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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: NNG2Q

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 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 196
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2108867.046098
FMO2-HF: Nuclear repulsion 2032526.37991
FMO2-HF: Total energy -76340.666189
FMO2-MP2: Total energy -76561.041862


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.
4.6721.4612.4652.415-1.667-0.012
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 : 0.034 / q_NPA : 0.030
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].
3A1MET00.0580.0582.5923.465-0.1742.4552.561-1.376-0.012
4A2ALA00.0760.0564.561-0.227-0.223-0.001-0.0060.0030.000
5A3ALA00.0280.0053.8360.1820.3110.002-0.057-0.0730.000
6A4SER0-0.079-0.0453.3440.2450.5180.010-0.081-0.2020.000
7A5LEU00.0310.0054.9610.3090.331-0.001-0.002-0.0190.000
8A6VAL00.0240.0288.0700.1040.1040.0000.0000.0000.000
9A7GLY0-0.002-0.00310.0820.0340.0340.0000.0000.0000.000
10A8LYS10.8120.9188.7070.2950.2950.0000.0000.0000.000
11A9LYS10.9100.96013.328-0.118-0.1180.0000.0000.0000.000
12A10ILE00.0140.00812.2580.0410.0410.0000.0000.0000.000
13A11VAL0-0.029-0.01415.768-0.035-0.0350.0000.0000.0000.000
14A12PHE0-0.0010.00118.5970.0100.0100.0000.0000.0000.000
15A13VAL00.025-0.00320.769-0.007-0.0070.0000.0000.0000.000
16A14THR0-0.024-0.00223.305-0.010-0.0100.0000.0000.0000.000
17A15GLY00.0280.00826.5340.0050.0050.0000.0000.0000.000
18A16ASN0-0.040-0.03029.384-0.009-0.0090.0000.0000.0000.000
19A17ALA00.0870.04028.552-0.001-0.0010.0000.0000.0000.000
20A18LYS10.8460.91128.7300.0320.0320.0000.0000.0000.000
21A19LYS10.8880.92628.0760.0030.0030.0000.0000.0000.000
22A20LEU00.0440.02722.2920.0010.0010.0000.0000.0000.000
23A21GLU-1-0.777-0.86624.951-0.060-0.0600.0000.0000.0000.000
24A22GLU-1-0.819-0.88626.963-0.034-0.0340.0000.0000.0000.000
25A23VAL00.0130.01621.228-0.009-0.0090.0000.0000.0000.000
26A24VAL00.0200.00121.719-0.016-0.0160.0000.0000.0000.000
27A25GLN0-0.093-0.06823.146-0.020-0.0200.0000.0000.0000.000
28A26ILE0-0.058-0.01823.468-0.010-0.0100.0000.0000.0000.000
29A27LEU0-0.0180.00118.041-0.010-0.0100.0000.0000.0000.000
30A28GLY00.0420.03720.443-0.032-0.0320.0000.0000.0000.000
31A29ASP-1-0.868-0.95020.568-0.268-0.2680.0000.0000.0000.000
32A30LYS10.8230.91118.4920.2970.2970.0000.0000.0000.000
33A31PHE00.0190.01614.796-0.068-0.0680.0000.0000.0000.000
34A32PRO00.0100.01211.9520.0290.0290.0000.0000.0000.000
35A33CYS0-0.044-0.02211.531-0.033-0.0330.0000.0000.0000.000
36A34THR00.0110.00614.4310.0250.0250.0000.0000.0000.000
37A35LEU00.0120.00616.6690.0460.0460.0000.0000.0000.000
38A36VAL0-0.024-0.01918.918-0.007-0.0070.0000.0000.0000.000
39A37ALA0-0.0080.00721.5490.0190.0190.0000.0000.0000.000
40A38GLN00.0330.00622.899-0.001-0.0010.0000.0000.0000.000
41A39LYS10.8400.91125.020-0.081-0.0810.0000.0000.0000.000
42A40ILE00.0030.00022.6790.0010.0010.0000.0000.0000.000
43A41ASP-1-0.890-0.92426.1760.0890.0890.0000.0000.0000.000
44A42LEU00.0200.00623.5650.0150.0150.0000.0000.0000.000
45A43PRO00.0020.00927.557-0.013-0.0130.0000.0000.0000.000
46A44GLU-1-0.851-0.90928.2770.0880.0880.0000.0000.0000.000
47A45TYR00.0140.00026.191-0.001-0.0010.0000.0000.0000.000
48A46GLN0-0.031-0.02730.155-0.012-0.0120.0000.0000.0000.000
49A47GLY00.0530.03529.2920.0110.0110.0000.0000.0000.000
50A48GLU-1-0.920-0.97127.4820.0900.0900.0000.0000.0000.000
51A49PRO0-0.003-0.02726.5940.0100.0100.0000.0000.0000.000
52A50ASP-1-0.786-0.85421.9470.1200.1200.0000.0000.0000.000
53A51GLU-1-0.816-0.89722.3260.1780.1780.0000.0000.0000.000
54A52ILE0-0.0190.00323.9070.0170.0170.0000.0000.0000.000
55A53SER00.000-0.01621.7200.0040.0040.0000.0000.0000.000
56A54ILE0-0.021-0.01818.3650.0200.0200.0000.0000.0000.000
57A55GLN0-0.0060.00320.2290.0180.0180.0000.0000.0000.000
58A56LYS10.8510.89722.848-0.095-0.0950.0000.0000.0000.000
59A57CYS0-0.031-0.01417.0540.0040.0040.0000.0000.0000.000
60A58GLN00.0020.00418.5210.0130.0130.0000.0000.0000.000
61A59GLU-1-0.850-0.89519.5350.2540.2540.0000.0000.0000.000
62A60ALA00.015-0.00119.601-0.003-0.0030.0000.0000.0000.000
63A61VAL0-0.018-0.00815.375-0.006-0.0060.0000.0000.0000.000
64A62ARG10.8510.91418.045-0.295-0.2950.0000.0000.0000.000
65A63GLN0-0.067-0.03321.051-0.018-0.0180.0000.0000.0000.000
66A64VAL0-0.074-0.04317.677-0.019-0.0190.0000.0000.0000.000
67A65GLN0-0.085-0.03617.4050.0020.0020.0000.0000.0000.000
68A66GLY00.0390.02014.2310.0250.0250.0000.0000.0000.000
69A67PRO0-0.036-0.01611.217-0.005-0.0050.0000.0000.0000.000
70A68VAL0-0.0110.00113.443-0.079-0.0790.0000.0000.0000.000
71A69LEU00.0040.00615.3730.0280.0280.0000.0000.0000.000
72A70VAL00.001-0.00617.582-0.017-0.0170.0000.0000.0000.000
73A71GLU-1-0.756-0.85520.6090.0050.0050.0000.0000.0000.000
74A72ASP-1-0.787-0.87323.4250.1170.1170.0000.0000.0000.000
75A73THR0-0.057-0.05325.955-0.017-0.0170.0000.0000.0000.000
76A74CYS0-0.080-0.00128.7420.0080.0080.0000.0000.0000.000
77A75LEU0-0.0080.00431.378-0.007-0.0070.0000.0000.0000.000
78A76CYS0-0.040-0.00231.2410.0060.0060.0000.0000.0000.000
79A77PHE00.0700.01134.797-0.005-0.0050.0000.0000.0000.000
80A78ASN0-0.017-0.02735.9170.0070.0070.0000.0000.0000.000
81A79ALA00.0110.01038.2650.0030.0030.0000.0000.0000.000
82A80LEU0-0.049-0.01039.7870.0010.0010.0000.0000.0000.000
83A81GLY00.0140.00637.5920.0050.0050.0000.0000.0000.000
84A82GLY0-0.016-0.00534.2880.0040.0040.0000.0000.0000.000
85A83LEU00.0050.00434.6780.0030.0030.0000.0000.0000.000
86A84PRO00.022-0.00137.090-0.005-0.0050.0000.0000.0000.000
87A85GLY00.0760.03933.4270.0060.0060.0000.0000.0000.000
88A86PRO00.022-0.01429.967-0.005-0.0050.0000.0000.0000.000
89A87TYR0-0.029-0.01731.9480.0010.0010.0000.0000.0000.000
90A88ILE0-0.006-0.00133.973-0.003-0.0030.0000.0000.0000.000
91A89LYS10.8850.94933.268-0.073-0.0730.0000.0000.0000.000
92A90TRP00.0640.01135.486-0.005-0.0050.0000.0000.0000.000
93A91PHE00.0110.01039.384-0.003-0.0030.0000.0000.0000.000
94A92LEU00.0060.01438.788-0.003-0.0030.0000.0000.0000.000
95A93GLU-1-0.838-0.89140.9550.0370.0370.0000.0000.0000.000
96A94LYS10.8150.89042.654-0.043-0.0430.0000.0000.0000.000
97A95LEU0-0.018-0.00344.158-0.002-0.0020.0000.0000.0000.000
98A96LYS10.8790.93444.974-0.028-0.0280.0000.0000.0000.000
99A97PRO00.0320.00043.4390.0010.0010.0000.0000.0000.000
100A98GLU-1-0.870-0.93845.0780.0080.0080.0000.0000.0000.000
101A99GLY00.0370.01448.0210.0000.0000.0000.0000.0000.000
102A100LEU0-0.055-0.03441.0110.0020.0020.0000.0000.0000.000
103A101HIS00.0420.02444.6080.0010.0010.0000.0000.0000.000
104A102GLN0-0.024-0.01346.5670.0010.0010.0000.0000.0000.000
105A103LEU0-0.039-0.01243.0700.0010.0010.0000.0000.0000.000
106A104LEU00.0070.00642.3880.0010.0010.0000.0000.0000.000
107A105ALA0-0.017-0.00746.720-0.002-0.0020.0000.0000.0000.000
108A106GLY0-0.055-0.02450.170-0.002-0.0020.0000.0000.0000.000
109A107PHE00.0460.02545.5880.0020.0020.0000.0000.0000.000
110A108GLU-1-0.879-0.92748.5560.0120.0120.0000.0000.0000.000
111A109ASP-1-0.831-0.88742.1720.0050.0050.0000.0000.0000.000
112A110LYS10.8120.88344.239-0.009-0.0090.0000.0000.0000.000
113A111SER0-0.042-0.03439.6770.0000.0000.0000.0000.0000.000
114A112ALA00.0220.00037.3190.0050.0050.0000.0000.0000.000
115A113TYR00.0160.00729.821-0.002-0.0020.0000.0000.0000.000
116A114ALA00.0310.04032.3930.0070.0070.0000.0000.0000.000
117A115LEU0-0.006-0.02525.538-0.006-0.0060.0000.0000.0000.000
118A116CYS0-0.081-0.00625.3170.0030.0030.0000.0000.0000.000
119A117THR00.0440.00321.288-0.015-0.0150.0000.0000.0000.000
120A118PHE00.0450.02618.9670.0060.0060.0000.0000.0000.000
121A119ALA0-0.010-0.00617.3590.0070.0070.0000.0000.0000.000
122A120LEU00.0190.01111.370-0.019-0.0190.0000.0000.0000.000
123A121SER00.0430.01111.6040.1000.1000.0000.0000.0000.000
124A122THR0-0.004-0.0276.880-0.105-0.1050.0000.0000.0000.000
125A123GLY0-0.0080.00810.288-0.056-0.0560.0000.0000.0000.000
126A124ASP-1-0.833-0.90911.1640.8940.8940.0000.0000.0000.000
127A125PRO0-0.043-0.0128.2600.0510.0510.0000.0000.0000.000
128A126SER00.015-0.02010.264-0.101-0.1010.0000.0000.0000.000
129A127GLN0-0.099-0.0367.4410.6080.6080.0000.0000.0000.000
130A128PRO00.0100.0119.851-0.207-0.2070.0000.0000.0000.000
131A129VAL0-0.004-0.00411.7120.0390.0390.0000.0000.0000.000
132A130ARG10.8020.91211.578-0.008-0.0080.0000.0000.0000.000
133A131LEU0-0.024-0.00613.634-0.036-0.0360.0000.0000.0000.000
134A132PHE0-0.0120.00012.584-0.014-0.0140.0000.0000.0000.000
135A133ARG10.8420.88418.379-0.083-0.0830.0000.0000.0000.000
136A134GLY00.0420.02121.992-0.020-0.0200.0000.0000.0000.000
137A135ARG10.8790.93025.085-0.018-0.0180.0000.0000.0000.000
138A136THR0-0.037-0.04028.519-0.012-0.0120.0000.0000.0000.000
139A137SER00.0040.01432.0430.0070.0070.0000.0000.0000.000
140A138GLY00.0980.05434.847-0.005-0.0050.0000.0000.0000.000
141A139ARG10.8560.93938.4740.0030.0030.0000.0000.0000.000
142A140ILE00.0020.01239.391-0.001-0.0010.0000.0000.0000.000
143A141VAL0-0.063-0.03442.811-0.001-0.0010.0000.0000.0000.000
144A142ALA00.0340.01446.1420.0010.0010.0000.0000.0000.000
145A143PRO0-0.059-0.01346.312-0.002-0.0020.0000.0000.0000.000
146A144ARG10.7960.86146.2340.0100.0100.0000.0000.0000.000
147A145GLY00.0360.02645.386-0.001-0.0010.0000.0000.0000.000
148A146CYS0-0.067-0.04744.2720.0010.0010.0000.0000.0000.000
149A147GLN00.0510.00144.0900.0020.0020.0000.0000.0000.000
150A148ASP-1-0.857-0.91443.6260.0030.0030.0000.0000.0000.000
151A149PHE0-0.081-0.02639.4620.0020.0020.0000.0000.0000.000
152A150GLY00.022-0.00438.7760.0000.0000.0000.0000.0000.000
153A151TRP00.0510.00633.022-0.002-0.0020.0000.0000.0000.000
154A152ASP-1-0.779-0.87936.772-0.006-0.0060.0000.0000.0000.000
155A153PRO0-0.018-0.00539.436-0.002-0.0020.0000.0000.0000.000
156A154CYS0-0.040-0.01141.4290.0000.0000.0000.0000.0000.000
157A155PHE00.0050.00935.9920.0020.0020.0000.0000.0000.000
158A156GLN00.0350.02340.690-0.001-0.0010.0000.0000.0000.000
159A157PRO0-0.049-0.00736.5330.0020.0020.0000.0000.0000.000
160A158ASP-1-0.847-0.95936.962-0.016-0.0160.0000.0000.0000.000
161A159GLY0-0.060-0.02937.753-0.004-0.0040.0000.0000.0000.000
162A160TYR0-0.090-0.06037.313-0.002-0.0020.0000.0000.0000.000
163A161GLU-1-0.905-0.95142.144-0.018-0.0180.0000.0000.0000.000
164A162GLN00.002-0.00242.9550.0030.0030.0000.0000.0000.000
165A163THR00.025-0.01142.270-0.002-0.0020.0000.0000.0000.000
166A164TYR0-0.033-0.04832.710-0.005-0.0050.0000.0000.0000.000
167A165ALA0-0.039-0.01139.191-0.001-0.0010.0000.0000.0000.000
168A166GLU-1-0.787-0.86241.851-0.013-0.0130.0000.0000.0000.000
169A167MET0-0.066-0.01437.802-0.002-0.0020.0000.0000.0000.000
170A168PRO00.0300.02840.2860.0010.0010.0000.0000.0000.000
171A169LYS10.8910.91432.7720.0320.0320.0000.0000.0000.000
172A170ALA0-0.012-0.01135.353-0.002-0.0020.0000.0000.0000.000
173A171GLU-1-0.829-0.88535.324-0.056-0.0560.0000.0000.0000.000
174A172LYS10.8050.89334.7670.0130.0130.0000.0000.0000.000
175A173ASN0-0.028-0.03331.2410.0060.0060.0000.0000.0000.000
176A174ALA00.0280.03430.835-0.004-0.0040.0000.0000.0000.000
177A175VAL00.015-0.00131.799-0.003-0.0030.0000.0000.0000.000
178A176SER00.0040.04030.0360.0100.0100.0000.0000.0000.000
179A177HIS00.0480.02928.428-0.014-0.0140.0000.0000.0000.000
180A178ARG10.7840.83925.7830.0070.0070.0000.0000.0000.000
181A179PHE00.0430.00524.855-0.004-0.0040.0000.0000.0000.000
182A180ARG10.8790.95424.2560.0380.0380.0000.0000.0000.000
183A181ALA00.0140.01122.051-0.009-0.0090.0000.0000.0000.000
184A182LEU0-0.029-0.01620.281-0.003-0.0030.0000.0000.0000.000
185A183LEU00.0180.01719.789-0.022-0.0220.0000.0000.0000.000
186A184GLU-1-0.853-0.92117.511-0.112-0.1120.0000.0000.0000.000
187A185LEU0-0.065-0.02614.577-0.018-0.0180.0000.0000.0000.000
188A186GLN0-0.054-0.04415.073-0.040-0.0400.0000.0000.0000.000
189A187GLU-1-0.957-0.98114.812-0.426-0.4260.0000.0000.0000.000
190A188TYR00.008-0.0338.670-0.071-0.0710.0000.0000.0000.000
191A189PHE0-0.055-0.0419.566-0.111-0.1110.0000.0000.0000.000
192A190GLY00.0310.03811.578-0.160-0.1600.0000.0000.0000.000
193A191SER0-0.008-0.01614.045-0.028-0.0280.0000.0000.0000.000
194A192LEU0-0.046-0.02714.1620.0350.0350.0000.0000.0000.000
195A193ALA00.0150.00511.3930.0100.0100.0000.0000.0000.000
196A194ALA0-0.0220.01513.3640.0980.0980.0000.0000.0000.000