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: KGN23

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 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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2420715.403422
FMO2-HF: Nuclear repulsion 2339109.860117
FMO2-HF: Total energy -81605.543305
FMO2-MP2: Total energy -81847.184654


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.
-80.272-77.1817.556-8.428-12.22-0.089
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 : 0.926 / q_NPA : 0.948
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].
3A12LYS10.9180.9663.50524.48226.3580.009-0.811-1.0740.003
4A13VAL0-0.025-0.0102.3581.5592.3281.038-0.704-1.102-0.003
5A14TYR0-0.028-0.0433.9740.5911.1770.000-0.252-0.3350.000
6A15ASN00.0420.0105.9011.0181.0180.0000.0000.0000.000
7A16LEU00.0220.0287.6791.2561.2560.0000.0000.0000.000
8A17LEU00.010-0.0166.9951.0821.0820.0000.0000.0000.000
9A18LYS10.7910.8799.73122.52222.5220.0000.0000.0000.000
10A19GLU-1-0.933-0.96111.751-15.492-15.4920.0000.0000.0000.000
11A20MET0-0.066-0.03812.4060.3290.3290.0000.0000.0000.000
12A21ILE0-0.0100.00613.0840.5640.5640.0000.0000.0000.000
13A22LEU0-0.017-0.00615.6690.7710.7710.0000.0000.0000.000
14A23ASN0-0.013-0.00416.9340.6510.6510.0000.0000.0000.000
15A24HIS0-0.015-0.00218.9760.5990.5990.0000.0000.0000.000
16A25GLU-1-0.842-0.90816.538-14.443-14.4430.0000.0000.0000.000
17A26LEU0-0.083-0.03213.5000.0720.0720.0000.0000.0000.000
18A27LYS10.7940.87018.02512.65712.6570.0000.0000.0000.000
19A28LEU00.0560.01520.132-0.537-0.5370.0000.0000.0000.000
20A29GLY00.0440.03121.4120.4300.4300.0000.0000.0000.000
21A30GLU-1-0.868-0.90718.819-13.586-13.5860.0000.0000.0000.000
22A31LYS10.8380.93018.56714.27214.2720.0000.0000.0000.000
23A32LEU00.0260.01113.296-0.266-0.2660.0000.0000.0000.000
24A33ASN0-0.055-0.06015.356-1.032-1.0320.0000.0000.0000.000
25A34VAL00.0020.0049.349-0.083-0.0830.0000.0000.0000.000
26A35ARG10.9550.97111.58717.82317.8230.0000.0000.0000.000
27A36GLU-1-0.822-0.89113.955-14.599-14.5990.0000.0000.0000.000
28A37LEU00.0290.00710.6790.2290.2290.0000.0000.0000.000
29A38SER0-0.117-0.07810.098-0.219-0.2190.0000.0000.0000.000
30A39GLU-1-0.913-0.97111.101-16.630-16.6300.0000.0000.0000.000
31A40LYS10.8200.91013.94315.61515.6150.0000.0000.0000.000
32A41LEU0-0.011-0.0109.1990.2460.2460.0000.0000.0000.000
33A42GLY00.0160.03210.973-0.213-0.2130.0000.0000.0000.000
34A43ILE0-0.037-0.0185.338-1.065-1.0650.0000.0000.0000.000
35A44SER00.0430.0397.419-0.771-0.7710.0000.0000.0000.000
36A45PHE00.0740.0117.041-2.310-2.3100.0000.0000.0000.000
37A46THR00.0060.0004.3261.2541.348-0.001-0.010-0.0830.000
38A47PRO00.001-0.0022.238-7.945-7.1512.847-1.231-2.411-0.003
39A48VAL00.0580.0412.961-1.248-1.650-0.0260.937-0.508-0.004
40A49ARG10.9410.9675.61139.86739.8670.0000.0000.0000.000
41A50ASP-1-0.870-0.9401.792-99.520-100.39713.690-6.313-6.500-0.082
42A51ALA00.0000.0123.9361.9862.2130.000-0.042-0.1850.000
43A52LEU00.0330.0195.1203.2903.315-0.001-0.002-0.0220.000
44A53LEU0-0.034-0.0226.9762.4472.4470.0000.0000.0000.000
45A54GLN0-0.031-0.0075.1853.6153.6150.0000.0000.0000.000
46A55LEU00.0580.0328.0562.4532.4530.0000.0000.0000.000
47A56ALA0-0.045-0.01310.5272.0152.0150.0000.0000.0000.000
48A57THR0-0.107-0.06510.8551.1871.1870.0000.0000.0000.000
49A58GLU-1-0.748-0.82510.978-23.029-23.0290.0000.0000.0000.000
50A59GLY0-0.0180.00614.0751.2191.2190.0000.0000.0000.000
51A60LEU00.0350.01212.9400.9130.9130.0000.0000.0000.000
52A61VAL0-0.017-0.00112.2980.4400.4400.0000.0000.0000.000
53A62LYS10.8800.94414.90514.97614.9760.0000.0000.0000.000
54A63VAL00.011-0.01113.595-0.481-0.4810.0000.0000.0000.000
55A64VAL00.0450.04016.8590.4860.4860.0000.0000.0000.000
56A65PRO00.017-0.00820.056-0.237-0.2370.0000.0000.0000.000
57A66ARG10.9300.95420.57312.81512.8150.0000.0000.0000.000
58A67VAL00.0100.02320.8910.3770.3770.0000.0000.0000.000
59A68GLY0-0.015-0.00917.019-0.171-0.1710.0000.0000.0000.000
60A69PHE00.006-0.01110.6390.2550.2550.0000.0000.0000.000
61A70PHE00.0140.00715.8540.8010.8010.0000.0000.0000.000
62A71VAL00.0460.03415.949-1.126-1.1260.0000.0000.0000.000
63A72THR0-0.097-0.06117.5670.6120.6120.0000.0000.0000.000
64A73ASP-1-0.864-0.93119.610-12.240-12.2400.0000.0000.0000.000
65A74VAL0-0.0100.00422.646-0.442-0.4420.0000.0000.0000.000
66A75ASP-1-0.785-0.89725.101-10.442-10.4420.0000.0000.0000.000
67A76GLU-1-0.728-0.83328.317-8.831-8.8310.0000.0000.0000.000
68A77LYS10.8210.89726.19911.54611.5460.0000.0000.0000.000
69A78PHE0-0.011-0.00620.283-0.156-0.1560.0000.0000.0000.000
70A79ILE00.0420.03825.597-0.305-0.3050.0000.0000.0000.000
71A80ARG10.8370.88027.8078.6988.6980.0000.0000.0000.000
72A81GLU-1-0.820-0.89225.729-11.769-11.7690.0000.0000.0000.000
73A82THR0-0.042-0.01123.464-0.414-0.4140.0000.0000.0000.000
74A83ILE00.013-0.00225.570-0.068-0.0680.0000.0000.0000.000
75A84GLU-1-0.939-0.96728.884-9.358-9.3580.0000.0000.0000.000
76A85THR0-0.018-0.02423.812-0.015-0.0150.0000.0000.0000.000
77A86ARG10.7980.89826.05610.77910.7790.0000.0000.0000.000
78A87ILE0-0.011-0.00827.7630.1820.1820.0000.0000.0000.000
79A88MET0-0.022-0.00926.8500.2010.2010.0000.0000.0000.000
80A89MET0-0.035-0.01322.4490.0130.0130.0000.0000.0000.000
81A90GLU-1-0.695-0.82327.623-10.528-10.5280.0000.0000.0000.000
82A91VAL0-0.0020.00129.7310.2490.2490.0000.0000.0000.000
83A92PHE00.0080.02129.6180.1680.1680.0000.0000.0000.000
84A93CYS0-0.051-0.01928.4400.0300.0300.0000.0000.0000.000
85A94LEU00.017-0.00231.1010.1370.1370.0000.0000.0000.000
86A95GLU-1-0.901-0.94933.829-7.950-7.9500.0000.0000.0000.000
87A96ASN0-0.096-0.06033.3670.2710.2710.0000.0000.0000.000
88A97TYR0-0.024-0.00330.458-0.143-0.1430.0000.0000.0000.000
89A98PHE00.0280.04134.392-0.060-0.0600.0000.0000.0000.000
90A99ASP-1-0.852-0.93736.965-7.780-7.7800.0000.0000.0000.000
91A100LYS10.8110.90429.75110.20710.2070.0000.0000.0000.000
92A101ILE0-0.0180.00331.956-0.178-0.1780.0000.0000.0000.000
93A102ALA00.0300.01434.288-0.009-0.0090.0000.0000.0000.000
94A103GLY0-0.0110.00437.5750.1510.1510.0000.0000.0000.000
95A104SER0-0.093-0.05332.456-0.121-0.1210.0000.0000.0000.000
96A105GLU-1-0.908-0.96833.077-8.672-8.6720.0000.0000.0000.000
97A106GLU-1-0.750-0.85227.396-10.639-10.6390.0000.0000.0000.000
98A107LEU00.0040.01431.7230.0010.0010.0000.0000.0000.000
99A108LEU0-0.002-0.00234.2510.1790.1790.0000.0000.0000.000
100A109GLU-1-0.876-0.92030.810-9.422-9.4220.0000.0000.0000.000
101A110ILE0-0.020-0.00329.6810.1030.1030.0000.0000.0000.000
102A111LYS10.8000.88033.1907.4937.4930.0000.0000.0000.000
103A112GLY00.0190.01236.6890.1830.1830.0000.0000.0000.000
104A113GLH0-0.086-0.08629.3110.0960.0960.0000.0000.0000.000
105A114ILE00.0240.01734.3780.0800.0800.0000.0000.0000.000
106A115ASP-1-0.795-0.86836.535-7.127-7.1270.0000.0000.0000.000
107A116ASP-1-0.845-0.89936.342-7.617-7.6170.0000.0000.0000.000
108A117VAL00.0130.00934.0030.1510.1510.0000.0000.0000.000
109A118GLU-1-0.899-0.95337.229-7.234-7.2340.0000.0000.0000.000
110A119LYS10.7460.87639.2757.5927.5920.0000.0000.0000.000
111A120SER0-0.087-0.06937.2010.0750.0750.0000.0000.0000.000
112A121ALA0-0.0050.00937.720-0.031-0.0310.0000.0000.0000.000
113A122LYS10.9240.98931.9668.5258.5250.0000.0000.0000.000
114A123ARG10.8470.90828.7699.5609.5600.0000.0000.0000.000
115A124GLU-1-0.842-0.94627.823-9.327-9.3270.0000.0000.0000.000
116A125ILE00.0040.00728.216-0.260-0.2600.0000.0000.0000.000
117A126PHE00.0050.00830.318-0.069-0.0690.0000.0000.0000.000
118A127ASP-1-0.776-0.86725.959-10.443-10.4430.0000.0000.0000.000
119A128ASP-1-0.802-0.86025.670-10.987-10.9870.0000.0000.0000.000
120A129SER0-0.012-0.01526.871-0.031-0.0310.0000.0000.0000.000
121A130ASP-1-0.820-0.93627.939-10.151-10.1510.0000.0000.0000.000
122A131GLU-1-0.832-0.90920.664-13.578-13.5780.0000.0000.0000.000
123A132ARG10.7750.85925.23310.07710.0770.0000.0000.0000.000
124A133LEU0-0.023-0.00526.7790.0240.0240.0000.0000.0000.000
125A134HIS10.7440.85227.00610.02010.0200.0000.0000.0000.000
126A135LYS10.8200.89418.88414.37314.3730.0000.0000.0000.000
127A136LEU0-0.043-0.00424.906-0.208-0.2080.0000.0000.0000.000
128A137PHE00.023-0.01027.7680.0510.0510.0000.0000.0000.000
129A138ILE00.0270.01223.5850.0590.0590.0000.0000.0000.000
130A139ARG10.8550.91523.57911.62911.6290.0000.0000.0000.000
131A140ALA00.0030.00925.475-0.010-0.0100.0000.0000.0000.000
132A141SER0-0.012-0.03226.2140.1190.1190.0000.0000.0000.000
133A142GLY0-0.049-0.01025.5520.2150.2150.0000.0000.0000.000
134A143ASN00.0090.00023.779-0.657-0.6570.0000.0000.0000.000
135A144GLU-1-0.831-0.93718.937-14.647-14.6470.0000.0000.0000.000
136A145LEU0-0.0380.01618.933-0.863-0.8630.0000.0000.0000.000
137A146ILE00.0190.00220.186-0.300-0.3000.0000.0000.0000.000
138A147ILE00.0390.02219.318-0.035-0.0350.0000.0000.0000.000
139A148SER0-0.051-0.04615.503-0.420-0.4200.0000.0000.0000.000
140A149LEU0-0.057-0.02916.440-0.761-0.7610.0000.0000.0000.000
141A150TYR0-0.001-0.03318.830-0.132-0.1320.0000.0000.0000.000
142A151GLU-1-0.833-0.90515.996-15.176-15.1760.0000.0000.0000.000
143A152LYS10.8770.92711.25322.99022.9900.0000.0000.0000.000
144A153ILE0-0.034-0.01716.5340.2670.2670.0000.0000.0000.000
145A154TRP00.018-0.00719.1300.6240.6240.0000.0000.0000.000
146A155ASP-1-0.792-0.88614.592-18.411-18.4110.0000.0000.0000.000
147A156ARG10.8110.89917.65913.74813.7480.0000.0000.0000.000
148A157ILE00.0040.00120.3950.6150.6150.0000.0000.0000.000
149A158ASP-1-0.773-0.86119.975-12.331-12.3310.0000.0000.0000.000
150A159LEU0-0.066-0.01818.3200.2210.2210.0000.0000.0000.000
151A160VAL0-0.011-0.02221.2230.3580.3580.0000.0000.0000.000
152A161ARG10.8140.87922.57212.35012.3500.0000.0000.0000.000
153A162HIS0-0.024-0.01425.2350.3260.3260.0000.0000.0000.000
154A163LEU00.0230.02527.5960.3010.3010.0000.0000.0000.000
155A164ASN0-0.0130.00828.5230.6550.6550.0000.0000.0000.000
156A165GLU-1-0.877-0.93930.809-8.411-8.4110.0000.0000.0000.000
157A166ARG10.8240.88333.6838.3588.3580.0000.0000.0000.000
158A167TYR0-0.049-0.05232.7610.1300.1300.0000.0000.0000.000
159A168VAL00.0430.01734.5640.0310.0310.0000.0000.0000.000
160A169VAL0-0.037-0.02137.9650.1570.1570.0000.0000.0000.000
161A170SER0-0.004-0.00533.4830.0850.0850.0000.0000.0000.000
162A171ASN0-0.023-0.01935.933-0.275-0.2750.0000.0000.0000.000
163A172ARG10.9790.99736.8117.1007.1000.0000.0000.0000.000
164A173GLU-1-0.772-0.83736.916-8.014-8.0140.0000.0000.0000.000
165A174HIS00.0590.03131.513-0.111-0.1110.0000.0000.0000.000
166A175LYS10.8510.94236.5857.0497.0490.0000.0000.0000.000
167A176GLU-1-0.788-0.88339.728-6.853-6.8530.0000.0000.0000.000
168A177LEU0-0.059-0.02034.5190.0160.0160.0000.0000.0000.000
169A178ILE00.021-0.00234.828-0.001-0.0010.0000.0000.0000.000
170A179GLU-1-0.840-0.91838.630-6.991-6.9910.0000.0000.0000.000
171A180ARG10.7820.88941.5527.2147.2140.0000.0000.0000.000
172A181ILE0-0.018-0.01335.9990.0520.0520.0000.0000.0000.000
173A182ILE0-0.024-0.01539.4350.0570.0570.0000.0000.0000.000
174A183SER0-0.077-0.04142.1620.1740.1740.0000.0000.0000.000
175A184GLY0-0.017-0.00543.5230.1440.1440.0000.0000.0000.000
176A185ASP-1-0.862-0.93244.178-6.946-6.9460.0000.0000.0000.000
177A186LYS10.8090.88239.7867.5057.5050.0000.0000.0000.000
178A187GLU-1-0.844-0.91740.759-7.529-7.5290.0000.0000.0000.000
179A188GLY00.0850.04242.064-0.118-0.1180.0000.0000.0000.000
180A189ALA0-0.0130.00238.750-0.092-0.0920.0000.0000.0000.000
181A190ILE00.0130.00136.924-0.219-0.2190.0000.0000.0000.000
182A191GLU-1-0.987-0.99138.062-7.219-7.2190.0000.0000.0000.000
183A192LYS10.8740.93439.2297.2487.2480.0000.0000.0000.000
184A193LEU0-0.042-0.01331.962-0.118-0.1180.0000.0000.0000.000
185A194LYS10.9380.96835.1627.8227.8220.0000.0000.0000.000
186A195GLU-1-0.845-0.91836.754-7.354-7.3540.0000.0000.0000.000
187A196HIS10.8040.90431.4578.9648.9640.0000.0000.0000.000
188A197LEU00.0060.00430.228-0.107-0.1070.0000.0000.0000.000
189A198LYS10.8830.92333.4398.5848.5840.0000.0000.0000.000
190A199ASN0-0.045-0.03936.0630.0920.0920.0000.0000.0000.000
191A200VAL0-0.008-0.00630.2340.0260.0260.0000.0000.0000.000
192A201GLU-1-0.837-0.87432.195-9.083-9.0830.0000.0000.0000.000
193A202ALA0-0.007-0.00533.296-0.042-0.0420.0000.0000.0000.000
194A203GLU-1-0.818-0.88834.486-8.045-8.0450.0000.0000.0000.000
195A204THR0-0.024-0.03228.698-0.094-0.0940.0000.0000.0000.000
196A205ILE0-0.033-0.01431.864-0.132-0.1320.0000.0000.0000.000
197A206LYS10.7900.87133.5497.9947.9940.0000.0000.0000.000
198A207ASN00.0210.00433.0770.3070.3070.0000.0000.0000.000
199A208LEU0-0.0280.00929.067-0.086-0.0860.0000.0000.0000.000
200A209TYR0-0.076-0.05632.196-0.063-0.0630.0000.0000.0000.000
201A210THR0-0.098-0.04034.2550.4050.4050.0000.0000.0000.000