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: 4J34N

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 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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2405902.686314
FMO2-HF: Nuclear repulsion 2325356.577297
FMO2-HF: Total energy -80546.109017
FMO2-MP2: Total energy -80784.963847


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.
-8.884-2.6313.256-3.518-5.988-0.02
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 : -0.011 / q_NPA : -0.001
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-1-0.874-0.8972.964-5.431-1.8720.196-1.691-2.064-0.003
4A27ILE00.002-0.0015.0970.4870.528-0.001-0.005-0.0350.000
5A28TYR0-0.041-0.0298.8220.0690.0690.0000.0000.0000.000
6A29TYR00.002-0.00211.7130.0490.0490.0000.0000.0000.000
7A30GLU-1-0.820-0.89015.491-0.495-0.4950.0000.0000.0000.000
8A31ARG10.8820.94418.2870.3070.3070.0000.0000.0000.000
9A32GLY00.0960.05521.1020.0190.0190.0000.0000.0000.000
10A33THR0-0.098-0.05418.7000.0040.0040.0000.0000.0000.000
11A34ILE00.0480.02312.661-0.005-0.0050.0000.0000.0000.000
12A35VAL0-0.064-0.03211.1880.0470.0470.0000.0000.0000.000
13A36VAL00.0320.0158.695-0.113-0.1130.0000.0000.0000.000
14A37LYS10.9010.9566.2141.6021.6020.0000.0000.0000.000
15A38GLY00.0490.0254.425-1.105-1.104-0.001-0.0340.0350.000
16A39ASP-1-0.782-0.8854.988-0.1220.060-0.001-0.007-0.1730.000
17A40ALA0-0.012-0.0037.413-0.011-0.0110.0000.0000.0000.000
18A41HIS0-0.077-0.04110.3780.1330.1330.0000.0000.0000.000
19A42VAL00.0460.04311.1340.0530.0530.0000.0000.0000.000
20A43PRO00.0300.00413.2610.0520.0520.0000.0000.0000.000
21A44HIS0-0.061-0.04316.803-0.054-0.0540.0000.0000.0000.000
22A45ALA00.0120.03414.6880.0040.0040.0000.0000.0000.000
23A46LYS10.9390.96716.6370.3340.3340.0000.0000.0000.000
24A47PHE00.0220.01013.624-0.033-0.0330.0000.0000.0000.000
25A48ASP-1-0.814-0.89916.614-0.309-0.3090.0000.0000.0000.000
26A49SER00.019-0.00217.708-0.024-0.0240.0000.0000.0000.000
27A50ARG10.8540.93619.5450.3740.3740.0000.0000.0000.000
28A51SER0-0.019-0.02216.1000.0310.0310.0000.0000.0000.000
29A52GLY0-0.030-0.00315.451-0.011-0.0110.0000.0000.0000.000
30A53THR0-0.007-0.00711.865-0.051-0.0510.0000.0000.0000.000
31A54TYR00.0130.01911.5410.1270.1270.0000.0000.0000.000
32A55ARG10.7320.83813.9680.4390.4390.0000.0000.0000.000
33A56ALA00.0510.02916.3620.0610.0610.0000.0000.0000.000
34A57LEU00.0000.00618.017-0.017-0.0170.0000.0000.0000.000
35A58ALA00.0700.02218.241-0.033-0.0330.0000.0000.0000.000
36A59PHE0-0.0270.00618.703-0.027-0.0270.0000.0000.0000.000
37A60ARG10.8090.91217.5350.3870.3870.0000.0000.0000.000
38A61TYR0-0.028-0.04712.9070.0250.0250.0000.0000.0000.000
39A62ARG10.7990.88015.1290.2620.2620.0000.0000.0000.000
40A63ASP-1-0.822-0.91016.275-0.390-0.3900.0000.0000.0000.000
41A64ILE0-0.027-0.02011.3520.0000.0000.0000.0000.0000.000
42A65ILE00.0190.02410.764-0.090-0.0900.0000.0000.0000.000
43A66GLU-1-0.818-0.90011.993-0.360-0.3600.0000.0000.0000.000
44A67TYR0-0.089-0.04410.3040.1290.1290.0000.0000.0000.000
45A68PHE00.012-0.0027.765-0.074-0.0740.0000.0000.0000.000
46A69GLU-1-0.874-0.9449.564-0.480-0.4800.0000.0000.0000.000
47A70SER0-0.080-0.05211.0260.1070.1070.0000.0000.0000.000
48A71ASN0-0.128-0.06210.9640.1430.1430.0000.0000.0000.000
49A72GLY0-0.003-0.00410.0310.0790.0790.0000.0000.0000.000
50A73ILE0-0.088-0.0345.1930.1400.1400.0000.0000.0000.000
51A74GLU-1-0.908-0.9542.306-0.981-1.1341.888-0.464-1.271-0.002
52A75PHE0-0.057-0.0712.819-2.878-1.0060.942-1.256-1.557-0.015
53A76VAL0-0.006-0.0152.699-0.1830.5700.234-0.060-0.9270.000
54A77ASP-1-0.741-0.8615.119-0.938-0.940-0.001-0.0010.0040.000
55A78ASN0-0.047-0.0287.4460.3340.3340.0000.0000.0000.000
56A79ALA0-0.052-0.03310.4900.1440.1440.0000.0000.0000.000
57A80ALA0-0.010-0.01313.0220.1200.1200.0000.0000.0000.000
58A81ASP-1-0.890-0.92714.685-0.428-0.4280.0000.0000.0000.000
59A82PRO00.0060.00316.6150.0540.0540.0000.0000.0000.000
60A83ILE00.0090.02119.8770.0100.0100.0000.0000.0000.000
61A84PRO0-0.009-0.01522.6730.0020.0020.0000.0000.0000.000
62A85THR0-0.021-0.02223.9190.0180.0180.0000.0000.0000.000
63A86PRO0-0.043-0.00425.419-0.007-0.0070.0000.0000.0000.000
64A87TYR0-0.048-0.03827.766-0.010-0.0100.0000.0000.0000.000
65A88PHE0-0.047-0.03828.9380.0070.0070.0000.0000.0000.000
66A89ASP-1-0.840-0.91731.786-0.109-0.1090.0000.0000.0000.000
67A90ALA0-0.030-0.01134.6020.0070.0070.0000.0000.0000.000
68A91GLU-1-0.942-0.96437.724-0.082-0.0820.0000.0000.0000.000
69A92ILE00.0130.02035.487-0.001-0.0010.0000.0000.0000.000
70A93SER0-0.033-0.02939.5170.0020.0020.0000.0000.0000.000
71A94LEU0-0.040-0.00538.444-0.001-0.0010.0000.0000.0000.000
72A95ARG10.8890.93742.9110.0760.0760.0000.0000.0000.000
73A96ASP-1-0.736-0.86343.600-0.074-0.0740.0000.0000.0000.000
74A97TYR00.032-0.00643.116-0.003-0.0030.0000.0000.0000.000
75A98GLN0-0.066-0.02641.497-0.003-0.0030.0000.0000.0000.000
76A99GLU-1-0.797-0.91738.574-0.099-0.0990.0000.0000.0000.000
77A100LYS10.8400.91238.4580.0700.0700.0000.0000.0000.000
78A101ALA0-0.061-0.03537.903-0.003-0.0030.0000.0000.0000.000
79A102LEU00.0590.04633.356-0.007-0.0070.0000.0000.0000.000
80A103GLU-1-0.868-0.94233.396-0.106-0.1060.0000.0000.0000.000
81A104ARG10.8620.93533.1570.0990.0990.0000.0000.0000.000
82A105TRP0-0.038-0.02628.240-0.004-0.0040.0000.0000.0000.000
83A106LEU00.0430.01829.232-0.015-0.0150.0000.0000.0000.000
84A107VAL0-0.065-0.00627.964-0.009-0.0090.0000.0000.0000.000
85A108ASP-1-0.871-0.94125.723-0.199-0.1990.0000.0000.0000.000
86A109LYS10.8340.93423.6400.1840.1840.0000.0000.0000.000
87A110ARG10.8760.93921.3280.3130.3130.0000.0000.0000.000
88A111GLY00.0010.01227.2100.0050.0050.0000.0000.0000.000
89A112CYS0-0.063-0.01830.8880.0010.0010.0000.0000.0000.000
90A113ILE0-0.0010.00234.3470.0060.0060.0000.0000.0000.000
91A114VAL0-0.0070.00537.1030.0010.0010.0000.0000.0000.000
92A115LEU0-0.014-0.02340.1090.0040.0040.0000.0000.0000.000
93A116PRO0-0.0220.00843.1800.0010.0010.0000.0000.0000.000
94A117THR0-0.033-0.04145.3640.0000.0000.0000.0000.0000.000
95A118GLY00.1570.07444.8900.0000.0000.0000.0000.0000.000
96A119SER00.0340.00544.392-0.003-0.0030.0000.0000.0000.000
97A120GLY00.009-0.00943.742-0.001-0.0010.0000.0000.0000.000
98A121LYS10.8070.91339.8730.1070.1070.0000.0000.0000.000
99A122THR00.0040.00139.164-0.004-0.0040.0000.0000.0000.000
100A123HIS00.0490.02239.948-0.003-0.0030.0000.0000.0000.000
101A124VAL00.0290.01436.318-0.002-0.0020.0000.0000.0000.000
102A125ALA0-0.0120.00434.871-0.006-0.0060.0000.0000.0000.000
103A126MET00.0080.01934.199-0.008-0.0080.0000.0000.0000.000
104A127ALA00.0240.00934.830-0.003-0.0030.0000.0000.0000.000
105A128ALA00.012-0.00131.083-0.003-0.0030.0000.0000.0000.000
106A129ILE0-0.044-0.02230.102-0.008-0.0080.0000.0000.0000.000
107A130ASN00.0570.01829.938-0.004-0.0040.0000.0000.0000.000
108A131GLU-1-0.939-0.95529.689-0.139-0.1390.0000.0000.0000.000
109A132LEU0-0.037-0.00825.086-0.008-0.0080.0000.0000.0000.000
110A133SER00.0210.03426.719-0.002-0.0020.0000.0000.0000.000
111A134THR0-0.029-0.02121.918-0.022-0.0220.0000.0000.0000.000
112A135PRO0-0.0030.01822.4010.0140.0140.0000.0000.0000.000
113A136THR0-0.020-0.04425.102-0.012-0.0120.0000.0000.0000.000
114A137LEU0-0.0390.00327.3610.0100.0100.0000.0000.0000.000
115A138ILE00.0110.00129.1440.0000.0000.0000.0000.0000.000
116A139VAL0-0.0020.00831.1380.0050.0050.0000.0000.0000.000
117A140VAL00.0270.01133.9260.0040.0040.0000.0000.0000.000
118A141PRO00.0010.02437.724-0.002-0.0020.0000.0000.0000.000
119A142THR00.002-0.02840.2430.0060.0060.0000.0000.0000.000
120A143LEU00.0730.02741.146-0.002-0.0020.0000.0000.0000.000
121A144ALA00.0050.01642.304-0.001-0.0010.0000.0000.0000.000
122A145LEU00.0620.02442.0400.0010.0010.0000.0000.0000.000
123A146ALA00.007-0.00638.622-0.002-0.0020.0000.0000.0000.000
124A147GLU-1-0.778-0.89240.286-0.100-0.1000.0000.0000.0000.000
125A148GLN0-0.046-0.02242.7600.0010.0010.0000.0000.0000.000
126A149TRP0-0.008-0.01936.200-0.002-0.0020.0000.0000.0000.000
127A150LYS10.8910.93537.8370.1090.1090.0000.0000.0000.000
128A151GLU-1-0.907-0.92639.523-0.085-0.0850.0000.0000.0000.000
129A152ARG10.8220.90840.8400.0990.0990.0000.0000.0000.000
130A153LEU0-0.012-0.02434.7270.0000.0000.0000.0000.0000.000
131A154GLY00.0290.01137.603-0.002-0.0020.0000.0000.0000.000
132A155ILE0-0.037-0.00538.1020.0020.0020.0000.0000.0000.000
133A156PHE0-0.004-0.01634.290-0.002-0.0020.0000.0000.0000.000
134A157GLY0-0.0150.00735.501-0.003-0.0030.0000.0000.0000.000
135A158GLU-1-0.951-0.98636.501-0.100-0.1000.0000.0000.0000.000
136A159GLU-1-0.898-0.94734.600-0.116-0.1160.0000.0000.0000.000
137A160TYR0-0.066-0.04631.198-0.012-0.0120.0000.0000.0000.000
138A161VAL00.0120.00232.443-0.011-0.0110.0000.0000.0000.000
139A162GLY0-0.044-0.01733.5800.0050.0050.0000.0000.0000.000
140A163GLU-1-0.726-0.82634.433-0.119-0.1190.0000.0000.0000.000
141A164PHE00.0060.00830.077-0.002-0.0020.0000.0000.0000.000
142A165SER0-0.013-0.05533.897-0.001-0.0010.0000.0000.0000.000
143A166GLY0-0.047-0.02336.644-0.001-0.0010.0000.0000.0000.000
144A167ARG10.7060.82538.8060.1080.1080.0000.0000.0000.000
145A168ILE00.0290.01836.5450.0040.0040.0000.0000.0000.000
146A169LYS10.8140.93632.5780.1530.1530.0000.0000.0000.000
147A170GLU-1-0.826-0.89532.344-0.138-0.1380.0000.0000.0000.000
148A171LEU0-0.040-0.03926.026-0.005-0.0050.0000.0000.0000.000
149A172LYS10.8350.92428.8570.1350.1350.0000.0000.0000.000
150A173PRO00.0220.01327.201-0.009-0.0090.0000.0000.0000.000
151A174LEU00.0400.04728.214-0.008-0.0080.0000.0000.0000.000
152A175THR0-0.0170.01329.8030.0060.0060.0000.0000.0000.000
153A176VAL00.0040.00431.703-0.008-0.0080.0000.0000.0000.000
154A177SER0-0.040-0.06532.4060.0010.0010.0000.0000.0000.000
155A178THR0-0.023-0.02634.4370.0020.0020.0000.0000.0000.000
156A179TYR00.020-0.00934.804-0.010-0.0100.0000.0000.0000.000
157A180ASP-1-0.860-0.91434.819-0.135-0.1350.0000.0000.0000.000
158A181SER0-0.0040.00133.621-0.005-0.0050.0000.0000.0000.000
159A182ALA00.0260.01730.840-0.009-0.0090.0000.0000.0000.000
160A183TYR0-0.014-0.00530.154-0.014-0.0140.0000.0000.0000.000
161A184VAL0-0.051-0.03230.755-0.009-0.0090.0000.0000.0000.000
162A185ASN0-0.044-0.01629.3250.0010.0010.0000.0000.0000.000
163A186ALA00.0810.04826.496-0.013-0.0130.0000.0000.0000.000
164A187GLU-1-0.906-0.95623.812-0.272-0.2720.0000.0000.0000.000
165A188LYS10.9460.97923.0530.1990.1990.0000.0000.0000.000
166A189LEU0-0.010-0.00924.332-0.007-0.0070.0000.0000.0000.000
167A190GLY00.0050.00822.332-0.007-0.0070.0000.0000.0000.000
168A191ASN00.013-0.01416.7240.0330.0330.0000.0000.0000.000
169A192ARG10.8310.91219.0030.3200.3200.0000.0000.0000.000
170A193PHE00.0110.00221.6470.0160.0160.0000.0000.0000.000
171A194MET00.0150.00316.870-0.034-0.0340.0000.0000.0000.000
172A195LEU00.001-0.00321.9410.0010.0010.0000.0000.0000.000
173A196LEU0-0.031-0.02125.4450.0060.0060.0000.0000.0000.000
174A197ILE00.0060.00427.6130.0080.0080.0000.0000.0000.000
175A198PHE00.001-0.00429.167-0.001-0.0010.0000.0000.0000.000
176A199ASP-1-0.761-0.86933.822-0.113-0.1130.0000.0000.0000.000
177A200GLU-1-0.903-0.97535.180-0.145-0.1450.0000.0000.0000.000
178A201VAL0-0.012-0.01339.0360.0050.0050.0000.0000.0000.000
179A202HIS0-0.055-0.03642.6520.0000.0000.0000.0000.0000.000
180A203HIS00.0080.00537.3210.0000.0000.0000.0000.0000.000
181A204LEU00.0050.00937.7040.0030.0030.0000.0000.0000.000
182A205PRO00.0260.00437.991-0.004-0.0040.0000.0000.0000.000
183A206ALA00.0140.01035.572-0.008-0.0080.0000.0000.0000.000
184A207GLU-1-0.876-0.95434.463-0.164-0.1640.0000.0000.0000.000
185A208SER0-0.060-0.02934.181-0.003-0.0030.0000.0000.0000.000
186A209TYR00.010-0.00631.468-0.014-0.0140.0000.0000.0000.000
187A210VAL0-0.0050.00230.302-0.012-0.0120.0000.0000.0000.000
188A211GLN00.0030.00929.267-0.020-0.0200.0000.0000.0000.000
189A212ILE0-0.0040.00728.104-0.018-0.0180.0000.0000.0000.000
190A213ALA00.0070.00726.787-0.020-0.0200.0000.0000.0000.000
191A214GLN0-0.041-0.00824.907-0.033-0.0330.0000.0000.0000.000
192A215MET00.0140.00923.068-0.034-0.0340.0000.0000.0000.000
193A216SER0-0.0040.00822.404-0.022-0.0220.0000.0000.0000.000
194A217ILE00.0470.02216.3560.0000.0000.0000.0000.0000.000
195A218ALA0-0.0310.00619.369-0.015-0.0150.0000.0000.0000.000
196A219PRO00.0100.01918.6120.0210.0210.0000.0000.0000.000
197A220PHE00.0180.00820.8170.0210.0210.0000.0000.0000.000
198A221ARG10.7680.86322.4760.3150.3150.0000.0000.0000.000
199A222LEU00.0660.03027.5490.0090.0090.0000.0000.0000.000
200A223GLY00.0210.03631.1310.0000.0000.0000.0000.0000.000
201A224LEU0-0.009-0.02334.0650.0080.0080.0000.0000.0000.000
202A225THR00.0270.01237.4860.0040.0040.0000.0000.0000.000
203A226ALA0-0.017-0.01041.0680.0010.0010.0000.0000.0000.000
204A227THR0-0.016-0.02044.4960.0020.0020.0000.0000.0000.000
205A228PHE0-0.098-0.03747.0360.0030.0030.0000.0000.0000.000
206A229GLU-1-0.931-0.94947.031-0.079-0.0790.0000.0000.0000.000