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: 5JNYZ

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 OptH
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 -2664793.820007
FMO2-HF: Nuclear repulsion 2578862.605252
FMO2-HF: Total energy -85931.214755
FMO2-MP2: Total energy -86185.018915


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.
-13.322-6.5545.101-6.013-5.856-0.052
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 : -0.026 / q_NPA : -0.016
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].
3A3GLN0-0.022-0.0033.569-0.2871.8990.001-1.160-1.027-0.001
4A4ILE0-0.013-0.0136.2040.1710.1710.0000.0000.0000.000
5A5ILE0-0.0160.0049.303-0.112-0.1120.0000.0000.0000.000
6A6ASP-1-0.866-0.92912.0700.0270.0270.0000.0000.0000.000
7A7ILE0-0.047-0.04515.055-0.022-0.0220.0000.0000.0000.000
8A8GLU-1-0.916-0.94517.7880.0210.0210.0000.0000.0000.000
9A9ASN0-0.081-0.04517.629-0.012-0.0120.0000.0000.0000.000
10A10TRP00.0310.00316.3560.0280.0280.0000.0000.0000.000
11A11GLU-1-0.904-0.95818.006-0.121-0.1210.0000.0000.0000.000
12A12ARG10.7650.85818.8060.0110.0110.0000.0000.0000.000
13A13LYS10.9411.00120.7380.0170.0170.0000.0000.0000.000
14A14GLU-1-0.901-0.96821.4990.0410.0410.0000.0000.0000.000
15A15ASN0-0.026-0.01622.7080.0030.0030.0000.0000.0000.000
16A16PHE00.012-0.00318.4820.0150.0150.0000.0000.0000.000
17A17ASN00.0370.01922.2250.0350.0350.0000.0000.0000.000
18A18PHE0-0.0340.00724.5950.0060.0060.0000.0000.0000.000
19A19PHE00.001-0.01824.2570.0050.0050.0000.0000.0000.000
20A20ARG10.8680.94320.192-0.120-0.1200.0000.0000.0000.000
21A21HIS00.0470.01324.8830.0190.0190.0000.0000.0000.000
22A22PHE0-0.029-0.00827.219-0.003-0.0030.0000.0000.0000.000
23A23GLN0-0.027-0.01127.6070.0080.0080.0000.0000.0000.000
24A24ASN00.0630.02227.4530.0200.0200.0000.0000.0000.000
25A25PRO0-0.0090.02023.555-0.014-0.0140.0000.0000.0000.000
26A26GLN00.0030.01422.7240.0170.0170.0000.0000.0000.000
27A27LEU0-0.039-0.01024.672-0.014-0.0140.0000.0000.0000.000
28A28SER0-0.009-0.01625.3010.0100.0100.0000.0000.0000.000
29A29ILE0-0.015-0.00225.754-0.013-0.0130.0000.0000.0000.000
30A30THR0-0.004-0.01127.5910.0120.0120.0000.0000.0000.000
31A31SER0-0.0050.01328.562-0.009-0.0090.0000.0000.0000.000
32A32GLU-1-0.960-0.98630.1670.0390.0390.0000.0000.0000.000
33A33VAL00.0090.02126.611-0.005-0.0050.0000.0000.0000.000
34A34GLU-1-0.919-0.97330.0700.0060.0060.0000.0000.0000.000
35A35CYS0-0.029-0.02829.4720.0000.0000.0000.0000.0000.000
36A36GLY0-0.012-0.01130.8290.0020.0020.0000.0000.0000.000
37A37GLY00.0490.01231.535-0.001-0.0010.0000.0000.0000.000
38A38ALA0-0.022-0.02227.573-0.002-0.0020.0000.0000.0000.000
39A39ARG10.9790.99729.477-0.039-0.0390.0000.0000.0000.000
40A40GLN0-0.034-0.01832.3250.0050.0050.0000.0000.0000.000
41A41ARG10.8990.95427.0350.0070.0070.0000.0000.0000.000
42A42ALA00.0220.03429.524-0.002-0.0020.0000.0000.0000.000
43A43LYS10.9500.97430.945-0.016-0.0160.0000.0000.0000.000
44A44ALA0-0.057-0.02834.2590.0000.0000.0000.0000.0000.000
45A45ALA0-0.017-0.00230.542-0.002-0.0020.0000.0000.0000.000
46A46GLY00.0030.00932.0120.0010.0010.0000.0000.0000.000
47A47GLN0-0.0050.00426.7060.0060.0060.0000.0000.0000.000
48A48SER00.0380.00526.9480.0000.0000.0000.0000.0000.000
49A49PHE00.011-0.02827.2380.0020.0020.0000.0000.0000.000
50A50PHE00.0140.00523.153-0.007-0.0070.0000.0000.0000.000
51A51LEU00.0690.04021.5650.0080.0080.0000.0000.0000.000
52A52HIS0-0.045-0.02622.3200.0000.0000.0000.0000.0000.000
53A53TYR00.010-0.00523.205-0.002-0.0020.0000.0000.0000.000
54A54LEU0-0.0140.00919.2870.0010.0010.0000.0000.0000.000
55A55TYR00.0210.02116.2650.0070.0070.0000.0000.0000.000
56A56ALA0-0.034-0.01318.208-0.001-0.0010.0000.0000.0000.000
57A57VAL00.0170.00318.482-0.013-0.0130.0000.0000.0000.000
58A58LEU00.0040.01712.957-0.013-0.0130.0000.0000.0000.000
59A59ARG10.8590.93314.2360.1100.1100.0000.0000.0000.000
60A60ALA0-0.013-0.01315.093-0.039-0.0390.0000.0000.0000.000
61A61ALA0-0.013-0.00614.236-0.032-0.0320.0000.0000.0000.000
62A62ASN0-0.011-0.0129.4670.0410.0410.0000.0000.0000.000
63A63GLU-1-0.851-0.93111.549-0.246-0.2460.0000.0000.0000.000
64A64ILE0-0.054-0.00514.178-0.047-0.0470.0000.0000.0000.000
65A65PRO00.0420.02512.1290.0420.0420.0000.0000.0000.000
66A66GLU-1-0.837-0.94012.748-0.096-0.0960.0000.0000.0000.000
67A67PHE0-0.059-0.04214.6940.0460.0460.0000.0000.0000.000
68A68ARG10.8790.9537.9860.4740.4740.0000.0000.0000.000
69A69TYR0-0.026-0.00110.0560.0130.0130.0000.0000.0000.000
70A70ARG10.7620.88110.659-0.437-0.4370.0000.0000.0000.000
71A71ILE0-0.034-0.01112.811-0.055-0.0550.0000.0000.0000.000
72A72ASP-1-0.707-0.8439.2011.1631.1630.0000.0000.0000.000
73A73PRO00.0180.02011.650-0.109-0.1090.0000.0000.0000.000
74A74ASP-1-0.846-0.90113.3590.6030.6030.0000.0000.0000.000
75A75GLY0-0.045-0.02515.759-0.061-0.0610.0000.0000.0000.000
76A76ARG10.8170.89010.576-0.738-0.7380.0000.0000.0000.000
77A77VAL0-0.0060.00413.2790.0530.0530.0000.0000.0000.000
78A78VAL0-0.0170.0038.278-0.045-0.0450.0000.0000.0000.000
79A79LEU0-0.022-0.0078.1120.0520.0520.0000.0000.0000.000
80A80TYR00.016-0.0214.885-0.747-0.7470.0000.0000.0000.000
81A81ASP-1-0.897-0.9602.219-17.644-13.2895.101-4.819-4.637-0.051
82A82THR0-0.076-0.0524.139-0.508-0.281-0.001-0.034-0.1920.000
83A83ILE0-0.053-0.0026.0360.5170.5170.0000.0000.0000.000
84A84ASP-1-0.745-0.8389.1751.0681.0680.0000.0000.0000.000
85A85MET0-0.068-0.03811.244-0.069-0.0690.0000.0000.0000.000
86A86LEU00.0640.04615.014-0.008-0.0080.0000.0000.0000.000
87A87SER0-0.026-0.04417.287-0.051-0.0510.0000.0000.0000.000
88A88PRO00.0120.01320.8770.0020.0020.0000.0000.0000.000
89A89ILE0-0.0040.00923.132-0.024-0.0240.0000.0000.0000.000
90A90LYS10.8940.95425.956-0.096-0.0960.0000.0000.0000.000
91A91ILE00.0160.00628.550-0.005-0.0050.0000.0000.0000.000
92A92LYS10.9210.96231.207-0.123-0.1230.0000.0000.0000.000
93A93GLU-1-0.854-0.95034.8440.0870.0870.0000.0000.0000.000
94A94ASN0-0.064-0.02936.501-0.001-0.0010.0000.0000.0000.000
95A95GLY0-0.016-0.00934.1400.0010.0010.0000.0000.0000.000
96A96LYS10.8960.96530.596-0.145-0.1450.0000.0000.0000.000
97A97PHE00.0240.01825.805-0.010-0.0100.0000.0000.0000.000
98A98PHE00.010-0.00122.6690.0000.0000.0000.0000.0000.000
99A99THR0-0.037-0.02019.876-0.010-0.0100.0000.0000.0000.000
100A100THR0-0.0040.00219.4990.0260.0260.0000.0000.0000.000
101A101ARG10.8340.8878.435-1.489-1.4890.0000.0000.0000.000
102A102PHE0-0.050-0.02515.467-0.058-0.0580.0000.0000.0000.000
103A103PRO00.0280.02911.6530.0820.0820.0000.0000.0000.000
104A104TYR00.035-0.01610.064-0.204-0.2040.0000.0000.0000.000
105A105HIS00.0300.01611.298-0.021-0.0210.0000.0000.0000.000
106A106ASN0-0.021-0.03512.8310.0460.0460.0000.0000.0000.000
107A107ASP-1-0.846-0.88114.463-0.099-0.0990.0000.0000.0000.000
108A108PHE0-0.030-0.01817.7830.0290.0290.0000.0000.0000.000
109A109ASP-1-0.879-0.93620.033-0.018-0.0180.0000.0000.0000.000
110A110THR0-0.039-0.05116.0900.0080.0080.0000.0000.0000.000
111A111PHE00.0000.00215.5720.0150.0150.0000.0000.0000.000
112A112TYR0-0.020-0.00217.8070.0280.0280.0000.0000.0000.000
113A113GLN0-0.056-0.04620.8580.0000.0000.0000.0000.0000.000
114A114GLU-1-0.865-0.94815.7280.1960.1960.0000.0000.0000.000
115A115ALA0-0.0140.00319.2510.0220.0220.0000.0000.0000.000
116A116ARG10.8850.93420.334-0.044-0.0440.0000.0000.0000.000
117A117LEU0-0.0040.00521.070-0.004-0.0040.0000.0000.0000.000
118A118ILE00.0190.02016.9150.0010.0010.0000.0000.0000.000
119A119ILE0-0.062-0.04821.4860.0030.0030.0000.0000.0000.000
120A120ASP-1-0.931-0.96824.5270.0780.0780.0000.0000.0000.000
121A121ALA0-0.044-0.01423.415-0.006-0.0060.0000.0000.0000.000
122A122ILE0-0.065-0.01723.7520.0130.0130.0000.0000.0000.000
123A123PRO0-0.0240.00725.119-0.015-0.0150.0000.0000.0000.000
124A124GLU-1-0.925-0.97428.1720.0990.0990.0000.0000.0000.000
125A125ASP-1-0.961-1.00031.0200.1270.1270.0000.0000.0000.000
126A126GLY00.002-0.00327.8000.0070.0070.0000.0000.0000.000
127A127ASP-1-0.898-0.95225.5810.2300.2300.0000.0000.0000.000
128A128PRO0-0.048-0.03225.2660.0120.0120.0000.0000.0000.000
129A129TYR00.010-0.00722.971-0.005-0.0050.0000.0000.0000.000
130A130ALA00.0170.03321.8230.0270.0270.0000.0000.0000.000
131A131ALA00.0430.02318.1460.0260.0260.0000.0000.0000.000
132A132GLU-1-0.847-0.93617.0880.4120.4120.0000.0000.0000.000
133A133ASN0-0.026-0.02617.4770.0490.0490.0000.0000.0000.000
134A134GLU-1-0.959-0.96215.1930.5180.5180.0000.0000.0000.000
135A135GLU-1-0.772-0.89112.0461.0331.0330.0000.0000.0000.000
136A136VAL0-0.085-0.04713.0910.0920.0920.0000.0000.0000.000
137A137ALA0-0.102-0.05315.3090.0140.0140.0000.0000.0000.000
138A138ASP-1-0.924-0.96010.5621.0911.0910.0000.0000.0000.000
139A139GLY0-0.122-0.05110.8920.1700.1700.0000.0000.0000.000
140A140ASP-1-0.804-0.8837.7362.4052.4050.0000.0000.0000.000
141A141TYR0-0.023-0.0419.320-0.251-0.2510.0000.0000.0000.000
142A142GLY00.0390.0237.731-0.282-0.2820.0000.0000.0000.000
143A143LEU0-0.015-0.0208.7810.0970.0970.0000.0000.0000.000
144A144ILE0-0.042-0.02512.009-0.122-0.1220.0000.0000.0000.000
145A145LEU00.0440.03515.3920.0240.0240.0000.0000.0000.000
146A146LEU0-0.017-0.00618.593-0.042-0.0420.0000.0000.0000.000
147A147SER00.0150.00721.5180.0000.0000.0000.0000.0000.000
148A148ALA00.0170.00724.940-0.013-0.0130.0000.0000.0000.000
149A149THR00.008-0.01127.5490.0000.0000.0000.0000.0000.000
150A150PRO00.0010.00330.559-0.008-0.0080.0000.0000.0000.000
151A151ASP-1-0.901-0.95432.5970.0640.0640.0000.0000.0000.000
152A152LEU0-0.036-0.02134.447-0.005-0.0050.0000.0000.0000.000
153A153TYR0-0.0420.00434.2840.0030.0030.0000.0000.0000.000
154A154PHE00.0150.00929.226-0.002-0.0020.0000.0000.0000.000
155A155THR00.006-0.01834.4420.0000.0000.0000.0000.0000.000
156A156SER0-0.033-0.02732.7640.0000.0000.0000.0000.0000.000
157A157ILE00.0110.02129.0550.0000.0000.0000.0000.0000.000
158A158THR00.0020.00229.352-0.002-0.0020.0000.0000.0000.000
159A159GLY0-0.0200.00525.9700.0040.0040.0000.0000.0000.000
160A160THR00.001-0.00425.787-0.009-0.0090.0000.0000.0000.000
161A161GLN0-0.052-0.05324.793-0.006-0.0060.0000.0000.0000.000
162A162GLU-1-0.920-0.94121.0610.3290.3290.0000.0000.0000.000
163A163LYS10.9500.98118.489-0.398-0.3980.0000.0000.0000.000
164A164ARG10.9210.95424.569-0.141-0.1410.0000.0000.0000.000
165A165SER00.0120.01120.035-0.013-0.0130.0000.0000.0000.000
166A166GLY0-0.019-0.01721.096-0.003-0.0030.0000.0000.0000.000
167A167ASN0-0.016-0.02719.9540.0180.0180.0000.0000.0000.000
168A168ASN00.0280.02015.096-0.023-0.0230.0000.0000.0000.000
169A169TYR0-0.013-0.00813.9150.0540.0540.0000.0000.0000.000
170A170PRO0-0.063-0.03015.316-0.045-0.0450.0000.0000.0000.000
171A171LEU00.0190.03418.2560.0250.0250.0000.0000.0000.000
172A172LEU00.000-0.01819.121-0.031-0.0310.0000.0000.0000.000
173A173ASN00.0090.00922.8420.0120.0120.0000.0000.0000.000
174A174ALA00.0370.02325.739-0.011-0.0110.0000.0000.0000.000
175A175GLY00.0160.00427.4510.0040.0040.0000.0000.0000.000
176A176LYS10.8800.92731.188-0.054-0.0540.0000.0000.0000.000
177A177ALA00.005-0.00732.557-0.003-0.0030.0000.0000.0000.000
178A178ILE0-0.066-0.04834.277-0.001-0.0010.0000.0000.0000.000
179A179ILE0-0.015-0.00137.424-0.002-0.0020.0000.0000.0000.000
180A180ARG10.9690.97338.260-0.034-0.0340.0000.0000.0000.000
181A181GLU-1-0.918-0.95540.3790.0100.0100.0000.0000.0000.000
182A182GLY0-0.019-0.00742.440-0.002-0.0020.0000.0000.0000.000
183A183ARG10.9280.97137.2220.0000.0000.0000.0000.0000.000
184A184LEU0-0.057-0.01733.7370.0030.0030.0000.0000.0000.000
185A185VAL00.1030.04533.322-0.002-0.0020.0000.0000.0000.000
186A186MET0-0.024-0.01427.4910.0000.0000.0000.0000.0000.000
187A187PRO0-0.0110.02630.759-0.003-0.0030.0000.0000.0000.000
188A188ILE00.023-0.00824.1410.0080.0080.0000.0000.0000.000
189A189ALA00.0190.03127.033-0.011-0.0110.0000.0000.0000.000
190A190MET0-0.014-0.00820.2700.0090.0090.0000.0000.0000.000
191A191THR00.0280.02322.980-0.023-0.0230.0000.0000.0000.000
192A192ILE00.0000.01419.3370.0250.0250.0000.0000.0000.000
193A193HIS00.1060.05519.162-0.025-0.0250.0000.0000.0000.000
194A194HIS10.8850.93220.790-0.076-0.0760.0000.0000.0000.000
195A195GLY00.007-0.00121.193-0.020-0.0200.0000.0000.0000.000
196A196PHE0-0.012-0.00115.734-0.024-0.0240.0000.0000.0000.000
197A197ILE00.0130.02517.405-0.025-0.0250.0000.0000.0000.000
198A198ASP-1-0.821-0.89920.8940.0240.0240.0000.0000.0000.000
199A199GLY00.030-0.00524.010-0.001-0.0010.0000.0000.0000.000
200A200HIS00.0070.00223.0870.0000.0000.0000.0000.0000.000
201A201HIS00.1020.04419.9600.0110.0110.0000.0000.0000.000
202A202LEU00.0270.01521.6920.0020.0020.0000.0000.0000.000
203A203SER0-0.022-0.01223.6530.0030.0030.0000.0000.0000.000
204A204LEU0-0.013-0.00720.767-0.001-0.0010.0000.0000.0000.000
205A205PHE00.0390.01117.905-0.007-0.0070.0000.0000.0000.000
206A206TYR00.010-0.02421.4670.0020.0020.0000.0000.0000.000
207A207LYS10.9220.97824.7910.0290.0290.0000.0000.0000.000
208A208LYS10.8930.96118.2150.0990.0990.0000.0000.0000.000
209A209VAL00.0160.00421.2470.0000.0000.0000.0000.0000.000
210A210GLU-1-0.847-0.92623.1630.0050.0050.0000.0000.0000.000
211A211ASP-1-0.908-0.94124.530-0.044-0.0440.0000.0000.0000.000
212A212PHE0-0.060-0.03119.017-0.006-0.0060.0000.0000.0000.000
213A213LEU00.012-0.00424.5470.0020.0020.0000.0000.0000.000
214A214LYS10.8900.98127.3700.0410.0410.0000.0000.0000.000