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: L7L89

Calculation Name: 2D8N-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2D8N

Chain ID: A

ChEMBL ID:

UniProt ID: P35243

Base Structure: X-ray

Registration Date: 2023-09-26

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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2282571.157026
FMO2-HF: Nuclear repulsion 2202358.265713
FMO2-HF: Total energy -80212.891313
FMO2-MP2: Total energy -80446.641292


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.
-19.603-20.86818.858-9.062-8.5330.027
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 : 0.091 / q_NPA : 0.066
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].
3A3ASN0-0.023-0.0263.276-4.661-1.3000.075-1.899-1.5380.002
4A4SER00.0080.0102.270-1.643-0.5231.401-0.872-1.650-0.005
5A5LYS10.8760.9122.203-12.875-18.62117.382-6.291-5.3450.030
6A6SER00.0350.0145.528-0.370-0.3700.0000.0000.0000.000
7A7GLY00.0630.0437.997-0.138-0.1380.0000.0000.0000.000
8A8ALA0-0.053-0.0218.6340.0130.0130.0000.0000.0000.000
9A9LEU00.0450.01810.394-0.045-0.0450.0000.0000.0000.000
10A10SER00.0240.01613.345-0.054-0.0540.0000.0000.0000.000
11A11LYS10.8350.87914.230-0.011-0.0110.0000.0000.0000.000
12A12GLU-1-0.893-0.93017.287-0.045-0.0450.0000.0000.0000.000
13A13ILE00.0390.01717.6410.0100.0100.0000.0000.0000.000
14A14LEU0-0.034-0.01716.4300.0110.0110.0000.0000.0000.000
15A15GLU-1-0.934-0.94819.850-0.008-0.0080.0000.0000.0000.000
16A16GLU-1-0.801-0.88922.7480.0310.0310.0000.0000.0000.000
17A17LEU00.0270.01120.6740.0050.0050.0000.0000.0000.000
18A18GLN0-0.040-0.01721.0180.0100.0100.0000.0000.0000.000
19A19LEU0-0.034-0.00625.290-0.003-0.0030.0000.0000.0000.000
20A20ASN0-0.119-0.06427.743-0.007-0.0070.0000.0000.0000.000
21A21THR0-0.046-0.02626.2480.0080.0080.0000.0000.0000.000
22A22LYS10.8370.90428.728-0.069-0.0690.0000.0000.0000.000
23A23PHE0-0.0040.02224.2170.0030.0030.0000.0000.0000.000
24A24SER00.003-0.03822.293-0.003-0.0030.0000.0000.0000.000
25A25GLU-1-0.770-0.89215.9840.1170.1170.0000.0000.0000.000
26A26GLU-1-0.935-0.95616.5110.2990.2990.0000.0000.0000.000
27A27GLU-1-0.808-0.87217.9370.1980.1980.0000.0000.0000.000
28A28LEU0-0.0020.00220.0620.0230.0230.0000.0000.0000.000
29A29CYS0-0.019-0.01514.5650.0200.0200.0000.0000.0000.000
30A30SER00.0030.00215.4230.0840.0840.0000.0000.0000.000
31A31TRP0-0.020-0.00417.1600.0190.0190.0000.0000.0000.000
32A32TYR0-0.009-0.00612.8760.0040.0040.0000.0000.0000.000
33A33GLN0-0.035-0.0329.6860.0530.0530.0000.0000.0000.000
34A34SER0-0.0070.00114.4080.0370.0370.0000.0000.0000.000
35A35PHE00.0560.02217.524-0.007-0.0070.0000.0000.0000.000
36A36LEU0-0.034-0.01612.212-0.003-0.0030.0000.0000.0000.000
37A37LYS10.7700.88211.896-0.703-0.7030.0000.0000.0000.000
38A38ASP-1-0.881-0.93116.6990.1760.1760.0000.0000.0000.000
39A39CYS0-0.102-0.03919.078-0.043-0.0430.0000.0000.0000.000
40A40PRO00.0110.00515.5410.0110.0110.0000.0000.0000.000
41A41THR0-0.045-0.02515.5130.0140.0140.0000.0000.0000.000
42A42GLY0-0.0100.00217.372-0.017-0.0170.0000.0000.0000.000
43A43ARG10.8150.88917.800-0.041-0.0410.0000.0000.0000.000
44A44ILE0-0.039-0.01321.6470.0110.0110.0000.0000.0000.000
45A45THR00.024-0.01624.345-0.014-0.0140.0000.0000.0000.000
46A46GLN00.0850.04727.7690.0110.0110.0000.0000.0000.000
47A47GLN0-0.030-0.00430.1270.0080.0080.0000.0000.0000.000
48A48GLN00.0920.06623.636-0.008-0.0080.0000.0000.0000.000
49A49PHE00.0430.03728.2870.0060.0060.0000.0000.0000.000
50A50GLN00.036-0.01029.9410.0020.0020.0000.0000.0000.000
51A51SER0-0.082-0.05531.093-0.005-0.0050.0000.0000.0000.000
52A52ILE0-0.038-0.01626.4020.0030.0030.0000.0000.0000.000
53A53TYR00.0470.02030.8980.0010.0010.0000.0000.0000.000
54A54ALA00.001-0.00834.283-0.001-0.0010.0000.0000.0000.000
55A55LYS10.8760.95028.740-0.122-0.1220.0000.0000.0000.000
56A56PHE0-0.033-0.02730.0830.0070.0070.0000.0000.0000.000
57A57PHE00.0130.01335.975-0.001-0.0010.0000.0000.0000.000
58A58PRO0-0.024-0.00539.402-0.002-0.0020.0000.0000.0000.000
59A59ASP-1-0.928-0.95941.4320.0510.0510.0000.0000.0000.000
60A60THR0-0.124-0.06743.105-0.002-0.0020.0000.0000.0000.000
61A61ASP-1-0.829-0.90841.4540.0420.0420.0000.0000.0000.000
62A62PRO00.0290.02137.954-0.003-0.0030.0000.0000.0000.000
63A63LYS10.8360.92035.091-0.056-0.0560.0000.0000.0000.000
64A64ALA00.0260.00938.206-0.001-0.0010.0000.0000.0000.000
65A65TYR00.011-0.02437.5120.0000.0000.0000.0000.0000.000
66A66ALA00.009-0.00234.527-0.001-0.0010.0000.0000.0000.000
67A67GLN0-0.030-0.01634.8990.0000.0000.0000.0000.0000.000
68A68HIS00.0200.00236.055-0.002-0.0020.0000.0000.0000.000
69A69VAL00.0110.01033.333-0.002-0.0020.0000.0000.0000.000
70A70PHE0-0.059-0.01028.4490.0000.0000.0000.0000.0000.000
71A71ARG10.8600.91232.576-0.018-0.0180.0000.0000.0000.000
72A72SER0-0.051-0.02434.986-0.003-0.0030.0000.0000.0000.000
73A73PHE00.007-0.01129.837-0.001-0.0010.0000.0000.0000.000
74A74ASP-1-0.806-0.89830.1990.0170.0170.0000.0000.0000.000
75A75SER0-0.018-0.01729.704-0.006-0.0060.0000.0000.0000.000
76A76ASN0-0.113-0.06427.702-0.002-0.0020.0000.0000.0000.000
77A77LEU0-0.026-0.00831.159-0.004-0.0040.0000.0000.0000.000
78A78ASP-1-0.831-0.88226.892-0.005-0.0050.0000.0000.0000.000
79A79GLY0-0.026-0.01130.1360.0010.0010.0000.0000.0000.000
80A80THR0-0.141-0.10325.4150.0100.0100.0000.0000.0000.000
81A81LEU00.0760.06625.986-0.006-0.0060.0000.0000.0000.000
82A82ASP-1-0.812-0.91620.9330.0900.0900.0000.0000.0000.000
83A83PHE0-0.0060.00219.2800.0090.0090.0000.0000.0000.000
84A84LYS10.8280.88721.253-0.027-0.0270.0000.0000.0000.000
85A85GLU-1-0.822-0.91122.9180.0300.0300.0000.0000.0000.000
86A86TYR0-0.014-0.00322.8670.0040.0040.0000.0000.0000.000
87A87VAL00.0060.00222.868-0.002-0.0020.0000.0000.0000.000
88A88ILE0-0.013-0.00325.872-0.004-0.0040.0000.0000.0000.000
89A89ALA00.0100.00828.696-0.004-0.0040.0000.0000.0000.000
90A90LEU0-0.039-0.02526.884-0.002-0.0020.0000.0000.0000.000
91A91HIS0-0.068-0.04927.3550.0000.0000.0000.0000.0000.000
92A92MET0-0.0400.00331.854-0.004-0.0040.0000.0000.0000.000
93A93THR00.0040.03234.053-0.003-0.0030.0000.0000.0000.000
94A94THR00.0200.00434.805-0.002-0.0020.0000.0000.0000.000
95A95ALA00.0210.00736.8160.0020.0020.0000.0000.0000.000
96A96GLY00.0480.05134.8630.0000.0000.0000.0000.0000.000
97A97LYS10.8330.89035.781-0.030-0.0300.0000.0000.0000.000
98A98THR00.0540.02837.6980.0000.0000.0000.0000.0000.000
99A99ASN0-0.006-0.01441.000-0.002-0.0020.0000.0000.0000.000
100A100GLN0-0.102-0.05937.108-0.002-0.0020.0000.0000.0000.000
101A101LYS10.8750.93132.095-0.017-0.0170.0000.0000.0000.000
102A102LEU0-0.004-0.00737.6800.0010.0010.0000.0000.0000.000
103A103GLU-1-0.712-0.83534.3450.0140.0140.0000.0000.0000.000
104A104TRP00.0320.02234.9780.0000.0000.0000.0000.0000.000
105A105ALA00.010-0.00637.1440.0000.0000.0000.0000.0000.000
106A106PHE00.007-0.00740.6370.0000.0000.0000.0000.0000.000
107A107SER00.016-0.00737.086-0.002-0.0020.0000.0000.0000.000
108A108LEU0-0.067-0.01338.2500.0010.0010.0000.0000.0000.000
109A109TYR0-0.035-0.04440.0320.0000.0000.0000.0000.0000.000
110A110ASP-1-0.817-0.87342.0220.0010.0010.0000.0000.0000.000
111A111VAL0-0.056-0.04541.6120.0020.0020.0000.0000.0000.000
112A112ASP-1-0.933-0.97441.5860.0040.0040.0000.0000.0000.000
113A113GLY0-0.043-0.00840.428-0.002-0.0020.0000.0000.0000.000
114A114ASN0-0.075-0.03541.231-0.004-0.0040.0000.0000.0000.000
115A115GLY00.005-0.00143.423-0.002-0.0020.0000.0000.0000.000
116A116THR0-0.164-0.10344.3460.0000.0000.0000.0000.0000.000
117A117ILE00.0240.03345.2280.0010.0010.0000.0000.0000.000
118A118SER0-0.004-0.05348.194-0.001-0.0010.0000.0000.0000.000
119A119LYS10.8120.88750.679-0.007-0.0070.0000.0000.0000.000
120A120ASN00.006-0.00851.5650.0020.0020.0000.0000.0000.000
121A121GLU-1-0.726-0.82346.2180.0070.0070.0000.0000.0000.000
122A122VAL00.007-0.00347.2080.0020.0020.0000.0000.0000.000
123A123LEU0-0.031-0.01148.7720.0020.0020.0000.0000.0000.000
124A124GLU-1-0.830-0.88844.7800.0220.0220.0000.0000.0000.000
125A125ILE00.0100.01142.0790.0030.0030.0000.0000.0000.000
126A126VAL0-0.025-0.00745.2560.0030.0030.0000.0000.0000.000
127A127MET0-0.019-0.02147.9220.0020.0020.0000.0000.0000.000
128A128ALA0-0.022-0.00742.6920.0020.0020.0000.0000.0000.000
129A129ILE0-0.0030.00343.0920.0030.0030.0000.0000.0000.000
130A130PHE0-0.017-0.02544.8310.0020.0020.0000.0000.0000.000
131A131LYS10.7960.89744.963-0.032-0.0320.0000.0000.0000.000
132A132MET00.0200.03040.3030.0030.0030.0000.0000.0000.000
133A133ILE0-0.0360.00743.7010.0030.0030.0000.0000.0000.000
134A134THR00.011-0.03346.546-0.002-0.0020.0000.0000.0000.000
135A135PRO00.021-0.01349.201-0.001-0.0010.0000.0000.0000.000
136A136GLU-1-0.828-0.90652.2330.0290.0290.0000.0000.0000.000
137A137ASP-1-0.749-0.82948.2750.0400.0400.0000.0000.0000.000
138A138VAL00.009-0.00151.368-0.001-0.0010.0000.0000.0000.000
139A139LYS10.7590.86153.688-0.030-0.0300.0000.0000.0000.000
140A140LEU0-0.0150.00052.655-0.001-0.0010.0000.0000.0000.000
141A141LEU0-0.0360.00351.190-0.001-0.0010.0000.0000.0000.000
142A142PRO0-0.002-0.00155.188-0.001-0.0010.0000.0000.0000.000
143A143ASP-1-0.788-0.89457.9360.0180.0180.0000.0000.0000.000
144A144ASP-1-0.877-0.93759.4980.0160.0160.0000.0000.0000.000
145A145GLU-1-0.755-0.85054.0770.0210.0210.0000.0000.0000.000
146A146ASN0-0.020-0.00154.5900.0000.0000.0000.0000.0000.000
147A147THR0-0.003-0.03154.9990.0000.0000.0000.0000.0000.000
148A148PRO00.0460.01351.3520.0000.0000.0000.0000.0000.000
149A149GLU-1-0.778-0.87653.0510.0170.0170.0000.0000.0000.000
150A150LYS10.7700.90356.060-0.019-0.0190.0000.0000.0000.000
151A151ARG10.8700.93049.468-0.024-0.0240.0000.0000.0000.000
152A152ALA00.0280.02352.689-0.001-0.0010.0000.0000.0000.000
153A153GLU-1-0.854-0.91653.8100.0090.0090.0000.0000.0000.000
154A154LYS10.7210.84255.952-0.018-0.0180.0000.0000.0000.000
155A155ILE00.006-0.01050.022-0.001-0.0010.0000.0000.0000.000
156A156TRP0-0.003-0.01551.3070.0000.0000.0000.0000.0000.000
157A157LYS10.9630.98455.759-0.011-0.0110.0000.0000.0000.000
158A158TYR0-0.099-0.05755.856-0.001-0.0010.0000.0000.0000.000
159A159PHE0-0.012-0.01149.2750.0000.0000.0000.0000.0000.000
160A160GLY0-0.048-0.00555.381-0.001-0.0010.0000.0000.0000.000
161A161LYS10.7640.87354.147-0.002-0.0020.0000.0000.0000.000
162A162ASN0-0.030-0.03658.1560.0010.0010.0000.0000.0000.000
163A163ASP-1-0.837-0.92158.2660.0060.0060.0000.0000.0000.000
164A164ASP-1-0.868-0.92356.6610.0010.0010.0000.0000.0000.000
165A165ASP-1-0.870-0.90056.5740.0000.0000.0000.0000.0000.000
166A166LYS10.8200.89451.4720.0000.0000.0000.0000.0000.000
167A167LEU0-0.044-0.00349.5140.0000.0000.0000.0000.0000.000
168A168THR00.039-0.02348.0270.0000.0000.0000.0000.0000.000
169A169GLU-1-0.855-0.93740.9410.0020.0020.0000.0000.0000.000
170A170LYS10.7880.87345.6210.0040.0040.0000.0000.0000.000
171A171GLU-1-0.734-0.82547.8430.0010.0010.0000.0000.0000.000
172A172PHE00.0280.02543.5040.0010.0010.0000.0000.0000.000
173A173ILE00.0060.01242.7460.0020.0020.0000.0000.0000.000
174A174GLU-1-0.823-0.90046.8150.0000.0000.0000.0000.0000.000
175A175GLY00.0160.00650.3730.0010.0010.0000.0000.0000.000
176A176THR0-0.064-0.06346.6750.0010.0010.0000.0000.0000.000
177A177LEU0-0.038-0.01345.5470.0020.0020.0000.0000.0000.000
178A178ALA0-0.029-0.00549.4350.0000.0000.0000.0000.0000.000
179A179ASN00.013-0.00152.5870.0010.0010.0000.0000.0000.000
180A180LYS10.9550.97648.644-0.020-0.0200.0000.0000.0000.000
181A181GLU-1-0.797-0.87351.4380.0190.0190.0000.0000.0000.000
182A182ILE00.0360.03250.2690.0010.0010.0000.0000.0000.000
183A183LEU00.0190.01244.6980.0010.0010.0000.0000.0000.000
184A184ARG10.6110.76547.462-0.019-0.0190.0000.0000.0000.000
185A185LEU0-0.029-0.01449.3840.0020.0020.0000.0000.0000.000
186A186ILE00.0520.03745.1910.0010.0010.0000.0000.0000.000
187A187GLN00.0110.00543.3520.0010.0010.0000.0000.0000.000
188A188PHE0-0.051-0.02944.9920.0010.0010.0000.0000.0000.000
189A189GLU-1-0.718-0.83041.0270.0430.0430.0000.0000.0000.000
190A190PRO0-0.082-0.02544.2000.0020.0020.0000.0000.0000.000
191A191GLN00.023-0.00542.788-0.002-0.0020.0000.0000.0000.000
192A192LYS10.8510.92045.302-0.039-0.0390.0000.0000.0000.000
193A193VAL0-0.065-0.02846.813-0.001-0.0010.0000.0000.0000.000
194A194LYS10.8540.91249.710-0.029-0.0290.0000.0000.0000.000
195A195GLU-1-0.782-0.86049.5340.0270.0270.0000.0000.0000.000
196A196LYS10.8350.88551.722-0.019-0.0190.0000.0000.0000.000
197A197MET0-0.0010.01354.894-0.001-0.0010.0000.0000.0000.000