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: K9N83

Calculation Name: 1SPX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1SPX

Chain ID: A

ChEMBL ID:

UniProt ID: Q18946

Base Structure: X-ray

Registration Date: 2023-09-20

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 237
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2742801.786441
FMO2-HF: Nuclear repulsion 2655513.122754
FMO2-HF: Total energy -87288.663687
FMO2-MP2: Total energy -87546.178814


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:2:THR)


Summations of interaction energy for fragment #1(A:2: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.
-28.737-27.88518.679-9.551-9.982-0.085
Interaction energy analysis for fragmet #1(A:2:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.054 / q_NPA : -0.035
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].
3A4PHE0-0.024-0.0353.253-4.471-2.6240.059-0.973-0.9330.000
4A5ALA00.0860.0573.079-0.1470.7530.034-0.389-0.5450.002
5A6GLU-1-0.956-0.9764.4420.5410.685-0.001-0.015-0.1280.000
6A7LYS10.8160.9267.2981.4581.4580.0000.0000.0000.000
7A8VAL00.0140.0128.948-0.272-0.2720.0000.0000.0000.000
8A9ALA0-0.003-0.00611.3110.0980.0980.0000.0000.0000.000
9A10ILE00.0120.01513.0500.0510.0510.0000.0000.0000.000
10A11ILE0-0.0010.00312.5740.0150.0150.0000.0000.0000.000
11A12THR00.0250.01616.6580.0710.0710.0000.0000.0000.000
12A13GLY00.0390.02419.871-0.022-0.0220.0000.0000.0000.000
13A14SER0-0.001-0.02017.5330.0270.0270.0000.0000.0000.000
14A15SER0-0.0110.01419.373-0.021-0.0210.0000.0000.0000.000
15A16ASN0-0.042-0.03421.4300.0440.0440.0000.0000.0000.000
16A17GLY00.0860.03520.276-0.041-0.0410.0000.0000.0000.000
17A18ILE00.0420.03917.908-0.055-0.0550.0000.0000.0000.000
18A19GLY00.0640.04516.492-0.096-0.0960.0000.0000.0000.000
19A20ARG10.8510.92215.7410.3780.3780.0000.0000.0000.000
20A21ALA00.0110.00614.432-0.100-0.1000.0000.0000.0000.000
21A22THR00.009-0.01812.172-0.154-0.1540.0000.0000.0000.000
22A23ALA0-0.009-0.00110.863-0.289-0.2890.0000.0000.0000.000
23A24VAL00.0210.00710.581-0.268-0.2680.0000.0000.0000.000
24A25LEU0-0.073-0.0246.985-0.257-0.2570.0000.0000.0000.000
25A26PHE00.037-0.0066.431-0.777-0.7770.0000.0000.0000.000
26A27ALA00.0040.0066.081-1.115-1.1150.0000.0000.0000.000
27A28ARG10.9140.9585.2701.3961.3960.0000.0000.0000.000
28A29GLU-1-0.844-0.9042.205-10.675-7.3784.709-3.666-4.341-0.029
29A30GLY00.0180.0271.736-14.729-20.17313.878-4.486-3.948-0.058
30A31ALA0-0.041-0.0103.7391.6501.7580.000-0.022-0.0870.000
31A32LYS10.8400.9306.6381.8091.8090.0000.0000.0000.000
32A33VAL0-0.003-0.0079.7200.0420.0420.0000.0000.0000.000
33A34THR00.0250.01212.3080.1640.1640.0000.0000.0000.000
34A35ILE0-0.025-0.00415.085-0.038-0.0380.0000.0000.0000.000
35A36THR00.009-0.01617.7040.0720.0720.0000.0000.0000.000
36A37GLY0-0.005-0.01321.451-0.011-0.0110.0000.0000.0000.000
37A38ARG10.8640.91324.7090.2510.2510.0000.0000.0000.000
38A39HIS00.0060.01126.9050.0140.0140.0000.0000.0000.000
39A40ALA00.0670.02126.011-0.022-0.0220.0000.0000.0000.000
40A41GLU-1-0.892-0.94225.113-0.258-0.2580.0000.0000.0000.000
41A42ARG10.9300.95724.4800.2580.2580.0000.0000.0000.000
42A43LEU0-0.0070.00620.102-0.027-0.0270.0000.0000.0000.000
43A44GLU-1-0.809-0.88120.342-0.475-0.4750.0000.0000.0000.000
44A45GLU-1-0.873-0.91920.377-0.403-0.4030.0000.0000.0000.000
45A46THR0-0.061-0.04616.419-0.009-0.0090.0000.0000.0000.000
46A47ARG10.8470.91616.0860.3480.3480.0000.0000.0000.000
47A48GLN0-0.019-0.02715.960-0.025-0.0250.0000.0000.0000.000
48A49GLN0-0.046-0.04115.283-0.045-0.0450.0000.0000.0000.000
49A50ILE0-0.025-0.01110.926-0.063-0.0630.0000.0000.0000.000
50A51LEU0-0.024-0.01011.681-0.044-0.0440.0000.0000.0000.000
51A52ALA0-0.012-0.00313.5450.0470.0470.0000.0000.0000.000
52A53ALA0-0.077-0.0329.5840.0480.0480.0000.0000.0000.000
53A54GLY00.0040.0049.172-0.047-0.0470.0000.0000.0000.000
54A55VAL0-0.065-0.0167.5460.0350.0350.0000.0000.0000.000
55A56SER00.0270.0049.9390.0940.0940.0000.0000.0000.000
56A57GLU-1-0.781-0.90612.064-0.524-0.5240.0000.0000.0000.000
57A58GLN0-0.042-0.01613.872-0.045-0.0450.0000.0000.0000.000
58A59ASN00.0060.0117.7440.1190.1190.0000.0000.0000.000
59A60VAL0-0.010-0.00411.439-0.168-0.1680.0000.0000.0000.000
60A61ASN0-0.011-0.01614.1940.1650.1650.0000.0000.0000.000
61A62SER00.0280.00317.319-0.041-0.0410.0000.0000.0000.000
62A63VAL00.0030.01719.9080.0450.0450.0000.0000.0000.000
63A64VAL00.0070.00322.607-0.007-0.0070.0000.0000.0000.000
64A65ALA00.0380.02825.6910.0250.0250.0000.0000.0000.000
65A66ASP-1-0.800-0.86227.372-0.265-0.2650.0000.0000.0000.000
66A67VAL00.0670.03824.9810.0120.0120.0000.0000.0000.000
67A68THR0-0.062-0.05127.7660.0090.0090.0000.0000.0000.000
68A69THR0-0.078-0.04330.9780.0170.0170.0000.0000.0000.000
69A70ASP-1-0.841-0.91930.594-0.237-0.2370.0000.0000.0000.000
70A71ALA00.0940.03730.355-0.014-0.0140.0000.0000.0000.000
71A72GLY00.0010.00928.595-0.012-0.0120.0000.0000.0000.000
72A73GLN0-0.046-0.04825.956-0.026-0.0260.0000.0000.0000.000
73A74ASP-1-0.805-0.89025.358-0.291-0.2910.0000.0000.0000.000
74A75GLU-1-0.907-0.92325.165-0.319-0.3190.0000.0000.0000.000
75A76ILE0-0.039-0.00720.833-0.035-0.0350.0000.0000.0000.000
76A77LEU0-0.020-0.00420.999-0.053-0.0530.0000.0000.0000.000
77A78SER0-0.012-0.03121.649-0.020-0.0200.0000.0000.0000.000
78A79THR0-0.003-0.02021.339-0.026-0.0260.0000.0000.0000.000
79A80THR00.0040.00516.329-0.058-0.0580.0000.0000.0000.000
80A81LEU0-0.039-0.00817.605-0.035-0.0350.0000.0000.0000.000
81A82GLY0-0.017-0.00419.8410.0140.0140.0000.0000.0000.000
82A83LYS10.8650.92617.3170.4920.4920.0000.0000.0000.000
83A84PHE0-0.023-0.02413.741-0.046-0.0460.0000.0000.0000.000
84A85GLY00.0040.01915.226-0.038-0.0380.0000.0000.0000.000
85A86LYS10.7860.87811.6800.9460.9460.0000.0000.0000.000
86A87LEU00.014-0.00115.574-0.057-0.0570.0000.0000.0000.000
87A88ASP-1-0.760-0.85112.447-0.880-0.8800.0000.0000.0000.000
88A89ILE00.0090.00610.2920.0080.0080.0000.0000.0000.000
89A90LEU0-0.0090.00914.691-0.005-0.0050.0000.0000.0000.000
90A91VAL00.0240.01714.2090.0440.0440.0000.0000.0000.000
91A92ASN00.010-0.00317.3890.0170.0170.0000.0000.0000.000
92A93ASN0-0.037-0.03619.6120.0530.0530.0000.0000.0000.000
93A94ALA00.0090.02321.6220.0110.0110.0000.0000.0000.000
94A95GLY00.0180.00725.0340.0190.0190.0000.0000.0000.000
95A109GLN00.0640.04341.0030.0040.0040.0000.0000.0000.000
96A110SER0-0.047-0.04444.152-0.001-0.0010.0000.0000.0000.000
97A111ILE00.0710.02743.250-0.006-0.0060.0000.0000.0000.000
98A112GLU-1-0.780-0.87142.649-0.127-0.1270.0000.0000.0000.000
99A113SER0-0.031-0.02239.877-0.010-0.0100.0000.0000.0000.000
100A114TYR0-0.0060.01538.479-0.014-0.0140.0000.0000.0000.000
101A115ASP-1-0.871-0.93638.053-0.154-0.1540.0000.0000.0000.000
102A116ALA0-0.051-0.02936.910-0.012-0.0120.0000.0000.0000.000
103A117THR0-0.040-0.02733.783-0.018-0.0180.0000.0000.0000.000
104A118LEU00.0520.02233.210-0.020-0.0200.0000.0000.0000.000
105A119ASN0-0.0030.00133.201-0.014-0.0140.0000.0000.0000.000
106A120LEU0-0.008-0.00928.690-0.016-0.0160.0000.0000.0000.000
107A121ASN0-0.041-0.03928.799-0.036-0.0360.0000.0000.0000.000
108A122LEU00.0240.01828.698-0.013-0.0130.0000.0000.0000.000
109A123ARG10.9250.95930.0720.1910.1910.0000.0000.0000.000
110A124SER0-0.018-0.01428.239-0.006-0.0060.0000.0000.0000.000
111A125VAL00.0240.02724.868-0.014-0.0140.0000.0000.0000.000
112A126ILE00.0060.01926.390-0.013-0.0130.0000.0000.0000.000
113A127ALA0-0.030-0.00728.709-0.001-0.0010.0000.0000.0000.000
114A128LEU00.0470.02022.1840.0000.0000.0000.0000.0000.000
115A129THR00.012-0.01923.445-0.030-0.0300.0000.0000.0000.000
116A130LYS10.9010.94524.8830.2190.2190.0000.0000.0000.000
117A131LYS10.7810.89226.2320.2730.2730.0000.0000.0000.000
118A132ALA00.0300.01121.118-0.001-0.0010.0000.0000.0000.000
119A133VAL00.0240.00722.266-0.017-0.0170.0000.0000.0000.000
120A134PRO00.0370.02523.466-0.002-0.0020.0000.0000.0000.000
121A135HIS00.0350.02520.2830.0020.0020.0000.0000.0000.000
122A136LEU00.0030.00817.395-0.019-0.0190.0000.0000.0000.000
123A137SER0-0.011-0.01019.5910.0010.0010.0000.0000.0000.000
124A138SER0-0.075-0.04320.9720.0280.0280.0000.0000.0000.000
125A139THR0-0.048-0.03815.6590.0270.0270.0000.0000.0000.000
126A140LYS10.8780.94216.3710.1490.1490.0000.0000.0000.000
127A141GLY00.0360.03415.610-0.029-0.0290.0000.0000.0000.000
128A142GLU-1-0.830-0.89913.663-0.535-0.5350.0000.0000.0000.000
129A143ILE0-0.024-0.00416.757-0.041-0.0410.0000.0000.0000.000
130A144VAL0-0.001-0.00215.3230.0310.0310.0000.0000.0000.000
131A145ASN0-0.013-0.02318.521-0.040-0.0400.0000.0000.0000.000
132A146ILE0-0.003-0.00318.3090.0130.0130.0000.0000.0000.000
133A147SER00.011-0.01922.3670.0280.0280.0000.0000.0000.000
134A148SER0-0.006-0.02125.258-0.008-0.0080.0000.0000.0000.000
135A149ILE00.0050.01327.1090.0120.0120.0000.0000.0000.000
136A150ALA0-0.008-0.01029.4540.0180.0180.0000.0000.0000.000
137A151SER0-0.034-0.02029.8350.0210.0210.0000.0000.0000.000
138A152GLY00.0420.01131.764-0.001-0.0010.0000.0000.0000.000
139A153LEU0-0.029-0.01233.2500.0040.0040.0000.0000.0000.000
140A154HIS10.8370.90932.8880.1620.1620.0000.0000.0000.000
141A155ALA00.0300.02337.739-0.005-0.0050.0000.0000.0000.000
142A156THR00.004-0.01134.625-0.001-0.0010.0000.0000.0000.000
143A157PRO00.0090.01137.816-0.006-0.0060.0000.0000.0000.000
144A158ASP-1-0.868-0.93337.640-0.130-0.1300.0000.0000.0000.000
145A159PHE0-0.024-0.01233.589-0.008-0.0080.0000.0000.0000.000
146A160PRO0-0.0010.02636.416-0.008-0.0080.0000.0000.0000.000
147A161TYR00.007-0.03537.618-0.001-0.0010.0000.0000.0000.000
148A162TYR0-0.009-0.00927.519-0.004-0.0040.0000.0000.0000.000
149A163SER00.024-0.00632.623-0.010-0.0100.0000.0000.0000.000
150A164ILE00.0050.01233.517-0.007-0.0070.0000.0000.0000.000
151A165ALA00.0060.00932.475-0.004-0.0040.0000.0000.0000.000
152A166LYS10.8430.92825.7500.3150.3150.0000.0000.0000.000
153A167ALA00.0310.02029.649-0.008-0.0080.0000.0000.0000.000
154A168ALA0-0.036-0.01332.0200.0020.0020.0000.0000.0000.000
155A169ILE00.0050.00525.975-0.003-0.0030.0000.0000.0000.000
156A170ASP-1-0.736-0.81126.903-0.272-0.2720.0000.0000.0000.000
157A171GLN0-0.0050.00228.6140.0040.0040.0000.0000.0000.000
158A172TYR00.006-0.00125.7380.0150.0150.0000.0000.0000.000
159A173THR00.0040.00523.851-0.017-0.0170.0000.0000.0000.000
160A174ARG10.8390.90726.6270.1850.1850.0000.0000.0000.000
161A175ASN0-0.017-0.00528.8050.0140.0140.0000.0000.0000.000
162A176THR0-0.006-0.03526.557-0.001-0.0010.0000.0000.0000.000
163A177ALA00.0020.00925.031-0.006-0.0060.0000.0000.0000.000
164A178ILE0-0.0060.00325.9730.0070.0070.0000.0000.0000.000
165A179ASP-1-0.862-0.92429.018-0.185-0.1850.0000.0000.0000.000
166A180LEU00.007-0.01224.3490.0010.0010.0000.0000.0000.000
167A181ILE0-0.0030.01722.232-0.011-0.0110.0000.0000.0000.000
168A182GLN0-0.073-0.03724.9610.0210.0210.0000.0000.0000.000
169A183HIS0-0.072-0.02725.3930.0110.0110.0000.0000.0000.000
170A184GLY0-0.041-0.02222.348-0.016-0.0160.0000.0000.0000.000
171A185ILE0-0.034-0.01420.075-0.032-0.0320.0000.0000.0000.000
172A186ARG10.7680.88215.3760.5150.5150.0000.0000.0000.000
173A187VAL00.0150.00219.528-0.056-0.0560.0000.0000.0000.000
174A188ASN0-0.019-0.01918.7140.0820.0820.0000.0000.0000.000
175A189SER0-0.021-0.01421.223-0.028-0.0280.0000.0000.0000.000
176A190ILE00.0180.01917.0620.0060.0060.0000.0000.0000.000
177A191SER0-0.002-0.00621.718-0.003-0.0030.0000.0000.0000.000
178A192PRO0-0.0040.00922.0670.0220.0220.0000.0000.0000.000
179A193GLY00.023-0.00223.9300.0220.0220.0000.0000.0000.000
180A194LEU0-0.017-0.00126.187-0.016-0.0160.0000.0000.0000.000
181A195VAL0-0.001-0.00521.736-0.006-0.0060.0000.0000.0000.000
182A196ALA00.0020.00024.2910.0130.0130.0000.0000.0000.000
183A197THR0-0.016-0.03121.915-0.034-0.0340.0000.0000.0000.000
184A198GLY00.0000.01121.468-0.049-0.0490.0000.0000.0000.000
185A213PHE00.0390.00833.4800.0020.0020.0000.0000.0000.000
186A214TYR00.0610.01637.526-0.004-0.0040.0000.0000.0000.000
187A215SER00.0500.03438.920-0.001-0.0010.0000.0000.0000.000
188A216THR00.0240.01835.3060.0010.0010.0000.0000.0000.000
189A217MET0-0.004-0.00230.891-0.008-0.0080.0000.0000.0000.000
190A218ALA0-0.0080.00135.023-0.002-0.0020.0000.0000.0000.000
191A219THR00.0380.00337.0950.0000.0000.0000.0000.0000.000
192A220MET0-0.061-0.01329.027-0.002-0.0020.0000.0000.0000.000
193A221LYS10.8420.89130.3050.0920.0920.0000.0000.0000.000
194A222GLU-1-0.960-0.96033.795-0.083-0.0830.0000.0000.0000.000
195A223CYS0-0.031-0.01133.936-0.001-0.0010.0000.0000.0000.000
196A224VAL0-0.0390.00027.721-0.011-0.0110.0000.0000.0000.000
197A225PRO00.0500.03530.7300.0040.0040.0000.0000.0000.000
198A226ALA0-0.0200.00125.7970.0090.0090.0000.0000.0000.000
199A227GLY0-0.019-0.00327.4690.0040.0040.0000.0000.0000.000
200A228VAL0-0.026-0.01523.9620.0080.0080.0000.0000.0000.000
201A229MET0-0.0030.01225.908-0.008-0.0080.0000.0000.0000.000
202A230GLY00.0810.05222.641-0.006-0.0060.0000.0000.0000.000
203A231GLN0-0.008-0.01018.758-0.002-0.0020.0000.0000.0000.000
204A232PRO0-0.013-0.02018.065-0.032-0.0320.0000.0000.0000.000
205A233GLN00.0480.00514.210-0.023-0.0230.0000.0000.0000.000
206A234ASP-1-0.803-0.88614.426-0.437-0.4370.0000.0000.0000.000
207A235ILE0-0.025-0.01916.155-0.022-0.0220.0000.0000.0000.000
208A236ALA00.0010.01312.490-0.038-0.0380.0000.0000.0000.000
209A237GLU-1-0.765-0.8809.089-1.440-1.4400.0000.0000.0000.000
210A238VAL0-0.0240.00512.307-0.009-0.0090.0000.0000.0000.000
211A239ILE0-0.015-0.01712.9910.0190.0190.0000.0000.0000.000
212A240ALA0-0.001-0.0048.548-0.058-0.0580.0000.0000.0000.000
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