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: KG5Q3

Calculation Name: 3PKV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3PKV

Chain ID: A

ChEMBL ID:

UniProt ID: E3SET7

Base Structure: X-ray

Registration Date: 2023-09-23

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 221
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2695701.104864
FMO2-HF: Nuclear repulsion 2610519.478488
FMO2-HF: Total energy -85181.626376
FMO2-MP2: Total energy -85433.621437


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:THR)


Summations of interaction energy for fragment #1(A:2:THR)
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.
-33.224-35.44426.492-12.846-11.422-0.048
Interaction energy analysis for fragmet #1(A:2:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.060 / q_NPA : -0.045
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].
3A4ILE00.0420.0093.502-0.0713.2560.014-1.818-1.5220.007
4A5LYS10.7970.9016.177-0.307-0.3070.0000.0000.0000.000
5A6GLN0-0.041-0.0387.5830.0070.0070.0000.0000.0000.000
6A7LEU00.0100.01610.1990.2160.2160.0000.0000.0000.000
7A8THR0-0.014-0.00612.254-0.073-0.0730.0000.0000.0000.000
8A9LEU00.0030.00614.7080.0430.0430.0000.0000.0000.000
9A10TYR0-0.010-0.01717.820-0.013-0.0130.0000.0000.0000.000
10A11THR00.0580.00521.535-0.010-0.0100.0000.0000.0000.000
11A12ALA0-0.019-0.01224.3450.0070.0070.0000.0000.0000.000
12A13GLU-1-0.846-0.90927.036-0.057-0.0570.0000.0000.0000.000
13A14LEU00.0430.02024.697-0.012-0.0120.0000.0000.0000.000
14A15ASP-1-0.881-0.93027.628-0.077-0.0770.0000.0000.0000.000
15A16ARG10.8330.89029.9690.0770.0770.0000.0000.0000.000
16A17MET0-0.0480.04321.981-0.014-0.0140.0000.0000.0000.000
17A18LEU00.0460.03725.861-0.020-0.0200.0000.0000.0000.000
18A19ALA0-0.015-0.00426.996-0.015-0.0150.0000.0000.0000.000
19A20PHE00.005-0.00623.524-0.007-0.0070.0000.0000.0000.000
20A21TYR00.036-0.03420.637-0.025-0.0250.0000.0000.0000.000
21A22THR0-0.040-0.02224.682-0.021-0.0210.0000.0000.0000.000
22A23ASN0-0.096-0.04826.898-0.008-0.0080.0000.0000.0000.000
23A24MET0-0.0100.01622.954-0.017-0.0170.0000.0000.0000.000
24A25LEU0-0.032-0.02720.059-0.021-0.0210.0000.0000.0000.000
25A26GLY00.0230.02223.873-0.014-0.0140.0000.0000.0000.000
26A27ALA00.007-0.02224.782-0.009-0.0090.0000.0000.0000.000
27A28GLN0-0.049-0.01323.3900.0310.0310.0000.0000.0000.000
28A29HIS0-0.070-0.03120.253-0.025-0.0250.0000.0000.0000.000
29A30VAL0-0.011-0.00520.405-0.017-0.0170.0000.0000.0000.000
30A31HIS0-0.036-0.00621.6830.0040.0040.0000.0000.0000.000
31A32GLU-1-0.914-0.95723.180-0.094-0.0940.0000.0000.0000.000
32A33GLN0-0.077-0.04821.652-0.008-0.0080.0000.0000.0000.000
33A34ALA0-0.013-0.01426.4260.0000.0000.0000.0000.0000.000
34A35ASP-1-0.852-0.91925.548-0.013-0.0130.0000.0000.0000.000
35A36ALA0-0.003-0.00922.2950.0100.0100.0000.0000.0000.000
36A37PHE0-0.0110.00922.587-0.004-0.0040.0000.0000.0000.000
37A38THR0-0.011-0.00317.654-0.001-0.0010.0000.0000.0000.000
38A39ILE00.0090.00917.3690.0020.0020.0000.0000.0000.000
39A40GLN0-0.025-0.02112.8630.0740.0740.0000.0000.0000.000
40A41LEU0-0.006-0.01613.9380.0330.0330.0000.0000.0000.000
41A42GLY00.0810.04913.119-0.155-0.1550.0000.0000.0000.000
42A43VAL0-0.073-0.0447.8350.1530.1530.0000.0000.0000.000
43A44SER0-0.027-0.0158.630-0.139-0.1390.0000.0000.0000.000
44A45GLN0-0.0350.00610.6630.1600.1600.0000.0000.0000.000
45A46ILE00.0260.01012.6390.0460.0460.0000.0000.0000.000
46A47GLN00.0040.00015.3040.0230.0230.0000.0000.0000.000
47A48PHE00.0230.00917.8710.0340.0340.0000.0000.0000.000
48A49ARG10.8460.90520.287-0.013-0.0130.0000.0000.0000.000
49A50ALA00.0470.01822.928-0.004-0.0040.0000.0000.0000.000
50A51ALA0-0.038-0.01225.2230.0150.0150.0000.0000.0000.000
51A52ALA00.0040.00726.090-0.001-0.0010.0000.0000.0000.000
52A53ASP-1-0.850-0.92328.640-0.003-0.0030.0000.0000.0000.000
53A54GLY0-0.068-0.03531.8630.0060.0060.0000.0000.0000.000
54A55THR0-0.084-0.04327.2320.0030.0030.0000.0000.0000.000
55A56LYS10.8990.92627.4860.0320.0320.0000.0000.0000.000
56A57PRO0-0.021-0.00322.160-0.004-0.0040.0000.0000.0000.000
57A58PHE0-0.043-0.01121.665-0.008-0.0080.0000.0000.0000.000
58A59TYR0-0.030-0.04016.4020.0220.0220.0000.0000.0000.000
59A60HIS0-0.041-0.01614.6330.0240.0240.0000.0000.0000.000
60A61ILE00.005-0.01513.562-0.001-0.0010.0000.0000.0000.000
61A62ALA00.0310.03413.2150.0130.0130.0000.0000.0000.000
62A63ILE0-0.006-0.01212.562-0.134-0.1340.0000.0000.0000.000
63A64ASN00.0070.0038.9710.3600.3600.0000.0000.0000.000
64A65ILE0-0.003-0.00113.2590.0300.0300.0000.0000.0000.000
65A66ALA00.0370.01015.269-0.050-0.0500.0000.0000.0000.000
66A67ALA00.0210.02916.4300.0590.0590.0000.0000.0000.000
67A68ASN0-0.016-0.01917.7650.0090.0090.0000.0000.0000.000
68A69HIS00.006-0.01419.625-0.008-0.0080.0000.0000.0000.000
69A70PHE00.0010.01720.6350.0140.0140.0000.0000.0000.000
70A71GLN00.020-0.00922.1760.0170.0170.0000.0000.0000.000
71A72GLU-1-0.864-0.92724.448-0.308-0.3080.0000.0000.0000.000
72A73GLY00.0190.00922.2910.0090.0090.0000.0000.0000.000
73A74LYS10.8210.87923.2950.2220.2220.0000.0000.0000.000
74A75ALA0-0.020-0.01025.4800.0170.0170.0000.0000.0000.000
75A76TRP0-0.025-0.00521.8220.0070.0070.0000.0000.0000.000
76A77LEU00.0260.00922.2810.0100.0100.0000.0000.0000.000
77A78SER0-0.038-0.02825.6900.0200.0200.0000.0000.0000.000
78A79GLY0-0.040-0.00929.0040.0170.0170.0000.0000.0000.000
79A80PHE0-0.056-0.03726.4400.0100.0100.0000.0000.0000.000
80A81GLY0-0.019-0.01828.9960.0110.0110.0000.0000.0000.000
81A82GLU-1-0.968-0.97429.822-0.146-0.1460.0000.0000.0000.000
82A83LEU0-0.031-0.00826.302-0.007-0.0070.0000.0000.0000.000
83A84LEU0-0.032-0.00724.4460.0130.0130.0000.0000.0000.000
84A85THR0-0.022-0.02727.687-0.010-0.0100.0000.0000.0000.000
85A86GLU-1-0.777-0.85726.653-0.098-0.0980.0000.0000.0000.000
86A87ASN0-0.087-0.05328.9790.0030.0030.0000.0000.0000.000
87A88ASP-1-0.948-0.96932.032-0.093-0.0930.0000.0000.0000.000
88A89GLU-1-0.945-0.95329.259-0.144-0.1440.0000.0000.0000.000
89A90ASP-1-0.797-0.89928.697-0.187-0.1870.0000.0000.0000.000
90A91GLN00.0090.00625.047-0.028-0.0280.0000.0000.0000.000
91A92ALA00.0220.01722.5290.0220.0220.0000.0000.0000.000
92A93TYR0-0.041-0.03820.880-0.015-0.0150.0000.0000.0000.000
93A94PHE0-0.001-0.00118.1960.0440.0440.0000.0000.0000.000
94A95PRO00.028-0.00418.804-0.030-0.0300.0000.0000.0000.000
95A96PHE0-0.088-0.03013.7610.0000.0000.0000.0000.0000.000
96A97PHE00.0440.01812.013-0.027-0.0270.0000.0000.0000.000
97A98ASN0-0.0410.00715.112-0.049-0.0490.0000.0000.0000.000
98A99ALA00.0300.01615.556-0.049-0.0490.0000.0000.0000.000
99A100TYR0-0.050-0.00317.6960.0670.0670.0000.0000.0000.000
100A101SER0-0.009-0.02917.929-0.062-0.0620.0000.0000.0000.000
101A102CYS0-0.050-0.01120.3970.0430.0430.0000.0000.0000.000
102A103TYR00.008-0.01919.072-0.026-0.0260.0000.0000.0000.000
103A104VAL00.0270.02722.8230.0190.0190.0000.0000.0000.000
104A105GLU-1-0.914-0.95123.281-0.126-0.1260.0000.0000.0000.000
105A106ASP-1-0.712-0.82222.275-0.161-0.1610.0000.0000.0000.000
106A107PRO0-0.021-0.02725.1470.0170.0170.0000.0000.0000.000
107A108SER0-0.040-0.05223.9460.0200.0200.0000.0000.0000.000
108A109GLY0-0.002-0.00825.5220.0160.0160.0000.0000.0000.000
109A110ASN0-0.066-0.04619.9180.0210.0210.0000.0000.0000.000
110A111ILE00.0300.01919.804-0.004-0.0040.0000.0000.0000.000
111A112ILE0-0.023-0.00418.752-0.026-0.0260.0000.0000.0000.000
112A113GLU-1-0.734-0.84517.064-0.396-0.3960.0000.0000.0000.000
113A114LEU0-0.049-0.01217.136-0.067-0.0670.0000.0000.0000.000
114A115ILE00.0420.01113.5360.0380.0380.0000.0000.0000.000
115A116SER0-0.055-0.03515.377-0.084-0.0840.0000.0000.0000.000
116A117ARG10.8990.9399.7581.2691.2690.0000.0000.0000.000
117A118GLN0-0.066-0.04615.0060.0180.0180.0000.0000.0000.000
118A119GLN0-0.046-0.03715.5990.0450.0450.0000.0000.0000.000
119A120ALA0-0.0240.00310.1990.0170.0170.0000.0000.0000.000
120A121ALA00.0640.03210.616-0.252-0.2520.0000.0000.0000.000
121A122PRO0-0.0130.00511.9330.1260.1260.0000.0000.0000.000
122A123VAL00.0180.00614.7220.0280.0280.0000.0000.0000.000
123A124LEU0-0.059-0.03516.1960.0070.0070.0000.0000.0000.000
124A125ASP-1-0.944-0.95919.816-0.268-0.2680.0000.0000.0000.000
125A126LYS10.8600.91119.1500.5240.5240.0000.0000.0000.000
126A127PRO0-0.0020.00824.061-0.015-0.0150.0000.0000.0000.000
127A128PHE00.0130.01119.315-0.020-0.0200.0000.0000.0000.000
128A129SER0-0.034-0.04022.4410.0260.0260.0000.0000.0000.000
129A130ALA00.0850.04221.716-0.039-0.0390.0000.0000.0000.000
130A131ASP-1-0.881-0.92920.095-0.404-0.4040.0000.0000.0000.000
131A132GLN0-0.061-0.01118.440-0.081-0.0810.0000.0000.0000.000
132A133LEU0-0.0070.01116.431-0.051-0.0510.0000.0000.0000.000
133A134LEU0-0.032-0.02211.822-0.022-0.0220.0000.0000.0000.000
134A135SER00.0320.0228.4580.0030.0030.0000.0000.0000.000
135A136ILE0-0.012-0.0039.1110.2000.2000.0000.0000.0000.000
136A137GLY00.001-0.0048.280-0.398-0.3980.0000.0000.0000.000
137A138GLU-1-0.878-0.9619.352-0.513-0.5130.0000.0000.0000.000
138A139ILE00.0110.0158.8170.0430.0430.0000.0000.0000.000
139A140ASN0-0.0030.00611.2890.0190.0190.0000.0000.0000.000
140A141ILE0-0.006-0.00810.0880.0500.0500.0000.0000.0000.000
141A142THR00.0150.00713.678-0.006-0.0060.0000.0000.0000.000
142A143THR0-0.014-0.02416.6270.0190.0190.0000.0000.0000.000
143A144SER0-0.041-0.05418.647-0.017-0.0170.0000.0000.0000.000
144A145ASP-1-0.896-0.94519.7870.2330.2330.0000.0000.0000.000
145A146VAL00.0100.01116.8860.0380.0380.0000.0000.0000.000
146A147GLU-1-0.899-0.94216.6150.2790.2790.0000.0000.0000.000
147A148GLN0-0.033-0.02217.0970.0730.0730.0000.0000.0000.000
148A149ALA00.0140.00014.0180.0670.0670.0000.0000.0000.000
149A150ALA00.0350.01312.6120.1080.1080.0000.0000.0000.000
150A151THR0-0.041-0.03412.4120.0970.0970.0000.0000.0000.000
151A152ARG10.7860.86912.951-0.358-0.3580.0000.0000.0000.000
152A153LEU00.0220.0117.4720.1450.1450.0000.0000.0000.000
153A154LYS10.8790.9448.235-0.486-0.4860.0000.0000.0000.000
154A155GLN0-0.068-0.04210.3240.0890.0890.0000.0000.0000.000
155A156ALA0-0.032-0.0017.776-0.025-0.0250.0000.0000.0000.000
156A157GLU-1-0.991-0.9946.8191.9531.9530.0000.0000.0000.000
157A158LEU0-0.0030.0143.4970.1660.5070.007-0.047-0.3000.000
158A159PRO0-0.029-0.0154.869-0.323-0.3230.0000.0000.0000.000
159A160VAL00.0400.0127.807-0.224-0.2240.0000.0000.0000.000
160A161LYS10.9150.96310.967-0.170-0.1700.0000.0000.0000.000
161A162LEU00.0550.01014.445-0.038-0.0380.0000.0000.0000.000
162A163ASP-1-0.926-0.95916.6260.2290.2290.0000.0000.0000.000
163A164GLN0-0.059-0.04117.008-0.042-0.0420.0000.0000.0000.000
164A165ILE0-0.0400.00114.028-0.017-0.0170.0000.0000.0000.000
165A166GLU-1-0.875-0.94218.0830.0880.0880.0000.0000.0000.000
166A167PRO0-0.005-0.01220.231-0.007-0.0070.0000.0000.0000.000
167A168ALA0-0.025-0.01521.523-0.003-0.0030.0000.0000.0000.000
168A169GLY0-0.044-0.02721.466-0.021-0.0210.0000.0000.0000.000
169A170LEU0-0.036-0.01616.4040.0210.0210.0000.0000.0000.000
170A171ASN0-0.023-0.00714.8210.0020.0020.0000.0000.0000.000
171A172PHE00.0070.00712.3780.0060.0060.0000.0000.0000.000
172A173ILE0-0.032-0.0167.5370.0440.0440.0000.0000.0000.000
173A174GLY00.0220.0095.773-0.045-0.0450.0000.0000.0000.000
174A175ASP-1-0.900-0.9595.6020.2170.2170.0000.0000.0000.000
175A176GLN0-0.089-0.0444.658-1.524-1.463-0.001-0.003-0.0560.000
176A177ASP-1-0.868-0.9455.661-3.443-3.4430.0000.0000.0000.000
177A178LEU00.0070.0332.657-0.1120.4450.221-0.194-0.584-0.001
178A179PHE0-0.036-0.0216.1750.2200.2200.0000.0000.0000.000
179A180LEU00.0030.0016.1590.0750.0750.0000.0000.0000.000
180A181LEU0-0.015-0.0089.0950.0500.0500.0000.0000.0000.000
181A182LEU0-0.0100.00912.3860.0310.0310.0000.0000.0000.000
182A183GLY00.0420.00814.118-0.020-0.0200.0000.0000.0000.000
183A184PRO0-0.0060.02417.8910.0150.0150.0000.0000.0000.000
184A185PRO0-0.012-0.01321.116-0.021-0.0210.0000.0000.0000.000
185A186GLY0-0.028-0.02123.1240.0040.0040.0000.0000.0000.000
186A187ARG10.9250.96324.0330.0010.0010.0000.0000.0000.000
187A188ARG10.7800.86624.5430.0870.0870.0000.0000.0000.000
188A189TRP00.0310.01316.4680.0010.0010.0000.0000.0000.000
189A190LEU0-0.029-0.01922.1960.0030.0030.0000.0000.0000.000
190A191PHE0-0.008-0.01223.045-0.015-0.0150.0000.0000.0000.000
191A192SER00.0640.04724.3000.0060.0060.0000.0000.0000.000
192A193GLU-1-0.912-0.95726.235-0.061-0.0610.0000.0000.0000.000
193A194ARG10.8240.93125.0460.0700.0700.0000.0000.0000.000
194A195VAL00.000-0.00925.380-0.006-0.0060.0000.0000.0000.000
195A196ALA0-0.019-0.00321.2620.0020.0020.0000.0000.0000.000
196A197VAL0-0.003-0.01122.2850.0130.0130.0000.0000.0000.000
197A198ILE0-0.0160.00620.563-0.004-0.0040.0000.0000.0000.000
198A199TYR00.0150.01020.034-0.013-0.0130.0000.0000.0000.000
199A200PRO0-0.0060.01618.8020.0140.0140.0000.0000.0000.000
200A201LEU00.0020.01712.731-0.037-0.0370.0000.0000.0000.000
201A202GLN0-0.023-0.01813.6300.0080.0080.0000.0000.0000.000
202A203MET00.0250.0216.308-0.243-0.2430.0000.0000.0000.000
203A204GLU-1-0.808-0.8767.6410.2950.2950.0000.0000.0000.000
204A205LEU00.0320.0092.337-3.674-2.0371.980-1.087-2.5300.013
205A206ASP-1-0.790-0.8561.567-23.585-34.41223.880-8.441-4.612-0.070
206A207ASN0-0.007-0.0062.525-2.1510.4510.390-1.231-1.7600.003
207A208GLY0-0.024-0.0094.1160.0790.1610.001-0.025-0.0580.000
208A209VAL0-0.028-0.0025.233-0.500-0.5000.0000.0000.0000.000
209A210SER00.0010.0117.0180.0180.0180.0000.0000.0000.000
210A211LEU0-0.0120.0008.072-0.061-0.0610.0000.0000.0000.000
211A212ALA00.0140.00311.298-0.090-0.0900.0000.0000.0000.000
212A213ILE0-0.0120.01614.0900.0380.0380.0000.0000.0000.000
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