Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 5J3KZ

Calculation Name: 2FZ4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FZ4

Chain ID: A

ChEMBL ID:

UniProt ID: O29889

Base Structure: X-ray

Registration Date: 2023-09-21

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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2400930.174777
FMO2-HF: Nuclear repulsion 2320382.697826
FMO2-HF: Total energy -80547.476951
FMO2-MP2: Total energy -80786.085968


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:24:ILE)


Summations of interaction energy for fragment #1(A:24:ILE)
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.
-10.911-3.7514.344-4.193-7.309-0.038
Interaction energy analysis for fragmet #1(A:24:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.018 / q_NPA : 0.002
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].
3A26GLU-1-0.886-0.9432.568-5.787-2.1600.971-2.083-2.515-0.010
4A27ILE00.0000.0024.9910.4330.472-0.001-0.007-0.0310.000
5A28TYR0-0.031-0.0388.6860.0750.0750.0000.0000.0000.000
6A29TYR00.0080.00011.4440.0310.0310.0000.0000.0000.000
7A30GLU-1-0.806-0.87115.253-0.438-0.4380.0000.0000.0000.000
8A31ARG10.8840.93718.1250.2870.2870.0000.0000.0000.000
9A32GLY00.1120.07020.8650.0220.0220.0000.0000.0000.000
10A33THR0-0.091-0.05418.6420.0030.0030.0000.0000.0000.000
11A34ILE00.0490.03112.694-0.003-0.0030.0000.0000.0000.000
12A35VAL0-0.048-0.02411.6350.0520.0520.0000.0000.0000.000
13A36VAL00.0240.0108.652-0.077-0.0770.0000.0000.0000.000
14A37LYS10.8850.9486.0131.5091.5090.0000.0000.0000.000
15A38GLY00.0460.0274.574-0.877-0.849-0.001-0.0270.0010.000
16A39ASP-1-0.744-0.8655.344-0.558-0.382-0.001-0.007-0.1690.000
17A40ALA0-0.048-0.0277.7610.0810.0810.0000.0000.0000.000
18A41HIS0-0.059-0.03110.6570.1910.1910.0000.0000.0000.000
19A42VAL00.0130.02911.2720.0840.0840.0000.0000.0000.000
20A43PRO00.0360.01413.2350.0570.0570.0000.0000.0000.000
21A44HIS0-0.064-0.04416.727-0.051-0.0510.0000.0000.0000.000
22A45ALA0-0.0020.02915.0600.0220.0220.0000.0000.0000.000
23A46LYS10.9120.95817.0010.3780.3780.0000.0000.0000.000
24A47PHE00.0320.01514.551-0.023-0.0230.0000.0000.0000.000
25A48ASP-1-0.805-0.88317.245-0.329-0.3290.0000.0000.0000.000
26A49SER00.019-0.00418.135-0.018-0.0180.0000.0000.0000.000
27A50ARG10.8110.90019.7810.3690.3690.0000.0000.0000.000
28A51SER0-0.012-0.02316.0640.0370.0370.0000.0000.0000.000
29A52GLY0-0.0220.01015.227-0.029-0.0290.0000.0000.0000.000
30A53THR00.0010.01211.516-0.055-0.0550.0000.0000.0000.000
31A54TYR00.007-0.00512.4530.1300.1300.0000.0000.0000.000
32A55ARG10.7450.84013.5990.4250.4250.0000.0000.0000.000
33A56ALA00.0440.02516.1530.0520.0520.0000.0000.0000.000
34A57LEU0-0.006-0.00617.964-0.011-0.0110.0000.0000.0000.000
35A58ALA00.0350.01418.238-0.031-0.0310.0000.0000.0000.000
36A59PHE0-0.020-0.00118.481-0.035-0.0350.0000.0000.0000.000
37A60ARG10.8340.92117.2920.4070.4070.0000.0000.0000.000
38A61TYR0-0.013-0.03612.6740.0130.0130.0000.0000.0000.000
39A62ARG10.7500.87014.8350.2560.2560.0000.0000.0000.000
40A63ASP-1-0.772-0.87315.901-0.417-0.4170.0000.0000.0000.000
41A64ILE0-0.045-0.02111.304-0.002-0.0020.0000.0000.0000.000
42A65ILE00.0180.02210.455-0.102-0.1020.0000.0000.0000.000
43A66GLU-1-0.785-0.88412.028-0.360-0.3600.0000.0000.0000.000
44A67TYR0-0.083-0.04610.4230.1360.1360.0000.0000.0000.000
45A68PHE00.012-0.0037.915-0.074-0.0740.0000.0000.0000.000
46A69GLU-1-0.903-0.9539.746-0.481-0.4810.0000.0000.0000.000
47A70SER0-0.098-0.07011.3770.1020.1020.0000.0000.0000.000
48A71ASN0-0.112-0.06311.2630.1310.1310.0000.0000.0000.000
49A72GLY0-0.0110.00210.0080.0750.0750.0000.0000.0000.000
50A73ILE0-0.088-0.0345.3620.1620.1620.0000.0000.0000.000
51A74GLU-1-0.891-0.9542.693-1.397-0.8420.761-0.339-0.976-0.002
52A75PHE0-0.054-0.0412.592-3.815-1.8661.889-1.727-2.111-0.023
53A76VAL00.0120.0092.564-0.4210.3620.7270.001-1.510-0.003
54A77ASP-1-0.744-0.8714.879-0.900-0.897-0.001-0.0040.0020.000
55A78ASN0-0.049-0.0277.3650.3160.3160.0000.0000.0000.000
56A79ALA0-0.049-0.03210.2720.1200.1200.0000.0000.0000.000
57A80ALA00.002-0.00812.8360.1150.1150.0000.0000.0000.000
58A81ASP-1-0.893-0.92614.601-0.354-0.3540.0000.0000.0000.000
59A82PRO00.0150.00716.3720.0440.0440.0000.0000.0000.000
60A83ILE0-0.0070.00919.5770.0140.0140.0000.0000.0000.000
61A84PRO0-0.010-0.00722.5260.0010.0010.0000.0000.0000.000
62A85THR0-0.021-0.02623.5590.0130.0130.0000.0000.0000.000
63A86PRO0-0.046-0.00325.033-0.005-0.0050.0000.0000.0000.000
64A87TYR0-0.053-0.05927.622-0.010-0.0100.0000.0000.0000.000
65A88PHE0-0.020-0.02028.5000.0070.0070.0000.0000.0000.000
66A89ASP-1-0.843-0.90831.562-0.092-0.0920.0000.0000.0000.000
67A90ALA0-0.0200.00134.4900.0060.0060.0000.0000.0000.000
68A91GLU-1-0.897-0.92337.604-0.075-0.0750.0000.0000.0000.000
69A92ILE00.0360.03235.312-0.002-0.0020.0000.0000.0000.000
70A93SER0-0.058-0.05539.1840.0010.0010.0000.0000.0000.000
71A94LEU0-0.065-0.01838.1200.0000.0000.0000.0000.0000.000
72A95ARG10.9110.94942.4540.0720.0720.0000.0000.0000.000
73A96ASP-1-0.777-0.88443.306-0.072-0.0720.0000.0000.0000.000
74A97TYR00.0250.00342.870-0.003-0.0030.0000.0000.0000.000
75A98GLN0-0.031-0.01541.011-0.003-0.0030.0000.0000.0000.000
76A99GLU-1-0.804-0.90638.475-0.095-0.0950.0000.0000.0000.000
77A100LYS10.8700.91937.8430.0650.0650.0000.0000.0000.000
78A101ALA0-0.096-0.05137.914-0.003-0.0030.0000.0000.0000.000
79A102LEU00.0530.03332.940-0.007-0.0070.0000.0000.0000.000
80A103GLU-1-0.899-0.95133.363-0.100-0.1000.0000.0000.0000.000
81A104ARG10.8720.92632.9270.0960.0960.0000.0000.0000.000
82A105TRP0-0.029-0.00528.263-0.003-0.0030.0000.0000.0000.000
83A106LEU00.0390.01429.030-0.015-0.0150.0000.0000.0000.000
84A107VAL0-0.0180.00827.984-0.009-0.0090.0000.0000.0000.000
85A108ASP-1-0.882-0.94524.590-0.238-0.2380.0000.0000.0000.000
86A109LYS10.8390.92523.5080.1800.1800.0000.0000.0000.000
87A110ARG10.8380.92221.0610.3300.3300.0000.0000.0000.000
88A111GLY00.0150.01026.7700.0010.0010.0000.0000.0000.000
89A112CYS0-0.103-0.03730.4580.0010.0010.0000.0000.0000.000
90A113ILE00.0010.01133.9560.0050.0050.0000.0000.0000.000
91A114VAL00.0000.00636.8560.0010.0010.0000.0000.0000.000
92A115LEU0-0.002-0.00540.3700.0030.0030.0000.0000.0000.000
93A116PRO00.0120.01443.1720.0000.0000.0000.0000.0000.000
94A117THR0-0.026-0.02044.7670.0020.0020.0000.0000.0000.000
95A118GLY00.1150.04644.746-0.004-0.0040.0000.0000.0000.000
96A119SER00.004-0.00644.190-0.004-0.0040.0000.0000.0000.000
97A120GLY00.006-0.01043.5280.0000.0000.0000.0000.0000.000
98A121LYS10.8030.90539.6300.1020.1020.0000.0000.0000.000
99A122THR00.0180.00838.760-0.004-0.0040.0000.0000.0000.000
100A123HIS00.0600.03538.595-0.004-0.0040.0000.0000.0000.000
101A124VAL0-0.011-0.01536.242-0.002-0.0020.0000.0000.0000.000
102A125ALA00.0040.00234.286-0.005-0.0050.0000.0000.0000.000
103A126MET00.0130.02833.668-0.008-0.0080.0000.0000.0000.000
104A127ALA00.0290.01334.395-0.002-0.0020.0000.0000.0000.000
105A128ALA0-0.007-0.00630.737-0.003-0.0030.0000.0000.0000.000
106A129ILE0-0.016-0.01029.727-0.009-0.0090.0000.0000.0000.000
107A130ASN00.0220.01329.7890.0000.0000.0000.0000.0000.000
108A131GLU-1-0.912-0.95829.345-0.127-0.1270.0000.0000.0000.000
109A132LEU0-0.085-0.03824.792-0.009-0.0090.0000.0000.0000.000
110A133SER00.0260.01826.343-0.003-0.0030.0000.0000.0000.000
111A134THR0-0.027-0.00721.737-0.021-0.0210.0000.0000.0000.000
112A135PRO0-0.0070.02921.9040.0120.0120.0000.0000.0000.000
113A136THR0-0.015-0.03324.341-0.019-0.0190.0000.0000.0000.000
114A137LEU0-0.054-0.00627.1520.0110.0110.0000.0000.0000.000
115A138ILE00.0150.00528.974-0.001-0.0010.0000.0000.0000.000
116A139VAL0-0.014-0.00730.8570.0030.0030.0000.0000.0000.000
117A140VAL00.0190.01133.7770.0040.0040.0000.0000.0000.000
118A141PRO00.0160.01337.609-0.002-0.0020.0000.0000.0000.000
119A142THR0-0.018-0.03040.4230.0070.0070.0000.0000.0000.000
120A143LEU00.0500.00540.871-0.002-0.0020.0000.0000.0000.000
121A144ALA00.0020.01042.2880.0000.0000.0000.0000.0000.000
122A145LEU00.0590.02741.6740.0010.0010.0000.0000.0000.000
123A146ALA00.0260.01638.670-0.002-0.0020.0000.0000.0000.000
124A147GLU-1-0.791-0.87340.116-0.091-0.0910.0000.0000.0000.000
125A148GLN0-0.016-0.01542.6530.0000.0000.0000.0000.0000.000
126A149TRP0-0.005-0.01636.2360.0000.0000.0000.0000.0000.000
127A150LYS10.8830.93537.8000.0980.0980.0000.0000.0000.000
128A151GLU-1-0.964-0.97239.467-0.075-0.0750.0000.0000.0000.000
129A152ARG10.7760.87340.4450.0920.0920.0000.0000.0000.000
130A153LEU00.028-0.00733.7170.0000.0000.0000.0000.0000.000
131A154GLY00.0080.01237.144-0.001-0.0010.0000.0000.0000.000
132A155ILE0-0.040-0.01737.3890.0030.0030.0000.0000.0000.000
133A156PHE0-0.007-0.00633.8800.0010.0010.0000.0000.0000.000
134A157GLY00.0050.01435.234-0.001-0.0010.0000.0000.0000.000
135A158GLU-1-0.958-0.98835.899-0.089-0.0890.0000.0000.0000.000
136A159GLU-1-0.878-0.93234.073-0.097-0.0970.0000.0000.0000.000
137A160TYR0-0.056-0.04930.736-0.011-0.0110.0000.0000.0000.000
138A161VAL00.0190.01731.890-0.011-0.0110.0000.0000.0000.000
139A162GLY00.0230.01234.0520.0050.0050.0000.0000.0000.000
140A163GLU-1-0.774-0.82634.854-0.108-0.1080.0000.0000.0000.000
141A164PHE00.0290.01729.840-0.001-0.0010.0000.0000.0000.000
142A165SER0-0.005-0.00933.775-0.005-0.0050.0000.0000.0000.000
143A166GLY00.000-0.01636.448-0.003-0.0030.0000.0000.0000.000
144A167ARG10.7150.82038.9560.0980.0980.0000.0000.0000.000
145A168ILE00.0000.00536.3460.0040.0040.0000.0000.0000.000
146A169LYS10.8330.92632.5260.1430.1430.0000.0000.0000.000
147A170GLU-1-0.814-0.88231.970-0.124-0.1240.0000.0000.0000.000
148A171LEU0-0.028-0.02925.703-0.004-0.0040.0000.0000.0000.000
149A172LYS10.8400.91228.2450.1140.1140.0000.0000.0000.000
150A173PRO00.0130.01426.646-0.010-0.0100.0000.0000.0000.000
151A174LEU00.0210.02227.797-0.010-0.0100.0000.0000.0000.000
152A175THR0-0.0320.00429.6510.0080.0080.0000.0000.0000.000
153A176VAL00.0280.00831.736-0.007-0.0070.0000.0000.0000.000
154A177SER0-0.038-0.04832.327-0.001-0.0010.0000.0000.0000.000
155A178THR0-0.029-0.03934.3710.0010.0010.0000.0000.0000.000
156A179TYR0-0.014-0.02634.527-0.010-0.0100.0000.0000.0000.000
157A180ASP-1-0.819-0.88634.425-0.133-0.1330.0000.0000.0000.000
158A181SER0-0.070-0.04934.228-0.006-0.0060.0000.0000.0000.000
159A182ALA00.0550.01530.625-0.007-0.0070.0000.0000.0000.000
160A183TYR0-0.028-0.01529.931-0.013-0.0130.0000.0000.0000.000
161A184VAL0-0.060-0.03330.671-0.008-0.0080.0000.0000.0000.000
162A185ASN0-0.040-0.01629.5350.0030.0030.0000.0000.0000.000
163A186ALA00.0680.04526.293-0.010-0.0100.0000.0000.0000.000
164A187GLU-1-0.869-0.93923.627-0.246-0.2460.0000.0000.0000.000
165A188LYS10.8490.93122.9530.1860.1860.0000.0000.0000.000
166A189LEU00.0100.00624.491-0.001-0.0010.0000.0000.0000.000
167A190GLY00.0380.02222.122-0.008-0.0080.0000.0000.0000.000
168A191ASN0-0.010-0.02116.6120.0320.0320.0000.0000.0000.000
169A192ARG10.8290.90518.8950.2800.2800.0000.0000.0000.000
170A193PHE00.0250.01021.5740.0170.0170.0000.0000.0000.000
171A194MET00.0040.00216.278-0.032-0.0320.0000.0000.0000.000
172A195LEU0-0.013-0.00921.375-0.002-0.0020.0000.0000.0000.000
173A196LEU0-0.012-0.00924.9430.0040.0040.0000.0000.0000.000
174A197ILE0-0.0020.00427.4250.0050.0050.0000.0000.0000.000
175A198PHE00.0280.00529.0570.0000.0000.0000.0000.0000.000
176A199ASP-1-0.729-0.85833.752-0.107-0.1070.0000.0000.0000.000
177A200GLU-1-0.786-0.88534.854-0.147-0.1470.0000.0000.0000.000
178A201VAL0-0.030-0.02838.8470.0060.0060.0000.0000.0000.000
179A202HIS0-0.062-0.03542.494-0.001-0.0010.0000.0000.0000.000
180A203HIS0-0.0070.00236.6440.0010.0010.0000.0000.0000.000
181A204LEU00.0050.01337.6080.0040.0040.0000.0000.0000.000
182A205PRO00.0050.00238.286-0.003-0.0030.0000.0000.0000.000
183A206ALA00.0530.02535.177-0.007-0.0070.0000.0000.0000.000
184A207GLU-1-0.872-0.94033.851-0.174-0.1740.0000.0000.0000.000
185A208SER0-0.055-0.02834.0040.0010.0010.0000.0000.0000.000
186A209TYR0-0.032-0.02932.397-0.014-0.0140.0000.0000.0000.000
187A210VAL00.0230.01529.838-0.011-0.0110.0000.0000.0000.000
188A211GLN0-0.043-0.02328.841-0.031-0.0310.0000.0000.0000.000
189A212ILE0-0.016-0.01027.675-0.018-0.0180.0000.0000.0000.000
190A213ALA00.0140.01526.594-0.017-0.0170.0000.0000.0000.000
191A214GLN0-0.044-0.01124.717-0.035-0.0350.0000.0000.0000.000
192A215MET0-0.009-0.00223.016-0.039-0.0390.0000.0000.0000.000
193A216SER0-0.021-0.00722.114-0.010-0.0100.0000.0000.0000.000
194A217ILE00.0440.01716.4300.0010.0010.0000.0000.0000.000
195A218ALA0-0.0260.01619.446-0.013-0.0130.0000.0000.0000.000
196A219PRO00.0150.01618.3470.0130.0130.0000.0000.0000.000
197A220PHE00.0320.01820.5180.0170.0170.0000.0000.0000.000
198A221ARG10.7630.83622.2080.3100.3100.0000.0000.0000.000
199A222LEU00.0440.03127.2840.0080.0080.0000.0000.0000.000
200A223GLY00.0510.03230.9770.0030.0030.0000.0000.0000.000
201A224LEU00.006-0.00533.8210.0060.0060.0000.0000.0000.000
202A225THR00.0210.00437.1760.0050.0050.0000.0000.0000.000
203A226ALA0-0.005-0.01240.7190.0010.0010.0000.0000.0000.000
204A227THR0-0.017-0.01244.2240.0010.0010.0000.0000.0000.000
205A228PHE0-0.073-0.02847.1120.0030.0030.0000.0000.0000.000
206A229GLU-1-0.947-0.96346.962-0.078-0.0780.0000.0000.0000.000