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: R8RY8

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 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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2406684.290518
FMO2-HF: Nuclear repulsion 2325080.912352
FMO2-HF: Total energy -81603.378166
FMO2-MP2: Total energy -81844.525962


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.
-73.224-63.6999.553-7.431-11.646-0.061
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 : 0.970
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].
3A12LYS10.9871.0113.74324.41326.524-0.014-0.975-1.1220.004
4A13VAL00.0190.0092.0280.244-0.0342.825-0.694-1.853-0.004
5A14TYR0-0.030-0.0413.8741.6322.1280.001-0.165-0.3320.000
6A15ASN00.018-0.0185.5792.3032.3030.0000.0000.0000.000
7A16LEU00.0210.0227.7211.4591.4590.0000.0000.0000.000
8A17LEU0-0.008-0.0166.6731.2421.2420.0000.0000.0000.000
9A18LYS10.7990.8849.56323.86423.8640.0000.0000.0000.000
10A19GLU-1-0.935-0.95311.545-15.995-15.9950.0000.0000.0000.000
11A20MET0-0.032-0.01312.7970.4490.4490.0000.0000.0000.000
12A21ILE0-0.015-0.00412.8580.8020.8020.0000.0000.0000.000
13A22LEU0-0.025-0.00715.4330.7730.7730.0000.0000.0000.000
14A23ASN0-0.013-0.00217.3690.6980.6980.0000.0000.0000.000
15A24HIS0-0.032-0.00818.8460.4570.4570.0000.0000.0000.000
16A25GLU-1-0.911-0.95816.993-14.246-14.2460.0000.0000.0000.000
17A26LEU0-0.133-0.07013.193-0.043-0.0430.0000.0000.0000.000
18A27LYS10.9400.96917.67811.60211.6020.0000.0000.0000.000
19A28LEU00.0590.01320.085-0.469-0.4690.0000.0000.0000.000
20A29GLY00.0560.03021.0410.4450.4450.0000.0000.0000.000
21A30GLU-1-0.936-0.94918.985-13.657-13.6570.0000.0000.0000.000
22A31LYS10.8850.94018.33313.81913.8190.0000.0000.0000.000
23A32LEU00.0460.03413.068-0.276-0.2760.0000.0000.0000.000
24A33ASN0-0.013-0.02515.391-0.572-0.5720.0000.0000.0000.000
25A34VAL00.004-0.0099.804-0.165-0.1650.0000.0000.0000.000
26A35ARG10.9610.96611.86517.07717.0770.0000.0000.0000.000
27A36GLU-1-0.910-0.94514.255-14.299-14.2990.0000.0000.0000.000
28A37LEU00.0290.01210.8620.0920.0920.0000.0000.0000.000
29A38SER0-0.105-0.08810.008-0.134-0.1340.0000.0000.0000.000
30A39GLU-1-0.904-0.97011.038-15.964-15.9640.0000.0000.0000.000
31A40LYS10.8920.96113.96215.82015.8200.0000.0000.0000.000
32A41LEU0-0.030-0.0288.9720.1340.1340.0000.0000.0000.000
33A42GLY00.0170.03810.509-0.207-0.2070.0000.0000.0000.000
34A43ILE0-0.046-0.0164.966-1.365-1.3650.0000.0000.0000.000
35A44SER00.0190.0577.351-0.259-0.2590.0000.0000.0000.000
36A45PHE00.0650.0007.353-1.945-1.9450.0000.0000.0000.000
37A46THR00.0190.0084.6031.6461.731-0.001-0.008-0.0760.000
38A47PRO00.0100.0192.501-5.907-4.1670.993-0.868-1.864-0.001
39A48VAL00.0530.0323.387-2.913-1.9980.020-0.364-0.571-0.005
40A49ARG10.9580.9806.02929.95529.9550.0000.0000.0000.000
41A50ASP-1-0.901-0.9702.299-77.132-73.0195.731-4.309-5.535-0.055
42A51ALA00.0000.0003.8250.8001.0200.000-0.040-0.1810.000
43A52LEU00.0350.0235.3103.0503.062-0.001-0.001-0.0090.000
44A53LEU0-0.025-0.0146.9352.3902.3900.0000.0000.0000.000
45A54GLN0-0.030-0.0114.7664.0344.145-0.001-0.007-0.1030.000
46A55LEU00.0730.0347.7322.3392.3390.0000.0000.0000.000
47A56ALA0-0.054-0.03110.7811.9871.9870.0000.0000.0000.000
48A57THR0-0.139-0.06410.0671.4451.4450.0000.0000.0000.000
49A58GLU-1-0.826-0.88610.603-24.470-24.4700.0000.0000.0000.000
50A59GLY0-0.0250.00514.0851.1961.1960.0000.0000.0000.000
51A60LEU00.0360.01213.6020.9020.9020.0000.0000.0000.000
52A61VAL0-0.0160.00312.1830.4850.4850.0000.0000.0000.000
53A62LYS10.9320.97315.25114.23814.2380.0000.0000.0000.000
54A63VAL00.0340.00713.598-0.361-0.3610.0000.0000.0000.000
55A64VAL0-0.0180.00316.8800.5960.5960.0000.0000.0000.000
56A65PRO00.028-0.01120.151-0.120-0.1200.0000.0000.0000.000
57A66ARG10.9280.96320.77212.17712.1770.0000.0000.0000.000
58A67VAL00.0060.01220.8660.4020.4020.0000.0000.0000.000
59A68GLY0-0.035-0.02617.276-0.207-0.2070.0000.0000.0000.000
60A69PHE0-0.0030.00511.180-0.088-0.0880.0000.0000.0000.000
61A70PHE00.0060.00215.9300.6100.6100.0000.0000.0000.000
62A71VAL00.0220.02415.847-1.009-1.0090.0000.0000.0000.000
63A72THR0-0.098-0.05417.5090.6900.6900.0000.0000.0000.000
64A73ASP-1-0.849-0.91919.772-11.814-11.8140.0000.0000.0000.000
65A74VAL0-0.026-0.01523.015-0.389-0.3890.0000.0000.0000.000
66A75ASP-1-0.851-0.93025.292-10.596-10.5960.0000.0000.0000.000
67A76GLU-1-0.759-0.87128.664-8.864-8.8640.0000.0000.0000.000
68A77LYS10.8510.92326.85211.09111.0910.0000.0000.0000.000
69A78PHE00.0140.01621.002-0.187-0.1870.0000.0000.0000.000
70A79ILE00.0380.01326.274-0.263-0.2630.0000.0000.0000.000
71A80ARG10.8520.89828.1858.8148.8140.0000.0000.0000.000
72A81GLU-1-0.846-0.90526.290-11.388-11.3880.0000.0000.0000.000
73A82THR0-0.031-0.00423.934-0.407-0.4070.0000.0000.0000.000
74A83ILE00.0120.00825.970-0.107-0.1070.0000.0000.0000.000
75A84GLU-1-0.941-0.96829.213-9.624-9.6240.0000.0000.0000.000
76A85THR0-0.013-0.01524.054-0.008-0.0080.0000.0000.0000.000
77A86ARG10.8690.93526.01610.95410.9540.0000.0000.0000.000
78A87ILE0-0.010-0.00427.7780.1960.1960.0000.0000.0000.000
79A88MET0-0.0210.00026.5360.1940.1940.0000.0000.0000.000
80A89MET0-0.035-0.01922.4000.0020.0020.0000.0000.0000.000
81A90GLU-1-0.715-0.82827.939-10.644-10.6440.0000.0000.0000.000
82A91VAL0-0.002-0.00329.7300.2510.2510.0000.0000.0000.000
83A92PHE00.0150.03329.2920.1670.1670.0000.0000.0000.000
84A93CYS0-0.055-0.02027.8880.0210.0210.0000.0000.0000.000
85A94LEU00.0250.00430.6360.1500.1500.0000.0000.0000.000
86A95GLU-1-0.950-0.97633.632-8.091-8.0910.0000.0000.0000.000
87A96ASN0-0.077-0.06232.5710.3820.3820.0000.0000.0000.000
88A97TYR0-0.034-0.00129.801-0.088-0.0880.0000.0000.0000.000
89A98PHE00.0200.02233.448-0.080-0.0800.0000.0000.0000.000
90A99ASP-1-0.841-0.93036.326-7.837-7.8370.0000.0000.0000.000
91A100LYS10.8380.93128.37910.50510.5050.0000.0000.0000.000
92A101ILE0-0.024-0.01031.563-0.115-0.1150.0000.0000.0000.000
93A102ALA00.0160.00833.903-0.014-0.0140.0000.0000.0000.000
94A103GLY0-0.0200.00036.9290.1490.1490.0000.0000.0000.000
95A104SER0-0.096-0.04932.334-0.095-0.0950.0000.0000.0000.000
96A105GLU-1-0.928-0.97632.927-9.044-9.0440.0000.0000.0000.000
97A106GLU-1-0.789-0.88827.881-10.676-10.6760.0000.0000.0000.000
98A107LEU0-0.0050.00231.8490.0090.0090.0000.0000.0000.000
99A108LEU0-0.021-0.02234.1980.1870.1870.0000.0000.0000.000
100A109GLU-1-0.910-0.95031.250-9.556-9.5560.0000.0000.0000.000
101A110ILE0-0.013-0.00929.6800.0790.0790.0000.0000.0000.000
102A111LYS10.9550.98133.3687.6227.6220.0000.0000.0000.000
103A112GLY00.0040.00636.7530.1770.1770.0000.0000.0000.000
104A113GLH0-0.077-0.09729.4320.1240.1240.0000.0000.0000.000
105A114ILE00.0140.00534.3070.0660.0660.0000.0000.0000.000
106A115ASP-1-0.896-0.94836.491-7.336-7.3360.0000.0000.0000.000
107A116ASP-1-0.977-0.98336.357-7.918-7.9180.0000.0000.0000.000
108A117VAL0-0.030-0.01634.1620.0940.0940.0000.0000.0000.000
109A118GLU-1-0.933-0.96837.259-7.309-7.3090.0000.0000.0000.000
110A119LYS10.9120.97140.6447.4037.4030.0000.0000.0000.000
111A120SER0-0.098-0.05937.4290.0610.0610.0000.0000.0000.000
112A121ALA00.0210.01537.4840.0140.0140.0000.0000.0000.000
113A122LYS10.9221.00232.6408.5628.5620.0000.0000.0000.000
114A123ARG10.8720.93128.7289.7429.7420.0000.0000.0000.000
115A124GLU-1-0.863-0.95328.024-9.486-9.4860.0000.0000.0000.000
116A125ILE0-0.011-0.00728.359-0.276-0.2760.0000.0000.0000.000
117A126PHE00.0160.03030.432-0.040-0.0400.0000.0000.0000.000
118A127ASP-1-0.826-0.92025.942-10.656-10.6560.0000.0000.0000.000
119A128ASP-1-0.821-0.85825.853-11.278-11.2780.0000.0000.0000.000
120A129SER0-0.005-0.01526.990-0.035-0.0350.0000.0000.0000.000
121A130ASP-1-0.938-0.98028.148-10.419-10.4190.0000.0000.0000.000
122A131GLU-1-0.832-0.91720.623-13.919-13.9190.0000.0000.0000.000
123A132ARG10.7990.88925.35610.35010.3500.0000.0000.0000.000
124A133LEU0-0.0250.00226.6990.0170.0170.0000.0000.0000.000
125A134HIS10.7450.83126.80310.30210.3020.0000.0000.0000.000
126A135LYS10.8460.91218.93214.83814.8380.0000.0000.0000.000
127A136LEU0-0.0200.01724.972-0.272-0.2720.0000.0000.0000.000
128A137PHE00.018-0.01027.6850.0460.0460.0000.0000.0000.000
129A138ILE00.0250.00423.2930.0380.0380.0000.0000.0000.000
130A139ARG10.9750.99523.07112.32412.3240.0000.0000.0000.000
131A140ALA0-0.020-0.00424.950-0.014-0.0140.0000.0000.0000.000
132A141SER0-0.001-0.02925.3730.1370.1370.0000.0000.0000.000
133A142GLY0-0.054-0.02024.4150.1660.1660.0000.0000.0000.000
134A143ASN00.0020.01322.272-0.866-0.8660.0000.0000.0000.000
135A144GLU-1-0.843-0.94717.558-15.693-15.6930.0000.0000.0000.000
136A145LEU0-0.0410.00617.803-0.814-0.8140.0000.0000.0000.000
137A146ILE00.021-0.00819.054-0.444-0.4440.0000.0000.0000.000
138A147ILE00.0490.02318.506-0.033-0.0330.0000.0000.0000.000
139A148SER0-0.053-0.02414.855-0.654-0.6540.0000.0000.0000.000
140A149LEU0-0.054-0.03316.549-0.606-0.6060.0000.0000.0000.000
141A150TYR0-0.006-0.03818.554-0.022-0.0220.0000.0000.0000.000
142A151GLU-1-0.907-0.94615.704-16.368-16.3680.0000.0000.0000.000
143A152LYS10.9580.97812.32622.32922.3290.0000.0000.0000.000
144A153ILE0-0.039-0.01716.7400.3910.3910.0000.0000.0000.000
145A154TRP00.011-0.00819.5990.7350.7350.0000.0000.0000.000
146A155ASP-1-0.750-0.86114.709-18.676-18.6760.0000.0000.0000.000
147A156ARG10.8150.89718.16114.09014.0900.0000.0000.0000.000
148A157ILE0-0.019-0.00820.7620.6290.6290.0000.0000.0000.000
149A158ASP-1-0.826-0.91819.753-13.292-13.2920.0000.0000.0000.000
150A159LEU0-0.059-0.01518.4740.2440.2440.0000.0000.0000.000
151A160VAL0-0.013-0.01921.2380.3720.3720.0000.0000.0000.000
152A161ARG10.9270.96822.37512.72112.7210.0000.0000.0000.000
153A162HIS0-0.027-0.01924.9380.2300.2300.0000.0000.0000.000
154A163LEU0-0.0030.00727.5980.3140.3140.0000.0000.0000.000
155A164ASN0-0.0060.01528.8240.6230.6230.0000.0000.0000.000
156A165GLU-1-0.850-0.93131.021-8.662-8.6620.0000.0000.0000.000
157A166ARG10.7970.87933.7338.4578.4570.0000.0000.0000.000
158A167TYR0-0.033-0.06532.8030.1540.1540.0000.0000.0000.000
159A168VAL00.0670.04334.7030.0470.0470.0000.0000.0000.000
160A169VAL0-0.038-0.02938.1230.1400.1400.0000.0000.0000.000
161A170SER0-0.002-0.00433.9290.0830.0830.0000.0000.0000.000
162A171ASN0-0.006-0.00135.806-0.287-0.2870.0000.0000.0000.000
163A172ARG10.9780.99736.7837.1947.1940.0000.0000.0000.000
164A173GLU-1-0.787-0.85337.365-8.074-8.0740.0000.0000.0000.000
165A174HIS00.0120.01431.602-0.089-0.0890.0000.0000.0000.000
166A175LYS10.9400.98236.5997.0707.0700.0000.0000.0000.000
167A176GLU-1-0.814-0.90639.502-6.978-6.9780.0000.0000.0000.000
168A177LEU0-0.076-0.03734.6600.0290.0290.0000.0000.0000.000
169A178ILE00.0250.00135.0240.0110.0110.0000.0000.0000.000
170A179GLU-1-0.915-0.95138.568-6.988-6.9880.0000.0000.0000.000
171A180ARG10.8100.89541.2697.2357.2350.0000.0000.0000.000
172A181ILE0-0.0040.00535.7620.0350.0350.0000.0000.0000.000
173A182ILE0-0.038-0.02639.7740.0590.0590.0000.0000.0000.000
174A183SER0-0.051-0.01941.9060.1650.1650.0000.0000.0000.000
175A184GLY0-0.035-0.01343.2570.1390.1390.0000.0000.0000.000
176A185ASP-1-0.899-0.94544.017-6.923-6.9230.0000.0000.0000.000
177A186LYS10.9430.97938.9797.7647.7640.0000.0000.0000.000
178A187GLU-1-0.898-0.96641.062-7.561-7.5610.0000.0000.0000.000
179A188GLY00.0690.04742.575-0.062-0.0620.0000.0000.0000.000
180A189ALA0-0.035-0.02038.657-0.087-0.0870.0000.0000.0000.000
181A190ILE00.0130.00737.265-0.219-0.2190.0000.0000.0000.000
182A191GLU-1-0.988-0.99338.393-7.203-7.2030.0000.0000.0000.000
183A192LYS10.9781.00039.3427.3017.3010.0000.0000.0000.000
184A193LEU0-0.0030.00532.219-0.097-0.0970.0000.0000.0000.000
185A194LYS10.9360.95135.3508.0438.0430.0000.0000.0000.000
186A195GLU-1-0.955-0.96636.827-7.408-7.4080.0000.0000.0000.000
187A196HIS10.8620.92631.8749.0159.0150.0000.0000.0000.000
188A197LEU0-0.001-0.00530.384-0.087-0.0870.0000.0000.0000.000
189A198LYS10.9830.98633.6778.1458.1450.0000.0000.0000.000
190A199ASN0-0.042-0.02236.2330.0910.0910.0000.0000.0000.000
191A200VAL0-0.035-0.02330.6520.0180.0180.0000.0000.0000.000
192A201GLU-1-0.882-0.91932.355-9.249-9.2490.0000.0000.0000.000
193A202ALA0-0.021-0.01033.378-0.012-0.0120.0000.0000.0000.000
194A203GLU-1-0.917-0.96134.455-8.214-8.2140.0000.0000.0000.000
195A204THR0-0.009-0.02529.301-0.094-0.0940.0000.0000.0000.000
196A205ILE0-0.055-0.03632.297-0.093-0.0930.0000.0000.0000.000
197A206LYS10.9310.97233.7767.5257.5250.0000.0000.0000.000
198A207ASN00.0450.00733.2610.2770.2770.0000.0000.0000.000
199A208LEU0-0.057-0.00229.395-0.105-0.1050.0000.0000.0000.000
200A209TYR0-0.145-0.07432.458-0.085-0.0850.0000.0000.0000.000
201A210THR0-0.033-0.00933.9800.2930.2930.0000.0000.0000.000