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: J3Y19

Calculation Name: 2JEU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2JEU

Chain ID: A

ChEMBL ID:

UniProt ID: P03122

Base Structure: X-ray

Registration Date: 2023-03-13

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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2077615.976491
FMO2-HF: Nuclear repulsion 1997467.182841
FMO2-HF: Total energy -80148.79365
FMO2-MP2: Total energy -80378.581443


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:3:THR)


Summations of interaction energy for fragment #1(A:3:THR)
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.
-16.394-9.9168.299-6.989-7.787-0.054
Interaction energy analysis for fragmet #1(A:3:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.062 / q_NPA : 0.024
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].
3A5CYS00.026-0.0033.242-2.190-0.275-0.003-0.818-1.0950.002
4A6GLU-1-0.837-0.9102.234-14.943-9.8164.465-5.187-4.405-0.057
5A7ARG10.9640.9722.0640.7950.1573.838-0.977-2.2220.001
6A8LEU0-0.037-0.0045.0370.6130.687-0.001-0.007-0.0650.000
7A9HIS00.0620.0277.7320.2690.2690.0000.0000.0000.000
8A10VAL00.0280.0257.5760.2250.2250.0000.0000.0000.000
9A11ALA0-0.046-0.0079.1020.2260.2260.0000.0000.0000.000
10A12GLN0-0.055-0.06410.9460.0230.0230.0000.0000.0000.000
11A13GLU-1-0.871-0.93412.837-0.492-0.4920.0000.0000.0000.000
12A14THR0-0.051-0.04012.5610.0890.0890.0000.0000.0000.000
13A15GLN0-0.099-0.07214.0320.1000.1000.0000.0000.0000.000
14A16MET0-0.005-0.00217.3500.0280.0280.0000.0000.0000.000
15A17GLN00.0330.02917.0670.0260.0260.0000.0000.0000.000
16A18LEU0-0.037-0.02918.0500.0340.0340.0000.0000.0000.000
17A19ILE0-0.056-0.03420.7910.0270.0270.0000.0000.0000.000
18A20GLU-1-0.927-0.96522.933-0.237-0.2370.0000.0000.0000.000
19A21LYS10.8210.93223.3740.1810.1810.0000.0000.0000.000
20A22SER0-0.022-0.01625.6210.0170.0170.0000.0000.0000.000
21A23SER0-0.088-0.05825.2100.0120.0120.0000.0000.0000.000
22A24ASP-1-0.797-0.89927.164-0.076-0.0760.0000.0000.0000.000
23A25LYS10.9130.95725.8150.1190.1190.0000.0000.0000.000
24A26LEU00.0920.04025.566-0.009-0.0090.0000.0000.0000.000
25A27GLN0-0.023-0.02122.342-0.013-0.0130.0000.0000.0000.000
26A28ASP-1-0.779-0.87520.941-0.159-0.1590.0000.0000.0000.000
27A29HIS0-0.006-0.00720.652-0.023-0.0230.0000.0000.0000.000
28A30ILE00.0070.01218.8610.0040.0040.0000.0000.0000.000
29A31LEU0-0.0170.01114.7070.0060.0060.0000.0000.0000.000
30A32TYR00.0460.01716.099-0.030-0.0300.0000.0000.0000.000
31A33TRP00.0030.00316.974-0.016-0.0160.0000.0000.0000.000
32A34THR0-0.024-0.02512.8020.0300.0300.0000.0000.0000.000
33A35ALA0-0.0160.01112.4060.0130.0130.0000.0000.0000.000
34A36VAL00.0660.04012.814-0.019-0.0190.0000.0000.0000.000
35A37ARG10.9240.95913.574-0.072-0.0720.0000.0000.0000.000
36A38THR0-0.072-0.0298.1630.0920.0920.0000.0000.0000.000
37A39GLU-1-0.802-0.87510.186-0.262-0.2620.0000.0000.0000.000
38A40ASN0-0.050-0.04411.5250.0610.0610.0000.0000.0000.000
39A41THR0-0.016-0.02011.1270.0680.0680.0000.0000.0000.000
40A42LEU0-0.058-0.0295.3240.1660.1660.0000.0000.0000.000
41A43LEU00.0350.0199.6690.1430.1430.0000.0000.0000.000
42A44TYR0-0.015-0.01112.6290.0380.0380.0000.0000.0000.000
43A45ALA0-0.022-0.02610.1910.0270.0270.0000.0000.0000.000
44A46ALA0-0.010-0.00110.6890.0840.0840.0000.0000.0000.000
45A47ARG10.9460.98111.951-0.120-0.1200.0000.0000.0000.000
46A48LYS10.8950.96115.076-0.241-0.2410.0000.0000.0000.000
47A49LYS10.9250.9699.256-1.115-1.1150.0000.0000.0000.000
48A50GLY0-0.0030.00614.712-0.002-0.0020.0000.0000.0000.000
49A51VAL0-0.0140.00511.169-0.030-0.0300.0000.0000.0000.000
50A52THR0-0.034-0.03514.397-0.038-0.0380.0000.0000.0000.000
51A53VAL00.0030.00714.108-0.042-0.0420.0000.0000.0000.000
52A54LEU00.0310.0257.5760.0860.0860.0000.0000.0000.000
53A55GLY00.0510.0319.698-0.088-0.0880.0000.0000.0000.000
54A56HIS0-0.009-0.01610.8600.1040.1040.0000.0000.0000.000
55A57CYS0-0.027-0.01413.4080.0140.0140.0000.0000.0000.000
56A58ARG10.9760.98114.6290.1450.1450.0000.0000.0000.000
57A59VAL0-0.0070.00813.295-0.028-0.0280.0000.0000.0000.000
58A60PRO00.0070.00416.1720.0240.0240.0000.0000.0000.000
59A61HIS00.1000.02418.5640.0330.0330.0000.0000.0000.000
60A62SER00.0420.01318.583-0.006-0.0060.0000.0000.0000.000
61A63VAL00.0200.00619.5750.0040.0040.0000.0000.0000.000
62A64VAL00.0140.01520.906-0.007-0.0070.0000.0000.0000.000
63A65CYS0-0.066-0.02116.165-0.013-0.0130.0000.0000.0000.000
64A66GLN00.008-0.00917.958-0.013-0.0130.0000.0000.0000.000
65A67GLU-1-0.879-0.94519.4230.0510.0510.0000.0000.0000.000
66A68ARG10.9891.00818.9120.0530.0530.0000.0000.0000.000
67A69ALA0-0.0020.00716.336-0.013-0.0130.0000.0000.0000.000
68A70LYS10.9410.96017.746-0.093-0.0930.0000.0000.0000.000
69A71GLN00.0010.00920.923-0.011-0.0110.0000.0000.0000.000
70A72ALA00.0230.00617.737-0.005-0.0050.0000.0000.0000.000
71A73ILE0-0.079-0.04117.3170.0000.0000.0000.0000.0000.000
72A74GLU-1-0.852-0.92319.6100.0250.0250.0000.0000.0000.000
73A75MET0-0.0040.01121.7940.0020.0020.0000.0000.0000.000
74A76GLN00.0340.03216.3420.0100.0100.0000.0000.0000.000
75A77LEU0-0.054-0.04119.2940.0010.0010.0000.0000.0000.000
76A78SER00.0160.01822.4620.0010.0010.0000.0000.0000.000
77A79LEU00.0440.02223.110-0.001-0.0010.0000.0000.0000.000
78A80GLN0-0.020-0.01419.023-0.011-0.0110.0000.0000.0000.000
79A81GLU-1-0.918-0.96223.8540.0330.0330.0000.0000.0000.000
80A82LEU00.0200.01827.134-0.001-0.0010.0000.0000.0000.000
81A83SER0-0.039-0.03225.603-0.001-0.0010.0000.0000.0000.000
82A84LYS10.8820.95324.414-0.029-0.0290.0000.0000.0000.000
83A85THR0-0.040-0.01629.4460.0030.0030.0000.0000.0000.000
84A86GLU-1-0.850-0.93832.750-0.013-0.0130.0000.0000.0000.000
85A87PHE00.0090.00233.473-0.003-0.0030.0000.0000.0000.000
86A88GLY0-0.094-0.03130.361-0.005-0.0050.0000.0000.0000.000
87A89ASP-1-0.895-0.93930.225-0.036-0.0360.0000.0000.0000.000
88A90GLU-1-0.925-0.96232.849-0.034-0.0340.0000.0000.0000.000
89A91PRO00.0140.01832.057-0.004-0.0040.0000.0000.0000.000
90A92TRP0-0.029-0.02028.9250.0050.0050.0000.0000.0000.000
91A93SER00.0510.03629.079-0.010-0.0100.0000.0000.0000.000
92A94LEU00.051-0.00123.4690.0060.0060.0000.0000.0000.000
93A95LEU0-0.023-0.00527.1860.0040.0040.0000.0000.0000.000
94A96ASP-1-0.818-0.91730.124-0.049-0.0490.0000.0000.0000.000
95A97THR0-0.0200.00524.5380.0100.0100.0000.0000.0000.000
96A98SER00.0090.01325.730-0.003-0.0030.0000.0000.0000.000
97A99TRP00.064-0.00225.2000.0090.0090.0000.0000.0000.000
98A100ASP-1-0.872-0.93727.142-0.039-0.0390.0000.0000.0000.000
99A101ARG10.8100.91330.3800.0530.0530.0000.0000.0000.000
100A102TYR0-0.035-0.01628.5430.0050.0050.0000.0000.0000.000
101A103MET0-0.040-0.03629.3260.0070.0070.0000.0000.0000.000
102A104SER0-0.054-0.00832.1320.0040.0040.0000.0000.0000.000
103A105GLU-1-0.845-0.91935.3910.0010.0010.0000.0000.0000.000
104A106PRO0-0.053-0.03038.304-0.003-0.0030.0000.0000.0000.000
105A107LYS10.9280.94434.234-0.006-0.0060.0000.0000.0000.000
106A108ARG10.9140.95629.052-0.022-0.0220.0000.0000.0000.000
107A109CYS0-0.0350.01532.3190.0020.0020.0000.0000.0000.000
108A110PHE00.0440.02026.895-0.004-0.0040.0000.0000.0000.000
109A111LYS10.8640.94932.6910.0180.0180.0000.0000.0000.000
110A112LYS10.8510.92933.2600.0380.0380.0000.0000.0000.000
111A113GLY00.0170.01936.6790.0030.0030.0000.0000.0000.000
112A114ALA0-0.017-0.01139.0150.0030.0030.0000.0000.0000.000
113A115ARG10.8610.90540.9890.0200.0200.0000.0000.0000.000
114A116VAL0-0.010-0.00343.9040.0010.0010.0000.0000.0000.000
115A117VAL0-0.0210.00546.0180.0010.0010.0000.0000.0000.000
116A118GLU-1-0.845-0.92548.598-0.022-0.0220.0000.0000.0000.000
117A119VAL0-0.028-0.01450.7100.0010.0010.0000.0000.0000.000
118A120GLU-1-0.902-0.93852.834-0.015-0.0150.0000.0000.0000.000
119A121PHE00.024-0.00451.5820.0020.0020.0000.0000.0000.000
120A122ASP-1-0.778-0.86457.332-0.008-0.0080.0000.0000.0000.000
121A123GLY0-0.0120.01260.2900.0000.0000.0000.0000.0000.000
122A124ASN0-0.032-0.01959.100-0.001-0.0010.0000.0000.0000.000
123A125ALA00.0650.03858.0750.0000.0000.0000.0000.0000.000
124A126SER0-0.065-0.04356.285-0.001-0.0010.0000.0000.0000.000
125A127ASN0-0.085-0.04053.849-0.001-0.0010.0000.0000.0000.000
126A128THR00.0410.02551.6170.0010.0010.0000.0000.0000.000
127A129ASN0-0.021-0.00348.188-0.002-0.0020.0000.0000.0000.000
128A130TRP0-0.052-0.03545.745-0.001-0.0010.0000.0000.0000.000
129A131TYR0-0.061-0.05244.3620.0000.0000.0000.0000.0000.000
130A132THR0-0.019-0.01839.893-0.002-0.0020.0000.0000.0000.000
131A133VAL0-0.0150.01342.1050.0020.0020.0000.0000.0000.000
132A134TYR00.017-0.01237.066-0.005-0.0050.0000.0000.0000.000
133A135SER0-0.006-0.01141.1100.0020.0020.0000.0000.0000.000
134A136ASN0-0.018-0.00639.0130.0040.0040.0000.0000.0000.000
135A137LEU0-0.002-0.01337.432-0.002-0.0020.0000.0000.0000.000
136A138TYR0-0.015-0.03233.8290.0010.0010.0000.0000.0000.000
137A139MET00.008-0.00834.0970.0010.0010.0000.0000.0000.000
138A140ARG10.9260.98627.261-0.032-0.0320.0000.0000.0000.000
139A141THR0-0.004-0.00933.8230.0010.0010.0000.0000.0000.000
140A142GLU-1-0.934-0.97035.4870.0420.0420.0000.0000.0000.000
141A143ASP-1-0.973-0.96936.8690.0230.0230.0000.0000.0000.000
142A144GLY0-0.021-0.00933.965-0.002-0.0020.0000.0000.0000.000
143A145TRP0-0.060-0.06129.050-0.004-0.0040.0000.0000.0000.000
144A146GLN0-0.004-0.00534.594-0.003-0.0030.0000.0000.0000.000
145A147LEU0-0.0220.00337.817-0.001-0.0010.0000.0000.0000.000
146A148ALA00.0140.01639.6240.0020.0020.0000.0000.0000.000
147A149LYS10.9390.96341.4870.0130.0130.0000.0000.0000.000
148A150ALA00.0220.01542.6510.0020.0020.0000.0000.0000.000
149A151GLY0-0.048-0.02544.753-0.002-0.0020.0000.0000.0000.000
150A152ALA00.0190.01147.5430.0010.0010.0000.0000.0000.000
151A153ASP-1-0.801-0.86450.051-0.005-0.0050.0000.0000.0000.000
152A154GLY00.0650.01253.3020.0000.0000.0000.0000.0000.000
153A155THR0-0.0300.03353.2030.0010.0010.0000.0000.0000.000
154A156GLY00.027-0.01250.4080.0010.0010.0000.0000.0000.000
155A157LEU0-0.0210.01344.388-0.001-0.0010.0000.0000.0000.000
156A158TYR0-0.006-0.01746.6720.0020.0020.0000.0000.0000.000
157A159TYR00.024-0.00642.006-0.002-0.0020.0000.0000.0000.000
158A160CYS0-0.039-0.01645.4110.0020.0020.0000.0000.0000.000
159A161THR00.0810.04042.500-0.001-0.0010.0000.0000.0000.000
160A162MET0-0.024-0.02445.2200.0000.0000.0000.0000.0000.000
161A163ALA00.0240.02244.9290.0010.0010.0000.0000.0000.000
162A164GLY00.006-0.01047.0540.0020.0020.0000.0000.0000.000
163A165ALA0-0.041-0.00250.163-0.001-0.0010.0000.0000.0000.000
164A166GLY00.012-0.00151.2360.0000.0000.0000.0000.0000.000
165A167ARG10.8670.94049.4320.0050.0050.0000.0000.0000.000
166A168ILE00.0190.01444.7450.0010.0010.0000.0000.0000.000
167A169TYR0-0.085-0.07846.175-0.001-0.0010.0000.0000.0000.000
168A170TYR0-0.004-0.00442.5450.0020.0020.0000.0000.0000.000
169A171SER0-0.0210.00144.3880.0000.0000.0000.0000.0000.000
170A172ARG10.9870.99146.392-0.004-0.0040.0000.0000.0000.000
171A173PHE00.0760.03348.6980.0000.0000.0000.0000.0000.000
172A174GLY00.0450.02452.0660.0000.0000.0000.0000.0000.000
173A175ASP-1-0.863-0.95550.4360.0030.0030.0000.0000.0000.000
174A176GLU-1-0.906-0.94647.157-0.007-0.0070.0000.0000.0000.000
175A177ALA00.0120.00950.993-0.001-0.0010.0000.0000.0000.000
176A178ALA0-0.0380.02553.5930.0000.0000.0000.0000.0000.000
177A179ARG10.8500.93944.7160.0030.0030.0000.0000.0000.000
178A180PHE0-0.024-0.01846.9550.0000.0000.0000.0000.0000.000
179A181SER0-0.078-0.05153.146-0.001-0.0010.0000.0000.0000.000
180A182THR0-0.062-0.03956.7880.0010.0010.0000.0000.0000.000
181A183THR0-0.064-0.07760.1370.0010.0010.0000.0000.0000.000
182A184GLY0-0.0070.01358.9350.0010.0010.0000.0000.0000.000
183A185HIS00.003-0.02759.0590.0000.0000.0000.0000.0000.000
184A186TYR0-0.026-0.03355.7600.0000.0000.0000.0000.0000.000
185A187SER0-0.055-0.02057.3780.0000.0000.0000.0000.0000.000
186A188VAL00.020-0.00652.472-0.001-0.0010.0000.0000.0000.000
187A189ARG10.9670.99554.1680.0200.0200.0000.0000.0000.000
188A190ASP-1-0.833-0.90050.376-0.019-0.0190.0000.0000.0000.000
189A191GLN0-0.046-0.03550.856-0.002-0.0020.0000.0000.0000.000
190A192ASP-1-0.923-0.96353.611-0.019-0.0190.0000.0000.0000.000
191A193ARG10.9230.96255.4860.0150.0150.0000.0000.0000.000
192A194VAL00.0330.02656.312-0.001-0.0010.0000.0000.0000.000
193A195TYR0-0.039-0.00954.5150.0010.0010.0000.0000.0000.000
194A196ALA00.0480.00758.490-0.001-0.0010.0000.0000.0000.000
195A197GLY0-0.029-0.00258.7370.0010.0010.0000.0000.0000.000
196A198VAL00.005-0.00459.7160.0000.0000.0000.0000.0000.000
197A199SER0-0.0420.01756.7450.0010.0010.0000.0000.0000.000