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: K9683

Calculation Name: 3BQ4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BQ4

Chain ID: A

ChEMBL ID:

UniProt ID: Q7T925

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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2081469.09447
FMO2-HF: Nuclear repulsion 2006111.670197
FMO2-HF: Total energy -75357.424273
FMO2-MP2: Total energy -75575.535754


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:131:ILE)


Summations of interaction energy for fragment #1(A:131: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.
-7.282-1.2060.693-2.565-4.204-0.006
Interaction energy analysis for fragmet #1(A:131:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.052 / q_NPA : 0.015
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].
3A133THR0-0.089-0.0563.549-1.6811.0800.013-1.386-1.3880.004
4A134LEU00.0480.0434.950-0.648-0.525-0.001-0.011-0.1110.000
5A135TRP00.019-0.0137.5470.3590.3590.0000.0000.0000.000
6A136THR00.0670.03510.520-0.068-0.0680.0000.0000.0000.000
7A137GLY0-0.073-0.02611.708-0.008-0.0080.0000.0000.0000.000
8A138ILE00.032-0.00612.607-0.007-0.0070.0000.0000.0000.000
9A139ASN0-0.0060.00315.128-0.034-0.0340.0000.0000.0000.000
10A140PRO00.0190.04316.762-0.005-0.0050.0000.0000.0000.000
11A141PRO00.0500.01218.4890.0070.0070.0000.0000.0000.000
12A142PRO00.010-0.01021.386-0.004-0.0040.0000.0000.0000.000
13A143ASN0-0.0070.00018.375-0.004-0.0040.0000.0000.0000.000
14A144CYS0-0.033-0.00421.615-0.020-0.0200.0000.0000.0000.000
15A145GLN00.0170.00323.9240.0000.0000.0000.0000.0000.000
16A146ILE00.004-0.01526.644-0.003-0.0030.0000.0000.0000.000
17A147VAL0-0.0110.00328.6310.0010.0010.0000.0000.0000.000
18A148GLU-1-0.917-0.95531.628-0.047-0.0470.0000.0000.0000.000
19A149ASN0-0.063-0.03732.787-0.002-0.0020.0000.0000.0000.000
20A150THR0-0.061-0.03730.990-0.001-0.0010.0000.0000.0000.000
21A151ASN00.0070.00731.377-0.002-0.0020.0000.0000.0000.000
22A152THR0-0.046-0.03029.689-0.003-0.0030.0000.0000.0000.000
23A153ASN0-0.014-0.00823.955-0.006-0.0060.0000.0000.0000.000
24A154ASP-1-0.783-0.87027.466-0.026-0.0260.0000.0000.0000.000
25A155GLY00.0610.02026.4690.0090.0090.0000.0000.0000.000
26A156LYS10.8100.89921.650-0.060-0.0600.0000.0000.0000.000
27A157LEU00.0390.02818.7070.0150.0150.0000.0000.0000.000
28A158THR0-0.042-0.01816.179-0.002-0.0020.0000.0000.0000.000
29A159LEU00.0330.01114.2810.0120.0120.0000.0000.0000.000
30A160VAL0-0.048-0.03410.237-0.009-0.0090.0000.0000.0000.000
31A161LEU00.0420.0379.6950.0330.0330.0000.0000.0000.000
32A162VAL0-0.014-0.0267.930-0.026-0.0260.0000.0000.0000.000
33A163LYS10.8820.9615.1950.4030.4030.0000.0000.0000.000
34A164ASN0-0.054-0.0326.9790.3470.3470.0000.0000.0000.000
35A165GLY00.0660.0359.030-0.064-0.0640.0000.0000.0000.000
36A166GLY00.0260.00710.353-0.097-0.0970.0000.0000.0000.000
37A167LEU0-0.019-0.01112.126-0.027-0.0270.0000.0000.0000.000
38A168VAL0-0.0050.0089.392-0.007-0.0070.0000.0000.0000.000
39A169ASN0-0.025-0.01411.2920.0810.0810.0000.0000.0000.000
40A170GLY00.0350.01312.244-0.020-0.0200.0000.0000.0000.000
41A171TYR0-0.027-0.01514.7590.0300.0300.0000.0000.0000.000
42A172VAL00.0140.00216.159-0.027-0.0270.0000.0000.0000.000
43A173SER00.0020.00118.8770.0120.0120.0000.0000.0000.000
44A174LEU00.0180.01820.918-0.008-0.0080.0000.0000.0000.000
45A175VAL0-0.019-0.00823.6580.0080.0080.0000.0000.0000.000
46A176GLY00.0390.03125.855-0.010-0.0100.0000.0000.0000.000
47A177VAL0-0.078-0.04426.6210.0060.0060.0000.0000.0000.000
48A178SER00.0070.00729.7410.0010.0010.0000.0000.0000.000
49A179ASP-1-0.828-0.91832.822-0.001-0.0010.0000.0000.0000.000
50A180THR0-0.024-0.01735.3550.0020.0020.0000.0000.0000.000
51A181VAL00.009-0.00229.8070.0010.0010.0000.0000.0000.000
52A182ASN00.000-0.00132.0330.0020.0020.0000.0000.0000.000
53A183GLN0-0.043-0.02634.2340.0020.0020.0000.0000.0000.000
54A184MET0-0.0210.00534.075-0.002-0.0020.0000.0000.0000.000
55A185PHE0-0.013-0.02731.2290.0010.0010.0000.0000.0000.000
56A186THR0-0.004-0.02236.6480.0040.0040.0000.0000.0000.000
57A187GLN00.0450.02539.4480.0000.0000.0000.0000.0000.000
58A188LYS10.8340.91839.425-0.004-0.0040.0000.0000.0000.000
59A189THR0-0.019-0.01339.0100.0010.0010.0000.0000.0000.000
60A190ALA0-0.0150.00035.190-0.002-0.0020.0000.0000.0000.000
61A191ASN0-0.031-0.02031.8700.0070.0070.0000.0000.0000.000
62A192ILE00.0190.01828.456-0.002-0.0020.0000.0000.0000.000
63A193GLN0-0.022-0.01727.0250.0060.0060.0000.0000.0000.000
64A194LEU0-0.0060.00022.594-0.002-0.0020.0000.0000.0000.000
65A195ARG10.8450.90622.8720.0860.0860.0000.0000.0000.000
66A196LEU00.0050.00216.618-0.003-0.0030.0000.0000.0000.000
67A197TYR00.0300.00519.1850.0070.0070.0000.0000.0000.000
68A198PHE00.009-0.00613.824-0.011-0.0110.0000.0000.0000.000
69A199ASP-1-0.642-0.78914.594-0.465-0.4650.0000.0000.0000.000
70A200SER0-0.007-0.02015.227-0.034-0.0340.0000.0000.0000.000
71A201SER0-0.076-0.05911.886-0.016-0.0160.0000.0000.0000.000
72A202GLY00.023-0.01010.763-0.132-0.1320.0000.0000.0000.000
73A203ASN0-0.071-0.05211.217-0.126-0.1260.0000.0000.0000.000
74A204LEU0-0.030-0.01513.2490.0460.0460.0000.0000.0000.000
75A205LEU00.0120.00915.8180.0030.0030.0000.0000.0000.000
76A206THR0-0.010-0.00118.3740.0150.0150.0000.0000.0000.000
77A207GLU-1-0.953-0.95720.772-0.106-0.1060.0000.0000.0000.000
78A208GLU-1-0.801-0.90623.211-0.165-0.1650.0000.0000.0000.000
79A209SER0-0.064-0.03520.4090.0070.0070.0000.0000.0000.000
80A210ASP-1-0.751-0.84422.646-0.078-0.0780.0000.0000.0000.000
81A211LEU0-0.056-0.03016.4770.0130.0130.0000.0000.0000.000
82A212LYS10.8860.94320.4680.0930.0930.0000.0000.0000.000
83A213ILE0-0.052-0.02816.4860.0010.0010.0000.0000.0000.000
84A214PRO00.0140.00514.0510.0020.0020.0000.0000.0000.000
85A215LEU0-0.0220.00010.9700.0300.0300.0000.0000.0000.000
86A216LYS10.9180.9649.191-0.022-0.0220.0000.0000.0000.000
87A217ASN00.0640.0383.542-0.0840.2940.004-0.051-0.3320.000
88A218LYS10.9320.9694.205-1.244-1.033-0.001-0.025-0.1850.000
89A219SER0-0.004-0.0192.676-1.8590.1540.673-0.966-1.720-0.010
90A220SER0-0.0010.0144.949-0.131-0.092-0.001-0.009-0.0280.000
91A221THR0-0.033-0.0198.7840.1160.1160.0000.0000.0000.000
92A222ALA0-0.0040.01010.480-0.078-0.0780.0000.0000.0000.000
93A223THR00.026-0.0037.4330.0870.0870.0000.0000.0000.000
94A224SER0-0.039-0.0224.0660.0880.2240.000-0.014-0.1220.000
95A225GLU-1-0.861-0.9106.044-0.694-0.6940.0000.0000.0000.000
96A226THR0-0.037-0.0345.938-0.145-0.1450.0000.0000.0000.000
97A227VAL00.0090.0056.819-0.291-0.2910.0000.0000.0000.000
98A228ALA0-0.023-0.0245.0980.0960.0960.0000.0000.0000.000
99A229SER00.0190.0197.2130.1050.1050.0000.0000.0000.000
100A230SER00.0070.0026.700-0.328-0.3280.0000.0000.0000.000
101A231LYS10.9030.9567.7430.5530.5530.0000.0000.0000.000
102A232ALA00.0090.0275.0990.1210.1210.0000.0000.0000.000
103A233PHE0-0.034-0.0323.615-0.1790.2360.006-0.103-0.3180.000
104A234MET0-0.0420.0268.3880.1590.1590.0000.0000.0000.000
105A235PRO0-0.0060.00611.9220.0140.0140.0000.0000.0000.000
106A236SER0-0.006-0.03515.0120.0020.0020.0000.0000.0000.000
107A237THR0-0.022-0.04716.5630.0340.0340.0000.0000.0000.000
108A238THR0-0.0220.00519.2510.0210.0210.0000.0000.0000.000
109A239ALA0-0.040-0.02219.3930.0180.0180.0000.0000.0000.000
110A240TYR0-0.022-0.01217.3770.0210.0210.0000.0000.0000.000
111A241PRO00.0580.02321.658-0.017-0.0170.0000.0000.0000.000
112A242PHE00.0330.03220.2480.0080.0080.0000.0000.0000.000
113A243ASN0-0.070-0.04525.2770.0070.0070.0000.0000.0000.000
114A244THR0-0.0070.00028.8000.0010.0010.0000.0000.0000.000
115A245THR00.0390.01930.8220.0010.0010.0000.0000.0000.000
116A246THR0-0.120-0.07133.076-0.003-0.0030.0000.0000.0000.000
117A247ARG10.8050.89025.2170.0760.0760.0000.0000.0000.000
118A248ASP-1-0.862-0.93029.685-0.057-0.0570.0000.0000.0000.000
119A249SER00.0000.00928.9880.0060.0060.0000.0000.0000.000
120A250GLU-1-0.819-0.87427.495-0.059-0.0590.0000.0000.0000.000
121A251ASN0-0.042-0.03423.2020.0140.0140.0000.0000.0000.000
122A252TYR00.033-0.00124.837-0.003-0.0030.0000.0000.0000.000
123A253ILE0-0.039-0.01319.4160.0110.0110.0000.0000.0000.000
124A254HIS00.0240.00223.8870.0040.0040.0000.0000.0000.000
125A255GLY0-0.015-0.00926.6530.0080.0080.0000.0000.0000.000
126A256ILE0-0.020-0.00327.745-0.006-0.0060.0000.0000.0000.000
127A257CYS0-0.087-0.01426.4710.0090.0090.0000.0000.0000.000
128A258TYR00.0470.00428.399-0.008-0.0080.0000.0000.0000.000
129A259TYR00.0580.02929.3500.0040.0040.0000.0000.0000.000
130A260MET0-0.033-0.01131.3220.0010.0010.0000.0000.0000.000
131A261THR0-0.012-0.01133.163-0.002-0.0020.0000.0000.0000.000
132A262SER00.0170.01235.7700.0040.0040.0000.0000.0000.000
133A263TYR0-0.013-0.00936.7810.0030.0030.0000.0000.0000.000
134A264ASP-1-0.809-0.90039.9970.0500.0500.0000.0000.0000.000
135A265ARG10.7880.86634.793-0.062-0.0620.0000.0000.0000.000
136A266SER00.0550.05136.4420.0050.0050.0000.0000.0000.000
137A267LEU0-0.019-0.01432.3270.0020.0020.0000.0000.0000.000
138A268PHE00.0510.03135.176-0.002-0.0020.0000.0000.0000.000
139A269PRO0-0.022-0.00833.2320.0030.0030.0000.0000.0000.000
140A270LEU0-0.025-0.01430.047-0.005-0.0050.0000.0000.0000.000
141A271ASN0-0.0040.00030.6170.0080.0080.0000.0000.0000.000
142A272ILE0-0.029-0.01223.528-0.002-0.0020.0000.0000.0000.000
143A273SER0-0.026-0.00525.914-0.001-0.0010.0000.0000.0000.000
144A274ILE00.016-0.00519.417-0.004-0.0040.0000.0000.0000.000
145A275MET0-0.0280.03022.705-0.002-0.0020.0000.0000.0000.000
146A276LEU0-0.008-0.00417.237-0.004-0.0040.0000.0000.0000.000
147A277ASN0-0.017-0.02917.943-0.003-0.0030.0000.0000.0000.000
148A278SER00.013-0.00221.3340.0070.0070.0000.0000.0000.000
149A279ARG10.9230.93424.7070.0890.0890.0000.0000.0000.000
150A280MET0-0.0180.00022.194-0.001-0.0010.0000.0000.0000.000
151A281ILE0-0.028-0.00324.7940.0060.0060.0000.0000.0000.000
152A282SER00.0270.00025.1150.0090.0090.0000.0000.0000.000
153A283SER0-0.003-0.00725.104-0.006-0.0060.0000.0000.0000.000
154A284ASN0-0.055-0.03421.9170.0030.0030.0000.0000.0000.000
155A285VAL0-0.051-0.01320.500-0.024-0.0240.0000.0000.0000.000
156A286ALA0-0.039-0.01917.3220.0090.0090.0000.0000.0000.000
157A287TYR0-0.022-0.03515.008-0.021-0.0210.0000.0000.0000.000
158A288ALA00.007-0.00517.6820.0040.0040.0000.0000.0000.000
159A289ILE0-0.026-0.00814.5510.0040.0040.0000.0000.0000.000
160A290GLN0-0.0270.00019.165-0.008-0.0080.0000.0000.0000.000
161A291PHE00.004-0.00117.0390.0080.0080.0000.0000.0000.000
162A292GLU-1-0.790-0.88523.141-0.043-0.0430.0000.0000.0000.000
163A293TRP00.010-0.01122.4570.0040.0040.0000.0000.0000.000
164A294ASN0-0.020-0.02228.9530.0000.0000.0000.0000.0000.000
165A295LEU00.0190.01532.6800.0050.0050.0000.0000.0000.000
166A296ASN00.002-0.01035.201-0.005-0.0050.0000.0000.0000.000
167A297ALA00.0020.00738.6700.0020.0020.0000.0000.0000.000
168A298SER0-0.031-0.02140.933-0.003-0.0030.0000.0000.0000.000
169A299GLU-1-0.907-0.97043.3500.0170.0170.0000.0000.0000.000
170A300SER00.0070.00838.1120.0030.0030.0000.0000.0000.000
171A301PRO0-0.069-0.04237.635-0.002-0.0020.0000.0000.0000.000
172A302GLU-1-0.843-0.87439.9350.0130.0130.0000.0000.0000.000
173A303SER0-0.049-0.03240.7260.0030.0030.0000.0000.0000.000
174A304ASN0-0.0050.00537.9980.0020.0020.0000.0000.0000.000
175A305ILE00.0070.00136.8160.0010.0010.0000.0000.0000.000
176A306ALA00.0010.01035.1840.0060.0060.0000.0000.0000.000
177A307THR0-0.044-0.03229.798-0.004-0.0040.0000.0000.0000.000
178A308LEU00.0070.02628.600-0.001-0.0010.0000.0000.0000.000
179A309THR0-0.019-0.03026.0010.0050.0050.0000.0000.0000.000
180A310THR00.0080.02124.529-0.001-0.0010.0000.0000.0000.000
181A311SER00.002-0.00625.1220.0070.0070.0000.0000.0000.000
182A312PRO0-0.055-0.03720.335-0.007-0.0070.0000.0000.0000.000
183A313PHE00.0390.03621.3670.0040.0040.0000.0000.0000.000
184A314PHE0-0.028-0.02518.7510.0100.0100.0000.0000.0000.000
185A315PHE00.0380.03215.924-0.015-0.0150.0000.0000.0000.000
186A316SER0-0.020-0.03215.7600.0510.0510.0000.0000.0000.000
187A317TYR0-0.026-0.00711.9480.0270.0270.0000.0000.0000.000
188A318ILE00.0270.00714.4940.0040.0040.0000.0000.0000.000
189A319THR0-0.051-0.03310.348-0.041-0.0410.0000.0000.0000.000
190A320GLU-1-0.729-0.80012.471-0.230-0.2300.0000.0000.0000.000
191A321ASP-1-0.937-0.95711.604-0.320-0.3200.0000.0000.0000.000
192A322ASP-1-0.977-0.9828.191-0.796-0.7960.0000.0000.0000.000