Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 1717Z

Calculation Name: 2FYI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FYI

Chain ID: A

ChEMBL ID:

UniProt ID: Q47083

Base Structure: X-ray

Registration Date: 2023-09-20

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 223
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2638335.452591
FMO2-HF: Nuclear repulsion 2551535.045952
FMO2-HF: Total energy -86800.40664
FMO2-MP2: Total energy -87058.707951


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:85:SER)


Summations of interaction energy for fragment #1(A:85:SER)
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.
-15.658-12.5079.222-5.106-7.2660.007
Interaction energy analysis for fragmet #1(A:85:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / q_NPA : -0.019
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].
3A87MET0-0.080-0.0292.147-6.287-4.8115.659-3.149-3.9860.019
4A88THR0-0.017-0.0272.619-2.580-0.9441.034-1.116-1.554-0.011
5A89ASN00.0380.0164.489-1.459-1.370-0.001-0.012-0.0750.000
6A90ASP-1-0.875-0.9186.451-0.361-0.3610.0000.0000.0000.000
7A91THR0-0.109-0.0477.6360.3270.3270.0000.0000.0000.000
8A92SER00.0710.0349.377-0.141-0.1410.0000.0000.0000.000
9A93GLY00.0210.00512.7360.1240.1240.0000.0000.0000.000
10A94VAL00.0220.01315.509-0.087-0.0870.0000.0000.0000.000
11A95LEU0-0.0310.00113.6500.0320.0320.0000.0000.0000.000
12A96THR00.0390.01416.782-0.034-0.0340.0000.0000.0000.000
13A97ILE0-0.030-0.01416.0780.0250.0250.0000.0000.0000.000
14A98ALA00.0260.02220.4780.0020.0020.0000.0000.0000.000
15A99THR0-0.030-0.03922.7420.0030.0030.0000.0000.0000.000
16A100THR00.0360.02024.8940.0050.0050.0000.0000.0000.000
17A101HIS00.0240.01126.275-0.020-0.0200.0000.0000.0000.000
18A102THR00.0260.00227.102-0.015-0.0150.0000.0000.0000.000
19A103GLN00.0340.00722.7390.0090.0090.0000.0000.0000.000
20A104ALA00.0290.01122.442-0.033-0.0330.0000.0000.0000.000
21A105ARG10.8370.91622.6350.2260.2260.0000.0000.0000.000
22A106TYR00.0160.01023.928-0.003-0.0030.0000.0000.0000.000
23A107SER0-0.034-0.02020.6850.0150.0150.0000.0000.0000.000
24A108LEU00.0040.00217.657-0.032-0.0320.0000.0000.0000.000
25A109PRO00.0150.03516.796-0.085-0.0850.0000.0000.0000.000
26A110GLU-1-0.960-0.97715.117-0.605-0.6050.0000.0000.0000.000
27A111VAL00.0660.02712.788-0.135-0.1350.0000.0000.0000.000
28A112ILE0-0.027-0.02012.058-0.175-0.1750.0000.0000.0000.000
29A113LYS10.9230.96012.0410.5980.5980.0000.0000.0000.000
30A114ALA00.0420.0268.980-0.258-0.2580.0000.0000.0000.000
31A115PHE0-0.005-0.0167.466-0.612-0.6120.0000.0000.0000.000
32A116ARG10.9390.9607.8430.7140.7140.0000.0000.0000.000
33A117GLU-1-0.940-0.9486.221-2.459-2.4590.0000.0000.0000.000
34A118LEU0-0.061-0.0282.342-1.007-1.4032.532-0.753-1.383-0.001
35A119PHE0-0.063-0.0574.115-0.902-0.674-0.001-0.056-0.1710.000
36A120PRO00.0220.0355.8350.6650.6650.0000.0000.0000.000
37A121GLU-1-0.911-0.9518.776-0.580-0.5800.0000.0000.0000.000
38A122VAL0-0.103-0.04810.5720.2650.2650.0000.0000.0000.000
39A123ARG10.8000.90812.3080.3490.3490.0000.0000.0000.000
40A124LEU0-0.007-0.00114.2520.0380.0380.0000.0000.0000.000
41A125GLU-1-0.837-0.91516.118-0.329-0.3290.0000.0000.0000.000
42A126LEU0-0.013-0.01818.2960.0020.0020.0000.0000.0000.000
43A127ILE00.0190.02021.8630.0170.0170.0000.0000.0000.000
44A128GLN0-0.034-0.02625.4050.0080.0080.0000.0000.0000.000
45A129GLY00.0310.01527.4940.0110.0110.0000.0000.0000.000
46A130THR0-0.030-0.02330.0530.0000.0000.0000.0000.0000.000
47A131PRO00.0570.00830.207-0.003-0.0030.0000.0000.0000.000
48A132GLN00.016-0.00331.0670.0030.0030.0000.0000.0000.000
49A133GLU-1-0.839-0.92131.242-0.142-0.1420.0000.0000.0000.000
50A134ILE0-0.054-0.00426.200-0.001-0.0010.0000.0000.0000.000
51A135ALA00.0150.00928.121-0.002-0.0020.0000.0000.0000.000
52A136THR0-0.0090.00130.0740.0080.0080.0000.0000.0000.000
53A137LEU0-0.017-0.01327.3870.0040.0040.0000.0000.0000.000
54A138LEU0-0.0200.00323.3130.0010.0010.0000.0000.0000.000
55A139GLN0-0.057-0.03026.9940.0090.0090.0000.0000.0000.000
56A140ASN0-0.036-0.03529.9870.0180.0180.0000.0000.0000.000
57A141GLY0-0.033-0.00325.6510.0040.0040.0000.0000.0000.000
58A142GLU-1-0.925-0.95825.222-0.165-0.1650.0000.0000.0000.000
59A143ALA0-0.059-0.03123.339-0.024-0.0240.0000.0000.0000.000
60A144ASP-1-0.853-0.89918.885-0.271-0.2710.0000.0000.0000.000
61A145ILE0-0.034-0.02015.9540.0240.0240.0000.0000.0000.000
62A146GLY00.0040.01120.474-0.013-0.0130.0000.0000.0000.000
63A147ILE0-0.010-0.01118.9060.0080.0080.0000.0000.0000.000
64A148ALA00.0260.00323.325-0.004-0.0040.0000.0000.0000.000
65A149SER00.0190.00326.5840.0060.0060.0000.0000.0000.000
66A150GLU-1-0.921-0.96028.894-0.090-0.0900.0000.0000.0000.000
67A151ARG10.8780.94030.4620.0850.0850.0000.0000.0000.000
68A152LEU00.0570.03525.4030.0010.0010.0000.0000.0000.000
69A153SER0-0.003-0.01328.6700.0030.0030.0000.0000.0000.000
70A154ASN0-0.028-0.01329.7930.0120.0120.0000.0000.0000.000
71A155ASP-1-0.833-0.90431.147-0.069-0.0690.0000.0000.0000.000
72A156PRO00.0000.00031.6070.0020.0020.0000.0000.0000.000
73A157GLN0-0.039-0.03431.3490.0010.0010.0000.0000.0000.000
74A158LEU0-0.049-0.01327.004-0.007-0.0070.0000.0000.0000.000
75A159VAL00.0090.00524.2730.0130.0130.0000.0000.0000.000
76A160ALA0-0.017-0.01424.196-0.016-0.0160.0000.0000.0000.000
77A161PHE00.008-0.00120.7140.0180.0180.0000.0000.0000.000
78A162PRO0-0.014-0.00422.601-0.023-0.0230.0000.0000.0000.000
79A163TRP00.008-0.00417.3080.0020.0020.0000.0000.0000.000
80A164PHE00.0120.00320.8450.0090.0090.0000.0000.0000.000
81A165ARG10.9040.94223.2960.0770.0770.0000.0000.0000.000
82A166TRP0-0.0030.01426.892-0.005-0.0050.0000.0000.0000.000
83A167HIS00.0560.02429.1360.0090.0090.0000.0000.0000.000
84A168HIS0-0.029-0.02532.578-0.007-0.0070.0000.0000.0000.000
85A169SER0-0.066-0.02934.9440.0040.0040.0000.0000.0000.000
86A170LEU00.0240.00936.675-0.002-0.0020.0000.0000.0000.000
87A171LEU0-0.0180.00437.105-0.002-0.0020.0000.0000.0000.000
88A172VAL0-0.013-0.01539.9240.0040.0040.0000.0000.0000.000
89A173PRO00.0460.00742.572-0.003-0.0030.0000.0000.0000.000
90A174HIS00.0260.03040.8490.0070.0070.0000.0000.0000.000
91A175ASP-1-0.915-0.93945.021-0.073-0.0730.0000.0000.0000.000
92A176HIS0-0.0170.01047.1430.0050.0050.0000.0000.0000.000
93A177PRO00.0510.01648.9920.0010.0010.0000.0000.0000.000
94A178LEU0-0.003-0.01246.6600.0020.0020.0000.0000.0000.000
95A179THR0-0.070-0.03544.9350.0010.0010.0000.0000.0000.000
96A180GLN0-0.025-0.01747.0540.0040.0040.0000.0000.0000.000
97A181ILE0-0.051-0.00549.7760.0040.0040.0000.0000.0000.000
98A182SER0-0.020-0.04648.161-0.003-0.0030.0000.0000.0000.000
99A183PRO0-0.0780.01347.4460.0020.0020.0000.0000.0000.000
100A184LEU00.0750.03543.2060.0010.0010.0000.0000.0000.000
101A185THR00.024-0.00446.2850.0000.0000.0000.0000.0000.000
102A186LEU00.0240.00944.276-0.002-0.0020.0000.0000.0000.000
103A187GLU-1-0.792-0.92947.638-0.048-0.0480.0000.0000.0000.000
104A188SER0-0.063-0.02349.4570.0010.0010.0000.0000.0000.000
105A189ILE00.0120.00443.944-0.001-0.0010.0000.0000.0000.000
106A190ALA0-0.034-0.02748.112-0.002-0.0020.0000.0000.0000.000
107A191LYS10.8650.95449.9860.0490.0490.0000.0000.0000.000
108A192TRP0-0.012-0.00548.8730.0000.0000.0000.0000.0000.000
109A193PRO00.0580.02749.2970.0000.0000.0000.0000.0000.000
110A194LEU00.0010.00344.275-0.004-0.0040.0000.0000.0000.000
111A195ILE0-0.0250.00641.8080.0000.0000.0000.0000.0000.000
112A196THR00.009-0.01639.165-0.004-0.0040.0000.0000.0000.000
113A197TYR00.0000.00533.3330.0010.0010.0000.0000.0000.000
114A198ARG10.9981.00238.4220.1170.1170.0000.0000.0000.000
115A199GLN0-0.011-0.01838.814-0.001-0.0010.0000.0000.0000.000
116A200GLY0-0.016-0.00537.736-0.002-0.0020.0000.0000.0000.000
117A201ILE0-0.070-0.03534.002-0.006-0.0060.0000.0000.0000.000
118A202THR00.017-0.00131.3510.0020.0020.0000.0000.0000.000
119A203GLY00.1340.08233.1550.0020.0020.0000.0000.0000.000
120A204ARG10.8070.91334.9050.0880.0880.0000.0000.0000.000
121A205SER00.0260.00137.9930.0030.0030.0000.0000.0000.000
122A206ARG10.9600.98233.5880.0830.0830.0000.0000.0000.000
123A207ILE0-0.0010.00438.3720.0050.0050.0000.0000.0000.000
124A208ASP-1-0.821-0.91241.157-0.068-0.0680.0000.0000.0000.000
125A209ASP-1-0.903-0.95741.755-0.054-0.0540.0000.0000.0000.000
126A210ALA0-0.044-0.03142.2140.0040.0040.0000.0000.0000.000
127A211PHE0-0.014-0.01644.0810.0030.0030.0000.0000.0000.000
128A212ALA00.0380.02546.8720.0030.0030.0000.0000.0000.000
129A213ARG10.9090.97941.4300.0540.0540.0000.0000.0000.000
130A214LYS10.8540.92948.7390.0440.0440.0000.0000.0000.000
131A215GLY0-0.015-0.00451.2130.0010.0010.0000.0000.0000.000
132A216LEU0-0.050-0.02350.5470.0000.0000.0000.0000.0000.000
133A217LEU0-0.006-0.00449.755-0.001-0.0010.0000.0000.0000.000
134A218ALA0-0.003-0.00146.5780.0000.0000.0000.0000.0000.000
135A219ASP-1-0.874-0.92948.541-0.066-0.0660.0000.0000.0000.000
136A220ILE0-0.084-0.03844.208-0.004-0.0040.0000.0000.0000.000
137A221VAL00.0510.02847.0310.0010.0010.0000.0000.0000.000
138A222LEU0-0.034-0.01541.760-0.002-0.0020.0000.0000.0000.000
139A223SER0-0.052-0.02742.480-0.001-0.0010.0000.0000.0000.000
140A224ALA00.0200.00838.328-0.001-0.0010.0000.0000.0000.000
141A225GLN00.001-0.03635.5230.0110.0110.0000.0000.0000.000
142A226ASP-1-0.855-0.93032.624-0.174-0.1740.0000.0000.0000.000
143A227SER00.0630.02331.9100.0110.0110.0000.0000.0000.000
144A228ASP-1-0.803-0.88031.653-0.206-0.2060.0000.0000.0000.000
145A229VAL00.0110.00934.8420.0080.0080.0000.0000.0000.000
146A230ILE0-0.034-0.02136.5440.0060.0060.0000.0000.0000.000
147A231LYS10.8850.95431.5170.1940.1940.0000.0000.0000.000
148A232THR0-0.0070.00938.3370.0040.0040.0000.0000.0000.000
149A233TYR0-0.016-0.02040.6170.0070.0070.0000.0000.0000.000
150A234VAL0-0.015-0.00141.1800.0060.0060.0000.0000.0000.000
151A235ALA00.0050.00441.5480.0050.0050.0000.0000.0000.000
152A236LEU0-0.083-0.03143.5180.0040.0040.0000.0000.0000.000
153A237GLY00.0310.01646.3460.0040.0040.0000.0000.0000.000
154A238LEU0-0.098-0.03946.4460.0030.0030.0000.0000.0000.000
155A239GLY00.0220.00347.1920.0040.0040.0000.0000.0000.000
156A240ILE0-0.0100.01444.396-0.004-0.0040.0000.0000.0000.000
157A241GLY00.0440.01540.6810.0000.0000.0000.0000.0000.000
158A242LEU0-0.0470.00239.0820.0010.0010.0000.0000.0000.000
159A243VAL00.016-0.00334.387-0.003-0.0030.0000.0000.0000.000
160A244ALA00.0310.00930.2390.0050.0050.0000.0000.0000.000
161A245GLU-1-0.825-0.91129.396-0.138-0.1380.0000.0000.0000.000
162A246GLN00.035-0.00626.1210.0130.0130.0000.0000.0000.000
163A247SER0-0.068-0.02927.436-0.014-0.0140.0000.0000.0000.000
164A248SER00.003-0.00529.790-0.001-0.0010.0000.0000.0000.000
165A249GLY0-0.029-0.00826.798-0.004-0.0040.0000.0000.0000.000
166A250GLU-1-0.941-0.97825.127-0.271-0.2710.0000.0000.0000.000
167A251GLN0-0.081-0.04027.859-0.002-0.0020.0000.0000.0000.000
168A252GLU-1-0.984-0.97230.966-0.147-0.1470.0000.0000.0000.000
169A253GLU-1-0.760-0.91732.718-0.156-0.1560.0000.0000.0000.000
170A254GLU-1-0.840-0.91536.367-0.120-0.1200.0000.0000.0000.000
171A255ASN0-0.085-0.06338.8690.0080.0080.0000.0000.0000.000
172A256LEU0-0.028-0.01138.6520.0070.0070.0000.0000.0000.000
173A257ILE00.0700.03738.903-0.003-0.0030.0000.0000.0000.000
174A258ARG10.8060.90633.1620.1550.1550.0000.0000.0000.000
175A259LEU0-0.003-0.00238.0470.0030.0030.0000.0000.0000.000
176A260ASP-1-0.891-0.94736.984-0.087-0.0870.0000.0000.0000.000
177A261THR00.051-0.00237.9500.0040.0040.0000.0000.0000.000
178A262ARG10.8940.92831.7020.1070.1070.0000.0000.0000.000
179A263HIS0-0.071-0.01537.3100.0020.0020.0000.0000.0000.000
180A264LEU0-0.068-0.03040.2600.0050.0050.0000.0000.0000.000
181A265PHE0-0.029-0.01338.0790.0020.0020.0000.0000.0000.000
182A266ASP-1-0.901-0.94036.687-0.055-0.0550.0000.0000.0000.000
183A267ALA0-0.067-0.03131.493-0.006-0.0060.0000.0000.0000.000
184A268ASN0-0.033-0.01830.7760.0110.0110.0000.0000.0000.000
185A269THR0-0.015-0.02626.1710.0030.0030.0000.0000.0000.000
186A270VAL0-0.0360.01023.3050.0010.0010.0000.0000.0000.000
187A271TRP00.014-0.00623.8830.0040.0040.0000.0000.0000.000
188A272LEU00.0240.01217.773-0.022-0.0220.0000.0000.0000.000
189A273GLY0-0.018-0.00321.5520.0290.0290.0000.0000.0000.000
190A274LEU00.0330.00818.700-0.024-0.0240.0000.0000.0000.000
191A275LYS10.9370.97522.8410.0870.0870.0000.0000.0000.000
192A276ARG10.9470.97124.6390.0250.0250.0000.0000.0000.000
193A277GLY0-0.0120.00126.097-0.002-0.0020.0000.0000.0000.000
194A278GLN0-0.0290.00722.7050.0140.0140.0000.0000.0000.000
195A279LEU0-0.008-0.01520.7810.0060.0060.0000.0000.0000.000
196A280GLN00.0440.00717.053-0.048-0.0480.0000.0000.0000.000
197A281ARG10.8720.93412.4970.3030.3030.0000.0000.0000.000
198A282ASN00.012-0.0158.224-0.050-0.0500.0000.0000.0000.000
199A283TYR00.0480.0019.7280.0360.0360.0000.0000.0000.000
200A284VAL00.0190.02710.698-0.080-0.0800.0000.0000.0000.000
201A285TRP0-0.017-0.02412.5470.0030.0030.0000.0000.0000.000
202A286ARG10.9560.9834.159-0.185-0.067-0.001-0.020-0.0970.000
203A287PHE00.0250.01610.122-0.030-0.0300.0000.0000.0000.000
204A288LEU00.019-0.00211.8170.0090.0090.0000.0000.0000.000
205A289GLU-1-0.922-0.9609.1120.1180.1180.0000.0000.0000.000
206A290LEU0-0.025-0.0137.598-0.008-0.0080.0000.0000.0000.000
207A291CYS0-0.052-0.00810.586-0.011-0.0110.0000.0000.0000.000
208A292ASN0-0.044-0.03914.0880.0230.0230.0000.0000.0000.000
209A293ALA00.0340.02214.0360.0300.0300.0000.0000.0000.000
210A294GLY0-0.055-0.01315.0530.0480.0480.0000.0000.0000.000
211A295LEU0-0.037-0.01516.3970.0340.0340.0000.0000.0000.000
212A296SER00.0990.06514.4550.0150.0150.0000.0000.0000.000
213A297VAL00.016-0.00211.291-0.057-0.0570.0000.0000.0000.000
214A298GLU-1-0.933-0.97914.2670.3430.3430.0000.0000.0000.000
215A299ASP-1-0.920-0.97017.1530.1450.1450.0000.0000.0000.000
216A300ILE0-0.0040.00815.512-0.027-0.0270.0000.0000.0000.000
217A301LYS10.9210.96214.372-0.235-0.2350.0000.0000.0000.000
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