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: G52Y1

Calculation Name: 2CAR-A-Xray372

Preferred Name: Inosine triphosphate pyrophosphatase

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2CAR

Chain ID: A

ChEMBL ID: CHEMBL4105788

UniProt ID: Q9BY32

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 196
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2103110.691383
FMO2-HF: Nuclear repulsion 2026772.29691
FMO2-HF: Total energy -76338.394474
FMO2-MP2: Total energy -76558.917172


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:-1:GLY)


Summations of interaction energy for fragment #1(A:-1:GLY)
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.
5.8651.8871.1033.838-0.964-0.005
Interaction energy analysis for fragmet #1(A:-1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.037 / q_NPA : 0.034
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].
3A1MET00.0260.0132.7834.2220.0611.1053.890-0.834-0.005
4A2ALA00.0590.0244.516-0.249-0.259-0.001-0.0090.0190.000
5A3ALA00.0210.0054.6180.1020.143-0.001-0.015-0.0250.000
6A4SER0-0.077-0.0283.7970.2890.4410.000-0.028-0.1240.000
7A5LEU0-0.010-0.0335.5560.4350.4350.0000.0000.0000.000
8A6VAL00.0560.0398.7100.1450.1450.0000.0000.0000.000
9A7GLY0-0.033-0.01310.796-0.019-0.0190.0000.0000.0000.000
10A8LYS10.8680.9548.4760.4380.4380.0000.0000.0000.000
11A9LYS10.9310.96613.764-0.006-0.0060.0000.0000.0000.000
12A10ILE00.0040.00512.9030.0370.0370.0000.0000.0000.000
13A11VAL0-0.014-0.00116.102-0.025-0.0250.0000.0000.0000.000
14A12PHE0-0.011-0.01018.9320.0130.0130.0000.0000.0000.000
15A13VAL00.0290.01021.090-0.004-0.0040.0000.0000.0000.000
16A14THR0-0.023-0.01523.661-0.004-0.0040.0000.0000.0000.000
17A15GLY0-0.007-0.00626.9970.0040.0040.0000.0000.0000.000
18A16ASN0-0.049-0.04129.560-0.008-0.0080.0000.0000.0000.000
19A17ALA00.1180.05229.325-0.002-0.0020.0000.0000.0000.000
20A18LYS10.8960.94029.5090.0500.0500.0000.0000.0000.000
21A19LYS10.9200.96928.0830.0140.0140.0000.0000.0000.000
22A20LEU00.0250.02022.974-0.002-0.0020.0000.0000.0000.000
23A21GLU-1-0.824-0.89125.605-0.083-0.0830.0000.0000.0000.000
24A22GLU-1-0.955-0.98827.322-0.052-0.0520.0000.0000.0000.000
25A23VAL00.0180.01421.802-0.009-0.0090.0000.0000.0000.000
26A24VAL00.0290.01122.366-0.016-0.0160.0000.0000.0000.000
27A25GLN0-0.041-0.02423.573-0.018-0.0180.0000.0000.0000.000
28A26ILE0-0.054-0.01523.341-0.010-0.0100.0000.0000.0000.000
29A27LEU0-0.024-0.01218.404-0.010-0.0100.0000.0000.0000.000
30A28GLY00.0270.03220.735-0.033-0.0330.0000.0000.0000.000
31A29ASP-1-0.950-0.99821.246-0.273-0.2730.0000.0000.0000.000
32A30LYS10.8880.95118.4430.3760.3760.0000.0000.0000.000
33A31PHE00.0230.01414.969-0.074-0.0740.0000.0000.0000.000
34A32PRO0-0.0080.00112.4210.0230.0230.0000.0000.0000.000
35A33CYS00.0020.02312.607-0.082-0.0820.0000.0000.0000.000
36A34THR00.0240.01914.9020.0310.0310.0000.0000.0000.000
37A35LEU00.0030.00217.2470.0350.0350.0000.0000.0000.000
38A36VAL0-0.008-0.01019.489-0.002-0.0020.0000.0000.0000.000
39A37ALA0-0.037-0.01321.9010.0170.0170.0000.0000.0000.000
40A38GLN00.0150.00223.827-0.002-0.0020.0000.0000.0000.000
41A39LYS10.9870.99625.496-0.038-0.0380.0000.0000.0000.000
42A40ILE0-0.016-0.01123.0750.0020.0020.0000.0000.0000.000
43A41ASP-1-0.982-0.98926.4640.0840.0840.0000.0000.0000.000
44A42LEU0-0.0060.00623.7670.0120.0120.0000.0000.0000.000
45A43PRO00.008-0.00127.100-0.012-0.0120.0000.0000.0000.000
46A44GLU-1-0.977-0.99028.4000.0790.0790.0000.0000.0000.000
47A45TYR00.009-0.00426.0330.0030.0030.0000.0000.0000.000
48A46GLN0-0.021-0.02329.954-0.008-0.0080.0000.0000.0000.000
49A47GLY00.0390.03229.0750.0110.0110.0000.0000.0000.000
50A48GLU-1-0.938-0.99627.4110.1000.1000.0000.0000.0000.000
51A49PRO0-0.010-0.01926.7080.0090.0090.0000.0000.0000.000
52A50ASP-1-0.726-0.85222.0070.1350.1350.0000.0000.0000.000
53A51GLU-1-0.849-0.88122.2810.1800.1800.0000.0000.0000.000
54A52ILE0-0.019-0.01923.9670.0130.0130.0000.0000.0000.000
55A53SER0-0.009-0.00221.1780.0000.0000.0000.0000.0000.000
56A54ILE0-0.012-0.01918.3080.0140.0140.0000.0000.0000.000
57A55GLN0-0.0080.00420.0990.0190.0190.0000.0000.0000.000
58A56LYS10.9000.95722.659-0.078-0.0780.0000.0000.0000.000
59A57CYS0-0.063-0.02517.0160.0140.0140.0000.0000.0000.000
60A58GLN00.008-0.01718.261-0.006-0.0060.0000.0000.0000.000
61A59GLU-1-0.874-0.92619.3720.2140.2140.0000.0000.0000.000
62A60ALA0-0.001-0.01619.651-0.009-0.0090.0000.0000.0000.000
63A61VAL0-0.047-0.01815.544-0.011-0.0110.0000.0000.0000.000
64A62ARG10.9420.99218.265-0.282-0.2820.0000.0000.0000.000
65A63GLN0-0.075-0.03221.093-0.017-0.0170.0000.0000.0000.000
66A64VAL0-0.040-0.02618.157-0.011-0.0110.0000.0000.0000.000
67A65GLN0-0.075-0.03017.3260.0010.0010.0000.0000.0000.000
68A66GLY00.0200.01014.3320.0120.0120.0000.0000.0000.000
69A67PRO0-0.053-0.02611.4380.0060.0060.0000.0000.0000.000
70A68VAL0-0.0110.00213.768-0.059-0.0590.0000.0000.0000.000
71A69LEU00.006-0.00315.6690.0190.0190.0000.0000.0000.000
72A70VAL00.006-0.00517.922-0.014-0.0140.0000.0000.0000.000
73A71GLU-1-0.767-0.84820.754-0.015-0.0150.0000.0000.0000.000
74A72ASP-1-0.810-0.90223.5170.0910.0910.0000.0000.0000.000
75A73THR0-0.064-0.04526.112-0.011-0.0110.0000.0000.0000.000
76A74CYS0-0.085-0.00828.8990.0050.0050.0000.0000.0000.000
77A75LEU00.0000.00631.150-0.007-0.0070.0000.0000.0000.000
78A76CYS0-0.076-0.01831.5970.0060.0060.0000.0000.0000.000
79A77PHE00.0630.01035.143-0.005-0.0050.0000.0000.0000.000
80A78ASN0-0.006-0.03836.3630.0080.0080.0000.0000.0000.000
81A79ALA00.0360.03738.7850.0030.0030.0000.0000.0000.000
82A80LEU0-0.073-0.03139.9300.0020.0020.0000.0000.0000.000
83A81GLY00.0230.01437.8310.0040.0040.0000.0000.0000.000
84A82GLY0-0.0030.00334.4380.0050.0050.0000.0000.0000.000
85A83LEU0-0.0150.00034.8140.0010.0010.0000.0000.0000.000
86A84PRO00.036-0.01737.058-0.004-0.0040.0000.0000.0000.000
87A85GLY00.0750.05333.3230.0060.0060.0000.0000.0000.000
88A86PRO00.054-0.00429.985-0.007-0.0070.0000.0000.0000.000
89A87TYR0-0.026-0.00931.9090.0020.0020.0000.0000.0000.000
90A88ILE00.0360.02233.844-0.004-0.0040.0000.0000.0000.000
91A89LYS10.9640.99134.538-0.054-0.0540.0000.0000.0000.000
92A90TRP00.0370.01435.392-0.005-0.0050.0000.0000.0000.000
93A91PHE00.0340.00939.144-0.003-0.0030.0000.0000.0000.000
94A92LEU00.0070.00839.091-0.003-0.0030.0000.0000.0000.000
95A93GLU-1-0.933-0.94841.1100.0270.0270.0000.0000.0000.000
96A94LYS10.8740.90842.895-0.036-0.0360.0000.0000.0000.000
97A95LEU0-0.0150.01244.236-0.001-0.0010.0000.0000.0000.000
98A96LYS10.8760.94144.938-0.020-0.0200.0000.0000.0000.000
99A97PRO00.0470.01143.4250.0010.0010.0000.0000.0000.000
100A98GLU-1-0.899-0.95545.1440.0060.0060.0000.0000.0000.000
101A99GLY00.0410.01747.8150.0000.0000.0000.0000.0000.000
102A100LEU0-0.055-0.03640.8750.0020.0020.0000.0000.0000.000
103A101HIS00.0350.01344.5480.0010.0010.0000.0000.0000.000
104A102GLN0-0.0030.00246.4230.0000.0000.0000.0000.0000.000
105A103LEU0-0.043-0.00843.0360.0010.0010.0000.0000.0000.000
106A104LEU00.0140.00142.8370.0020.0020.0000.0000.0000.000
107A105ALA0-0.079-0.04046.968-0.001-0.0010.0000.0000.0000.000
108A106GLY0-0.022-0.00850.094-0.001-0.0010.0000.0000.0000.000
109A107PHE00.0170.02146.2010.0010.0010.0000.0000.0000.000
110A108GLU-1-0.894-0.96548.4750.0140.0140.0000.0000.0000.000
111A109ASP-1-0.862-0.88042.1750.0110.0110.0000.0000.0000.000
112A110LYS10.8570.92844.302-0.010-0.0100.0000.0000.0000.000
113A111SER0-0.031-0.03239.790-0.001-0.0010.0000.0000.0000.000
114A112ALA00.0210.00437.5380.0040.0040.0000.0000.0000.000
115A113TYR0-0.014-0.01430.168-0.003-0.0030.0000.0000.0000.000
116A114ALA00.0130.03532.2990.0060.0060.0000.0000.0000.000
117A115LEU00.005-0.02725.548-0.006-0.0060.0000.0000.0000.000
118A116CYS0-0.0670.00225.1530.0020.0020.0000.0000.0000.000
119A117THR00.023-0.01020.975-0.006-0.0060.0000.0000.0000.000
120A118PHE00.0310.01518.8530.0010.0010.0000.0000.0000.000
121A119ALA00.003-0.00817.1930.0110.0110.0000.0000.0000.000
122A120LEU0-0.004-0.01211.291-0.021-0.0210.0000.0000.0000.000
123A121SER00.0650.03311.9180.0820.0820.0000.0000.0000.000
124A122THR00.0630.0187.320-0.145-0.1450.0000.0000.0000.000
125A123GLY0-0.053-0.03810.573-0.050-0.0500.0000.0000.0000.000
126A124ASP-1-0.746-0.86710.6061.1001.1000.0000.0000.0000.000
127A125PRO00.0230.0297.418-0.054-0.0540.0000.0000.0000.000
128A126SER0-0.134-0.0549.659-0.031-0.0310.0000.0000.0000.000
129A127GLN0-0.094-0.0786.8430.6510.6510.0000.0000.0000.000
130A128PRO0-0.031-0.0019.343-0.217-0.2170.0000.0000.0000.000
131A129VAL00.0230.00211.4580.0110.0110.0000.0000.0000.000
132A130ARG10.9030.97311.624-0.069-0.0690.0000.0000.0000.000
133A131LEU0-0.021-0.00213.699-0.043-0.0430.0000.0000.0000.000
134A132PHE0-0.024-0.01012.546-0.010-0.0100.0000.0000.0000.000
135A133ARG10.8210.87618.495-0.096-0.0960.0000.0000.0000.000
136A134GLY00.0510.03022.166-0.018-0.0180.0000.0000.0000.000
137A135ARG10.9100.95525.215-0.023-0.0230.0000.0000.0000.000
138A136THR0-0.006-0.00928.662-0.009-0.0090.0000.0000.0000.000
139A137SER00.0100.00532.0380.0070.0070.0000.0000.0000.000
140A138GLY00.1030.05535.051-0.006-0.0060.0000.0000.0000.000
141A139ARG10.9290.97138.4730.0050.0050.0000.0000.0000.000
142A140ILE0-0.029-0.00139.385-0.002-0.0020.0000.0000.0000.000
143A141VAL0-0.074-0.03442.9650.0000.0000.0000.0000.0000.000
144A142ALA00.0390.01446.1160.0010.0010.0000.0000.0000.000
145A143PRO0-0.061-0.03246.410-0.002-0.0020.0000.0000.0000.000
146A144ARG10.8850.94246.3000.0120.0120.0000.0000.0000.000
147A145GLY00.0670.03145.679-0.001-0.0010.0000.0000.0000.000
148A146CYS0-0.051-0.01044.9960.0030.0030.0000.0000.0000.000
149A147GLN00.044-0.00644.4470.0010.0010.0000.0000.0000.000
150A148ASP-1-0.872-0.94143.463-0.004-0.0040.0000.0000.0000.000
151A149PHE0-0.076-0.02539.6550.0010.0010.0000.0000.0000.000
152A150GLY00.008-0.01138.5620.0000.0000.0000.0000.0000.000
153A151TRP00.0460.00633.3160.0000.0000.0000.0000.0000.000
154A152ASP-1-0.797-0.89036.999-0.014-0.0140.0000.0000.0000.000
155A153PRO0-0.001-0.01739.582-0.002-0.0020.0000.0000.0000.000
156A154CYS0-0.0300.00241.3360.0000.0000.0000.0000.0000.000
157A155PHE00.0040.01035.7250.0020.0020.0000.0000.0000.000
158A156GLN00.0240.01940.422-0.002-0.0020.0000.0000.0000.000
159A157PRO0-0.055-0.00336.6860.0030.0030.0000.0000.0000.000
160A158ASP-1-0.831-0.95537.496-0.016-0.0160.0000.0000.0000.000
161A159GLY0-0.068-0.03738.039-0.004-0.0040.0000.0000.0000.000
162A160TYR0-0.077-0.04337.413-0.002-0.0020.0000.0000.0000.000
163A161GLU-1-0.923-0.95742.410-0.018-0.0180.0000.0000.0000.000
164A162GLN0-0.041-0.02243.3150.0020.0020.0000.0000.0000.000
165A163THR00.013-0.00542.182-0.001-0.0010.0000.0000.0000.000
166A164TYR00.000-0.03532.902-0.005-0.0050.0000.0000.0000.000
167A165ALA0-0.063-0.01839.474-0.003-0.0030.0000.0000.0000.000
168A166GLU-1-0.846-0.91741.848-0.019-0.0190.0000.0000.0000.000
169A167MET0-0.084-0.00338.118-0.002-0.0020.0000.0000.0000.000
170A168PRO00.0290.02240.7990.0000.0000.0000.0000.0000.000
171A169LYS10.9860.97632.8400.0530.0530.0000.0000.0000.000
172A170ALA0-0.012-0.01135.496-0.002-0.0020.0000.0000.0000.000
173A171GLU-1-0.833-0.90735.605-0.062-0.0620.0000.0000.0000.000
174A172LYS10.8540.91733.6260.0250.0250.0000.0000.0000.000
175A173ASN0-0.059-0.05731.4310.0060.0060.0000.0000.0000.000
176A174ALA00.0110.02231.032-0.005-0.0050.0000.0000.0000.000
177A175VAL0-0.0020.00632.003-0.002-0.0020.0000.0000.0000.000
178A176SER0-0.0130.02930.0390.0090.0090.0000.0000.0000.000
179A177HIS00.0710.03228.483-0.012-0.0120.0000.0000.0000.000
180A178ARG10.8080.83926.0500.0300.0300.0000.0000.0000.000
181A179PHE00.015-0.00724.958-0.005-0.0050.0000.0000.0000.000
182A180ARG10.9070.95924.5370.0390.0390.0000.0000.0000.000
183A181ALA00.0100.00922.030-0.009-0.0090.0000.0000.0000.000
184A182LEU0-0.015-0.01020.397-0.006-0.0060.0000.0000.0000.000
185A183LEU00.0190.01519.883-0.025-0.0250.0000.0000.0000.000
186A184GLU-1-0.905-0.94418.276-0.143-0.1430.0000.0000.0000.000
187A185LEU0-0.073-0.02914.444-0.022-0.0220.0000.0000.0000.000
188A186GLN0-0.046-0.05015.027-0.055-0.0550.0000.0000.0000.000
189A187GLU-1-0.964-0.98115.600-0.393-0.3930.0000.0000.0000.000
190A188TYR0-0.034-0.0248.134-0.032-0.0320.0000.0000.0000.000
191A189PHE0-0.058-0.03710.103-0.111-0.1110.0000.0000.0000.000
192A190GLY00.0120.02611.939-0.168-0.1680.0000.0000.0000.000
193A191SER0-0.025-0.02814.4360.0270.0270.0000.0000.0000.000
194A192LEU0-0.017-0.02414.3130.0430.0430.0000.0000.0000.000
195A193ALA00.0040.00812.262-0.038-0.0380.0000.0000.0000.000
196A194ALA00.0050.03114.2820.0810.0810.0000.0000.0000.000