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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: K3NQ3

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 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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1693605.323416
FMO2-HF: Nuclear repulsion 1620244.888927
FMO2-HF: Total energy -73360.434489
FMO2-MP2: Total energy -73574.963591


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.
-29.867-25.41211.087-5.383-10.163-0.01
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 : 0.983 / q_NPA : 0.984
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].
3D50PHE0-0.029-0.0183.791-2.3770.167-0.029-1.265-1.2500.005
4D51VAL00.0380.0326.2452.2412.2410.0000.0000.0000.000
5D52SER0-0.010-0.0248.633-0.535-0.5350.0000.0000.0000.000
6D53VAL0-0.005-0.00212.0160.5340.5340.0000.0000.0000.000
7D54TYR00.0140.01014.445-0.169-0.1690.0000.0000.0000.000
8D55ASN0-0.001-0.01918.0050.3390.3390.0000.0000.0000.000
9D56ILE0-0.0040.01317.752-0.164-0.1640.0000.0000.0000.000
10D57GLN0-0.055-0.02920.9310.0780.0780.0000.0000.0000.000
11D58ASP-1-0.831-0.93224.610-10.392-10.3920.0000.0000.0000.000
12D59GLU-1-0.851-0.89926.556-10.763-10.7630.0000.0000.0000.000
13D60THR00.0210.00829.4510.3900.3900.0000.0000.0000.000
14D61GLY0-0.017-0.00131.4730.2900.2900.0000.0000.0000.000
15D62GLN0-0.041-0.01633.5750.4880.4880.0000.0000.0000.000
16D63PHE0-0.009-0.02234.559-0.255-0.2550.0000.0000.0000.000
17D64LYS10.8310.92233.7939.2029.2020.0000.0000.0000.000
18D65PRO00.0380.03038.5820.1210.1210.0000.0000.0000.000
19D66TYR00.0310.02042.269-0.042-0.0420.0000.0000.0000.000
20D67PRO00.008-0.02744.396-0.024-0.0240.0000.0000.0000.000
21D68ALA0-0.058-0.00640.1320.0090.0090.0000.0000.0000.000
22D69SER00.0540.02340.2230.1450.1450.0000.0000.0000.000
23D70ASN00.0520.02740.262-0.107-0.1070.0000.0000.0000.000
24D71PHE0-0.005-0.00838.243-0.058-0.0580.0000.0000.0000.000
25D72SER0-0.091-0.04235.862-0.273-0.2730.0000.0000.0000.000
26D73THR00.0850.04530.9900.2310.2310.0000.0000.0000.000
27D74ALA0-0.037-0.01333.7380.0030.0030.0000.0000.0000.000
28D75VAL00.008-0.00427.403-0.132-0.1320.0000.0000.0000.000
29D76PRO0-0.012-0.00425.5220.0440.0440.0000.0000.0000.000
30D77GLN00.0540.03026.069-0.007-0.0070.0000.0000.0000.000
31D78SER00.0000.00122.135-0.187-0.1870.0000.0000.0000.000
32D79ALA00.0450.02219.766-0.827-0.8270.0000.0000.0000.000
33D80THR00.0220.01416.7250.2050.2050.0000.0000.0000.000
34D81ALA00.0130.01716.550-0.499-0.4990.0000.0000.0000.000
35D82MET00.0070.00615.599-1.099-1.0990.0000.0000.0000.000
36D83LEU00.0440.02913.077-0.851-0.8510.0000.0000.0000.000
37D84VAL00.0220.01311.678-1.562-1.5620.0000.0000.0000.000
38D85THR00.023-0.02010.982-2.239-2.2390.0000.0000.0000.000
39D86ALA00.0440.04011.727-1.353-1.3530.0000.0000.0000.000
40D87LEU00.0010.0088.349-1.485-1.4850.0000.0000.0000.000
41D88LYS10.9070.9585.79936.89236.8920.0000.0000.0000.000
42D89ASP-1-0.874-0.9486.993-32.051-32.0510.0000.0000.0000.000
43D90SER0-0.042-0.0198.5900.5070.5070.0000.0000.0000.000
44D91ARG10.6970.8733.23635.02035.6700.025-0.133-0.543-0.001
45D92TRP00.049-0.0012.025-3.301-2.7897.632-4.001-4.144-0.005
46D93PHE00.0680.0313.0314.0534.1580.1910.925-1.221-0.006
47D94ILE0-0.119-0.0572.149-9.081-8.4993.269-0.890-2.962-0.003
48D95PRO00.0330.0164.5022.4332.495-0.001-0.019-0.0430.000
49D96LEU0-0.053-0.0268.037-0.942-0.9420.0000.0000.0000.000
50D97GLU-1-0.865-0.93810.391-16.298-16.2980.0000.0000.0000.000
51D98ARG10.8430.92012.64920.26020.2600.0000.0000.0000.000
52D99GLN00.0370.04316.6790.5560.5560.0000.0000.0000.000
53D100GLY0-0.010-0.00919.0040.7760.7760.0000.0000.0000.000
54D101LEU00.010-0.00718.080-0.195-0.1950.0000.0000.0000.000
55D102GLN00.0440.02120.023-0.229-0.2290.0000.0000.0000.000
56D103ASN00.0450.00622.2980.6130.6130.0000.0000.0000.000
57D104LEU00.0430.04016.1490.1180.1180.0000.0000.0000.000
58D105LEU0-0.008-0.01520.8490.0580.0580.0000.0000.0000.000
59D106ASN0-0.015-0.01123.0450.4880.4880.0000.0000.0000.000
60D107GLU-1-0.866-0.92121.588-12.781-12.7810.0000.0000.0000.000
61D108ARG10.9040.95217.21216.55616.5560.0000.0000.0000.000
62D109LYS10.8320.91823.48411.73511.7350.0000.0000.0000.000
63D110ILE00.0370.02426.4890.3750.3750.0000.0000.0000.000
64D111ILE0-0.018-0.01121.4580.1640.1640.0000.0000.0000.000
65D112ARG10.9170.95023.78812.41612.4160.0000.0000.0000.000
66D113ALA00.0220.01927.3060.2830.2830.0000.0000.0000.000
67D114ALA0-0.030-0.01228.2140.3050.3050.0000.0000.0000.000
68D115GLN0-0.065-0.03223.7570.0040.0040.0000.0000.0000.000
69D116GLU-1-0.977-0.97029.566-10.063-10.0630.0000.0000.0000.000
70D129GLN00.0220.00118.778-0.479-0.4790.0000.0000.0000.000
71D130SER00.000-0.01217.1260.7360.7360.0000.0000.0000.000
72D131LEU0-0.025-0.02014.901-0.831-0.8310.0000.0000.0000.000
73D132THR00.0210.0269.8121.1071.1070.0000.0000.0000.000
74D133ALA00.0510.03012.4370.2600.2600.0000.0000.0000.000
75D134ALA0-0.015-0.01710.207-1.912-1.9120.0000.0000.0000.000
76D135ASN00.0350.01410.2382.1532.1530.0000.0000.0000.000
77D136ILE00.0260.0237.7090.8390.8390.0000.0000.0000.000
78D137MET0-0.002-0.01011.616-0.996-0.9960.0000.0000.0000.000
79D138VAL0-0.026-0.00511.7190.2950.2950.0000.0000.0000.000
80D139GLU-1-0.836-0.91314.458-13.016-13.0160.0000.0000.0000.000
81D140GLY0-0.013-0.00118.123-0.318-0.3180.0000.0000.0000.000
82D141SER0-0.056-0.06020.824-0.176-0.1760.0000.0000.0000.000
83D142ILE0-0.032-0.02923.149-0.246-0.2460.0000.0000.0000.000
84D143ILE00.0220.00825.1720.3170.3170.0000.0000.0000.000
85D144GLY00.0200.01127.4540.3740.3740.0000.0000.0000.000
86D145TYR0-0.095-0.08429.607-0.320-0.3200.0000.0000.0000.000
87D146GLU-1-0.895-0.92732.211-8.350-8.3500.0000.0000.0000.000
88D147SER00.0730.03235.392-0.108-0.1080.0000.0000.0000.000
89D148ASN0-0.010-0.02338.2270.1000.1000.0000.0000.0000.000
90D149VAL00.0080.01635.768-0.087-0.0870.0000.0000.0000.000
91D150LYS10.9090.97338.5577.6717.6710.0000.0000.0000.000
92D151SER0-0.024-0.02339.967-0.091-0.0910.0000.0000.0000.000
93D152GLY0-0.013-0.00342.6150.1370.1370.0000.0000.0000.000
94D153GLY00.0370.01445.326-0.139-0.1390.0000.0000.0000.000
95D154VAL0-0.071-0.02047.6120.1370.1370.0000.0000.0000.000
96D155GLY00.0880.03150.704-0.081-0.0810.0000.0000.0000.000
97D156ALA0-0.064-0.01653.3040.1010.1010.0000.0000.0000.000
98D157ARG10.9690.96956.6975.2335.2330.0000.0000.0000.000
99D158TYR00.0090.02159.3890.0940.0940.0000.0000.0000.000
100D159PHE00.0280.04662.046-0.049-0.0490.0000.0000.0000.000
101D160GLY00.027-0.03163.4060.0490.0490.0000.0000.0000.000
102D161ILE0-0.047-0.02457.343-0.027-0.0270.0000.0000.0000.000
103D162GLY0-0.006-0.00557.4430.0340.0340.0000.0000.0000.000
104D163ALA00.004-0.00252.287-0.049-0.0490.0000.0000.0000.000
105D164ASP-1-0.897-0.94950.467-6.219-6.2190.0000.0000.0000.000
106D165THR0-0.038-0.02745.383-0.139-0.1390.0000.0000.0000.000
107D166GLN00.0450.02145.9320.0320.0320.0000.0000.0000.000
108D167TYR00.002-0.00139.978-0.172-0.1720.0000.0000.0000.000
109D168GLN00.0210.00439.7300.1270.1270.0000.0000.0000.000
110D169LEU0-0.058-0.02035.430-0.185-0.1850.0000.0000.0000.000
111D170ASP-1-0.774-0.84833.627-8.587-8.5870.0000.0000.0000.000
112D171GLN0-0.110-0.07831.315-0.318-0.3180.0000.0000.0000.000
113D172ILE0-0.0080.00126.0580.0370.0370.0000.0000.0000.000
114D173ALA0-0.024-0.01626.164-0.254-0.2540.0000.0000.0000.000
115D174VAL0-0.039-0.01920.6980.0350.0350.0000.0000.0000.000
116D175ASN00.013-0.00421.891-0.067-0.0670.0000.0000.0000.000
117D176LEU0-0.0140.00615.118-0.344-0.3440.0000.0000.0000.000
118D177ARG10.8660.89917.65113.07113.0710.0000.0000.0000.000
119D178VAL00.0130.02512.314-0.707-0.7070.0000.0000.0000.000
120D179VAL00.0120.00514.8910.7730.7730.0000.0000.0000.000
121D180ASN00.008-0.00614.915-1.353-1.3530.0000.0000.0000.000
122D181VAL0-0.027-0.01114.3340.6400.6400.0000.0000.0000.000
123D182SER0-0.058-0.02315.8620.6200.6200.0000.0000.0000.000
124D183THR0-0.043-0.06318.2390.3400.3400.0000.0000.0000.000
125D184GLY0-0.0080.01119.5340.5720.5720.0000.0000.0000.000
126D185GLU-1-0.890-0.90219.944-12.131-12.1310.0000.0000.0000.000
127D186ILE0-0.007-0.02318.735-0.746-0.7460.0000.0000.0000.000
128D187LEU0-0.040-0.01213.7990.2050.2050.0000.0000.0000.000
129D188SER00.0350.01615.0680.1080.1080.0000.0000.0000.000
130D189SER0-0.016-0.01817.845-0.029-0.0290.0000.0000.0000.000
131D190VAL0-0.019-0.00118.1450.4020.4020.0000.0000.0000.000
132D191ASN00.0400.02920.619-0.468-0.4680.0000.0000.0000.000
133D192THR0-0.041-0.01120.1590.1900.1900.0000.0000.0000.000
134D193SER00.0480.00423.2260.1340.1340.0000.0000.0000.000
135D194LYS10.8060.93421.76513.10713.1070.0000.0000.0000.000
136D195THR00.012-0.00527.0030.1690.1690.0000.0000.0000.000
137D196ILE0-0.014-0.02529.942-0.287-0.2870.0000.0000.0000.000
138D197LEU00.0030.02132.1990.3000.3000.0000.0000.0000.000
139D198SER00.0460.02534.970-0.081-0.0810.0000.0000.0000.000
140D199TYR0-0.033-0.02836.4550.2220.2220.0000.0000.0000.000
141D200GLU-1-0.891-0.94140.802-7.213-7.2130.0000.0000.0000.000
142D201VAL0-0.037-0.01343.5620.1050.1050.0000.0000.0000.000
143D202GLN00.0060.00246.124-0.064-0.0640.0000.0000.0000.000
144D203ALA0-0.023-0.01749.5420.0700.0700.0000.0000.0000.000
145D204GLY00.0630.03752.506-0.028-0.0280.0000.0000.0000.000
146D205VAL0-0.093-0.05055.8560.0780.0780.0000.0000.0000.000
147D206PHE00.0280.03159.1580.0510.0510.0000.0000.0000.000
148D207ARG10.8380.91662.6884.9964.9960.0000.0000.0000.000
149D208PHE00.0360.02065.803-0.019-0.0190.0000.0000.0000.000
150D209ILE0-0.059-0.02867.9740.0050.0050.0000.0000.0000.000
151D210ASP-1-0.820-0.89471.790-4.369-4.3690.0000.0000.0000.000
152D211TYR0-0.041-0.00873.8290.0650.0650.0000.0000.0000.000
153D212GLN00.015-0.03772.955-0.133-0.1330.0000.0000.0000.000
154D213ARG10.8530.94467.8124.7024.7020.0000.0000.0000.000
155D214LEU00.0180.00366.6500.0280.0280.0000.0000.0000.000
156D215LEU0-0.031-0.01961.823-0.015-0.0150.0000.0000.0000.000
157D216GLU-1-0.899-0.95960.478-5.288-5.2880.0000.0000.0000.000
158D217GLY0-0.022-0.00457.589-0.009-0.0090.0000.0000.0000.000
159D218GLU-1-0.918-0.95853.459-5.827-5.8270.0000.0000.0000.000
160D219VAL0-0.042-0.02049.444-0.063-0.0630.0000.0000.0000.000
161D220GLY00.0540.01847.7470.0620.0620.0000.0000.0000.000
162D221TYR0-0.061-0.01737.366-0.063-0.0630.0000.0000.0000.000
163D222THR00.0210.01241.0250.0920.0920.0000.0000.0000.000
164D223SER0-0.035-0.00935.454-0.161-0.1610.0000.0000.0000.000
165D224ASN00.006-0.01235.6310.1800.1800.0000.0000.0000.000
166D225GLU-1-0.919-0.94930.791-10.168-10.1680.0000.0000.0000.000
167D226PRO00.018-0.00228.0630.0440.0440.0000.0000.0000.000
168D227VAL00.0780.04327.983-0.507-0.5070.0000.0000.0000.000
169D228MET0-0.010-0.01124.479-0.373-0.3730.0000.0000.0000.000
170D229LEU00.005-0.00623.466-0.582-0.5820.0000.0000.0000.000
171D230CYS00.0110.01923.739-0.417-0.4170.0000.0000.0000.000
172D231LEU00.0200.01021.947-0.268-0.2680.0000.0000.0000.000
173D232MET00.0130.01018.438-0.686-0.6860.0000.0000.0000.000
174D233SER00.0380.03519.508-0.457-0.4570.0000.0000.0000.000
175D234ALA0-0.008-0.01220.275-0.364-0.3640.0000.0000.0000.000
176D235ILE00.0260.01016.527-0.306-0.3060.0000.0000.0000.000
177D236GLU-1-0.899-0.95115.733-17.202-17.2020.0000.0000.0000.000
178D237THR0-0.047-0.03715.646-0.302-0.3020.0000.0000.0000.000
179D238GLY00.0310.01417.2370.0120.0120.0000.0000.0000.000
180D239VAL00.015-0.00510.948-0.276-0.2760.0000.0000.0000.000
181D240ILE0-0.022-0.00812.408-0.717-0.7170.0000.0000.0000.000
182D241PHE0-0.033-0.02313.976-0.007-0.0070.0000.0000.0000.000
183D242LEU0-0.0010.01212.5510.1110.1110.0000.0000.0000.000
184D243ILE0-0.026-0.0088.547-0.546-0.5460.0000.0000.0000.000
185D244ASN0-0.023-0.02811.028-0.797-0.7970.0000.0000.0000.000
186D245ASP-1-0.840-0.90714.001-14.098-14.0980.0000.0000.0000.000
187D246GLY00.0150.00811.3260.2700.2700.0000.0000.0000.000
188D247ILE0-0.061-0.03910.942-0.134-0.1340.0000.0000.0000.000
189D248ASP-1-0.911-0.92912.617-13.942-13.9420.0000.0000.0000.000
190D249ARG10.7200.84313.62415.16815.1680.0000.0000.0000.000
191D250GLY0-0.045-0.0069.9230.5450.5450.0000.0000.0000.000