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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: 89VNY

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 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 196
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2103976.254906
FMO2-HF: Nuclear repulsion 2027636.359532
FMO2-HF: Total energy -76339.895374
FMO2-MP2: Total energy -76560.34773


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.
5.7281.7821.113.809-0.973-0.005
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 : 0.038 / 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].
3A1MET00.0570.0512.7824.2530.1181.1113.863-0.840-0.005
4A2ALA00.0770.0504.517-0.238-0.251-0.001-0.0090.0230.000
5A3ALA00.0180.0034.6170.1050.149-0.001-0.015-0.0270.000
6A4SER0-0.077-0.0363.7450.2960.4540.001-0.030-0.1290.000
7A5LEU00.0250.0005.5530.4280.4280.0000.0000.0000.000
8A6VAL00.0380.0418.7070.1410.1410.0000.0000.0000.000
9A7GLY0-0.027-0.01410.793-0.011-0.0110.0000.0000.0000.000
10A8LYS10.8380.9218.7360.4730.4730.0000.0000.0000.000
11A9LYS10.9280.96613.761-0.049-0.0490.0000.0000.0000.000
12A10ILE0-0.007-0.00112.6250.0430.0430.0000.0000.0000.000
13A11VAL0-0.0070.00116.100-0.030-0.0300.0000.0000.0000.000
14A12PHE0-0.013-0.01318.9320.0130.0130.0000.0000.0000.000
15A13VAL00.0270.00821.089-0.005-0.0050.0000.0000.0000.000
16A14THR0-0.022-0.01823.661-0.007-0.0070.0000.0000.0000.000
17A15GLY00.0260.01726.9970.0040.0040.0000.0000.0000.000
18A16ASN0-0.040-0.03029.579-0.009-0.0090.0000.0000.0000.000
19A17ALA00.1000.04429.310-0.002-0.0020.0000.0000.0000.000
20A18LYS10.8550.91529.5070.0450.0450.0000.0000.0000.000
21A19LYS10.8650.92328.0980.0120.0120.0000.0000.0000.000
22A20LEU00.0300.01922.930-0.003-0.0030.0000.0000.0000.000
23A21GLU-1-0.770-0.86625.604-0.074-0.0740.0000.0000.0000.000
24A22GLU-1-0.839-0.90727.321-0.044-0.0440.0000.0000.0000.000
25A23VAL00.0110.01321.708-0.009-0.0090.0000.0000.0000.000
26A24VAL00.0300.00922.238-0.016-0.0160.0000.0000.0000.000
27A25GLN0-0.079-0.04823.571-0.021-0.0210.0000.0000.0000.000
28A26ILE0-0.049-0.01423.655-0.011-0.0110.0000.0000.0000.000
29A27LEU0-0.022-0.00818.444-0.010-0.0100.0000.0000.0000.000
30A28GLY00.0330.03720.734-0.033-0.0330.0000.0000.0000.000
31A29ASP-1-0.907-0.97321.244-0.286-0.2860.0000.0000.0000.000
32A30LYS10.8120.90018.6550.3350.3350.0000.0000.0000.000
33A31PHE00.0440.02215.284-0.070-0.0700.0000.0000.0000.000
34A32PRO0-0.0010.00812.4050.0260.0260.0000.0000.0000.000
35A33CYS0-0.0200.00211.987-0.069-0.0690.0000.0000.0000.000
36A34THR00.0110.00814.9000.0280.0280.0000.0000.0000.000
37A35LEU00.0120.01417.1890.0370.0370.0000.0000.0000.000
38A36VAL0-0.015-0.02119.487-0.003-0.0030.0000.0000.0000.000
39A37ALA0-0.034-0.00621.9000.0170.0170.0000.0000.0000.000
40A38GLN00.007-0.00123.676-0.003-0.0030.0000.0000.0000.000
41A39LYS10.8990.94425.495-0.069-0.0690.0000.0000.0000.000
42A40ILE00.0130.00223.0110.0030.0030.0000.0000.0000.000
43A41ASP-1-0.919-0.95626.4640.0830.0830.0000.0000.0000.000
44A42LEU00.0040.01323.5750.0130.0130.0000.0000.0000.000
45A43PRO00.0090.00627.194-0.013-0.0130.0000.0000.0000.000
46A44GLU-1-0.887-0.93428.4010.0780.0780.0000.0000.0000.000
47A45TYR00.0220.00026.1580.0020.0020.0000.0000.0000.000
48A46GLN0-0.029-0.02729.955-0.009-0.0090.0000.0000.0000.000
49A47GLY00.0670.04829.0770.0110.0110.0000.0000.0000.000
50A48GLU-1-0.936-0.98827.6340.1020.1020.0000.0000.0000.000
51A49PRO00.013-0.00726.5270.0100.0100.0000.0000.0000.000
52A50ASP-1-0.769-0.85922.0610.1340.1340.0000.0000.0000.000
53A51GLU-1-0.841-0.88722.2830.1850.1850.0000.0000.0000.000
54A52ILE0-0.029-0.02023.9690.0140.0140.0000.0000.0000.000
55A53SER0-0.033-0.02221.3770.0010.0010.0000.0000.0000.000
56A54ILE0-0.004-0.01518.2200.0170.0170.0000.0000.0000.000
57A55GLN0-0.0090.00420.1010.0180.0180.0000.0000.0000.000
58A56LYS10.8620.90922.661-0.090-0.0900.0000.0000.0000.000
59A57CYS0-0.040-0.02017.0240.0040.0040.0000.0000.0000.000
60A58GLN00.010-0.00618.2350.0030.0030.0000.0000.0000.000
61A59GLU-1-0.826-0.88319.3740.2380.2380.0000.0000.0000.000
62A60ALA0-0.001-0.02019.796-0.008-0.0080.0000.0000.0000.000
63A61VAL0-0.040-0.01715.452-0.011-0.0110.0000.0000.0000.000
64A62ARG10.9000.96018.266-0.291-0.2910.0000.0000.0000.000
65A63GLN0-0.099-0.04521.094-0.020-0.0200.0000.0000.0000.000
66A64VAL0-0.047-0.03418.056-0.011-0.0110.0000.0000.0000.000
67A65GLN0-0.082-0.03417.2920.0060.0060.0000.0000.0000.000
68A66GLY00.0290.01414.3320.0170.0170.0000.0000.0000.000
69A67PRO0-0.047-0.02411.4270.0010.0010.0000.0000.0000.000
70A68VAL0-0.022-0.00813.768-0.064-0.0640.0000.0000.0000.000
71A69LEU00.0090.00415.6700.0200.0200.0000.0000.0000.000
72A70VAL00.008-0.00217.922-0.015-0.0150.0000.0000.0000.000
73A71GLU-1-0.759-0.85020.755-0.005-0.0050.0000.0000.0000.000
74A72ASP-1-0.800-0.87423.5170.1050.1050.0000.0000.0000.000
75A73THR0-0.064-0.05426.113-0.011-0.0110.0000.0000.0000.000
76A74CYS0-0.0650.00528.6360.0060.0060.0000.0000.0000.000
77A75LEU0-0.010-0.00331.151-0.007-0.0070.0000.0000.0000.000
78A76CYS0-0.062-0.00931.5900.0060.0060.0000.0000.0000.000
79A77PHE00.0710.01535.145-0.006-0.0060.0000.0000.0000.000
80A78ASN0-0.014-0.03436.4260.0080.0080.0000.0000.0000.000
81A79ALA00.0420.03838.7870.0030.0030.0000.0000.0000.000
82A80LEU0-0.079-0.03339.9460.0020.0020.0000.0000.0000.000
83A81GLY00.0220.01337.8340.0050.0050.0000.0000.0000.000
84A82GLY0-0.0080.00034.4400.0050.0050.0000.0000.0000.000
85A83LEU0-0.0090.00334.8160.0020.0020.0000.0000.0000.000
86A84PRO00.035-0.01437.060-0.005-0.0050.0000.0000.0000.000
87A85GLY00.0760.04933.3260.0060.0060.0000.0000.0000.000
88A86PRO00.026-0.01329.966-0.006-0.0060.0000.0000.0000.000
89A87TYR0-0.030-0.01931.9110.0020.0020.0000.0000.0000.000
90A88ILE00.0270.02333.807-0.004-0.0040.0000.0000.0000.000
91A89LYS10.8910.94933.513-0.066-0.0660.0000.0000.0000.000
92A90TRP00.0430.01235.378-0.005-0.0050.0000.0000.0000.000
93A91PHE00.0390.01639.404-0.003-0.0030.0000.0000.0000.000
94A92LEU00.0000.01039.104-0.003-0.0030.0000.0000.0000.000
95A93GLU-1-0.863-0.90741.1190.0330.0330.0000.0000.0000.000
96A94LYS10.8330.89242.896-0.040-0.0400.0000.0000.0000.000
97A95LEU0-0.0210.01144.074-0.001-0.0010.0000.0000.0000.000
98A96LYS10.8650.91844.945-0.024-0.0240.0000.0000.0000.000
99A97PRO00.0530.01143.4930.0010.0010.0000.0000.0000.000
100A98GLU-1-0.885-0.94745.1450.0080.0080.0000.0000.0000.000
101A99GLY00.0350.01447.8110.0000.0000.0000.0000.0000.000
102A100LEU0-0.058-0.03940.8650.0020.0020.0000.0000.0000.000
103A101HIS00.0360.01544.5490.0010.0010.0000.0000.0000.000
104A102GLN0-0.0060.00046.4250.0010.0010.0000.0000.0000.000
105A103LEU0-0.041-0.00443.0400.0010.0010.0000.0000.0000.000
106A104LEU00.010-0.00542.7480.0020.0020.0000.0000.0000.000
107A105ALA0-0.072-0.03646.969-0.001-0.0010.0000.0000.0000.000
108A106GLY0-0.021-0.00750.095-0.001-0.0010.0000.0000.0000.000
109A107PHE00.0120.01446.0820.0010.0010.0000.0000.0000.000
110A108GLU-1-0.868-0.93948.4770.0140.0140.0000.0000.0000.000
111A109ASP-1-0.868-0.90042.0100.0120.0120.0000.0000.0000.000
112A110LYS10.8340.91344.304-0.011-0.0110.0000.0000.0000.000
113A111SER0-0.025-0.02339.738-0.001-0.0010.0000.0000.0000.000
114A112ALA00.0210.00337.6090.0050.0050.0000.0000.0000.000
115A113TYR0-0.008-0.01430.123-0.003-0.0030.0000.0000.0000.000
116A114ALA00.0160.03532.3470.0060.0060.0000.0000.0000.000
117A115LEU00.002-0.02625.485-0.007-0.0070.0000.0000.0000.000
118A116CYS0-0.0740.00225.2230.0020.0020.0000.0000.0000.000
119A117THR00.039-0.00720.991-0.012-0.0120.0000.0000.0000.000
120A118PHE00.0360.02018.8730.0010.0010.0000.0000.0000.000
121A119ALA0-0.010-0.01717.1840.0110.0110.0000.0000.0000.000
122A120LEU00.003-0.00511.468-0.020-0.0200.0000.0000.0000.000
123A121SER00.0640.02311.8770.0970.0970.0000.0000.0000.000
124A122THR00.0450.0157.069-0.133-0.1330.0000.0000.0000.000
125A123GLY0-0.031-0.01710.573-0.045-0.0450.0000.0000.0000.000
126A124ASP-1-0.786-0.87410.7090.9260.9260.0000.0000.0000.000
127A125PRO0-0.0020.0007.5330.0040.0040.0000.0000.0000.000
128A126SER0-0.096-0.05510.178-0.048-0.0480.0000.0000.0000.000
129A127GLN0-0.112-0.0716.9390.6040.6040.0000.0000.0000.000
130A128PRO00.0090.0199.492-0.211-0.2110.0000.0000.0000.000
131A129VAL00.0160.00511.4600.0160.0160.0000.0000.0000.000
132A130ARG10.8890.96311.611-0.038-0.0380.0000.0000.0000.000
133A131LEU0-0.016-0.00113.701-0.040-0.0400.0000.0000.0000.000
134A132PHE0-0.026-0.00412.615-0.012-0.0120.0000.0000.0000.000
135A133ARG10.8360.87718.496-0.099-0.0990.0000.0000.0000.000
136A134GLY00.0560.03422.167-0.018-0.0180.0000.0000.0000.000
137A135ARG10.9100.95725.216-0.026-0.0260.0000.0000.0000.000
138A136THR0-0.026-0.03228.663-0.009-0.0090.0000.0000.0000.000
139A137SER0-0.0030.01032.0390.0070.0070.0000.0000.0000.000
140A138GLY00.1080.05835.053-0.005-0.0050.0000.0000.0000.000
141A139ARG10.9280.97038.4740.0030.0030.0000.0000.0000.000
142A140ILE0-0.0360.00039.391-0.002-0.0020.0000.0000.0000.000
143A141VAL0-0.073-0.03642.9660.0000.0000.0000.0000.0000.000
144A142ALA00.0360.01446.1170.0010.0010.0000.0000.0000.000
145A143PRO0-0.065-0.02746.405-0.002-0.0020.0000.0000.0000.000
146A144ARG10.8610.92346.1190.0100.0100.0000.0000.0000.000
147A145GLY00.0520.02245.680-0.001-0.0010.0000.0000.0000.000
148A146CYS0-0.068-0.04144.8480.0020.0020.0000.0000.0000.000
149A147GLN00.0500.00344.4470.0010.0010.0000.0000.0000.000
150A148ASP-1-0.876-0.92943.722-0.001-0.0010.0000.0000.0000.000
151A149PHE0-0.064-0.01539.6440.0010.0010.0000.0000.0000.000
152A150GLY00.021-0.00638.5620.0000.0000.0000.0000.0000.000
153A151TRP00.0500.01033.142-0.001-0.0010.0000.0000.0000.000
154A152ASP-1-0.775-0.87236.861-0.010-0.0100.0000.0000.0000.000
155A153PRO0-0.003-0.01339.582-0.002-0.0020.0000.0000.0000.000
156A154CYS0-0.036-0.01141.4340.0000.0000.0000.0000.0000.000
157A155PHE00.0040.00835.8130.0020.0020.0000.0000.0000.000
158A156GLN00.0340.02740.423-0.001-0.0010.0000.0000.0000.000
159A157PRO0-0.051-0.00936.6470.0020.0020.0000.0000.0000.000
160A158ASP-1-0.857-0.96837.449-0.015-0.0150.0000.0000.0000.000
161A159GLY0-0.054-0.02938.039-0.004-0.0040.0000.0000.0000.000
162A160TYR0-0.099-0.07137.373-0.002-0.0020.0000.0000.0000.000
163A161GLU-1-0.896-0.94642.411-0.017-0.0170.0000.0000.0000.000
164A162GLN0-0.044-0.02143.1620.0020.0020.0000.0000.0000.000
165A163THR00.020-0.00942.196-0.001-0.0010.0000.0000.0000.000
166A164TYR00.005-0.03232.847-0.005-0.0050.0000.0000.0000.000
167A165ALA0-0.066-0.01839.474-0.003-0.0030.0000.0000.0000.000
168A166GLU-1-0.811-0.89441.848-0.016-0.0160.0000.0000.0000.000
169A167MET0-0.074-0.00537.770-0.001-0.0010.0000.0000.0000.000
170A168PRO00.0290.02540.8520.0000.0000.0000.0000.0000.000
171A169LYS10.9200.93933.0260.0420.0420.0000.0000.0000.000
172A170ALA0-0.013-0.01535.502-0.002-0.0020.0000.0000.0000.000
173A171GLU-1-0.813-0.87935.604-0.058-0.0580.0000.0000.0000.000
174A172LYS10.8010.89234.0490.0180.0180.0000.0000.0000.000
175A173ASN0-0.062-0.05831.5500.0060.0060.0000.0000.0000.000
176A174ALA00.0120.02231.032-0.005-0.0050.0000.0000.0000.000
177A175VAL00.0030.00732.003-0.003-0.0030.0000.0000.0000.000
178A176SER0-0.0060.03530.3180.0090.0090.0000.0000.0000.000
179A177HIS00.0650.02728.490-0.013-0.0130.0000.0000.0000.000
180A178ARG10.8100.84726.0780.0210.0210.0000.0000.0000.000
181A179PHE00.030-0.00124.958-0.005-0.0050.0000.0000.0000.000
182A180ARG10.9120.96424.5370.0360.0360.0000.0000.0000.000
183A181ALA00.0020.00522.108-0.009-0.0090.0000.0000.0000.000
184A182LEU0-0.008-0.00720.397-0.005-0.0050.0000.0000.0000.000
185A183LEU00.0180.01719.883-0.024-0.0240.0000.0000.0000.000
186A184GLU-1-0.916-0.95118.195-0.125-0.1250.0000.0000.0000.000
187A185LEU0-0.078-0.03314.487-0.022-0.0220.0000.0000.0000.000
188A186GLN0-0.049-0.05315.026-0.051-0.0510.0000.0000.0000.000
189A187GLU-1-0.960-0.97815.561-0.387-0.3870.0000.0000.0000.000
190A188TYR0-0.047-0.0628.448-0.044-0.0440.0000.0000.0000.000
191A189PHE0-0.066-0.0379.973-0.103-0.1030.0000.0000.0000.000
192A190GLY00.0080.02311.937-0.169-0.1690.0000.0000.0000.000
193A191SER0-0.006-0.02214.4350.0110.0110.0000.0000.0000.000
194A192LEU0-0.019-0.01614.2200.0390.0390.0000.0000.0000.000
195A193ALA0-0.006-0.00112.289-0.043-0.0430.0000.0000.0000.000
196A194ALA00.0210.04714.2800.0830.0830.0000.0000.0000.000