FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 5J5JZ

Calculation Name: 2GK9-C-Xray372

Preferred Name: Phosphatidylinositol-5-phosphate 4-kinase type-2 gamma

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2GK9

Chain ID: C

ChEMBL ID: CHEMBL1770034

UniProt ID: Q8TBX8

Base Structure: X-ray

Registration Date: 2023-09-23

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 252
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3496436.092802
FMO2-HF: Nuclear repulsion 3391789.983269
FMO2-HF: Total energy -104646.109533
FMO2-MP2: Total energy -104950.902553


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(C:45:ASP)


Summations of interaction energy for fragment #1(C:45: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.
-18.509-7.33220.116-14.188-17.1050.123
Interaction energy analysis for fragmet #1(C:45:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.789 / q_NPA : -0.914
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].
3C47LEU00.0490.0122.036-33.882-27.8185.358-4.894-6.5280.062
4C48VAL00.0510.0231.898-26.875-28.42113.789-5.567-6.6750.062
5C49GLY00.003-0.0172.727-19.592-15.4840.413-2.384-2.1370.013
6C50VAL0-0.041-0.0133.350-8.252-7.8670.023-0.014-0.395-0.001
7C51PHE00.0210.0126.446-5.754-5.7540.0000.0000.0000.000
8C52LEU0-0.0220.0105.399-4.170-4.1700.0000.0000.0000.000
9C53TRP0-0.020-0.0137.286-3.221-3.2210.0000.0000.0000.000
10C54GLY0-0.023-0.0298.981-2.316-2.3160.0000.0000.0000.000
11C55VAL00.0160.00511.245-1.891-1.8910.0000.0000.0000.000
12C56ALA00.0470.05212.243-1.644-1.6440.0000.0000.0000.000
13C57HIS00.0020.00713.368-0.807-0.8070.0000.0000.0000.000
14C58SER0-0.074-0.05915.218-0.831-0.8310.0000.0000.0000.000
15C59ILE00.0270.00016.647-1.016-1.0160.0000.0000.0000.000
16C60ASN0-0.040-0.04516.689-0.052-0.0520.0000.0000.0000.000
17C61GLU-1-0.895-0.93819.29612.72812.7280.0000.0000.0000.000
18C62LEU00.0030.00120.929-0.829-0.8290.0000.0000.0000.000
19C63SER0-0.093-0.05622.419-0.591-0.5910.0000.0000.0000.000
20C64GLN0-0.075-0.01724.224-0.395-0.3950.0000.0000.0000.000
21C65VAL00.0020.00926.243-0.312-0.3120.0000.0000.0000.000
22C66PRO00.0030.02128.0240.1610.1610.0000.0000.0000.000
23C67PRO00.0290.00329.4740.0880.0880.0000.0000.0000.000
24C68PRO0-0.0180.00430.290-0.341-0.3410.0000.0000.0000.000
25C69VAL00.0160.00333.5480.0470.0470.0000.0000.0000.000
26C70MET0-0.042-0.02236.129-0.088-0.0880.0000.0000.0000.000
27C71LEU00.0130.01430.0990.1100.1100.0000.0000.0000.000
28C72LEU0-0.026-0.01633.437-0.322-0.3220.0000.0000.0000.000
29C73PRO00.0450.01132.5800.3230.3230.0000.0000.0000.000
30C74ASP-1-0.855-0.95731.4309.8499.8490.0000.0000.0000.000
31C75ASP-1-0.819-0.91329.19710.55310.5530.0000.0000.0000.000
32C76PHE0-0.014-0.04627.5740.4830.4830.0000.0000.0000.000
33C77LYS10.8260.94727.235-9.322-9.3220.0000.0000.0000.000
34C78ALA00.0210.02925.9410.1070.1070.0000.0000.0000.000
35C79SER0-0.073-0.06021.8390.7610.7610.0000.0000.0000.000
36C80SER00.0500.02420.095-0.326-0.3260.0000.0000.0000.000
37C81LYS10.9120.97118.015-14.425-14.4250.0000.0000.0000.000
38C82ILE00.0550.04615.167-0.750-0.7500.0000.0000.0000.000
39C83LYS10.8870.92215.605-14.285-14.2850.0000.0000.0000.000
40C84VAL00.0370.04413.570-1.035-1.0350.0000.0000.0000.000
41C85ASN0-0.017-0.01114.6750.9470.9470.0000.0000.0000.000
42C86ASN00.0080.01712.345-1.816-1.8160.0000.0000.0000.000
43C87HIS00.016-0.00315.2381.1561.1560.0000.0000.0000.000
44C88LEU0-0.077-0.04616.498-0.193-0.1930.0000.0000.0000.000
45C89PHE00.0610.02415.047-0.446-0.4460.0000.0000.0000.000
46C90HIS00.0140.0168.9301.3751.3750.0000.0000.0000.000
47C91ARG10.9350.9509.353-19.623-19.6230.0000.0000.0000.000
48C92GLU-1-0.907-0.9346.65625.86325.8630.0000.0000.0000.000
49C93ASN0-0.0010.0092.6751.0011.5480.167-0.158-0.5560.001
50C94LEU0-0.012-0.0112.7371.6923.3110.366-1.171-0.814-0.014
51C95PRO00.0030.0135.225-3.423-3.4230.0000.0000.0000.000
52C96SER00.006-0.0058.112-1.148-1.1480.0000.0000.0000.000
53C97HIS0-0.039-0.03411.442-2.913-2.9130.0000.0000.0000.000
54C98PHE00.0080.0339.4412.0612.0610.0000.0000.0000.000
55C99LYS10.8950.92411.194-20.252-20.2520.0000.0000.0000.000
56C100PHE00.0740.04910.3141.8411.8410.0000.0000.0000.000
57C101LYS10.9000.93213.548-17.383-17.3830.0000.0000.0000.000
58C102GLU-1-0.846-0.92515.83617.08817.0880.0000.0000.0000.000
59C103TYR0-0.076-0.03216.109-1.157-1.1570.0000.0000.0000.000
60C104CYS0-0.0640.00120.628-0.103-0.1030.0000.0000.0000.000
61C105PRO00.0560.03621.364-0.216-0.2160.0000.0000.0000.000
62C106GLN00.0800.03222.7790.0650.0650.0000.0000.0000.000
63C107VAL0-0.0110.01725.426-0.265-0.2650.0000.0000.0000.000
64C108PHE00.0150.00021.410-0.256-0.2560.0000.0000.0000.000
65C109ARG10.8460.89623.366-11.580-11.5800.0000.0000.0000.000
66C110ASN00.0000.00924.245-0.354-0.3540.0000.0000.0000.000
67C111LEU0-0.014-0.01024.664-0.377-0.3770.0000.0000.0000.000
68C112ARG10.8630.95420.152-14.742-14.7420.0000.0000.0000.000
69C113ASP-1-0.870-0.91924.9629.9179.9170.0000.0000.0000.000
70C114ARG10.9520.98528.347-9.982-9.9820.0000.0000.0000.000
71C115PHE0-0.118-0.03825.000-0.315-0.3150.0000.0000.0000.000
72C116GLY00.0330.01227.1650.2100.2100.0000.0000.0000.000
73C117ILE0-0.101-0.06821.7180.2500.2500.0000.0000.0000.000
74C118ASP-1-0.826-0.90724.46111.95811.9580.0000.0000.0000.000
75C119ASP-1-0.813-0.92321.73413.92613.9260.0000.0000.0000.000
76C120GLN0-0.026-0.00819.3060.7780.7780.0000.0000.0000.000
77C121ASP-1-0.868-0.94820.19913.16213.1620.0000.0000.0000.000
78C122TYR00.001-0.02216.5991.1651.1650.0000.0000.0000.000
79C123LEU00.0300.03413.9371.0761.0760.0000.0000.0000.000
80C124VAL00.0090.04914.4581.4661.4660.0000.0000.0000.000
81C125SER0-0.062-0.04415.6580.3080.3080.0000.0000.0000.000
82C126LEU0-0.079-0.05310.3110.5950.5950.0000.0000.0000.000
83C127THR0-0.046-0.08510.1051.6551.6550.0000.0000.0000.000
84C128ARG10.8910.97110.139-14.616-14.6160.0000.0000.0000.000
85C129ASN0-0.021-0.02811.091-1.313-1.3130.0000.0000.0000.000
86C130PRO00.0180.0166.504-0.130-0.1300.0000.0000.0000.000
87C131PRO00.0130.0096.942-2.129-2.1290.0000.0000.0000.000
88C132SER0-0.058-0.0358.6391.8821.8820.0000.0000.0000.000
89C133GLU-1-0.959-0.9737.42735.09535.0950.0000.0000.0000.000
90C134SER0-0.043-0.0629.759-3.260-3.2600.0000.0000.0000.000
91C135GLU-1-0.858-0.91611.63523.87223.8720.0000.0000.0000.000
92C136GLY00.0180.00713.221-1.329-1.3290.0000.0000.0000.000
93C137SER0-0.088-0.04216.751-1.259-1.2590.0000.0000.0000.000
94C138ASP-1-0.857-0.94218.72216.30416.3040.0000.0000.0000.000
95C139GLY00.0170.01815.896-0.007-0.0070.0000.0000.0000.000
96C140ARG10.9421.0025.782-40.756-40.7560.0000.0000.0000.000
97C141PHE0-0.079-0.05311.1401.9791.9790.0000.0000.0000.000
98C142LEU0-0.0080.0027.5001.9741.9740.0000.0000.0000.000
99C143ILE0-0.0090.00811.527-0.777-0.7770.0000.0000.0000.000
100C144SER00.0480.02411.9721.1781.1780.0000.0000.0000.000
101C145TYR00.0130.00512.313-0.950-0.9500.0000.0000.0000.000
102C146ASP-1-0.835-0.89613.73415.00615.0060.0000.0000.0000.000
103C147ARG10.8680.93016.081-16.568-16.5680.0000.0000.0000.000
104C148THR00.0110.03017.844-0.475-0.4750.0000.0000.0000.000
105C149LEU0-0.0010.00215.751-0.550-0.5500.0000.0000.0000.000
106C150VAL00.0070.00415.2130.9000.9000.0000.0000.0000.000
107C151ILE00.003-0.00510.450-0.843-0.8430.0000.0000.0000.000
108C152LYS10.9040.96412.465-15.996-15.9960.0000.0000.0000.000
109C153GLU-1-0.925-0.97610.22330.72830.7280.0000.0000.0000.000
110C154VAL0-0.043-0.01912.686-1.545-1.5450.0000.0000.0000.000
111C155SER00.017-0.00814.6790.9720.9720.0000.0000.0000.000
112C156SER00.012-0.03117.1710.1150.1150.0000.0000.0000.000
113C157GLU-1-0.938-0.96818.38812.61512.6150.0000.0000.0000.000
114C158ASP-1-0.718-0.84118.95415.50815.5080.0000.0000.0000.000
115C159ILE0-0.037-0.03716.572-0.270-0.2700.0000.0000.0000.000
116C160ALA0-0.010-0.00120.230-0.532-0.5320.0000.0000.0000.000
117C161ASP-1-0.827-0.89923.75112.39912.3990.0000.0000.0000.000
118C162MET0-0.063-0.03420.579-0.570-0.5700.0000.0000.0000.000
119C163HIS0-0.030-0.04322.0250.0400.0400.0000.0000.0000.000
120C164SER0-0.078-0.06425.226-0.523-0.5230.0000.0000.0000.000
121C165ASN0-0.013-0.02427.580-0.739-0.7390.0000.0000.0000.000
122C166LEU0-0.0160.02224.637-0.317-0.3170.0000.0000.0000.000
123C167SER00.001-0.00827.904-0.230-0.2300.0000.0000.0000.000
124C168ASN0-0.004-0.00331.088-0.348-0.3480.0000.0000.0000.000
125C169TYR00.009-0.01326.417-0.172-0.1720.0000.0000.0000.000
126C170HIS0-0.023-0.00629.668-0.110-0.1100.0000.0000.0000.000
127C171GLN00.016-0.01331.155-0.344-0.3440.0000.0000.0000.000
128C172TYR0-0.050-0.02332.904-0.479-0.4790.0000.0000.0000.000
129C173ILE00.0420.02428.085-0.210-0.2100.0000.0000.0000.000
130C174VAL0-0.041-0.00132.696-0.124-0.1240.0000.0000.0000.000
131C175LYS10.9530.97335.412-8.263-8.2630.0000.0000.0000.000
132C176CYS0-0.126-0.01434.176-0.165-0.1650.0000.0000.0000.000
133C177HIS0-0.069-0.04135.212-0.131-0.1310.0000.0000.0000.000
134C178GLY00.0680.06830.9850.0970.0970.0000.0000.0000.000
135C179ASN0-0.022-0.02431.0470.2660.2660.0000.0000.0000.000
136C180THR00.004-0.03931.177-0.273-0.2730.0000.0000.0000.000
137C181LEU0-0.048-0.01530.5130.2630.2630.0000.0000.0000.000
138C182LEU0-0.035-0.00128.8270.2170.2170.0000.0000.0000.000
139C183PRO00.0410.02923.453-0.005-0.0050.0000.0000.0000.000
140C184GLN00.0410.04024.4990.0980.0980.0000.0000.0000.000
141C185PHE0-0.0070.00121.3150.5560.5560.0000.0000.0000.000
142C186LEU0-0.001-0.00419.000-0.464-0.4640.0000.0000.0000.000
143C187GLY00.0560.01317.619-0.375-0.3750.0000.0000.0000.000
144C188MET00.0400.04016.3690.6140.6140.0000.0000.0000.000
145C189TYR00.0320.01912.872-0.767-0.7670.0000.0000.0000.000
146C190ARG10.9170.96512.877-20.056-20.0560.0000.0000.0000.000
147C191VAL0-0.036-0.0046.950-2.090-2.0900.0000.0000.0000.000
148C192SER0-0.028-0.0149.7810.4340.4340.0000.0000.0000.000
149C193VAL0-0.003-0.0166.458-0.429-0.4290.0000.0000.0000.000
150C194ASP-1-0.910-0.9409.40424.85624.8560.0000.0000.0000.000
151C195ASN0-0.091-0.05111.747-1.870-1.8700.0000.0000.0000.000
152C196GLU-1-0.908-0.9419.88324.55024.5500.0000.0000.0000.000
153C197ASP-1-0.990-1.00910.05824.42124.4210.0000.0000.0000.000
154C198SER00.0200.0248.4680.3160.3160.0000.0000.0000.000
155C199TYR0-0.040-0.01910.581-0.171-0.1710.0000.0000.0000.000
156C200MET00.0130.0248.6362.0022.0020.0000.0000.0000.000
157C201LEU00.0280.00312.446-1.440-1.4400.0000.0000.0000.000
158C202VAL0-0.054-0.00314.3230.8490.8490.0000.0000.0000.000
159C203MET00.023-0.00616.389-1.330-1.3300.0000.0000.0000.000
160C204ARG10.8540.91518.764-11.909-11.9090.0000.0000.0000.000
161C205ASN0-0.018-0.03419.576-0.124-0.1240.0000.0000.0000.000
162C206MET00.0030.00221.217-0.395-0.3950.0000.0000.0000.000
163C207PHE0-0.011-0.00822.407-0.605-0.6050.0000.0000.0000.000
164C208SER00.0130.00824.460-0.032-0.0320.0000.0000.0000.000
165C209HIS00.0220.00721.4410.3990.3990.0000.0000.0000.000
166C210ARG10.9560.97322.134-10.768-10.7680.0000.0000.0000.000
167C211LEU0-0.049-0.02524.7030.0810.0810.0000.0000.0000.000
168C212PRO0-0.0010.01524.0200.2300.2300.0000.0000.0000.000
169C213VAL0-0.0180.00825.000-0.471-0.4710.0000.0000.0000.000
170C214HIS0-0.030-0.02326.1670.0950.0950.0000.0000.0000.000
171C215ARG10.9050.95228.493-9.611-9.6110.0000.0000.0000.000
172C216LYS10.9950.99521.815-14.151-14.1510.0000.0000.0000.000
173C217TYR0-0.034-0.01028.419-0.004-0.0040.0000.0000.0000.000
174C218ASP-1-0.872-0.94027.05011.46711.4670.0000.0000.0000.000
175C239THR0-0.018-0.04023.1280.0180.0180.0000.0000.0000.000
176C240LEU0-0.0450.03325.899-0.023-0.0230.0000.0000.0000.000
177C241ARG11.0471.02427.255-11.326-11.3260.0000.0000.0000.000
178C242ASP-1-0.784-0.93130.9048.8148.8140.0000.0000.0000.000
179C243MET0-0.080-0.00734.105-0.139-0.1390.0000.0000.0000.000
180C244ASP-1-0.973-1.01531.8469.6739.6730.0000.0000.0000.000
181C245PHE00.021-0.00133.0670.1280.1280.0000.0000.0000.000
182C246LEU00.0110.00335.561-0.150-0.1500.0000.0000.0000.000
183C247ASN00.0440.03137.501-0.137-0.1370.0000.0000.0000.000
184C248LYS10.8380.93634.194-9.333-9.3330.0000.0000.0000.000
185C249ASN0-0.030-0.02139.875-0.016-0.0160.0000.0000.0000.000
186C250GLN00.0280.00536.1670.1370.1370.0000.0000.0000.000
187C251LYS10.9730.97538.741-8.342-8.3420.0000.0000.0000.000
188C252VAL0-0.0110.00538.7300.2390.2390.0000.0000.0000.000
189C253TYR00.000-0.01840.385-0.159-0.1590.0000.0000.0000.000
190C254ILE0-0.056-0.02337.2280.1450.1450.0000.0000.0000.000
191C255GLY00.0640.02341.382-0.079-0.0790.0000.0000.0000.000
192C256GLU-1-1.013-1.00643.9656.7256.7250.0000.0000.0000.000
193C257GLU-1-0.926-0.98145.3986.8386.8380.0000.0000.0000.000
194C258GLU-1-0.856-0.90040.3867.7597.7590.0000.0000.0000.000
195C259LYS10.9620.98039.253-7.894-7.8940.0000.0000.0000.000
196C260LYS11.0211.00241.423-6.631-6.6310.0000.0000.0000.000
197C261ILE00.0130.01139.465-0.009-0.0090.0000.0000.0000.000
198C262PHE0-0.058-0.03433.7510.1190.1190.0000.0000.0000.000
199C263LEU00.012-0.00337.9590.1940.1940.0000.0000.0000.000
200C264GLU-1-0.953-0.96340.5577.4227.4220.0000.0000.0000.000
201C265LYS10.8410.89933.292-9.393-9.3930.0000.0000.0000.000
202C266LEU00.0640.05035.2680.0830.0830.0000.0000.0000.000
203C267LYS10.9340.90636.968-7.418-7.4180.0000.0000.0000.000
204C268ARG10.9470.96635.904-8.707-8.7070.0000.0000.0000.000
205C269ASP-1-0.798-0.89533.5869.6619.6610.0000.0000.0000.000
206C270VAL0-0.007-0.02035.1910.1980.1980.0000.0000.0000.000
207C271GLU-1-0.825-0.94136.8927.8577.8570.0000.0000.0000.000
208C272PHE00.0120.00831.366-0.008-0.0080.0000.0000.0000.000
209C273LEU00.0500.02632.3580.0300.0300.0000.0000.0000.000
210C274VAL00.0570.04634.1680.0290.0290.0000.0000.0000.000
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215C279MET00.010-0.00430.666-0.451-0.4510.0000.0000.0000.000
216C280ASP-1-0.946-0.99232.05310.15510.1550.0000.0000.0000.000
217C281TYR00.0610.03829.5950.2020.2020.0000.0000.0000.000
218C282SER00.0680.04528.039-0.389-0.3890.0000.0000.0000.000
219C283LEU0-0.061-0.03229.2420.1520.1520.0000.0000.0000.000
220C284LEU00.0080.02923.564-0.125-0.1250.0000.0000.0000.000
221C285LEU00.0220.01127.845-0.142-0.1420.0000.0000.0000.000
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224C288HIS00.0050.00729.3690.1480.1480.0000.0000.0000.000
225C289ASP-1-0.865-0.90931.2658.9038.9030.0000.0000.0000.000
226C290ILE0-0.058-0.01732.9380.1870.1870.0000.0000.0000.000
227C366GLU-1-0.946-1.01734.9708.9948.9940.0000.0000.0000.000
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229C368TYR00.0320.01432.1790.1780.1780.0000.0000.0000.000
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234C373ILE00.004-0.02323.4940.3080.3080.0000.0000.0000.000
235C374ASP-1-0.945-0.92524.63313.21013.2100.0000.0000.0000.000
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247C412PHE00.0500.03733.6080.0890.0890.0000.0000.0000.000
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