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: LNGL9

Calculation Name: 3F5T-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3F5T

Chain ID: A

ChEMBL ID:

UniProt ID: A5A5U1

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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1816437.126545
FMO2-HF: Nuclear repulsion 1739934.997445
FMO2-HF: Total energy -76502.1291
FMO2-MP2: Total energy -76722.793811


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:5:THR)


Summations of interaction energy for fragment #1(A:5: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.
-8.04-3.5931.645-2.491-3.6010.01
Interaction energy analysis for fragmet #1(A:5:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / q_NPA : 0.005
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].
3A7SER00.0500.0173.358-0.9821.6650.186-1.259-1.5740.006
4A8SER00.016-0.0072.245-3.728-2.6501.438-1.020-1.4950.004
5A9PHE0-0.0120.0124.099-1.200-0.8850.000-0.094-0.2210.000
6A10GLN00.027-0.0026.014-0.248-0.2480.0000.0000.0000.000
7A11VAL00.0180.0217.333-0.388-0.3880.0000.0000.0000.000
8A12ASP-1-0.852-0.9278.0660.7150.7150.0000.0000.0000.000
9A13CYS0-0.101-0.0529.745-0.224-0.2240.0000.0000.0000.000
10A14PHE0-0.0640.00711.822-0.139-0.1390.0000.0000.0000.000
11A15LEU00.0360.00212.008-0.124-0.1240.0000.0000.0000.000
12A16TRP0-0.054-0.03714.180-0.088-0.0880.0000.0000.0000.000
13A17HIS0-0.044-0.02916.014-0.050-0.0500.0000.0000.0000.000
14A18VAL0-0.0150.00717.247-0.044-0.0440.0000.0000.0000.000
15A19ARG10.8150.91315.107-0.403-0.4030.0000.0000.0000.000
16A20LYS10.8990.95320.251-0.288-0.2880.0000.0000.0000.000
17A21ARG11.0140.99422.323-0.262-0.2620.0000.0000.0000.000
18A22PHE00.0580.02924.817-0.013-0.0130.0000.0000.0000.000
19A23ALA0-0.007-0.01225.404-0.014-0.0140.0000.0000.0000.000
20A24ASP-1-1.002-0.98325.9500.1940.1940.0000.0000.0000.000
21A25GLN0-0.131-0.05327.6200.0010.0010.0000.0000.0000.000
22A26GLU-1-0.850-0.93529.9120.1460.1460.0000.0000.0000.000
23A27LEU0-0.053-0.00531.696-0.003-0.0030.0000.0000.0000.000
24A28GLY00.0370.01328.014-0.002-0.0020.0000.0000.0000.000
25A29ASP-1-0.780-0.91026.7630.0990.0990.0000.0000.0000.000
26A30ALA0-0.0040.01127.3480.0100.0100.0000.0000.0000.000
27A31PRO00.0790.02525.0470.0090.0090.0000.0000.0000.000
28A32PHE0-0.056-0.04422.0480.0170.0170.0000.0000.0000.000
29A33LEU00.0230.00222.2980.0270.0270.0000.0000.0000.000
30A34ASP-1-0.914-0.94623.1380.1200.1200.0000.0000.0000.000
31A35ARG10.8900.95818.852-0.138-0.1380.0000.0000.0000.000
32A36LEU00.0280.03718.1840.0350.0350.0000.0000.0000.000
33A37ARG10.9870.99618.993-0.116-0.1160.0000.0000.0000.000
34A38ALA0-0.014-0.00117.8830.0180.0180.0000.0000.0000.000
35A39ASP-1-0.791-0.90914.6710.3520.3520.0000.0000.0000.000
36A40GLN0-0.045-0.01414.4320.0780.0780.0000.0000.0000.000
37A41ALA0-0.012-0.01415.9560.0350.0350.0000.0000.0000.000
38A42SER0-0.034-0.02112.3510.0460.0460.0000.0000.0000.000
39A43LEU00.015-0.00610.4810.1010.1010.0000.0000.0000.000
40A44ARG10.9270.96811.756-0.230-0.2300.0000.0000.0000.000
41A45GLY00.0200.00912.8930.0230.0230.0000.0000.0000.000
42A46ARG10.9170.9555.648-1.130-1.1300.0000.0000.0000.000
43A47GLY00.0510.0298.0790.1670.1670.0000.0000.0000.000
44A48ASN0-0.046-0.03010.151-0.076-0.0760.0000.0000.0000.000
45A49THR0-0.012-0.0087.098-0.010-0.0100.0000.0000.0000.000
46A50LEU0-0.081-0.0353.275-0.4030.0040.021-0.118-0.3110.000
47A51GLY0-0.0040.0347.307-0.014-0.0140.0000.0000.0000.000
48A52LEU0-0.066-0.0407.9850.0890.0890.0000.0000.0000.000
49A53ASP-1-0.824-0.92010.8350.4800.4800.0000.0000.0000.000
50A54ILE00.0460.03912.9970.0240.0240.0000.0000.0000.000
51A55GLU-1-0.947-0.92214.2230.4420.4420.0000.0000.0000.000
52A56THR0-0.037-0.06913.2920.0620.0620.0000.0000.0000.000
53A57ALA00.0000.00110.2300.0390.0390.0000.0000.0000.000
54A58THR0-0.002-0.03611.7180.0840.0840.0000.0000.0000.000
55A59ARG10.8760.93314.162-0.551-0.5510.0000.0000.0000.000
56A60ALA00.0380.01611.309-0.042-0.0420.0000.0000.0000.000
57A61GLY00.0490.00311.6940.0870.0870.0000.0000.0000.000
58A62LYS10.9610.97612.604-0.548-0.5480.0000.0000.0000.000
59A63GLN00.0150.01514.446-0.048-0.0480.0000.0000.0000.000
60A64ILE0-0.055-0.0157.6770.0140.0140.0000.0000.0000.000
61A65VAL0-0.014-0.00612.108-0.002-0.0020.0000.0000.0000.000
62A66GLU-1-0.911-0.98914.1760.3700.3700.0000.0000.0000.000
63A67ARG10.8950.96115.683-0.447-0.4470.0000.0000.0000.000
64A68ILE00.0390.02012.608-0.040-0.0400.0000.0000.0000.000
65A69LEU0-0.108-0.03116.100-0.051-0.0510.0000.0000.0000.000
66A70GLU-1-0.964-1.02519.1280.2170.2170.0000.0000.0000.000
67A71GLY0-0.093-0.04419.8170.0140.0140.0000.0000.0000.000
68A72GLU-1-0.840-0.88723.1360.1600.1600.0000.0000.0000.000
69A73SER0-0.062-0.02920.5790.0090.0090.0000.0000.0000.000
70A74ASP-1-0.768-0.85723.0430.1700.1700.0000.0000.0000.000
71A75LYS10.8970.94218.841-0.275-0.2750.0000.0000.0000.000
72A76ALA0-0.018-0.01224.593-0.004-0.0040.0000.0000.0000.000
73A77LEU0-0.0040.01227.763-0.003-0.0030.0000.0000.0000.000
74A78LYS10.8190.88829.342-0.151-0.1510.0000.0000.0000.000
75A79MET00.044-0.00534.130-0.007-0.0070.0000.0000.0000.000
76A80PRO00.0620.05231.977-0.007-0.0070.0000.0000.0000.000
77A81ALA0-0.061-0.01832.8420.0070.0070.0000.0000.0000.000
78A82SER00.0150.01131.428-0.009-0.0090.0000.0000.0000.000
79A83ARG10.9740.98333.593-0.050-0.0500.0000.0000.0000.000
80A84TYR0-0.042-0.04233.563-0.002-0.0020.0000.0000.0000.000
81A85LEU0-0.0190.00035.6110.0010.0010.0000.0000.0000.000
82A86THR0-0.035-0.02536.6500.0000.0000.0000.0000.0000.000
83A87ASP-1-0.715-0.78739.4530.0220.0220.0000.0000.0000.000
84A88MET0-0.064-0.02038.649-0.003-0.0030.0000.0000.0000.000
85A89THR00.0180.00638.9180.0030.0030.0000.0000.0000.000
86A90LEU00.025-0.01832.881-0.002-0.0020.0000.0000.0000.000
87A91GLU-1-0.831-0.91036.264-0.004-0.0040.0000.0000.0000.000
88A92GLU-1-0.792-0.89738.8060.0080.0080.0000.0000.0000.000
89A93MET0-0.060-0.03334.049-0.002-0.0020.0000.0000.0000.000
90A94SER0-0.077-0.02934.224-0.004-0.0040.0000.0000.0000.000
91A95ARG10.8240.93035.8090.0000.0000.0000.0000.0000.000
92A96ASP-1-0.894-0.94237.664-0.031-0.0310.0000.0000.0000.000
93A97TRP0-0.086-0.05238.8340.0030.0030.0000.0000.0000.000
94A98PHE0-0.021-0.01141.311-0.003-0.0030.0000.0000.0000.000
95A99MET0-0.0350.00341.5400.0020.0020.0000.0000.0000.000
96A100LEU0-0.017-0.02345.617-0.003-0.0030.0000.0000.0000.000
97A101MET0-0.061-0.03648.734-0.002-0.0020.0000.0000.0000.000
98A102PRO00.0060.00143.4740.0020.0020.0000.0000.0000.000
99A103LYS10.9801.00644.5500.0160.0160.0000.0000.0000.000
100A104GLN0-0.002-0.01238.4030.0020.0020.0000.0000.0000.000
101A105LYS10.9310.97539.8090.0140.0140.0000.0000.0000.000
102A106VAL00.0520.02033.7720.0010.0010.0000.0000.0000.000
103A107ALA0-0.072-0.04636.8920.0000.0000.0000.0000.0000.000
104A108GLY00.0570.03835.0780.0040.0040.0000.0000.0000.000
105A109SER0-0.028-0.02230.431-0.005-0.0050.0000.0000.0000.000
106A110LEU00.0030.02132.1820.0020.0020.0000.0000.0000.000
107A111CYS0-0.038-0.01233.955-0.004-0.0040.0000.0000.0000.000
108A112ILE00.0050.00935.9090.0030.0030.0000.0000.0000.000
109A113LYS10.9170.94636.1930.0280.0280.0000.0000.0000.000
110A114MET00.0160.00641.4600.0030.0030.0000.0000.0000.000
111A115ASP-1-0.726-0.84345.099-0.023-0.0230.0000.0000.0000.000
112A116GLN0-0.026-0.03747.6120.0010.0010.0000.0000.0000.000
113A117ALA00.0080.00550.5900.0010.0010.0000.0000.0000.000
114A118ILE0-0.070-0.02350.1580.0010.0010.0000.0000.0000.000
115A119MET00.0220.00153.0480.0000.0000.0000.0000.0000.000
116A120ASP-1-0.881-0.91856.395-0.007-0.0070.0000.0000.0000.000
117A121LYS10.8280.92754.4990.0090.0090.0000.0000.0000.000
118A122THR00.001-0.00755.0720.0000.0000.0000.0000.0000.000
119A123ILE0-0.015-0.01449.3710.0000.0000.0000.0000.0000.000
120A124ILE0-0.041-0.01448.4980.0010.0010.0000.0000.0000.000
121A125LEU0-0.026-0.00544.964-0.001-0.0010.0000.0000.0000.000
122A126LYS10.9190.96043.247-0.008-0.0080.0000.0000.0000.000
123A127ALA0-0.007-0.01439.656-0.002-0.0020.0000.0000.0000.000
124A128ASN00.0410.04035.9500.0010.0010.0000.0000.0000.000
125A129PHE0-0.002-0.01135.027-0.002-0.0020.0000.0000.0000.000
126A130SER00.0330.02332.2640.0010.0010.0000.0000.0000.000
127A131VAL0-0.012-0.01034.955-0.004-0.0040.0000.0000.0000.000
128A132ILE00.0090.00634.5520.0060.0060.0000.0000.0000.000
129A133PHE0-0.033-0.02137.780-0.003-0.0030.0000.0000.0000.000
130A134ASP-1-0.929-0.97041.3240.0390.0390.0000.0000.0000.000
131A135ARG10.9720.99237.099-0.046-0.0460.0000.0000.0000.000
132A136LEU00.0040.00936.6680.0040.0040.0000.0000.0000.000
133A137GLU-1-1.001-1.00032.6810.0530.0530.0000.0000.0000.000
134A138THR0-0.015-0.01329.8110.0000.0000.0000.0000.0000.000
135A139LEU0-0.022-0.01033.1530.0020.0020.0000.0000.0000.000
136A140ILE0-0.036-0.02730.2020.0000.0000.0000.0000.0000.000
137A141LEU0-0.022-0.02332.947-0.005-0.0050.0000.0000.0000.000
138A142LEU00.0010.01435.7650.0040.0040.0000.0000.0000.000
139A143ARG10.7720.84937.2300.0050.0050.0000.0000.0000.000
140A144ALA00.0130.01341.8760.0020.0020.0000.0000.0000.000
141A145PHE0-0.020-0.01942.293-0.002-0.0020.0000.0000.0000.000
142A146THR00.0160.02047.6350.0010.0010.0000.0000.0000.000
143A147GLU-1-0.833-0.92950.9270.0050.0050.0000.0000.0000.000
144A148GLU-1-0.927-0.97053.216-0.003-0.0030.0000.0000.0000.000
145A149GLY0-0.023-0.00349.1420.0000.0000.0000.0000.0000.000
146A150ALA0-0.026-0.01947.365-0.001-0.0010.0000.0000.0000.000
147A151ILE0-0.005-0.00541.3730.0020.0020.0000.0000.0000.000
148A152VAL00.0350.00945.238-0.002-0.0020.0000.0000.0000.000
149A153GLY00.013-0.01043.949-0.001-0.0010.0000.0000.0000.000
150A154GLU-1-0.838-0.89137.148-0.014-0.0140.0000.0000.0000.000
151A155ILE0-0.013-0.00537.398-0.002-0.0020.0000.0000.0000.000
152A156SER00.0530.01833.1940.0030.0030.0000.0000.0000.000
153A157PRO0-0.0210.00330.375-0.004-0.0040.0000.0000.0000.000
154A158LEU0-0.002-0.00729.125-0.004-0.0040.0000.0000.0000.000
155A159PRO0-0.004-0.01324.0870.0070.0070.0000.0000.0000.000
156A160SER0-0.032-0.01425.223-0.010-0.0100.0000.0000.0000.000
157A161LEU00.012-0.01120.8130.0080.0080.0000.0000.0000.000
158A162PRO0-0.058-0.00724.5270.0090.0090.0000.0000.0000.000
159A163GLY00.0700.05428.1240.0090.0090.0000.0000.0000.000
160A164HIS0-0.004-0.00128.937-0.002-0.0020.0000.0000.0000.000
161A165THR00.0670.03232.7040.0060.0060.0000.0000.0000.000
162A166GLY00.0530.01235.465-0.003-0.0030.0000.0000.0000.000
163A167GLU-1-0.867-0.92138.4620.0150.0150.0000.0000.0000.000
164A168ASP-1-0.872-0.93335.7640.0070.0070.0000.0000.0000.000
165A169VAL0-0.001-0.01336.671-0.004-0.0040.0000.0000.0000.000
166A170LYS10.8830.93639.290-0.016-0.0160.0000.0000.0000.000
167A171ASN0-0.041-0.03341.8500.0000.0000.0000.0000.0000.000
168A172ALA0-0.002-0.00339.895-0.002-0.0020.0000.0000.0000.000
169A173ILE00.0380.01842.026-0.002-0.0020.0000.0000.0000.000
170A174GLY00.0230.02444.346-0.001-0.0010.0000.0000.0000.000
171A175VAL0-0.040-0.02444.486-0.002-0.0020.0000.0000.0000.000
172A176LEU0-0.047-0.01743.345-0.002-0.0020.0000.0000.0000.000
173A177ILE0-0.003-0.01046.197-0.001-0.0010.0000.0000.0000.000
174A178GLY00.0480.02849.377-0.001-0.0010.0000.0000.0000.000
175A179GLY0-0.080-0.05049.145-0.001-0.0010.0000.0000.0000.000
176A180LEU00.001-0.01847.862-0.001-0.0010.0000.0000.0000.000
177A181GLU-1-0.909-0.95751.2380.0000.0000.0000.0000.0000.000
178A182TRP0-0.056-0.01353.8120.0000.0000.0000.0000.0000.000
179A183ASN0-0.094-0.02853.3280.0000.0000.0000.0000.0000.000
180A184ASP-1-0.856-0.93156.463-0.007-0.0070.0000.0000.0000.000
181A185ASN0-0.069-0.03753.7700.0010.0010.0000.0000.0000.000
182A186THR0-0.003-0.00255.9760.0010.0010.0000.0000.0000.000
183A187VAL00.0030.00149.9790.0000.0000.0000.0000.0000.000
184A188ARG10.8890.95651.838-0.006-0.0060.0000.0000.0000.000
185A189VAL00.002-0.00547.487-0.001-0.0010.0000.0000.0000.000
186A190THR0-0.020-0.04445.2570.0000.0000.0000.0000.0000.000
187A191GLU-1-0.883-0.95448.2630.0210.0210.0000.0000.0000.000
188A192THR0-0.078-0.08142.3170.0010.0010.0000.0000.0000.000
189A193ILE0-0.005-0.00543.1340.0020.0020.0000.0000.0000.000
190A194GLN0-0.010-0.00345.0710.0000.0000.0000.0000.0000.000
191A195ARG10.9120.97446.672-0.034-0.0340.0000.0000.0000.000
192A196PHE0-0.044-0.02642.1890.0030.0030.0000.0000.0000.000
193A197ALA0-0.0220.00442.4410.0010.0010.0000.0000.0000.000