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: J3V29

Calculation Name: 3D3J-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3D3J

Chain ID: A

ChEMBL ID:

UniProt ID: Q96F86

Base Structure: X-ray

Registration Date: 2023-03-14

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 239
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3001660.230652
FMO2-HF: Nuclear repulsion 2908587.548382
FMO2-HF: Total energy -93072.68227
FMO2-MP2: Total energy -93341.945138


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:258:TYR)


Summations of interaction energy for fragment #1(A:258:TYR)
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.
-9.744-1.4351.033-3.399-5.940.005
Interaction energy analysis for fragmet #1(A:258:TYR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.073 / q_NPA : 0.034
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].
3A260ARG10.9280.9763.176-6.836-1.6610.642-2.138-3.6790.008
4A261ILE00.0090.0075.342-0.191-0.008-0.001-0.011-0.1700.000
5A262ILE0-0.030-0.0135.872-0.200-0.2000.0000.0000.0000.000
6A263VAL00.0140.0019.6680.1160.1160.0000.0000.0000.000
7A264PRO00.0110.01213.283-0.019-0.0190.0000.0000.0000.000
8A265HIS0-0.070-0.03215.8360.0420.0420.0000.0000.0000.000
9A266ASN00.029-0.00115.162-0.047-0.0470.0000.0000.0000.000
10A267VAL00.0120.01516.4440.0050.0050.0000.0000.0000.000
11A268SER0-0.032-0.02216.0700.0190.0190.0000.0000.0000.000
12A269LYS10.9550.99414.8450.2520.2520.0000.0000.0000.000
13A270GLU-1-0.840-0.9158.648-1.033-1.0330.0000.0000.0000.000
14A271PHE0-0.0260.00510.7700.1030.1030.0000.0000.0000.000
15A272CYS00.013-0.0036.273-0.186-0.1860.0000.0000.0000.000
16A273THR00.0330.0236.8060.2040.2040.0000.0000.0000.000
17A274ASP-1-0.863-0.9457.914-0.106-0.1060.0000.0000.0000.000
18A275SER0-0.057-0.0236.622-0.031-0.0310.0000.0000.0000.000
19A276GLY00.0210.0074.7690.4240.526-0.001-0.008-0.0920.000
20A277LEU0-0.079-0.0282.538-3.769-1.6150.362-1.071-1.445-0.003
21A278VAL0-0.006-0.0063.2850.9221.6170.031-0.171-0.5540.000
22A279VAL0-0.026-0.0105.5130.1620.1620.0000.0000.0000.000
23A280PRO00.0170.0108.9520.1360.1360.0000.0000.0000.000
24A281SER0-0.044-0.02611.3330.0830.0830.0000.0000.0000.000
25A282ILE0-0.004-0.00315.064-0.022-0.0220.0000.0000.0000.000
26A283SER00.021-0.00117.8690.0260.0260.0000.0000.0000.000
27A284TYR00.023-0.01521.451-0.006-0.0060.0000.0000.0000.000
28A285GLU-1-0.851-0.94024.340-0.183-0.1830.0000.0000.0000.000
29A286LEU0-0.059-0.01617.9650.0080.0080.0000.0000.0000.000
30A287HIS00.0130.00420.1520.0060.0060.0000.0000.0000.000
31A288LYS10.9090.93322.6730.1510.1510.0000.0000.0000.000
32A289LYS10.9370.96423.5010.2550.2550.0000.0000.0000.000
33A290LEU00.0090.00519.3510.0070.0070.0000.0000.0000.000
34A291LEU0-0.004-0.01323.0470.0130.0130.0000.0000.0000.000
35A292SER0-0.046-0.00925.7470.0140.0140.0000.0000.0000.000
36A293VAL0-0.018-0.00723.2960.0130.0130.0000.0000.0000.000
37A294ALA00.0190.00524.0200.0100.0100.0000.0000.0000.000
38A295GLU-1-0.912-0.95925.600-0.106-0.1060.0000.0000.0000.000
39A296LYS10.8880.94728.8740.1560.1560.0000.0000.0000.000
40A297HIS0-0.082-0.03525.4300.0170.0170.0000.0000.0000.000
41A298GLY00.0090.01627.6150.0030.0030.0000.0000.0000.000
42A299LEU0-0.060-0.02924.5330.0100.0100.0000.0000.0000.000
43A300THR00.0660.02128.598-0.008-0.0080.0000.0000.0000.000
44A301LEU00.0500.01730.254-0.005-0.0050.0000.0000.0000.000
45A302GLU-1-0.907-0.96131.194-0.069-0.0690.0000.0000.0000.000
46A303ARG10.9570.99129.3810.0780.0780.0000.0000.0000.000
47A304ARG10.9170.96725.4750.1380.1380.0000.0000.0000.000
48A305LEU0-0.019-0.00227.690-0.004-0.0040.0000.0000.0000.000
49A306GLU-1-0.794-0.85330.188-0.056-0.0560.0000.0000.0000.000
50A307MET0-0.038-0.00721.7410.0030.0030.0000.0000.0000.000
51A308THR0-0.026-0.04025.162-0.005-0.0050.0000.0000.0000.000
52A309GLY00.0280.02226.2210.0000.0000.0000.0000.0000.000
53A310VAL00.0340.01926.3310.0030.0030.0000.0000.0000.000
54A311CYS0-0.0170.00722.5500.0050.0050.0000.0000.0000.000
55A312ALA00.012-0.00124.180-0.001-0.0010.0000.0000.0000.000
56A313SER0-0.034-0.03625.6420.0060.0060.0000.0000.0000.000
57A314GLN00.0330.00024.5200.0000.0000.0000.0000.0000.000
58A315MET0-0.047-0.00421.3290.0010.0010.0000.0000.0000.000
59A316ALA00.0350.00124.2780.0060.0060.0000.0000.0000.000
60A317LEU00.010-0.00227.5960.0050.0050.0000.0000.0000.000
61A318THR0-0.059-0.02122.9360.0090.0090.0000.0000.0000.000
62A319LEU0-0.114-0.06023.6090.0040.0040.0000.0000.0000.000
63A320LEU0-0.022-0.00127.1000.0030.0030.0000.0000.0000.000
64A321GLY0-0.0450.00229.3210.0070.0070.0000.0000.0000.000
65A333GLN0-0.005-0.00942.221-0.001-0.0010.0000.0000.0000.000
66A334ARG10.8970.94540.0070.0110.0110.0000.0000.0000.000
67A335PRO00.0700.05935.6190.0000.0000.0000.0000.0000.000
68A336THR0-0.032-0.02537.869-0.001-0.0010.0000.0000.0000.000
69A337VAL00.012-0.00733.309-0.002-0.0020.0000.0000.0000.000
70A338ALA0-0.0130.00835.9860.0010.0010.0000.0000.0000.000
71A339LEU00.004-0.01032.883-0.004-0.0040.0000.0000.0000.000
72A340LEU00.0100.01134.7200.0020.0020.0000.0000.0000.000
73A341CYS0-0.0050.02034.462-0.007-0.0070.0000.0000.0000.000
74A342GLY00.0620.02735.2440.0040.0040.0000.0000.0000.000
75A343PRO0-0.026-0.00836.997-0.001-0.0010.0000.0000.0000.000
76A344HIS0-0.004-0.03033.460-0.003-0.0030.0000.0000.0000.000
77A345VAL00.020-0.00830.8190.0020.0020.0000.0000.0000.000
78A346LYS10.9640.98927.1230.1530.1530.0000.0000.0000.000
79A347GLY00.0110.02031.0180.0010.0010.0000.0000.0000.000
80A348ALA0-0.013-0.02033.7790.0040.0040.0000.0000.0000.000
81A349GLN0-0.002-0.00126.7390.0040.0040.0000.0000.0000.000
82A350GLY00.0770.02730.7800.0030.0030.0000.0000.0000.000
83A351ILE0-0.0170.00031.9460.0050.0050.0000.0000.0000.000
84A352SER00.0000.00131.4630.0070.0070.0000.0000.0000.000
85A353CYS0-0.047-0.02229.2070.0060.0060.0000.0000.0000.000
86A354GLY00.015-0.00531.3030.0050.0050.0000.0000.0000.000
87A355ARG10.8800.92934.4580.0590.0590.0000.0000.0000.000
88A356HIS0-0.042-0.01631.5970.0090.0090.0000.0000.0000.000
89A357LEU0-0.023-0.01330.4440.0050.0050.0000.0000.0000.000
90A358ALA0-0.009-0.00134.1230.0040.0040.0000.0000.0000.000
91A359ASN0-0.022-0.01235.7310.0040.0040.0000.0000.0000.000
92A360HIS0-0.119-0.04732.8250.0070.0070.0000.0000.0000.000
93A361ASP-1-0.929-0.96036.298-0.012-0.0120.0000.0000.0000.000
94A362VAL0-0.022-0.00734.2640.0010.0010.0000.0000.0000.000
95A363GLN0-0.020-0.02037.6900.0010.0010.0000.0000.0000.000
96A364VAL0-0.0010.01836.298-0.002-0.0020.0000.0000.0000.000
97A365ILE0-0.0020.01038.8920.0020.0020.0000.0000.0000.000
98A366LEU0-0.021-0.02737.356-0.003-0.0030.0000.0000.0000.000
99A367PHE0-0.023-0.00939.1590.0020.0020.0000.0000.0000.000
100A368LEU0-0.014-0.02038.815-0.004-0.0040.0000.0000.0000.000
101A369PRO0-0.0160.01540.5590.0040.0040.0000.0000.0000.000
102A370ASN00.014-0.01343.633-0.001-0.0010.0000.0000.0000.000
103A371PHE0-0.019-0.01142.495-0.002-0.0020.0000.0000.0000.000
104A372VAL00.0210.01346.2080.0010.0010.0000.0000.0000.000
105A373LYS10.9110.95045.0920.0590.0590.0000.0000.0000.000
106A374MET00.0650.02543.779-0.003-0.0030.0000.0000.0000.000
107A375LEU00.0090.01737.646-0.002-0.0020.0000.0000.0000.000
108A376GLU-1-0.936-0.94439.946-0.070-0.0700.0000.0000.0000.000
109A377SER00.0570.01935.4980.0040.0040.0000.0000.0000.000
110A378ILE00.0160.00736.8760.0020.0020.0000.0000.0000.000
111A379THR0-0.030-0.02839.0090.0040.0040.0000.0000.0000.000
112A380ASN0-0.013-0.01838.8210.0000.0000.0000.0000.0000.000
113A381GLU-1-0.807-0.92834.486-0.065-0.0650.0000.0000.0000.000
114A382LEU0-0.0030.00438.2710.0030.0030.0000.0000.0000.000
115A383SER0-0.0370.01441.2030.0040.0040.0000.0000.0000.000
116A384LEU00.024-0.00437.4280.0040.0040.0000.0000.0000.000
117A385PHE00.0000.00837.8680.0020.0020.0000.0000.0000.000
118A386SER0-0.061-0.03940.6400.0030.0030.0000.0000.0000.000
119A387LYS10.8570.94043.2560.0360.0360.0000.0000.0000.000
120A388THR0-0.037-0.01239.1960.0020.0020.0000.0000.0000.000
121A389GLN00.0300.00541.942-0.002-0.0020.0000.0000.0000.000
122A390GLY0-0.0130.00340.9450.0010.0010.0000.0000.0000.000
123A391GLN0-0.006-0.01241.8590.0000.0000.0000.0000.0000.000
124A392GLN00.0120.01342.408-0.002-0.0020.0000.0000.0000.000
125A393VAL0-0.010-0.00843.3120.0020.0020.0000.0000.0000.000
126A394SER00.0280.01343.792-0.002-0.0020.0000.0000.0000.000
127A395SER0-0.021-0.00745.872-0.001-0.0010.0000.0000.0000.000
128A396LEU00.0160.00241.4310.0000.0000.0000.0000.0000.000
129A397LYS10.8830.92544.8300.0310.0310.0000.0000.0000.000
130A398ASP-1-0.855-0.91746.721-0.030-0.0300.0000.0000.0000.000
131A399LEU0-0.070-0.01740.9710.0000.0000.0000.0000.0000.000
132A400PRO00.0100.00142.2830.0010.0010.0000.0000.0000.000
133A401THR0-0.006-0.01143.650-0.002-0.0020.0000.0000.0000.000
134A402SER0-0.046-0.01843.6610.0000.0000.0000.0000.0000.000
135A403PRO0-0.027-0.01339.150-0.001-0.0010.0000.0000.0000.000
136A404VAL0-0.0300.00036.6430.0020.0020.0000.0000.0000.000
137A405ASP-1-0.834-0.92234.658-0.022-0.0220.0000.0000.0000.000
138A406LEU0-0.055-0.03029.103-0.002-0.0020.0000.0000.0000.000
139A407VAL00.0130.02232.4470.0010.0010.0000.0000.0000.000
140A408ILE0-0.001-0.00729.406-0.006-0.0060.0000.0000.0000.000
141A409ASN00.014-0.01529.6660.0080.0080.0000.0000.0000.000
142A410CYS0-0.058-0.01729.711-0.010-0.0100.0000.0000.0000.000
143A411LEU00.0770.02031.5350.0020.0020.0000.0000.0000.000
144A412ASP-1-0.803-0.90231.218-0.105-0.1050.0000.0000.0000.000
145A413CYS0-0.054-0.00730.891-0.011-0.0110.0000.0000.0000.000
146A414PRO00.0400.01228.3400.0040.0040.0000.0000.0000.000
147A415GLU-1-0.808-0.88431.364-0.130-0.1300.0000.0000.0000.000
148A416ASN0-0.094-0.04334.0060.0040.0040.0000.0000.0000.000
149A417VAL00.0600.03135.9480.0030.0030.0000.0000.0000.000
150A418PHE00.0510.00136.8820.0010.0010.0000.0000.0000.000
151A419LEU0-0.054-0.01938.3920.0050.0050.0000.0000.0000.000
152A420ARG10.9350.98131.1080.1080.1080.0000.0000.0000.000
153A421ASP-1-0.885-0.93138.739-0.067-0.0670.0000.0000.0000.000
154A422GLN0-0.055-0.01742.0180.0060.0060.0000.0000.0000.000
155A423PRO00.0290.00643.2550.0000.0000.0000.0000.0000.000
156A424TRP00.033-0.00238.9240.0010.0010.0000.0000.0000.000
157A425TYR0-0.028-0.02034.4820.0010.0010.0000.0000.0000.000
158A426LYS10.9920.98339.8000.0560.0560.0000.0000.0000.000
159A427ALA0-0.029-0.00341.5870.0010.0010.0000.0000.0000.000
160A428ALA00.0220.00239.0000.0020.0020.0000.0000.0000.000
161A429VAL00.0280.01435.8650.0020.0020.0000.0000.0000.000
162A430ALA0-0.056-0.02837.9970.0010.0010.0000.0000.0000.000
163A431TRP0-0.003-0.00237.8190.0010.0010.0000.0000.0000.000
164A432ALA00.018-0.00635.0110.0030.0030.0000.0000.0000.000
165A433ASN00.0100.01135.212-0.001-0.0010.0000.0000.0000.000
166A434GLN0-0.062-0.01937.3790.0030.0030.0000.0000.0000.000
167A435ASN00.0290.01437.9320.0030.0030.0000.0000.0000.000
168A436ARG10.9130.95036.9660.0310.0310.0000.0000.0000.000
169A437ALA00.0200.03234.9540.0000.0000.0000.0000.0000.000
170A438PRO0-0.033-0.00829.629-0.004-0.0040.0000.0000.0000.000
171A439VAL00.0740.03329.8180.0000.0000.0000.0000.0000.000
172A440LEU0-0.017-0.00124.356-0.006-0.0060.0000.0000.0000.000
173A441SER00.0300.01325.9780.0080.0080.0000.0000.0000.000
174A442ILE00.007-0.00424.876-0.015-0.0150.0000.0000.0000.000
175A443ASP-1-0.911-0.96123.906-0.173-0.1730.0000.0000.0000.000
176A444PRO0-0.0160.00023.3110.0080.0080.0000.0000.0000.000
177A445PRO0-0.006-0.00725.031-0.016-0.0160.0000.0000.0000.000
178A446VAL0-0.031-0.02122.606-0.003-0.0030.0000.0000.0000.000
179A447HIS00.015-0.00525.0160.0090.0090.0000.0000.0000.000
180A448GLU-1-0.897-0.96127.997-0.089-0.0890.0000.0000.0000.000
181A449VAL0-0.0170.02526.9470.0060.0060.0000.0000.0000.000
182A450GLU-1-0.832-0.89830.359-0.083-0.0830.0000.0000.0000.000
183A451GLN0-0.168-0.07733.2040.0080.0080.0000.0000.0000.000
184A452GLY00.0280.00932.1300.0040.0040.0000.0000.0000.000
185A453ILE0-0.061-0.04231.7400.0030.0030.0000.0000.0000.000
186A454ASP-1-0.896-0.94129.432-0.083-0.0830.0000.0000.0000.000
187A455ALA0-0.053-0.02125.8810.0050.0050.0000.0000.0000.000
188A456LYS10.9240.97525.4090.0440.0440.0000.0000.0000.000
189A457TRP0-0.002-0.02522.028-0.005-0.0050.0000.0000.0000.000
190A458SER00.021-0.01421.5460.0080.0080.0000.0000.0000.000
191A459LEU0-0.044-0.02519.558-0.016-0.0160.0000.0000.0000.000
192A460ALA00.0300.01617.6860.0050.0050.0000.0000.0000.000
193A461LEU00.0420.01019.3840.0030.0030.0000.0000.0000.000
194A462GLY00.0160.01917.914-0.005-0.0050.0000.0000.0000.000
195A463LEU0-0.042-0.04513.358-0.056-0.0560.0000.0000.0000.000
196A464PRO00.0090.02013.9640.0480.0480.0000.0000.0000.000
197A465LEU00.0780.04617.110-0.028-0.0280.0000.0000.0000.000
198A466PRO0-0.023-0.02917.669-0.015-0.0150.0000.0000.0000.000
199A467LEU0-0.0090.00418.6490.0270.0270.0000.0000.0000.000
200A468GLY00.024-0.00119.285-0.015-0.0150.0000.0000.0000.000
201A469GLU-1-0.941-0.98421.682-0.107-0.1070.0000.0000.0000.000
202A470HIS00.0430.00922.5630.0020.0020.0000.0000.0000.000
203A471ALA0-0.0200.01021.5280.0050.0050.0000.0000.0000.000
204A472GLY00.0440.07122.7370.0050.0050.0000.0000.0000.000
205A473ARG10.8700.91418.9960.0510.0510.0000.0000.0000.000
206A474ILE00.0370.02316.2640.0020.0020.0000.0000.0000.000
207A475TYR00.014-0.00116.239-0.015-0.0150.0000.0000.0000.000
208A476LEU0-0.054-0.01913.171-0.016-0.0160.0000.0000.0000.000
209A477CYS00.0130.00216.3840.0220.0220.0000.0000.0000.000
210A478ASP-1-0.861-0.92717.464-0.185-0.1850.0000.0000.0000.000
211A479ILE0-0.031-0.02418.8290.0180.0180.0000.0000.0000.000
212A480GLY00.0300.01220.5900.0090.0090.0000.0000.0000.000
213A481ILE0-0.035-0.01819.2720.0080.0080.0000.0000.0000.000
214A482PRO00.0320.01118.926-0.010-0.0100.0000.0000.0000.000
215A483GLN00.005-0.01311.396-0.013-0.0130.0000.0000.0000.000
216A484GLN00.0360.00216.078-0.040-0.0400.0000.0000.0000.000
217A485VAL00.0340.03118.318-0.009-0.0090.0000.0000.0000.000
218A486PHE0-0.010-0.01615.277-0.015-0.0150.0000.0000.0000.000
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