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: QY3MY

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 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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2081096.683863
FMO2-HF: Nuclear repulsion 2005740.617289
FMO2-HF: Total energy -75356.066574
FMO2-MP2: Total energy -75574.303267


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.
-8.063-1.3360.588-2.35-4.964-0.002
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 : 0.059 / q_NPA : 0.020
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].
3A133THR0-0.062-0.0232.892-2.0470.9040.076-1.155-1.8710.007
4A134LEU00.0850.0664.514-0.598-0.345-0.001-0.021-0.2320.000
5A135TRP00.009-0.0197.0530.3450.3450.0000.0000.0000.000
6A136THR00.0840.0639.890-0.072-0.0720.0000.0000.0000.000
7A137GLY0-0.089-0.03711.563-0.014-0.0140.0000.0000.0000.000
8A138ILE00.023-0.01012.504-0.006-0.0060.0000.0000.0000.000
9A139ASN0-0.0210.00814.777-0.035-0.0350.0000.0000.0000.000
10A140PRO00.0310.03816.430-0.006-0.0060.0000.0000.0000.000
11A141PRO00.0190.01418.1580.0090.0090.0000.0000.0000.000
12A142PRO00.018-0.02320.895-0.006-0.0060.0000.0000.0000.000
13A143ASN0-0.0160.01217.808-0.005-0.0050.0000.0000.0000.000
14A144CYS0-0.0100.00321.338-0.016-0.0160.0000.0000.0000.000
15A145GLN00.0260.02923.594-0.004-0.0040.0000.0000.0000.000
16A146ILE0-0.017-0.03226.265-0.003-0.0030.0000.0000.0000.000
17A147VAL00.0040.01528.343-0.001-0.0010.0000.0000.0000.000
18A148GLU-1-0.947-0.96231.100-0.039-0.0390.0000.0000.0000.000
19A149ASN0-0.064-0.04432.163-0.003-0.0030.0000.0000.0000.000
20A150THR0-0.053-0.03530.745-0.003-0.0030.0000.0000.0000.000
21A151ASN00.0390.02931.169-0.002-0.0020.0000.0000.0000.000
22A152THR0-0.057-0.04029.393-0.003-0.0030.0000.0000.0000.000
23A153ASN00.013-0.01224.130-0.004-0.0040.0000.0000.0000.000
24A154ASP-1-0.759-0.86327.157-0.013-0.0130.0000.0000.0000.000
25A155GLY00.0700.02225.7160.0070.0070.0000.0000.0000.000
26A156LYS10.7730.87921.251-0.079-0.0790.0000.0000.0000.000
27A157LEU00.0410.00918.1630.0120.0120.0000.0000.0000.000
28A158THR0-0.056-0.02915.5470.0030.0030.0000.0000.0000.000
29A159LEU00.0470.01313.6340.0060.0060.0000.0000.0000.000
30A160VAL0-0.055-0.0409.7630.0050.0050.0000.0000.0000.000
31A161LEU00.0260.0169.3010.0310.0310.0000.0000.0000.000
32A162VAL0-0.025-0.0317.2040.0000.0000.0000.0000.0000.000
33A163LYS10.8850.9635.0170.3680.3680.0000.0000.0000.000
34A164ASN0-0.053-0.0316.8020.3710.3710.0000.0000.0000.000
35A165GLY00.0580.0368.828-0.057-0.0570.0000.0000.0000.000
36A166GLY00.0310.00610.236-0.089-0.0890.0000.0000.0000.000
37A167LEU0-0.004-0.00212.324-0.036-0.0360.0000.0000.0000.000
38A168VAL0-0.0020.0039.2620.0070.0070.0000.0000.0000.000
39A169ASN0-0.047-0.01511.0240.0800.0800.0000.0000.0000.000
40A170GLY00.0670.02112.1540.0030.0030.0000.0000.0000.000
41A171TYR0-0.027-0.02814.2360.0340.0340.0000.0000.0000.000
42A172VAL00.0070.00715.633-0.014-0.0140.0000.0000.0000.000
43A173SER0-0.009-0.00318.3830.0100.0100.0000.0000.0000.000
44A174LEU00.0090.01520.387-0.008-0.0080.0000.0000.0000.000
45A175VAL0-0.016-0.00923.0700.0080.0080.0000.0000.0000.000
46A176GLY00.0720.05425.276-0.010-0.0100.0000.0000.0000.000
47A177VAL0-0.085-0.04426.0110.0050.0050.0000.0000.0000.000
48A178SER00.0480.02129.1300.0010.0010.0000.0000.0000.000
49A179ASP-1-0.854-0.92732.3740.0050.0050.0000.0000.0000.000
50A180THR0-0.039-0.02334.6940.0010.0010.0000.0000.0000.000
51A181VAL00.0160.00929.4410.0010.0010.0000.0000.0000.000
52A182ASN00.006-0.01731.5840.0030.0030.0000.0000.0000.000
53A183GLN0-0.067-0.01333.8360.0030.0030.0000.0000.0000.000
54A184MET00.0030.00833.667-0.004-0.0040.0000.0000.0000.000
55A185PHE0-0.060-0.03830.7220.0000.0000.0000.0000.0000.000
56A186THR00.0370.00136.4110.0030.0030.0000.0000.0000.000
57A187GLN00.0430.02539.050-0.001-0.0010.0000.0000.0000.000
58A188LYS10.8250.91439.163-0.008-0.0080.0000.0000.0000.000
59A189THR0-0.008-0.01838.3000.0000.0000.0000.0000.0000.000
60A190ALA0-0.0010.01334.301-0.001-0.0010.0000.0000.0000.000
61A191ASN00.003-0.00731.6700.0060.0060.0000.0000.0000.000
62A192ILE0-0.0010.01927.734-0.003-0.0030.0000.0000.0000.000
63A193GLN0-0.041-0.02926.8270.0050.0050.0000.0000.0000.000
64A194LEU0-0.0140.00922.262-0.003-0.0030.0000.0000.0000.000
65A195ARG10.8550.90022.6880.0710.0710.0000.0000.0000.000
66A196LEU0-0.001-0.00616.314-0.003-0.0030.0000.0000.0000.000
67A197TYR00.0340.00618.9990.0040.0040.0000.0000.0000.000
68A198PHE00.030-0.01813.258-0.008-0.0080.0000.0000.0000.000
69A199ASP-1-0.685-0.81214.797-0.411-0.4110.0000.0000.0000.000
70A200SER00.000-0.03514.870-0.036-0.0360.0000.0000.0000.000
71A201SER0-0.101-0.07512.159-0.029-0.0290.0000.0000.0000.000
72A202GLY00.013-0.02210.357-0.096-0.0960.0000.0000.0000.000
73A203ASN0-0.027-0.00511.093-0.090-0.0900.0000.0000.0000.000
74A204LEU0-0.0360.00113.0640.0470.0470.0000.0000.0000.000
75A205LEU0-0.0040.00615.377-0.004-0.0040.0000.0000.0000.000
76A206THR0-0.022-0.01818.2100.0160.0160.0000.0000.0000.000
77A207GLU-1-0.961-0.97220.348-0.096-0.0960.0000.0000.0000.000
78A208GLU-1-0.793-0.89422.610-0.154-0.1540.0000.0000.0000.000
79A209SER0-0.064-0.01719.9810.0050.0050.0000.0000.0000.000
80A210ASP-1-0.751-0.84722.192-0.063-0.0630.0000.0000.0000.000
81A211LEU0-0.064-0.02816.0210.0110.0110.0000.0000.0000.000
82A212LYS10.8780.93820.1080.0800.0800.0000.0000.0000.000
83A213ILE0-0.039-0.02415.9310.0020.0020.0000.0000.0000.000
84A214PRO00.0160.00813.6080.0040.0040.0000.0000.0000.000
85A215LEU0-0.0100.01010.4640.0400.0400.0000.0000.0000.000
86A216LYS10.9780.9788.742-0.036-0.0360.0000.0000.0000.000
87A217ASN00.0960.0443.342-0.0130.5350.022-0.125-0.4450.000
88A218LYS10.9010.9614.329-1.641-1.419-0.001-0.023-0.1990.000
89A219SER00.028-0.0152.658-1.9650.0470.474-0.842-1.644-0.009
90A220SER00.0020.0155.050-0.203-0.178-0.001-0.007-0.0170.000
91A221THR0-0.044-0.0168.8410.1090.1090.0000.0000.0000.000
92A222ALA0-0.081-0.02710.083-0.050-0.0500.0000.0000.0000.000
93A223THR00.0510.0097.2250.0650.0650.0000.0000.0000.000
94A224SER0-0.023-0.0073.8140.0270.1710.001-0.019-0.1240.000
95A225GLU-1-0.914-0.9345.974-0.662-0.6620.0000.0000.0000.000
96A226THR0-0.046-0.0416.024-0.219-0.2190.0000.0000.0000.000
97A227VAL00.0490.0117.314-0.128-0.1280.0000.0000.0000.000
98A228ALA0-0.059-0.0214.8990.1130.1130.0000.0000.0000.000
99A229SER00.0510.0217.0620.0580.0580.0000.0000.0000.000
100A230SER0-0.0100.0076.128-0.397-0.3970.0000.0000.0000.000
101A231LYS10.9570.9687.2160.5910.5910.0000.0000.0000.000
102A232ALA00.0060.0234.8620.1190.1190.0000.0000.0000.000
103A233PHE0-0.014-0.0193.282-0.3310.2410.018-0.158-0.4320.000
104A234MET0-0.0710.0158.1950.1540.1540.0000.0000.0000.000
105A235PRO0-0.012-0.00611.4970.0130.0130.0000.0000.0000.000
106A236SER00.0530.00914.4540.0070.0070.0000.0000.0000.000
107A237THR0-0.079-0.04315.8910.0340.0340.0000.0000.0000.000
108A238THR00.0020.00518.8280.0150.0150.0000.0000.0000.000
109A239ALA0-0.066-0.03219.4080.0170.0170.0000.0000.0000.000
110A240TYR0-0.016-0.00617.0310.0210.0210.0000.0000.0000.000
111A241PRO00.0280.01421.218-0.017-0.0170.0000.0000.0000.000
112A242PHE00.0560.03520.1710.0070.0070.0000.0000.0000.000
113A243ASN0-0.029-0.03325.0080.0110.0110.0000.0000.0000.000
114A244THR0-0.042-0.00928.471-0.003-0.0030.0000.0000.0000.000
115A245THR00.0950.06330.7990.0020.0020.0000.0000.0000.000
116A246THR0-0.118-0.06432.202-0.003-0.0030.0000.0000.0000.000
117A247ARG10.8500.88825.3610.0640.0640.0000.0000.0000.000
118A248ASP-1-0.922-0.97129.497-0.045-0.0450.0000.0000.0000.000
119A249SER00.0310.04228.2010.0060.0060.0000.0000.0000.000
120A250GLU-1-0.886-0.90627.283-0.047-0.0470.0000.0000.0000.000
121A251ASN0-0.045-0.03622.9390.0120.0120.0000.0000.0000.000
122A252TYR00.0680.02723.755-0.007-0.0070.0000.0000.0000.000
123A253ILE0-0.061-0.02619.4990.0100.0100.0000.0000.0000.000
124A254HIS00.0380.01223.8100.0040.0040.0000.0000.0000.000
125A255GLY0-0.003-0.00426.3700.0080.0080.0000.0000.0000.000
126A256ILE0-0.005-0.00227.330-0.006-0.0060.0000.0000.0000.000
127A257CYS0-0.0780.00425.6520.0090.0090.0000.0000.0000.000
128A258TYR00.035-0.01227.539-0.010-0.0100.0000.0000.0000.000
129A259TYR00.0790.03028.6790.0040.0040.0000.0000.0000.000
130A260MET0-0.048-0.01730.9030.0010.0010.0000.0000.0000.000
131A261THR0-0.007-0.01432.8310.0000.0000.0000.0000.0000.000
132A262SER00.0040.00235.5250.0040.0040.0000.0000.0000.000
133A263TYR0-0.0160.00236.5100.0040.0040.0000.0000.0000.000
134A264ASP-1-0.823-0.90439.3930.0560.0560.0000.0000.0000.000
135A265ARG10.8430.89533.709-0.072-0.0720.0000.0000.0000.000
136A266SER00.0270.02835.9400.0060.0060.0000.0000.0000.000
137A267LEU0-0.003-0.00932.1600.0010.0010.0000.0000.0000.000
138A268PHE00.0320.01634.220-0.004-0.0040.0000.0000.0000.000
139A269PRO0-0.020-0.01132.7680.0040.0040.0000.0000.0000.000
140A270LEU0-0.036-0.02029.495-0.005-0.0050.0000.0000.0000.000
141A271ASN0-0.0160.00029.7720.0060.0060.0000.0000.0000.000
142A272ILE00.0040.00923.160-0.003-0.0030.0000.0000.0000.000
143A273SER0-0.025-0.01825.5090.0000.0000.0000.0000.0000.000
144A274ILE0-0.025-0.02619.135-0.005-0.0050.0000.0000.0000.000
145A275MET0-0.041-0.00522.579-0.004-0.0040.0000.0000.0000.000
146A276LEU00.0000.00317.205-0.002-0.0020.0000.0000.0000.000
147A277ASN0-0.023-0.03017.741-0.013-0.0130.0000.0000.0000.000
148A278SER00.0180.00921.0780.0080.0080.0000.0000.0000.000
149A279ARG10.9450.94324.5410.0770.0770.0000.0000.0000.000
150A280MET0-0.023-0.00321.4850.0020.0020.0000.0000.0000.000
151A281ILE0-0.051-0.00524.7060.0040.0040.0000.0000.0000.000
152A282SER00.012-0.02424.6530.0050.0050.0000.0000.0000.000
153A283SER00.0350.01524.862-0.004-0.0040.0000.0000.0000.000
154A284ASN0-0.098-0.05121.7700.0010.0010.0000.0000.0000.000
155A285VAL0-0.0030.01420.332-0.016-0.0160.0000.0000.0000.000
156A286ALA0-0.053-0.02216.7160.0060.0060.0000.0000.0000.000
157A287TYR0-0.030-0.05214.452-0.016-0.0160.0000.0000.0000.000
158A288ALA00.0050.00217.561-0.001-0.0010.0000.0000.0000.000
159A289ILE0-0.0200.01014.1900.0080.0080.0000.0000.0000.000
160A290GLN0-0.028-0.01118.813-0.010-0.0100.0000.0000.0000.000
161A291PHE0-0.0020.01016.9540.0100.0100.0000.0000.0000.000
162A292GLU-1-0.777-0.89723.004-0.032-0.0320.0000.0000.0000.000
163A293TRP00.001-0.00621.7280.0030.0030.0000.0000.0000.000
164A294ASN0-0.011-0.01228.530-0.001-0.0010.0000.0000.0000.000
165A295LEU0-0.011-0.00632.2590.0050.0050.0000.0000.0000.000
166A296ASN0-0.026-0.03434.841-0.006-0.0060.0000.0000.0000.000
167A297ALA00.0120.01738.2990.0010.0010.0000.0000.0000.000
168A298SER0-0.035-0.03040.289-0.003-0.0030.0000.0000.0000.000
169A299GLU-1-0.897-0.94543.0330.0210.0210.0000.0000.0000.000
170A300SER0-0.034-0.01937.7710.0040.0040.0000.0000.0000.000
171A301PRO0-0.050-0.04036.778-0.001-0.0010.0000.0000.0000.000
172A302GLU-1-0.859-0.88239.2860.0190.0190.0000.0000.0000.000
173A303SER0-0.070-0.03740.7780.0010.0010.0000.0000.0000.000
174A304ASN00.0600.01437.6650.0000.0000.0000.0000.0000.000
175A305ILE0-0.0160.00235.5290.0020.0020.0000.0000.0000.000
176A306ALA00.0080.01134.3970.0050.0050.0000.0000.0000.000
177A307THR0-0.029-0.01228.992-0.002-0.0020.0000.0000.0000.000
178A308LEU0-0.0110.02228.067-0.001-0.0010.0000.0000.0000.000
179A309THR0-0.036-0.04725.3750.0050.0050.0000.0000.0000.000
180A310THR00.0320.03723.8550.0000.0000.0000.0000.0000.000
181A311SER0-0.0090.00724.6260.0070.0070.0000.0000.0000.000
182A312PRO0-0.042-0.04519.624-0.008-0.0080.0000.0000.0000.000
183A313PHE00.0240.02720.8140.0020.0020.0000.0000.0000.000
184A314PHE0-0.012-0.01918.2640.0090.0090.0000.0000.0000.000
185A315PHE00.0170.02815.939-0.016-0.0160.0000.0000.0000.000
186A316SER0-0.007-0.02415.5120.0520.0520.0000.0000.0000.000
187A317TYR0-0.0280.00311.6140.0260.0260.0000.0000.0000.000
188A318ILE00.027-0.00914.2930.0100.0100.0000.0000.0000.000
189A319THR0-0.0010.0049.862-0.048-0.0480.0000.0000.0000.000
190A320GLU-1-0.780-0.86411.557-0.235-0.2350.0000.0000.0000.000
191A321ASP-1-0.962-0.96111.134-0.307-0.3070.0000.0000.0000.000
192A322ASP-1-1.000-1.0038.686-0.749-0.7490.0000.0000.0000.000