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: KG363

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 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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2406727.97693
FMO2-HF: Nuclear repulsion 2326184.01438
FMO2-HF: Total energy -80543.962549
FMO2-MP2: Total energy -80783.036725


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.
-8.971-4.1684.305-3.193-5.914-0.023
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 : -0.039 / q_NPA : -0.031
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-1-0.885-0.9082.829-6.167-3.1740.335-1.334-1.995-0.009
4A27ILE0-0.011-0.0075.0710.7550.801-0.001-0.006-0.0390.000
5A28TYR0-0.012-0.0088.7910.0030.0030.0000.0000.0000.000
6A29TYR00.0150.01811.6400.1050.1050.0000.0000.0000.000
7A30GLU-1-0.897-0.95915.421-0.408-0.4080.0000.0000.0000.000
8A31ARG10.8830.95918.1380.2660.2660.0000.0000.0000.000
9A32GLY00.0920.05020.9480.0250.0250.0000.0000.0000.000
10A33THR0-0.114-0.07618.4010.0230.0230.0000.0000.0000.000
11A34ILE00.0590.02312.760-0.025-0.0250.0000.0000.0000.000
12A35VAL0-0.052-0.03110.9530.0970.0970.0000.0000.0000.000
13A36VAL00.0410.0188.778-0.176-0.1760.0000.0000.0000.000
14A37LYS10.9010.9566.2671.2961.2960.0000.0000.0000.000
15A38GLY00.0630.0314.676-0.920-0.919-0.001-0.0340.0340.000
16A39ASP-1-0.801-0.8745.2440.5660.741-0.001-0.007-0.1670.000
17A40ALA00.006-0.0217.916-0.284-0.2840.0000.0000.0000.000
18A41HIS0-0.113-0.06011.025-0.142-0.1420.0000.0000.0000.000
19A42VAL00.0530.05511.411-0.031-0.0310.0000.0000.0000.000
20A43PRO00.0420.00613.2630.0040.0040.0000.0000.0000.000
21A44HIS0-0.050-0.03616.821-0.063-0.0630.0000.0000.0000.000
22A45ALA00.0040.02714.860-0.033-0.0330.0000.0000.0000.000
23A46LYS10.9330.96416.8530.1330.1330.0000.0000.0000.000
24A47PHE00.0220.01113.548-0.048-0.0480.0000.0000.0000.000
25A48ASP-1-0.812-0.91116.509-0.150-0.1500.0000.0000.0000.000
26A49SER00.022-0.00517.446-0.014-0.0140.0000.0000.0000.000
27A50ARG10.9250.97919.1470.2120.2120.0000.0000.0000.000
28A51SER0-0.072-0.03015.949-0.013-0.0130.0000.0000.0000.000
29A52GLY0-0.026-0.00215.171-0.012-0.0120.0000.0000.0000.000
30A53THR0-0.051-0.03611.362-0.032-0.0320.0000.0000.0000.000
31A54TYR00.0640.05011.2320.0880.0880.0000.0000.0000.000
32A55ARG10.8270.90913.7810.2300.2300.0000.0000.0000.000
33A56ALA00.0390.02116.1950.0670.0670.0000.0000.0000.000
34A57LEU0-0.022-0.00117.891-0.032-0.0320.0000.0000.0000.000
35A58ALA00.0730.02818.164-0.018-0.0180.0000.0000.0000.000
36A59PHE0-0.052-0.00718.596-0.022-0.0220.0000.0000.0000.000
37A60ARG10.8850.94617.5470.1850.1850.0000.0000.0000.000
38A61TYR0-0.042-0.05812.8250.0560.0560.0000.0000.0000.000
39A62ARG10.8260.90114.9590.1780.1780.0000.0000.0000.000
40A63ASP-1-0.873-0.92916.378-0.202-0.2020.0000.0000.0000.000
41A64ILE0-0.067-0.04111.0870.0250.0250.0000.0000.0000.000
42A65ILE00.0130.01611.136-0.049-0.0490.0000.0000.0000.000
43A66GLU-1-0.886-0.95212.057-0.220-0.2200.0000.0000.0000.000
44A67TYR0-0.098-0.08110.0520.0610.0610.0000.0000.0000.000
45A68PHE0-0.019-0.0157.835-0.005-0.0050.0000.0000.0000.000
46A69GLU-1-0.899-0.9589.643-0.376-0.3760.0000.0000.0000.000
47A70SER0-0.077-0.01611.0260.1050.1050.0000.0000.0000.000
48A71ASN0-0.082-0.03010.8560.0770.0770.0000.0000.0000.000
49A72GLY0-0.013-0.0119.9460.1290.1290.0000.0000.0000.000
50A73ILE0-0.081-0.0335.1260.1680.1680.0000.0000.0000.000
51A74GLU-1-0.901-0.9482.150-0.804-1.7403.150-0.691-1.522-0.002
52A75PHE0-0.040-0.0782.916-2.470-0.6700.721-1.052-1.469-0.012
53A76VAL0-0.004-0.0043.002-0.1310.5910.103-0.068-0.7560.000
54A77ASP-1-0.740-0.8575.157-0.827-0.825-0.001-0.0010.0000.000
55A78ASN0-0.045-0.0207.1060.2570.2570.0000.0000.0000.000
56A79ALA0-0.058-0.03610.5900.1650.1650.0000.0000.0000.000
57A80ALA0-0.019-0.01613.0470.1190.1190.0000.0000.0000.000
58A81ASP-1-0.929-0.95314.746-0.522-0.5220.0000.0000.0000.000
59A82PRO0-0.021-0.01116.6260.0670.0670.0000.0000.0000.000
60A83ILE0-0.0100.01419.923-0.001-0.0010.0000.0000.0000.000
61A84PRO0-0.004-0.00522.8380.0040.0040.0000.0000.0000.000
62A85THR0-0.022-0.03324.1080.0230.0230.0000.0000.0000.000
63A86PRO0-0.0310.00525.599-0.010-0.0100.0000.0000.0000.000
64A87TYR00.0140.00227.466-0.008-0.0080.0000.0000.0000.000
65A88PHE0-0.056-0.04829.0930.0060.0060.0000.0000.0000.000
66A89ASP-1-0.899-0.95431.943-0.118-0.1180.0000.0000.0000.000
67A90ALA0-0.035-0.01234.7450.0060.0060.0000.0000.0000.000
68A91GLU-1-0.996-1.00937.876-0.080-0.0800.0000.0000.0000.000
69A92ILE00.0050.01035.0250.0000.0000.0000.0000.0000.000
70A93SER0-0.0340.00239.6550.0040.0040.0000.0000.0000.000
71A94LEU0-0.024-0.00338.4800.0000.0000.0000.0000.0000.000
72A95ARG10.8880.94343.0440.0640.0640.0000.0000.0000.000
73A96ASP-1-0.799-0.91143.719-0.058-0.0580.0000.0000.0000.000
74A97TYR00.016-0.03343.221-0.002-0.0020.0000.0000.0000.000
75A98GLN0-0.0540.00741.691-0.002-0.0020.0000.0000.0000.000
76A99GLU-1-0.726-0.89738.860-0.085-0.0850.0000.0000.0000.000
77A100LYS10.8900.98738.5600.0510.0510.0000.0000.0000.000
78A101ALA0-0.066-0.04837.983-0.001-0.0010.0000.0000.0000.000
79A102LEU00.0630.04533.665-0.003-0.0030.0000.0000.0000.000
80A103GLU-1-0.852-0.94233.504-0.085-0.0850.0000.0000.0000.000
81A104ARG10.8490.94333.2410.0670.0670.0000.0000.0000.000
82A105TRP0-0.047-0.02428.476-0.001-0.0010.0000.0000.0000.000
83A106LEU00.027-0.00329.378-0.010-0.0100.0000.0000.0000.000
84A107VAL0-0.088-0.01028.054-0.008-0.0080.0000.0000.0000.000
85A108ASP-1-0.859-0.92825.814-0.117-0.1170.0000.0000.0000.000
86A109LYS10.9170.97023.1440.1670.1670.0000.0000.0000.000
87A110ARG10.8610.93221.6560.2040.2040.0000.0000.0000.000
88A111GLY0-0.0030.01227.3350.0100.0100.0000.0000.0000.000
89A112CYS0-0.057-0.01331.011-0.004-0.0040.0000.0000.0000.000
90A113ILE00.0070.00334.4010.0050.0050.0000.0000.0000.000
91A114VAL00.0000.00937.2340.0000.0000.0000.0000.0000.000
92A115LEU0-0.024-0.02340.6320.0020.0020.0000.0000.0000.000
93A116PRO0-0.029-0.00243.3170.0000.0000.0000.0000.0000.000
94A117THR00.014-0.03345.408-0.001-0.0010.0000.0000.0000.000
95A118GLY00.1520.07244.9250.0010.0010.0000.0000.0000.000
96A119SER00.017-0.00644.448-0.003-0.0030.0000.0000.0000.000
97A120GLY00.015-0.04443.972-0.002-0.0020.0000.0000.0000.000
98A121LYS10.8890.96839.8530.0850.0850.0000.0000.0000.000
99A122THR0-0.024-0.00839.327-0.003-0.0030.0000.0000.0000.000
100A123HIS0-0.016-0.00340.120-0.004-0.0040.0000.0000.0000.000
101A124VAL00.0370.01536.224-0.003-0.0030.0000.0000.0000.000
102A125ALA0-0.0120.00235.033-0.005-0.0050.0000.0000.0000.000
103A126MET00.0200.01434.362-0.009-0.0090.0000.0000.0000.000
104A127ALA00.0220.01534.990-0.005-0.0050.0000.0000.0000.000
105A128ALA00.016-0.00231.202-0.004-0.0040.0000.0000.0000.000
106A129ILE0-0.053-0.02330.276-0.008-0.0080.0000.0000.0000.000
107A130ASN00.0590.01330.098-0.009-0.0090.0000.0000.0000.000
108A131GLU-1-0.958-0.96029.793-0.136-0.1360.0000.0000.0000.000
109A132LEU0-0.032-0.00825.351-0.009-0.0090.0000.0000.0000.000
110A133SER00.0220.04726.8390.0000.0000.0000.0000.0000.000
111A134THR0-0.023-0.01922.069-0.026-0.0260.0000.0000.0000.000
112A135PRO0-0.0210.01122.3090.0180.0180.0000.0000.0000.000
113A136THR00.006-0.03525.137-0.005-0.0050.0000.0000.0000.000
114A137LEU0-0.046-0.00327.5230.0070.0070.0000.0000.0000.000
115A138ILE00.0010.00029.1250.0050.0050.0000.0000.0000.000
116A139VAL0-0.0070.00131.1130.0030.0030.0000.0000.0000.000
117A140VAL00.0410.02333.8870.0060.0060.0000.0000.0000.000
118A141PRO0-0.0130.01937.684-0.002-0.0020.0000.0000.0000.000
119A142THR00.003-0.02340.2050.0030.0030.0000.0000.0000.000
120A143LEU00.0870.03041.250-0.002-0.0020.0000.0000.0000.000
121A144ALA00.0020.01242.313-0.002-0.0020.0000.0000.0000.000
122A145LEU00.0610.01741.8460.0000.0000.0000.0000.0000.000
123A146ALA0-0.003-0.00938.707-0.003-0.0030.0000.0000.0000.000
124A147GLU-1-0.935-1.00040.283-0.098-0.0980.0000.0000.0000.000
125A148GLN0-0.025-0.00142.7740.0020.0020.0000.0000.0000.000
126A149TRP0-0.016-0.00836.838-0.001-0.0010.0000.0000.0000.000
127A150LYS10.9600.97737.8880.1090.1090.0000.0000.0000.000
128A151GLU-1-0.887-0.91739.536-0.086-0.0860.0000.0000.0000.000
129A152ARG10.8190.91340.8190.0930.0930.0000.0000.0000.000
130A153LEU00.005-0.01735.3950.0000.0000.0000.0000.0000.000
131A154GLY00.0240.00737.795-0.004-0.0040.0000.0000.0000.000
132A155ILE0-0.0210.00337.8580.0000.0000.0000.0000.0000.000
133A156PHE0-0.009-0.00834.270-0.001-0.0010.0000.0000.0000.000
134A157GLY0-0.0020.00635.685-0.005-0.0050.0000.0000.0000.000
135A158GLU-1-0.939-0.98236.701-0.108-0.1080.0000.0000.0000.000
136A159GLU-1-0.966-0.98134.741-0.140-0.1400.0000.0000.0000.000
137A160TYR0-0.008-0.01231.380-0.015-0.0150.0000.0000.0000.000
138A161VAL00.001-0.00532.489-0.010-0.0100.0000.0000.0000.000
139A162GLY0-0.070-0.03733.6050.0030.0030.0000.0000.0000.000
140A163GLU-1-0.774-0.87934.489-0.114-0.1140.0000.0000.0000.000
141A164PHE00.0290.02030.103-0.004-0.0040.0000.0000.0000.000
142A165SER0-0.019-0.06833.9490.0020.0020.0000.0000.0000.000
143A166GLY0-0.083-0.05436.690-0.002-0.0020.0000.0000.0000.000
144A167ARG10.8610.94438.8660.1050.1050.0000.0000.0000.000
145A168ILE00.0290.02136.5420.0030.0030.0000.0000.0000.000
146A169LYS10.8830.97732.6350.1380.1380.0000.0000.0000.000
147A170GLU-1-0.875-0.90032.513-0.148-0.1480.0000.0000.0000.000
148A171LEU0-0.049-0.04226.292-0.002-0.0020.0000.0000.0000.000
149A172LYS10.9100.97228.9490.1490.1490.0000.0000.0000.000
150A173PRO00.0330.00727.226-0.005-0.0050.0000.0000.0000.000
151A174LEU00.0420.05028.255-0.004-0.0040.0000.0000.0000.000
152A175THR0-0.055-0.00429.2490.0090.0090.0000.0000.0000.000
153A176VAL00.0510.02631.706-0.004-0.0040.0000.0000.0000.000
154A177SER0-0.029-0.06832.324-0.001-0.0010.0000.0000.0000.000
155A178THR00.0050.00534.4420.0030.0030.0000.0000.0000.000
156A179TYR00.040-0.00734.918-0.006-0.0060.0000.0000.0000.000
157A180ASP-1-0.919-0.95934.796-0.107-0.1070.0000.0000.0000.000
158A181SER0-0.022-0.00433.827-0.004-0.0040.0000.0000.0000.000
159A182ALA00.0210.02130.789-0.009-0.0090.0000.0000.0000.000
160A183TYR0-0.007-0.00130.153-0.012-0.0120.0000.0000.0000.000
161A184VAL0-0.029-0.01930.754-0.006-0.0060.0000.0000.0000.000
162A185ASN0-0.074-0.04229.246-0.007-0.0070.0000.0000.0000.000
163A186ALA00.0650.03726.415-0.015-0.0150.0000.0000.0000.000
164A187GLU-1-0.977-0.98923.727-0.245-0.2450.0000.0000.0000.000
165A188LYS10.9640.98123.0580.2100.2100.0000.0000.0000.000
166A189LEU0-0.006-0.01224.397-0.013-0.0130.0000.0000.0000.000
167A190GLY0-0.0050.00622.333-0.009-0.0090.0000.0000.0000.000
168A191ASN00.0380.00517.0300.0430.0430.0000.0000.0000.000
169A192ARG10.8960.94519.0300.3270.3270.0000.0000.0000.000
170A193PHE00.0170.00421.6850.0120.0120.0000.0000.0000.000
171A194MET00.0250.00917.330-0.027-0.0270.0000.0000.0000.000
172A195LEU0-0.016-0.00521.9560.0100.0100.0000.0000.0000.000
173A196LEU0-0.026-0.02225.4970.0030.0030.0000.0000.0000.000
174A197ILE00.0060.00727.5390.0100.0100.0000.0000.0000.000
175A198PHE0-0.019-0.01529.202-0.002-0.0020.0000.0000.0000.000
176A199ASP-1-0.801-0.92033.738-0.091-0.0910.0000.0000.0000.000
177A200GLU-1-0.920-0.97435.222-0.101-0.1010.0000.0000.0000.000
178A201VAL0-0.037-0.02238.9400.0050.0050.0000.0000.0000.000
179A202HIS0-0.065-0.04442.5640.0010.0010.0000.0000.0000.000
180A203HIS00.0230.01037.7650.0000.0000.0000.0000.0000.000
181A204LEU0-0.0040.00037.7170.0020.0020.0000.0000.0000.000
182A205PRO00.0290.00737.886-0.001-0.0010.0000.0000.0000.000
183A206ALA00.0280.00335.507-0.007-0.0070.0000.0000.0000.000
184A207GLU-1-0.869-0.95234.389-0.094-0.0940.0000.0000.0000.000
185A208SER0-0.059-0.02534.114-0.004-0.0040.0000.0000.0000.000
186A209TYR00.013-0.01731.515-0.008-0.0080.0000.0000.0000.000
187A210VAL0-0.0100.02030.267-0.010-0.0100.0000.0000.0000.000
188A211GLN0-0.0190.00529.165-0.006-0.0060.0000.0000.0000.000
189A212ILE0-0.0060.00528.035-0.014-0.0140.0000.0000.0000.000
190A213ALA0-0.008-0.00226.725-0.019-0.0190.0000.0000.0000.000
191A214GLN0-0.031-0.01724.813-0.021-0.0210.0000.0000.0000.000
192A215MET00.0130.00723.014-0.017-0.0170.0000.0000.0000.000
193A216SER0-0.0130.00422.368-0.026-0.0260.0000.0000.0000.000
194A217ILE00.0430.00516.5920.0130.0130.0000.0000.0000.000
195A218ALA0-0.0280.00719.269-0.010-0.0100.0000.0000.0000.000
196A219PRO00.0240.01818.8730.0340.0340.0000.0000.0000.000
197A220PHE00.0340.03220.9650.0270.0270.0000.0000.0000.000
198A221ARG10.8170.91022.3620.2290.2290.0000.0000.0000.000
199A222LEU00.0810.03627.5270.0100.0100.0000.0000.0000.000
200A223GLY00.0060.02331.185-0.002-0.0020.0000.0000.0000.000
201A224LEU00.014-0.01133.9540.0060.0060.0000.0000.0000.000
202A225THR00.0490.02037.4360.0030.0030.0000.0000.0000.000
203A226ALA0-0.040-0.01540.9720.0010.0010.0000.0000.0000.000
204A227THR0-0.068-0.01444.4750.0020.0020.0000.0000.0000.000
205A228PHE0-0.067-0.03147.0160.0030.0030.0000.0000.0000.000
206A229GLU-1-0.931-0.95046.783-0.066-0.0660.0000.0000.0000.000