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: N213Q

Calculation Name: 2NN6-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NN6

Chain ID: D

ChEMBL ID:

UniProt ID: Q9Y3B2

Base Structure: X-ray

Registration Date: 2023-09-26

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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2303320.012856
FMO2-HF: Nuclear repulsion 2222473.658493
FMO2-HF: Total energy -80846.354363
FMO2-MP2: Total energy -81077.930478


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:25:GLY)


Summations of interaction energy for fragment #1(D:25:GLY)
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.
0.1861.404-0.01-0.54-0.6680
Interaction energy analysis for fragmet #1(D:25:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.033 / q_NPA : 0.005
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].
3D27SER0-0.028-0.0213.8240.8592.077-0.010-0.540-0.6680.000
4D28LEU0-0.010-0.0275.421-0.141-0.1410.0000.0000.0000.000
5D29ARG10.7860.9198.8220.3610.3610.0000.0000.0000.000
6D30HIS00.0080.02410.8930.0680.0680.0000.0000.0000.000
7D31PHE00.0620.00913.4090.0320.0320.0000.0000.0000.000
8D32ALA0-0.050-0.01915.6840.0220.0220.0000.0000.0000.000
9D33CYS0-0.008-0.01519.4490.0050.0050.0000.0000.0000.000
10D34GLU-1-0.944-0.96122.783-0.104-0.1040.0000.0000.0000.000
11D35GLN00.044-0.01226.4640.0000.0000.0000.0000.0000.000
12D36ASN0-0.038-0.01128.9940.0010.0010.0000.0000.0000.000
13D37LEU0-0.0170.00029.137-0.001-0.0010.0000.0000.0000.000
14D38LEU0-0.031-0.03833.2680.0030.0030.0000.0000.0000.000
15D39SER00.0490.02736.0960.0020.0020.0000.0000.0000.000
16D40ARG10.8660.94339.2510.0400.0400.0000.0000.0000.000
17D41PRO0-0.027-0.02137.0290.0030.0030.0000.0000.0000.000
18D42ASP-1-0.868-0.93238.439-0.031-0.0310.0000.0000.0000.000
19D43GLY00.0250.01534.7420.0010.0010.0000.0000.0000.000
20D44SER0-0.0830.00132.742-0.004-0.0040.0000.0000.0000.000
21D45ALA00.0260.01427.4790.0010.0010.0000.0000.0000.000
22D46SER00.0120.01626.764-0.004-0.0040.0000.0000.0000.000
23D47PHE0-0.0030.00218.1650.0020.0020.0000.0000.0000.000
24D48LEU00.0520.00320.546-0.003-0.0030.0000.0000.0000.000
25D49GLN0-0.0020.00815.1190.0460.0460.0000.0000.0000.000
26D50GLY00.092-0.00715.290-0.029-0.0290.0000.0000.0000.000
27D51ASP-1-0.959-0.95816.212-0.269-0.2690.0000.0000.0000.000
28D52THR0-0.0160.02418.1090.0130.0130.0000.0000.0000.000
29D53SER00.014-0.00919.802-0.003-0.0030.0000.0000.0000.000
30D54VAL0-0.0310.00122.4210.0070.0070.0000.0000.0000.000
31D55LEU00.0160.02625.4660.0000.0000.0000.0000.0000.000
32D56ALA0-0.047-0.03828.3020.0020.0020.0000.0000.0000.000
33D57GLY0-0.024-0.02430.1090.0020.0020.0000.0000.0000.000
34D58VAL00.005-0.01432.8680.0010.0010.0000.0000.0000.000
35D59TYR0-0.061-0.02135.5100.0000.0000.0000.0000.0000.000
36D60GLY00.0510.00637.9270.0020.0020.0000.0000.0000.000
37D61PRO00.0130.02138.8410.0000.0000.0000.0000.0000.000
38D62ALA00.0440.02241.5330.0000.0000.0000.0000.0000.000
39D63GLU-1-0.875-0.94144.634-0.012-0.0120.0000.0000.0000.000
40D64VAL0-0.051-0.02246.042-0.001-0.0010.0000.0000.0000.000
41D65LYS11.0251.01149.0370.0200.0200.0000.0000.0000.000
42D66VAL0-0.021-0.02052.5490.0000.0000.0000.0000.0000.000
43D67SER0-0.009-0.00450.940-0.002-0.0020.0000.0000.0000.000
44D68LYS10.7980.89053.0380.0120.0120.0000.0000.0000.000
45D69GLU-1-0.784-0.87452.993-0.011-0.0110.0000.0000.0000.000
46D70ILE0-0.015-0.01052.022-0.001-0.0010.0000.0000.0000.000
47D71PHE00.0290.02744.7970.0000.0000.0000.0000.0000.000
48D72ASN0-0.023-0.07347.1750.0020.0020.0000.0000.0000.000
49D73LYS10.8630.99741.6470.0030.0030.0000.0000.0000.000
50D74ALA00.1790.07940.186-0.001-0.0010.0000.0000.0000.000
51D75THR0-0.061-0.04440.4690.0010.0010.0000.0000.0000.000
52D76LEU00.0220.01733.271-0.001-0.0010.0000.0000.0000.000
53D77GLU-1-0.945-0.97337.292-0.039-0.0390.0000.0000.0000.000
54D78VAL00.004-0.01031.881-0.001-0.0010.0000.0000.0000.000
55D79ILE00.0020.02534.787-0.002-0.0020.0000.0000.0000.000
56D80LEU00.0340.02428.187-0.002-0.0020.0000.0000.0000.000
57D81ARG10.8990.94532.2600.0610.0610.0000.0000.0000.000
58D82PRO00.048-0.02030.238-0.005-0.0050.0000.0000.0000.000
59D83LYN00.0040.03425.5220.0010.0010.0000.0000.0000.000
60D84ILE0-0.033-0.00529.4280.0060.0060.0000.0000.0000.000
61D85GLY00.006-0.00532.5610.0010.0010.0000.0000.0000.000
62D86LEU00.0210.01435.1730.0000.0000.0000.0000.0000.000
63D87PRO00.008-0.01534.610-0.003-0.0030.0000.0000.0000.000
64D88GLY00.0590.03634.1940.0040.0040.0000.0000.0000.000
65D89VAL00.040-0.00735.3610.0010.0010.0000.0000.0000.000
66D90ALA00.0200.01230.3700.0010.0010.0000.0000.0000.000
67D91GLU-1-0.861-0.91730.997-0.089-0.0890.0000.0000.0000.000
68D92LYS10.9260.98332.1630.0460.0460.0000.0000.0000.000
69D93SER0-0.072-0.05331.7310.0020.0020.0000.0000.0000.000
70D94ARG10.9400.95624.4350.1140.1140.0000.0000.0000.000
71D95GLU-1-0.837-0.93629.442-0.051-0.0510.0000.0000.0000.000
72D96ARG10.9240.96631.6510.0340.0340.0000.0000.0000.000
73D97LEU00.0280.03826.5710.0030.0030.0000.0000.0000.000
74D98ILE00.0270.06526.3870.0050.0050.0000.0000.0000.000
75D99ARG10.9400.97329.0270.0380.0380.0000.0000.0000.000
76D100ASN0-0.026-0.03931.2460.0010.0010.0000.0000.0000.000
77D101THR0-0.090-0.09325.7630.0040.0040.0000.0000.0000.000
78D102CYS0-0.040-0.01729.1370.0030.0030.0000.0000.0000.000
79D103GLU-1-0.841-0.90031.040-0.017-0.0170.0000.0000.0000.000
80D104ALA0-0.047-0.01230.1620.0040.0040.0000.0000.0000.000
81D105VAL00.025-0.01227.4910.0050.0050.0000.0000.0000.000
82D106VAL00.0300.02030.9470.0020.0020.0000.0000.0000.000
83D107LEU00.0190.02533.7170.0020.0020.0000.0000.0000.000
84D108GLY00.0830.00235.9610.0000.0000.0000.0000.0000.000
85D109THR0-0.091-0.06337.1870.0010.0010.0000.0000.0000.000
86D110LEU0-0.079-0.04639.5070.0010.0010.0000.0000.0000.000
87D111HIS0-0.038-0.01341.6220.0010.0010.0000.0000.0000.000
88D112PRO00.014-0.03344.130-0.001-0.0010.0000.0000.0000.000
89D113ARG10.8740.97546.8480.0060.0060.0000.0000.0000.000
90D114THR0-0.0520.00443.075-0.001-0.0010.0000.0000.0000.000
91D115SER0-0.057-0.02342.7520.0000.0000.0000.0000.0000.000
92D116ILE00.0500.02536.9740.0000.0000.0000.0000.0000.000
93D117THR0-0.026-0.01337.862-0.001-0.0010.0000.0000.0000.000
94D118VAL00.0230.01231.368-0.001-0.0010.0000.0000.0000.000
95D119VAL0-0.030-0.01833.8450.0010.0010.0000.0000.0000.000
96D120LEU0-0.034-0.01627.619-0.003-0.0030.0000.0000.0000.000
97D121GLN00.018-0.00629.899-0.003-0.0030.0000.0000.0000.000
98D122VAL00.0220.04126.315-0.007-0.0070.0000.0000.0000.000
99D123VAL0-0.0130.00225.9500.0040.0040.0000.0000.0000.000
100D124SER0-0.089-0.11421.3880.0010.0010.0000.0000.0000.000
101D125ASP-1-0.845-0.91521.850-0.213-0.2130.0000.0000.0000.000
102D126ALA00.000-0.01718.424-0.005-0.0050.0000.0000.0000.000
103D127GLY00.0370.01816.233-0.052-0.0520.0000.0000.0000.000
104D128SER0-0.014-0.02414.3770.0000.0000.0000.0000.0000.000
105D129LEU00.0480.03617.1520.0300.0300.0000.0000.0000.000
106D130LEU00.024-0.04320.8900.0120.0120.0000.0000.0000.000
107D131ALA0-0.018-0.01817.7380.0170.0170.0000.0000.0000.000
108D132CYS00.0350.05019.6530.0180.0180.0000.0000.0000.000
109D133CYS0-0.023-0.00620.9080.0170.0170.0000.0000.0000.000
110D134LEU0-0.0230.04721.1210.0150.0150.0000.0000.0000.000
111D135ASN00.0920.04319.9650.0180.0180.0000.0000.0000.000
112D136ALA00.0230.03222.7950.0090.0090.0000.0000.0000.000
113D137ALA00.059-0.00725.1730.0090.0090.0000.0000.0000.000
114D138CYS0-0.088-0.01424.8470.0110.0110.0000.0000.0000.000
115D139MET0-0.018-0.02924.0670.0100.0100.0000.0000.0000.000
116D140ALA00.0010.00027.2540.0040.0040.0000.0000.0000.000
117D141LEU0-0.027-0.03429.9700.0050.0050.0000.0000.0000.000
118D142VAL0-0.038-0.01927.0070.0040.0040.0000.0000.0000.000
119D143ASP-1-0.818-0.91230.423-0.041-0.0410.0000.0000.0000.000
120D144ALA0-0.0280.00232.2700.0030.0030.0000.0000.0000.000
121D145GLY0-0.037-0.03034.0300.0030.0030.0000.0000.0000.000
122D146VAL0-0.054-0.00634.8290.0040.0040.0000.0000.0000.000
123D147PRO0-0.0640.01134.4380.0010.0010.0000.0000.0000.000
124D148MET00.0620.01529.829-0.001-0.0010.0000.0000.0000.000
125D149ARG10.8380.95430.877-0.006-0.0060.0000.0000.0000.000
126D150ALA0-0.016-0.01227.0310.0050.0050.0000.0000.0000.000
127D151LEU00.016-0.01024.309-0.007-0.0070.0000.0000.0000.000
128D152PHE00.0360.00523.3070.0090.0090.0000.0000.0000.000
129D153CYS0-0.056-0.00118.231-0.011-0.0110.0000.0000.0000.000
130D154GLY00.0610.00719.1570.0160.0160.0000.0000.0000.000
131D155VAL0-0.059-0.01813.665-0.025-0.0250.0000.0000.0000.000
132D156ALA00.021-0.00314.2200.0350.0350.0000.0000.0000.000
133D157CYS0-0.054-0.02112.085-0.054-0.0540.0000.0000.0000.000
134D158ALA00.016-0.00311.7710.0730.0730.0000.0000.0000.000
135D159LEU00.0120.01111.485-0.069-0.0690.0000.0000.0000.000
136D160ASP-1-0.591-0.78711.738-0.246-0.2460.0000.0000.0000.000
137D161SER0-0.101-0.05114.3690.0330.0330.0000.0000.0000.000
138D162ASP-1-0.939-0.96613.253-0.108-0.1080.0000.0000.0000.000
139D163GLY0-0.124-0.05213.4050.0310.0310.0000.0000.0000.000
140D164THR0-0.025-0.0187.6810.0490.0490.0000.0000.0000.000
141D165LEU0-0.053-0.0297.861-0.026-0.0260.0000.0000.0000.000
142D166VAL00.024-0.0076.279-0.247-0.2470.0000.0000.0000.000
143D167LEU0-0.031-0.0167.1820.3970.3970.0000.0000.0000.000
144D168ASP-1-0.865-0.8928.931-0.694-0.6940.0000.0000.0000.000
145D169PRO00.0150.01711.173-0.086-0.0860.0000.0000.0000.000
146D170THR0-0.046-0.02812.346-0.032-0.0320.0000.0000.0000.000
147D171SER00.1240.05514.4400.0230.0230.0000.0000.0000.000
148D172LYS10.8850.94813.7540.4370.4370.0000.0000.0000.000
149D173GLN00.1330.0399.5470.1850.1850.0000.0000.0000.000
150D174GLU-1-0.914-0.96613.993-0.233-0.2330.0000.0000.0000.000
151D175LYS10.9070.97316.8780.1950.1950.0000.0000.0000.000
152D176GLU-1-0.979-0.99015.443-0.313-0.3130.0000.0000.0000.000
153D177ALA0-0.0360.00814.5440.0110.0110.0000.0000.0000.000
154D178ARG10.9060.94716.3650.1130.1130.0000.0000.0000.000
155D179ALA0-0.040-0.03316.4470.0300.0300.0000.0000.0000.000
156D180VAL00.0720.05016.075-0.039-0.0390.0000.0000.0000.000
157D181LEU0-0.011-0.03616.1070.0380.0380.0000.0000.0000.000
158D182THR0-0.012-0.00116.756-0.041-0.0410.0000.0000.0000.000
159D183PHE0-0.056-0.00416.0360.0210.0210.0000.0000.0000.000
160D184ALA00.0190.00619.721-0.010-0.0100.0000.0000.0000.000
161D185LEU0-0.058-0.04017.9770.0180.0180.0000.0000.0000.000
162D186ASP-1-0.727-0.87421.7860.0270.0270.0000.0000.0000.000
163D187SER00.0160.01522.0500.0090.0090.0000.0000.0000.000
164D188VAL0-0.081-0.02722.9520.0110.0110.0000.0000.0000.000
165D189GLU-1-0.902-0.95324.5550.0680.0680.0000.0000.0000.000
166D190ARG10.8120.94017.663-0.134-0.1340.0000.0000.0000.000
167D191LYS10.9610.90921.566-0.047-0.0470.0000.0000.0000.000
168D192LEU0-0.0040.01020.696-0.012-0.0120.0000.0000.0000.000
169D193LEU0-0.0600.01523.096-0.002-0.0020.0000.0000.0000.000
170D194MET00.0170.00524.329-0.010-0.0100.0000.0000.0000.000
171D195SER00.0070.01021.529-0.007-0.0070.0000.0000.0000.000
172D196SER0-0.009-0.00222.5470.0040.0040.0000.0000.0000.000
173D197THR0-0.0150.00720.001-0.012-0.0120.0000.0000.0000.000
174D198LYS10.8840.95921.9430.0870.0870.0000.0000.0000.000
175D199GLY00.0540.01520.707-0.020-0.0200.0000.0000.0000.000
176D200LEU0-0.054-0.01820.6830.0120.0120.0000.0000.0000.000
177D201TYR00.0310.01218.338-0.002-0.0020.0000.0000.0000.000
178D202SER00.0000.00220.3450.0070.0070.0000.0000.0000.000
179D203ASP-1-0.845-0.95720.7860.0720.0720.0000.0000.0000.000
180D204THR0-0.021-0.02419.2260.0050.0050.0000.0000.0000.000
181D205GLU-1-0.907-0.92016.7530.0000.0000.0000.0000.0000.000
182D206LEU0-0.059-0.03816.7000.0120.0120.0000.0000.0000.000
183D207GLN00.0210.03616.9230.0180.0180.0000.0000.0000.000
184D208GLN00.0920.02612.6150.0000.0000.0000.0000.0000.000
185D209CYS00.0080.02012.4390.0250.0250.0000.0000.0000.000
186D210LEU00.0990.03113.496-0.012-0.0120.0000.0000.0000.000
187D211ALA00.0850.02014.9470.0030.0030.0000.0000.0000.000
188D212ALA0-0.088-0.03310.1780.0540.0540.0000.0000.0000.000
189D213ALA0-0.038-0.03712.156-0.007-0.0070.0000.0000.0000.000
190D214GLN0-0.069-0.00413.768-0.014-0.0140.0000.0000.0000.000
191D215ALA00.1110.04410.794-0.032-0.0320.0000.0000.0000.000
192D216ALA00.0390.01310.741-0.017-0.0170.0000.0000.0000.000
193D217SER00.015-0.02011.581-0.040-0.0400.0000.0000.0000.000
194D218GLN00.0930.06414.002-0.015-0.0150.0000.0000.0000.000
195D219HIS0-0.016-0.0088.999-0.050-0.0500.0000.0000.0000.000
196D220VAL00.0300.05313.669-0.018-0.0180.0000.0000.0000.000
197D221PHE0-0.002-0.00515.945-0.004-0.0040.0000.0000.0000.000
198D222ARG10.7430.83612.002-0.211-0.2110.0000.0000.0000.000
199D223PHE00.0040.00116.072-0.004-0.0040.0000.0000.0000.000
200D224TYR0-0.019-0.01317.801-0.004-0.0040.0000.0000.0000.000
201D225ARG10.9790.99521.041-0.038-0.0380.0000.0000.0000.000
202D226GLU-1-0.856-0.92619.062-0.026-0.0260.0000.0000.0000.000
203D227SER00.027-0.00920.807-0.006-0.0060.0000.0000.0000.000
204D228LEU0-0.033-0.03023.2510.0010.0010.0000.0000.0000.000
205D229GLN0-0.050-0.02524.1070.0010.0010.0000.0000.0000.000
206D230ARG10.9170.96223.8400.0410.0410.0000.0000.0000.000
207D231ARG10.8680.99925.1410.0710.0710.0000.0000.0000.000
208D232TYR00.0170.00329.8290.0010.0010.0000.0000.0000.000
209D233SER0-0.093-0.06629.2550.0030.0030.0000.0000.0000.000
210D234LYS10.9250.98131.2880.0280.0280.0000.0000.0000.000