FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: 6YMZZ

Calculation Name: 2EAY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2EAY

Chain ID: A

ChEMBL ID:

UniProt ID: O66837

Base Structure: X-ray

Registration Date: 2023-09-24

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 219
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2723251.847789
FMO2-HF: Nuclear repulsion 2637137.266634
FMO2-HF: Total energy -86114.581155
FMO2-MP2: Total energy -86371.265713


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-9.252-4.0233.64-3.08-5.789-0.018
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : -0.002
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].
3A3LYS10.9150.9602.238-5.911-2.6092.729-1.958-4.073-0.007
4A4ASN00.0110.0133.4730.5700.7740.0120.122-0.3370.000
5A5LEU00.0220.0246.940-0.184-0.1840.0000.0000.0000.000
6A6ILE00.0050.0149.6160.1750.1750.0000.0000.0000.000
7A7TRP0-0.017-0.03112.265-0.071-0.0710.0000.0000.0000.000
8A8LEU0-0.0060.00015.4020.0690.0690.0000.0000.0000.000
9A9LYS10.8490.91419.0430.2740.2740.0000.0000.0000.000
10A10GLU-1-0.842-0.91021.872-0.220-0.2200.0000.0000.0000.000
11A11VAL00.0020.01020.6880.0020.0020.0000.0000.0000.000
12A12ASP-1-0.753-0.83023.883-0.275-0.2750.0000.0000.0000.000
13A13SER00.002-0.01822.500-0.015-0.0150.0000.0000.0000.000
14A14THR00.030-0.00516.8630.0220.0220.0000.0000.0000.000
15A15GLN00.0200.00816.959-0.084-0.0840.0000.0000.0000.000
16A16GLU-1-0.873-0.95819.184-0.266-0.2660.0000.0000.0000.000
17A17ARG10.8090.85019.9760.2710.2710.0000.0000.0000.000
18A18LEU0-0.0210.02313.7830.0030.0030.0000.0000.0000.000
19A19LYS10.8110.91617.8960.3200.3200.0000.0000.0000.000
20A20GLU-1-0.913-0.92020.573-0.209-0.2090.0000.0000.0000.000
21A21TRP0-0.044-0.03618.5810.0120.0120.0000.0000.0000.000
22A22ASN0-0.083-0.04516.493-0.053-0.0530.0000.0000.0000.000
23A23VAL00.0360.02912.2800.0280.0280.0000.0000.0000.000
24A24SER00.0300.01510.8060.0740.0740.0000.0000.0000.000
25A25TYR00.026-0.0027.306-0.146-0.1460.0000.0000.0000.000
26A26GLY0-0.021-0.0095.2910.2420.2420.0000.0000.0000.000
27A27THR0-0.013-0.0196.113-0.447-0.4470.0000.0000.0000.000
28A28ALA0-0.037-0.0078.6430.0480.0480.0000.0000.0000.000
29A29LEU0-0.025-0.00710.3730.0940.0940.0000.0000.0000.000
30A30VAL00.004-0.01312.122-0.006-0.0060.0000.0000.0000.000
31A31ALA00.0310.01215.0450.0650.0650.0000.0000.0000.000
32A32ASP-1-0.792-0.86818.641-0.413-0.4130.0000.0000.0000.000
33A33ARG10.7590.84820.5010.2620.2620.0000.0000.0000.000
34A34GLN00.0270.02521.012-0.019-0.0190.0000.0000.0000.000
35A35THR0-0.046-0.02524.4380.0150.0150.0000.0000.0000.000
36A36LYS10.9971.00527.1090.2080.2080.0000.0000.0000.000
37A49GLU-1-0.832-0.92324.933-0.272-0.2720.0000.0000.0000.000
38A50GLY00.0500.02423.2420.0130.0130.0000.0000.0000.000
39A51GLY00.0230.02822.171-0.013-0.0130.0000.0000.0000.000
40A52LEU0-0.021-0.00914.405-0.006-0.0060.0000.0000.0000.000
41A53TYR00.0070.00717.4730.0070.0070.0000.0000.0000.000
42A54PHE00.0380.00910.212-0.054-0.0540.0000.0000.0000.000
43A55SER00.0210.00713.7050.0530.0530.0000.0000.0000.000
44A56PHE0-0.006-0.0149.018-0.175-0.1750.0000.0000.0000.000
45A57LEU0-0.0090.01010.5830.1240.1240.0000.0000.0000.000
46A58LEU00.0070.0018.080-0.242-0.2420.0000.0000.0000.000
47A59ASN00.0560.02110.3060.1130.1130.0000.0000.0000.000
48A60PRO0-0.003-0.01912.156-0.001-0.0010.0000.0000.0000.000
49A61LYS10.9140.95915.2310.2000.2000.0000.0000.0000.000
50A62GLU-1-0.842-0.8979.841-0.313-0.3130.0000.0000.0000.000
51A63PHE0-0.018-0.0249.193-0.031-0.0310.0000.0000.0000.000
52A64GLU-1-0.888-0.93715.090-0.171-0.1710.0000.0000.0000.000
53A65ASN0-0.032-0.00118.2940.0060.0060.0000.0000.0000.000
54A66LEU00.002-0.02517.289-0.035-0.0350.0000.0000.0000.000
55A67LEU00.0030.01919.774-0.005-0.0050.0000.0000.0000.000
56A68GLN0-0.030-0.02918.564-0.023-0.0230.0000.0000.0000.000
57A69LEU00.0030.00712.467-0.024-0.0240.0000.0000.0000.000
58A70PRO00.0360.01315.298-0.062-0.0620.0000.0000.0000.000
59A71LEU00.0220.03217.094-0.017-0.0170.0000.0000.0000.000
60A72VAL00.0110.01012.471-0.002-0.0020.0000.0000.0000.000
61A73LEU0-0.035-0.00610.854-0.063-0.0630.0000.0000.0000.000
62A74GLY00.0640.02613.475-0.031-0.0310.0000.0000.0000.000
63A75LEU0-0.0090.00115.4670.0130.0130.0000.0000.0000.000
64A76SER0-0.003-0.01010.572-0.007-0.0070.0000.0000.0000.000
65A77VAL0-0.0190.00212.692-0.018-0.0180.0000.0000.0000.000
66A78SER0-0.038-0.03114.2590.0470.0470.0000.0000.0000.000
67A79GLU-1-0.816-0.91014.048-0.342-0.3420.0000.0000.0000.000
68A80ALA00.0060.00411.9460.0290.0290.0000.0000.0000.000
69A81LEU00.012-0.00613.9740.0270.0270.0000.0000.0000.000
70A82GLU-1-0.832-0.88717.247-0.200-0.2000.0000.0000.0000.000
71A83GLU-1-0.877-0.91914.030-0.286-0.2860.0000.0000.0000.000
72A84ILE0-0.074-0.02513.9530.0150.0150.0000.0000.0000.000
73A85THR0-0.062-0.06217.7170.0320.0320.0000.0000.0000.000
74A86GLU-1-0.942-0.96620.768-0.112-0.1120.0000.0000.0000.000
75A87ILE0-0.046-0.01322.4680.0190.0190.0000.0000.0000.000
76A88PRO0-0.0040.00922.052-0.024-0.0240.0000.0000.0000.000
77A89PHE0-0.018-0.02620.552-0.003-0.0030.0000.0000.0000.000
78A90SER0-0.013-0.02022.5730.0060.0060.0000.0000.0000.000
79A91LEU0-0.048-0.02518.801-0.030-0.0300.0000.0000.0000.000
80A92LYS10.8640.94022.6860.2180.2180.0000.0000.0000.000
81A93TRP0-0.0270.00323.951-0.018-0.0180.0000.0000.0000.000
82A94PRO00.017-0.01823.3620.0120.0120.0000.0000.0000.000
83A95ASN0-0.055-0.07020.288-0.001-0.0010.0000.0000.0000.000
84A96ASP-1-0.730-0.84220.314-0.337-0.3370.0000.0000.0000.000
85A97VAL0-0.028-0.01717.7690.0110.0110.0000.0000.0000.000
86A98TYR00.0480.00321.1840.0040.0040.0000.0000.0000.000
87A99PHE00.0510.04324.156-0.004-0.0040.0000.0000.0000.000
88A100GLN0-0.009-0.01226.2500.0110.0110.0000.0000.0000.000
89A101GLU-1-0.789-0.89429.004-0.162-0.1620.0000.0000.0000.000
90A102LYS10.7860.91128.9700.1620.1620.0000.0000.0000.000
91A103LYS10.8050.90323.1000.2880.2880.0000.0000.0000.000
92A104VAL0-0.011-0.00820.8860.0020.0020.0000.0000.0000.000
93A105SER0-0.049-0.05117.882-0.038-0.0380.0000.0000.0000.000
94A106GLY0-0.0060.00819.6810.0320.0320.0000.0000.0000.000
95A107VAL0-0.016-0.00415.454-0.058-0.0580.0000.0000.0000.000
96A108LEU00.0260.02417.4490.0530.0530.0000.0000.0000.000
97A109CYS0-0.032-0.00515.510-0.064-0.0640.0000.0000.0000.000
98A110GLU-1-0.779-0.87318.039-0.307-0.3070.0000.0000.0000.000
99A111LEU00.0080.00518.501-0.032-0.0320.0000.0000.0000.000
100A112SER0-0.007-0.01219.8200.0300.0300.0000.0000.0000.000
101A113LYS10.9360.95520.7410.1710.1710.0000.0000.0000.000
102A114ASP-1-0.863-0.92318.916-0.174-0.1740.0000.0000.0000.000
103A115LYS10.8230.90916.4030.3110.3110.0000.0000.0000.000
104A116LEU00.0140.02613.7660.0280.0280.0000.0000.0000.000
105A117ILE0-0.024-0.02613.872-0.085-0.0850.0000.0000.0000.000
106A118VAL00.0150.00912.2070.0740.0740.0000.0000.0000.000
107A119GLY00.0530.02513.951-0.071-0.0710.0000.0000.0000.000
108A120ILE0-0.042-0.02512.0830.0330.0330.0000.0000.0000.000
109A121GLY00.0160.01115.932-0.013-0.0130.0000.0000.0000.000
110A122ILE0-0.0230.00214.5750.0090.0090.0000.0000.0000.000
111A123ASN0-0.0120.00319.092-0.014-0.0140.0000.0000.0000.000
112A124VAL0-0.006-0.00318.3480.0080.0080.0000.0000.0000.000
113A125ASN00.0410.00221.4540.0230.0230.0000.0000.0000.000
114A126GLN0-0.014-0.00824.1130.0110.0110.0000.0000.0000.000
115A127ARG10.7880.85826.7550.1970.1970.0000.0000.0000.000
116A128GLU-1-0.912-0.94830.515-0.141-0.1410.0000.0000.0000.000
117A129ILE0-0.024-0.00330.058-0.012-0.0120.0000.0000.0000.000
118A130PRO0-0.036-0.02732.2320.0100.0100.0000.0000.0000.000
119A131GLU-1-0.830-0.93335.248-0.124-0.1240.0000.0000.0000.000
120A132GLU-1-0.902-0.92535.936-0.138-0.1380.0000.0000.0000.000
121A133ILE0-0.029-0.02730.095-0.004-0.0040.0000.0000.0000.000
122A134LYN00.0560.05732.694-0.011-0.0110.0000.0000.0000.000
123A135ASP-1-0.872-0.94633.686-0.151-0.1510.0000.0000.0000.000
124A136ARG10.8300.91031.3430.1610.1610.0000.0000.0000.000
125A137ALA0-0.050-0.02528.165-0.018-0.0180.0000.0000.0000.000
126A138THR00.0430.02226.0590.0110.0110.0000.0000.0000.000
127A139THR0-0.016-0.02424.751-0.021-0.0210.0000.0000.0000.000
128A140LEU00.0550.02519.4220.0100.0100.0000.0000.0000.000
129A141TYR0-0.0070.01724.1390.0190.0190.0000.0000.0000.000
130A142GLU-1-0.926-0.96126.554-0.152-0.1520.0000.0000.0000.000
131A143ILE0-0.044-0.00324.9700.0090.0090.0000.0000.0000.000
132A144THR0-0.025-0.03324.3040.0090.0090.0000.0000.0000.000
133A145GLY00.0060.00927.6210.0120.0120.0000.0000.0000.000
134A146LYS10.8490.93523.7610.1920.1920.0000.0000.0000.000
135A147ASP-1-0.805-0.86023.697-0.228-0.2280.0000.0000.0000.000
136A148TRP00.004-0.02719.1360.0020.0020.0000.0000.0000.000
137A149ASP-1-0.822-0.90715.685-0.453-0.4530.0000.0000.0000.000
138A150ARG10.8500.88716.1300.3720.3720.0000.0000.0000.000
139A151LYS10.8910.94610.3100.5940.5940.0000.0000.0000.000
140A152GLU-1-0.851-0.92511.339-0.773-0.7730.0000.0000.0000.000
141A153VAL00.0010.00511.906-0.061-0.0610.0000.0000.0000.000
142A154LEU0-0.0060.0019.894-0.073-0.0730.0000.0000.0000.000
143A155LEU0-0.026-0.0176.010-0.274-0.2740.0000.0000.0000.000
144A156LYS10.8520.9277.5930.1620.1620.0000.0000.0000.000
145A157VAL00.0380.0029.478-0.019-0.0190.0000.0000.0000.000
146A158LEU0-0.026-0.0115.696-0.087-0.0870.0000.0000.0000.000
147A159LYN00.0280.0424.802-0.470-0.4700.0000.0000.0000.000
148A160ARG10.8320.9105.8550.5550.5550.0000.0000.0000.000
149A161ILE0-0.0060.0006.7300.0640.0640.0000.0000.0000.000
150A162SER0-0.084-0.0652.647-2.713-1.0360.900-1.229-1.349-0.011
151A163GLU-1-0.904-0.9364.465-0.285-0.239-0.001-0.015-0.0300.000
152A164ASN0-0.025-0.0427.1550.2260.2260.0000.0000.0000.000
153A165LEU00.004-0.0037.2040.1470.1470.0000.0000.0000.000
154A166LYS10.8000.8975.5030.1400.1400.0000.0000.0000.000
155A167LYS10.9270.9557.8540.3450.3450.0000.0000.0000.000
156A168PHE0-0.084-0.03411.1800.0940.0940.0000.0000.0000.000
157A169LYS10.8020.8837.5160.5070.5070.0000.0000.0000.000
158A170GLU-1-0.847-0.88910.5400.0870.0870.0000.0000.0000.000
159A171LYS10.8270.90813.3740.0980.0980.0000.0000.0000.000
160A172SER00.0480.02016.2300.0030.0030.0000.0000.0000.000
161A173PHE00.0940.03517.439-0.009-0.0090.0000.0000.0000.000
162A174LYS10.8540.93118.9170.0910.0910.0000.0000.0000.000
163A175GLU-1-0.838-0.89216.436-0.088-0.0880.0000.0000.0000.000
164A176PHE0-0.029-0.03212.820-0.005-0.0050.0000.0000.0000.000
165A177LYS10.7890.90918.6390.1390.1390.0000.0000.0000.000
166A178GLY00.0670.03322.0830.0000.0000.0000.0000.0000.000
167A179LYS10.9010.93815.9820.2570.2570.0000.0000.0000.000
168A180ILE00.0040.00117.985-0.004-0.0040.0000.0000.0000.000
169A181GLU-1-0.744-0.87621.548-0.140-0.1400.0000.0000.0000.000
170A182SER0-0.079-0.03723.6130.0070.0070.0000.0000.0000.000
171A183LYS10.8920.93919.2190.2780.2780.0000.0000.0000.000
172A184MET0-0.0450.00224.336-0.012-0.0120.0000.0000.0000.000
173A185LEU0-0.0030.01326.0550.0140.0140.0000.0000.0000.000
174A186TYR0-0.075-0.07528.521-0.003-0.0030.0000.0000.0000.000
175A187LEU00.0080.02528.6170.0090.0090.0000.0000.0000.000
176A188GLY0-0.057-0.03931.3580.0050.0050.0000.0000.0000.000
177A189GLU-1-0.941-0.97634.437-0.098-0.0980.0000.0000.0000.000
178A190GLU-1-0.891-0.94836.273-0.092-0.0920.0000.0000.0000.000
179A191VAL0-0.026-0.02833.737-0.004-0.0040.0000.0000.0000.000
180A192LYS10.8760.92636.8550.1230.1230.0000.0000.0000.000
181A193LEU0-0.019-0.00932.916-0.007-0.0070.0000.0000.0000.000
182A194LEU0-0.022-0.00233.9430.0080.0080.0000.0000.0000.000
183A195GLY00.0240.01536.463-0.002-0.0020.0000.0000.0000.000
184A196GLU-1-0.939-0.98236.279-0.120-0.1200.0000.0000.0000.000
185A197GLY0-0.025-0.02040.0370.0010.0010.0000.0000.0000.000
186A198LYS10.9100.96342.0170.0870.0870.0000.0000.0000.000
187A199ILE0-0.015-0.01236.7970.0040.0040.0000.0000.0000.000
188A200THR00.0480.02739.215-0.005-0.0050.0000.0000.0000.000
189A201GLY00.0330.01239.2630.0050.0050.0000.0000.0000.000
190A202LYS10.9551.01136.5760.0790.0790.0000.0000.0000.000
191A203LEU00.0050.01829.6790.0010.0010.0000.0000.0000.000
192A204VAL0-0.045-0.03433.3650.0010.0010.0000.0000.0000.000
193A205GLY00.0500.03529.2190.0020.0020.0000.0000.0000.000
194A206LEU0-0.058-0.02823.777-0.004-0.0040.0000.0000.0000.000
195A207SER0-0.048-0.05627.7920.0070.0070.0000.0000.0000.000
196A208GLU-1-0.866-0.94025.404-0.112-0.1120.0000.0000.0000.000
197A209LYS10.8430.90224.1750.1130.1130.0000.0000.0000.000
198A210GLY00.0430.01523.425-0.018-0.0180.0000.0000.0000.000
199A211GLY00.0340.02924.344-0.011-0.0110.0000.0000.0000.000
200A212ALA00.0170.02527.6580.0040.0040.0000.0000.0000.000
201A213LEU0-0.044-0.02029.4080.0090.0090.0000.0000.0000.000
202A214ILE00.0350.02132.522-0.001-0.0010.0000.0000.0000.000
203A215LEU0-0.015-0.01235.6570.0050.0050.0000.0000.0000.000
204A216THR0-0.038-0.02938.7900.0010.0010.0000.0000.0000.000
205A217GLU-1-0.871-0.94741.533-0.063-0.0630.0000.0000.0000.000
206A218GLU-1-0.962-0.97344.509-0.056-0.0560.0000.0000.0000.000
207A219GLY00.0050.00942.2910.0000.0000.0000.0000.0000.000
208A220ILE0-0.046-0.02635.512-0.004-0.0040.0000.0000.0000.000
209A221LYS10.8540.93737.0700.0820.0820.0000.0000.0000.000
210A222GLU-1-0.759-0.84729.803-0.131-0.1310.0000.0000.0000.000
211A223ILE0-0.024-0.00830.9780.0020.0020.0000.0000.0000.000
212A224LEU0-0.002-0.02327.934-0.009-0.0090.0000.0000.0000.000
213A225SER00.0090.00727.909-0.011-0.0110.0000.0000.0000.000
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