Manual

About

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: L7JJ9

Calculation Name: 2PET-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2PET

Chain ID: A

ChEMBL ID:

UniProt ID: P50895

Base Structure: X-ray

Registration Date: 2023-09-26

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 229
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2461173.306567
FMO2-HF: Nuclear repulsion 2369818.563794
FMO2-HF: Total energy -91354.742773
FMO2-MP2: Total energy -91616.737041


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:GLU)


Summations of interaction energy for fragment #1(A:1:GLU)
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.
-84.036-85.31330.412-16.286-12.8490.126
Interaction energy analysis for fragmet #1(A:1:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.820 / q_NPA : -0.887
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].
3A3ARG10.7870.8641.737-127.871-132.03129.351-14.497-10.6940.142
4A4LEU00.0320.0034.827-4.171-4.131-0.001-0.008-0.0300.000
5A5SER0-0.0230.0038.4530.5800.5800.0000.0000.0000.000
6A6VAL00.0260.00911.451-0.621-0.6210.0000.0000.0000.000
7A7PRO00.002-0.00815.0630.0100.0100.0000.0000.0000.000
8A8PRO00.0340.02217.927-0.323-0.3230.0000.0000.0000.000
9A9LEU0-0.038-0.01219.368-0.525-0.5250.0000.0000.0000.000
10A10VAL0-0.0010.00822.0140.0720.0720.0000.0000.0000.000
11A11GLU-1-0.845-0.92624.72410.18510.1850.0000.0000.0000.000
12A12VAL00.0100.00728.569-0.016-0.0160.0000.0000.0000.000
13A13MET0-0.0180.00330.965-0.158-0.1580.0000.0000.0000.000
14A14ARG10.9520.94934.438-7.652-7.6520.0000.0000.0000.000
15A15GLY0-0.061-0.03335.814-0.194-0.1940.0000.0000.0000.000
16A16LYS10.8880.95333.415-8.388-8.3880.0000.0000.0000.000
17A17SER00.0460.02330.635-0.009-0.0090.0000.0000.0000.000
18A18VAL0-0.018-0.00325.2580.0360.0360.0000.0000.0000.000
19A19ILE00.0150.01022.311-0.157-0.1570.0000.0000.0000.000
20A20LEU0-0.039-0.00720.3230.2320.2320.0000.0000.0000.000
21A21ASP-1-0.841-0.91516.11417.66317.6630.0000.0000.0000.000
22A22CYS00.0120.00213.8510.0190.0190.0000.0000.0000.000
23A23THR00.0100.00612.891-0.407-0.4070.0000.0000.0000.000
24A24PRO0-0.027-0.0058.4101.1681.1680.0000.0000.0000.000
25A25THR00.0100.0056.147-1.431-1.4310.0000.0000.0000.000
26A26GLY00.002-0.0133.5602.5462.6670.001-0.060-0.0630.000
27A27THR0-0.0080.0074.2622.1072.2390.000-0.052-0.0800.000
28A28HIS0-0.015-0.0085.429-1.643-1.6430.0000.0000.0000.000
29A29ASP-1-0.864-0.9608.50116.41716.4170.0000.0000.0000.000
30A30HIS0-0.078-0.03311.402-0.186-0.1860.0000.0000.0000.000
31A31TYR0-0.051-0.0359.7331.7021.7020.0000.0000.0000.000
32A32MET0-0.0230.00211.604-1.281-1.2810.0000.0000.0000.000
33A33LEU0-0.0020.00512.6931.6181.6180.0000.0000.0000.000
34A34GLU-1-0.777-0.85615.05014.19014.1900.0000.0000.0000.000
35A35TRP00.0150.00016.6170.6540.6540.0000.0000.0000.000
36A36PHE0-0.026-0.02316.571-0.728-0.7280.0000.0000.0000.000
37A37LEU0-0.0150.00720.9960.0820.0820.0000.0000.0000.000
38A38THR0-0.021-0.03020.5240.3160.3160.0000.0000.0000.000
39A39ASP-1-0.781-0.87023.39110.35110.3510.0000.0000.0000.000
40A40ARG10.8690.91924.752-9.848-9.8480.0000.0000.0000.000
41A41SER0-0.037-0.02726.3290.1460.1460.0000.0000.0000.000
42A42GLY00.0130.01322.7070.0990.0990.0000.0000.0000.000
43A43ALA0-0.0060.00122.4210.3790.3790.0000.0000.0000.000
44A44ARG10.8120.86015.402-16.616-16.6160.0000.0000.0000.000
45A45PRO0-0.055-0.02322.803-0.008-0.0080.0000.0000.0000.000
46A46ARG10.9220.94318.636-13.662-13.6620.0000.0000.0000.000
47A47LEU0-0.049-0.01222.749-0.470-0.4700.0000.0000.0000.000
48A48ALA00.020-0.00922.275-0.488-0.4880.0000.0000.0000.000
49A49SER0-0.032-0.02019.4670.4040.4040.0000.0000.0000.000
50A50ALA00.0100.00618.135-0.715-0.7150.0000.0000.0000.000
51A51GLU-1-0.841-0.91815.87515.99915.9990.0000.0000.0000.000
52A52MET0-0.018-0.00214.592-0.790-0.7900.0000.0000.0000.000
53A53GLN00.0540.00914.8380.5660.5660.0000.0000.0000.000
54A54GLY00.0180.02116.042-0.841-0.8410.0000.0000.0000.000
55A55SER0-0.126-0.05917.992-0.145-0.1450.0000.0000.0000.000
56A56GLU-1-0.894-0.93220.12011.47111.4710.0000.0000.0000.000
57A57LEU0-0.038-0.00819.2300.6470.6470.0000.0000.0000.000
58A58GLN0-0.042-0.02420.316-0.743-0.7430.0000.0000.0000.000
59A59VAL00.016-0.00320.9670.5690.5690.0000.0000.0000.000
60A60THR0-0.033-0.00323.194-0.558-0.5580.0000.0000.0000.000
61A61MET0-0.040-0.01624.3270.5040.5040.0000.0000.0000.000
62A62HIS0-0.019-0.02822.521-0.520-0.5200.0000.0000.0000.000
63A63ASP-1-0.885-0.96427.3889.7559.7550.0000.0000.0000.000
64A64THR0-0.033-0.04429.152-0.237-0.2370.0000.0000.0000.000
65A65ARG10.8650.97229.498-10.195-10.1950.0000.0000.0000.000
66A66GLY00.0160.01633.313-0.096-0.0960.0000.0000.0000.000
67A67ARG10.7520.85830.496-9.748-9.7480.0000.0000.0000.000
68A68SER0-0.0130.01433.956-0.084-0.0840.0000.0000.0000.000
69A69PRO00.011-0.00833.823-0.064-0.0640.0000.0000.0000.000
70A70PRO00.0200.00132.1060.1770.1770.0000.0000.0000.000
71A71TYR00.0190.01326.7230.0980.0980.0000.0000.0000.000
72A72GLN0-0.014-0.01227.464-0.245-0.2450.0000.0000.0000.000
73A73LEU00.0150.01520.9320.2860.2860.0000.0000.0000.000
74A74ASP-1-0.792-0.88221.73113.21613.2160.0000.0000.0000.000
75A75SER0-0.015-0.01822.6670.3310.3310.0000.0000.0000.000
76A76GLN0-0.018-0.00718.0680.6840.6840.0000.0000.0000.000
77A77GLY00.0420.02117.7860.8060.8060.0000.0000.0000.000
78A78ARG10.8080.90318.063-14.369-14.3690.0000.0000.0000.000
79A79LEU00.0170.01720.120-0.717-0.7170.0000.0000.0000.000
80A80VAL0-0.003-0.00422.511-0.022-0.0220.0000.0000.0000.000
81A81LEU0-0.051-0.02824.922-0.275-0.2750.0000.0000.0000.000
82A82ALA00.0630.02128.548-0.070-0.0700.0000.0000.0000.000
83A83GLU-1-0.944-0.97531.8668.1438.1430.0000.0000.0000.000
84A84ALA00.0200.02031.132-0.071-0.0710.0000.0000.0000.000
85A85GLN00.0520.01232.791-0.533-0.5330.0000.0000.0000.000
86A86VAL00.0580.02833.1570.2610.2610.0000.0000.0000.000
87A87GLY00.0040.01133.2230.1850.1850.0000.0000.0000.000
88A88ASP-1-0.737-0.84029.1719.9999.9990.0000.0000.0000.000
89A89GLU-1-0.846-0.89828.32110.09710.0970.0000.0000.0000.000
90A90ARG10.7990.89525.948-10.549-10.5490.0000.0000.0000.000
91A91ASP-1-0.828-0.92021.80612.76312.7630.0000.0000.0000.000
92A92TYR0-0.065-0.05420.890-0.403-0.4030.0000.0000.0000.000
93A93VAL0-0.018-0.01215.3690.5400.5400.0000.0000.0000.000
94A95VAL0-0.008-0.01511.8731.2801.2800.0000.0000.0000.000
95A96VAL00.0410.0248.054-1.085-1.0850.0000.0000.0000.000
96A97ARG10.8610.9119.362-15.594-15.5940.0000.0000.0000.000
97A98ALA00.0710.0215.924-1.450-1.4500.0000.0000.0000.000
98A99GLY00.0500.0366.9841.0321.0320.0000.0000.0000.000
99A100ALA0-0.022-0.0207.1001.1861.1860.0000.0000.0000.000
100A101ALA00.0000.0133.0022.2862.7980.127-0.174-0.4640.000
101A102GLY00.0180.0152.8034.0196.0390.935-1.491-1.464-0.016
102A103THR0-0.014-0.0254.908-3.313-3.255-0.001-0.004-0.0540.000
103A104ALA0-0.0250.0025.4833.0143.0140.0000.0000.0000.000
104A105GLU-1-0.795-0.8657.51216.96816.9680.0000.0000.0000.000
105A106ALA0-0.0140.00210.6861.2751.2750.0000.0000.0000.000
106A107THR0-0.012-0.01213.077-1.194-1.1940.0000.0000.0000.000
107A108ALA00.0040.01216.8020.2930.2930.0000.0000.0000.000
108A109ARG10.8490.93819.607-11.751-11.7510.0000.0000.0000.000
109A110LEU0-0.020-0.00923.2600.0330.0330.0000.0000.0000.000
110A111ASN00.011-0.00325.798-0.195-0.1950.0000.0000.0000.000
111A112VAL0-0.015-0.01629.1940.0060.0060.0000.0000.0000.000
112A113PHE0-0.0110.00131.182-0.275-0.2750.0000.0000.0000.000
113A114ALA0-0.043-0.03735.392-0.058-0.0580.0000.0000.0000.000
114A115LYS10.9250.97738.863-7.035-7.0350.0000.0000.0000.000
115A116PRO00.0070.00941.875-0.042-0.0420.0000.0000.0000.000
116A117GLU-1-0.863-0.93044.7206.4586.4580.0000.0000.0000.000
117A118ALA0-0.025-0.02348.0710.0150.0150.0000.0000.0000.000
118A119THR0-0.037-0.03750.5350.0170.0170.0000.0000.0000.000
119A120GLU-1-0.835-0.88851.9915.6505.6500.0000.0000.0000.000
120A121VAL0-0.013-0.02955.0370.0630.0630.0000.0000.0000.000
121A122SER0-0.033-0.01357.694-0.058-0.0580.0000.0000.0000.000
122A123PRO0-0.030-0.01760.579-0.002-0.0020.0000.0000.0000.000
123A124ASN00.0460.02363.240-0.098-0.0980.0000.0000.0000.000
124A125LYS10.9460.95765.545-4.857-4.8570.0000.0000.0000.000
125A126GLY0-0.012-0.00268.639-0.086-0.0860.0000.0000.0000.000
126A127THR00.016-0.00469.241-0.049-0.0490.0000.0000.0000.000
127A128LEU0-0.0230.02766.192-0.029-0.0290.0000.0000.0000.000
128A129SER00.055-0.00470.413-0.079-0.0790.0000.0000.0000.000
129A130VAL0-0.047-0.01571.7240.0410.0410.0000.0000.0000.000
130A131MET0-0.037-0.02573.449-0.016-0.0160.0000.0000.0000.000
131A132GLU-1-0.875-0.89770.9274.4484.4480.0000.0000.0000.000
132A133ASP-1-0.875-0.91571.9264.5264.5260.0000.0000.0000.000
133A134SER0-0.045-0.05668.2080.0450.0450.0000.0000.0000.000
134A135ALA0-0.007-0.00563.424-0.001-0.0010.0000.0000.0000.000
135A136GLN00.000-0.00264.9950.0200.0200.0000.0000.0000.000
136A137GLU-1-0.832-0.89761.2205.2945.2940.0000.0000.0000.000
137A138ILE0-0.020-0.01361.563-0.078-0.0780.0000.0000.0000.000
138A139ALA00.013-0.00660.042-0.065-0.0650.0000.0000.0000.000
139A140THR00.0180.03055.6550.0840.0840.0000.0000.0000.000
140A141CYS0-0.0380.00753.1380.0090.0090.0000.0000.0000.000
141A142ASN0-0.019-0.01251.5890.0640.0640.0000.0000.0000.000
142A143SER00.0440.02447.2790.0270.0270.0000.0000.0000.000
143A144ARG10.8790.91147.180-5.911-5.9110.0000.0000.0000.000
144A145ASN0-0.018-0.03143.8650.1700.1700.0000.0000.0000.000
145A146GLY00.0320.02341.5750.0350.0350.0000.0000.0000.000
146A147ASN0-0.102-0.04634.266-0.147-0.1470.0000.0000.0000.000
147A148PRO00.0830.02735.4220.0410.0410.0000.0000.0000.000
148A149ALA00.001-0.00737.385-0.181-0.1810.0000.0000.0000.000
149A150PRO00.0110.01640.6990.0960.0960.0000.0000.0000.000
150A151LYS10.9430.96740.489-7.739-7.7390.0000.0000.0000.000
151A152ILE00.0170.00445.224-0.014-0.0140.0000.0000.0000.000
152A153THR0-0.0110.01848.7760.0500.0500.0000.0000.0000.000
153A154TRP00.0300.00651.361-0.074-0.0740.0000.0000.0000.000
154A155TYR0-0.014-0.00650.9830.0760.0760.0000.0000.0000.000
155A156ARG10.9050.92957.434-5.119-5.1190.0000.0000.0000.000
156A157ASN00.0060.00661.0710.0170.0170.0000.0000.0000.000
157A158GLY00.0060.00458.893-0.006-0.0060.0000.0000.0000.000
158A159GLN0-0.042-0.01457.4230.1130.1130.0000.0000.0000.000
159A160ARG10.8240.88850.731-6.258-6.2580.0000.0000.0000.000
160A161LEU0-0.013-0.01155.246-0.071-0.0710.0000.0000.0000.000
161A162GLU-1-0.865-0.91652.8446.1876.1870.0000.0000.0000.000
162A163VAL0-0.0160.00254.410-0.081-0.0810.0000.0000.0000.000
163A164PRO00.0090.01952.4530.1330.1330.0000.0000.0000.000
164A165VAL00.006-0.01949.553-0.049-0.0490.0000.0000.0000.000
165A166GLU-1-0.919-0.95650.9786.1896.1890.0000.0000.0000.000
166A167MET0-0.005-0.00254.780-0.095-0.0950.0000.0000.0000.000
167A168ASN0-0.049-0.03558.008-0.085-0.0850.0000.0000.0000.000
168A169PRO00.016-0.01061.033-0.002-0.0020.0000.0000.0000.000
169A170GLU-1-0.837-0.90362.3044.8274.8270.0000.0000.0000.000
170A171GLY00.027-0.00360.642-0.045-0.0450.0000.0000.0000.000
171A172TYR0-0.0320.00756.3860.0480.0480.0000.0000.0000.000
172A173MET0-0.0120.00250.417-0.075-0.0750.0000.0000.0000.000
173A174THR00.0450.03253.1600.0990.0990.0000.0000.0000.000
174A175SER0-0.014-0.02748.6910.0730.0730.0000.0000.0000.000
175A176ARG10.9640.98348.590-6.296-6.2960.0000.0000.0000.000
176A177THR00.0040.00842.5090.0220.0220.0000.0000.0000.000
177A178VAL0-0.005-0.00545.663-0.022-0.0220.0000.0000.0000.000
178A179ARG10.8710.94336.464-8.110-8.1100.0000.0000.0000.000
179A180GLU-1-0.810-0.86642.9456.5296.5290.0000.0000.0000.000
180A181ALA00.014-0.00442.6930.1770.1770.0000.0000.0000.000
181A182SER0-0.0030.00341.7510.1500.1500.0000.0000.0000.000
182A183GLY00.0190.00638.5620.2150.2150.0000.0000.0000.000
183A184LEU0-0.057-0.01438.7570.2140.2140.0000.0000.0000.000
184A185LEU0-0.047-0.02338.215-0.102-0.1020.0000.0000.0000.000
185A186SER0-0.019-0.04042.2120.0100.0100.0000.0000.0000.000
186A187LEU0-0.060-0.02045.5380.0060.0060.0000.0000.0000.000
187A188THR00.0290.00547.454-0.129-0.1290.0000.0000.0000.000
188A189SER0-0.029-0.02750.8190.0680.0680.0000.0000.0000.000
189A190THR00.0250.01352.779-0.030-0.0300.0000.0000.0000.000
190A191LEU00.0000.01756.2720.0580.0580.0000.0000.0000.000
191A192TYR0-0.040-0.05257.882-0.060-0.0600.0000.0000.0000.000
192A193LEU0-0.009-0.01660.4170.0670.0670.0000.0000.0000.000
193A194ARG10.8140.90663.232-4.755-4.7550.0000.0000.0000.000
194A195LEU0-0.072-0.02166.3950.0200.0200.0000.0000.0000.000
195A196ARG10.9000.93067.970-4.727-4.7270.0000.0000.0000.000
196A197LYS10.9530.95370.875-4.265-4.2650.0000.0000.0000.000
197A198ASP-1-0.808-0.90570.7424.4314.4310.0000.0000.0000.000
198A199ASP-1-0.743-0.85366.7744.9034.9030.0000.0000.0000.000
199A200ARG10.7840.88569.269-4.242-4.2420.0000.0000.0000.000
200A201ASP-1-0.861-0.92171.0664.3754.3750.0000.0000.0000.000
201A202ALA0-0.057-0.00665.5970.0360.0360.0000.0000.0000.000
202A203SER0-0.0230.00063.613-0.004-0.0040.0000.0000.0000.000
203A204PHE00.0320.00260.9970.0480.0480.0000.0000.0000.000
204A205HIS0-0.037-0.01554.494-0.135-0.1350.0000.0000.0000.000
205A207ALA00.002-0.00350.791-0.016-0.0160.0000.0000.0000.000
206A208ALA00.0370.02646.9500.0440.0440.0000.0000.0000.000
207A209HIS0-0.020-0.03344.3780.0900.0900.0000.0000.0000.000
208A210TYR00.019-0.00440.9760.0710.0710.0000.0000.0000.000
209A211SER00.0190.00036.4790.0020.0020.0000.0000.0000.000
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