Manual

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: 3J6GL

Calculation Name: 2QOP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2QOP

Chain ID: A

ChEMBL ID:

UniProt ID: P0ACS9

Base Structure: X-ray

Registration Date: 2023-09-24

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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2358002.803069
FMO2-HF: Nuclear repulsion 2273897.695126
FMO2-HF: Total energy -84105.107943
FMO2-MP2: Total energy -84346.608177


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:7:GLN)


Summations of interaction energy for fragment #1(A:7:GLN)
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.
-3.3150.3910.049-1.56-2.1950.004
Interaction energy analysis for fragmet #1(A:7:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.037 / q_NPA : -0.036
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].
3A9ALA0-0.024-0.0133.340-1.6871.0220.018-1.322-1.4050.005
4A10GLN00.030-0.0093.633-0.0950.6520.032-0.207-0.572-0.001
5A11GLU-1-0.918-0.9394.650-3.568-3.318-0.001-0.031-0.2180.000
6A12THR0-0.055-0.0386.5420.7440.7440.0000.0000.0000.000
7A13ARG10.9080.9718.061-0.250-0.2500.0000.0000.0000.000
8A14GLN00.0840.0239.5520.2780.2780.0000.0000.0000.000
9A15HIS00.0130.02111.1730.0400.0400.0000.0000.0000.000
10A16ILE0-0.029-0.02112.6400.0720.0720.0000.0000.0000.000
11A17LEU00.0130.01413.3900.0400.0400.0000.0000.0000.000
12A18ASP-1-0.854-0.92014.943-0.523-0.5230.0000.0000.0000.000
13A19VAL0-0.078-0.04317.0870.0330.0330.0000.0000.0000.000
14A20ALA00.008-0.00418.6100.0350.0350.0000.0000.0000.000
15A21LEU00.0180.02120.1550.0230.0230.0000.0000.0000.000
16A22ARG10.9350.97318.6490.5230.5230.0000.0000.0000.000
17A23LEU00.0310.01122.1930.0160.0160.0000.0000.0000.000
18A24PHE0-0.030-0.01922.3330.0200.0200.0000.0000.0000.000
19A25SER0-0.011-0.01026.4230.0160.0160.0000.0000.0000.000
20A26GLN0-0.072-0.04226.620-0.004-0.0040.0000.0000.0000.000
21A27GLN0-0.036-0.01428.432-0.008-0.0080.0000.0000.0000.000
22A28GLY00.0340.04129.9740.0130.0130.0000.0000.0000.000
23A29VAL00.0220.00126.512-0.012-0.0120.0000.0000.0000.000
24A30SER0-0.0070.00028.8050.0010.0010.0000.0000.0000.000
25A31SER0-0.061-0.02531.5800.0090.0090.0000.0000.0000.000
26A32THR00.0300.02525.397-0.014-0.0140.0000.0000.0000.000
27A33SER0-0.054-0.03126.1490.0160.0160.0000.0000.0000.000
28A34LEU00.1010.02319.769-0.029-0.0290.0000.0000.0000.000
29A35GLY0-0.061-0.04921.202-0.024-0.0240.0000.0000.0000.000
30A36GLU-1-0.890-0.95223.166-0.191-0.1910.0000.0000.0000.000
31A37ILE00.0390.03118.595-0.032-0.0320.0000.0000.0000.000
32A38ALA0-0.024-0.00418.317-0.053-0.0530.0000.0000.0000.000
33A39LYS10.9190.94918.4660.2520.2520.0000.0000.0000.000
34A40ALA00.0120.01219.5720.0160.0160.0000.0000.0000.000
35A41ALA00.0230.02015.062-0.036-0.0360.0000.0000.0000.000
36A42GLY0-0.062-0.00915.287-0.137-0.1370.0000.0000.0000.000
37A43VAL00.0110.01012.930-0.117-0.1170.0000.0000.0000.000
38A44THR00.0130.00115.3320.0890.0890.0000.0000.0000.000
39A45ARG11.0070.98116.8580.1360.1360.0000.0000.0000.000
40A46GLY0-0.011-0.01018.0680.0370.0370.0000.0000.0000.000
41A47ALA00.0300.02012.6610.0770.0770.0000.0000.0000.000
42A48ILE0-0.013-0.00213.8470.0770.0770.0000.0000.0000.000
43A49TYR0-0.013-0.01716.0370.0010.0010.0000.0000.0000.000
44A50TRP0-0.0480.00010.852-0.065-0.0650.0000.0000.0000.000
45A51HIS0-0.041-0.0168.2460.1770.1770.0000.0000.0000.000
46A52PHE00.0300.01313.2500.0340.0340.0000.0000.0000.000
47A53LYS10.9360.96816.745-0.291-0.2910.0000.0000.0000.000
48A54ASP-1-0.860-0.95920.0370.0940.0940.0000.0000.0000.000
49A55LYS10.9230.95521.6280.0290.0290.0000.0000.0000.000
50A56SER00.0430.02423.536-0.021-0.0210.0000.0000.0000.000
51A57ASP-1-0.854-0.90818.3780.2560.2560.0000.0000.0000.000
52A58LEU0-0.021-0.00117.5480.0060.0060.0000.0000.0000.000
53A59PHE0-0.004-0.01419.422-0.023-0.0230.0000.0000.0000.000
54A60SER0-0.008-0.03421.449-0.012-0.0120.0000.0000.0000.000
55A61GLU-1-0.907-0.94514.7730.3110.3110.0000.0000.0000.000
56A62ILE0-0.037-0.00617.211-0.018-0.0180.0000.0000.0000.000
57A63TRP00.006-0.01719.315-0.025-0.0250.0000.0000.0000.000
58A64GLU-1-0.948-0.95016.8930.2130.2130.0000.0000.0000.000
59A65LEU0-0.053-0.01512.1780.0150.0150.0000.0000.0000.000
60A66SER0-0.107-0.06416.267-0.039-0.0390.0000.0000.0000.000
61A67GLU-1-0.809-0.89518.325-0.067-0.0670.0000.0000.0000.000
62A68SER0-0.006-0.01120.9140.0210.0210.0000.0000.0000.000
63A69ASN00.0450.02220.3850.0040.0040.0000.0000.0000.000
64A70ILE0-0.023-0.03822.5490.0010.0010.0000.0000.0000.000
65A71GLY0-0.0040.00725.2540.0000.0000.0000.0000.0000.000
66A72GLU-1-0.905-0.95419.7820.1420.1420.0000.0000.0000.000
67A73LEU0-0.012-0.01023.640-0.008-0.0080.0000.0000.0000.000
68A74GLU-1-0.988-0.98826.0450.0680.0680.0000.0000.0000.000
69A75LEU00.0190.00324.988-0.002-0.0020.0000.0000.0000.000
70A76GLU-1-0.977-0.96524.591-0.046-0.0460.0000.0000.0000.000
71A77TYR0-0.002-0.03426.854-0.004-0.0040.0000.0000.0000.000
72A78GLN00.015-0.00430.3010.0020.0020.0000.0000.0000.000
73A79ALA0-0.0310.00229.0550.0030.0030.0000.0000.0000.000
74A80LYS10.8780.94829.0300.0300.0300.0000.0000.0000.000
75A81PHE0-0.057-0.02232.545-0.007-0.0070.0000.0000.0000.000
76A82PRO00.0250.01935.4010.0070.0070.0000.0000.0000.000
77A83GLY0-0.029-0.01736.790-0.003-0.0030.0000.0000.0000.000
78A84ASP-1-0.841-0.91338.1990.0120.0120.0000.0000.0000.000
79A85PRO00.0300.01437.291-0.003-0.0030.0000.0000.0000.000
80A86LEU00.057-0.00237.717-0.002-0.0020.0000.0000.0000.000
81A87SER0-0.057-0.05437.679-0.008-0.0080.0000.0000.0000.000
82A88VAL00.0190.03132.325-0.007-0.0070.0000.0000.0000.000
83A89LEU0-0.008-0.00833.814-0.003-0.0030.0000.0000.0000.000
84A90ARG10.8880.95235.8860.0120.0120.0000.0000.0000.000
85A91GLU-1-0.856-0.96132.424-0.046-0.0460.0000.0000.0000.000
86A92ILE00.0110.02329.457-0.011-0.0110.0000.0000.0000.000
87A93LEU0-0.016-0.01731.208-0.008-0.0080.0000.0000.0000.000
88A94ILE0-0.0020.00033.284-0.007-0.0070.0000.0000.0000.000
89A95HIS00.0720.04624.831-0.004-0.0040.0000.0000.0000.000
90A96VAL0-0.0050.01029.191-0.014-0.0140.0000.0000.0000.000
91A97LEU0-0.0060.00030.403-0.010-0.0100.0000.0000.0000.000
92A98GLU-1-0.933-0.96430.722-0.106-0.1060.0000.0000.0000.000
93A99SER00.000-0.01426.024-0.016-0.0160.0000.0000.0000.000
94A100THR0-0.019-0.03227.297-0.015-0.0150.0000.0000.0000.000
95A101VAL0-0.0260.00229.464-0.007-0.0070.0000.0000.0000.000
96A102THR0-0.064-0.06127.186-0.014-0.0140.0000.0000.0000.000
97A103GLU-1-0.915-0.94422.753-0.199-0.1990.0000.0000.0000.000
98A104GLU-1-0.873-0.95821.937-0.307-0.3070.0000.0000.0000.000
99A105ARG10.8740.93014.3680.4120.4120.0000.0000.0000.000
100A106ARG10.8750.95021.8060.1100.1100.0000.0000.0000.000
101A107ARG10.8380.94724.9400.2390.2390.0000.0000.0000.000
102A108LEU0-0.039-0.03323.1370.0120.0120.0000.0000.0000.000
103A109LEU00.0330.02723.6250.0100.0100.0000.0000.0000.000
104A110MET0-0.003-0.01425.4950.0190.0190.0000.0000.0000.000
105A111GLU-1-0.871-0.93528.767-0.115-0.1150.0000.0000.0000.000
106A112ILE0-0.030-0.01525.8630.0060.0060.0000.0000.0000.000
107A113ILE0-0.055-0.02827.2570.0110.0110.0000.0000.0000.000
108A114PHE0-0.003-0.01330.9560.0100.0100.0000.0000.0000.000
109A115HIS00.0090.02533.0270.0050.0050.0000.0000.0000.000
110A116LYS10.8260.93730.3080.1360.1360.0000.0000.0000.000
111A117CYS0-0.022-0.01130.437-0.001-0.0010.0000.0000.0000.000
112A118GLU-1-0.930-0.97431.022-0.032-0.0320.0000.0000.0000.000
113A119PHE0-0.027-0.03131.4830.0050.0050.0000.0000.0000.000
114A120VAL00.0080.01034.2310.0040.0040.0000.0000.0000.000
115A121GLY00.0170.00534.5270.0060.0060.0000.0000.0000.000
116A122GLU-1-0.902-0.97029.1020.0710.0710.0000.0000.0000.000
117A123MET0-0.046-0.00126.7180.0100.0100.0000.0000.0000.000
118A124ALA00.0300.01630.710-0.001-0.0010.0000.0000.0000.000
119A125VAL00.003-0.00228.6940.0060.0060.0000.0000.0000.000
120A126VAL00.0550.02125.6810.0100.0100.0000.0000.0000.000
121A127GLN00.0150.02528.5940.0040.0040.0000.0000.0000.000
122A128GLN0-0.060-0.04431.953-0.006-0.0060.0000.0000.0000.000
123A129ALA00.0130.01527.2260.0070.0070.0000.0000.0000.000
124A130GLN00.0350.00228.2560.0040.0040.0000.0000.0000.000
125A131ARG10.9030.96730.138-0.046-0.0460.0000.0000.0000.000
126A132ASN00.0370.00131.246-0.007-0.0070.0000.0000.0000.000
127A133LEU00.0270.04026.1350.0020.0020.0000.0000.0000.000
128A134CYS0-0.080-0.03930.407-0.007-0.0070.0000.0000.0000.000
129A135LEU0-0.011-0.03533.575-0.004-0.0040.0000.0000.0000.000
130A136GLU-1-0.867-0.92331.7570.1070.1070.0000.0000.0000.000
131A137SER0-0.053-0.01032.133-0.002-0.0020.0000.0000.0000.000
132A138TYR0-0.046-0.03333.518-0.006-0.0060.0000.0000.0000.000
133A139ASP-1-0.838-0.91336.0940.0710.0710.0000.0000.0000.000
134A140ARG10.9540.98327.568-0.096-0.0960.0000.0000.0000.000
135A141ILE00.0040.01534.196-0.002-0.0020.0000.0000.0000.000
136A142GLU-1-0.890-0.96936.8100.0480.0480.0000.0000.0000.000
137A143GLN00.012-0.00337.247-0.002-0.0020.0000.0000.0000.000
138A144THR00.0290.01635.5550.0020.0020.0000.0000.0000.000
139A145LEU0-0.025-0.01937.871-0.004-0.0040.0000.0000.0000.000
140A146LYS10.9210.95241.373-0.053-0.0530.0000.0000.0000.000
141A147HIS00.0540.04437.299-0.001-0.0010.0000.0000.0000.000
142A148CYS0-0.011-0.00540.370-0.003-0.0030.0000.0000.0000.000
143A149ILE0-0.078-0.03042.976-0.003-0.0030.0000.0000.0000.000
144A150GLU-1-0.971-0.99143.0900.0650.0650.0000.0000.0000.000
145A151ALA0-0.019-0.00143.3970.0000.0000.0000.0000.0000.000
146A152LYS10.8680.93645.507-0.035-0.0350.0000.0000.0000.000
147A153MET0-0.0010.01642.544-0.003-0.0030.0000.0000.0000.000
148A154LEU0-0.0010.00143.423-0.004-0.0040.0000.0000.0000.000
149A155PRO0-0.038-0.01547.5580.0030.0030.0000.0000.0000.000
150A156ALA00.0340.00349.8770.0010.0010.0000.0000.0000.000
151A157ASP-1-0.911-0.94551.2770.0230.0230.0000.0000.0000.000
152A158LEU00.0100.01846.025-0.002-0.0020.0000.0000.0000.000
153A159MET0-0.034-0.01148.7970.0030.0030.0000.0000.0000.000
154A160THR00.0260.00943.391-0.003-0.0030.0000.0000.0000.000
155A161ARG10.9931.00940.638-0.052-0.0520.0000.0000.0000.000
156A162ARG10.8930.92644.121-0.019-0.0190.0000.0000.0000.000
157A163ALA00.0460.02743.874-0.004-0.0040.0000.0000.0000.000
158A164ALA00.0310.02039.735-0.004-0.0040.0000.0000.0000.000
159A165ILE0-0.055-0.03240.035-0.002-0.0020.0000.0000.0000.000
160A166ILE0-0.0130.00141.864-0.004-0.0040.0000.0000.0000.000
161A167MET00.0150.02336.018-0.004-0.0040.0000.0000.0000.000
162A168ARG10.9660.97531.404-0.025-0.0250.0000.0000.0000.000
163A169GLY00.004-0.00337.716-0.005-0.0050.0000.0000.0000.000
164A170TYR0-0.048-0.04540.278-0.005-0.0050.0000.0000.0000.000
165A171ILE00.0020.00634.598-0.006-0.0060.0000.0000.0000.000
166A172SER0-0.004-0.02534.809-0.007-0.0070.0000.0000.0000.000
167A173GLY00.0150.02636.100-0.005-0.0050.0000.0000.0000.000
168A174LEU00.0280.01038.516-0.005-0.0050.0000.0000.0000.000
169A175MET0-0.050-0.01930.789-0.004-0.0040.0000.0000.0000.000
170A176GLU-1-0.928-0.96535.279-0.059-0.0590.0000.0000.0000.000
171A177ASN0-0.031-0.02736.564-0.004-0.0040.0000.0000.0000.000
172A178TRP0-0.0230.00032.178-0.008-0.0080.0000.0000.0000.000
173A179LEU0-0.058-0.03531.236-0.007-0.0070.0000.0000.0000.000
174A180PHE0-0.0370.01835.219-0.005-0.0050.0000.0000.0000.000
175A181ALA0-0.034-0.02738.325-0.004-0.0040.0000.0000.0000.000
176A182PRO00.0540.05036.0240.0040.0040.0000.0000.0000.000
177A183GLN0-0.032-0.03638.077-0.004-0.0040.0000.0000.0000.000
178A184SER0-0.101-0.04341.1870.0050.0050.0000.0000.0000.000
179A185PHE00.013-0.00139.3460.0040.0040.0000.0000.0000.000
180A186ASP-1-0.863-0.94137.651-0.120-0.1200.0000.0000.0000.000
181A187LEU00.0290.01034.3700.0060.0060.0000.0000.0000.000
182A188LYS10.9530.97731.6600.1420.1420.0000.0000.0000.000
183A189LYS10.8650.92035.3000.1150.1150.0000.0000.0000.000
184A190GLU-1-0.871-0.91538.359-0.063-0.0630.0000.0000.0000.000
185A191ALA00.0030.01835.5690.0080.0080.0000.0000.0000.000
186A192ARG10.8990.92935.5100.0600.0600.0000.0000.0000.000
187A193ASP-1-0.860-0.91438.942-0.046-0.0460.0000.0000.0000.000
188A194TYR0-0.026-0.01739.0880.0070.0070.0000.0000.0000.000
189A195VAL0-0.0100.00136.6500.0070.0070.0000.0000.0000.000
190A196ALA00.0160.01240.0540.0070.0070.0000.0000.0000.000
191A197ILE00.0560.03443.1440.0050.0050.0000.0000.0000.000
192A198LEU0-0.077-0.03039.9960.0050.0050.0000.0000.0000.000
193A199LEU00.000-0.02139.8400.0050.0050.0000.0000.0000.000
194A200GLU-1-0.939-0.96943.837-0.014-0.0140.0000.0000.0000.000
195A201MET0-0.049-0.01844.8680.0020.0020.0000.0000.0000.000
196A202TYR0-0.010-0.01542.1990.0020.0020.0000.0000.0000.000
197A203LEU00.0370.00546.7680.0040.0040.0000.0000.0000.000
198A204LEU0-0.054-0.02150.0220.0000.0000.0000.0000.0000.000
199A205CYS0-0.045-0.00151.1410.0000.0000.0000.0000.0000.000
200A206PRO00.0950.05153.0590.0030.0030.0000.0000.0000.000
201A207THR0-0.085-0.02853.901-0.001-0.0010.0000.0000.0000.000
202A208LEU0-0.007-0.03048.1130.0020.0020.0000.0000.0000.000
203A209ARG10.8950.96751.696-0.010-0.0100.0000.0000.0000.000
204A210ASN0-0.024-0.02153.414-0.002-0.0020.0000.0000.0000.000
205A211PRO00.0110.01056.0210.0010.0010.0000.0000.0000.000
206A212ALA00.0040.01057.3030.0020.0020.0000.0000.0000.000