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: MN8MZ

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 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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1821898.000368
FMO2-HF: Nuclear repulsion 1745393.299711
FMO2-HF: Total energy -76504.700657
FMO2-MP2: Total energy -76725.111448


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.
-9.015-3.5353.147-3.572-5.053-0.02
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 : 0.012 / q_NPA : -0.002
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].
3A7SER00.0420.0262.230-6.889-4.3272.600-2.240-2.921-0.013
4A8SER00.0390.0072.622-1.7510.3210.531-1.048-1.554-0.007
5A9PHE00.0100.0234.1230.4590.8220.000-0.127-0.2350.000
6A10GLN00.0140.0076.153-0.076-0.0760.0000.0000.0000.000
7A11VAL00.0150.0117.2470.0810.0810.0000.0000.0000.000
8A12ASP-1-0.809-0.8868.1550.4490.4490.0000.0000.0000.000
9A13CYS0-0.090-0.0379.9860.0140.0140.0000.0000.0000.000
10A14PHE0-0.0040.00112.089-0.004-0.0040.0000.0000.0000.000
11A15LEU00.021-0.00111.484-0.004-0.0040.0000.0000.0000.000
12A16TRP0-0.048-0.03714.006-0.006-0.0060.0000.0000.0000.000
13A17HIS0-0.017-0.01615.879-0.001-0.0010.0000.0000.0000.000
14A18VAL0-0.028-0.01017.331-0.006-0.0060.0000.0000.0000.000
15A19ARG10.7930.88614.834-0.105-0.1050.0000.0000.0000.000
16A20LYS10.8000.87519.903-0.077-0.0770.0000.0000.0000.000
17A21ARG10.9410.95822.132-0.048-0.0480.0000.0000.0000.000
18A22PHE00.0410.03124.586-0.001-0.0010.0000.0000.0000.000
19A23ALA0-0.019-0.01925.354-0.003-0.0030.0000.0000.0000.000
20A24ASP-1-0.864-0.89826.1690.0650.0650.0000.0000.0000.000
21A25GLN0-0.073-0.04427.8900.0030.0030.0000.0000.0000.000
22A26GLU-1-0.859-0.91629.3490.0250.0250.0000.0000.0000.000
23A27LEU0-0.034-0.01331.3830.0020.0020.0000.0000.0000.000
24A28GLY00.0320.02427.8200.0020.0020.0000.0000.0000.000
25A29ASP-1-0.765-0.92326.4110.0230.0230.0000.0000.0000.000
26A30ALA00.0040.02627.1690.0050.0050.0000.0000.0000.000
27A31PRO00.0370.00325.0960.0070.0070.0000.0000.0000.000
28A32PHE0-0.016-0.00322.5180.0080.0080.0000.0000.0000.000
29A33LEU00.0280.01522.4090.0100.0100.0000.0000.0000.000
30A34ASP-1-0.814-0.90523.2230.0750.0750.0000.0000.0000.000
31A35ARG10.8830.95419.148-0.027-0.0270.0000.0000.0000.000
32A36LEU0-0.0080.01218.2950.0210.0210.0000.0000.0000.000
33A37ARG10.8590.92018.863-0.058-0.0580.0000.0000.0000.000
34A38ALA00.0130.00917.9030.0180.0180.0000.0000.0000.000
35A39ASP-1-0.758-0.86113.9290.2250.2250.0000.0000.0000.000
36A40GLN0-0.0250.01014.2720.0490.0490.0000.0000.0000.000
37A41ALA00.000-0.00215.4950.0290.0290.0000.0000.0000.000
38A42SER00.002-0.00311.9580.0620.0620.0000.0000.0000.000
39A43LEU0-0.0070.00210.0920.1370.1370.0000.0000.0000.000
40A44ARG10.9110.94011.459-0.137-0.1370.0000.0000.0000.000
41A45GLY00.0150.01712.4870.0070.0070.0000.0000.0000.000
42A46ARG10.8100.8746.490-0.956-0.9560.0000.0000.0000.000
43A47GLY00.0540.0248.1060.1050.1050.0000.0000.0000.000
44A48ASN0-0.046-0.03910.080-0.051-0.0510.0000.0000.0000.000
45A49THR0-0.060-0.0347.865-0.053-0.0530.0000.0000.0000.000
46A50LEU0-0.054-0.0213.616-0.528-0.0450.016-0.157-0.3430.000
47A51GLY0-0.0160.0177.2170.0120.0120.0000.0000.0000.000
48A52LEU0-0.052-0.0267.412-0.005-0.0050.0000.0000.0000.000
49A53ASP-1-0.832-0.90710.3690.3080.3080.0000.0000.0000.000
50A54ILE00.028-0.00113.147-0.003-0.0030.0000.0000.0000.000
51A55GLU-1-0.803-0.84414.2800.1340.1340.0000.0000.0000.000
52A56THR0-0.043-0.03813.1060.0000.0000.0000.0000.0000.000
53A57ALA00.0230.01010.036-0.006-0.0060.0000.0000.0000.000
54A58THR00.023-0.02111.369-0.062-0.0620.0000.0000.0000.000
55A59ARG10.7530.84413.900-0.184-0.1840.0000.0000.0000.000
56A60ALA00.0210.01310.269-0.021-0.0210.0000.0000.0000.000
57A61GLY00.0360.00010.482-0.050-0.0500.0000.0000.0000.000
58A62LYS10.8220.90411.457-0.088-0.0880.0000.0000.0000.000
59A63GLN00.0190.01513.328-0.038-0.0380.0000.0000.0000.000
60A64ILE0-0.032-0.0156.614-0.033-0.0330.0000.0000.0000.000
61A65VAL00.0010.00410.914-0.070-0.0700.0000.0000.0000.000
62A66GLU-1-0.845-0.93013.0670.0290.0290.0000.0000.0000.000
63A67ARG10.7690.86514.5380.0200.0200.0000.0000.0000.000
64A68ILE0-0.0070.00311.521-0.008-0.0080.0000.0000.0000.000
65A69LEU0-0.058-0.02314.993-0.001-0.0010.0000.0000.0000.000
66A70GLU-1-0.802-0.85618.044-0.002-0.0020.0000.0000.0000.000
67A71GLY0-0.022-0.01919.583-0.013-0.0130.0000.0000.0000.000
68A72GLU-1-0.903-0.94423.146-0.027-0.0270.0000.0000.0000.000
69A73SER0-0.053-0.04020.344-0.002-0.0020.0000.0000.0000.000
70A74ASP-1-0.772-0.84622.529-0.018-0.0180.0000.0000.0000.000
71A75LYS10.8780.92918.5020.0680.0680.0000.0000.0000.000
72A76ALA0-0.030-0.03424.3890.0020.0020.0000.0000.0000.000
73A77LEU0-0.0080.01527.6570.0000.0000.0000.0000.0000.000
74A78LYS10.8120.88228.5790.0180.0180.0000.0000.0000.000
75A79MET00.0240.00133.6830.0020.0020.0000.0000.0000.000
76A80PRO00.0800.05531.8290.0000.0000.0000.0000.0000.000
77A81ALA0-0.043-0.01832.905-0.001-0.0010.0000.0000.0000.000
78A82SER0-0.018-0.01430.7140.0010.0010.0000.0000.0000.000
79A83ARG10.9370.97633.3630.0190.0190.0000.0000.0000.000
80A84TYR0-0.002-0.01333.344-0.003-0.0030.0000.0000.0000.000
81A85LEU0-0.0020.01135.4490.0030.0030.0000.0000.0000.000
82A86THR0-0.031-0.02736.599-0.002-0.0020.0000.0000.0000.000
83A87ASP-1-0.690-0.77939.299-0.018-0.0180.0000.0000.0000.000
84A88MET0-0.087-0.02038.2580.0010.0010.0000.0000.0000.000
85A89THR00.023-0.01938.754-0.001-0.0010.0000.0000.0000.000
86A90LEU00.036-0.00733.177-0.001-0.0010.0000.0000.0000.000
87A91GLU-1-0.785-0.82836.399-0.022-0.0220.0000.0000.0000.000
88A92GLU-1-0.723-0.81738.963-0.020-0.0200.0000.0000.0000.000
89A93MET0-0.042-0.01633.951-0.002-0.0020.0000.0000.0000.000
90A94SER0-0.072-0.05534.278-0.002-0.0020.0000.0000.0000.000
91A95ARG10.7740.86935.8580.0200.0200.0000.0000.0000.000
92A96ASP-1-0.878-0.93837.818-0.034-0.0340.0000.0000.0000.000
93A97TRP0-0.082-0.05839.3090.0020.0020.0000.0000.0000.000
94A98PHE0-0.030-0.01441.321-0.002-0.0020.0000.0000.0000.000
95A99MET0-0.041-0.00541.6520.0010.0010.0000.0000.0000.000
96A100LEU0-0.003-0.00146.172-0.001-0.0010.0000.0000.0000.000
97A101MET0-0.048-0.02949.3460.0000.0000.0000.0000.0000.000
98A102PRO0-0.016-0.01544.1210.0000.0000.0000.0000.0000.000
99A103LYS10.8930.96045.5510.0260.0260.0000.0000.0000.000
100A104GLN00.0290.00239.5160.0000.0000.0000.0000.0000.000
101A105LYS10.9100.96640.1310.0360.0360.0000.0000.0000.000
102A106VAL00.0540.02634.352-0.001-0.0010.0000.0000.0000.000
103A107ALA0-0.046-0.03637.2100.0020.0020.0000.0000.0000.000
104A108GLY00.0410.02535.4450.0000.0000.0000.0000.0000.000
105A109SER0-0.011-0.03031.177-0.002-0.0020.0000.0000.0000.000
106A110LEU0-0.0040.01832.558-0.002-0.0020.0000.0000.0000.000
107A111CYS0-0.062-0.02834.8780.0010.0010.0000.0000.0000.000
108A112ILE00.0140.00536.5870.0020.0020.0000.0000.0000.000
109A113LYS10.8470.90737.2320.0390.0390.0000.0000.0000.000
110A114MET00.0230.01542.0460.0010.0010.0000.0000.0000.000
111A115ASP-1-0.728-0.86145.540-0.026-0.0260.0000.0000.0000.000
112A116GLN00.0090.00248.1800.0010.0010.0000.0000.0000.000
113A117ALA00.0190.00651.3060.0010.0010.0000.0000.0000.000
114A118ILE0-0.040-0.00750.2040.0010.0010.0000.0000.0000.000
115A119MET00.0410.04353.3240.0000.0000.0000.0000.0000.000
116A120ASP-1-0.855-0.90556.645-0.015-0.0150.0000.0000.0000.000
117A121LYS10.7780.88054.4740.0170.0170.0000.0000.0000.000
118A122THR0-0.028-0.00755.7040.0000.0000.0000.0000.0000.000
119A123ILE00.020-0.00149.6830.0000.0000.0000.0000.0000.000
120A124ILE0-0.042-0.01648.5160.0010.0010.0000.0000.0000.000
121A125LEU0-0.021-0.00345.137-0.001-0.0010.0000.0000.0000.000
122A126LYS10.8470.89142.9530.0190.0190.0000.0000.0000.000
123A127ALA0-0.010-0.02639.847-0.002-0.0020.0000.0000.0000.000
124A128ASN00.0180.01135.8250.0030.0030.0000.0000.0000.000
125A129PHE00.000-0.00935.033-0.003-0.0030.0000.0000.0000.000
126A130SER00.0420.02432.4030.0030.0030.0000.0000.0000.000
127A131VAL0-0.003-0.00434.7990.0000.0000.0000.0000.0000.000
128A132ILE0-0.015-0.01034.5140.0010.0010.0000.0000.0000.000
129A133PHE0-0.017-0.01337.8170.0000.0000.0000.0000.0000.000
130A134ASP-1-0.919-0.96041.170-0.017-0.0170.0000.0000.0000.000
131A135ARG10.8150.87636.7890.0280.0280.0000.0000.0000.000
132A136LEU00.0000.00737.230-0.001-0.0010.0000.0000.0000.000
133A137GLU-1-0.863-0.90233.263-0.034-0.0340.0000.0000.0000.000
134A138THR0-0.021-0.01830.145-0.003-0.0030.0000.0000.0000.000
135A139LEU0-0.0050.00233.5530.0020.0020.0000.0000.0000.000
136A140ILE0-0.048-0.03030.123-0.004-0.0040.0000.0000.0000.000
137A141LEU0-0.017-0.01532.943-0.003-0.0030.0000.0000.0000.000
138A142LEU0-0.0090.00235.7710.0020.0020.0000.0000.0000.000
139A143ARG10.7720.87037.7140.0290.0290.0000.0000.0000.000
140A144ALA00.0120.00841.9490.0010.0010.0000.0000.0000.000
141A145PHE0-0.025-0.01842.238-0.001-0.0010.0000.0000.0000.000
142A146THR00.004-0.02947.7170.0000.0000.0000.0000.0000.000
143A147GLU-1-0.784-0.86051.070-0.015-0.0150.0000.0000.0000.000
144A148GLU-1-0.897-0.91752.892-0.016-0.0160.0000.0000.0000.000
145A149GLY0-0.005-0.00449.3130.0000.0000.0000.0000.0000.000
146A150ALA0-0.009-0.00647.481-0.001-0.0010.0000.0000.0000.000
147A151ILE0-0.013-0.00241.4160.0000.0000.0000.0000.0000.000
148A152VAL00.014-0.00145.411-0.001-0.0010.0000.0000.0000.000
149A153GLY00.029-0.00444.1320.0000.0000.0000.0000.0000.000
150A154GLU-1-0.791-0.86438.012-0.036-0.0360.0000.0000.0000.000
151A155ILE0-0.008-0.00237.848-0.001-0.0010.0000.0000.0000.000
152A156SER00.0300.01233.6140.0000.0000.0000.0000.0000.000
153A157PRO0-0.0050.01230.461-0.001-0.0010.0000.0000.0000.000
154A158LEU00.0200.00629.772-0.002-0.0020.0000.0000.0000.000
155A159PRO0-0.020-0.01724.428-0.001-0.0010.0000.0000.0000.000
156A160SER0-0.039-0.02325.578-0.004-0.0040.0000.0000.0000.000
157A161LEU00.009-0.00521.3840.0020.0020.0000.0000.0000.000
158A162PRO0-0.0110.00325.0940.0000.0000.0000.0000.0000.000
159A163GLY00.0340.03627.9130.0040.0040.0000.0000.0000.000
160A164HIS0-0.0180.01229.2090.0040.0040.0000.0000.0000.000
161A165THR00.023-0.01332.9160.0010.0010.0000.0000.0000.000
162A166GLY00.0620.01135.6810.0000.0000.0000.0000.0000.000
163A167GLU-1-0.794-0.86338.687-0.025-0.0250.0000.0000.0000.000
164A168ASP-1-0.844-0.89936.552-0.039-0.0390.0000.0000.0000.000
165A169VAL00.002-0.00437.1000.0000.0000.0000.0000.0000.000
166A170LYS10.8400.91539.7750.0260.0260.0000.0000.0000.000
167A171ASN0-0.041-0.03142.5690.0020.0020.0000.0000.0000.000
168A172ALA0-0.025-0.01840.3650.0010.0010.0000.0000.0000.000
169A173ILE00.0170.00042.1790.0010.0010.0000.0000.0000.000
170A174GLY00.0170.01644.6580.0010.0010.0000.0000.0000.000
171A175VAL0-0.051-0.03044.9050.0010.0010.0000.0000.0000.000
172A176LEU0-0.033-0.01143.5090.0000.0000.0000.0000.0000.000
173A177ILE0-0.0060.00246.6010.0010.0010.0000.0000.0000.000
174A178GLY00.0670.03949.7700.0010.0010.0000.0000.0000.000
175A179GLY0-0.063-0.03749.4350.0000.0000.0000.0000.0000.000
176A180LEU0-0.001-0.01747.9220.0000.0000.0000.0000.0000.000
177A181GLU-1-0.871-0.94951.614-0.018-0.0180.0000.0000.0000.000
178A182TRP0-0.080-0.02754.3660.0010.0010.0000.0000.0000.000
179A183ASN0-0.095-0.05554.3690.0000.0000.0000.0000.0000.000
180A184ASP-1-0.872-0.93856.692-0.016-0.0160.0000.0000.0000.000
181A185ASN0-0.098-0.06153.8790.0010.0010.0000.0000.0000.000
182A186THR0-0.006-0.00656.0880.0000.0000.0000.0000.0000.000
183A187VAL0-0.007-0.00150.4740.0000.0000.0000.0000.0000.000
184A188ARG10.7950.87052.0180.0160.0160.0000.0000.0000.000
185A189VAL00.002-0.00247.619-0.001-0.0010.0000.0000.0000.000
186A190THR0-0.012-0.02745.1080.0010.0010.0000.0000.0000.000
187A191GLU-1-0.850-0.93148.230-0.014-0.0140.0000.0000.0000.000
188A192THR0-0.052-0.05642.5240.0000.0000.0000.0000.0000.000
189A193ILE00.0130.00443.305-0.001-0.0010.0000.0000.0000.000
190A194GLN0-0.016-0.01345.186-0.001-0.0010.0000.0000.0000.000
191A195ARG10.8560.94047.0350.0130.0130.0000.0000.0000.000
192A196PHE0-0.048-0.02142.2910.0010.0010.0000.0000.0000.000
193A197ALA00.0070.01242.477-0.001-0.0010.0000.0000.0000.000