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: V54G1

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 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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2431912.33063
FMO2-HF: Nuclear repulsion 2350571.190421
FMO2-HF: Total energy -81341.140208
FMO2-MP2: Total energy -81578.554042


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.
-60.778-58.59710.045-6.358-5.8690.061
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 : -0.901 / q_NPA : -0.954
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].
3A9ILE0-0.076-0.0263.350-10.707-7.6480.015-1.465-1.6090.005
4A10VAL00.0360.0244.3064.4534.650-0.001-0.027-0.1700.000
5A11VAL0-0.026-0.0226.516-1.504-1.5040.0000.0000.0000.000
6A12ARG10.7920.8658.670-18.630-18.6300.0000.0000.0000.000
7A13GLN00.0040.00512.148-0.881-0.8810.0000.0000.0000.000
8A14VAL0-0.035-0.01115.6720.1470.1470.0000.0000.0000.000
9A15ASP-1-0.812-0.90518.14212.61212.6120.0000.0000.0000.000
10A16VAL00.008-0.01420.964-0.112-0.1120.0000.0000.0000.000
11A17GLY0-0.022-0.00224.031-0.369-0.3690.0000.0000.0000.000
12A18GLU-1-0.835-0.87817.59216.55716.5570.0000.0000.0000.000
13A19THR00.007-0.01321.2820.3900.3900.0000.0000.0000.000
14A20GLU-1-0.903-0.93923.55610.80410.8040.0000.0000.0000.000
15A21GLN00.0180.01019.830-0.251-0.2510.0000.0000.0000.000
16A22LEU00.0090.01218.9210.3850.3850.0000.0000.0000.000
17A23MET00.0090.01420.7820.0970.0970.0000.0000.0000.000
18A24THR0-0.021-0.02922.800-0.282-0.2820.0000.0000.0000.000
19A25PHE0-0.048-0.01516.2870.1390.1390.0000.0000.0000.000
20A26LEU0-0.002-0.00520.9110.0480.0480.0000.0000.0000.000
21A27LEU0-0.012-0.01422.714-0.308-0.3080.0000.0000.0000.000
22A28ALA0-0.054-0.01622.247-0.393-0.3930.0000.0000.0000.000
23A29HIS0-0.036-0.01518.427-0.187-0.1870.0000.0000.0000.000
24A30TYR00.022-0.01920.4680.8460.8460.0000.0000.0000.000
25A31TYR0-0.001-0.03623.062-0.166-0.1660.0000.0000.0000.000
26A32PRO0-0.049-0.00925.250-0.426-0.4260.0000.0000.0000.000
27A33GLU-1-0.914-0.96523.74212.22312.2230.0000.0000.0000.000
28A34GLU-1-0.817-0.87026.73510.37110.3710.0000.0000.0000.000
29A35PRO0-0.011-0.01327.671-0.432-0.4320.0000.0000.0000.000
30A36LEU0-0.003-0.00830.843-0.454-0.4540.0000.0000.0000.000
31A37THR0-0.005-0.01830.649-0.436-0.4360.0000.0000.0000.000
32A38ALA0-0.021-0.01431.578-0.317-0.3170.0000.0000.0000.000
33A39GLY0-0.022-0.00533.459-0.250-0.2500.0000.0000.0000.000
34A40THR0-0.013-0.01735.818-0.241-0.2410.0000.0000.0000.000
35A41HIS00.0190.00137.7850.1330.1330.0000.0000.0000.000
36A42PRO00.0050.01539.531-0.052-0.0520.0000.0000.0000.000
37A43PRO00.0180.02935.7130.1640.1640.0000.0000.0000.000
38A44GLU-1-0.890-0.95533.0959.3669.3660.0000.0000.0000.000
39A45PRO00.0270.01830.062-0.236-0.2360.0000.0000.0000.000
40A46GLU-1-0.766-0.88533.2527.9997.9990.0000.0000.0000.000
41A47ALA0-0.042-0.02333.7030.2700.2700.0000.0000.0000.000
42A48ALA00.0830.03233.3520.2530.2530.0000.0000.0000.000
43A49ASP-1-0.858-0.89530.79910.22310.2230.0000.0000.0000.000
44A50LYS10.8660.91529.084-9.188-9.1880.0000.0000.0000.000
45A51GLU-1-0.929-0.97828.7239.2949.2940.0000.0000.0000.000
46A52PHE00.0240.02429.2580.2610.2610.0000.0000.0000.000
47A53LEU00.0030.01224.9300.4130.4130.0000.0000.0000.000
48A54LEU0-0.001-0.01224.6160.5050.5050.0000.0000.0000.000
49A55SER0-0.071-0.04626.3790.1520.1520.0000.0000.0000.000
50A56ASN0-0.005-0.01624.5930.0170.0170.0000.0000.0000.000
51A57VAL0-0.012-0.01121.6840.4400.4400.0000.0000.0000.000
52A58PRO0-0.009-0.01223.1310.4140.4140.0000.0000.0000.000
53A59PHE0-0.0070.01324.582-0.063-0.0630.0000.0000.0000.000
54A60GLY00.0470.02920.8300.2620.2620.0000.0000.0000.000
55A61THR0-0.037-0.05019.7520.6550.6550.0000.0000.0000.000
56A62CYS0-0.0190.04519.1870.2280.2280.0000.0000.0000.000
57A63PHE0-0.004-0.00813.5700.5090.5090.0000.0000.0000.000
58A64VAL00.0280.01213.546-0.513-0.5130.0000.0000.0000.000
59A65ALA00.0040.0069.0931.8221.8220.0000.0000.0000.000
60A66LEU0-0.024-0.0249.040-2.279-2.2790.0000.0000.0000.000
61A67HIS0-0.006-0.0187.6281.6451.6450.0000.0000.0000.000
62A68GLU-1-0.880-0.9329.76317.33317.3330.0000.0000.0000.000
63A69GLY00.0240.01511.736-1.132-1.1320.0000.0000.0000.000
64A70ARG10.8330.92012.989-20.250-20.2500.0000.0000.0000.000
65A71ILE00.0190.01013.0871.6881.6880.0000.0000.0000.000
66A72VAL0-0.045-0.02710.106-0.582-0.5820.0000.0000.0000.000
67A73ALA0-0.007-0.01512.306-0.025-0.0250.0000.0000.0000.000
68A74ALA00.0350.02214.0050.5680.5680.0000.0000.0000.000
69A75VAL0-0.035-0.01015.543-0.401-0.4010.0000.0000.0000.000
70A76VAL00.0310.01017.8740.1350.1350.0000.0000.0000.000
71A77ALA00.026-0.00520.813-0.253-0.2530.0000.0000.0000.000
72A78GLY00.0590.04922.5030.1280.1280.0000.0000.0000.000
73A79PRO0-0.097-0.03025.2150.0440.0440.0000.0000.0000.000
74A80LYS10.8550.92827.439-10.784-10.7840.0000.0000.0000.000
75A81ASP-1-0.782-0.92730.7219.0629.0620.0000.0000.0000.000
76A82SER0-0.040-0.03533.783-0.088-0.0880.0000.0000.0000.000
77A83HIS0-0.064-0.03437.059-0.204-0.2040.0000.0000.0000.000
78A84GLU-1-0.893-0.94231.7419.7409.7400.0000.0000.0000.000
79A85PRO0-0.036-0.03135.834-0.071-0.0710.0000.0000.0000.000
80A86GLU-1-0.914-0.93038.5947.3617.3610.0000.0000.0000.000
81A87HIS00.0150.00135.572-0.273-0.2730.0000.0000.0000.000
82A88MET00.003-0.00233.876-0.028-0.0280.0000.0000.0000.000
83A89ALA00.0290.02737.723-0.100-0.1000.0000.0000.0000.000
84A90GLU-1-0.792-0.85741.4616.8596.8590.0000.0000.0000.000
85A91GLU-1-0.822-0.90336.5258.3178.3170.0000.0000.0000.000
86A92ALA00.011-0.00639.744-0.078-0.0780.0000.0000.0000.000
87A93ARG10.7230.81641.017-6.996-6.9960.0000.0000.0000.000
88A94LYS10.7520.87138.784-8.237-8.2370.0000.0000.0000.000
89A95TYR0-0.0040.00138.093-0.051-0.0510.0000.0000.0000.000
90A96ALA00.0110.02442.3480.0360.0360.0000.0000.0000.000
91A97GLY0-0.061-0.02544.605-0.130-0.1300.0000.0000.0000.000
92A98GLY00.0220.00642.112-0.060-0.0600.0000.0000.0000.000
93A99LYS10.7580.87934.389-8.857-8.8570.0000.0000.0000.000
94A100TRP00.0350.00831.7430.1420.1420.0000.0000.0000.000
95A101GLY00.0540.02437.2810.0820.0820.0000.0000.0000.000
96A102SER0-0.049-0.02939.343-0.083-0.0830.0000.0000.0000.000
97A103ILE0-0.015-0.01533.0910.0140.0140.0000.0000.0000.000
98A104LEU0-0.0070.00435.1130.1250.1250.0000.0000.0000.000
99A105HIS0-0.038-0.01637.099-0.172-0.1720.0000.0000.0000.000
100A106LEU0-0.029-0.00834.167-0.032-0.0320.0000.0000.0000.000
101A107LEU00.023-0.00331.3290.0360.0360.0000.0000.0000.000
102A108SER00.0630.03535.0660.0750.0750.0000.0000.0000.000
103A109ALA0-0.042-0.00437.871-0.104-0.1040.0000.0000.0000.000
104A110VAL0-0.011-0.00932.633-0.067-0.0670.0000.0000.0000.000
105A111GLU-1-0.773-0.85832.7659.9609.9600.0000.0000.0000.000
106A112THR0-0.018-0.02435.669-0.115-0.1150.0000.0000.0000.000
107A113ALA0-0.051-0.01037.704-0.134-0.1340.0000.0000.0000.000
108A114THR0-0.104-0.07833.3240.0920.0920.0000.0000.0000.000
109A115ASP-1-0.825-0.92535.9508.6128.6120.0000.0000.0000.000
110A116VAL00.023-0.00530.517-0.062-0.0620.0000.0000.0000.000
111A117CYS0-0.0130.02433.2010.1440.1440.0000.0000.0000.000
112A118ARG10.9080.95734.733-8.325-8.3250.0000.0000.0000.000
113A119ARG10.8130.91735.600-8.832-8.8320.0000.0000.0000.000
114A120PHE0-0.005-0.01631.9210.0290.0290.0000.0000.0000.000
115A121SER0-0.049-0.01435.060-0.014-0.0140.0000.0000.0000.000
116A122VAL0-0.031-0.00430.4540.0730.0730.0000.0000.0000.000
117A123PRO0-0.022-0.00832.274-0.151-0.1510.0000.0000.0000.000
118A124SER0-0.005-0.02528.955-0.215-0.2150.0000.0000.0000.000
119A125CYS0-0.048-0.01027.6890.2760.2760.0000.0000.0000.000
120A126LEU0-0.0280.00520.577-0.120-0.1200.0000.0000.0000.000
121A127HIS00.0510.04224.7170.4230.4230.0000.0000.0000.000
122A128VAL0-0.035-0.03620.5540.3330.3330.0000.0000.0000.000
123A129HIS00.0450.02023.368-0.332-0.3320.0000.0000.0000.000
124A130ALA00.0000.00822.984-0.329-0.3290.0000.0000.0000.000
125A131LEU0-0.051-0.03415.8920.8430.8430.0000.0000.0000.000
126A132GLY00.0450.04218.504-0.566-0.5660.0000.0000.0000.000
127A133VAL0-0.081-0.06513.5181.4721.4720.0000.0000.0000.000
128A134ASP-1-0.780-0.88214.44516.43416.4340.0000.0000.0000.000
129A135PRO0-0.020-0.01014.6621.3211.3210.0000.0000.0000.000
130A136GLN0-0.033-0.02315.8060.0040.0040.0000.0000.0000.000
131A137LEU0-0.020-0.0019.1390.6090.6090.0000.0000.0000.000
132A138ARG10.9700.97610.923-14.841-14.8410.0000.0000.0000.000
133A139GLY0-0.009-0.00310.4910.6170.6170.0000.0000.0000.000
134A140ARG10.8250.8815.230-33.537-33.5370.0000.0000.0000.000
135A141ASN00.0070.0026.8730.7750.7750.0000.0000.0000.000
136A142LEU00.0400.0347.9960.7390.7390.0000.0000.0000.000
137A143GLY00.0900.04210.040-0.162-0.1620.0000.0000.0000.000
138A144GLY0-0.0010.00111.875-0.913-0.9130.0000.0000.0000.000
139A145ARG10.8540.9111.996-86.050-87.12510.031-4.866-4.0900.056
140A146LEU00.0170.0289.726-0.525-0.5250.0000.0000.0000.000
141A147MET00.0100.00812.621-1.196-1.1960.0000.0000.0000.000
142A148GLU-1-0.837-0.92512.09820.26720.2670.0000.0000.0000.000
143A149THR0-0.055-0.02611.0750.1400.1400.0000.0000.0000.000
144A150VAL0-0.001-0.00113.325-1.021-1.0210.0000.0000.0000.000
145A151ALA00.0100.01216.805-0.970-0.9700.0000.0000.0000.000
146A152GLN0-0.038-0.02214.434-0.375-0.3750.0000.0000.0000.000
147A153ARG10.8700.93316.691-15.947-15.9470.0000.0000.0000.000
148A154GLY00.0320.00118.377-0.930-0.9300.0000.0000.0000.000
149A155ARG10.8040.88315.687-20.109-20.1090.0000.0000.0000.000
150A156ASP-1-0.893-0.93917.65317.70317.7030.0000.0000.0000.000
151A157LEU0-0.093-0.04621.013-0.595-0.5950.0000.0000.0000.000
152A158GLY0-0.0060.01324.015-0.611-0.6110.0000.0000.0000.000
153A159HIS00.0040.01924.059-0.687-0.6870.0000.0000.0000.000
154A160GLN00.024-0.00525.1640.2560.2560.0000.0000.0000.000
155A161LEU0-0.033-0.00726.4100.0440.0440.0000.0000.0000.000
156A162VAL00.0310.02121.2550.1390.1390.0000.0000.0000.000
157A163SER0-0.010-0.04624.553-0.336-0.3360.0000.0000.0000.000
158A164VAL00.0070.00122.4090.3140.3140.0000.0000.0000.000
159A165ASP-1-0.737-0.85025.50010.60310.6030.0000.0000.0000.000
160A166CYS0-0.084-0.02924.3500.3730.3730.0000.0000.0000.000
161A167THR00.0720.03726.320-0.468-0.4680.0000.0000.0000.000
162A168SER00.0190.00824.152-0.037-0.0370.0000.0000.0000.000
163A169VAL00.0450.00925.1520.3010.3010.0000.0000.0000.000
164A170TYR0-0.0020.00316.0260.6710.6710.0000.0000.0000.000
165A171SER00.0600.03520.6940.4890.4890.0000.0000.0000.000
166A172ALA00.0840.03921.6970.4060.4060.0000.0000.0000.000
167A173ARG10.8450.90821.209-12.592-12.5920.0000.0000.0000.000
168A174LEU0-0.048-0.02615.0020.5770.5770.0000.0000.0000.000
169A175VAL00.0490.01918.4030.7210.7210.0000.0000.0000.000
170A176GLN00.0640.05120.6060.1820.1820.0000.0000.0000.000
171A177ARG10.8320.91712.843-21.423-21.4230.0000.0000.0000.000
172A178LEU0-0.041-0.02414.4011.2571.2570.0000.0000.0000.000
173A179GLY00.0090.01318.466-0.058-0.0580.0000.0000.0000.000
174A180TYR0-0.0020.00419.152-0.722-0.7220.0000.0000.0000.000
175A181GLN0-0.032-0.02823.808-0.258-0.2580.0000.0000.0000.000
176A182LEU0-0.052-0.01827.5970.0660.0660.0000.0000.0000.000
177A183ILE00.0130.00829.784-0.358-0.3580.0000.0000.0000.000
178A184ASN0-0.007-0.01032.331-0.348-0.3480.0000.0000.0000.000
179A185THR0-0.038-0.02332.6950.4110.4110.0000.0000.0000.000
180A186LEU00.0370.04534.758-0.280-0.2800.0000.0000.0000.000
181A187ARG10.7930.84435.859-7.645-7.6450.0000.0000.0000.000
182A188TYR0-0.009-0.01231.541-0.193-0.1930.0000.0000.0000.000
183A189VAL0-0.046-0.02838.387-0.173-0.1730.0000.0000.0000.000
184A190ASP-1-0.800-0.86341.0097.4987.4980.0000.0000.0000.000
185A191HIS0-0.0140.00940.004-0.053-0.0530.0000.0000.0000.000
186A192LEU0-0.016-0.00442.0580.0200.0200.0000.0000.0000.000
187A193ASP-1-0.736-0.85845.2676.6526.6520.0000.0000.0000.000
188A194ALA0-0.016-0.00646.804-0.092-0.0920.0000.0000.0000.000
189A195SER0-0.080-0.05750.234-0.189-0.1890.0000.0000.0000.000
190A196GLY0-0.032-0.00749.914-0.100-0.1000.0000.0000.0000.000
191A197GLN0-0.080-0.05247.7580.0590.0590.0000.0000.0000.000
192A198GLN0-0.014-0.00540.404-0.084-0.0840.0000.0000.0000.000
193A199VAL00.0100.00940.5550.0100.0100.0000.0000.0000.000
194A200ILE00.0040.01535.5590.0980.0980.0000.0000.0000.000
195A201ARG10.8340.89638.609-7.295-7.2950.0000.0000.0000.000
196A202PRO00.0490.04033.906-0.062-0.0620.0000.0000.0000.000
197A203PRO00.0040.01532.779-0.204-0.2040.0000.0000.0000.000
198A204PRO00.010-0.00533.7860.2320.2320.0000.0000.0000.000
199A205PRO0-0.054-0.02430.1120.1370.1370.0000.0000.0000.000
200A206HIS0-0.020-0.02428.9430.3770.3770.0000.0000.0000.000
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