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: QVQNY

Calculation Name: 3SXY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3SXY

Chain ID: A

ChEMBL ID:

UniProt ID: Q9WYS0

Base Structure: X-ray

Registration Date: 2023-09-24

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 OptHSide
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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2408504.984252
FMO2-HF: Nuclear repulsion 2326899.974648
FMO2-HF: Total energy -81605.009604
FMO2-MP2: Total energy -81846.275017


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:10:ARG)


Summations of interaction energy for fragment #1(A:10:ARG)
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.
-64.219-55.7267.517-5.854-10.156-0.035
Interaction energy analysis for fragmet #1(A:10:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.965 / q_NPA : 0.968
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].
3A12LYS10.9901.0113.62724.34726.457-0.013-0.942-1.1550.003
4A13VAL00.0310.0092.378-0.6180.0631.987-1.019-1.6500.002
5A14TYR0-0.024-0.0303.8340.7081.1860.001-0.167-0.3110.000
6A15ASN00.011-0.0145.5621.3831.3830.0000.0000.0000.000
7A16LEU00.0140.0187.8121.3931.3930.0000.0000.0000.000
8A17LEU0-0.001-0.0156.6791.0691.0690.0000.0000.0000.000
9A18LYS10.7680.8609.54022.89922.8990.0000.0000.0000.000
10A19GLU-1-0.934-0.95311.527-15.438-15.4380.0000.0000.0000.000
11A20MET0-0.039-0.01612.5200.3600.3600.0000.0000.0000.000
12A21ILE0-0.013-0.00212.8630.7280.7280.0000.0000.0000.000
13A22LEU0-0.028-0.00615.4190.7510.7510.0000.0000.0000.000
14A23ASN0-0.005-0.00117.2130.6730.6730.0000.0000.0000.000
15A24HIS0-0.019-0.00318.7990.5850.5850.0000.0000.0000.000
16A25GLU-1-0.846-0.91416.834-14.041-14.0410.0000.0000.0000.000
17A26LEU0-0.126-0.06513.186-0.013-0.0130.0000.0000.0000.000
18A27LYS10.9260.96317.65311.74111.7410.0000.0000.0000.000
19A28LEU00.0510.00920.073-0.463-0.4630.0000.0000.0000.000
20A29GLY00.0590.03521.0190.4370.4370.0000.0000.0000.000
21A30GLU-1-0.930-0.94718.634-13.427-13.4270.0000.0000.0000.000
22A31LYS10.8630.93418.20213.81513.8150.0000.0000.0000.000
23A32LEU00.0350.02813.031-0.242-0.2420.0000.0000.0000.000
24A33ASN0-0.071-0.06515.388-0.958-0.9580.0000.0000.0000.000
25A34VAL00.000-0.0119.685-0.202-0.2020.0000.0000.0000.000
26A35ARG10.9700.97511.84817.16017.1600.0000.0000.0000.000
27A36GLU-1-0.834-0.90114.239-14.036-14.0360.0000.0000.0000.000
28A37LEU00.0350.01710.8070.1380.1380.0000.0000.0000.000
29A38SER0-0.088-0.05710.265-0.052-0.0520.0000.0000.0000.000
30A39GLU-1-0.909-0.96711.229-15.933-15.9330.0000.0000.0000.000
31A40LYS10.8020.90314.13215.26415.2640.0000.0000.0000.000
32A41LEU0-0.027-0.0289.2900.1690.1690.0000.0000.0000.000
33A42GLY00.0230.04011.296-0.152-0.1520.0000.0000.0000.000
34A43ILE0-0.064-0.0315.545-1.077-1.0770.0000.0000.0000.000
35A44SER00.0280.0387.219-0.412-0.4120.0000.0000.0000.000
36A45PHE00.0640.0007.412-1.824-1.8240.0000.0000.0000.000
37A46THR00.0200.0064.4721.5561.631-0.001-0.007-0.0670.000
38A47PRO00.0060.0062.414-6.871-5.5151.987-0.998-2.345-0.003
39A48VAL00.0660.0453.190-1.700-1.1450.009-0.016-0.548-0.005
40A49ARG10.9470.9776.01933.47633.4760.0000.0000.0000.000
41A50ASP-1-0.918-0.9812.392-71.807-68.7803.547-2.668-3.906-0.032
42A51ALA0-0.0020.0073.7690.8761.0700.001-0.036-0.1590.000
43A52LEU00.0370.0245.3342.8322.849-0.001-0.001-0.0150.000
44A53LEU0-0.023-0.0167.1212.2132.2130.0000.0000.0000.000
45A54GLN0-0.037-0.0115.1733.1783.1780.0000.0000.0000.000
46A55LEU00.0590.0268.2062.2552.2550.0000.0000.0000.000
47A56ALA0-0.046-0.02610.7651.8971.8970.0000.0000.0000.000
48A57THR0-0.121-0.05811.0401.1101.1100.0000.0000.0000.000
49A58GLU-1-0.770-0.84310.875-23.610-23.6100.0000.0000.0000.000
50A59GLY0-0.0120.01314.2041.1371.1370.0000.0000.0000.000
51A60LEU00.0350.01513.4230.8580.8580.0000.0000.0000.000
52A61VAL0-0.016-0.00212.3200.4510.4510.0000.0000.0000.000
53A62LYS10.9090.96115.26814.13414.1340.0000.0000.0000.000
54A63VAL00.0280.00613.767-0.324-0.3240.0000.0000.0000.000
55A64VAL0-0.0080.01017.0640.5690.5690.0000.0000.0000.000
56A65PRO00.034-0.01120.215-0.146-0.1460.0000.0000.0000.000
57A66ARG10.9240.95820.76112.16512.1650.0000.0000.0000.000
58A67VAL00.0170.02320.8590.4120.4120.0000.0000.0000.000
59A68GLY0-0.045-0.03317.426-0.212-0.2120.0000.0000.0000.000
60A69PHE00.0010.00611.160-0.008-0.0080.0000.0000.0000.000
61A70PHE00.0260.00716.1560.6080.6080.0000.0000.0000.000
62A71VAL00.0210.02515.875-0.981-0.9810.0000.0000.0000.000
63A72THR0-0.093-0.05517.5110.6240.6240.0000.0000.0000.000
64A73ASP-1-0.853-0.91519.781-11.790-11.7900.0000.0000.0000.000
65A74VAL0-0.024-0.01322.991-0.386-0.3860.0000.0000.0000.000
66A75ASP-1-0.810-0.91925.298-10.331-10.3310.0000.0000.0000.000
67A76GLU-1-0.751-0.85528.615-8.790-8.7900.0000.0000.0000.000
68A77LYS10.8300.90626.90911.16811.1680.0000.0000.0000.000
69A78PHE00.0170.01620.794-0.201-0.2010.0000.0000.0000.000
70A79ILE00.0390.02026.150-0.274-0.2740.0000.0000.0000.000
71A80ARG10.8360.88328.0708.7048.7040.0000.0000.0000.000
72A81GLU-1-0.850-0.89926.399-11.400-11.4000.0000.0000.0000.000
73A82THR0-0.037-0.01423.620-0.388-0.3880.0000.0000.0000.000
74A83ILE00.0230.01025.914-0.092-0.0920.0000.0000.0000.000
75A84GLU-1-0.942-0.96729.189-9.484-9.4840.0000.0000.0000.000
76A85THR0-0.010-0.01924.027-0.031-0.0310.0000.0000.0000.000
77A86ARG10.8290.89926.05810.77910.7790.0000.0000.0000.000
78A87ILE0-0.023-0.00727.8270.1840.1840.0000.0000.0000.000
79A88MET0-0.015-0.00127.0230.1850.1850.0000.0000.0000.000
80A89MET0-0.025-0.01022.4640.0170.0170.0000.0000.0000.000
81A90GLU-1-0.712-0.82327.948-10.582-10.5820.0000.0000.0000.000
82A91VAL0-0.007-0.00529.8640.2510.2510.0000.0000.0000.000
83A92PHE00.0150.03029.3250.1600.1600.0000.0000.0000.000
84A93CYS0-0.057-0.02028.4160.0110.0110.0000.0000.0000.000
85A94LEU00.025-0.00131.1210.1450.1450.0000.0000.0000.000
86A95GLU-1-0.914-0.95733.912-7.971-7.9710.0000.0000.0000.000
87A96ASN0-0.079-0.05633.0300.3170.3170.0000.0000.0000.000
88A97TYR0-0.0320.00129.776-0.081-0.0810.0000.0000.0000.000
89A98PHE00.0310.03233.956-0.081-0.0810.0000.0000.0000.000
90A99ASP-1-0.847-0.93236.852-7.843-7.8430.0000.0000.0000.000
91A100LYS10.8120.90328.79510.46410.4640.0000.0000.0000.000
92A101ILE0-0.025-0.00732.016-0.111-0.1110.0000.0000.0000.000
93A102ALA00.0170.00934.438-0.011-0.0110.0000.0000.0000.000
94A103GLY0-0.0110.00437.4730.1520.1520.0000.0000.0000.000
95A104SER0-0.094-0.04932.859-0.107-0.1070.0000.0000.0000.000
96A105GLU-1-0.922-0.97533.419-8.902-8.9020.0000.0000.0000.000
97A106GLU-1-0.764-0.86327.666-10.836-10.8360.0000.0000.0000.000
98A107LEU00.0070.01432.1480.0010.0010.0000.0000.0000.000
99A108LEU0-0.007-0.01334.4870.1710.1710.0000.0000.0000.000
100A109GLU-1-0.871-0.91531.139-9.563-9.5630.0000.0000.0000.000
101A110ILE0-0.028-0.01329.7860.0870.0870.0000.0000.0000.000
102A111LYS10.8190.90933.4827.5497.5490.0000.0000.0000.000
103A112GLY00.0200.01236.8110.1750.1750.0000.0000.0000.000
104A113GLH0-0.098-0.09529.5030.1030.1030.0000.0000.0000.000
105A114ILE00.0250.01234.1760.0720.0720.0000.0000.0000.000
106A115ASP-1-0.790-0.87436.491-7.207-7.2070.0000.0000.0000.000
107A116ASP-1-0.867-0.92636.391-7.679-7.6790.0000.0000.0000.000
108A117VAL0-0.011-0.01034.0210.1010.1010.0000.0000.0000.000
109A118GLU-1-0.903-0.95137.259-7.270-7.2700.0000.0000.0000.000
110A119LYS10.7680.90339.4017.6287.6280.0000.0000.0000.000
111A120SER0-0.077-0.05337.3500.0640.0640.0000.0000.0000.000
112A121ALA00.0130.01237.4480.0100.0100.0000.0000.0000.000
113A122LYS10.9220.98432.4628.5008.5000.0000.0000.0000.000
114A123ARG10.8570.91028.6139.6289.6280.0000.0000.0000.000
115A124GLU-1-0.852-0.95228.138-9.303-9.3030.0000.0000.0000.000
116A125ILE0-0.018-0.01428.359-0.259-0.2590.0000.0000.0000.000
117A126PHE00.0230.03130.471-0.055-0.0550.0000.0000.0000.000
118A127ASP-1-0.762-0.86325.956-10.519-10.5190.0000.0000.0000.000
119A128ASP-1-0.822-0.87025.853-11.091-11.0910.0000.0000.0000.000
120A129SER00.001-0.01326.990-0.035-0.0350.0000.0000.0000.000
121A130ASP-1-0.910-0.97328.166-10.183-10.1830.0000.0000.0000.000
122A131GLU-1-0.853-0.92620.860-13.712-13.7120.0000.0000.0000.000
123A132ARG10.7900.87825.55510.19910.1990.0000.0000.0000.000
124A133LEU0-0.0230.00126.9350.0250.0250.0000.0000.0000.000
125A134HIS10.7970.88226.94210.15710.1570.0000.0000.0000.000
126A135LYS10.8290.89519.04414.67314.6730.0000.0000.0000.000
127A136LEU0-0.0080.02125.189-0.244-0.2440.0000.0000.0000.000
128A137PHE00.011-0.01327.9450.0470.0470.0000.0000.0000.000
129A138ILE00.0240.00723.4670.0420.0420.0000.0000.0000.000
130A139ARG10.8650.92223.65211.87211.8720.0000.0000.0000.000
131A140ALA0-0.0060.00425.503-0.013-0.0130.0000.0000.0000.000
132A141SER00.004-0.02025.9290.1500.1500.0000.0000.0000.000
133A142GLY0-0.058-0.02324.9280.1650.1650.0000.0000.0000.000
134A143ASN00.0000.00822.795-0.840-0.8400.0000.0000.0000.000
135A144GLU-1-0.838-0.94318.053-15.370-15.3700.0000.0000.0000.000
136A145LEU0-0.0380.00518.071-0.768-0.7680.0000.0000.0000.000
137A146ILE00.015-0.00219.464-0.424-0.4240.0000.0000.0000.000
138A147ILE00.0530.02419.129-0.039-0.0390.0000.0000.0000.000
139A148SER0-0.058-0.02815.342-0.617-0.6170.0000.0000.0000.000
140A149LEU0-0.038-0.02916.738-0.534-0.5340.0000.0000.0000.000
141A150TYR0-0.006-0.03718.835-0.014-0.0140.0000.0000.0000.000
142A151GLU-1-0.854-0.90715.917-15.590-15.5900.0000.0000.0000.000
143A152LYS10.8690.91911.52923.49523.4950.0000.0000.0000.000
144A153ILE0-0.034-0.01616.7860.3850.3850.0000.0000.0000.000
145A154TRP00.026-0.00219.6820.7360.7360.0000.0000.0000.000
146A155ASP-1-0.756-0.86314.830-18.281-18.2810.0000.0000.0000.000
147A156ARG10.8160.90318.17413.73413.7340.0000.0000.0000.000
148A157ILE0-0.016-0.01020.7080.6050.6050.0000.0000.0000.000
149A158ASP-1-0.785-0.88219.925-12.617-12.6170.0000.0000.0000.000
150A159LEU0-0.059-0.01218.4560.2190.2190.0000.0000.0000.000
151A160VAL0-0.027-0.03021.2290.3570.3570.0000.0000.0000.000
152A161ARG10.8280.89722.55612.41412.4140.0000.0000.0000.000
153A162HIS0-0.020-0.01224.9370.2880.2880.0000.0000.0000.000
154A163LEU0-0.0010.01027.5790.3200.3200.0000.0000.0000.000
155A164ASN0-0.0120.00528.7560.6190.6190.0000.0000.0000.000
156A165GLU-1-0.858-0.93231.008-8.513-8.5130.0000.0000.0000.000
157A166ARG10.7870.85933.7158.3748.3740.0000.0000.0000.000
158A167TYR0-0.015-0.03832.8040.1430.1430.0000.0000.0000.000
159A168VAL00.0680.04334.6840.0420.0420.0000.0000.0000.000
160A169VAL0-0.037-0.02538.1070.1290.1290.0000.0000.0000.000
161A170SER0-0.005-0.00433.7830.0790.0790.0000.0000.0000.000
162A171ASN0-0.017-0.01235.859-0.287-0.2870.0000.0000.0000.000
163A172ARG10.9730.99236.7877.1107.1100.0000.0000.0000.000
164A173GLU-1-0.768-0.82837.426-8.002-8.0020.0000.0000.0000.000
165A174HIS00.000-0.00131.927-0.090-0.0900.0000.0000.0000.000
166A175LYS10.8780.93836.7577.0827.0820.0000.0000.0000.000
167A176GLU-1-0.817-0.89239.686-6.900-6.9000.0000.0000.0000.000
168A177LEU0-0.059-0.02734.9870.0230.0230.0000.0000.0000.000
169A178ILE00.0240.00135.0410.0030.0030.0000.0000.0000.000
170A179GLU-1-0.860-0.92538.785-7.048-7.0480.0000.0000.0000.000
171A180ARG10.7930.89141.4887.1917.1910.0000.0000.0000.000
172A181ILE0-0.0040.00135.9640.0330.0330.0000.0000.0000.000
173A182ILE0-0.032-0.02239.8960.0570.0570.0000.0000.0000.000
174A183SER0-0.072-0.03742.1660.1610.1610.0000.0000.0000.000
175A184GLY0-0.022-0.01043.5550.1380.1380.0000.0000.0000.000
176A185ASP-1-0.894-0.94444.245-6.909-6.9090.0000.0000.0000.000
177A186LYS10.8200.89339.7637.5957.5950.0000.0000.0000.000
178A187GLU-1-0.811-0.91341.234-7.583-7.5830.0000.0000.0000.000
179A188GLY00.0780.04842.714-0.062-0.0620.0000.0000.0000.000
180A189ALA0-0.036-0.01838.877-0.086-0.0860.0000.0000.0000.000
181A190ILE00.0090.00137.324-0.212-0.2120.0000.0000.0000.000
182A191GLU-1-0.979-0.98838.504-7.180-7.1800.0000.0000.0000.000
183A192LYS10.8920.94839.7457.2477.2470.0000.0000.0000.000
184A193LEU0-0.0060.00232.278-0.107-0.1070.0000.0000.0000.000
185A194LYS10.9230.95235.4347.9407.9400.0000.0000.0000.000
186A195GLU-1-0.861-0.91636.896-7.370-7.3700.0000.0000.0000.000
187A196HIS10.8520.92131.9808.9118.9110.0000.0000.0000.000
188A197LEU00.0090.00430.447-0.084-0.0840.0000.0000.0000.000
189A198LYS10.9800.98533.6828.1168.1160.0000.0000.0000.000
190A199ASN0-0.042-0.02836.2320.0970.0970.0000.0000.0000.000
191A200VAL0-0.026-0.02130.6520.0230.0230.0000.0000.0000.000
192A201GLU-1-0.887-0.90932.302-9.066-9.0660.0000.0000.0000.000
193A202ALA0-0.014-0.00233.332-0.017-0.0170.0000.0000.0000.000
194A203GLU-1-0.843-0.89734.859-7.949-7.9490.0000.0000.0000.000
195A204THR0-0.010-0.02929.220-0.090-0.0900.0000.0000.0000.000
196A205ILE0-0.054-0.03532.294-0.101-0.1010.0000.0000.0000.000
197A206LYS10.8050.89533.7777.9117.9110.0000.0000.0000.000
198A207ASN00.027-0.00433.2220.3180.3180.0000.0000.0000.000
199A208LEU0-0.0180.02129.332-0.100-0.1000.0000.0000.0000.000
200A209TYR0-0.150-0.09032.453-0.088-0.0880.0000.0000.0000.000
201A210THR0-0.031-0.00834.0910.2690.2690.0000.0000.0000.000