FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: KGMG3

Calculation Name: 3B8P-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3B8P

Chain ID: A

ChEMBL ID:

UniProt ID: Q04866

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 207
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2004019.833114
FMO2-HF: Nuclear repulsion 1923481.582466
FMO2-HF: Total energy -80538.250648
FMO2-MP2: Total energy -80778.398343


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:54:GLU)


Summations of interaction energy for fragment #1(A:54:GLU)
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.
-0.0110000000000174.5766.844-5.201-6.2310.024
Interaction energy analysis for fragmet #1(A:54:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.863 / q_NPA : -0.929
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].
3A56TRP0-0.016-0.0182.674-4.830-2.3560.292-1.079-1.687-0.002
4A57THR0-0.031-0.0136.405-2.179-2.1790.0000.0000.0000.000
5A58SER0-0.029-0.03610.114-1.112-1.1120.0000.0000.0000.000
6A59THR00.047-0.00812.761-0.063-0.0630.0000.0000.0000.000
7A60ALA00.0230.01216.335-0.255-0.2550.0000.0000.0000.000
8A61ILE0-0.014-0.00219.7930.0470.0470.0000.0000.0000.000
9A62ILE00.0350.02023.262-0.295-0.2950.0000.0000.0000.000
10A63THR00.017-0.01325.953-0.104-0.1040.0000.0000.0000.000
11A64GLN00.0390.01829.6590.0720.0720.0000.0000.0000.000
12A65PRO0-0.0280.02032.822-0.003-0.0030.0000.0000.0000.000
13A66ASP-1-0.839-0.92333.9888.3988.3980.0000.0000.0000.000
14A67ALA00.0530.00336.678-0.016-0.0160.0000.0000.0000.000
15A68ALA00.0160.00938.701-0.088-0.0880.0000.0000.0000.000
16A69GLN00.006-0.00631.778-0.104-0.1040.0000.0000.0000.000
17A70VAL00.0370.02337.2460.0790.0790.0000.0000.0000.000
18A71ALA0-0.029-0.00839.486-0.167-0.1670.0000.0000.0000.000
19A72THR00.022-0.00441.145-0.192-0.1920.0000.0000.0000.000
20A73TYR00.021-0.01140.172-0.204-0.2040.0000.0000.0000.000
21A74THR00.0120.00342.538-0.098-0.0980.0000.0000.0000.000
22A75ASN0-0.037-0.00944.644-0.188-0.1880.0000.0000.0000.000
23A76ALA00.0160.00645.519-0.161-0.1610.0000.0000.0000.000
24A77LEU00.0370.02743.432-0.107-0.1070.0000.0000.0000.000
25A78ASN0-0.034-0.02547.593-0.088-0.0880.0000.0000.0000.000
26A79VAL00.0050.00950.753-0.132-0.1320.0000.0000.0000.000
27A80LEU00.010-0.00348.419-0.128-0.1280.0000.0000.0000.000
28A81TYR0-0.037-0.01448.720-0.020-0.0200.0000.0000.0000.000
29A82GLY0-0.044-0.02652.892-0.102-0.1020.0000.0000.0000.000
30A83GLY0-0.061-0.02153.7350.0380.0380.0000.0000.0000.000
31A84ASN0-0.012-0.02252.8240.1240.1240.0000.0000.0000.000
32A85ALA00.0020.01949.6560.1220.1220.0000.0000.0000.000
33A86PRO00.0130.01745.213-0.038-0.0380.0000.0000.0000.000
34A87LYS10.9370.96745.737-6.971-6.9710.0000.0000.0000.000
35A88ILE00.0540.01341.9670.1500.1500.0000.0000.0000.000
36A89SER0-0.047-0.02241.6400.0930.0930.0000.0000.0000.000
37A90GLU-1-0.812-0.91540.6727.2997.2990.0000.0000.0000.000
38A91VAL00.0020.02039.8580.2010.2010.0000.0000.0000.000
39A92GLN0-0.057-0.05137.4070.0230.0230.0000.0000.0000.000
40A93ALA00.0190.01836.1220.3110.3110.0000.0000.0000.000
41A94ASN0-0.014-0.01335.9270.3130.3130.0000.0000.0000.000
42A95PHE00.0480.02234.4620.2030.2030.0000.0000.0000.000
43A96ILE00.0380.02229.0720.2740.2740.0000.0000.0000.000
44A97SER0-0.069-0.02230.9100.3400.3400.0000.0000.0000.000
45A98ARG10.7930.86131.338-8.419-8.4190.0000.0000.0000.000
46A99PHE00.0150.01224.2480.3320.3320.0000.0000.0000.000
47A100SER0-0.057-0.04126.6970.4100.4100.0000.0000.0000.000
48A101SER00.0140.01226.4120.3930.3930.0000.0000.0000.000
49A102ALA00.0730.04726.9390.3090.3090.0000.0000.0000.000
50A103PHE00.0420.00319.5630.6180.6180.0000.0000.0000.000
51A104SER0-0.092-0.05621.8890.7120.7120.0000.0000.0000.000
52A105ALA00.0170.01522.9680.2450.2450.0000.0000.0000.000
53A106LEU00.0270.00519.1090.4860.4860.0000.0000.0000.000
54A107SER0-0.090-0.05818.0620.7190.7190.0000.0000.0000.000
55A108GLU-1-0.911-0.96317.86515.97415.9740.0000.0000.0000.000
56A109VAL0-0.033-0.01319.2090.4300.4300.0000.0000.0000.000
57A110LEU00.006-0.01315.0370.5020.5020.0000.0000.0000.000
58A111ASP-1-0.779-0.83913.90323.44123.4410.0000.0000.0000.000
59A112ASN0-0.074-0.02915.3030.7510.7510.0000.0000.0000.000
60A113GLN0-0.020-0.00714.202-1.626-1.6260.0000.0000.0000.000
61A114LYS10.8520.91013.500-20.906-20.9060.0000.0000.0000.000
62A115GLU-1-0.944-0.97010.00526.81526.8150.0000.0000.0000.000
63A116ARG10.7880.87010.098-21.749-21.7490.0000.0000.0000.000
64A117GLU-1-0.722-0.8009.55925.56025.5600.0000.0000.0000.000
65A118LYS10.8380.91610.827-22.434-22.4340.0000.0000.0000.000
66A119LEU00.0390.02912.3871.0311.0310.0000.0000.0000.000
67A120THR00.0050.00815.411-0.532-0.5320.0000.0000.0000.000
68A121ILE00.0290.00818.043-0.127-0.1270.0000.0000.0000.000
69A122GLU-1-0.814-0.87920.86914.72814.7280.0000.0000.0000.000
70A123GLN00.0380.01923.6250.0390.0390.0000.0000.0000.000
71A124SER00.003-0.01724.1920.1610.1610.0000.0000.0000.000
72A125VAL0-0.0030.00925.5000.1530.1530.0000.0000.0000.000
73A126LYS10.7920.88322.254-14.338-14.3380.0000.0000.0000.000
74A127GLY00.0350.01828.586-0.286-0.2860.0000.0000.0000.000
75A128GLN0-0.071-0.02731.330-0.448-0.4480.0000.0000.0000.000
76A129ALA0-0.020-0.00631.0860.2860.2860.0000.0000.0000.000
77A130LEU00.0120.01730.4050.2680.2680.0000.0000.0000.000
78A131PRO0-0.037-0.02927.194-0.253-0.2530.0000.0000.0000.000
79A132LEU00.0450.02425.5260.1160.1160.0000.0000.0000.000
80A133SER0-0.019-0.00520.969-0.174-0.1740.0000.0000.0000.000
81A134VAL00.0060.01619.7380.2960.2960.0000.0000.0000.000
82A135SER0-0.053-0.02814.8620.5810.5810.0000.0000.0000.000
83A136TYR0-0.027-0.04110.9620.3600.3600.0000.0000.0000.000
84A137VAL00.0010.0147.2500.5870.5870.0000.0000.0000.000
85A138SER0-0.0030.0117.0500.0790.0790.0000.0000.0000.000
86A139THR00.0160.0023.3094.7935.2630.027-0.152-0.3450.000
87A140THR0-0.021-0.0403.3692.1423.0040.058-0.452-0.469-0.003
88A141ALA00.0460.0305.919-1.111-1.1110.0000.0000.0000.000
89A142GLU-1-0.730-0.8608.16623.15123.1510.0000.0000.0000.000
90A143GLY0-0.0010.0119.126-1.471-1.4710.0000.0000.0000.000
91A144ALA00.0210.0038.911-1.326-1.3260.0000.0000.0000.000
92A145GLN0-0.052-0.03610.742-1.086-1.0860.0000.0000.0000.000
93A146ARG10.7900.89811.222-21.928-21.9280.0000.0000.0000.000
94A147ARG10.9350.94012.497-19.647-19.6470.0000.0000.0000.000
95A148LEU0-0.044-0.00214.645-0.947-0.9470.0000.0000.0000.000
96A149ALA00.028-0.00816.348-0.844-0.8440.0000.0000.0000.000
97A150GLU-1-0.892-0.91916.39516.69816.6980.0000.0000.0000.000
98A151TYR00.021-0.02714.120-1.136-1.1360.0000.0000.0000.000
99A152ILE0-0.063-0.01319.453-0.537-0.5370.0000.0000.0000.000
100A153GLN0-0.087-0.05822.145-0.486-0.4860.0000.0000.0000.000
101A154GLN00.0120.00820.597-0.083-0.0830.0000.0000.0000.000
102A155VAL00.0250.02222.794-0.393-0.3930.0000.0000.0000.000
103A156ASP-1-0.791-0.91725.28710.12610.1260.0000.0000.0000.000
104A157GLU-1-0.876-0.92927.10411.02111.0210.0000.0000.0000.000
105A158GLU-1-0.956-0.97126.44011.48211.4820.0000.0000.0000.000
106A159VAL0-0.026-0.02028.986-0.373-0.3730.0000.0000.0000.000
107A160ALA00.0350.01431.248-0.387-0.3870.0000.0000.0000.000
108A161LYS10.7730.86932.519-8.995-8.9950.0000.0000.0000.000
109A162GLU-1-0.818-0.90633.4849.0509.0500.0000.0000.0000.000
110A163LEU00.0370.03434.854-0.314-0.3140.0000.0000.0000.000
111A164GLU-1-0.847-0.91137.1997.8867.8860.0000.0000.0000.000
112A165VAL00.011-0.00737.596-0.252-0.2520.0000.0000.0000.000
113A166ASP-1-0.764-0.87639.3067.9907.9900.0000.0000.0000.000
114A167LEU0-0.084-0.01341.199-0.239-0.2390.0000.0000.0000.000
115A168LYS10.9360.94943.048-7.402-7.4020.0000.0000.0000.000
116A169ASP-1-0.844-0.90843.6667.0797.0790.0000.0000.0000.000
117A170ASN0-0.077-0.06444.673-0.288-0.2880.0000.0000.0000.000
118A171ILE0-0.033-0.01346.837-0.172-0.1720.0000.0000.0000.000
119A172THR0-0.051-0.01848.123-0.216-0.2160.0000.0000.0000.000
120A173LEU00.014-0.00648.545-0.181-0.1810.0000.0000.0000.000
121A174GLN0-0.0090.01151.597-0.144-0.1440.0000.0000.0000.000
122A175THR0-0.025-0.02153.286-0.170-0.1700.0000.0000.0000.000
123A176LYS10.8180.91554.851-5.732-5.7320.0000.0000.0000.000
124A177THR00.0270.01756.001-0.121-0.1210.0000.0000.0000.000
125A178LEU00.0430.01056.926-0.128-0.1280.0000.0000.0000.000
126A179GLN0-0.0140.00859.008-0.020-0.0200.0000.0000.0000.000
127A180GLU-1-0.770-0.87959.9805.3455.3450.0000.0000.0000.000
128A181SER0-0.074-0.03262.304-0.101-0.1010.0000.0000.0000.000
129A182LEU0-0.009-0.01963.402-0.111-0.1110.0000.0000.0000.000
130A183GLU-1-0.880-0.93563.4695.0205.0200.0000.0000.0000.000
131A184THR0-0.018-0.00766.117-0.069-0.0690.0000.0000.0000.000
132A185GLN0-0.066-0.04268.179-0.141-0.1410.0000.0000.0000.000
133A186GLU-1-0.875-0.95168.9364.6414.6410.0000.0000.0000.000
134A187VAL00.0160.03371.122-0.049-0.0490.0000.0000.0000.000
135A188VAL00.0560.03072.806-0.070-0.0700.0000.0000.0000.000
136A189ALA0-0.100-0.05073.971-0.084-0.0840.0000.0000.0000.000
137A190GLN00.0050.00475.764-0.022-0.0220.0000.0000.0000.000
138A191GLU-1-0.828-0.92576.6504.2064.2060.0000.0000.0000.000
139A192GLN0-0.049-0.02878.595-0.050-0.0500.0000.0000.0000.000
140A193LYS10.8360.89877.172-4.246-4.2460.0000.0000.0000.000
141A194ASP-1-0.828-0.88881.5773.9103.9100.0000.0000.0000.000
142A195LEU00.0110.02383.057-0.053-0.0530.0000.0000.0000.000
143A196ARG11.0240.98983.753-3.923-3.9230.0000.0000.0000.000
144A197ILE0-0.0260.00185.856-0.045-0.0450.0000.0000.0000.000
145A198LYS10.8170.87785.092-3.837-3.8370.0000.0000.0000.000
146A199GLN0-0.033-0.00186.5050.0120.0120.0000.0000.0000.000
147A200ILE0-0.042-0.02089.455-0.024-0.0240.0000.0000.0000.000
148A201GLU-1-0.836-0.89291.7413.3903.3900.0000.0000.0000.000
149A202GLU-1-0.862-0.88193.4953.4593.4590.0000.0000.0000.000
150A203ALA0-0.011-0.01295.174-0.013-0.0130.0000.0000.0000.000
151A204LEU00.003-0.00898.086-0.027-0.0270.0000.0000.0000.000
152A205ARG10.7880.85495.047-3.415-3.4150.0000.0000.0000.000
153A206TYR0-0.031-0.02694.535-0.011-0.0110.0000.0000.0000.000
154A207ALA0-0.051-0.043100.9810.0060.0060.0000.0000.0000.000
155A208ASP-1-0.839-0.900100.8833.1453.1450.0000.0000.0000.000
156A209GLU-1-0.882-0.95597.7273.3293.3290.0000.0000.0000.000
157A210ALA0-0.027-0.01096.2590.0420.0420.0000.0000.0000.000
158A211LYS10.8100.89195.476-3.330-3.3300.0000.0000.0000.000
159A212ILE0-0.0250.00295.1590.0170.0170.0000.0000.0000.000
160A213THR0-0.068-0.01391.0270.0370.0370.0000.0000.0000.000
161A214GLN0-0.0120.00590.7610.0220.0220.0000.0000.0000.000
162A247PRO00.017-0.02080.5030.0140.0140.0000.0000.0000.000
163A248LEU0-0.039-0.00876.7780.0010.0010.0000.0000.0000.000
164A249VAL00.0410.03875.3780.0510.0510.0000.0000.0000.000
165A250PHE0-0.006-0.00972.063-0.020-0.0200.0000.0000.0000.000
166A251SER00.0340.01171.3880.0010.0010.0000.0000.0000.000
167A252PRO00.0470.01069.7950.0430.0430.0000.0000.0000.000
168A253ALA00.0110.01467.1140.0750.0750.0000.0000.0000.000
169A254TYR00.032-0.01265.9440.0510.0510.0000.0000.0000.000
170A255TYR0-0.022-0.00366.4400.0300.0300.0000.0000.0000.000
171A256GLN00.0110.01462.2860.0670.0670.0000.0000.0000.000
172A257THR00.0160.00761.3900.0850.0850.0000.0000.0000.000
173A258LYS10.8570.92161.187-4.725-4.7250.0000.0000.0000.000
174A259GLN0-0.046-0.01159.643-0.029-0.0290.0000.0000.0000.000
175A260THR00.0180.00357.5250.0490.0490.0000.0000.0000.000
176A261LEU00.0130.00656.9290.1120.1120.0000.0000.0000.000
177A262LEU0-0.0060.00657.4030.0520.0520.0000.0000.0000.000
178A263ASP-1-0.826-0.93054.9785.6875.6870.0000.0000.0000.000
179A264ILE0-0.036-0.01152.3990.1320.1320.0000.0000.0000.000
180A265LYS10.8650.93852.192-5.534-5.5340.0000.0000.0000.000
181A266ASN0-0.112-0.04552.9580.0770.0770.0000.0000.0000.000
182A267LEU00.0680.06046.5830.0170.0170.0000.0000.0000.000
183A268LYS10.8070.87346.980-6.173-6.1730.0000.0000.0000.000
184A269VAL00.0220.00841.0370.0220.0220.0000.0000.0000.000
185A270THR0-0.0090.01239.1120.0140.0140.0000.0000.0000.000
186A271ALA00.0530.02736.1660.0420.0420.0000.0000.0000.000
187A272ASP-1-0.872-0.93034.9098.7458.7450.0000.0000.0000.000
188A273THR0-0.147-0.08535.979-0.068-0.0680.0000.0000.0000.000
189A274VAL0-0.035-0.01135.548-0.016-0.0160.0000.0000.0000.000
190A275HIS0-0.033-0.01430.2170.1020.1020.0000.0000.0000.000
191A276VAL00.0250.01629.941-0.188-0.1880.0000.0000.0000.000
192A277TYR0-0.064-0.03425.5670.2110.2110.0000.0000.0000.000
193A278ARG10.8990.95629.720-9.480-9.4800.0000.0000.0000.000
194A279TYR0-0.025-0.02122.0600.3820.3820.0000.0000.0000.000
195A280VAL0-0.048-0.01825.876-0.429-0.4290.0000.0000.0000.000
196A281MET0-0.045-0.02219.091-0.278-0.2780.0000.0000.0000.000
197A282LYS10.9800.98921.168-12.076-12.0760.0000.0000.0000.000
198A283PRO00.0100.00916.7280.1230.1230.0000.0000.0000.000
199A284THR00.0160.02714.079-0.091-0.0910.0000.0000.0000.000
200A285LEU00.0000.02111.7251.0111.0110.0000.0000.0000.000
201A286PRO0-0.066-0.0249.004-0.690-0.6900.0000.0000.0000.000
202A287VAL00.0300.02310.1510.9810.9810.0000.0000.0000.000
203A288ARG10.8280.9209.509-24.449-24.4490.0000.0000.0000.000
204A289ARG10.9590.9672.165-68.185-67.4186.468-3.515-3.7200.029
205A290ASP-1-0.813-0.9086.94632.41632.4160.0000.0000.0000.000
206A291SER00.001-0.0125.7927.7367.750-0.001-0.003-0.0100.000
207A292PRO00.0020.0237.706-3.690-3.6900.0000.0000.0000.000