Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: Q17YY

Calculation Name: 3MSQ-A-Xray317

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MSQ

Chain ID: A

ChEMBL ID:

UniProt ID: B2J5W7

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 218
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2623271.605539
FMO2-HF: Nuclear repulsion 2537448.862
FMO2-HF: Total energy -85822.743539
FMO2-MP2: Total energy -86074.253276


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:ACE )


Summations of interaction energy for fragment #1(A:5:ACE )
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.
-0.0731.611-0.006-0.885-0.793-0.002
Interaction energy analysis for fragmet #1(A:5:ACE )
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 : -0.011
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].
3A7TYR 00.0530.0413.828-0.2961.388-0.006-0.885-0.793-0.002
4A8ASN 0-0.007-0.0045.2980.5670.5670.0000.0000.0000.000
5A9ASN 00.0780.0147.156-0.190-0.1900.0000.0000.0000.000
6A10ASP -1-0.878-0.9279.3680.4190.4190.0000.0000.0000.000
7A11LYS 10.9000.94511.110-0.007-0.0070.0000.0000.0000.000
8A12GLY 00.0540.03912.563-0.024-0.0240.0000.0000.0000.000
9A13LEU 0-0.002-0.00214.016-0.010-0.0100.0000.0000.0000.000
10A14LEU 0-0.014-0.01814.661-0.014-0.0140.0000.0000.0000.000
11A15ALA 00.0380.02616.982-0.010-0.0100.0000.0000.0000.000
12A16TYR 00.0090.00718.579-0.007-0.0070.0000.0000.0000.000
13A17ILE 00.002-0.00419.029-0.004-0.0040.0000.0000.0000.000
14A18GLN 00.0070.01221.400-0.005-0.0050.0000.0000.0000.000
15A19PHE 00.0110.00722.888-0.004-0.0040.0000.0000.0000.000
16A20LEU 0-0.023-0.00323.451-0.002-0.0020.0000.0000.0000.000
17A21ALA 00.0130.00925.965-0.002-0.0020.0000.0000.0000.000
18A22SER 0-0.055-0.03327.037-0.004-0.0040.0000.0000.0000.000
19A23SER 0-0.061-0.06028.339-0.004-0.0040.0000.0000.0000.000
20A24ALA 00.0190.02630.8120.0000.0000.0000.0000.0000.000
21A25GLN 0-0.029-0.01031.486-0.001-0.0010.0000.0000.0000.000
22A26LYS 10.8420.91234.934-0.013-0.0130.0000.0000.0000.000
23A27ILE 00.0270.01937.1040.0000.0000.0000.0000.0000.000
24A28GLY 00.005-0.01235.5750.0000.0000.0000.0000.0000.000
25A29ASP -1-0.954-0.94936.650-0.013-0.0130.0000.0000.0000.000
26A30GLY 00.0800.04934.029-0.001-0.0010.0000.0000.0000.000
27A31ASN 0-0.006-0.02432.2530.0010.0010.0000.0000.0000.000
28A32THR 00.0120.01231.1600.0000.0000.0000.0000.0000.000
29A33ASP -1-0.878-0.94729.357-0.027-0.0270.0000.0000.0000.000
30A34ARG 10.9200.95827.333-0.001-0.0010.0000.0000.0000.000
31A35VAL 0-0.019-0.01325.6430.0010.0010.0000.0000.0000.000
32A36PHE 00.016-0.00124.543-0.005-0.0050.0000.0000.0000.000
33A37ASP -1-0.872-0.93223.323-0.049-0.0490.0000.0000.0000.000
34A38PHE 0-0.032-0.02319.072-0.003-0.0030.0000.0000.0000.000
35A39GLU -1-0.850-0.97519.701-0.065-0.0650.0000.0000.0000.000
36A40ASP -1-0.824-0.89519.275-0.099-0.0990.0000.0000.0000.000
37A41ALA 0-0.0410.00316.795-0.023-0.0230.0000.0000.0000.000
38A42LEU 0-0.005-0.00115.0420.0000.0000.0000.0000.0000.000
39A43ASP -1-0.773-0.84614.474-0.155-0.1550.0000.0000.0000.000
40A44GLN 0-0.070-0.04610.855-0.072-0.0720.0000.0000.0000.000
41A45THR 0-0.082-0.0709.634-0.065-0.0650.0000.0000.0000.000
42A46GLN 00.0350.0127.4790.0510.0510.0000.0000.0000.000
43A47MET 0-0.018-0.0139.474-0.012-0.0120.0000.0000.0000.000
44A48ALA 00.0180.02012.9540.0040.0040.0000.0000.0000.000
45A49GLN 00.002-0.00611.146-0.016-0.0160.0000.0000.0000.000
46A50LEU 00.0250.00511.4140.0200.0200.0000.0000.0000.000
47A51ALA 00.0100.01514.0860.0160.0160.0000.0000.0000.000
48A52VAL 0-0.016-0.00616.4710.0120.0120.0000.0000.0000.000
49A53ASP -1-0.902-0.95513.852-0.228-0.2280.0000.0000.0000.000
50A54GLU -1-0.921-0.97717.305-0.038-0.0380.0000.0000.0000.000
51A55LEU 0-0.033-0.01519.7000.0110.0110.0000.0000.0000.000
52A56LYS 10.9010.94520.0690.1680.1680.0000.0000.0000.000
53A57LYS 10.8680.96018.6110.0700.0700.0000.0000.0000.000
54A58ILE 0-0.035-0.00323.5560.0090.0090.0000.0000.0000.000
55A59PRO 00.009-0.00826.815-0.006-0.0060.0000.0000.0000.000
56A60GLU -1-0.872-0.95229.243-0.044-0.0440.0000.0000.0000.000
57A61VAL 0-0.0050.00725.057-0.001-0.0010.0000.0000.0000.000
58A62ASN 00.0270.00324.422-0.014-0.0140.0000.0000.0000.000
59A63ALA 0-0.0060.02326.461-0.007-0.0070.0000.0000.0000.000
60A64LEU 00.0210.01128.412-0.003-0.0030.0000.0000.0000.000
61A65PHE 0-0.038-0.03021.312-0.005-0.0050.0000.0000.0000.000
62A66SER 0-0.101-0.05525.885-0.009-0.0090.0000.0000.0000.000
63A67GLU -1-0.865-0.92327.838-0.063-0.0630.0000.0000.0000.000
64A68ARG 10.8630.95322.2860.1460.1460.0000.0000.0000.000
65A69TRP 00.0100.02528.4590.0030.0030.0000.0000.0000.000
66A70LEU 0-0.001-0.01628.714-0.003-0.0030.0000.0000.0000.000
67A71PRO 0-0.051-0.00732.4170.0020.0020.0000.0000.0000.000
68A72ALA 00.004-0.00435.787-0.001-0.0010.0000.0000.0000.000
69A73PRO 0-0.048-0.02338.9180.0010.0010.0000.0000.0000.000
70A74PHE 00.0180.00338.3680.0020.0020.0000.0000.0000.000
71A75ASN 00.003-0.00443.1980.0000.0000.0000.0000.0000.000
72A76LEU 00.0480.00243.0890.0010.0010.0000.0000.0000.000
73A77ASP -1-0.914-0.96246.333-0.019-0.0190.0000.0000.0000.000
74A78ASP -1-0.898-0.95248.739-0.022-0.0220.0000.0000.0000.000
75A79LEU 0-0.035-0.00343.2830.0010.0010.0000.0000.0000.000
76A80ALA 00.003-0.01247.9580.0010.0010.0000.0000.0000.000
77A81LYS 10.8810.94850.3970.0200.0200.0000.0000.0000.000
78A82LEU 0-0.0130.02947.7480.0000.0000.0000.0000.0000.000
79A83PRO 00.000-0.01651.6570.0010.0010.0000.0000.0000.000
80A84GLU -1-0.790-0.87251.762-0.012-0.0120.0000.0000.0000.000
81A85GLY 0-0.001-0.00550.3980.0000.0000.0000.0000.0000.000
82A86THR 0-0.053-0.02047.917-0.001-0.0010.0000.0000.0000.000
83A87LEU 00.0230.00440.2430.0010.0010.0000.0000.0000.000
84A88GLY 00.004-0.01344.3170.0000.0000.0000.0000.0000.000
85A89HIS 0-0.0180.00745.7210.0010.0010.0000.0000.0000.000
86A90VAL 0-0.010-0.01544.9560.0010.0010.0000.0000.0000.000
87A91TYR 0-0.034-0.01038.1700.0000.0000.0000.0000.0000.000
88A92ALA 00.0300.00543.7840.0000.0000.0000.0000.0000.000
89A93ARG 10.7940.88146.1620.0130.0130.0000.0000.0000.000
90A94GLU -1-0.863-0.92642.310-0.013-0.0130.0000.0000.0000.000
91A95MET 0-0.047-0.00239.3910.0010.0010.0000.0000.0000.000
92A96LYS 10.8570.94244.2630.0170.0170.0000.0000.0000.000
93A97ALA 0-0.0140.00747.2780.0010.0010.0000.0000.0000.000
94A98ARG 10.8750.96837.5320.0180.0180.0000.0000.0000.000
95A99GLY 0-0.031-0.04742.525-0.001-0.0010.0000.0000.0000.000
96A100PHE 0-0.080-0.05833.9700.0010.0010.0000.0000.0000.000
97A101ASP -1-0.858-0.93437.126-0.022-0.0220.0000.0000.0000.000
98A102PRO 00.010-0.02038.911-0.002-0.0020.0000.0000.0000.000
99A103TYR 0-0.0060.03433.278-0.002-0.0020.0000.0000.0000.000
100A104PHE 0-0.014-0.01336.254-0.003-0.0030.0000.0000.0000.000
101A105TYR 0-0.011-0.00730.2430.0000.0000.0000.0000.0000.000
102A106LYS 10.9440.98625.4530.0560.0560.0000.0000.0000.000
103A107LYS 10.9530.97728.5550.0570.0570.0000.0000.0000.000
104A108VAL 00.020-0.00123.119-0.001-0.0010.0000.0000.0000.000
105A109PRO 0-0.014-0.00524.6970.0030.0030.0000.0000.0000.000
106A110VAL 0-0.012-0.01224.284-0.011-0.0110.0000.0000.0000.000
107A111VAL 0-0.002-0.00619.9600.0040.0040.0000.0000.0000.000
108A112ASP -1-0.870-0.91516.908-0.267-0.2670.0000.0000.0000.000
109A113ASP -1-0.818-0.92818.435-0.163-0.1630.0000.0000.0000.000
110A114ILE 00.0360.02614.0100.0270.0270.0000.0000.0000.000
111A115SER 0-0.016-0.03318.5280.0300.0300.0000.0000.0000.000
112A116TYR 0-0.049-0.03221.3550.0170.0170.0000.0000.0000.000
113A117LEU 00.0230.01220.0410.0150.0150.0000.0000.0000.000
114A118LYS 10.7860.88020.1000.1350.1350.0000.0000.0000.000
115A119MET 00.0050.01723.5210.0150.0150.0000.0000.0000.000
116A120LEU 00.0310.04826.4240.0100.0100.0000.0000.0000.000
117A121TRP 00.0090.02325.5060.0100.0100.0000.0000.0000.000
118A122ARG 10.7910.89523.9160.0780.0780.0000.0000.0000.000
119A123SER 0-0.086-0.06929.2950.0040.0040.0000.0000.0000.000
120A124THR 0-0.020-0.03530.6150.0050.0050.0000.0000.0000.000
121A125HIS 10.9330.97729.7010.0350.0350.0000.0000.0000.000
122A126ASP -1-0.843-0.92931.897-0.019-0.0190.0000.0000.0000.000
123A127ILE 00.0130.01235.2160.0030.0030.0000.0000.0000.000
124A128TYR 00.0080.00229.3770.0020.0020.0000.0000.0000.000
125A129HIS 10.8710.92835.2530.0190.0190.0000.0000.0000.000
126A130VAL 00.0360.02937.2260.0020.0020.0000.0000.0000.000
127A131VAL 0-0.011-0.00137.9780.0020.0020.0000.0000.0000.000
128A132ALA 0-0.008-0.00935.8910.0020.0020.0000.0000.0000.000
129A133GLY 0-0.053-0.00537.9740.0020.0020.0000.0000.0000.000
130A134PHE 0-0.039-0.01236.1980.0020.0020.0000.0000.0000.000
131A135ASP -1-0.852-0.92839.251-0.004-0.0040.0000.0000.0000.000
132A136THR 00.007-0.00938.4890.0000.0000.0000.0000.0000.000
133A137ASN 0-0.041-0.00738.3400.0010.0010.0000.0000.0000.000
134A138VAL 00.0710.01434.687-0.001-0.0010.0000.0000.0000.000
135A139PHE 00.006-0.01035.0520.0010.0010.0000.0000.0000.000
136A140GLY 00.0410.04135.9660.0010.0010.0000.0000.0000.000
137A141GLU -1-0.888-0.95432.385-0.016-0.0160.0000.0000.0000.000
138A142ILE 0-0.055-0.03430.0300.0000.0000.0000.0000.0000.000
139A143GLY 00.0230.01231.5000.0010.0010.0000.0000.0000.000
140A144LEU 00.0030.00131.9400.0000.0000.0000.0000.0000.000
141A145GLN 00.0190.00727.126-0.003-0.0030.0000.0000.0000.000
142A146ALA 0-0.0050.00928.0670.0000.0000.0000.0000.0000.000
143A147PHE 00.0100.00429.6350.0010.0010.0000.0000.0000.000
144A148PHE 0-0.003-0.02224.912-0.002-0.0020.0000.0000.0000.000
145A149LEU 0-0.023-0.01722.645-0.003-0.0030.0000.0000.0000.000
146A150ALA 0-0.028-0.00425.6780.0010.0010.0000.0000.0000.000
147A151GLN 0-0.056-0.01028.295-0.004-0.0040.0000.0000.0000.000
148A152THR 0-0.013-0.02124.720-0.003-0.0030.0000.0000.0000.000
149A153PRO 00.0240.01820.826-0.003-0.0030.0000.0000.0000.000
150A154ILE 00.0460.03319.732-0.010-0.0100.0000.0000.0000.000
151A155PRO 00.021-0.00116.2990.0150.0150.0000.0000.0000.000
152A156ILE 00.0350.01718.7180.0150.0150.0000.0000.0000.000
153A157SER 00.0590.02821.8740.0060.0060.0000.0000.0000.000
154A158VAL 00.0020.00619.4970.0080.0080.0000.0000.0000.000
155A159MET 0-0.045-0.01718.4080.0120.0120.0000.0000.0000.000
156A160LEU 00.013-0.01222.1110.0050.0050.0000.0000.0000.000
157A161LEU 00.0190.01425.2940.0020.0020.0000.0000.0000.000
158A162SER 0-0.044-0.02123.2400.0050.0050.0000.0000.0000.000
159A163PHE 00.0140.00725.4250.0020.0020.0000.0000.0000.000
160A164GLY 00.0480.02826.8840.0000.0000.0000.0000.0000.000
161A165MET 0-0.025-0.02027.3000.0000.0000.0000.0000.0000.000
162A166VAL 00.0120.03526.6510.0000.0000.0000.0000.0000.000
163A167MET 00.0000.00728.855-0.001-0.0010.0000.0000.0000.000
164A168ILE 0-0.035-0.00632.073-0.002-0.0020.0000.0000.0000.000
165A169SER 0-0.065-0.05832.6320.0010.0010.0000.0000.0000.000
166A170LEU 0-0.024-0.01230.5970.0000.0000.0000.0000.0000.000
167A171TYR 0-0.004-0.01132.306-0.001-0.0010.0000.0000.0000.000
168A172GLN 0-0.0140.00437.065-0.003-0.0030.0000.0000.0000.000
169A173PRO 00.0620.03138.440-0.001-0.0010.0000.0000.0000.000
170A174THR 0-0.034-0.01839.4220.0000.0000.0000.0000.0000.000
171A175ASN 0-0.043-0.01840.029-0.001-0.0010.0000.0000.0000.000
172A176PHE 00.0580.02433.270-0.001-0.0010.0000.0000.0000.000
173A177LYS 10.9800.98537.764-0.016-0.0160.0000.0000.0000.000
174A178ALA 00.0140.00439.859-0.001-0.0010.0000.0000.0000.000
175A179LEU 00.0360.03332.820-0.001-0.0010.0000.0000.0000.000
176A180MET 00.002-0.00832.007-0.001-0.0010.0000.0000.0000.000
177A181THR 0-0.052-0.02236.1730.0000.0000.0000.0000.0000.000
178A182GLU -1-0.792-0.90936.5800.0020.0020.0000.0000.0000.000
179A183ILE 0-0.012-0.00731.103-0.002-0.0020.0000.0000.0000.000
180A184SER 0-0.045-0.02333.338-0.001-0.0010.0000.0000.0000.000
181A185ARG 10.7920.89735.194-0.001-0.0010.0000.0000.0000.000
182A186GLY 00.0560.01734.151-0.002-0.0020.0000.0000.0000.000
183A187TYR 00.0070.00827.061-0.002-0.0020.0000.0000.0000.000
184A188ARG 10.9420.97532.358-0.008-0.0080.0000.0000.0000.000
185A189VAL 0-0.008-0.01235.365-0.001-0.0010.0000.0000.0000.000
186A190GLY 00.0300.03832.561-0.002-0.0020.0000.0000.0000.000
187A191SER 0-0.047-0.04531.656-0.002-0.0020.0000.0000.0000.000
188A192HIS 0-0.050-0.02032.716-0.001-0.0010.0000.0000.0000.000
189A193THR 0-0.0040.00834.672-0.001-0.0010.0000.0000.0000.000
190A194PRO 0-0.046-0.01333.652-0.002-0.0020.0000.0000.0000.000
191A195GLY 00.0300.01333.239-0.003-0.0030.0000.0000.0000.000
192A196LYS 10.8980.94928.3960.0240.0240.0000.0000.0000.000
193A197LEU 00.0170.00731.093-0.002-0.0020.0000.0000.0000.000
194A198ILE 0-0.005-0.01225.978-0.001-0.0010.0000.0000.0000.000
195A199ALA 00.008-0.00229.497-0.005-0.0050.0000.0000.0000.000
196A200GLN 0-0.052-0.02131.0780.0000.0000.0000.0000.0000.000
197A201LYS 10.8570.93533.8230.0510.0510.0000.0000.0000.000
198A202TRP 00.026-0.01933.0580.0040.0040.0000.0000.0000.000
199A203ASP -1-0.810-0.89537.563-0.042-0.0420.0000.0000.0000.000
200A204GLN 0-0.003-0.00739.1490.0000.0000.0000.0000.0000.000
201A205LEU 0-0.021-0.02038.8200.0020.0020.0000.0000.0000.000
202A206TRP 00.0420.01839.8530.0030.0030.0000.0000.0000.000
203A207ASP -1-0.896-0.94144.252-0.023-0.0230.0000.0000.0000.000
204A208VAL 0-0.0110.00444.6710.0010.0010.0000.0000.0000.000
205A209GLN 0-0.003-0.00246.1410.0000.0000.0000.0000.0000.000
206A210VAL 00.0670.02543.107-0.001-0.0010.0000.0000.0000.000
207A211SER 0-0.028-0.02044.2640.0000.0000.0000.0000.0000.000
208A212GLU -1-0.839-0.91345.936-0.016-0.0160.0000.0000.0000.000
209A213ILE 0-0.007-0.00140.163-0.001-0.0010.0000.0000.0000.000
210A214ARG 10.8640.91541.0570.0110.0110.0000.0000.0000.000
211A215GLU -1-0.942-0.96341.695-0.010-0.0100.0000.0000.0000.000
212A216ARG 10.8770.94641.2740.0220.0220.0000.0000.0000.000
213A217LEU 0-0.068-0.02835.917-0.001-0.0010.0000.0000.0000.000
214A218GLY 00.0400.02437.8810.0000.0000.0000.0000.0000.000
215A219VAL 0-0.016-0.03538.3790.0010.0010.0000.0000.0000.000
216A220ASN 0-0.037-0.00639.6040.0020.0020.0000.0000.0000.000
217A221SER 00.0030.01239.2960.0020.0020.0000.0000.0000.000
218A222NME 0-0.044-0.00938.7210.0000.0000.0000.0000.0000.000