940.0140.0140.0000.0000.0000.000
184A191CYS0-0.0060.02317.7800.0020.0020.0000.0000.0000.000
185A192LYS10.9670.98520.0740.2950.2950.0000.0000.0000.000
186A193GLY00.0280.01923.6390.0060.0060.0000.0000.0000.000
187A194ASP-1-0.817-0.91121.814-0.355-0.3550.0000.0000.0000.000
188A195ALA00.0200.01523.8780.0130.0130.0000.0000.0000.000
189A196GLY00.019-0.01526.9060.0140.0140.0000.0000.0000.000
190A197GLY00.0090.01625.8980.0160.0160.0000.0000.0000.000
191A198PRO0-0.058-0.01825.780-0.003-0.0030.0000.0000.0000.000
192A199LEU00.0130.01622.275-0.019-0.0190.0000.0000.0000.000
193A200ILE0-0.006-0.01723.7260.0250.0250.0000.0000.0000.000
194A202LYS10.9450.95523.6120.1200.1200.0000.0000.0000.000
195A207GLY00.0540.03825.6870.0130.0130.0000.0000.0000.000
196A208VAL0-0.035-0.00627.5580.0070.0070.0000.0000.0000.000
197A209PHE00.0460.01628.029-0.017-0.0170.0000.0000.0000.000
198A210HIS00.010-0.00827.3570.0080.0080.0000.0000.0000.000
199A211ALA0-0.006-0.00427.1510.0050.0050.0000.0000.0000.000
200A212ILE00.0070.02228.2850.0010.0010.0000.0000.0000.000
201A213VAL0-0.025-0.01123.554-0.006-0.0060.0000.0000.0000.000
202A214SER00.0250.00726.4090.0130.0130.0000.0000.0000.000
203A215GLY00.004-0.00426.824-0.024-0.0240.0000.0000.0000.000
204A216GLY0-0.014-0.01028.4940.0020.0020.0000.0000.0000.000
205A217HIS0-0.031-0.01923.6240.0040.0040.0000.0000.0000.000
206A219GLU-1-0.861-0.93121.787-0.442-0.4420.0000.0000.0000.000
207A221GLY00.0480.02014.7350.0080.0080.0000.0000.0000.000
208A222VAL00.0040.01515.734-0.047-0.0470.0000.0000.0000.000
209A223ALA00.0250.00114.4520.0110.0110.0000.0000.0000.000
210A223THR0-0.075-0.06316.1880.0830.0830.0000.0000.0000.000
211A224LYS10.9150.98018.6330.5900.5900.0000.0000.0000.000
212A225PRO0-0.0160.01218.694-0.020-0.0200.0000.0000.0000.000
213A226GLY00.0230.01919.6620.0420.0420.0000.0000.0000.000
214A227ILE00.0210.00121.7270.0130.0130.0000.0000.0000.000
215A228TYR0-0.020-0.00820.857-0.002-0.0020.0000.0000.0000.000
216A229THR00.005-0.01026.9910.0050.0050.0000.0000.0000.000
217A230LEU0-0.033-0.01528.8270.0070.0070.0000.0000.0000.000
218A231LEU00.0650.03531.2130.0130.0130.0000.0000.0000.000
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