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: YZ2G2

Calculation Name: 5K9N-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 5K9N

Chain ID: A

ChEMBL ID:
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UniProt ID: Q9W469

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 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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2424945.533008
FMO2-HF: Nuclear repulsion 2343604.876722
FMO2-HF: Total energy -81340.656286
FMO2-MP2: Total energy -81578.106427


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:7:ASP)


Summations of interaction energy for fragment #1(A:7:ASP)
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.
-32.56-27.6310.022-2.432-2.520.011
Interaction energy analysis for fragmet #1(A:7:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.930 / q_NPA : -0.977
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].
3A9ILE0-0.073-0.0243.429-10.569-7.416-0.012-1.510-1.6310.002
4A10VAL00.0220.0144.5204.0074.108-0.001-0.011-0.0890.000
5A11VAL0-0.026-0.0077.131-2.581-2.5810.0000.0000.0000.000
6A12ARG10.8280.8939.134-18.023-18.0230.0000.0000.0000.000
7A13GLN0-0.013-0.00512.490-1.110-1.1100.0000.0000.0000.000
8A14VAL0-0.023-0.00916.0550.0360.0360.0000.0000.0000.000
9A15ASP-1-0.815-0.91318.57012.80012.8000.0000.0000.0000.000
10A16VAL0-0.020-0.02621.470-0.192-0.1920.0000.0000.0000.000
11A17GLY0-0.017-0.00324.433-0.380-0.3800.0000.0000.0000.000
12A18GLU-1-0.883-0.90617.99216.17216.1720.0000.0000.0000.000
13A19THR00.0430.00921.5170.3910.3910.0000.0000.0000.000
14A20GLU-1-0.899-0.93423.72210.74610.7460.0000.0000.0000.000
15A21GLN00.0230.00820.637-0.285-0.2850.0000.0000.0000.000
16A22LEU00.0190.01719.2200.3910.3910.0000.0000.0000.000
17A23MET0-0.0010.00221.2060.0540.0540.0000.0000.0000.000
18A24THR0-0.033-0.03923.318-0.244-0.2440.0000.0000.0000.000
19A25PHE0-0.046-0.01717.2510.0190.0190.0000.0000.0000.000
20A26LEU00.0150.01321.375-0.017-0.0170.0000.0000.0000.000
21A27LEU0-0.011-0.01523.250-0.264-0.2640.0000.0000.0000.000
22A28ALA0-0.039-0.01022.759-0.318-0.3180.0000.0000.0000.000
23A29HIS0-0.035-0.02219.556-0.270-0.2700.0000.0000.0000.000
24A30TYR0-0.025-0.02621.7540.6630.6630.0000.0000.0000.000
25A31TYR0-0.026-0.05923.806-0.128-0.1280.0000.0000.0000.000
26A32PRO0-0.0290.01226.089-0.360-0.3600.0000.0000.0000.000
27A33GLU-1-0.922-0.97325.15311.83011.8300.0000.0000.0000.000
28A34GLU-1-0.814-0.87027.54310.20110.2010.0000.0000.0000.000
29A35PRO00.001-0.00928.749-0.400-0.4000.0000.0000.0000.000
30A36LEU0-0.011-0.01331.584-0.462-0.4620.0000.0000.0000.000
31A37THR0-0.032-0.03930.993-0.378-0.3780.0000.0000.0000.000
32A38ALA00.0020.00832.878-0.298-0.2980.0000.0000.0000.000
33A39GLY0-0.028-0.01234.589-0.250-0.2500.0000.0000.0000.000
34A40THR0-0.0030.00436.676-0.259-0.2590.0000.0000.0000.000
35A41HIS00.017-0.01338.4210.1770.1770.0000.0000.0000.000
36A42PRO00.0240.03139.898-0.057-0.0570.0000.0000.0000.000
37A43PRO0-0.0050.02736.6700.1570.1570.0000.0000.0000.000
38A44GLU-1-0.942-0.98334.0979.0709.0700.0000.0000.0000.000
39A45PRO0-0.0050.00930.621-0.214-0.2140.0000.0000.0000.000
40A46GLU-1-0.776-0.90333.6477.9087.9080.0000.0000.0000.000
41A47ALA0-0.016-0.02233.9150.2880.2880.0000.0000.0000.000
42A48ALA00.0720.03333.7630.2070.2070.0000.0000.0000.000
43A49ASP-1-0.862-0.88830.97510.10910.1090.0000.0000.0000.000
44A50LYS10.9100.93029.319-9.200-9.2000.0000.0000.0000.000
45A51GLU-1-0.938-0.97529.0699.2389.2380.0000.0000.0000.000
46A52PHE00.0180.02029.6390.1880.1880.0000.0000.0000.000
47A53LEU0-0.0050.00725.3530.4150.4150.0000.0000.0000.000
48A54LEU0-0.003-0.02224.9500.4460.4460.0000.0000.0000.000
49A55SER0-0.064-0.02426.6870.1990.1990.0000.0000.0000.000
50A56ASN00.003-0.01724.886-0.008-0.0080.0000.0000.0000.000
51A57VAL00.003-0.00322.1770.3820.3820.0000.0000.0000.000
52A58PRO0-0.028-0.00823.5910.4190.4190.0000.0000.0000.000
53A59PHE0-0.0090.00924.940-0.080-0.0800.0000.0000.0000.000
54A60GLY00.0330.01421.2630.2450.2450.0000.0000.0000.000
55A61THR0-0.066-0.05719.9800.7540.7540.0000.0000.0000.000
56A62CYS0-0.0200.03619.3160.0430.0430.0000.0000.0000.000
57A63PHE00.0110.00313.7160.5720.5720.0000.0000.0000.000
58A64VAL00.0340.01613.878-0.576-0.5760.0000.0000.0000.000
59A65ALA0-0.003-0.0089.5581.8581.8580.0000.0000.0000.000
60A66LEU0-0.046-0.0279.646-1.744-1.7440.0000.0000.0000.000
61A67HIS0-0.013-0.0118.1891.2871.2870.0000.0000.0000.000
62A68GLU-1-0.826-0.90410.02317.48217.4820.0000.0000.0000.000
63A69GLY0-0.015-0.00511.701-1.458-1.4580.0000.0000.0000.000
64A70ARG10.8660.92413.692-19.793-19.7930.0000.0000.0000.000
65A71ILE00.0000.00113.4141.5891.5890.0000.0000.0000.000
66A72VAL0-0.022-0.01910.789-0.624-0.6240.0000.0000.0000.000
67A73ALA0-0.023-0.02312.761-0.305-0.3050.0000.0000.0000.000
68A74ALA00.0280.01714.4660.5260.5260.0000.0000.0000.000
69A75VAL0-0.031-0.01415.908-0.303-0.3030.0000.0000.0000.000
70A76VAL00.018-0.00118.1550.1540.1540.0000.0000.0000.000
71A77ALA00.0330.00521.130-0.269-0.2690.0000.0000.0000.000
72A78GLY00.0590.04922.7660.1060.1060.0000.0000.0000.000
73A79PRO0-0.083-0.02625.5360.0310.0310.0000.0000.0000.000
74A80LYS10.8700.93027.643-10.563-10.5630.0000.0000.0000.000
75A81ASP-1-0.771-0.93931.0329.0229.0220.0000.0000.0000.000
76A82SER0-0.057-0.02634.124-0.106-0.1060.0000.0000.0000.000
77A83HIS0-0.059-0.03837.339-0.220-0.2200.0000.0000.0000.000
78A84GLU-1-0.908-0.94732.3999.5109.5100.0000.0000.0000.000
79A85PRO0-0.012-0.00736.326-0.094-0.0940.0000.0000.0000.000
80A86GLU-1-0.905-0.93238.8927.3337.3330.0000.0000.0000.000
81A87HIS00.0150.01236.274-0.254-0.2540.0000.0000.0000.000
82A88MET0-0.007-0.01234.709-0.029-0.0290.0000.0000.0000.000
83A89ALA0-0.0070.00238.249-0.111-0.1110.0000.0000.0000.000
84A90GLU-1-0.782-0.86441.9206.7856.7850.0000.0000.0000.000
85A91GLU-1-0.845-0.92937.1178.2398.2390.0000.0000.0000.000
86A92ALA00.002-0.00440.421-0.043-0.0430.0000.0000.0000.000
87A93ARG10.7250.83341.578-6.919-6.9190.0000.0000.0000.000
88A94LYS10.7750.88339.579-8.037-8.0370.0000.0000.0000.000
89A95TYR0-0.004-0.00738.685-0.095-0.0950.0000.0000.0000.000
90A96ALA0-0.0120.02742.9200.0380.0380.0000.0000.0000.000
91A97GLY0-0.002-0.01145.025-0.097-0.0970.0000.0000.0000.000
92A98GLY00.0120.00743.082-0.108-0.1080.0000.0000.0000.000
93A99LYS10.7750.86835.137-8.657-8.6570.0000.0000.0000.000
94A100TRP00.0470.01032.2060.1060.1060.0000.0000.0000.000
95A101GLY00.0400.03137.9720.0760.0760.0000.0000.0000.000
96A102SER0-0.046-0.02239.915-0.073-0.0730.0000.0000.0000.000
97A103ILE0-0.014-0.01333.6880.0220.0220.0000.0000.0000.000
98A104LEU00.0100.01135.5960.1160.1160.0000.0000.0000.000
99A105HIS0-0.053-0.01537.618-0.154-0.1540.0000.0000.0000.000
100A106LEU0-0.028-0.01535.143-0.036-0.0360.0000.0000.0000.000
101A107LEU00.031-0.00131.8490.0470.0470.0000.0000.0000.000
102A108SER00.0330.02635.5490.1200.1200.0000.0000.0000.000
103A109ALA00.0030.00738.259-0.050-0.0500.0000.0000.0000.000
104A110VAL0-0.007-0.00233.236-0.054-0.0540.0000.0000.0000.000
105A111GLU-1-0.802-0.86733.1269.7879.7870.0000.0000.0000.000
106A112THR0-0.020-0.03035.908-0.111-0.1110.0000.0000.0000.000
107A113ALA0-0.035-0.00138.371-0.110-0.1100.0000.0000.0000.000
108A114THR0-0.111-0.07933.6500.0500.0500.0000.0000.0000.000
109A115ASP-1-0.858-0.92736.1568.4408.4400.0000.0000.0000.000
110A116VAL00.043-0.00530.890-0.067-0.0670.0000.0000.0000.000
111A117CYS0-0.0290.02433.1170.0840.0840.0000.0000.0000.000
112A118ARG10.9540.98134.870-8.192-8.1920.0000.0000.0000.000
113A119ARG10.8090.92736.082-8.751-8.7510.0000.0000.0000.000
114A120PHE0-0.015-0.03132.647-0.012-0.0120.0000.0000.0000.000
115A121SER0-0.070-0.01435.0690.0080.0080.0000.0000.0000.000
116A122VAL0-0.015-0.01330.7660.1140.1140.0000.0000.0000.000
117A123PRO0-0.034-0.01432.396-0.192-0.1920.0000.0000.0000.000
118A124SER00.000-0.03029.220-0.185-0.1850.0000.0000.0000.000
119A125CYS0-0.077-0.02028.0930.3030.3030.0000.0000.0000.000
120A126LEU0-0.0080.01120.968-0.088-0.0880.0000.0000.0000.000
121A127HIS00.0520.05324.9670.3490.3490.0000.0000.0000.000
122A128VAL0-0.025-0.04320.7480.2890.2890.0000.0000.0000.000
123A129HIS00.0280.01023.513-0.326-0.3260.0000.0000.0000.000
124A130ALA00.0120.01723.068-0.259-0.2590.0000.0000.0000.000
125A131LEU0-0.048-0.02216.2670.8510.8510.0000.0000.0000.000
126A132GLY00.0510.03418.734-0.618-0.6180.0000.0000.0000.000
127A133VAL0-0.079-0.06114.5711.3661.3660.0000.0000.0000.000
128A134ASP-1-0.753-0.86715.64115.57915.5790.0000.0000.0000.000
129A135PRO0-0.017-0.01415.5921.2501.2500.0000.0000.0000.000
130A136GLN0-0.058-0.02916.9330.1160.1160.0000.0000.0000.000
131A137LEU0-0.0110.00510.3130.7050.7050.0000.0000.0000.000
132A138ARG10.9660.97512.047-14.565-14.5650.0000.0000.0000.000
133A139GLY0-0.009-0.00911.1200.4760.4760.0000.0000.0000.000
134A140ARG10.8680.9246.317-31.345-31.3450.0000.0000.0000.000
135A141ASN0-0.024-0.0157.9750.2000.2000.0000.0000.0000.000
136A142LEU00.0590.0339.0840.9230.9230.0000.0000.0000.000
137A143GLY00.0770.04011.171-0.145-0.1450.0000.0000.0000.000
138A144GLY00.0080.00713.098-0.528-0.5280.0000.0000.0000.000
139A145ARG10.9430.9713.247-59.050-57.3750.035-0.911-0.8000.009
140A146LEU00.0080.03010.510-0.149-0.1490.0000.0000.0000.000
141A147MET00.0230.00512.981-0.941-0.9410.0000.0000.0000.000
142A148GLU-1-0.915-0.96812.25420.80420.8040.0000.0000.0000.000
143A149THR0-0.064-0.04111.4240.2940.2940.0000.0000.0000.000
144A150VAL0-0.014-0.01013.626-0.850-0.8500.0000.0000.0000.000
145A151ALA00.0130.01716.969-0.940-0.9400.0000.0000.0000.000
146A152GLN0-0.008-0.00814.271-0.478-0.4780.0000.0000.0000.000
147A153ARG10.8760.94916.832-15.907-15.9070.0000.0000.0000.000
148A154GLY00.025-0.00518.346-0.883-0.8830.0000.0000.0000.000
149A155ARG10.8780.93016.106-19.232-19.2320.0000.0000.0000.000
150A156ASP-1-0.899-0.94017.95617.44417.4440.0000.0000.0000.000
151A157LEU0-0.095-0.05521.020-0.647-0.6470.0000.0000.0000.000
152A158GLY00.0050.02323.932-0.595-0.5950.0000.0000.0000.000
153A159HIS00.0090.02124.374-0.668-0.6680.0000.0000.0000.000
154A160GLN00.020-0.00525.4820.1700.1700.0000.0000.0000.000
155A161LEU0-0.026-0.00726.5740.0030.0030.0000.0000.0000.000
156A162VAL00.0260.01721.3900.2060.2060.0000.0000.0000.000
157A163SER0-0.009-0.04224.696-0.289-0.2890.0000.0000.0000.000
158A164VAL00.0030.00522.9870.3680.3680.0000.0000.0000.000
159A165ASP-1-0.756-0.86125.82710.32810.3280.0000.0000.0000.000
160A166CYS0-0.110-0.04025.1870.3960.3960.0000.0000.0000.000
161A167THR00.0990.04326.999-0.486-0.4860.0000.0000.0000.000
162A168SER00.0330.01925.133-0.104-0.1040.0000.0000.0000.000
163A169VAL00.0510.00825.5910.2180.2180.0000.0000.0000.000
164A170TYR00.0080.00216.7560.6650.6650.0000.0000.0000.000
165A171SER00.0280.02021.7230.4060.4060.0000.0000.0000.000
166A172ALA00.0830.03922.6460.3380.3380.0000.0000.0000.000
167A173ARG10.8400.91921.604-12.308-12.3080.0000.0000.0000.000
168A174LEU0-0.022-0.02215.9440.4770.4770.0000.0000.0000.000
169A175VAL00.0580.02319.4270.5930.5930.0000.0000.0000.000
170A176GLN00.0520.04121.5100.1790.1790.0000.0000.0000.000
171A177ARG10.8530.92913.656-20.370-20.3700.0000.0000.0000.000
172A178LEU0-0.070-0.02315.1640.8550.8550.0000.0000.0000.000
173A179GLY0-0.0020.00319.111-0.001-0.0010.0000.0000.0000.000
174A180TYR0-0.016-0.01019.686-0.554-0.5540.0000.0000.0000.000
175A181GLN0-0.040-0.02824.692-0.299-0.2990.0000.0000.0000.000
176A182LEU0-0.040-0.00828.4600.0130.0130.0000.0000.0000.000
177A183ILE00.0100.00130.616-0.309-0.3090.0000.0000.0000.000
178A184ASN0-0.018-0.01433.327-0.328-0.3280.0000.0000.0000.000
179A185THR0-0.018-0.01333.7180.3710.3710.0000.0000.0000.000
180A186LEU00.0440.04735.759-0.268-0.2680.0000.0000.0000.000
181A187ARG10.8490.88136.818-7.448-7.4480.0000.0000.0000.000
182A188TYR00.0280.01932.662-0.190-0.1900.0000.0000.0000.000
183A189VAL0-0.044-0.02639.411-0.165-0.1650.0000.0000.0000.000
184A190ASP-1-0.814-0.87141.9497.3437.3430.0000.0000.0000.000
185A191HIS0-0.0030.01140.761-0.047-0.0470.0000.0000.0000.000
186A192LEU0-0.029-0.00643.0420.0190.0190.0000.0000.0000.000
187A193ASP-1-0.723-0.86645.8676.5916.5910.0000.0000.0000.000
188A194ALA0-0.0100.00747.295-0.103-0.1030.0000.0000.0000.000
189A195SER0-0.083-0.06150.532-0.180-0.1800.0000.0000.0000.000
190A196GLY0-0.047-0.02550.385-0.115-0.1150.0000.0000.0000.000
191A197GLN0-0.071-0.03948.6180.0660.0660.0000.0000.0000.000
192A198GLN0-0.028-0.01241.334-0.073-0.0730.0000.0000.0000.000
193A199VAL00.0000.01440.913-0.013-0.0130.0000.0000.0000.000
194A200ILE00.0100.01236.2240.0600.0600.0000.0000.0000.000
195A201ARG10.8620.91239.678-7.171-7.1710.0000.0000.0000.000
196A202PRO00.0280.03934.677-0.053-0.0530.0000.0000.0000.000
197A203PRO00.0020.00834.013-0.179-0.1790.0000.0000.0000.000
198A204PRO00.0090.00935.1850.1740.1740.0000.0000.0000.000
199A205PRO0-0.063-0.03531.2060.1110.1110.0000.0000.0000.000
200A206HIS00.006-0.01129.7280.4320.4320.0000.0000.0000.000
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