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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: Q1Q5Y

Calculation Name: 3X2R-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3X2R

Chain ID: D

ChEMBL ID:

UniProt ID: A0A0F6

Base Structure: X-ray

Registration Date: 2023-06-20

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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1694382.215996
FMO2-HF: Nuclear repulsion 1621022.935487
FMO2-HF: Total energy -73359.280509
FMO2-MP2: Total energy -73573.919603


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(D:48:LYS)


Summations of interaction energy for fragment #1(D:48:LYS)
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.
-23.62-26.82324.974-6.695-15.077-0.048
Interaction energy analysis for fragmet #1(D:48:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.947 / q_NPA : 0.983
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].
3D50PHE0-0.033-0.0193.791-3.151-0.464-0.032-1.348-1.3080.006
4D51VAL00.0530.0346.0182.3932.3930.0000.0000.0000.000
5D52SER0-0.027-0.0288.492-0.475-0.4750.0000.0000.0000.000
6D53VAL0-0.0020.00111.8220.5520.5520.0000.0000.0000.000
7D54TYR00.0200.01114.361-0.016-0.0160.0000.0000.0000.000
8D55ASN00.009-0.00917.9110.3890.3890.0000.0000.0000.000
9D56ILE0-0.0020.02317.973-0.166-0.1660.0000.0000.0000.000
10D57GLN0-0.039-0.01420.9150.0220.0220.0000.0000.0000.000
11D58ASP-1-0.836-0.92424.601-10.645-10.6450.0000.0000.0000.000
12D59GLU-1-0.918-0.96927.058-10.830-10.8300.0000.0000.0000.000
13D60THR00.0050.00729.4560.3940.3940.0000.0000.0000.000
14D61GLY0-0.018-0.00231.5080.3150.3150.0000.0000.0000.000
15D62GLN0-0.042-0.02433.6180.5430.5430.0000.0000.0000.000
16D63PHE0-0.005-0.01834.611-0.262-0.2620.0000.0000.0000.000
17D64LYS10.8920.95334.4849.1949.1940.0000.0000.0000.000
18D65PRO00.0430.03438.3740.1310.1310.0000.0000.0000.000
19D66TYR00.0260.02042.035-0.057-0.0570.0000.0000.0000.000
20D67PRO00.002-0.03443.584-0.021-0.0210.0000.0000.0000.000
21D68ALA0-0.062-0.00739.6580.0060.0060.0000.0000.0000.000
22D69SER00.0520.03139.9200.1440.1440.0000.0000.0000.000
23D70ASN00.0720.04140.113-0.169-0.1690.0000.0000.0000.000
24D71PHE0-0.012-0.01338.123-0.056-0.0560.0000.0000.0000.000
25D72SER0-0.100-0.05735.713-0.277-0.2770.0000.0000.0000.000
26D73THR00.0720.04230.8610.2620.2620.0000.0000.0000.000
27D74ALA0-0.036-0.02133.5810.0140.0140.0000.0000.0000.000
28D75VAL00.0170.00227.337-0.175-0.1750.0000.0000.0000.000
29D76PRO0-0.033-0.00725.2110.0520.0520.0000.0000.0000.000
30D77GLN00.0610.01726.137-0.040-0.0400.0000.0000.0000.000
31D78SER00.0070.00421.690-0.204-0.2040.0000.0000.0000.000
32D79ALA00.0390.02519.831-0.912-0.9120.0000.0000.0000.000
33D80THR00.003-0.00416.7870.3370.3370.0000.0000.0000.000
34D81ALA00.0140.02416.314-0.514-0.5140.0000.0000.0000.000
35D82MET00.0020.00015.314-1.287-1.2870.0000.0000.0000.000
36D83LEU00.0520.04113.425-0.919-0.9190.0000.0000.0000.000
37D84VAL00.0220.00811.371-1.750-1.7500.0000.0000.0000.000
38D85THR00.024-0.02410.809-2.597-2.5970.0000.0000.0000.000
39D86ALA00.0530.04810.882-1.645-1.6450.0000.0000.0000.000
40D87LEU0-0.006-0.0118.374-1.821-1.8210.0000.0000.0000.000
41D88LYS10.9120.9563.79947.38247.526-0.001-0.007-0.1360.000
42D89ASP-1-0.930-0.9725.932-35.745-35.7450.0000.0000.0000.000
43D90SER0-0.0180.0037.7620.4160.4160.0000.0000.0000.000
44D91ARG10.7320.8911.93638.45838.5832.723-0.861-1.987-0.010
45D92TRP00.065-0.0031.914-1.949-3.97413.857-6.429-5.404-0.016
46D93PHE00.0790.0342.5387.6315.1290.4423.824-1.763-0.012
47D94ILE0-0.126-0.0591.960-12.153-13.9067.986-1.839-4.393-0.016
48D95PRO00.0550.0264.4613.2083.329-0.001-0.035-0.0860.000
49D96LEU0-0.038-0.0247.924-0.677-0.6770.0000.0000.0000.000
50D97GLU-1-0.910-0.95910.261-17.471-17.4710.0000.0000.0000.000
51D98ARG10.8440.92312.98420.39620.3960.0000.0000.0000.000
52D99GLN00.0880.07916.5560.2410.2410.0000.0000.0000.000
53D100GLY0-0.004-0.00418.9260.8020.8020.0000.0000.0000.000
54D101LEU00.003-0.00918.053-0.190-0.1900.0000.0000.0000.000
55D102GLN00.0340.01619.891-0.123-0.1230.0000.0000.0000.000
56D103ASN00.0500.00821.7750.7300.7300.0000.0000.0000.000
57D104LEU00.0500.04515.8060.1910.1910.0000.0000.0000.000
58D105LEU0-0.013-0.02320.5020.1010.1010.0000.0000.0000.000
59D106ASN0-0.029-0.02522.8810.5880.5880.0000.0000.0000.000
60D107GLU-1-0.854-0.92021.085-12.956-12.9560.0000.0000.0000.000
61D108ARG10.9140.95317.94916.22816.2280.0000.0000.0000.000
62D109LYS10.8670.94423.30811.62111.6210.0000.0000.0000.000
63D110ILE00.0440.03426.1200.3720.3720.0000.0000.0000.000
64D111ILE0-0.030-0.01721.2620.1860.1860.0000.0000.0000.000
65D112ARG10.9080.94623.32412.65312.6530.0000.0000.0000.000
66D113ALA00.0300.02227.4230.2860.2860.0000.0000.0000.000
67D114ALA0-0.031-0.01228.1720.3060.3060.0000.0000.0000.000
68D115GLN0-0.083-0.03724.2290.1120.1120.0000.0000.0000.000
69D116GLU-1-0.990-0.97629.837-9.853-9.8530.0000.0000.0000.000
70D129GLN00.0440.00919.021-0.195-0.1950.0000.0000.0000.000
71D130SER0-0.017-0.01417.5120.6210.6210.0000.0000.0000.000
72D131LEU0-0.029-0.02615.212-0.734-0.7340.0000.0000.0000.000
73D132THR0-0.0110.0129.5620.9560.9560.0000.0000.0000.000
74D133ALA00.0620.02312.5750.2010.2010.0000.0000.0000.000
75D134ALA0-0.013-0.0189.971-1.851-1.8510.0000.0000.0000.000
76D135ASN00.0340.01310.1802.1322.1320.0000.0000.0000.000
77D136ILE00.0010.0128.3840.8420.8420.0000.0000.0000.000
78D137MET00.009-0.00211.445-1.218-1.2180.0000.0000.0000.000
79D138VAL0-0.047-0.01211.7060.2640.2640.0000.0000.0000.000
80D139GLU-1-0.893-0.96014.419-14.437-14.4370.0000.0000.0000.000
81D140GLY0-0.026-0.01618.088-0.324-0.3240.0000.0000.0000.000
82D141SER0-0.031-0.03320.789-0.216-0.2160.0000.0000.0000.000
83D142ILE0-0.032-0.02623.131-0.267-0.2670.0000.0000.0000.000
84D143ILE00.0120.00325.1710.3290.3290.0000.0000.0000.000
85D144GLY00.0220.01227.4260.3910.3910.0000.0000.0000.000
86D145TYR0-0.145-0.14429.584-0.438-0.4380.0000.0000.0000.000
87D146GLU-1-0.912-0.95332.187-8.529-8.5290.0000.0000.0000.000
88D147SER00.1000.05435.268-0.122-0.1220.0000.0000.0000.000
89D148ASN00.008-0.01838.1040.0210.0210.0000.0000.0000.000
90D149VAL0-0.0120.01635.736-0.074-0.0740.0000.0000.0000.000
91D150LYS10.8750.95138.5127.8857.8850.0000.0000.0000.000
92D151SER00.011-0.00639.639-0.107-0.1070.0000.0000.0000.000
93D152GLY0-0.035-0.01142.1740.1490.1490.0000.0000.0000.000
94D153GLY00.0310.00944.440-0.143-0.1430.0000.0000.0000.000
95D154VAL0-0.064-0.01446.6560.1430.1430.0000.0000.0000.000
96D155GLY00.0870.02749.567-0.086-0.0860.0000.0000.0000.000
97D156ALA0-0.065-0.01752.1550.1050.1050.0000.0000.0000.000
98D157ARG10.9680.98155.5885.3265.3260.0000.0000.0000.000
99D158TYR00.0000.01858.2730.1080.1080.0000.0000.0000.000
100D159PHE00.0240.04360.974-0.051-0.0510.0000.0000.0000.000
101D160GLY00.010-0.03662.3420.0530.0530.0000.0000.0000.000
102D161ILE0-0.038-0.02456.351-0.027-0.0270.0000.0000.0000.000
103D162GLY0-0.007-0.00856.3480.0350.0350.0000.0000.0000.000
104D163ALA0-0.005-0.00851.201-0.050-0.0500.0000.0000.0000.000
105D164ASP-1-0.920-0.96649.800-6.324-6.3240.0000.0000.0000.000
106D165THR0-0.037-0.01244.140-0.142-0.1420.0000.0000.0000.000
107D166GLN00.0490.01444.7400.0020.0020.0000.0000.0000.000
108D167TYR0-0.011-0.00538.946-0.177-0.1770.0000.0000.0000.000
109D168GLN00.014-0.00239.0560.0590.0590.0000.0000.0000.000
110D169LEU0-0.055-0.02535.013-0.195-0.1950.0000.0000.0000.000
111D170ASP-1-0.712-0.78733.371-8.749-8.7490.0000.0000.0000.000
112D171GLN0-0.061-0.03731.001-0.005-0.0050.0000.0000.0000.000
113D172ILE0-0.008-0.00226.3880.0260.0260.0000.0000.0000.000
114D173ALA0-0.034-0.01926.139-0.270-0.2700.0000.0000.0000.000
115D174VAL0-0.020-0.00720.4190.0470.0470.0000.0000.0000.000
116D175ASN00.006-0.02321.837-0.117-0.1170.0000.0000.0000.000
117D176LEU0-0.0120.00615.614-0.354-0.3540.0000.0000.0000.000
118D177ARG10.9710.96717.61713.42613.4260.0000.0000.0000.000
119D178VAL00.0000.02312.170-0.751-0.7510.0000.0000.0000.000
120D179VAL00.0230.01414.8580.8580.8580.0000.0000.0000.000
121D180ASN00.0100.00214.876-0.952-0.9520.0000.0000.0000.000
122D181VAL0-0.018-0.00714.0430.6420.6420.0000.0000.0000.000
123D182SER0-0.059-0.02415.9250.6170.6170.0000.0000.0000.000
124D183THR00.006-0.01518.2390.3650.3650.0000.0000.0000.000
125D184GLY0-0.0010.01319.4910.5720.5720.0000.0000.0000.000
126D185GLU-1-0.963-0.96920.035-12.002-12.0020.0000.0000.0000.000
127D186ILE0-0.007-0.01718.700-0.774-0.7740.0000.0000.0000.000
128D187LEU0-0.035-0.01413.8070.2090.2090.0000.0000.0000.000
129D188SER00.0170.00214.9470.0910.0910.0000.0000.0000.000
130D189SER0-0.041-0.02717.8190.0400.0400.0000.0000.0000.000
131D190VAL00.0340.03017.8860.4130.4130.0000.0000.0000.000
132D191ASN00.0330.03120.598-0.477-0.4770.0000.0000.0000.000
133D192THR0-0.051-0.01320.0290.2600.2600.0000.0000.0000.000
134D193SER00.029-0.02423.2090.2530.2530.0000.0000.0000.000
135D194LYS10.8480.98122.02613.40213.4020.0000.0000.0000.000
136D195THR00.012-0.00326.8770.1650.1650.0000.0000.0000.000
137D196ILE0-0.028-0.02829.073-0.300-0.3000.0000.0000.0000.000
138D197LEU0-0.0010.01631.3650.3090.3090.0000.0000.0000.000
139D198SER00.0230.01533.776-0.097-0.0970.0000.0000.0000.000
140D199TYR0-0.018-0.02135.5330.2250.2250.0000.0000.0000.000
141D200GLU-1-0.884-0.93939.603-7.367-7.3670.0000.0000.0000.000
142D201VAL0-0.038-0.02242.4180.1120.1120.0000.0000.0000.000
143D202GLN00.0240.01145.004-0.115-0.1150.0000.0000.0000.000
144D203ALA0-0.012-0.00848.4270.0730.0730.0000.0000.0000.000
145D204GLY00.0520.03051.437-0.029-0.0290.0000.0000.0000.000
146D205VAL0-0.082-0.04554.7800.0810.0810.0000.0000.0000.000
147D206PHE00.0340.02958.3850.0560.0560.0000.0000.0000.000
148D207ARG10.8450.91661.6025.0985.0980.0000.0000.0000.000
149D208PHE00.0630.02364.752-0.013-0.0130.0000.0000.0000.000
150D209ILE0-0.069-0.01367.3090.0030.0030.0000.0000.0000.000
151D210ASP-1-0.838-0.90170.773-4.412-4.4120.0000.0000.0000.000
152D211TYR0-0.040-0.02673.0680.0650.0650.0000.0000.0000.000
153D212GLN00.014-0.03772.216-0.128-0.1280.0000.0000.0000.000
154D213ARG10.8510.94367.0394.7414.7410.0000.0000.0000.000
155D214LEU00.0120.00265.5510.0250.0250.0000.0000.0000.000
156D215LEU0-0.038-0.01560.855-0.015-0.0150.0000.0000.0000.000
157D216GLU-1-0.883-0.95459.349-5.444-5.4440.0000.0000.0000.000
158D217GLY0-0.0130.00056.550-0.007-0.0070.0000.0000.0000.000
159D218GLU-1-0.921-0.95852.376-5.916-5.9160.0000.0000.0000.000
160D219VAL0-0.038-0.01548.427-0.065-0.0650.0000.0000.0000.000
161D220GLY00.0500.01246.6520.0640.0640.0000.0000.0000.000
162D221TYR0-0.071-0.02136.495-0.092-0.0920.0000.0000.0000.000
163D222THR00.0190.00940.4760.0150.0150.0000.0000.0000.000
164D223SER0-0.0270.00134.473-0.212-0.2120.0000.0000.0000.000
165D224ASN00.0380.00034.5660.2170.2170.0000.0000.0000.000
166D225GLU-1-0.916-0.95229.312-10.694-10.6940.0000.0000.0000.000
167D226PRO00.004-0.00826.9510.0480.0480.0000.0000.0000.000
168D227VAL00.0790.05226.944-0.556-0.5560.0000.0000.0000.000
169D228MET00.001-0.01323.392-0.429-0.4290.0000.0000.0000.000
170D229LEU0-0.002-0.00422.478-0.649-0.6490.0000.0000.0000.000
171D230CYS00.0050.02022.641-0.455-0.4550.0000.0000.0000.000
172D231LEU00.0280.01521.711-0.278-0.2780.0000.0000.0000.000
173D232MET00.0330.00917.525-0.789-0.7890.0000.0000.0000.000
174D233SER00.0010.01518.693-0.535-0.5350.0000.0000.0000.000
175D234ALA00.0120.00519.862-0.432-0.4320.0000.0000.0000.000
176D235ILE00.0050.00616.302-0.313-0.3130.0000.0000.0000.000
177D236GLU-1-0.923-0.95914.806-18.837-18.8370.0000.0000.0000.000
178D237THR0-0.033-0.05715.563-0.301-0.3010.0000.0000.0000.000
179D238GLY00.0310.01617.2280.0070.0070.0000.0000.0000.000
180D239VAL00.016-0.00510.997-0.304-0.3040.0000.0000.0000.000
181D240ILE0-0.034-0.01112.396-0.756-0.7560.0000.0000.0000.000
182D241PHE0-0.040-0.02313.9720.0520.0520.0000.0000.0000.000
183D242LEU00.0060.01212.6160.1190.1190.0000.0000.0000.000
184D243ILE0-0.026-0.0088.599-0.519-0.5190.0000.0000.0000.000
185D244ASN0-0.004-0.02311.020-0.769-0.7690.0000.0000.0000.000
186D245ASP-1-0.902-0.94114.000-14.404-14.4040.0000.0000.0000.000
187D246GLY0-0.029-0.01511.3140.3840.3840.0000.0000.0000.000
188D247ILE0-0.069-0.03911.106-0.090-0.0900.0000.0000.0000.000
189D248ASP-1-0.963-0.97312.614-14.341-14.3410.0000.0000.0000.000
190D249ARG10.8670.94913.41715.42915.4290.0000.0000.0000.000
191D250GLY0-0.050-0.01610.0210.5200.5200.0000.0000.0000.000