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: YY4V2

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 OptAll
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 -2338367.122551
FMO2-HF: Nuclear repulsion 2255124.663918
FMO2-HF: Total energy -83242.458634
FMO2-MP2: Total energy -83487.363609


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.
-2.410.3290.025-1.246-1.5170.004
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 : 0.039 / q_NPA : 0.017
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].
3A107PRO00.025-0.0023.577-1.9260.4400.016-1.195-1.1870.004
4A108PHE00.023-0.0015.2820.2340.312-0.001-0.003-0.0730.000
5A109SER00.0100.0143.5610.1760.4710.010-0.048-0.2570.000
6A110PHE00.0130.0085.4970.2350.2350.0000.0000.0000.000
7A111VAL0-0.0080.0007.5520.1420.1420.0000.0000.0000.000
8A112ARG10.8370.9019.3970.1760.1760.0000.0000.0000.000
9A113ASP-1-0.929-0.9528.411-0.026-0.0260.0000.0000.0000.000
10A114THR0-0.065-0.02811.6320.0120.0120.0000.0000.0000.000
11A115ASP-1-0.873-0.93814.004-0.152-0.1520.0000.0000.0000.000
12A116PRO0-0.007-0.00617.805-0.022-0.0220.0000.0000.0000.000
13A117VAL00.031-0.00119.363-0.013-0.0130.0000.0000.0000.000
14A118GLN0-0.010-0.00319.287-0.005-0.0050.0000.0000.0000.000
15A119LEU00.0060.01514.646-0.020-0.0200.0000.0000.0000.000
16A120VAL00.0200.00617.952-0.022-0.0220.0000.0000.0000.000
17A121ASN0-0.034-0.02120.8810.0030.0030.0000.0000.0000.000
18A122PHE0-0.001-0.01017.8880.0070.0070.0000.0000.0000.000
19A123LEU00.0100.00716.123-0.010-0.0100.0000.0000.0000.000
20A124GLN0-0.022-0.01020.0560.0110.0110.0000.0000.0000.000
21A125SER0-0.065-0.02222.4910.0150.0150.0000.0000.0000.000
22A126GLU-1-0.849-0.90318.162-0.349-0.3490.0000.0000.0000.000
23A127HIS00.0010.00421.4320.0100.0100.0000.0000.0000.000
24A128PRO00.037-0.00221.103-0.027-0.0270.0000.0000.0000.000
25A129GLN00.0280.02919.7680.0150.0150.0000.0000.0000.000
26A130THR0-0.013-0.02416.150-0.041-0.0410.0000.0000.0000.000
27A131ILE00.0120.01516.400-0.058-0.0580.0000.0000.0000.000
28A132ALA00.0030.00417.150-0.027-0.0270.0000.0000.0000.000
29A133VAL0-0.007-0.00813.005-0.034-0.0340.0000.0000.0000.000
30A134VAL00.0060.01212.380-0.085-0.0850.0000.0000.0000.000
31A135LEU00.0100.00112.648-0.061-0.0610.0000.0000.0000.000
32A136SER0-0.071-0.03614.248-0.006-0.0060.0000.0000.0000.000
33A137TYR00.003-0.0138.613-0.141-0.1410.0000.0000.0000.000
34A138LEU0-0.050-0.0039.342-0.111-0.1110.0000.0000.0000.000
35A139ASP-1-0.811-0.91411.323-0.166-0.1660.0000.0000.0000.000
36A140PRO00.0610.03213.1700.0060.0060.0000.0000.0000.000
37A141PRO00.0360.01916.2210.0010.0010.0000.0000.0000.000
38A142VAL0-0.011-0.00113.7620.0040.0040.0000.0000.0000.000
39A143ALA0-0.010-0.01015.451-0.008-0.0080.0000.0000.0000.000
40A144ALA00.0420.02016.9840.0040.0040.0000.0000.0000.000
41A145GLN0-0.030-0.01419.0630.0050.0050.0000.0000.0000.000
42A146ILE0-0.034-0.02215.5980.0060.0060.0000.0000.0000.000
43A147LEU0-0.037-0.01820.1150.0070.0070.0000.0000.0000.000
44A148GLY00.0220.00422.2540.0090.0090.0000.0000.0000.000
45A149ALA0-0.046-0.01122.9640.0130.0130.0000.0000.0000.000
46A150LEU0-0.032-0.00920.9080.0010.0010.0000.0000.0000.000
47A151PRO00.0110.01025.1050.0090.0090.0000.0000.0000.000
48A152GLU-1-0.783-0.86328.205-0.112-0.1120.0000.0000.0000.000
49A153GLU-1-0.929-0.97430.129-0.129-0.1290.0000.0000.0000.000
50A154LEU0-0.038-0.01924.615-0.007-0.0070.0000.0000.0000.000
51A155GLN0-0.013-0.00425.725-0.009-0.0090.0000.0000.0000.000
52A156THR00.0660.02425.982-0.009-0.0090.0000.0000.0000.000
53A157GLU-1-0.811-0.90527.240-0.159-0.1590.0000.0000.0000.000
54A158VAL0-0.0120.00321.006-0.016-0.0160.0000.0000.0000.000
55A159LEU00.0040.01422.550-0.025-0.0250.0000.0000.0000.000
56A160LYS10.8900.94323.8520.1430.1430.0000.0000.0000.000
57A161ARG10.9050.92922.0470.2370.2370.0000.0000.0000.000
58A162ILE0-0.0180.00718.632-0.029-0.0290.0000.0000.0000.000
59A163ALA0-0.0030.00320.659-0.016-0.0160.0000.0000.0000.000
60A164LEU0-0.022-0.02523.4530.0060.0060.0000.0000.0000.000
61A165LEU0-0.0340.01015.8940.0010.0010.0000.0000.0000.000
62A166GLU-1-0.817-0.90716.923-0.461-0.4610.0000.0000.0000.000
63A167ARG10.7380.81521.3030.2050.2050.0000.0000.0000.000
64A168THR0-0.029-0.02723.1280.0290.0290.0000.0000.0000.000
65A169SER00.0130.00525.9830.0200.0200.0000.0000.0000.000
66A173VAL00.0540.01727.434-0.011-0.0110.0000.0000.0000.000
67A174LYS10.8620.91128.1010.1570.1570.0000.0000.0000.000
68A175GLU-1-0.834-0.86822.352-0.311-0.3110.0000.0000.0000.000
69A176ILE00.0240.01423.269-0.018-0.0180.0000.0000.0000.000
70A177GLU-1-0.847-0.90224.065-0.169-0.1690.0000.0000.0000.000
71A178ARG10.8930.93722.7020.2660.2660.0000.0000.0000.000
72A179ASN0-0.002-0.01019.250-0.036-0.0360.0000.0000.0000.000
73A180LEU0-0.0030.00919.935-0.016-0.0160.0000.0000.0000.000
74A181GLU-1-0.878-0.95322.086-0.196-0.1960.0000.0000.0000.000
75A182LYS10.8540.94116.4640.4720.4720.0000.0000.0000.000
76A183LYS10.8070.89315.9830.4140.4140.0000.0000.0000.000
77A184ILE0-0.030-0.00118.6360.0190.0190.0000.0000.0000.000
78A185SER0-0.072-0.04920.5930.0170.0170.0000.0000.0000.000
79A186GLY0-0.041-0.01014.4410.0080.0080.0000.0000.0000.000
80A195VAL00.0160.01012.092-0.018-0.0180.0000.0000.0000.000
81A196GLY0-0.003-0.01314.7230.0440.0440.0000.0000.0000.000
82A197GLY0-0.0120.01317.4220.0170.0170.0000.0000.0000.000
83A198ILE0-0.003-0.01220.795-0.003-0.0030.0000.0000.0000.000
84A199ASP-1-0.809-0.88320.066-0.168-0.1680.0000.0000.0000.000
85A200THR00.007-0.00216.4360.0010.0010.0000.0000.0000.000
86A201ALA00.003-0.00518.8740.0050.0050.0000.0000.0000.000
87A202ALA00.0210.01221.9760.0140.0140.0000.0000.0000.000
88A203GLU-1-0.912-0.96018.041-0.161-0.1610.0000.0000.0000.000
89A204ILE0-0.035-0.01617.3940.0110.0110.0000.0000.0000.000
90A205MET0-0.020-0.01621.0970.0120.0120.0000.0000.0000.000
91A206ASN0-0.052-0.04423.9370.0110.0110.0000.0000.0000.000
92A207ASN0-0.087-0.05020.9990.0240.0240.0000.0000.0000.000
93A208LEU0-0.0140.01323.339-0.001-0.0010.0000.0000.0000.000
94A209ASP-1-0.829-0.85125.489-0.084-0.0840.0000.0000.0000.000
95A210ARG10.9830.96428.7360.0540.0540.0000.0000.0000.000
96A211THR0-0.022-0.03231.5960.0030.0030.0000.0000.0000.000
97A212THR0-0.026-0.04627.483-0.001-0.0010.0000.0000.0000.000
98A213GLU-1-0.825-0.89128.669-0.095-0.0950.0000.0000.0000.000
99A214LYS10.8290.88829.7490.0790.0790.0000.0000.0000.000
100A215LYS10.8550.91431.9970.0970.0970.0000.0000.0000.000
101A216ILE00.0040.00726.582-0.002-0.0020.0000.0000.0000.000
102A217MET0-0.0080.01030.417-0.001-0.0010.0000.0000.0000.000
103A218ASP-1-0.899-0.95932.353-0.081-0.0810.0000.0000.0000.000
104A219LYS10.8170.89932.2590.1320.1320.0000.0000.0000.000
105A220LEU0-0.030-0.02128.736-0.001-0.0010.0000.0000.0000.000
106A221VAL0-0.017-0.01433.4410.0010.0010.0000.0000.0000.000
107A222GLN0-0.049-0.01336.6490.0050.0050.0000.0000.0000.000
108A223GLU-1-0.891-0.95734.333-0.120-0.1200.0000.0000.0000.000
109A224ASN0-0.098-0.05332.422-0.007-0.0070.0000.0000.0000.000
110A225PRO00.0720.03333.751-0.005-0.0050.0000.0000.0000.000
111A226GLU-1-0.894-0.94333.868-0.097-0.0970.0000.0000.0000.000
112A227LEU0-0.019-0.00627.231-0.003-0.0030.0000.0000.0000.000
113A228ALA0-0.008-0.01329.943-0.005-0.0050.0000.0000.0000.000
114A229ASP-1-0.781-0.88131.817-0.084-0.0840.0000.0000.0000.000
115A230GLU-1-0.755-0.84528.220-0.156-0.1560.0000.0000.0000.000
116A231ILE0-0.010-0.02026.045-0.002-0.0020.0000.0000.0000.000
117A232ARG10.8130.89027.9690.0930.0930.0000.0000.0000.000
118A233ARG10.7500.84030.6110.0910.0910.0000.0000.0000.000
119A234ARG10.7770.87223.9820.1470.1470.0000.0000.0000.000
120A235MET0-0.039-0.00225.755-0.002-0.0020.0000.0000.0000.000
121A236PHE00.0110.03727.3310.0080.0080.0000.0000.0000.000
122A237VAL00.0330.00725.612-0.001-0.0010.0000.0000.0000.000
123A238PHE00.0690.01727.9390.0050.0050.0000.0000.0000.000
124A239GLU-1-0.734-0.85829.909-0.007-0.0070.0000.0000.0000.000
125A240ASP-1-0.831-0.89830.952-0.054-0.0540.0000.0000.0000.000
126A241ILE00.0190.01232.7330.0000.0000.0000.0000.0000.000
127A242LEU0-0.032-0.01835.6020.0020.0020.0000.0000.0000.000
128A243LYS10.8130.89434.0860.0450.0450.0000.0000.0000.000
129A244LEU00.0200.03935.816-0.001-0.0010.0000.0000.0000.000
130A245ASP-1-0.764-0.86739.367-0.022-0.0220.0000.0000.0000.000
131A246ASP-1-0.772-0.87942.268-0.012-0.0120.0000.0000.0000.000
132A247ARG10.8230.90044.0260.0180.0180.0000.0000.0000.000
133A248SER00.0650.01140.1530.0000.0000.0000.0000.0000.000
134A249ILE0-0.035-0.00638.9410.0000.0000.0000.0000.0000.000
135A250GLN0-0.028-0.02740.2840.0010.0010.0000.0000.0000.000
136A251LEU0-0.061-0.02040.5710.0020.0020.0000.0000.0000.000
137A252VAL00.0500.01935.3590.0000.0000.0000.0000.0000.000
138A253LEU0-0.031-0.02337.5520.0020.0020.0000.0000.0000.000
139A254ARG10.7270.86339.3840.0260.0260.0000.0000.0000.000
140A255GLU-1-0.807-0.86236.179-0.024-0.0240.0000.0000.0000.000
141A256VAL0-0.0180.00133.1800.0000.0000.0000.0000.0000.000
142A257ASH0-0.082-0.06931.8260.0050.0050.0000.0000.0000.000
143A258THR00.0360.00134.7010.0000.0000.0000.0000.0000.000
144A259ARG10.9090.95429.955-0.054-0.0540.0000.0000.0000.000
145A260ASP-1-0.729-0.82528.9260.0200.0200.0000.0000.0000.000
146A261LEU00.0250.00930.980-0.001-0.0010.0000.0000.0000.000
147A262ALA0-0.006-0.01633.4160.0000.0000.0000.0000.0000.000
148A263LEU0-0.032-0.01727.2280.0030.0030.0000.0000.0000.000
149A264ALA00.0220.01428.8920.0020.0020.0000.0000.0000.000
150A265LEU00.005-0.00129.931-0.001-0.0010.0000.0000.0000.000
151A266LYS10.8390.92130.084-0.052-0.0520.0000.0000.0000.000
152A267GLY0-0.0120.00428.1460.0060.0060.0000.0000.0000.000
153A268ALA00.0090.02729.034-0.006-0.0060.0000.0000.0000.000
154A269SER0-0.015-0.04731.8280.0060.0060.0000.0000.0000.000
155A270ASP-1-0.857-0.93534.4860.0160.0160.0000.0000.0000.000
156A271GLU-1-0.926-0.95337.901-0.013-0.0130.0000.0000.0000.000
157A272LEU00.0180.01333.310-0.001-0.0010.0000.0000.0000.000
158A273LYS10.7810.87334.611-0.018-0.0180.0000.0000.0000.000
159A274GLU-1-0.898-0.95138.0220.0040.0040.0000.0000.0000.000
160A275LYS10.7610.88539.6570.0210.0210.0000.0000.0000.000
161A276ILE00.0460.02735.381-0.002-0.0020.0000.0000.0000.000
162A277PHE00.000-0.02039.8740.0010.0010.0000.0000.0000.000
163A278LYS10.7660.87942.3330.0100.0100.0000.0000.0000.000
164A279ASN0-0.039-0.03042.571-0.002-0.0020.0000.0000.0000.000
165A280MET0-0.0160.02939.9870.0000.0000.0000.0000.0000.000
166A281SER0-0.012-0.00744.1320.0010.0010.0000.0000.0000.000
167A282LYS11.0060.97746.066-0.003-0.0030.0000.0000.0000.000
168A283ARG10.9900.99545.916-0.006-0.0060.0000.0000.0000.000
169A284ALA00.0100.01342.2110.0020.0020.0000.0000.0000.000
170A285ALA00.0470.01942.3790.0020.0020.0000.0000.0000.000
171A286ALA0-0.033-0.00943.5390.0020.0020.0000.0000.0000.000
172A287LEU00.0400.00941.4020.0020.0020.0000.0000.0000.000
173A288LEU00.0010.00036.8030.0030.0030.0000.0000.0000.000
174A289LYS10.9260.97439.214-0.016-0.0160.0000.0000.0000.000
175A290ASP-1-0.865-0.92940.8680.0300.0300.0000.0000.0000.000
176A291GLU-1-0.836-0.91234.5160.0480.0480.0000.0000.0000.000
177A292LEU0-0.043-0.03535.0170.0050.0050.0000.0000.0000.000
178A293GLU-1-0.996-0.99637.0360.0340.0340.0000.0000.0000.000
179A294TYR0-0.063-0.02938.3320.0040.0040.0000.0000.0000.000
180A295MET0-0.087-0.01131.6990.0050.0050.0000.0000.0000.000
181A296GLY00.0150.01732.9100.0070.0070.0000.0000.0000.000
182A297PRO0-0.047-0.04629.413-0.004-0.0040.0000.0000.0000.000
183A298VAL00.0020.01126.8750.0000.0000.0000.0000.0000.000
184A299ARG10.8920.94520.769-0.186-0.1860.0000.0000.0000.000
185A300LEU00.0460.02120.052-0.008-0.0080.0000.0000.0000.000
186A301LYN00.0530.01217.766-0.017-0.0170.0000.0000.0000.000
187A302ASP-1-0.795-0.90220.4970.0900.0900.0000.0000.0000.000
188A303VAL0-0.026-0.01323.797-0.012-0.0120.0000.0000.0000.000
189A304GLU-1-0.905-0.94420.036-0.003-0.0030.0000.0000.0000.000
190A305GLU-1-0.898-0.94921.4290.0170.0170.0000.0000.0000.000
191A306ALA0-0.0130.00323.088-0.011-0.0110.0000.0000.0000.000
192A307GLN0-0.046-0.03625.761-0.013-0.0130.0000.0000.0000.000
193A308GLN00.0490.02521.338-0.008-0.0080.0000.0000.0000.000
194A309LYS10.7730.87325.056-0.027-0.0270.0000.0000.0000.000
195A310ILE0-0.008-0.00427.430-0.005-0.0050.0000.0000.0000.000
196A311ILE00.0230.02126.079-0.002-0.0020.0000.0000.0000.000
197A312ASN0-0.035-0.02524.532-0.016-0.0160.0000.0000.0000.000
198A313ILE0-0.064-0.01728.674-0.003-0.0030.0000.0000.0000.000
199A314ILE00.0190.00132.0130.0000.0000.0000.0000.0000.000
200A315ARG10.9300.95826.4120.0910.0910.0000.0000.0000.000
201A316ARG10.8280.88932.0170.0340.0340.0000.0000.0000.000
202A317LEU0-0.021-0.01133.6790.0010.0010.0000.0000.0000.000
203A318GLU-1-0.864-0.91733.047-0.070-0.0700.0000.0000.0000.000
204A319GLU-1-0.849-0.90331.886-0.089-0.0890.0000.0000.0000.000
205A320ALA0-0.078-0.03435.9950.0000.0000.0000.0000.0000.000
206A321GLY0-0.024-0.00338.9760.0030.0030.0000.0000.0000.000
207A322GLU-1-0.905-0.95440.455-0.029-0.0290.0000.0000.0000.000
208A323ILE0-0.046-0.01836.5050.0040.0040.0000.0000.0000.000
209A324VAL0-0.014-0.00940.323-0.002-0.0020.0000.0000.0000.000
210A325ILE0-0.0060.00237.2270.0030.0030.0000.0000.0000.000