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: VQKV1

Calculation Name: 2I9D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2I9D

Chain ID: A

ChEMBL ID:

UniProt ID: Q8A336

Base Structure: X-ray

Registration Date: 2023-09-22

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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2668633.687991
FMO2-HF: Nuclear repulsion 2582700.610522
FMO2-HF: Total energy -85933.077469
FMO2-MP2: Total energy -86186.792661


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.
-10.494-8.0849.619-6.094-5.936-0.049
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 : -0.003 / q_NPA : 0.000
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].
3A3GLN0-0.062-0.0243.6760.5903.121-0.002-1.353-1.1770.003
4A4ILE00.009-0.0116.3410.1450.1450.0000.0000.0000.000
5A5ILE0-0.038-0.0029.315-0.039-0.0390.0000.0000.0000.000
6A6ASP-1-0.844-0.91412.421-0.138-0.1380.0000.0000.0000.000
7A7ILE0-0.064-0.04715.583-0.031-0.0310.0000.0000.0000.000
8A8GLU-1-0.851-0.90818.115-0.145-0.1450.0000.0000.0000.000
9A9ASN0-0.075-0.04318.1240.0000.0000.0000.0000.0000.000
10A10TRP00.0510.01316.1250.0270.0270.0000.0000.0000.000
11A11GLU-1-0.897-0.95218.249-0.475-0.4750.0000.0000.0000.000
12A12ARG10.7610.85918.2910.4100.4100.0000.0000.0000.000
13A13LYS10.8370.93420.6910.1960.1960.0000.0000.0000.000
14A14GLU-1-0.820-0.91821.539-0.144-0.1440.0000.0000.0000.000
15A15ASN0-0.030-0.01222.5520.0210.0210.0000.0000.0000.000
16A16PHE00.0270.00218.6150.0180.0180.0000.0000.0000.000
17A17ASN0-0.019-0.02322.0720.0310.0310.0000.0000.0000.000
18A18PHE0-0.044-0.00524.4780.0240.0240.0000.0000.0000.000
19A19PHE0-0.003-0.02223.9750.0170.0170.0000.0000.0000.000
20A20ARG10.8740.94919.9640.1530.1530.0000.0000.0000.000
21A21HIS00.0550.02624.5080.0200.0200.0000.0000.0000.000
22A22PHE0-0.024-0.00427.1300.0130.0130.0000.0000.0000.000
23A23GLN0-0.021-0.01027.8300.0080.0080.0000.0000.0000.000
24A24ASN00.1020.03626.4630.0000.0000.0000.0000.0000.000
25A25PRO0-0.0220.02123.077-0.004-0.0040.0000.0000.0000.000
26A26GLN0-0.021-0.00422.030-0.037-0.0370.0000.0000.0000.000
27A27LEU0-0.056-0.01624.1000.0150.0150.0000.0000.0000.000
28A28SER00.002-0.00924.426-0.010-0.0100.0000.0000.0000.000
29A29ILE0-0.013-0.00624.7450.0050.0050.0000.0000.0000.000
30A30THR0-0.039-0.03226.7070.0060.0060.0000.0000.0000.000
31A31SER00.0260.03027.9500.0070.0070.0000.0000.0000.000
32A32GLU-1-0.777-0.83329.231-0.091-0.0910.0000.0000.0000.000
33A33VAL00.0230.02726.085-0.007-0.0070.0000.0000.0000.000
34A34GLU-1-0.770-0.84429.372-0.099-0.0990.0000.0000.0000.000
35A35CYS0-0.045-0.01228.737-0.006-0.0060.0000.0000.0000.000
36A36GLY00.0290.01830.0470.0070.0070.0000.0000.0000.000
37A37GLY00.0330.01231.0440.0070.0070.0000.0000.0000.000
38A38ALA00.0200.01127.0200.0050.0050.0000.0000.0000.000
39A39ARG10.9440.97628.8190.0670.0670.0000.0000.0000.000
40A40GLN0-0.014-0.01231.7170.0110.0110.0000.0000.0000.000
41A41ARG10.8100.89725.2290.1380.1380.0000.0000.0000.000
42A42ALA00.0100.01628.7680.0060.0060.0000.0000.0000.000
43A43LYS10.9360.96730.1300.0500.0500.0000.0000.0000.000
44A44ALA0-0.046-0.02533.3650.0060.0060.0000.0000.0000.000
45A45ALA00.0020.00629.6720.0040.0040.0000.0000.0000.000
46A46GLY0-0.0040.01131.0590.0050.0050.0000.0000.0000.000
47A47GLN00.0000.01325.674-0.004-0.0040.0000.0000.0000.000
48A48SER00.035-0.00125.727-0.007-0.0070.0000.0000.0000.000
49A49PHE00.008-0.02625.955-0.008-0.0080.0000.0000.0000.000
50A50PHE00.0180.01222.056-0.014-0.0140.0000.0000.0000.000
51A51LEU00.0570.03320.592-0.016-0.0160.0000.0000.0000.000
52A52HIS00.0010.00521.245-0.031-0.0310.0000.0000.0000.000
53A53TYR00.0210.00122.070-0.017-0.0170.0000.0000.0000.000
54A54LEU0-0.0150.00318.191-0.027-0.0270.0000.0000.0000.000
55A55TYR00.0130.02015.639-0.042-0.0420.0000.0000.0000.000
56A56ALA0-0.032-0.01717.334-0.047-0.0470.0000.0000.0000.000
57A57VAL00.0140.00017.484-0.039-0.0390.0000.0000.0000.000
58A58LEU00.0000.02011.721-0.052-0.0520.0000.0000.0000.000
59A59ARG10.7890.89113.3900.2740.2740.0000.0000.0000.000
60A60ALA0-0.042-0.03014.637-0.080-0.0800.0000.0000.0000.000
61A61ALA0-0.009-0.00813.255-0.032-0.0320.0000.0000.0000.000
62A62ASN0-0.007-0.0128.783-0.424-0.4240.0000.0000.0000.000
63A63GLU-1-0.810-0.89411.350-0.607-0.6070.0000.0000.0000.000
64A64ILE0-0.030-0.00614.0210.0520.0520.0000.0000.0000.000
65A65PRO00.0400.02711.697-0.031-0.0310.0000.0000.0000.000
66A66GLU-1-0.803-0.92212.243-0.727-0.7270.0000.0000.0000.000
67A67PHE0-0.047-0.03314.0040.0620.0620.0000.0000.0000.000
68A68ARG10.8520.9307.4922.1502.1500.0000.0000.0000.000
69A69TYR00.0150.0259.484-0.281-0.2810.0000.0000.0000.000
70A70ARG10.7380.85210.2430.8320.8320.0000.0000.0000.000
71A71ILE0-0.036-0.01112.671-0.012-0.0120.0000.0000.0000.000
72A72ASP-1-0.707-0.8309.2780.2360.2360.0000.0000.0000.000
73A73PRO00.0350.02311.416-0.018-0.0180.0000.0000.0000.000
74A74ASP-1-0.843-0.88312.8050.3150.3150.0000.0000.0000.000
75A75GLY0-0.027-0.01615.604-0.027-0.0270.0000.0000.0000.000
76A76ARG10.7860.86410.735-0.447-0.4470.0000.0000.0000.000
77A77VAL0-0.021-0.00313.429-0.011-0.0110.0000.0000.0000.000
78A78VAL0-0.005-0.0058.1260.0280.0280.0000.0000.0000.000
79A79LEU0-0.014-0.0068.0920.1280.1280.0000.0000.0000.000
80A80TYR00.0340.0194.829-0.603-0.6030.0000.0000.0000.000
81A81ASP-1-0.841-0.9081.988-16.256-16.6509.622-4.701-4.526-0.052
82A82THR0-0.106-0.0623.9081.8782.151-0.001-0.040-0.2330.000
83A83ILE0-0.049-0.0065.309-0.326-0.3260.0000.0000.0000.000
84A84ASP-1-0.746-0.8508.0060.1650.1650.0000.0000.0000.000
85A85MET0-0.073-0.04110.154-0.050-0.0500.0000.0000.0000.000
86A86LEU00.0570.03313.9240.0640.0640.0000.0000.0000.000
87A87SER0-0.021-0.04916.295-0.038-0.0380.0000.0000.0000.000
88A88PRO00.0090.01519.9790.0230.0230.0000.0000.0000.000
89A89ILE0-0.0160.00121.823-0.013-0.0130.0000.0000.0000.000
90A90LYS10.8220.89124.8390.0100.0100.0000.0000.0000.000
91A91ILE00.0080.01127.6780.0000.0000.0000.0000.0000.000
92A92LYS10.8370.90530.326-0.055-0.0550.0000.0000.0000.000
93A93GLU-1-0.809-0.90533.9920.0010.0010.0000.0000.0000.000
94A94ASN0-0.053-0.02235.496-0.003-0.0030.0000.0000.0000.000
95A95GLY00.0050.00733.416-0.001-0.0010.0000.0000.0000.000
96A96LYS10.8380.93530.047-0.068-0.0680.0000.0000.0000.000
97A97PHE00.014-0.00325.318-0.004-0.0040.0000.0000.0000.000
98A98PHE0-0.002-0.00521.9890.0060.0060.0000.0000.0000.000
99A99THR0-0.041-0.02419.196-0.017-0.0170.0000.0000.0000.000
100A100THR0-0.0010.00718.6600.0380.0380.0000.0000.0000.000
101A101ARG10.7720.8487.770-0.528-0.5280.0000.0000.0000.000
102A102PHE0-0.041-0.01914.3570.0210.0210.0000.0000.0000.000
103A103PRO00.0410.03310.798-0.081-0.0810.0000.0000.0000.000
104A104TYR00.038-0.0039.3420.0000.0000.0000.0000.0000.000
105A105HIS00.0430.01810.418-0.001-0.0010.0000.0000.0000.000
106A106ASN00.014-0.00312.655-0.055-0.0550.0000.0000.0000.000
107A107ASP-1-0.804-0.87614.118-0.105-0.1050.0000.0000.0000.000
108A108PHE0-0.029-0.00517.0650.0100.0100.0000.0000.0000.000
109A109ASP-1-0.839-0.93219.435-0.057-0.0570.0000.0000.0000.000
110A110THR0-0.090-0.05916.0000.0290.0290.0000.0000.0000.000
111A111PHE00.0270.01814.6950.0180.0180.0000.0000.0000.000
112A112TYR0-0.025-0.00517.2820.0220.0220.0000.0000.0000.000
113A113GLN0-0.066-0.05320.3200.0250.0250.0000.0000.0000.000
114A114GLU-1-0.872-0.93715.3450.1900.1900.0000.0000.0000.000
115A115ALA00.002-0.00118.2070.0160.0160.0000.0000.0000.000
116A116ARG10.7870.87119.436-0.022-0.0220.0000.0000.0000.000
117A117LEU0-0.018-0.01321.1140.0030.0030.0000.0000.0000.000
118A118ILE00.0000.00516.3540.0060.0060.0000.0000.0000.000
119A119ILE0-0.044-0.03320.8450.0010.0010.0000.0000.0000.000
120A120ASP-1-0.863-0.91923.7600.0410.0410.0000.0000.0000.000
121A121ALA0-0.0220.00323.0000.0020.0020.0000.0000.0000.000
122A122ILE0-0.051-0.01123.0520.0130.0130.0000.0000.0000.000
123A123PRO0-0.0250.00124.883-0.007-0.0070.0000.0000.0000.000
124A124GLU-1-0.888-0.95727.8670.0530.0530.0000.0000.0000.000
125A125ASP-1-0.878-0.93730.2440.0580.0580.0000.0000.0000.000
126A126GLY00.0260.01227.1930.0110.0110.0000.0000.0000.000
127A127ASP-1-0.862-0.93924.6880.1100.1100.0000.0000.0000.000
128A128PRO0-0.028-0.01124.9950.0070.0070.0000.0000.0000.000
129A129TYR00.004-0.01322.549-0.012-0.0120.0000.0000.0000.000
130A130ALA00.0030.02321.3010.0110.0110.0000.0000.0000.000
131A131ALA00.0690.03617.0590.0230.0230.0000.0000.0000.000
132A132GLU-1-0.846-0.90916.6670.0400.0400.0000.0000.0000.000
133A133ASN0-0.045-0.03117.3050.0090.0090.0000.0000.0000.000
134A134GLU-1-0.967-0.97215.2660.3870.3870.0000.0000.0000.000
135A135GLU-1-0.775-0.89311.4690.5300.5300.0000.0000.0000.000
136A136VAL0-0.082-0.04812.7880.0560.0560.0000.0000.0000.000
137A137ALA0-0.075-0.02915.2020.0130.0130.0000.0000.0000.000
138A138ASP-1-0.955-0.9659.6541.2321.2320.0000.0000.0000.000
139A139GLY0-0.030-0.01611.0830.1720.1720.0000.0000.0000.000
140A140ASP-1-0.797-0.8896.9090.5470.5470.0000.0000.0000.000
141A141TYR0-0.006-0.0268.724-0.161-0.1610.0000.0000.0000.000
142A142GLY00.0480.0146.833-0.306-0.3060.0000.0000.0000.000
143A143LEU0-0.032-0.0167.7640.0220.0220.0000.0000.0000.000
144A144ILE0-0.032-0.01510.991-0.093-0.0930.0000.0000.0000.000
145A145LEU00.0260.03414.2780.0500.0500.0000.0000.0000.000
146A146LEU0-0.005-0.00817.557-0.018-0.0180.0000.0000.0000.000
147A147SER00.0340.02820.3740.0240.0240.0000.0000.0000.000
148A148ALA0-0.003-0.01323.825-0.016-0.0160.0000.0000.0000.000
149A149THR00.0140.00526.5570.0100.0100.0000.0000.0000.000
150A150PRO00.0240.00929.368-0.004-0.0040.0000.0000.0000.000
151A151ASP-1-0.850-0.92331.565-0.033-0.0330.0000.0000.0000.000
152A152LEU0-0.017-0.00633.1240.0020.0020.0000.0000.0000.000
153A153TYR0-0.037-0.04733.181-0.005-0.0050.0000.0000.0000.000
154A154PHE0-0.005-0.00427.9850.0060.0060.0000.0000.0000.000
155A155THR00.015-0.01233.337-0.004-0.0040.0000.0000.0000.000
156A156SER0-0.006-0.01431.517-0.009-0.0090.0000.0000.0000.000
157A157ILE00.0000.01028.0900.0100.0100.0000.0000.0000.000
158A158THR0-0.024-0.00228.130-0.011-0.0110.0000.0000.0000.000
159A159GLY00.0030.01125.0470.0090.0090.0000.0000.0000.000
160A160THR00.010-0.00124.745-0.001-0.0010.0000.0000.0000.000
161A161GLN0-0.072-0.06024.379-0.019-0.0190.0000.0000.0000.000
162A162GLU-1-0.795-0.87019.9880.0540.0540.0000.0000.0000.000
163A163LYS10.8460.90918.534-0.029-0.0290.0000.0000.0000.000
164A164ARG10.8750.94124.2920.0260.0260.0000.0000.0000.000
165A165SER00.0340.01220.240-0.001-0.0010.0000.0000.0000.000
166A166GLY0-0.027-0.02021.119-0.032-0.0320.0000.0000.0000.000
167A167ASN0-0.017-0.03019.3970.0420.0420.0000.0000.0000.000
168A168ASN00.0100.01514.632-0.032-0.0320.0000.0000.0000.000
169A169TYR0-0.003-0.03113.258-0.073-0.0730.0000.0000.0000.000
170A170PRO0-0.056-0.02514.2720.0490.0490.0000.0000.0000.000
171A171LEU00.0100.02717.0630.0110.0110.0000.0000.0000.000
172A172LEU0-0.016-0.02017.911-0.014-0.0140.0000.0000.0000.000
173A173ASN00.0080.00621.7690.0170.0170.0000.0000.0000.000
174A174ALA00.0160.01324.570-0.015-0.0150.0000.0000.0000.000
175A175GLY00.0130.00726.3700.0130.0130.0000.0000.0000.000
176A176LYS10.7780.87530.1480.0380.0380.0000.0000.0000.000
177A177ALA00.0150.00031.173-0.004-0.0040.0000.0000.0000.000
178A178ILE0-0.060-0.03232.9180.0090.0090.0000.0000.0000.000
179A179ILE0-0.018-0.00736.291-0.005-0.0050.0000.0000.0000.000
180A180ARG10.8350.88636.1580.0860.0860.0000.0000.0000.000
181A181GLU-1-0.918-0.95939.832-0.078-0.0780.0000.0000.0000.000
182A182GLY0-0.0080.00542.102-0.001-0.0010.0000.0000.0000.000
183A183ARG10.7830.85235.3980.0960.0960.0000.0000.0000.000
184A184LEU0-0.029-0.01132.9400.0030.0030.0000.0000.0000.000
185A185VAL00.0550.01532.406-0.008-0.0080.0000.0000.0000.000
186A186MET00.003-0.00726.4250.0080.0080.0000.0000.0000.000
187A187PRO0-0.0220.03029.705-0.011-0.0110.0000.0000.0000.000
188A188ILE00.035-0.00823.2780.0030.0030.0000.0000.0000.000
189A189ALA00.0110.02425.822-0.006-0.0060.0000.0000.0000.000
190A190MET00.0020.01019.837-0.004-0.0040.0000.0000.0000.000
191A191THR00.0280.02021.7910.0180.0180.0000.0000.0000.000
192A192ILE00.0030.01118.491-0.019-0.0190.0000.0000.0000.000
193A193HIS00.1170.05718.5440.0110.0110.0000.0000.0000.000
194A194HIS10.8740.94020.1180.1870.1870.0000.0000.0000.000
195A195GLY00.0310.00921.087-0.004-0.0040.0000.0000.0000.000
196A196PHE0-0.0120.00415.736-0.026-0.0260.0000.0000.0000.000
197A197ILE00.0280.02016.550-0.031-0.0310.0000.0000.0000.000
198A198ASP-1-0.813-0.88520.197-0.242-0.2420.0000.0000.0000.000
199A199GLY00.028-0.00723.468-0.011-0.0110.0000.0000.0000.000
200A200HIS00.0100.00122.2310.0190.0190.0000.0000.0000.000
201A201HIS00.0260.01519.2420.0370.0370.0000.0000.0000.000
202A202LEU00.0290.00921.221-0.012-0.0120.0000.0000.0000.000
203A203SER0-0.034-0.00622.9980.0100.0100.0000.0000.0000.000
204A204LEU00.0070.00121.4360.0060.0060.0000.0000.0000.000
205A205PHE00.0200.00617.0540.0050.0050.0000.0000.0000.000
206A206TYR0-0.011-0.03720.8390.0070.0070.0000.0000.0000.000
207A207LYS10.7990.89524.0280.2020.2020.0000.0000.0000.000
208A208LYS10.8820.94117.7760.4350.4350.0000.0000.0000.000
209A209VAL00.0180.00920.3160.0090.0090.0000.0000.0000.000
210A210GLU-1-0.819-0.91222.385-0.144-0.1440.0000.0000.0000.000
211A211ASP-1-0.863-0.90924.291-0.192-0.1920.0000.0000.0000.000
212A212PHE00.0000.01118.5240.0210.0210.0000.0000.0000.000
213A213LEU0-0.0110.00123.7830.0230.0230.0000.0000.0000.000
214A214LYS10.8250.90126.5120.2010.2010.0000.0000.0000.000