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: 984G2

Calculation Name: 2O8V-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2O8V

Chain ID: A

ChEMBL ID:

UniProt ID: P17854

Base Structure: X-ray

Registration Date: 2023-09-21

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 229
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2851038.588311
FMO2-HF: Nuclear repulsion 2760908.244334
FMO2-HF: Total energy -90130.343977
FMO2-MP2: Total energy -90399.610082


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:2:SER)


Summations of interaction energy for fragment #1(A:2: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.
1.3112.32-0.006-0.414-0.5890.002
Interaction energy analysis for fragmet #1(A:2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / 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].
3A4LEU00.0100.0073.8750.1491.158-0.006-0.414-0.5890.002
4A5ASP-1-0.749-0.8705.9841.4331.4330.0000.0000.0000.000
5A6LEU0-0.022-0.0127.865-0.356-0.3560.0000.0000.0000.000
6A7ASN0-0.064-0.03711.299-0.229-0.2290.0000.0000.0000.000
7A8ALA00.0580.0199.986-0.112-0.1120.0000.0000.0000.000
8A9LEU0-0.015-0.0179.354-0.115-0.1150.0000.0000.0000.000
9A10ASN0-0.108-0.06712.612-0.097-0.0970.0000.0000.0000.000
10A11GLU-1-0.915-0.94015.3040.1510.1510.0000.0000.0000.000
11A12LEU0-0.0100.01412.696-0.043-0.0430.0000.0000.0000.000
12A13PRO00.0380.01816.8430.0160.0160.0000.0000.0000.000
13A14LYS10.9450.96918.9480.0710.0710.0000.0000.0000.000
14A15VAL00.0000.00220.096-0.018-0.0180.0000.0000.0000.000
15A16ASP-1-0.792-0.91516.981-0.200-0.2000.0000.0000.0000.000
16A17ARG10.8400.93415.036-0.055-0.0550.0000.0000.0000.000
17A18ILE0-0.058-0.03715.372-0.044-0.0440.0000.0000.0000.000
18A19LEU0-0.003-0.00217.182-0.032-0.0320.0000.0000.0000.000
19A20ALA00.0740.04111.775-0.049-0.0490.0000.0000.0000.000
20A21LEU0-0.015-0.01712.075-0.115-0.1150.0000.0000.0000.000
21A22ALA0-0.0350.00113.506-0.020-0.0200.0000.0000.0000.000
22A23GLU-1-0.920-0.95612.060-0.810-0.8100.0000.0000.0000.000
23A24THR0-0.0120.0019.379-0.132-0.1320.0000.0000.0000.000
24A25ASN0-0.030-0.06211.3700.0720.0720.0000.0000.0000.000
25A26ALA0-0.0060.01414.8520.0540.0540.0000.0000.0000.000
26A27GLU-1-0.842-0.89312.225-0.660-0.6600.0000.0000.0000.000
27A28LEU00.0120.00111.5950.0800.0800.0000.0000.0000.000
28A29GLU-1-0.820-0.88515.134-0.177-0.1770.0000.0000.0000.000
29A30LYS10.7780.86916.2330.6110.6110.0000.0000.0000.000
30A31LEU0-0.0480.00113.7290.0210.0210.0000.0000.0000.000
31A32ASP-1-0.815-0.90218.350-0.172-0.1720.0000.0000.0000.000
32A33ALA0-0.025-0.01219.554-0.010-0.0100.0000.0000.0000.000
33A34GLU-1-0.839-0.94919.967-0.072-0.0720.0000.0000.0000.000
34A35GLY00.0340.01717.1890.0200.0200.0000.0000.0000.000
35A36ARG10.7190.81815.5100.2070.2070.0000.0000.0000.000
36A37VAL0-0.034-0.02115.2710.0100.0100.0000.0000.0000.000
37A38ALA00.0090.00015.4320.0530.0530.0000.0000.0000.000
38A39TRP00.0130.0137.9800.1980.1980.0000.0000.0000.000
39A40ALA00.004-0.01210.9260.0640.0640.0000.0000.0000.000
40A41LEU0-0.044-0.03012.3850.1220.1220.0000.0000.0000.000
41A42ASP-1-0.820-0.8869.0481.4731.4730.0000.0000.0000.000
42A43ASN0-0.057-0.0276.569-0.050-0.0500.0000.0000.0000.000
43A44LEU0-0.020-0.0037.160-0.182-0.1820.0000.0000.0000.000
44A45PRO0-0.0040.0028.9470.1940.1940.0000.0000.0000.000
45A46GLY00.0140.00410.682-0.190-0.1900.0000.0000.0000.000
46A47GLU-1-0.756-0.85513.7060.3180.3180.0000.0000.0000.000
47A48TYR0-0.021-0.01811.448-0.037-0.0370.0000.0000.0000.000
48A49VAL00.0070.00518.204-0.027-0.0270.0000.0000.0000.000
49A50LEU00.0200.00421.380-0.022-0.0220.0000.0000.0000.000
50A51SER0-0.0430.00524.1150.0000.0000.0000.0000.0000.000
51A52SER0-0.001-0.00526.753-0.019-0.0190.0000.0000.0000.000
52A53SER0-0.007-0.01230.0330.0050.0050.0000.0000.0000.000
53A54PHE00.0340.00632.233-0.002-0.0020.0000.0000.0000.000
54A55GLY00.0540.02734.788-0.002-0.0020.0000.0000.0000.000
55A56ILE0-0.024-0.03135.9470.0010.0010.0000.0000.0000.000
56A57GLN00.1070.05632.477-0.004-0.0040.0000.0000.0000.000
57A58ALA0-0.0090.01031.519-0.003-0.0030.0000.0000.0000.000
58A59ALA00.0460.02331.0530.0040.0040.0000.0000.0000.000
59A60VAL00.0020.01028.5250.0020.0020.0000.0000.0000.000
60A61SER00.0250.00526.2050.0010.0010.0000.0000.0000.000
61A62LEU0-0.014-0.00426.4460.0090.0090.0000.0000.0000.000
62A63HIS00.0180.00527.8870.0170.0170.0000.0000.0000.000
63A64LEU0-0.048-0.01022.7510.0080.0080.0000.0000.0000.000
64A65VAL00.015-0.00521.3360.0010.0010.0000.0000.0000.000
65A66ASN0-0.012-0.00723.0680.0310.0310.0000.0000.0000.000
66A67GLN0-0.037-0.01325.1900.0090.0090.0000.0000.0000.000
67A68ILE0-0.053-0.01718.8600.0000.0000.0000.0000.0000.000
68A69ARG10.8260.89317.528-0.317-0.3170.0000.0000.0000.000
69A70PRO00.0460.01621.814-0.001-0.0010.0000.0000.0000.000
70A71ASP-1-0.888-0.93524.5240.1580.1580.0000.0000.0000.000
71A72ILE0-0.0270.01121.2200.0230.0230.0000.0000.0000.000
72A73PRO0-0.015-0.02022.671-0.022-0.0220.0000.0000.0000.000
73A74VAL00.0130.01825.309-0.006-0.0060.0000.0000.0000.000
74A75ILE0-0.022-0.00724.629-0.004-0.0040.0000.0000.0000.000
75A76LEU00.0180.00928.650-0.014-0.0140.0000.0000.0000.000
76A77THR0-0.044-0.01631.0730.0040.0040.0000.0000.0000.000
77A78ASP-1-0.845-0.90133.6910.0500.0500.0000.0000.0000.000
78A79THR0-0.024-0.03937.3320.0030.0030.0000.0000.0000.000
79A80GLY0-0.0060.00839.542-0.001-0.0010.0000.0000.0000.000
80A81TYR0-0.052-0.05442.268-0.002-0.0020.0000.0000.0000.000
81A82LEU00.0030.01637.760-0.005-0.0050.0000.0000.0000.000
82A83PHE00.0250.00042.3650.0000.0000.0000.0000.0000.000
83A84PRO00.0240.00843.7500.0020.0020.0000.0000.0000.000
84A85GLU-1-0.771-0.87044.8450.0230.0230.0000.0000.0000.000
85A86THR0-0.051-0.01338.906-0.002-0.0020.0000.0000.0000.000
86A87TYR0-0.025-0.02540.1770.0000.0000.0000.0000.0000.000
87A88ARG10.9160.93341.222-0.023-0.0230.0000.0000.0000.000
88A89PHE00.0080.01136.7300.0010.0010.0000.0000.0000.000
89A90ILE0-0.019-0.01836.0470.0010.0010.0000.0000.0000.000
90A91ASP-1-0.906-0.93937.4450.0560.0560.0000.0000.0000.000
91A92GLU-1-0.909-0.93939.5970.0230.0230.0000.0000.0000.000
92A93LEU0-0.037-0.03734.7040.0010.0010.0000.0000.0000.000
93A94THR0-0.034-0.04133.7820.0040.0040.0000.0000.0000.000
94A95ASP-1-0.866-0.90734.8830.0620.0620.0000.0000.0000.000
95A96LYS10.8700.93136.352-0.018-0.0180.0000.0000.0000.000
96A97LEU0-0.059-0.04631.360-0.002-0.0020.0000.0000.0000.000
97A98LYS10.8400.91931.527-0.057-0.0570.0000.0000.0000.000
98A99LEU0-0.0070.01429.3540.0060.0060.0000.0000.0000.000
99A100ASN00.0680.03826.242-0.010-0.0100.0000.0000.0000.000
100A101LEU0-0.033-0.02129.0680.0090.0090.0000.0000.0000.000
101A102LYS10.8100.90227.562-0.151-0.1510.0000.0000.0000.000
102A103VAL00.0310.00731.028-0.005-0.0050.0000.0000.0000.000
103A104TYR0-0.062-0.06329.0730.0040.0040.0000.0000.0000.000
104A105ARG10.9880.99933.379-0.089-0.0890.0000.0000.0000.000
105A106ALA00.0580.02136.1110.0070.0070.0000.0000.0000.000
106A107THR0-0.040-0.01938.0890.0030.0030.0000.0000.0000.000
107A108GLU-1-0.755-0.84739.3590.0630.0630.0000.0000.0000.000
108A109SER00.0200.00842.645-0.002-0.0020.0000.0000.0000.000
109A110ALA00.0810.03844.645-0.001-0.0010.0000.0000.0000.000
110A111ALA00.0390.01746.287-0.002-0.0020.0000.0000.0000.000
111A112TRP0-0.023-0.00345.0070.0000.0000.0000.0000.0000.000
112A113GLN0-0.004-0.01941.743-0.004-0.0040.0000.0000.0000.000
113A114GLU-1-0.794-0.90346.8170.0290.0290.0000.0000.0000.000
114A115ALA0-0.031-0.01250.100-0.002-0.0020.0000.0000.0000.000
115A116ARG10.7890.89743.245-0.059-0.0590.0000.0000.0000.000
116A117TYR0-0.084-0.06143.7500.0010.0010.0000.0000.0000.000
117A118GLY00.0350.04549.164-0.003-0.0030.0000.0000.0000.000
118A119LYS10.9010.95148.927-0.020-0.0200.0000.0000.0000.000
119A120LEU0-0.017-0.00343.525-0.002-0.0020.0000.0000.0000.000
120A121TRP0-0.027-0.02545.4690.0000.0000.0000.0000.0000.000
121A122GLU-1-0.897-0.95746.7010.0150.0150.0000.0000.0000.000
122A123GLN0-0.070-0.03848.2460.0000.0000.0000.0000.0000.000
123A124GLY00.0320.02847.7360.0000.0000.0000.0000.0000.000
124A125VAL0-0.012-0.00742.6650.0020.0020.0000.0000.0000.000
125A126GLU-1-0.780-0.89742.1600.0140.0140.0000.0000.0000.000
126A127GLY00.0120.02242.6140.0050.0050.0000.0000.0000.000
127A128ILE00.009-0.01040.8470.0040.0040.0000.0000.0000.000
128A129GLU-1-0.953-0.97038.1940.0170.0170.0000.0000.0000.000
129A130LYS10.8610.93738.516-0.045-0.0450.0000.0000.0000.000
130A131TYR0-0.007-0.04340.0150.0070.0070.0000.0000.0000.000
131A132ASN00.021-0.00736.3090.0060.0060.0000.0000.0000.000
132A133ASP-1-0.877-0.94834.9880.0660.0660.0000.0000.0000.000
133A134ILE0-0.0110.00135.1260.0070.0070.0000.0000.0000.000
134A135ASN0-0.062-0.04537.3050.0070.0070.0000.0000.0000.000
135A136LYS10.8350.90833.185-0.034-0.0340.0000.0000.0000.000
136A137VAL0-0.044-0.01230.2920.0070.0070.0000.0000.0000.000
137A138GLU-1-0.749-0.83830.2930.1150.1150.0000.0000.0000.000
138A139PRO00.0370.02830.8120.0120.0120.0000.0000.0000.000
139A140MET0-0.0030.00426.6850.0140.0140.0000.0000.0000.000
140A141ASN0-0.094-0.05926.1760.0230.0230.0000.0000.0000.000
141A142ARG10.7850.86626.351-0.092-0.0920.0000.0000.0000.000
142A143ALA00.0250.01527.4820.0180.0180.0000.0000.0000.000
143A144LEU0-0.058-0.03821.5090.0160.0160.0000.0000.0000.000
144A145LYS10.9250.97222.467-0.177-0.1770.0000.0000.0000.000
145A146GLU-1-0.829-0.89024.0500.1890.1890.0000.0000.0000.000
146A147LEU0-0.043-0.03023.3250.0140.0140.0000.0000.0000.000
147A148ASN0-0.075-0.04020.0430.0450.0450.0000.0000.0000.000
148A149ALA00.0060.02918.5250.0610.0610.0000.0000.0000.000
149A150GLN0-0.059-0.04013.936-0.052-0.0520.0000.0000.0000.000
150A151THR00.0030.00913.773-0.083-0.0830.0000.0000.0000.000
151A152TRP00.000-0.03016.097-0.006-0.0060.0000.0000.0000.000
152A153PHE00.0360.02116.718-0.044-0.0440.0000.0000.0000.000
153A154ALA0-0.011-0.01820.9670.0130.0130.0000.0000.0000.000
154A155GLY00.008-0.00123.828-0.019-0.0190.0000.0000.0000.000
155A156LEU0-0.073-0.03125.2860.0030.0030.0000.0000.0000.000
156A157ARG10.8450.89925.7430.0470.0470.0000.0000.0000.000
157A158ARG10.7330.82721.6580.1950.1950.0000.0000.0000.000
158A159GLU-1-0.801-0.89228.673-0.067-0.0670.0000.0000.0000.000
159A160GLN0-0.043-0.00729.9380.0010.0010.0000.0000.0000.000
160A161SER0-0.028-0.01733.0090.0090.0090.0000.0000.0000.000
161A162GLY00.0360.01332.295-0.001-0.0010.0000.0000.0000.000
162A163SER0-0.032-0.02127.4880.0040.0040.0000.0000.0000.000
163A164ARG10.9850.99327.2600.1260.1260.0000.0000.0000.000
164A165ALA00.0560.01024.7650.0030.0030.0000.0000.0000.000
165A166ASN0-0.0160.00123.902-0.022-0.0220.0000.0000.0000.000
166A167LEU0-0.045-0.01222.9440.0070.0070.0000.0000.0000.000
167A168PRO00.0120.00718.032-0.001-0.0010.0000.0000.0000.000
168A169VAL00.0510.03516.8080.0380.0380.0000.0000.0000.000
169A170LEU0-0.0130.01611.5590.0450.0450.0000.0000.0000.000
170A171ALA0-0.010-0.01016.080-0.036-0.0360.0000.0000.0000.000
171A172ILE00.0430.02813.0420.0280.0280.0000.0000.0000.000
172A173GLN0-0.053-0.01217.402-0.017-0.0170.0000.0000.0000.000
173A174ARG10.9080.94320.294-0.098-0.0980.0000.0000.0000.000
174A175GLY00.0460.03217.8500.0160.0160.0000.0000.0000.000
175A176VAL0-0.0140.00316.7840.0440.0440.0000.0000.0000.000
176A177PHE00.0390.00710.026-0.087-0.0870.0000.0000.0000.000
177A178LYS10.8240.92915.5980.0130.0130.0000.0000.0000.000
178A179VAL00.0490.01015.528-0.048-0.0480.0000.0000.0000.000
179A180LEU0-0.039-0.02318.1990.0360.0360.0000.0000.0000.000
180A181PRO00.0510.03119.611-0.026-0.0260.0000.0000.0000.000
181A182ILE00.0160.01020.725-0.019-0.0190.0000.0000.0000.000
182A183ILE00.0020.00621.3470.0080.0080.0000.0000.0000.000
183A184ASP-1-0.819-0.88723.821-0.165-0.1650.0000.0000.0000.000
184A185TRP0-0.016-0.00124.9740.0160.0160.0000.0000.0000.000
185A186ASP-1-0.717-0.84028.261-0.072-0.0720.0000.0000.0000.000
186A187ASN0-0.042-0.03331.9130.0110.0110.0000.0000.0000.000
187A188ARG10.8930.94635.0240.0750.0750.0000.0000.0000.000
188A189THR0-0.025-0.03128.9850.0020.0020.0000.0000.0000.000
189A190ILE0-0.027-0.01529.7430.0060.0060.0000.0000.0000.000
190A191TYR00.0050.01432.8150.0070.0070.0000.0000.0000.000
191A192GLN00.0420.01034.2890.0040.0040.0000.0000.0000.000
192A193TYR0-0.0050.00527.6120.0010.0010.0000.0000.0000.000
193A194LEU0-0.011-0.01932.7240.0070.0070.0000.0000.0000.000
194A195GLN0-0.038-0.02335.4630.0010.0010.0000.0000.0000.000
195A196LYS10.9310.97529.8310.0640.0640.0000.0000.0000.000
196A197HIS00.0330.02929.2830.0070.0070.0000.0000.0000.000
197A198GLY00.0130.01634.5470.0060.0060.0000.0000.0000.000
198A199LEU0-0.0280.01032.5200.0040.0040.0000.0000.0000.000
199A200LYS10.8380.89237.253-0.001-0.0010.0000.0000.0000.000
200A201TYR00.0320.01337.3200.0000.0000.0000.0000.0000.000
201A202HIS00.0040.00539.0220.0000.0000.0000.0000.0000.000
202A203PRO00.0440.00740.545-0.003-0.0030.0000.0000.0000.000
203A204LEU00.0170.02143.934-0.001-0.0010.0000.0000.0000.000
204A205TRP0-0.063-0.03340.667-0.002-0.0020.0000.0000.0000.000
205A206ASP-1-0.890-0.95543.645-0.012-0.0120.0000.0000.0000.000
206A207GLU-1-0.907-0.95146.4890.0050.0050.0000.0000.0000.000
207A208GLY0-0.026-0.00747.057-0.001-0.0010.0000.0000.0000.000
208A209TYR0-0.101-0.06244.5760.0000.0000.0000.0000.0000.000
209A210LEU00.0040.00141.8030.0010.0010.0000.0000.0000.000
210A211SER0-0.009-0.02738.589-0.003-0.0030.0000.0000.0000.000
211A212VAL00.0430.04439.3210.0020.0020.0000.0000.0000.000
212A213GLY0-0.001-0.02539.049-0.001-0.0010.0000.0000.0000.000
213A214ASP-1-0.739-0.80039.9330.0330.0330.0000.0000.0000.000
214A215THR00.0190.00442.278-0.004-0.0040.0000.0000.0000.000
215A216HIS10.7840.88343.049-0.031-0.0310.0000.0000.0000.000
216A217THR00.0480.03646.9610.0010.0010.0000.0000.0000.000
217A218THR0-0.030-0.01342.0210.0000.0000.0000.0000.0000.000
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