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: 37QNL

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 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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2293874.262568
FMO2-HF: Nuclear repulsion 2213020.794811
FMO2-HF: Total energy -80853.467757
FMO2-MP2: Total energy -81083.700348


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.
0.4181.807-0.004-0.687-0.6970
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 : 0.041 / q_NPA : 0.006
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].
3D27SER0-0.045-0.0383.7890.6071.996-0.004-0.687-0.6970.000
4D28LEU0-0.0090.0035.4230.0650.0650.0000.0000.0000.000
5D29ARG10.8500.9198.6650.2780.2780.0000.0000.0000.000
6D30HIS00.0450.01710.8650.0420.0420.0000.0000.0000.000
7D31PHE00.0250.00013.4930.0280.0280.0000.0000.0000.000
8D32ALA0-0.030-0.01116.4060.0140.0140.0000.0000.0000.000
9D33CYS0-0.046-0.01720.1030.0090.0090.0000.0000.0000.000
10D34GLU-1-0.835-0.88423.271-0.128-0.1280.0000.0000.0000.000
11D35GLN0-0.039-0.06426.994-0.005-0.0050.0000.0000.0000.000
12D36ASN0-0.0040.01029.7140.0010.0010.0000.0000.0000.000
13D37LEU0-0.0190.00929.4130.0010.0010.0000.0000.0000.000
14D38LEU0-0.007-0.00433.6430.0030.0030.0000.0000.0000.000
15D39SER00.0350.02336.7270.0010.0010.0000.0000.0000.000
16D40ARG10.8650.92139.4570.0490.0490.0000.0000.0000.000
17D41PRO0-0.021-0.01736.9940.0040.0040.0000.0000.0000.000
18D42ASP-1-0.868-0.93839.410-0.043-0.0430.0000.0000.0000.000
19D43GLY00.0240.02435.2760.0010.0010.0000.0000.0000.000
20D44SER0-0.065-0.04132.958-0.002-0.0020.0000.0000.0000.000
21D45ALA0-0.015-0.00727.5030.0000.0000.0000.0000.0000.000
22D46SER0-0.035-0.02026.598-0.001-0.0010.0000.0000.0000.000
23D47PHE00.0330.00518.3240.0020.0020.0000.0000.0000.000
24D48LEU00.020-0.00520.5010.0020.0020.0000.0000.0000.000
25D49GLN0-0.033-0.03915.4820.0410.0410.0000.0000.0000.000
26D50GLY00.0250.00915.371-0.025-0.0250.0000.0000.0000.000
27D51ASP-1-0.920-0.95216.191-0.334-0.3340.0000.0000.0000.000
28D52THR0-0.0470.01518.0970.0200.0200.0000.0000.0000.000
29D53SER00.020-0.01519.794-0.007-0.0070.0000.0000.0000.000
30D54VAL0-0.039-0.02222.6110.0110.0110.0000.0000.0000.000
31D55LEU00.0070.02025.419-0.001-0.0010.0000.0000.0000.000
32D56ALA0-0.012-0.01528.6490.0040.0040.0000.0000.0000.000
33D57GLY00.0120.01230.530-0.001-0.0010.0000.0000.0000.000
34D58VAL0-0.034-0.02933.6930.0010.0010.0000.0000.0000.000
35D59TYR0-0.050-0.01936.2770.0000.0000.0000.0000.0000.000
36D60GLY00.0870.04238.9770.0030.0030.0000.0000.0000.000
37D61PRO0-0.023-0.01139.8810.0000.0000.0000.0000.0000.000
38D62ALA00.0430.03941.9360.0020.0020.0000.0000.0000.000
39D63GLU-1-0.842-0.93544.970-0.018-0.0180.0000.0000.0000.000
40D64VAL0-0.068-0.02546.298-0.001-0.0010.0000.0000.0000.000
41D65LYS10.9200.95149.4910.0250.0250.0000.0000.0000.000
42D66VAL00.016-0.00452.599-0.001-0.0010.0000.0000.0000.000
43D67SER0-0.0040.00651.176-0.002-0.0020.0000.0000.0000.000
44D68LYS10.8250.90453.1960.0150.0150.0000.0000.0000.000
45D69GLU-1-0.772-0.86552.991-0.014-0.0140.0000.0000.0000.000
46D70ILE0-0.030-0.01752.398-0.001-0.0010.0000.0000.0000.000
47D71PHE00.0340.02445.1680.0010.0010.0000.0000.0000.000
48D72ASN00.012-0.02247.6380.0010.0010.0000.0000.0000.000
49D73LYS10.8880.95840.9900.0110.0110.0000.0000.0000.000
50D74ALA00.0710.04840.824-0.001-0.0010.0000.0000.0000.000
51D75THR0-0.012-0.00740.7710.0010.0010.0000.0000.0000.000
52D76LEU00.0120.00533.942-0.002-0.0020.0000.0000.0000.000
53D77GLU-1-0.796-0.86837.706-0.039-0.0390.0000.0000.0000.000
54D78VAL00.013-0.00431.546-0.002-0.0020.0000.0000.0000.000
55D79ILE0-0.046-0.01334.9750.0010.0010.0000.0000.0000.000
56D80LEU0-0.005-0.00128.377-0.004-0.0040.0000.0000.0000.000
57D81ARG10.9220.94632.0120.0690.0690.0000.0000.0000.000
58D82PRO00.0250.02330.101-0.007-0.0070.0000.0000.0000.000
59D83LYN00.0480.04126.2020.0030.0030.0000.0000.0000.000
60D84ILE0-0.022-0.00829.6240.0040.0040.0000.0000.0000.000
61D85GLY00.0060.00532.9390.0010.0010.0000.0000.0000.000
62D86LEU0-0.001-0.00235.6510.0020.0020.0000.0000.0000.000
63D87PRO00.017-0.00334.641-0.003-0.0030.0000.0000.0000.000
64D88GLY00.0440.02934.7500.0050.0050.0000.0000.0000.000
65D89VAL00.020-0.01235.295-0.001-0.0010.0000.0000.0000.000
66D90ALA00.0130.01530.8270.0020.0020.0000.0000.0000.000
67D91GLU-1-0.772-0.85730.251-0.093-0.0930.0000.0000.0000.000
68D92LYS10.8410.90832.4590.0470.0470.0000.0000.0000.000
69D93SER0-0.082-0.04931.8590.0030.0030.0000.0000.0000.000
70D94ARG10.8630.90324.8740.1100.1100.0000.0000.0000.000
71D95GLU-1-0.762-0.87929.404-0.060-0.0600.0000.0000.0000.000
72D96ARG10.9290.97331.6610.0310.0310.0000.0000.0000.000
73D97LEU00.0230.01227.0440.0040.0040.0000.0000.0000.000
74D98ILE00.0020.03826.4300.0040.0040.0000.0000.0000.000
75D99ARG10.8350.90828.9400.0400.0400.0000.0000.0000.000
76D100ASN0-0.031-0.03732.0110.0030.0030.0000.0000.0000.000
77D101THR0-0.032-0.03326.0920.0040.0040.0000.0000.0000.000
78D102CYS0-0.042-0.01429.4600.0010.0010.0000.0000.0000.000
79D103GLU-1-0.849-0.93431.188-0.024-0.0240.0000.0000.0000.000
80D104ALA0-0.0030.01830.5050.0040.0040.0000.0000.0000.000
81D105VAL00.0020.00628.0380.0050.0050.0000.0000.0000.000
82D106VAL00.0310.02031.5090.0010.0010.0000.0000.0000.000
83D107LEU00.0090.01834.2420.0030.0030.0000.0000.0000.000
84D108GLY00.0290.00936.6180.0020.0020.0000.0000.0000.000
85D109THR0-0.083-0.06037.6280.0020.0020.0000.0000.0000.000
86D110LEU0-0.031-0.01340.0390.0020.0020.0000.0000.0000.000
87D111HIS00.0200.01842.2960.0020.0020.0000.0000.0000.000
88D112PRO0-0.010-0.00544.850-0.001-0.0010.0000.0000.0000.000
89D113ARG10.8590.92947.5150.0150.0150.0000.0000.0000.000
90D114THR0-0.042-0.01444.168-0.001-0.0010.0000.0000.0000.000
91D115SER0-0.022-0.01942.7800.0010.0010.0000.0000.0000.000
92D116ILE00.0470.03036.769-0.001-0.0010.0000.0000.0000.000
93D117THR0-0.049-0.03438.4390.0010.0010.0000.0000.0000.000
94D118VAL00.0220.01832.046-0.001-0.0010.0000.0000.0000.000
95D119VAL0-0.044-0.02234.5940.0020.0020.0000.0000.0000.000
96D120LEU00.001-0.00727.922-0.003-0.0030.0000.0000.0000.000
97D121GLN0-0.012-0.01530.0320.0010.0010.0000.0000.0000.000
98D122VAL00.0360.01125.337-0.007-0.0070.0000.0000.0000.000
99D123VAL0-0.024-0.01126.3940.0040.0040.0000.0000.0000.000
100D124SER0-0.011-0.02422.2370.0100.0100.0000.0000.0000.000
101D125ASP-1-0.831-0.93021.658-0.213-0.2130.0000.0000.0000.000
102D126ALA0-0.015-0.00118.363-0.001-0.0010.0000.0000.0000.000
103D127GLY00.0430.03617.022-0.046-0.0460.0000.0000.0000.000
104D128SER0-0.032-0.06114.566-0.001-0.0010.0000.0000.0000.000
105D129LEU00.0000.01817.4770.0270.0270.0000.0000.0000.000
106D130LEU00.024-0.00721.2920.0140.0140.0000.0000.0000.000
107D131ALA0-0.0070.00217.9280.0170.0170.0000.0000.0000.000
108D132CYS00.0310.03619.8640.0100.0100.0000.0000.0000.000
109D133CYS0-0.061-0.02221.0880.0180.0180.0000.0000.0000.000
110D134LEU0-0.011-0.01221.7470.0130.0130.0000.0000.0000.000
111D135ASN00.0480.02518.5640.0350.0350.0000.0000.0000.000
112D136ALA00.0100.01222.7820.0090.0090.0000.0000.0000.000
113D137ALA00.021-0.00125.5970.0100.0100.0000.0000.0000.000
114D138CYS0-0.0590.00425.0220.0110.0110.0000.0000.0000.000
115D139MET00.0360.00024.3990.0080.0080.0000.0000.0000.000
116D140ALA00.0180.01827.4030.0060.0060.0000.0000.0000.000
117D141LEU0-0.023-0.02430.4820.0060.0060.0000.0000.0000.000
118D142VAL0-0.046-0.02628.0480.0050.0050.0000.0000.0000.000
119D143ASP-1-0.782-0.88731.176-0.066-0.0660.0000.0000.0000.000
120D144ALA0-0.023-0.00132.7850.0030.0030.0000.0000.0000.000
121D145GLY0-0.0130.00134.8330.0040.0040.0000.0000.0000.000
122D146VAL0-0.035-0.01134.9410.0050.0050.0000.0000.0000.000
123D147PRO0-0.0080.00234.519-0.001-0.0010.0000.0000.0000.000
124D148MET0-0.013-0.01230.1280.0000.0000.0000.0000.0000.000
125D149ARG10.8320.89931.4820.0110.0110.0000.0000.0000.000
126D150ALA0-0.0150.00227.2120.0050.0050.0000.0000.0000.000
127D151LEU00.006-0.00124.812-0.006-0.0060.0000.0000.0000.000
128D152PHE00.032-0.00223.8910.0080.0080.0000.0000.0000.000
129D153CYS0-0.0420.00718.873-0.011-0.0110.0000.0000.0000.000
130D154GLY00.0150.00119.7850.0200.0200.0000.0000.0000.000
131D155VAL0-0.020-0.01414.314-0.033-0.0330.0000.0000.0000.000
132D156ALA00.0210.00714.6740.0440.0440.0000.0000.0000.000
133D157CYS0-0.042-0.02411.732-0.046-0.0460.0000.0000.0000.000
134D158ALA00.0170.01511.9910.0640.0640.0000.0000.0000.000
135D159LEU00.0300.01411.584-0.052-0.0520.0000.0000.0000.000
136D160ASP-1-0.689-0.81311.697-0.074-0.0740.0000.0000.0000.000
137D161SER0-0.033-0.05414.1680.0250.0250.0000.0000.0000.000
138D162ASP-1-0.915-0.92313.6650.0130.0130.0000.0000.0000.000
139D163GLY0-0.061-0.03613.2300.0440.0440.0000.0000.0000.000
140D164THR0-0.075-0.0517.3190.1010.1010.0000.0000.0000.000
141D165LEU0-0.027-0.0097.787-0.100-0.1000.0000.0000.0000.000
142D166VAL00.007-0.0057.024-0.175-0.1750.0000.0000.0000.000
143D167LEU0-0.014-0.0197.5250.3040.3040.0000.0000.0000.000
144D168ASP-1-0.831-0.8719.199-0.688-0.6880.0000.0000.0000.000
145D169PRO00.0000.02211.438-0.092-0.0920.0000.0000.0000.000
146D170THR00.020-0.00512.422-0.014-0.0140.0000.0000.0000.000
147D171SER00.029-0.00114.7670.0120.0120.0000.0000.0000.000
148D172LYS10.8180.90513.8130.3700.3700.0000.0000.0000.000
149D173GLN00.0680.02710.3210.1250.1250.0000.0000.0000.000
150D174GLU-1-0.848-0.93114.126-0.234-0.2340.0000.0000.0000.000
151D175LYS10.8350.90416.8940.1710.1710.0000.0000.0000.000
152D176GLU-1-0.791-0.87014.926-0.282-0.2820.0000.0000.0000.000
153D177ALA0-0.0350.00914.8780.0210.0210.0000.0000.0000.000
154D178ARG10.7850.87616.180-0.003-0.0030.0000.0000.0000.000
155D179ALA0-0.032-0.02417.1720.0200.0200.0000.0000.0000.000
156D180VAL00.0240.02616.332-0.030-0.0300.0000.0000.0000.000
157D181LEU00.006-0.00115.6270.0300.0300.0000.0000.0000.000
158D182THR0-0.046-0.03417.127-0.045-0.0450.0000.0000.0000.000
159D183PHE0-0.001-0.00516.2160.0230.0230.0000.0000.0000.000
160D184ALA00.0350.01919.807-0.021-0.0210.0000.0000.0000.000
161D185LEU0-0.033-0.01418.1890.0180.0180.0000.0000.0000.000
162D186ASP-1-0.744-0.88022.036-0.009-0.0090.0000.0000.0000.000
163D187SER00.026-0.00822.1580.0070.0070.0000.0000.0000.000
164D188VAL0-0.064-0.01822.7880.0080.0080.0000.0000.0000.000
165D189GLU-1-0.815-0.90724.2480.0420.0420.0000.0000.0000.000
166D190ARG10.7780.89418.544-0.050-0.0500.0000.0000.0000.000
167D191LYS10.8430.90621.473-0.027-0.0270.0000.0000.0000.000
168D192LEU00.0050.00620.972-0.012-0.0120.0000.0000.0000.000
169D193LEU0-0.037-0.01723.6220.0030.0030.0000.0000.0000.000
170D194MET0-0.0310.00124.694-0.003-0.0030.0000.0000.0000.000
171D195SER00.0210.00622.830-0.007-0.0070.0000.0000.0000.000
172D196SER0-0.008-0.01322.6900.0030.0030.0000.0000.0000.000
173D197THR00.0090.01220.501-0.015-0.0150.0000.0000.0000.000
174D198LYS10.8890.95421.6390.0740.0740.0000.0000.0000.000
175D199GLY00.0340.00820.875-0.017-0.0170.0000.0000.0000.000
176D200LEU0-0.033-0.00421.0240.0110.0110.0000.0000.0000.000
177D201TYR0-0.0050.00119.014-0.003-0.0030.0000.0000.0000.000
178D202SER00.002-0.01020.3950.0030.0030.0000.0000.0000.000
179D203ASP-1-0.827-0.93120.6980.1130.1130.0000.0000.0000.000
180D204THR0-0.007-0.00519.5320.0130.0130.0000.0000.0000.000
181D205GLU-1-0.781-0.86316.2580.0840.0840.0000.0000.0000.000
182D206LEU00.002-0.00516.3920.0110.0110.0000.0000.0000.000
183D207GLN0-0.026-0.02018.1360.0230.0230.0000.0000.0000.000
184D208GLN00.0080.00713.3140.0200.0200.0000.0000.0000.000
185D209CYS0-0.029-0.01212.8450.0280.0280.0000.0000.0000.000
186D210LEU0-0.0080.00913.899-0.036-0.0360.0000.0000.0000.000
187D211ALA00.0330.01715.052-0.010-0.0100.0000.0000.0000.000
188D212ALA0-0.006-0.00910.2550.0270.0270.0000.0000.0000.000
189D213ALA00.0180.00911.904-0.064-0.0640.0000.0000.0000.000
190D214GLN00.0170.00814.256-0.019-0.0190.0000.0000.0000.000
191D215ALA0-0.0010.01410.879-0.036-0.0360.0000.0000.0000.000
192D216ALA00.0040.00311.126-0.050-0.0500.0000.0000.0000.000
193D217SER00.000-0.02312.023-0.041-0.0410.0000.0000.0000.000
194D218GLN00.0550.02014.415-0.014-0.0140.0000.0000.0000.000
195D219HIS0-0.0230.0148.870-0.019-0.0190.0000.0000.0000.000
196D220VAL00.0360.03213.808-0.013-0.0130.0000.0000.0000.000
197D221PHE00.0100.01016.5220.0050.0050.0000.0000.0000.000
198D222ARG10.8500.90112.364-0.013-0.0130.0000.0000.0000.000
199D223PHE00.0450.02816.3780.0030.0030.0000.0000.0000.000
200D224TYR0-0.006-0.02918.2730.0030.0030.0000.0000.0000.000
201D225ARG10.9570.97721.4450.0260.0260.0000.0000.0000.000
202D226GLU-1-0.831-0.88419.458-0.111-0.1110.0000.0000.0000.000
203D227SER00.005-0.01521.212-0.001-0.0010.0000.0000.0000.000
204D228LEU0-0.021-0.02523.6590.0060.0060.0000.0000.0000.000
205D229GLN0-0.0070.00124.2270.0020.0020.0000.0000.0000.000
206D230ARG10.7940.88222.5850.1000.1000.0000.0000.0000.000
207D231ARG10.8380.92125.2070.1130.1130.0000.0000.0000.000
208D232TYR00.0410.02630.2010.0050.0050.0000.0000.0000.000
209D233SER0-0.061-0.02830.0970.0040.0040.0000.0000.0000.000
210D234LYS10.9070.96432.0060.0570.0570.0000.0000.0000.000