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: 435LN

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 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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2332357.144929
FMO2-HF: Nuclear repulsion 2249117.70126
FMO2-HF: Total energy -83239.443669
FMO2-MP2: Total energy -83484.639614


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.
-2.338-0.096-0.005-0.89-1.3470.001
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 : 0.005 / q_NPA : -0.008
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].
3A107PRO00.0420.0103.609-2.117-0.161-0.011-0.847-1.0980.001
4A108PHE00.0260.0066.0090.3510.3510.0000.0000.0000.000
5A109SER00.0010.0063.542-0.0860.2000.006-0.043-0.2490.000
6A110PHE0-0.0020.0085.5710.2130.2130.0000.0000.0000.000
7A111VAL00.046-0.0057.8470.1970.1970.0000.0000.0000.000
8A112ARG10.8960.9509.8530.2740.2740.0000.0000.0000.000
9A113ASP-1-0.931-0.9568.836-0.606-0.6060.0000.0000.0000.000
10A114THR0-0.136-0.04611.9010.0260.0260.0000.0000.0000.000
11A115ASP-1-0.877-0.94014.192-0.327-0.3270.0000.0000.0000.000
12A116PRO00.0040.00617.302-0.014-0.0140.0000.0000.0000.000
13A117VAL00.0300.01319.8630.0000.0000.0000.0000.0000.000
14A118GLN0-0.013-0.01719.7840.0090.0090.0000.0000.0000.000
15A119LEU00.0350.03815.099-0.012-0.0120.0000.0000.0000.000
16A120VAL00.0450.01118.489-0.011-0.0110.0000.0000.0000.000
17A121ASN0-0.085-0.04921.3270.0190.0190.0000.0000.0000.000
18A122PHE0-0.001-0.00618.5060.0110.0110.0000.0000.0000.000
19A123LEU00.0320.01416.4850.0040.0040.0000.0000.0000.000
20A124GLN0-0.020-0.00820.4410.0280.0280.0000.0000.0000.000
21A125SER0-0.068-0.02323.8200.0140.0140.0000.0000.0000.000
22A126GLU-1-0.923-0.94219.505-0.354-0.3540.0000.0000.0000.000
23A127HIS0-0.009-0.01122.4670.0140.0140.0000.0000.0000.000
24A128PRO00.0740.01522.148-0.019-0.0190.0000.0000.0000.000
25A129GLN00.0130.01019.6550.0140.0140.0000.0000.0000.000
26A130THR00.022-0.00517.433-0.009-0.0090.0000.0000.0000.000
27A131ILE00.0200.02017.477-0.050-0.0500.0000.0000.0000.000
28A132ALA0-0.016-0.02117.735-0.020-0.0200.0000.0000.0000.000
29A133VAL0-0.015-0.00913.850-0.004-0.0040.0000.0000.0000.000
30A134VAL00.0120.01112.630-0.056-0.0560.0000.0000.0000.000
31A135LEU00.007-0.00512.935-0.042-0.0420.0000.0000.0000.000
32A136SER0-0.053-0.00414.7400.0300.0300.0000.0000.0000.000
33A137TYR0-0.018-0.0279.187-0.013-0.0130.0000.0000.0000.000
34A138LEU0-0.092-0.0389.914-0.073-0.0730.0000.0000.0000.000
35A139ASP-1-0.888-0.94311.8760.0450.0450.0000.0000.0000.000
36A140PRO00.0800.03013.563-0.044-0.0440.0000.0000.0000.000
37A141PRO00.0360.02316.653-0.019-0.0190.0000.0000.0000.000
38A142VAL0-0.028-0.00713.775-0.008-0.0080.0000.0000.0000.000
39A143ALA00.0060.00116.082-0.015-0.0150.0000.0000.0000.000
40A144ALA00.0240.01017.4310.0000.0000.0000.0000.0000.000
41A145GLN0-0.029-0.01419.228-0.011-0.0110.0000.0000.0000.000
42A146ILE0-0.017-0.01415.838-0.001-0.0010.0000.0000.0000.000
43A147LEU0-0.017-0.00920.2950.0050.0050.0000.0000.0000.000
44A148GLY00.0220.00122.4280.0080.0080.0000.0000.0000.000
45A149ALA0-0.059-0.01923.2760.0090.0090.0000.0000.0000.000
46A150LEU0-0.054-0.02321.576-0.007-0.0070.0000.0000.0000.000
47A151PRO00.0060.00425.3320.0130.0130.0000.0000.0000.000
48A152GLU-1-0.889-0.95328.595-0.090-0.0900.0000.0000.0000.000
49A153GLU-1-0.927-0.96230.585-0.110-0.1100.0000.0000.0000.000
50A154LEU0-0.085-0.04725.363-0.002-0.0020.0000.0000.0000.000
51A155GLN0-0.0040.01226.0660.0050.0050.0000.0000.0000.000
52A156THR00.0690.02826.3320.0010.0010.0000.0000.0000.000
53A157GLU-1-0.883-0.95927.507-0.099-0.0990.0000.0000.0000.000
54A158VAL0-0.018-0.01221.542-0.004-0.0040.0000.0000.0000.000
55A159LEU00.0120.01722.923-0.009-0.0090.0000.0000.0000.000
56A160LYS10.9600.97824.2410.0950.0950.0000.0000.0000.000
57A161ARG10.9010.94122.7910.1640.1640.0000.0000.0000.000
58A162ILE0-0.0070.02219.036-0.008-0.0080.0000.0000.0000.000
59A163ALA0-0.0130.00421.0700.0110.0110.0000.0000.0000.000
60A164LEU0-0.083-0.05423.7330.0160.0160.0000.0000.0000.000
61A165LEU0-0.0220.01116.597-0.003-0.0030.0000.0000.0000.000
62A166GLU-1-0.931-0.96416.378-0.151-0.1510.0000.0000.0000.000
63A167ARG10.8630.92221.2060.0450.0450.0000.0000.0000.000
64A168THR0-0.047-0.02223.8080.0130.0130.0000.0000.0000.000
65A169SER00.0140.00426.4190.0060.0060.0000.0000.0000.000
66A173VAL00.0720.02127.3890.0010.0010.0000.0000.0000.000
67A174LYS10.9040.95427.7540.0540.0540.0000.0000.0000.000
68A175GLU-1-0.927-0.93522.124-0.148-0.1480.0000.0000.0000.000
69A176ILE00.0520.03223.1820.0020.0020.0000.0000.0000.000
70A177GLU-1-0.927-0.96724.244-0.023-0.0230.0000.0000.0000.000
71A178ARG11.0050.99522.1560.1230.1230.0000.0000.0000.000
72A179ASN0-0.005-0.01618.0160.0040.0040.0000.0000.0000.000
73A180LEU0-0.032-0.00819.9210.0200.0200.0000.0000.0000.000
74A181GLU-1-0.869-0.94821.865-0.012-0.0120.0000.0000.0000.000
75A182LYS10.8890.94514.8730.1810.1810.0000.0000.0000.000
76A183LYS10.9460.96716.899-0.021-0.0210.0000.0000.0000.000
77A184ILE0-0.0170.00818.5020.0290.0290.0000.0000.0000.000
78A185SER0-0.077-0.02420.2040.0090.0090.0000.0000.0000.000
79A186GLY0-0.0160.00014.8240.0110.0110.0000.0000.0000.000
80A195VAL0-0.0020.00012.4800.0290.0290.0000.0000.0000.000
81A196GLY00.0330.00414.536-0.014-0.0140.0000.0000.0000.000
82A197GLY0-0.039-0.01117.5570.0400.0400.0000.0000.0000.000
83A198ILE00.015-0.01920.832-0.011-0.0110.0000.0000.0000.000
84A199ASP-1-0.848-0.91619.9610.0590.0590.0000.0000.0000.000
85A200THR00.0260.02717.052-0.005-0.0050.0000.0000.0000.000
86A201ALA00.006-0.00419.172-0.011-0.0110.0000.0000.0000.000
87A202ALA00.0420.01922.366-0.006-0.0060.0000.0000.0000.000
88A203GLU-1-0.891-0.95018.0060.0420.0420.0000.0000.0000.000
89A204ILE0-0.050-0.02118.206-0.008-0.0080.0000.0000.0000.000
90A205MET0-0.036-0.02221.588-0.008-0.0080.0000.0000.0000.000
91A206ASN0-0.025-0.01724.368-0.003-0.0030.0000.0000.0000.000
92A207ASN0-0.114-0.05921.2270.0080.0080.0000.0000.0000.000
93A208LEU0-0.0090.01623.947-0.012-0.0120.0000.0000.0000.000
94A209ASP-1-0.865-0.90025.798-0.065-0.0650.0000.0000.0000.000
95A210ARG10.9850.95429.0080.0240.0240.0000.0000.0000.000
96A211THR0-0.019-0.00631.9370.0030.0030.0000.0000.0000.000
97A212THR00.001-0.01427.7910.0010.0010.0000.0000.0000.000
98A213GLU-1-0.871-0.94728.721-0.039-0.0390.0000.0000.0000.000
99A214LYS10.9610.96630.0070.0280.0280.0000.0000.0000.000
100A215LYS10.9540.99032.6610.0710.0710.0000.0000.0000.000
101A216ILE00.0040.00727.008-0.001-0.0010.0000.0000.0000.000
102A217MET0-0.0100.00130.5250.0010.0010.0000.0000.0000.000
103A218ASP-1-0.906-0.95732.681-0.035-0.0350.0000.0000.0000.000
104A219LYS10.8960.95132.3190.0860.0860.0000.0000.0000.000
105A220LEU0-0.026-0.01928.8710.0000.0000.0000.0000.0000.000
106A221VAL0-0.023-0.00533.4980.0040.0040.0000.0000.0000.000
107A222GLN0-0.036-0.02936.5780.0030.0030.0000.0000.0000.000
108A223GLU-1-0.947-0.96235.300-0.052-0.0520.0000.0000.0000.000
109A224ASN0-0.140-0.06832.810-0.007-0.0070.0000.0000.0000.000
110A225PRO00.0620.02734.0780.0020.0020.0000.0000.0000.000
111A226GLU-1-0.910-0.95633.972-0.003-0.0030.0000.0000.0000.000
112A227LEU00.0320.01927.3940.0020.0020.0000.0000.0000.000
113A228ALA0-0.008-0.01030.3190.0010.0010.0000.0000.0000.000
114A229ASP-1-0.800-0.93531.8750.0030.0030.0000.0000.0000.000
115A230GLU-1-0.924-0.96328.768-0.004-0.0040.0000.0000.0000.000
116A231ILE0-0.041-0.03526.4920.0060.0060.0000.0000.0000.000
117A232ARG10.8610.96028.3180.0160.0160.0000.0000.0000.000
118A233ARG10.8690.93530.543-0.013-0.0130.0000.0000.0000.000
119A234ARG10.7800.88223.369-0.037-0.0370.0000.0000.0000.000
120A235MET0-0.072-0.01825.9790.0030.0030.0000.0000.0000.000
121A236PHE0-0.0010.02327.6280.0010.0010.0000.0000.0000.000
122A237VAL00.021-0.00225.9790.0100.0100.0000.0000.0000.000
123A238PHE00.0680.00527.877-0.001-0.0010.0000.0000.0000.000
124A239GLU-1-0.771-0.90129.8180.0450.0450.0000.0000.0000.000
125A240ASP-1-0.828-0.87930.8830.0170.0170.0000.0000.0000.000
126A241ILE0-0.0040.00032.726-0.003-0.0030.0000.0000.0000.000
127A242LEU0-0.035-0.01435.473-0.001-0.0010.0000.0000.0000.000
128A243LYS10.8230.89236.057-0.014-0.0140.0000.0000.0000.000
129A244LEU00.0100.03236.156-0.002-0.0020.0000.0000.0000.000
130A245ASP-1-0.813-0.91239.9620.0260.0260.0000.0000.0000.000
131A246ASP-1-0.840-0.95642.8480.0330.0330.0000.0000.0000.000
132A247ARG10.8820.95544.289-0.027-0.0270.0000.0000.0000.000
133A248SER00.0670.02940.4530.0030.0030.0000.0000.0000.000
134A249ILE00.0070.00939.2400.0040.0040.0000.0000.0000.000
135A250GLN0-0.059-0.04640.2310.0040.0040.0000.0000.0000.000
136A251LEU0-0.095-0.05140.3560.0040.0040.0000.0000.0000.000
137A252VAL00.0560.02835.5060.0030.0030.0000.0000.0000.000
138A253LEU0-0.010-0.00337.5570.0060.0060.0000.0000.0000.000
139A254ARG10.8320.93339.120-0.044-0.0440.0000.0000.0000.000
140A255GLU-1-0.907-0.94536.2500.0700.0700.0000.0000.0000.000
141A256VAL0-0.040-0.01233.4220.0080.0080.0000.0000.0000.000
142A257ASH0-0.126-0.12631.952-0.003-0.0030.0000.0000.0000.000
143A258THR00.047-0.00634.9720.0010.0010.0000.0000.0000.000
144A259ARG11.0001.01128.492-0.158-0.1580.0000.0000.0000.000
145A260ASP-1-0.788-0.82929.2630.1470.1470.0000.0000.0000.000
146A261LEU00.0190.01531.1590.0000.0000.0000.0000.0000.000
147A262ALA00.015-0.01033.428-0.003-0.0030.0000.0000.0000.000
148A263LEU0-0.036-0.02327.626-0.001-0.0010.0000.0000.0000.000
149A264ALA00.0480.02228.9970.0000.0000.0000.0000.0000.000
150A265LEU0-0.0030.00330.047-0.007-0.0070.0000.0000.0000.000
151A266LYS10.8350.92929.929-0.113-0.1130.0000.0000.0000.000
152A267GLY00.0140.01328.3590.0010.0010.0000.0000.0000.000
153A268ALA00.0050.02229.336-0.004-0.0040.0000.0000.0000.000
154A269SER00.009-0.00632.2180.0000.0000.0000.0000.0000.000
155A270ASP-1-0.869-0.94634.7650.0490.0490.0000.0000.0000.000
156A271GLU-1-0.937-0.96538.1650.0250.0250.0000.0000.0000.000
157A272LEU00.0110.01033.2890.0000.0000.0000.0000.0000.000
158A273LYS10.7770.87634.571-0.059-0.0590.0000.0000.0000.000
159A274GLU-1-0.899-0.95538.1010.0410.0410.0000.0000.0000.000
160A275LYS10.8310.93640.131-0.029-0.0290.0000.0000.0000.000
161A276ILE00.0530.04635.5050.0000.0000.0000.0000.0000.000
162A277PHE00.050-0.02040.0630.0000.0000.0000.0000.0000.000
163A278LYS10.8280.92842.421-0.031-0.0310.0000.0000.0000.000
164A279ASN0-0.033-0.02342.713-0.004-0.0040.0000.0000.0000.000
165A280MET0-0.0010.04939.5450.0030.0030.0000.0000.0000.000
166A281SER0-0.0060.00444.167-0.002-0.0020.0000.0000.0000.000
167A282LYS11.0130.97846.088-0.039-0.0390.0000.0000.0000.000
168A283ARG10.9730.98446.388-0.057-0.0570.0000.0000.0000.000
169A284ALA00.0280.01742.2690.0020.0020.0000.0000.0000.000
170A285ALA00.0500.02642.5160.0030.0030.0000.0000.0000.000
171A286ALA0-0.037-0.01843.4110.0020.0020.0000.0000.0000.000
172A287LEU00.0120.00841.5620.0020.0020.0000.0000.0000.000
173A288LEU00.0050.00636.8760.0040.0040.0000.0000.0000.000
174A289LYS10.9070.94239.523-0.050-0.0500.0000.0000.0000.000
175A290ASP-1-0.865-0.92841.2990.0710.0710.0000.0000.0000.000
176A291GLU-1-0.890-0.95434.5900.1170.1170.0000.0000.0000.000
177A292LEU0-0.070-0.05535.5400.0040.0040.0000.0000.0000.000
178A293GLU-1-0.999-0.99137.4580.0690.0690.0000.0000.0000.000
179A294TYR0-0.072-0.02338.6510.0000.0000.0000.0000.0000.000
180A295MET0-0.0760.00731.1970.0050.0050.0000.0000.0000.000
181A296GLY00.0020.00133.6590.0060.0060.0000.0000.0000.000
182A297PRO0-0.057-0.05829.2270.0020.0020.0000.0000.0000.000
183A298VAL00.0170.01226.9640.0050.0050.0000.0000.0000.000
184A299ARG10.9380.97220.108-0.315-0.3150.0000.0000.0000.000
185A300LEU00.0610.02920.072-0.003-0.0030.0000.0000.0000.000
186A301LYN00.0300.00218.330-0.019-0.0190.0000.0000.0000.000
187A302ASP-1-0.833-0.92520.5970.2450.2450.0000.0000.0000.000
188A303VAL0-0.063-0.03223.731-0.013-0.0130.0000.0000.0000.000
189A304GLU-1-0.898-0.95320.5050.1290.1290.0000.0000.0000.000
190A305GLU-1-0.952-0.96520.7480.2670.2670.0000.0000.0000.000
191A306ALA0-0.039-0.00423.251-0.013-0.0130.0000.0000.0000.000
192A307GLN0-0.057-0.04625.895-0.011-0.0110.0000.0000.0000.000
193A308GLN00.0540.03421.444-0.022-0.0220.0000.0000.0000.000
194A309LYS10.9030.94125.236-0.183-0.1830.0000.0000.0000.000
195A310ILE0-0.024-0.01027.551-0.009-0.0090.0000.0000.0000.000
196A311ILE00.0310.02226.173-0.009-0.0090.0000.0000.0000.000
197A312ASN0-0.049-0.02924.789-0.015-0.0150.0000.0000.0000.000
198A313ILE0-0.064-0.01728.900-0.006-0.0060.0000.0000.0000.000
199A314ILE00.003-0.00332.208-0.006-0.0060.0000.0000.0000.000
200A315ARG11.0040.99825.381-0.079-0.0790.0000.0000.0000.000
201A316ARG10.8700.93631.955-0.076-0.0760.0000.0000.0000.000
202A317LEU0-0.016-0.01933.700-0.003-0.0030.0000.0000.0000.000
203A318GLU-1-0.859-0.93933.2680.0270.0270.0000.0000.0000.000
204A319GLU-1-0.905-0.92732.6060.0270.0270.0000.0000.0000.000
205A320ALA0-0.092-0.03336.364-0.003-0.0030.0000.0000.0000.000
206A321GLY0-0.028-0.02239.179-0.001-0.0010.0000.0000.0000.000
207A322GLU-1-0.992-0.99240.5370.0390.0390.0000.0000.0000.000
208A323ILE0-0.036-0.01336.4490.0020.0020.0000.0000.0000.000
209A324VAL0-0.032-0.01640.366-0.004-0.0040.0000.0000.0000.000
210A325ILE0-0.019-0.00737.8030.0010.0010.0000.0000.0000.000