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: 7M6YK

Calculation Name: 1YW5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YW5

Chain ID: A

ChEMBL ID:

UniProt ID: Q59KZ2

Base Structure: X-ray

Registration Date: 2023-09-27

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 177
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1822017.60418
FMO2-HF: Nuclear repulsion 1752755.163576
FMO2-HF: Total energy -69262.440604
FMO2-MP2: Total energy -69466.849085


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.
-1.4540.044-0.003-0.625-0.870.002
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 : 0.028 / q_NPA : 0.003
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].
3A3SER00.0640.0293.817-1.405-0.037-0.003-0.599-0.7660.002
4A4THR0-0.013-0.0086.0060.3270.3270.0000.0000.0000.000
5A5SER0-0.016-0.0098.8220.0710.0710.0000.0000.0000.000
6A6THR00.0680.02210.1720.0900.0900.0000.0000.0000.000
7A7GLY00.0330.01312.4700.0500.0500.0000.0000.0000.000
8A8LEU0-0.0200.00512.959-0.024-0.0240.0000.0000.0000.000
9A9PRO00.0190.02416.657-0.019-0.0190.0000.0000.0000.000
10A10PRO00.025-0.01119.1530.0080.0080.0000.0000.0000.000
11A11ASN0-0.017-0.01220.944-0.001-0.0010.0000.0000.0000.000
12A12TRP0-0.0010.02220.4700.0080.0080.0000.0000.0000.000
13A13THR0-0.037-0.03119.4130.0090.0090.0000.0000.0000.000
14A14ILE00.0040.00115.2460.0020.0020.0000.0000.0000.000
15A15ARG10.8010.89219.718-0.101-0.1010.0000.0000.0000.000
16A16VAL00.0310.01120.7370.0090.0090.0000.0000.0000.000
17A17SER0-0.0070.00123.364-0.006-0.0060.0000.0000.0000.000
18A18ARG10.9620.96326.641-0.082-0.0820.0000.0000.0000.000
19A19SER00.0320.00729.163-0.001-0.0010.0000.0000.0000.000
20A20HIS00.0140.01827.5440.0040.0040.0000.0000.0000.000
21A21ASN0-0.022-0.00622.675-0.002-0.0020.0000.0000.0000.000
22A22LYS10.9330.97222.401-0.107-0.1070.0000.0000.0000.000
23A23GLU-1-0.811-0.89917.7690.1900.1900.0000.0000.0000.000
24A24TYR0-0.029-0.01121.169-0.003-0.0030.0000.0000.0000.000
25A25PHE00.008-0.00717.6280.0120.0120.0000.0000.0000.000
26A26LEU0-0.012-0.00522.329-0.009-0.0090.0000.0000.0000.000
27A27ASN00.0600.03823.9770.0010.0010.0000.0000.0000.000
28A28GLN00.002-0.03924.375-0.001-0.0010.0000.0000.0000.000
29A29SER0-0.057-0.02427.363-0.003-0.0030.0000.0000.0000.000
30A30THR0-0.004-0.00929.292-0.001-0.0010.0000.0000.0000.000
31A31ASN0-0.061-0.03129.8550.0020.0020.0000.0000.0000.000
32A32GLU-1-0.919-0.94628.4480.0390.0390.0000.0000.0000.000
33A33SER0-0.027-0.02827.0250.0070.0070.0000.0000.0000.000
34A34SER0-0.004-0.01624.147-0.008-0.0080.0000.0000.0000.000
35A35TRP0-0.014-0.01723.9640.0120.0120.0000.0000.0000.000
36A36ASP-1-0.883-0.92322.2290.0810.0810.0000.0000.0000.000
37A37PRO0-0.022-0.02017.793-0.001-0.0010.0000.0000.0000.000
38A38PRO00.0270.03919.633-0.012-0.0120.0000.0000.0000.000
39A39TYR00.0320.01620.3140.0040.0040.0000.0000.0000.000
40A40GLY00.001-0.00619.754-0.002-0.0020.0000.0000.0000.000
41A41THR0-0.023-0.02515.2000.0000.0000.0000.0000.0000.000
42A42ASP-1-0.861-0.91511.2120.1180.1180.0000.0000.0000.000
43A43LYS10.8810.90112.0570.0180.0180.0000.0000.0000.000
44A44GLU-1-0.946-0.9567.1410.1090.1090.0000.0000.0000.000
45A45VAL0-0.003-0.0047.6270.2500.2500.0000.0000.0000.000
46A46LEU00.0430.0278.7650.0540.0540.0000.0000.0000.000
47A47ASN0-0.031-0.01810.752-0.021-0.0210.0000.0000.0000.000
48A48ALA0-0.0120.0006.0670.0090.0090.0000.0000.0000.000
49A49TYR0-0.031-0.0368.210-0.072-0.0720.0000.0000.0000.000
50A50ILE00.016-0.0109.734-0.059-0.0590.0000.0000.0000.000
51A51ALA0-0.032-0.0079.806-0.053-0.0530.0000.0000.0000.000
52A52LYS10.9600.9743.757-1.192-1.0620.000-0.026-0.1040.000
53A53PHE00.0140.01310.520-0.055-0.0550.0000.0000.0000.000
54A54LYS10.8330.90313.529-0.267-0.2670.0000.0000.0000.000
55A55ASN0-0.046-0.00912.775-0.055-0.0550.0000.0000.0000.000
56A56ASN0-0.058-0.02613.0690.0130.0130.0000.0000.0000.000
57A57GLY0-0.018-0.01715.102-0.021-0.0210.0000.0000.0000.000
58A58TYR0-0.029-0.02017.404-0.022-0.0220.0000.0000.0000.000
59A59LYS10.9721.00117.016-0.200-0.2000.0000.0000.0000.000
60A60PRO00.0090.01115.3760.0340.0340.0000.0000.0000.000
61A61LEU0-0.0240.0108.8210.0170.0170.0000.0000.0000.000
62A62VAL0-0.0150.00312.204-0.064-0.0640.0000.0000.0000.000
63A63ASN0-0.046-0.0659.0090.0280.0280.0000.0000.0000.000
64A64GLU-1-0.887-0.9296.1560.5850.5850.0000.0000.0000.000
65A65ASP-1-0.852-0.9028.8200.4150.4150.0000.0000.0000.000
66A66GLY0-0.067-0.04012.049-0.065-0.0650.0000.0000.0000.000
67A67GLN0-0.074-0.04713.239-0.063-0.0630.0000.0000.0000.000
68A68VAL0-0.021-0.01213.4620.0050.0050.0000.0000.0000.000
69A69ARG10.8590.90714.8710.0020.0020.0000.0000.0000.000
70A70VAL0-0.005-0.01016.805-0.005-0.0050.0000.0000.0000.000
71A71SER00.0050.01519.945-0.003-0.0030.0000.0000.0000.000
72A72HIS00.007-0.06522.7580.0080.0080.0000.0000.0000.000
73A73LEU00.0090.01226.242-0.005-0.0050.0000.0000.0000.000
74A74LEU0-0.071-0.03029.8210.0030.0030.0000.0000.0000.000
75A75ILE00.0190.02532.342-0.003-0.0030.0000.0000.0000.000
76A76LYS10.8220.90535.565-0.027-0.0270.0000.0000.0000.000
77A77ASN00.028-0.01138.095-0.001-0.0010.0000.0000.0000.000
78A78ASN0-0.034-0.02741.5830.0020.0020.0000.0000.0000.000
79A79GLN00.0170.02542.277-0.001-0.0010.0000.0000.0000.000
80A80SER0-0.063-0.01338.1450.0020.0020.0000.0000.0000.000
81A81ARG10.9420.94235.031-0.051-0.0510.0000.0000.0000.000
82A82LYS10.9240.96536.055-0.032-0.0320.0000.0000.0000.000
83A83PRO00.0920.05839.2770.0000.0000.0000.0000.0000.000
84A84LYS11.0030.99940.169-0.023-0.0230.0000.0000.0000.000
85A85SER0-0.080-0.06537.1140.0020.0020.0000.0000.0000.000
86A86TRP00.014-0.00134.471-0.002-0.0020.0000.0000.0000.000
87A87LYS10.8750.96237.097-0.016-0.0160.0000.0000.0000.000
88A88SER0-0.060-0.03240.0890.0000.0000.0000.0000.0000.000
89A89PRO00.0170.01042.4300.0020.0020.0000.0000.0000.000
90A90ASP-1-0.911-0.95743.3130.0140.0140.0000.0000.0000.000
91A91GLY0-0.046-0.01444.6600.0000.0000.0000.0000.0000.000
92A92ILE0-0.085-0.03639.934-0.001-0.0010.0000.0000.0000.000
93A93SER00.025-0.00444.1780.0010.0010.0000.0000.0000.000
94A94ARG10.8450.92539.146-0.021-0.0210.0000.0000.0000.000
95A95THR00.026-0.02744.5650.0020.0020.0000.0000.0000.000
96A96ARG10.8600.90039.909-0.036-0.0360.0000.0000.0000.000
97A97ASP-1-0.849-0.92541.7360.0290.0290.0000.0000.0000.000
98A98GLU-1-0.818-0.87443.1210.0190.0190.0000.0000.0000.000
99A99SER0-0.066-0.04438.8520.0000.0000.0000.0000.0000.000
100A100ILE00.0080.00438.3770.0000.0000.0000.0000.0000.000
101A101GLN00.008-0.00438.8600.0000.0000.0000.0000.0000.000
102A102ILE0-0.033-0.00838.131-0.001-0.0010.0000.0000.0000.000
103A103LEU00.0020.00332.547-0.001-0.0010.0000.0000.0000.000
104A104LYS10.8980.94035.144-0.027-0.0270.0000.0000.0000.000
105A105LYS10.9540.98736.465-0.017-0.0170.0000.0000.0000.000
106A106HIS00.0390.01533.480-0.002-0.0020.0000.0000.0000.000
107A107LEU00.002-0.00629.992-0.001-0.0010.0000.0000.0000.000
108A108GLU-1-0.890-0.94332.1970.0240.0240.0000.0000.0000.000
109A109ARG10.8610.92734.076-0.008-0.0080.0000.0000.0000.000
110A110ILE0-0.045-0.01527.836-0.002-0.0020.0000.0000.0000.000
111A111LEU0-0.041-0.02528.032-0.001-0.0010.0000.0000.0000.000
112A112SER00.0060.01330.1800.0000.0000.0000.0000.0000.000
113A113GLY0-0.019-0.00529.695-0.002-0.0020.0000.0000.0000.000
114A114GLU-1-0.844-0.89830.6850.0050.0050.0000.0000.0000.000
115A115VAL0-0.023-0.00631.378-0.003-0.0030.0000.0000.0000.000
116A116LYS10.9790.99424.4930.0030.0030.0000.0000.0000.000
117A117LEU00.0490.02424.9890.0000.0000.0000.0000.0000.000
118A118SER00.002-0.00924.5560.0020.0020.0000.0000.0000.000
119A119GLU-1-0.932-0.96526.645-0.006-0.0060.0000.0000.0000.000
120A120LEU00.0270.01229.9260.0010.0010.0000.0000.0000.000
121A121ALA0-0.030-0.02428.5080.0010.0010.0000.0000.0000.000
122A122ASN00.0110.00430.3780.0020.0020.0000.0000.0000.000
123A123THR0-0.029-0.02931.6570.0000.0000.0000.0000.0000.000
124A124GLU-1-0.825-0.91134.2610.0120.0120.0000.0000.0000.000
125A125SER00.0140.02730.3180.0030.0030.0000.0000.0000.000
126A126ASP-1-0.759-0.85633.2800.0200.0200.0000.0000.0000.000
127A127CYM-1-0.835-0.73629.5820.0340.0340.0000.0000.0000.000
128A128SER00.026-0.00529.908-0.003-0.0030.0000.0000.0000.000
129A129SER0-0.050-0.14226.229-0.003-0.0030.0000.0000.0000.000
130A130HIS10.8020.90027.584-0.012-0.0120.0000.0000.0000.000
131A131ASP-1-0.878-0.92229.6860.0060.0060.0000.0000.0000.000
132A132ARG10.8380.90521.433-0.016-0.0160.0000.0000.0000.000
133A133GLY00.0120.01324.257-0.001-0.0010.0000.0000.0000.000
134A134GLY00.0470.01324.9780.0010.0010.0000.0000.0000.000
135A135ASP-1-0.829-0.86319.8050.0220.0220.0000.0000.0000.000
136A136LEU0-0.008-0.01621.8180.0000.0000.0000.0000.0000.000
137A137GLY0-0.0200.00118.5470.0060.0060.0000.0000.0000.000
138A138PHE0-0.001-0.02411.620-0.005-0.0050.0000.0000.0000.000
139A139PHE00.0210.01616.932-0.001-0.0010.0000.0000.0000.000
140A140SER00.0760.04217.8320.0110.0110.0000.0000.0000.000
141A141LYS10.8750.94319.334-0.199-0.1990.0000.0000.0000.000
142A142GLY0-0.009-0.01221.9390.0050.0050.0000.0000.0000.000
143A143GLN0-0.0200.00121.6220.0010.0010.0000.0000.0000.000
144A144MET0-0.0190.00223.136-0.012-0.0120.0000.0000.0000.000
145A145GLN00.0380.00626.2570.0010.0010.0000.0000.0000.000
146A146PRO00.0830.02627.9910.0010.0010.0000.0000.0000.000
147A147PRO00.0310.01528.1050.0040.0040.0000.0000.0000.000
148A148PHE00.0100.00723.6920.0010.0010.0000.0000.0000.000
149A149GLU-1-0.864-0.92822.9970.1290.1290.0000.0000.0000.000
150A150GLU-1-0.898-0.95623.3730.1190.1190.0000.0000.0000.000
151A151ALA0-0.0060.00024.3190.0050.0050.0000.0000.0000.000
152A152ALA00.0340.00820.8910.0030.0030.0000.0000.0000.000
153A153PHE0-0.052-0.04316.9170.0060.0060.0000.0000.0000.000
154A154ASN0-0.078-0.03719.3570.0250.0250.0000.0000.0000.000
155A155LEU0-0.0450.01420.068-0.004-0.0040.0000.0000.0000.000
156A156HIS00.0470.03816.3560.0290.0290.0000.0000.0000.000
157A157VAL0-0.031-0.02912.500-0.012-0.0120.0000.0000.0000.000
158A158GLY0-0.004-0.00615.7990.0030.0030.0000.0000.0000.000
159A159GLU-1-0.800-0.85018.5480.0960.0960.0000.0000.0000.000
160A160VAL0-0.019-0.02221.311-0.004-0.0040.0000.0000.0000.000
161A161SER0-0.0060.00324.4690.0040.0040.0000.0000.0000.000
162A162ASN00.0280.00926.479-0.007-0.0070.0000.0000.0000.000
163A163ILE00.020-0.00229.7720.0010.0010.0000.0000.0000.000
164A164ILE0-0.0140.00827.9560.0030.0030.0000.0000.0000.000
165A165GLU-1-0.808-0.87731.4580.0370.0370.0000.0000.0000.000
166A166THR0-0.025-0.03030.4990.0040.0040.0000.0000.0000.000
167A167ASN0-0.011-0.01433.856-0.005-0.0050.0000.0000.0000.000
168A168SER0-0.023-0.02532.999-0.002-0.0020.0000.0000.0000.000
169A169GLY00.0160.02435.236-0.003-0.0030.0000.0000.0000.000
170A170VAL0-0.0060.01034.2230.0030.0030.0000.0000.0000.000
171A171HIS00.002-0.01929.277-0.001-0.0010.0000.0000.0000.000
172A172ILE00.0210.03727.5280.0020.0020.0000.0000.0000.000
173A173LEU0-0.002-0.00723.585-0.003-0.0030.0000.0000.0000.000
174A174GLN00.0470.02320.445-0.001-0.0010.0000.0000.0000.000
175A175ARG10.8010.90613.032-0.139-0.1390.0000.0000.0000.000
176A176THR00.004-0.01216.562-0.002-0.0020.0000.0000.0000.000
177A177GLY00.0290.04812.092-0.026-0.0260.0000.0000.0000.000