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: 534NZ

Calculation Name: 3AJC-A-Xray372

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: 2023-06-19

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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2332445.582304
FMO2-HF: Nuclear repulsion 2249203.951306
FMO2-HF: Total energy -83241.630998
FMO2-MP2: Total energy -83486.652953


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:105:VAL)


Summations of interaction energy for fragment #1(A:105:VAL)
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.
-2.7510.511-0.016-1.491-1.7560.007
Interaction energy analysis for fragmet #1(A:105:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.032 / q_NPA : 0.016
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].
3A107PRO00.0340.0033.765-2.3790.633-0.020-1.455-1.5380.007
4A108PHE00.010-0.0025.4750.3140.3140.0000.0000.0000.000
5A109SER00.0210.0103.7040.1660.4160.004-0.036-0.2180.000
6A110PHE0-0.0200.0085.6890.1930.1930.0000.0000.0000.000
7A111VAL00.0210.0017.8960.1300.1300.0000.0000.0000.000
8A112ARG10.8460.9179.8600.1550.1550.0000.0000.0000.000
9A113ASP-1-0.926-0.9588.728-0.113-0.1130.0000.0000.0000.000
10A114THR0-0.099-0.04311.8880.0080.0080.0000.0000.0000.000
11A115ASP-1-0.899-0.95514.185-0.170-0.1700.0000.0000.0000.000
12A116PRO0-0.011-0.00917.404-0.020-0.0200.0000.0000.0000.000
13A117VAL00.0320.00819.934-0.009-0.0090.0000.0000.0000.000
14A118GLN00.0330.01619.699-0.010-0.0100.0000.0000.0000.000
15A119LEU00.0300.02615.331-0.019-0.0190.0000.0000.0000.000
16A120VAL00.0230.00118.614-0.020-0.0200.0000.0000.0000.000
17A121ASN0-0.079-0.04221.4420.0080.0080.0000.0000.0000.000
18A122PHE0-0.003-0.00817.9050.0070.0070.0000.0000.0000.000
19A123LEU00.0090.00416.193-0.007-0.0070.0000.0000.0000.000
20A124GLN00.0010.00120.1110.0130.0130.0000.0000.0000.000
21A125SER0-0.045-0.01123.1820.0130.0130.0000.0000.0000.000
22A126GLU-1-0.883-0.93518.697-0.334-0.3340.0000.0000.0000.000
23A127HIS0-0.0090.00021.8500.0090.0090.0000.0000.0000.000
24A128PRO00.0680.01221.567-0.024-0.0240.0000.0000.0000.000
25A129GLN00.0200.02620.1820.0100.0100.0000.0000.0000.000
26A130THR00.000-0.01016.828-0.033-0.0330.0000.0000.0000.000
27A131ILE00.0030.00716.895-0.052-0.0520.0000.0000.0000.000
28A132ALA0-0.019-0.01717.544-0.024-0.0240.0000.0000.0000.000
29A133VAL0-0.007-0.01113.392-0.026-0.0260.0000.0000.0000.000
30A134VAL00.0040.01312.530-0.082-0.0820.0000.0000.0000.000
31A135LEU00.0220.00713.020-0.044-0.0440.0000.0000.0000.000
32A136SER0-0.054-0.01114.879-0.002-0.0020.0000.0000.0000.000
33A137TYR00.015-0.0148.645-0.151-0.1510.0000.0000.0000.000
34A138LEU0-0.059-0.01010.012-0.081-0.0810.0000.0000.0000.000
35A139ASP-1-0.836-0.90611.944-0.090-0.0900.0000.0000.0000.000
36A140PRO00.1020.03613.505-0.009-0.0090.0000.0000.0000.000
37A141PRO00.0330.02716.517-0.002-0.0020.0000.0000.0000.000
38A142VAL0-0.035-0.00913.8870.0050.0050.0000.0000.0000.000
39A143ALA0-0.001-0.00616.068-0.003-0.0030.0000.0000.0000.000
40A144ALA00.0180.00917.5040.0040.0040.0000.0000.0000.000
41A145GLN0-0.029-0.01119.5380.0030.0030.0000.0000.0000.000
42A146ILE0-0.030-0.02215.8820.0030.0030.0000.0000.0000.000
43A147LEU0-0.011-0.00920.4100.0060.0060.0000.0000.0000.000
44A148GLY00.0220.00422.5670.0090.0090.0000.0000.0000.000
45A149ALA0-0.057-0.01523.3680.0120.0120.0000.0000.0000.000
46A150LEU0-0.043-0.01321.413-0.002-0.0020.0000.0000.0000.000
47A151PRO00.0220.01625.5230.0100.0100.0000.0000.0000.000
48A152GLU-1-0.763-0.85628.653-0.104-0.1040.0000.0000.0000.000
49A153GLU-1-0.947-0.98430.515-0.122-0.1220.0000.0000.0000.000
50A154LEU0-0.061-0.03625.173-0.006-0.0060.0000.0000.0000.000
51A155GLN0-0.016-0.00126.233-0.007-0.0070.0000.0000.0000.000
52A156THR00.0690.02526.488-0.006-0.0060.0000.0000.0000.000
53A157GLU-1-0.825-0.91027.406-0.151-0.1510.0000.0000.0000.000
54A158VAL0-0.012-0.00821.419-0.014-0.0140.0000.0000.0000.000
55A159LEU00.0120.01522.902-0.022-0.0220.0000.0000.0000.000
56A160LYS10.9060.95024.3840.1390.1390.0000.0000.0000.000
57A161ARG10.8940.92322.5370.2220.2220.0000.0000.0000.000
58A162ILE0-0.0100.01819.081-0.024-0.0240.0000.0000.0000.000
59A163ALA0-0.0110.00421.070-0.014-0.0140.0000.0000.0000.000
60A164LEU0-0.056-0.03923.7340.0040.0040.0000.0000.0000.000
61A165LEU0-0.0310.00716.3730.0000.0000.0000.0000.0000.000
62A166GLU-1-0.827-0.92116.504-0.451-0.4510.0000.0000.0000.000
63A167ARG10.7570.84621.2830.1810.1810.0000.0000.0000.000
64A168THR0-0.030-0.02723.6580.0280.0280.0000.0000.0000.000
65A169SER00.0190.01126.4500.0180.0180.0000.0000.0000.000
66A173VAL00.0650.01727.485-0.009-0.0090.0000.0000.0000.000
67A174LYS10.8390.90228.1350.1450.1450.0000.0000.0000.000
68A175GLU-1-0.814-0.86122.517-0.292-0.2920.0000.0000.0000.000
69A176ILE00.0210.01623.280-0.017-0.0170.0000.0000.0000.000
70A177GLU-1-0.846-0.90524.199-0.154-0.1540.0000.0000.0000.000
71A178ARG10.8800.92422.4890.2580.2580.0000.0000.0000.000
72A179ASN0-0.059-0.04818.428-0.002-0.0020.0000.0000.0000.000
73A180LEU0-0.026-0.00219.833-0.014-0.0140.0000.0000.0000.000
74A181GLU-1-0.878-0.94821.688-0.178-0.1780.0000.0000.0000.000
75A182LYS10.8920.96215.0960.4950.4950.0000.0000.0000.000
76A183LYS10.8490.92416.2820.3520.3520.0000.0000.0000.000
77A184ILE0-0.0220.00318.2540.0190.0190.0000.0000.0000.000
78A185SER0-0.055-0.03420.7060.0130.0130.0000.0000.0000.000
79A186GLY0-0.029-0.00414.5580.0140.0140.0000.0000.0000.000
80A195VAL0-0.0020.00112.217-0.022-0.0220.0000.0000.0000.000
81A196GLY00.023-0.00114.4930.0250.0250.0000.0000.0000.000
82A197GLY0-0.034-0.00817.5560.0170.0170.0000.0000.0000.000
83A198ILE00.006-0.01920.828-0.002-0.0020.0000.0000.0000.000
84A199ASP-1-0.800-0.88019.957-0.136-0.1360.0000.0000.0000.000
85A200THR00.0130.01416.971-0.004-0.0040.0000.0000.0000.000
86A201ALA00.0170.00119.1800.0090.0090.0000.0000.0000.000
87A202ALA00.0350.01722.3820.0100.0100.0000.0000.0000.000
88A203GLU-1-0.901-0.95018.204-0.138-0.1380.0000.0000.0000.000
89A204ILE0-0.049-0.02318.0650.0090.0090.0000.0000.0000.000
90A205MET0-0.026-0.01921.6130.0090.0090.0000.0000.0000.000
91A206ASN0-0.034-0.02924.3730.0100.0100.0000.0000.0000.000
92A207ASN0-0.102-0.05821.3260.0220.0220.0000.0000.0000.000
93A208LEU0-0.0040.02023.897-0.001-0.0010.0000.0000.0000.000
94A209ASP-1-0.844-0.86225.803-0.078-0.0780.0000.0000.0000.000
95A210ARG11.0060.96629.0000.0470.0470.0000.0000.0000.000
96A211THR0-0.027-0.02531.9300.0010.0010.0000.0000.0000.000
97A212THR0-0.015-0.03527.974-0.001-0.0010.0000.0000.0000.000
98A213GLU-1-0.804-0.88028.729-0.085-0.0850.0000.0000.0000.000
99A214LYS10.8200.87030.0620.0710.0710.0000.0000.0000.000
100A215LYS10.8430.91532.7000.0920.0920.0000.0000.0000.000
101A216ILE0-0.012-0.00727.111-0.003-0.0030.0000.0000.0000.000
102A217MET0-0.0170.00230.641-0.002-0.0020.0000.0000.0000.000
103A218ASP-1-0.898-0.95232.782-0.072-0.0720.0000.0000.0000.000
104A219LYS10.8780.93332.4300.1230.1230.0000.0000.0000.000
105A220LEU0-0.023-0.01728.976-0.001-0.0010.0000.0000.0000.000
106A221VAL0-0.015-0.00733.6590.0010.0010.0000.0000.0000.000
107A222GLN0-0.046-0.02536.7140.0030.0030.0000.0000.0000.000
108A223GLU-1-0.950-0.96935.099-0.100-0.1000.0000.0000.0000.000
109A224ASN0-0.126-0.07032.652-0.009-0.0090.0000.0000.0000.000
110A225PRO00.0680.02634.082-0.004-0.0040.0000.0000.0000.000
111A226GLU-1-0.912-0.94934.132-0.087-0.0870.0000.0000.0000.000
112A227LEU00.0040.00627.423-0.002-0.0020.0000.0000.0000.000
113A228ALA0-0.023-0.01730.322-0.003-0.0030.0000.0000.0000.000
114A229ASP-1-0.783-0.89331.882-0.072-0.0720.0000.0000.0000.000
115A230GLU-1-0.783-0.86828.505-0.135-0.1350.0000.0000.0000.000
116A231ILE0-0.022-0.03326.398-0.002-0.0020.0000.0000.0000.000
117A232ARG10.8540.91428.3250.0820.0820.0000.0000.0000.000
118A233ARG10.7700.87430.5500.0770.0770.0000.0000.0000.000
119A234ARG10.7650.87123.5750.1270.1270.0000.0000.0000.000
120A235MET0-0.059-0.00925.985-0.004-0.0040.0000.0000.0000.000
121A236PHE00.0040.03227.6370.0070.0070.0000.0000.0000.000
122A237VAL00.0300.01325.9570.0010.0010.0000.0000.0000.000
123A238PHE00.0680.01627.8890.0040.0040.0000.0000.0000.000
124A239GLU-1-0.748-0.87329.8280.0000.0000.0000.0000.0000.000
125A240ASP-1-0.837-0.91231.201-0.044-0.0440.0000.0000.0000.000
126A241ILE0-0.0130.00032.5280.0000.0000.0000.0000.0000.000
127A242LEU0-0.038-0.01335.4810.0010.0010.0000.0000.0000.000
128A243LYS10.8370.90635.4090.0350.0350.0000.0000.0000.000
129A244LEU00.0040.02836.209-0.001-0.0010.0000.0000.0000.000
130A245ASP-1-0.789-0.87839.969-0.016-0.0160.0000.0000.0000.000
131A246ASP-1-0.794-0.91542.852-0.008-0.0080.0000.0000.0000.000
132A247ARG10.8350.92044.2910.0120.0120.0000.0000.0000.000
133A248SER00.0680.01540.5200.0000.0000.0000.0000.0000.000
134A249ILE0-0.0030.00539.1780.0010.0010.0000.0000.0000.000
135A250GLN0-0.028-0.01940.2300.0010.0010.0000.0000.0000.000
136A251LEU0-0.066-0.02640.6490.0030.0030.0000.0000.0000.000
137A252VAL00.0650.02235.5240.0010.0010.0000.0000.0000.000
138A253LEU00.003-0.00137.5500.0020.0020.0000.0000.0000.000
139A254ARG10.7870.91239.1120.0140.0140.0000.0000.0000.000
140A255GLU-1-0.836-0.89636.241-0.013-0.0130.0000.0000.0000.000
141A256VAL0-0.034-0.00833.3320.0010.0010.0000.0000.0000.000
142A257ASH0-0.097-0.07731.9420.0040.0040.0000.0000.0000.000
143A258THR00.0500.00134.9630.0000.0000.0000.0000.0000.000
144A259ARG10.9670.99028.810-0.067-0.0670.0000.0000.0000.000
145A260ASP-1-0.750-0.83828.8620.0340.0340.0000.0000.0000.000
146A261LEU00.0310.01931.1560.0000.0000.0000.0000.0000.000
147A262ALA00.013-0.00933.4290.0000.0000.0000.0000.0000.000
148A263LEU0-0.038-0.02127.4350.0020.0020.0000.0000.0000.000
149A264ALA00.0400.01929.0000.0010.0010.0000.0000.0000.000
150A265LEU00.0020.00430.050-0.003-0.0030.0000.0000.0000.000
151A266LYS10.8500.93630.003-0.058-0.0580.0000.0000.0000.000
152A267GLY00.0080.00928.3710.0050.0050.0000.0000.0000.000
153A268ALA0-0.0030.01829.348-0.006-0.0060.0000.0000.0000.000
154A269SER0-0.009-0.03232.2320.0050.0050.0000.0000.0000.000
155A270ASP-1-0.850-0.93034.7840.0190.0190.0000.0000.0000.000
156A271GLU-1-0.941-0.96238.187-0.008-0.0080.0000.0000.0000.000
157A272LEU00.0090.00733.365-0.001-0.0010.0000.0000.0000.000
158A273LYS10.7700.86134.795-0.023-0.0230.0000.0000.0000.000
159A274GLU-1-0.916-0.96338.1120.0080.0080.0000.0000.0000.000
160A275LYS10.8180.91840.1350.0140.0140.0000.0000.0000.000
161A276ILE00.0550.03235.604-0.001-0.0010.0000.0000.0000.000
162A277PHE00.023-0.00640.0680.0010.0010.0000.0000.0000.000
163A278LYS10.7990.91042.4260.0040.0040.0000.0000.0000.000
164A279ASN0-0.051-0.04042.744-0.002-0.0020.0000.0000.0000.000
165A280MET00.0040.03939.7390.0000.0000.0000.0000.0000.000
166A281SER0-0.016-0.00444.1670.0010.0010.0000.0000.0000.000
167A282LYS11.0110.97946.085-0.008-0.0080.0000.0000.0000.000
168A283ARG10.9800.98546.150-0.012-0.0120.0000.0000.0000.000
169A284ALA00.0210.01742.2760.0020.0020.0000.0000.0000.000
170A285ALA00.0430.02442.5120.0020.0020.0000.0000.0000.000
171A286ALA0-0.031-0.01443.4100.0020.0020.0000.0000.0000.000
172A287LEU00.0260.01241.5390.0020.0020.0000.0000.0000.000
173A288LEU0-0.004-0.00136.9920.0030.0030.0000.0000.0000.000
174A289LYS10.9280.95339.522-0.018-0.0180.0000.0000.0000.000
175A290ASP-1-0.868-0.93341.3000.0340.0340.0000.0000.0000.000
176A291GLU-1-0.888-0.95034.4010.0540.0540.0000.0000.0000.000
177A292LEU0-0.060-0.05335.3550.0040.0040.0000.0000.0000.000
178A293GLU-1-1.000-0.99037.4610.0380.0380.0000.0000.0000.000
179A294TYR0-0.071-0.02138.6490.0040.0040.0000.0000.0000.000
180A295MET0-0.0640.00932.0890.0050.0050.0000.0000.0000.000
181A296GLY00.0020.00133.6570.0060.0060.0000.0000.0000.000
182A297PRO0-0.060-0.05729.318-0.002-0.0020.0000.0000.0000.000
183A298VAL00.0060.00527.0610.0030.0030.0000.0000.0000.000
184A299ARG10.9360.97320.337-0.206-0.2060.0000.0000.0000.000
185A300LEU00.0560.02820.656-0.007-0.0070.0000.0000.0000.000
186A301LYN00.0480.01017.983-0.015-0.0150.0000.0000.0000.000
187A302ASP-1-0.841-0.92920.6000.1040.1040.0000.0000.0000.000
188A303VAL0-0.055-0.02823.728-0.012-0.0120.0000.0000.0000.000
189A304GLU-1-0.901-0.95120.5740.0080.0080.0000.0000.0000.000
190A305GLU-1-0.889-0.93421.5250.0430.0430.0000.0000.0000.000
191A306ALA0-0.0180.00223.246-0.011-0.0110.0000.0000.0000.000
192A307GLN0-0.037-0.03225.918-0.012-0.0120.0000.0000.0000.000
193A308GLN00.0400.02121.196-0.006-0.0060.0000.0000.0000.000
194A309LYS10.7520.86325.234-0.044-0.0440.0000.0000.0000.000
195A310ILE0-0.029-0.01527.543-0.004-0.0040.0000.0000.0000.000
196A311ILE00.0330.02226.372-0.003-0.0030.0000.0000.0000.000
197A312ASN0-0.007-0.00224.638-0.016-0.0160.0000.0000.0000.000
198A313ILE0-0.060-0.01428.892-0.004-0.0040.0000.0000.0000.000
199A314ILE00.0200.00732.231-0.001-0.0010.0000.0000.0000.000
200A315ARG10.9480.96426.2750.0700.0700.0000.0000.0000.000
201A316ARG10.8290.89331.9490.0220.0220.0000.0000.0000.000
202A317LEU0-0.024-0.02433.6890.0000.0000.0000.0000.0000.000
203A318GLU-1-0.835-0.91333.128-0.058-0.0580.0000.0000.0000.000
204A319GLU-1-0.863-0.89532.184-0.076-0.0760.0000.0000.0000.000
205A320ALA0-0.090-0.03436.3550.0000.0000.0000.0000.0000.000
206A321GLY0-0.031-0.02339.1680.0030.0030.0000.0000.0000.000
207A322GLU-1-0.986-0.99040.522-0.023-0.0230.0000.0000.0000.000
208A323ILE0-0.031-0.02036.6560.0030.0030.0000.0000.0000.000
209A324VAL0-0.024-0.01040.364-0.003-0.0030.0000.0000.0000.000
210A325ILE0-0.0050.00037.4920.0030.0030.0000.0000.0000.000