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: LJG19

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 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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2083127.322878
FMO2-HF: Nuclear repulsion 2002977.034909
FMO2-HF: Total energy -80150.287969
FMO2-MP2: Total energy -80380.058367


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.
-25.705-23.98516.261-8.98-9-0.091
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 : 0.010 / q_NPA : -0.017
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].
3A5CYS00.0030.0023.064-0.4521.490-0.002-0.856-1.0840.002
4A6GLU-1-0.754-0.8701.919-26.989-28.22115.532-7.728-6.572-0.095
5A7ARG10.9520.9682.5880.8041.7410.732-0.393-1.2760.002
6A8LEU0-0.033-0.0065.4000.7850.858-0.001-0.003-0.0680.000
7A9HIS0-0.007-0.0037.9270.2610.2610.0000.0000.0000.000
8A10VAL00.0280.0097.8810.3620.3620.0000.0000.0000.000
9A11ALA0-0.0220.0049.4400.3050.3050.0000.0000.0000.000
10A12GLN0-0.044-0.03511.2200.0510.0510.0000.0000.0000.000
11A13GLU-1-0.809-0.88013.061-0.736-0.7360.0000.0000.0000.000
12A14THR0-0.043-0.03712.5770.1360.1360.0000.0000.0000.000
13A15GLN0-0.082-0.08214.4030.1580.1580.0000.0000.0000.000
14A16MET0-0.025-0.00217.3700.0500.0500.0000.0000.0000.000
15A17GLN00.018-0.01217.2110.0900.0900.0000.0000.0000.000
16A18LEU0-0.050-0.02817.7480.0490.0490.0000.0000.0000.000
17A19ILE0-0.030-0.01820.9750.0390.0390.0000.0000.0000.000
18A20GLU-1-0.923-0.96723.000-0.354-0.3540.0000.0000.0000.000
19A21LYS10.7910.88722.2780.2440.2440.0000.0000.0000.000
20A22SER0-0.039-0.02625.2050.0250.0250.0000.0000.0000.000
21A23SER0-0.063-0.04725.2270.0200.0200.0000.0000.0000.000
22A24ASP-1-0.834-0.91827.162-0.104-0.1040.0000.0000.0000.000
23A25LYS10.8710.93425.4150.1250.1250.0000.0000.0000.000
24A26LEU00.0920.05125.251-0.013-0.0130.0000.0000.0000.000
25A27GLN00.0230.00122.512-0.013-0.0130.0000.0000.0000.000
26A28ASP-1-0.760-0.84020.855-0.207-0.2070.0000.0000.0000.000
27A29HIS00.0300.00520.371-0.035-0.0350.0000.0000.0000.000
28A30ILE0-0.0090.00618.804-0.001-0.0010.0000.0000.0000.000
29A31LEU0-0.0090.01614.3280.0080.0080.0000.0000.0000.000
30A32TYR00.0490.02215.945-0.027-0.0270.0000.0000.0000.000
31A33TRP00.020-0.00316.986-0.031-0.0310.0000.0000.0000.000
32A34THR0-0.031-0.03412.7730.0320.0320.0000.0000.0000.000
33A35ALA0-0.0200.01312.484-0.002-0.0020.0000.0000.0000.000
34A36VAL00.0340.02513.153-0.047-0.0470.0000.0000.0000.000
35A37ARG10.9110.95113.739-0.107-0.1070.0000.0000.0000.000
36A38THR0-0.058-0.0208.2530.0970.0970.0000.0000.0000.000
37A39GLU-1-0.763-0.86910.230-0.643-0.6430.0000.0000.0000.000
38A40ASN0-0.040-0.04011.8450.0530.0530.0000.0000.0000.000
39A41THR0-0.016-0.02411.2690.0910.0910.0000.0000.0000.000
40A42LEU0-0.040-0.0145.7560.2160.2160.0000.0000.0000.000
41A43LEU00.0030.0079.9960.1160.1160.0000.0000.0000.000
42A44TYR00.013-0.00313.0010.0590.0590.0000.0000.0000.000
43A45ALA0-0.021-0.02010.0580.0530.0530.0000.0000.0000.000
44A46ALA00.0020.00810.8060.1180.1180.0000.0000.0000.000
45A47ARG10.8890.93612.0500.0770.0770.0000.0000.0000.000
46A48LYS10.8450.92814.866-0.160-0.1600.0000.0000.0000.000
47A49LYS10.9110.9599.300-0.896-0.8960.0000.0000.0000.000
48A50GLY00.0230.02414.661-0.003-0.0030.0000.0000.0000.000
49A51VAL0-0.021-0.00511.287-0.048-0.0480.0000.0000.0000.000
50A52THR00.010-0.00414.566-0.047-0.0470.0000.0000.0000.000
51A53VAL0-0.026-0.01214.573-0.031-0.0310.0000.0000.0000.000
52A54LEU00.0280.0177.5770.0790.0790.0000.0000.0000.000
53A55GLY00.0660.03910.138-0.113-0.1130.0000.0000.0000.000
54A56HIS0-0.018-0.02011.1640.1730.1730.0000.0000.0000.000
55A57CYS0-0.0010.00813.5620.0980.0980.0000.0000.0000.000
56A58ARG10.9520.97314.8620.3490.3490.0000.0000.0000.000
57A59VAL00.0170.02213.354-0.029-0.0290.0000.0000.0000.000
58A60PRO00.0340.01716.0820.0620.0620.0000.0000.0000.000
59A61HIS00.0900.03518.6160.0300.0300.0000.0000.0000.000
60A62SER00.0140.01418.4220.0040.0040.0000.0000.0000.000
61A63VAL00.0660.02119.4050.0050.0050.0000.0000.0000.000
62A64VAL00.0130.01021.425-0.001-0.0010.0000.0000.0000.000
63A65CYS0-0.055-0.02016.518-0.027-0.0270.0000.0000.0000.000
64A66GLN00.0220.00118.364-0.006-0.0060.0000.0000.0000.000
65A67GLU-1-0.794-0.88819.8830.0410.0410.0000.0000.0000.000
66A68ARG10.9600.99419.0530.2020.2020.0000.0000.0000.000
67A69ALA00.0040.00516.606-0.008-0.0080.0000.0000.0000.000
68A70LYS10.8050.88718.040-0.041-0.0410.0000.0000.0000.000
69A71GLN00.0010.01021.305-0.010-0.0100.0000.0000.0000.000
70A72ALA00.0230.01217.8020.0010.0010.0000.0000.0000.000
71A73ILE0-0.048-0.02517.1010.0090.0090.0000.0000.0000.000
72A74GLU-1-0.754-0.81919.6900.0180.0180.0000.0000.0000.000
73A75MET00.0020.02621.9550.0080.0080.0000.0000.0000.000
74A76GLN00.0320.01815.6920.0120.0120.0000.0000.0000.000
75A77LEU0-0.060-0.03919.8520.0080.0080.0000.0000.0000.000
76A78SER00.0280.00822.3740.0050.0050.0000.0000.0000.000
77A79LEU00.0260.02422.993-0.002-0.0020.0000.0000.0000.000
78A80GLN00.0070.01318.551-0.006-0.0060.0000.0000.0000.000
79A81GLU-1-0.826-0.85623.4460.0620.0620.0000.0000.0000.000
80A82LEU00.0230.02126.8830.0000.0000.0000.0000.0000.000
81A83SER0-0.022-0.03225.1000.0020.0020.0000.0000.0000.000
82A84LYS10.8110.90723.952-0.055-0.0550.0000.0000.0000.000
83A85THR0-0.024-0.02329.2930.0040.0040.0000.0000.0000.000
84A86GLU-1-0.841-0.92232.422-0.007-0.0070.0000.0000.0000.000
85A87PHE0-0.005-0.01433.358-0.005-0.0050.0000.0000.0000.000
86A88GLY0-0.060-0.03330.172-0.008-0.0080.0000.0000.0000.000
87A89ASP-1-0.909-0.94630.038-0.033-0.0330.0000.0000.0000.000
88A90GLU-1-0.880-0.90832.559-0.043-0.0430.0000.0000.0000.000
89A91PRO0-0.0010.01231.816-0.004-0.0040.0000.0000.0000.000
90A92TRP0-0.030-0.03528.9370.0060.0060.0000.0000.0000.000
91A93SER00.0400.00729.095-0.013-0.0130.0000.0000.0000.000
92A94LEU00.0340.01823.7220.0090.0090.0000.0000.0000.000
93A95LEU0-0.0110.00527.2950.0040.0040.0000.0000.0000.000
94A96ASP-1-0.790-0.86330.257-0.076-0.0760.0000.0000.0000.000
95A97THR0-0.025-0.01224.9710.0150.0150.0000.0000.0000.000
96A98SER0-0.001-0.00125.805-0.006-0.0060.0000.0000.0000.000
97A99TRP00.047-0.00825.2810.0160.0160.0000.0000.0000.000
98A100ASP-1-0.879-0.94427.242-0.093-0.0930.0000.0000.0000.000
99A101ARG10.7920.89530.5130.0860.0860.0000.0000.0000.000
100A102TYR0-0.048-0.03428.3900.0080.0080.0000.0000.0000.000
101A103MET0-0.028-0.02029.6220.0130.0130.0000.0000.0000.000
102A104SER0-0.036-0.01232.3810.0050.0050.0000.0000.0000.000
103A105GLU-1-0.752-0.84635.560-0.015-0.0150.0000.0000.0000.000
104A106PRO0-0.025-0.00138.680-0.004-0.0040.0000.0000.0000.000
105A107LYS10.8460.88134.5720.0140.0140.0000.0000.0000.000
106A108ARG10.8360.88128.151-0.008-0.0080.0000.0000.0000.000
107A109CYS0-0.0500.00132.4980.0050.0050.0000.0000.0000.000
108A110PHE00.0540.02326.702-0.008-0.0080.0000.0000.0000.000
109A111LYS10.8140.89732.3890.0410.0410.0000.0000.0000.000
110A112LYS10.8220.91133.2740.0460.0460.0000.0000.0000.000
111A113GLY00.0360.03236.9160.0050.0050.0000.0000.0000.000
112A114ALA0-0.030-0.01738.7460.0040.0040.0000.0000.0000.000
113A115ARG10.8600.91240.7620.0330.0330.0000.0000.0000.000
114A116VAL0-0.002-0.00343.7010.0000.0000.0000.0000.0000.000
115A117VAL0-0.0230.00545.8110.0020.0020.0000.0000.0000.000
116A118GLU-1-0.782-0.86848.426-0.042-0.0420.0000.0000.0000.000
117A119VAL0-0.015-0.01650.6030.0020.0020.0000.0000.0000.000
118A120GLU-1-0.871-0.91452.858-0.030-0.0300.0000.0000.0000.000
119A121PHE00.037-0.00251.5810.0030.0030.0000.0000.0000.000
120A122ASP-1-0.735-0.84757.358-0.022-0.0220.0000.0000.0000.000
121A123GLY0-0.0050.01360.6370.0000.0000.0000.0000.0000.000
122A124ASN0-0.079-0.03859.899-0.001-0.0010.0000.0000.0000.000
123A125ALA00.0980.04957.975-0.001-0.0010.0000.0000.0000.000
124A126SER0-0.060-0.02956.355-0.002-0.0020.0000.0000.0000.000
125A127ASN0-0.076-0.03354.603-0.003-0.0030.0000.0000.0000.000
126A128THR00.013-0.01252.1760.0030.0030.0000.0000.0000.000
127A129ASN0-0.0270.00048.428-0.004-0.0040.0000.0000.0000.000
128A130TRP0-0.074-0.05745.798-0.001-0.0010.0000.0000.0000.000
129A131TYR0-0.022-0.03844.395-0.001-0.0010.0000.0000.0000.000
130A132THR0-0.012-0.00539.4050.0000.0000.0000.0000.0000.000
131A133VAL0-0.0140.00442.5520.0040.0040.0000.0000.0000.000
132A134TYR00.008-0.01836.795-0.007-0.0070.0000.0000.0000.000
133A135SER00.008-0.00440.9560.0030.0030.0000.0000.0000.000
134A136ASN0-0.024-0.00539.0390.0050.0050.0000.0000.0000.000
135A137LEU00.012-0.00537.459-0.005-0.0050.0000.0000.0000.000
136A138TYR0-0.017-0.03833.8960.0020.0020.0000.0000.0000.000
137A139MET0-0.022-0.02234.145-0.001-0.0010.0000.0000.0000.000
138A140ARG10.8520.91327.501-0.041-0.0410.0000.0000.0000.000
139A141THR0-0.023-0.01133.588-0.002-0.0020.0000.0000.0000.000
140A142GLU-1-0.908-0.95335.1470.0590.0590.0000.0000.0000.000
141A143ASP-1-0.964-0.97736.4290.0350.0350.0000.0000.0000.000
142A144GLY0-0.0150.00133.764-0.001-0.0010.0000.0000.0000.000
143A145TRP0-0.080-0.07128.870-0.008-0.0080.0000.0000.0000.000
144A146GLN00.0460.04434.170-0.004-0.0040.0000.0000.0000.000
145A147LEU0-0.029-0.00537.417-0.003-0.0030.0000.0000.0000.000
146A148ALA00.0050.01139.1940.0030.0030.0000.0000.0000.000
147A149LYS10.8880.93441.2610.0210.0210.0000.0000.0000.000
148A150ALA00.0030.00643.0950.0030.0030.0000.0000.0000.000
149A151GLY0-0.037-0.01644.950-0.003-0.0030.0000.0000.0000.000
150A152ALA00.0520.03447.8200.0010.0010.0000.0000.0000.000
151A153ASP-1-0.787-0.85350.346-0.012-0.0120.0000.0000.0000.000
152A154GLY00.0750.02253.716-0.001-0.0010.0000.0000.0000.000
153A155THR0-0.025-0.00853.6990.0010.0010.0000.0000.0000.000
154A156GLY0-0.026-0.02650.5810.0010.0010.0000.0000.0000.000
155A157LEU0-0.0270.02044.763-0.001-0.0010.0000.0000.0000.000
156A158TYR0-0.002-0.01646.6640.0030.0030.0000.0000.0000.000
157A159TYR00.014-0.00641.235-0.003-0.0030.0000.0000.0000.000
158A160CYS0-0.056-0.02845.2560.0020.0020.0000.0000.0000.000
159A161THR00.066-0.00642.738-0.002-0.0020.0000.0000.0000.000
160A162MET0-0.011-0.00945.2400.0000.0000.0000.0000.0000.000
161A163ALA00.0270.02744.4700.0020.0020.0000.0000.0000.000
162A164GLY00.000-0.00846.6120.0020.0020.0000.0000.0000.000
163A165ALA0-0.038-0.00349.738-0.002-0.0020.0000.0000.0000.000
164A166GLY00.013-0.00151.0000.0000.0000.0000.0000.0000.000
165A167ARG10.8770.94349.4980.0110.0110.0000.0000.0000.000
166A168ILE00.0310.01944.3680.0010.0010.0000.0000.0000.000
167A169TYR0-0.079-0.08146.039-0.002-0.0020.0000.0000.0000.000
168A170TYR0-0.027-0.01342.3250.0030.0030.0000.0000.0000.000
169A171SER0-0.033-0.00444.269-0.001-0.0010.0000.0000.0000.000
170A172ARG10.9940.99146.5080.0060.0060.0000.0000.0000.000
171A173PHE00.0430.02048.9500.0000.0000.0000.0000.0000.000
172A174GLY00.0600.05052.461-0.001-0.0010.0000.0000.0000.000
173A175ASP-1-0.873-0.94650.547-0.008-0.0080.0000.0000.0000.000
174A176GLU-1-0.812-0.86147.398-0.025-0.0250.0000.0000.0000.000
175A177ALA00.0440.02051.015-0.001-0.0010.0000.0000.0000.000
176A178ALA0-0.046-0.00753.6460.0000.0000.0000.0000.0000.000
177A179ARG10.7730.86347.4260.0200.0200.0000.0000.0000.000
178A180PHE0-0.033-0.01147.198-0.002-0.0020.0000.0000.0000.000
179A181SER0-0.072-0.02053.445-0.001-0.0010.0000.0000.0000.000
180A182THR0-0.061-0.06057.2060.0010.0010.0000.0000.0000.000
181A183THR0-0.075-0.05360.5130.0010.0010.0000.0000.0000.000
182A184GLY00.0250.02359.2060.0010.0010.0000.0000.0000.000
183A185HIS00.002-0.01459.3870.0000.0000.0000.0000.0000.000
184A186TYR0-0.050-0.03555.990-0.001-0.0010.0000.0000.0000.000
185A187SER0-0.058-0.02457.5020.0010.0010.0000.0000.0000.000
186A188VAL00.0070.00152.547-0.001-0.0010.0000.0000.0000.000
187A189ARG10.8620.91254.0150.0370.0370.0000.0000.0000.000
188A190ASP-1-0.834-0.88850.330-0.032-0.0320.0000.0000.0000.000
189A191GLN0-0.019-0.03450.413-0.003-0.0030.0000.0000.0000.000
190A192ASP-1-0.840-0.90053.585-0.029-0.0290.0000.0000.0000.000
191A193ARG10.8250.90655.0700.0260.0260.0000.0000.0000.000
192A194VAL00.0460.01456.631-0.002-0.0020.0000.0000.0000.000
193A195TYR0-0.035-0.00353.9710.0020.0020.0000.0000.0000.000
194A196ALA00.025-0.00258.630-0.001-0.0010.0000.0000.0000.000
195A197GLY0-0.022-0.00259.0620.0010.0010.0000.0000.0000.000
196A198VAL00.0340.01460.012-0.001-0.0010.0000.0000.0000.000
197A199SER0-0.117-0.05856.5210.0020.0020.0000.0000.0000.000