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: R5NN8

Calculation Name: 3AJC-A-Xray317

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3AJC

Chain ID: A

ChEMBL ID:

UniProt ID: Q9WY63

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 214
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2349887.938154
FMO2-HF: Nuclear repulsion 2266306.625963
FMO2-HF: Total energy -83581.312191
FMO2-MP2: Total energy -83827.573259


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:104:ACE )


Summations of interaction energy for fragment #1(A:104:ACE )
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.
0.8681.515-0.005-0.305-0.3370
Interaction energy analysis for fragmet #1(A:104:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : -0.010
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].
3A106LYS 10.9750.9913.8821.7162.363-0.005-0.305-0.3370.000
4A107PRO 00.0390.0087.0350.0160.0160.0000.0000.0000.000
5A108PHE 00.0260.0059.387-0.004-0.0040.0000.0000.0000.000
6A109SER 00.0030.0098.989-0.027-0.0270.0000.0000.0000.000
7A110PHE 0-0.0020.00711.0780.0110.0110.0000.0000.0000.000
8A111VAL 00.046-0.00613.1120.0640.0640.0000.0000.0000.000
9A112ARG 10.8970.95215.4800.3240.3240.0000.0000.0000.000
10A113ASP -1-0.930-0.95514.301-0.414-0.4140.0000.0000.0000.000
11A114THR 0-0.138-0.04817.2980.0330.0330.0000.0000.0000.000
12A115ASP -1-0.877-0.94119.481-0.147-0.1470.0000.0000.0000.000
13A116PRO 00.0030.00622.713-0.004-0.0040.0000.0000.0000.000
14A117VAL 00.0310.01225.3770.0020.0020.0000.0000.0000.000
15A118GLN 0-0.013-0.01824.6640.0020.0020.0000.0000.0000.000
16A119LEU 00.0360.04020.1970.0050.0050.0000.0000.0000.000
17A120VAL 00.0460.01123.5590.0040.0040.0000.0000.0000.000
18A121ASN 0-0.086-0.05026.3240.0130.0130.0000.0000.0000.000
19A122PHE 0-0.001-0.00623.1180.0080.0080.0000.0000.0000.000
20A123LEU 00.0320.01420.7930.0070.0070.0000.0000.0000.000
21A124GLN 0-0.022-0.00824.7350.0090.0090.0000.0000.0000.000
22A125SER 0-0.067-0.02227.8950.0060.0060.0000.0000.0000.000
23A126GLU -1-0.921-0.94323.175-0.053-0.0530.0000.0000.0000.000
24A127HIS 0-0.011-0.01225.7690.0010.0010.0000.0000.0000.000
25A128PRO 00.0760.01625.423-0.005-0.0050.0000.0000.0000.000
26A129GLN 00.0090.00921.898-0.007-0.0070.0000.0000.0000.000
27A130THR 00.025-0.00420.584-0.001-0.0010.0000.0000.0000.000
28A131ILE 00.0200.02020.775-0.015-0.0150.0000.0000.0000.000
29A132ALA 0-0.011-0.01921.526-0.015-0.0150.0000.0000.0000.000
30A133VAL 0-0.020-0.01116.636-0.011-0.0110.0000.0000.0000.000
31A134VAL 00.0100.01116.786-0.024-0.0240.0000.0000.0000.000
32A135LEU 00.010-0.00517.044-0.035-0.0350.0000.0000.0000.000
33A136SER 0-0.053-0.00317.474-0.014-0.0140.0000.0000.0000.000
34A137TYR 0-0.022-0.02811.073-0.011-0.0110.0000.0000.0000.000
35A138LEU 0-0.089-0.03713.768-0.079-0.0790.0000.0000.0000.000
36A139ASP -1-0.889-0.94416.255-0.239-0.2390.0000.0000.0000.000
37A140PRO 00.0820.03017.7950.0140.0140.0000.0000.0000.000
38A141PRO 00.0330.02321.0060.0140.0140.0000.0000.0000.000
39A142VAL 0-0.028-0.00619.0060.0070.0070.0000.0000.0000.000
40A143ALA 00.0090.00220.4320.0140.0140.0000.0000.0000.000
41A144ALA 00.0220.00822.1140.0150.0150.0000.0000.0000.000
42A145GLN 0-0.029-0.01324.6640.0010.0010.0000.0000.0000.000
43A146ILE 0-0.017-0.01521.1300.0090.0090.0000.0000.0000.000
44A147LEU 0-0.017-0.00925.4720.0110.0110.0000.0000.0000.000
45A148GLY 00.0190.00127.1580.0090.0090.0000.0000.0000.000
46A149ALA 0-0.059-0.01928.5280.0060.0060.0000.0000.0000.000
47A150LEU 0-0.055-0.02426.1050.0030.0030.0000.0000.0000.000
48A151PRO 00.0050.00330.1760.0030.0030.0000.0000.0000.000
49A152GLU -1-0.891-0.95333.108-0.044-0.0440.0000.0000.0000.000
50A153GLU -1-0.924-0.95934.890-0.042-0.0420.0000.0000.0000.000
51A154LEU 0-0.085-0.04829.4420.0020.0020.0000.0000.0000.000
52A155GLN 0-0.0070.01030.2550.0020.0020.0000.0000.0000.000
53A156THR 00.0590.02430.142-0.001-0.0010.0000.0000.0000.000
54A157GLU -1-0.876-0.95530.836-0.032-0.0320.0000.0000.0000.000
55A158VAL 0-0.019-0.01125.1710.0020.0020.0000.0000.0000.000
56A159LEU 00.0150.01626.115-0.004-0.0040.0000.0000.0000.000
57A160LYS 10.9550.97627.0590.0290.0290.0000.0000.0000.000
58A161ARG 10.8970.94025.2370.0340.0340.0000.0000.0000.000
59A162ILE 0-0.0040.02321.6940.0010.0010.0000.0000.0000.000
60A163ALA 0-0.0140.00523.0840.0000.0000.0000.0000.0000.000
61A164LEU 0-0.082-0.05425.5050.0050.0050.0000.0000.0000.000
62A165LEU 0-0.0210.01318.3150.0070.0070.0000.0000.0000.000
63A166GLU -1-0.935-0.96617.5660.0000.0000.0000.0000.0000.000
64A167ARG 10.8630.92222.4150.0280.0280.0000.0000.0000.000
65A168THR 0-0.048-0.02125.2790.0020.0020.0000.0000.0000.000
66A169SER 00.0150.00327.7170.0020.0020.0000.0000.0000.000
67A173VAL 00.0720.02128.3470.0020.0020.0000.0000.0000.000
68A174LYS 10.9040.95428.724-0.031-0.0310.0000.0000.0000.000
69A175GLU -1-0.925-0.93423.3790.0160.0160.0000.0000.0000.000
70A176ILE 00.0500.03223.9300.0050.0050.0000.0000.0000.000
71A177GLU -1-0.925-0.96624.6600.0470.0470.0000.0000.0000.000
72A178ARG 11.0060.99522.784-0.034-0.0340.0000.0000.0000.000
73A179ASN 0-0.007-0.01718.6980.0080.0080.0000.0000.0000.000
74A180LEU 0-0.034-0.00820.0640.0110.0110.0000.0000.0000.000
75A181GLU -1-0.869-0.94821.6450.0830.0830.0000.0000.0000.000
76A182LYS 10.8860.94315.265-0.137-0.1370.0000.0000.0000.000
77A183LYS 10.9490.96816.714-0.028-0.0280.0000.0000.0000.000
78A184ILE 0-0.0150.01018.0740.0080.0080.0000.0000.0000.000
79A185SER 0-0.071-0.02219.7200.0110.0110.0000.0000.0000.000
80A186GLY 00.0040.00716.3550.0130.0130.0000.0000.0000.000
81A187NME 0-0.032-0.01112.234-0.018-0.0180.0000.0000.0000.000
82A194ACE 0-0.037-0.03214.1200.0090.0090.0000.0000.0000.000
83A195VAL 0-0.009-0.00813.894-0.037-0.0370.0000.0000.0000.000
84A196GLY 00.0800.04415.9460.0210.0210.0000.0000.0000.000
85A197GLY 0-0.035-0.00819.3930.0010.0010.0000.0000.0000.000
86A198ILE 00.011-0.02022.540-0.008-0.0080.0000.0000.0000.000
87A199ASP -1-0.848-0.91622.278-0.072-0.0720.0000.0000.0000.000
88A200THR 00.0260.02719.704-0.012-0.0120.0000.0000.0000.000
89A201ALA 00.003-0.00521.828-0.005-0.0050.0000.0000.0000.000
90A202ALA 00.0440.01925.108-0.001-0.0010.0000.0000.0000.000
91A203GLU -1-0.885-0.94721.037-0.137-0.1370.0000.0000.0000.000
92A204ILE 0-0.051-0.02121.767-0.004-0.0040.0000.0000.0000.000
93A205MET 0-0.040-0.02425.2870.0020.0020.0000.0000.0000.000
94A206ASN 0-0.025-0.01727.8260.0080.0080.0000.0000.0000.000
95A207ASN 0-0.114-0.05924.960-0.001-0.0010.0000.0000.0000.000
96A208LEU 0-0.0120.01428.142-0.003-0.0030.0000.0000.0000.000
97A209ASP -1-0.861-0.89830.253-0.068-0.0680.0000.0000.0000.000
98A210ARG 10.9860.95433.6840.0660.0660.0000.0000.0000.000
99A211THR 0-0.018-0.00536.2800.0030.0030.0000.0000.0000.000
100A212THR 00.002-0.01332.4050.0050.0050.0000.0000.0000.000
101A213GLU -1-0.871-0.94632.436-0.054-0.0540.0000.0000.0000.000
102A214LYS 10.9620.96634.0320.0530.0530.0000.0000.0000.000
103A215LYS 10.9590.99436.8740.0500.0500.0000.0000.0000.000
104A216ILE 0-0.012-0.00330.8880.0030.0030.0000.0000.0000.000
105A217MET 00.0020.00733.3400.0040.0040.0000.0000.0000.000
106A218ASP -1-0.904-0.95535.963-0.034-0.0340.0000.0000.0000.000
107A219LYS 10.8980.95235.6250.0370.0370.0000.0000.0000.000
108A220LEU 0-0.025-0.01931.7740.0030.0030.0000.0000.0000.000
109A221VAL 0-0.028-0.00636.3050.0030.0030.0000.0000.0000.000
110A222GLN 0-0.033-0.02739.2200.0030.0030.0000.0000.0000.000
111A223GLU -1-0.946-0.96237.912-0.017-0.0170.0000.0000.0000.000
112A224ASN 0-0.139-0.07034.7670.0000.0000.0000.0000.0000.000
113A225PRO 00.0610.02736.117-0.002-0.0020.0000.0000.0000.000
114A226GLU -1-0.909-0.95735.475-0.022-0.0220.0000.0000.0000.000
115A227LEU 00.0340.01929.289-0.002-0.0020.0000.0000.0000.000
116A228ALA 0-0.007-0.01032.449-0.004-0.0040.0000.0000.0000.000
117A229ASP -1-0.801-0.93634.296-0.032-0.0320.0000.0000.0000.000
118A230GLU -1-0.922-0.96230.611-0.027-0.0270.0000.0000.0000.000
119A231ILE 0-0.044-0.03728.966-0.004-0.0040.0000.0000.0000.000
120A232ARG 10.8610.96030.8170.0310.0310.0000.0000.0000.000
121A233ARG 10.8700.93633.2420.0260.0260.0000.0000.0000.000
122A234ARG 10.7790.88225.1720.0490.0490.0000.0000.0000.000
123A235MET 0-0.074-0.02028.625-0.004-0.0040.0000.0000.0000.000
124A236PHE 0-0.0010.02430.517-0.002-0.0020.0000.0000.0000.000
125A237VAL 00.024-0.00229.168-0.005-0.0050.0000.0000.0000.000
126A238PHE 00.0660.00430.9200.0060.0060.0000.0000.0000.000
127A239GLU -1-0.771-0.90132.798-0.056-0.0560.0000.0000.0000.000
128A240ASP -1-0.828-0.87934.017-0.055-0.0550.0000.0000.0000.000
129A241ILE 0-0.007-0.00135.3490.0050.0050.0000.0000.0000.000
130A242LEU 0-0.037-0.01538.3730.0040.0040.0000.0000.0000.000
131A243LYS 10.8230.89139.3270.0440.0440.0000.0000.0000.000
132A244LEU 00.0120.03438.7160.0020.0020.0000.0000.0000.000
133A245ASP -1-0.806-0.90742.754-0.025-0.0250.0000.0000.0000.000
134A246ASP -1-0.840-0.95845.437-0.028-0.0280.0000.0000.0000.000
135A247ARG 10.8800.95446.7360.0190.0190.0000.0000.0000.000
136A248SER 00.0670.03042.8110.0010.0010.0000.0000.0000.000
137A249ILE 00.0020.00741.8560.0000.0000.0000.0000.0000.000
138A250GLN 0-0.056-0.04542.4730.0010.0010.0000.0000.0000.000
139A251LEU 0-0.094-0.05142.2480.0010.0010.0000.0000.0000.000
140A252VAL 00.0530.02737.6070.0010.0010.0000.0000.0000.000
141A253LEU 0-0.010-0.00339.4100.0000.0000.0000.0000.0000.000
142A254ARG 10.8330.93440.8960.0190.0190.0000.0000.0000.000
143A255GLU -1-0.908-0.94537.680-0.017-0.0170.0000.0000.0000.000
144A256VAL 0-0.040-0.01335.224-0.001-0.0010.0000.0000.0000.000
145A257ASH 0-0.127-0.12733.3330.0010.0010.0000.0000.0000.000
146A258THR 00.048-0.00536.664-0.002-0.0020.0000.0000.0000.000
147A259ARG 11.0001.01129.9700.0430.0430.0000.0000.0000.000
148A260ASP -1-0.786-0.82930.860-0.045-0.0450.0000.0000.0000.000
149A261LEU 00.0160.01433.206-0.004-0.0040.0000.0000.0000.000
150A262ALA 00.016-0.00935.787-0.003-0.0030.0000.0000.0000.000
151A263LEU 0-0.038-0.02329.514-0.003-0.0030.0000.0000.0000.000
152A264ALA 00.0520.02331.573-0.005-0.0050.0000.0000.0000.000
153A265LEU 00.0000.00432.583-0.003-0.0030.0000.0000.0000.000
154A266LYS 10.8330.92932.6390.0560.0560.0000.0000.0000.000
155A267GLY 00.0140.01431.447-0.004-0.0040.0000.0000.0000.000
156A268ALA 00.0050.02132.455-0.002-0.0020.0000.0000.0000.000
157A269SER 00.008-0.00735.4200.0020.0020.0000.0000.0000.000
158A270ASP -1-0.869-0.94638.196-0.048-0.0480.0000.0000.0000.000
159A271GLU -1-0.937-0.96441.524-0.042-0.0420.0000.0000.0000.000
160A272LEU 00.0090.00936.4240.0030.0030.0000.0000.0000.000
161A273LYS 10.7800.87737.8930.0570.0570.0000.0000.0000.000
162A274GLU -1-0.899-0.95541.113-0.030-0.0300.0000.0000.0000.000
163A275LYS 10.8320.93643.1320.0370.0370.0000.0000.0000.000
164A276ILE 00.0540.04638.2420.0020.0020.0000.0000.0000.000
165A277PHE 00.049-0.02042.7630.0030.0030.0000.0000.0000.000
166A278LYS 10.8270.92845.0600.0310.0310.0000.0000.0000.000
167A279ASN 0-0.029-0.02145.2670.0030.0030.0000.0000.0000.000
168A280MET 0-0.0040.04741.9880.0010.0010.0000.0000.0000.000
169A281SER 0-0.0070.00346.4100.0010.0010.0000.0000.0000.000
170A282LYS 11.0140.97948.1480.0210.0210.0000.0000.0000.000
171A283ARG 10.9720.98447.6690.0150.0150.0000.0000.0000.000
172A284ALA 00.0280.01744.1550.0000.0000.0000.0000.0000.000
173A285ALA 00.0520.02744.467-0.001-0.0010.0000.0000.0000.000
174A286ALA 0-0.038-0.01845.569-0.001-0.0010.0000.0000.0000.000
175A287LEU 00.0130.00843.2160.0000.0000.0000.0000.0000.000
176A288LEU 00.0070.00639.155-0.001-0.0010.0000.0000.0000.000
177A289LYS 10.9060.94241.6250.0260.0260.0000.0000.0000.000
178A290ASP -1-0.864-0.92743.460-0.025-0.0250.0000.0000.0000.000
179A291GLU -1-0.892-0.95536.242-0.036-0.0360.0000.0000.0000.000
180A292LEU 0-0.071-0.05637.875-0.002-0.0020.0000.0000.0000.000
181A293GLU -1-0.996-0.98939.694-0.030-0.0300.0000.0000.0000.000
182A294TYR 0-0.073-0.02340.5030.0000.0000.0000.0000.0000.000
183A295MET 0-0.0770.00633.128-0.002-0.0020.0000.0000.0000.000
184A296GLY 00.0030.00135.539-0.001-0.0010.0000.0000.0000.000
185A297PRO 0-0.059-0.05831.853-0.002-0.0020.0000.0000.0000.000
186A298VAL 00.0180.01229.2920.0030.0030.0000.0000.0000.000
187A299ARG 10.9380.97121.9630.1030.1030.0000.0000.0000.000
188A300LEU 00.0640.03023.5880.0030.0030.0000.0000.0000.000
189A301LYN 00.0300.00220.6860.0050.0050.0000.0000.0000.000
190A302ASP -1-0.833-0.92523.094-0.077-0.0770.0000.0000.0000.000
191A303VAL 0-0.063-0.03225.8350.0070.0070.0000.0000.0000.000
192A304GLU -1-0.896-0.95223.497-0.111-0.1110.0000.0000.0000.000
193A305GLU -1-0.952-0.96522.375-0.076-0.0760.0000.0000.0000.000
194A306ALA 0-0.042-0.00425.3400.0090.0090.0000.0000.0000.000
195A307GLN 0-0.055-0.04628.5740.0020.0020.0000.0000.0000.000
196A308GLN 00.0530.03423.4860.0070.0070.0000.0000.0000.000
197A309LYS 10.9030.94127.4360.0490.0490.0000.0000.0000.000
198A310ILE 0-0.026-0.01129.3520.0060.0060.0000.0000.0000.000
199A311ILE 00.0290.02128.7840.0040.0040.0000.0000.0000.000
200A312ASN 0-0.046-0.02826.4560.0020.0020.0000.0000.0000.000
201A313ILE 0-0.065-0.01830.6960.0040.0040.0000.0000.0000.000
202A314ILE 00.006-0.00334.1730.0030.0030.0000.0000.0000.000
203A315ARG 10.9980.99627.0760.0490.0490.0000.0000.0000.000
204A316ARG 10.8730.93733.7520.0230.0230.0000.0000.0000.000
205A317LEU 0-0.016-0.02035.2000.0030.0030.0000.0000.0000.000
206A318GLU -1-0.858-0.93935.458-0.034-0.0340.0000.0000.0000.000
207A319GLU -1-0.906-0.92734.120-0.021-0.0210.0000.0000.0000.000
208A320ALA 0-0.093-0.03337.9000.0020.0020.0000.0000.0000.000
209A321GLY 0-0.028-0.02240.7940.0010.0010.0000.0000.0000.000
210A322GLU -1-0.992-0.99242.251-0.016-0.0160.0000.0000.0000.000
211A323ILE 0-0.032-0.01238.498-0.001-0.0010.0000.0000.0000.000
212A324VAL 0-0.032-0.02042.5010.0000.0000.0000.0000.0000.000
213A325ILE 0-0.008-0.00440.370-0.001-0.0010.0000.0000.0000.000
214A326NME 0-0.016-0.00343.7000.0000.0000.0000.0000.0000.000