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: J23M9

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 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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2300789.811888
FMO2-HF: Nuclear repulsion 2219939.455889
FMO2-HF: Total energy -80850.355999
FMO2-MP2: Total energy -81081.226


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.
0.2451.473-0.009-0.545-0.6740
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 : 0.032 / 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].
3D27SER0-0.022-0.0153.8240.8992.127-0.009-0.545-0.6740.000
4D28LEU0-0.012-0.0055.404-0.117-0.1170.0000.0000.0000.000
5D29ARG10.8640.9098.8120.3830.3830.0000.0000.0000.000
6D30HIS00.0300.01510.8860.0670.0670.0000.0000.0000.000
7D31PHE00.0440.00213.4050.0350.0350.0000.0000.0000.000
8D32ALA0-0.036-0.00915.6750.0220.0220.0000.0000.0000.000
9D33CYS0-0.037-0.01819.4410.0060.0060.0000.0000.0000.000
10D34GLU-1-0.884-0.91922.773-0.105-0.1050.0000.0000.0000.000
11D35GLN0-0.020-0.03926.454-0.002-0.0020.0000.0000.0000.000
12D36ASN0-0.0310.00028.9820.0000.0000.0000.0000.0000.000
13D37LEU0-0.0080.00529.062-0.001-0.0010.0000.0000.0000.000
14D38LEU0-0.026-0.03333.2580.0040.0040.0000.0000.0000.000
15D39SER00.0520.02536.0860.0020.0020.0000.0000.0000.000
16D40ARG10.8700.94639.2410.0400.0400.0000.0000.0000.000
17D41PRO0-0.005-0.01436.7880.0030.0030.0000.0000.0000.000
18D42ASP-1-0.867-0.93538.426-0.033-0.0330.0000.0000.0000.000
19D43GLY00.0210.01734.7150.0010.0010.0000.0000.0000.000
20D44SER0-0.053-0.00132.729-0.005-0.0050.0000.0000.0000.000
21D45ALA00.0240.02327.4290.0010.0010.0000.0000.0000.000
22D46SER0-0.036-0.02826.701-0.004-0.0040.0000.0000.0000.000
23D47PHE00.005-0.00218.0810.0020.0020.0000.0000.0000.000
24D48LEU00.039-0.00720.497-0.002-0.0020.0000.0000.0000.000
25D49GLN0-0.059-0.03315.0990.0410.0410.0000.0000.0000.000
26D50GLY00.0750.02215.407-0.027-0.0270.0000.0000.0000.000
27D51ASP-1-1.003-0.97916.215-0.308-0.3080.0000.0000.0000.000
28D52THR0-0.026-0.02118.0090.0170.0170.0000.0000.0000.000
29D53SER00.0560.00219.806-0.005-0.0050.0000.0000.0000.000
30D54VAL0-0.038-0.00922.4240.0070.0070.0000.0000.0000.000
31D55LEU00.0230.02625.4690.0000.0000.0000.0000.0000.000
32D56ALA0-0.060-0.04428.2900.0030.0030.0000.0000.0000.000
33D57GLY0-0.014-0.01430.0950.0020.0020.0000.0000.0000.000
34D58VAL00.003-0.01232.9990.0010.0010.0000.0000.0000.000
35D59TYR0-0.074-0.01935.4930.0000.0000.0000.0000.0000.000
36D60GLY00.043-0.00837.9150.0020.0020.0000.0000.0000.000
37D61PRO0-0.0020.01538.8230.0000.0000.0000.0000.0000.000
38D62ALA00.0340.02241.5140.0000.0000.0000.0000.0000.000
39D63GLU-1-0.866-0.93344.615-0.012-0.0120.0000.0000.0000.000
40D64VAL0-0.034-0.01546.080-0.001-0.0010.0000.0000.0000.000
41D65LYS10.9560.97649.0170.0210.0210.0000.0000.0000.000
42D66VAL0-0.002-0.00352.5290.0000.0000.0000.0000.0000.000
43D67SER00.012-0.00350.903-0.002-0.0020.0000.0000.0000.000
44D68LYS10.8140.89852.9320.0120.0120.0000.0000.0000.000
45D69GLU-1-0.783-0.87252.728-0.012-0.0120.0000.0000.0000.000
46D70ILE0-0.012-0.01151.894-0.001-0.0010.0000.0000.0000.000
47D71PHE00.0270.02744.8990.0000.0000.0000.0000.0000.000
48D72ASN0-0.019-0.07647.1510.0020.0020.0000.0000.0000.000
49D73LYS10.8710.99841.1160.0040.0040.0000.0000.0000.000
50D74ALA00.1600.07440.204-0.001-0.0010.0000.0000.0000.000
51D75THR0-0.044-0.02440.4470.0010.0010.0000.0000.0000.000
52D76LEU00.0180.01333.262-0.001-0.0010.0000.0000.0000.000
53D77GLU-1-0.854-0.91337.276-0.039-0.0390.0000.0000.0000.000
54D78VAL0-0.004-0.01031.676-0.001-0.0010.0000.0000.0000.000
55D79ILE0-0.057-0.01934.787-0.001-0.0010.0000.0000.0000.000
56D80LEU00.0190.03328.287-0.002-0.0020.0000.0000.0000.000
57D81ARG10.9270.95332.2600.0620.0620.0000.0000.0000.000
58D82PRO00.021-0.00430.163-0.005-0.0050.0000.0000.0000.000
59D83LYN00.0470.03025.7600.0010.0010.0000.0000.0000.000
60D84ILE0-0.037-0.00929.4590.0060.0060.0000.0000.0000.000
61D85GLY00.010-0.00232.5630.0010.0010.0000.0000.0000.000
62D86LEU00.0080.01535.1750.0000.0000.0000.0000.0000.000
63D87PRO00.030-0.00534.611-0.004-0.0040.0000.0000.0000.000
64D88GLY00.0400.03134.1960.0040.0040.0000.0000.0000.000
65D89VAL00.035-0.00735.3610.0010.0010.0000.0000.0000.000
66D90ALA00.0060.00830.3910.0020.0020.0000.0000.0000.000
67D91GLU-1-0.770-0.86730.116-0.096-0.0960.0000.0000.0000.000
68D92LYS10.8910.95232.1630.0470.0470.0000.0000.0000.000
69D93SER0-0.069-0.04631.8030.0020.0020.0000.0000.0000.000
70D94ARG10.8890.92024.7040.1160.1160.0000.0000.0000.000
71D95GLU-1-0.803-0.90229.442-0.056-0.0560.0000.0000.0000.000
72D96ARG10.9330.96631.6510.0340.0340.0000.0000.0000.000
73D97LEU00.0290.01726.7820.0040.0040.0000.0000.0000.000
74D98ILE00.0060.03926.0580.0050.0050.0000.0000.0000.000
75D99ARG10.8820.92929.0270.0400.0400.0000.0000.0000.000
76D100ASN0-0.075-0.05331.4250.0020.0020.0000.0000.0000.000
77D101THR0-0.046-0.04525.7520.0040.0040.0000.0000.0000.000
78D102CYS0-0.035-0.01329.1370.0030.0030.0000.0000.0000.000
79D103GLU-1-0.853-0.91231.017-0.017-0.0170.0000.0000.0000.000
80D104ALA0-0.0190.00530.1930.0040.0040.0000.0000.0000.000
81D105VAL00.0320.01527.4540.0060.0060.0000.0000.0000.000
82D106VAL00.0250.01230.9230.0020.0020.0000.0000.0000.000
83D107LEU00.0360.03233.6940.0020.0020.0000.0000.0000.000
84D108GLY00.0620.01835.9350.0010.0010.0000.0000.0000.000
85D109THR0-0.107-0.07137.1550.0010.0010.0000.0000.0000.000
86D110LEU0-0.066-0.04439.4840.0010.0010.0000.0000.0000.000
87D111HIS00.0040.01641.5990.0010.0010.0000.0000.0000.000
88D112PRO00.013-0.02444.108-0.001-0.0010.0000.0000.0000.000
89D113ARG10.8300.95846.8260.0070.0070.0000.0000.0000.000
90D114THR0-0.018-0.00842.659-0.002-0.0020.0000.0000.0000.000
91D115SER0-0.031-0.01342.7220.0010.0010.0000.0000.0000.000
92D116ILE00.0060.01036.7790.0000.0000.0000.0000.0000.000
93D117THR0-0.025-0.01337.8590.0000.0000.0000.0000.0000.000
94D118VAL00.0280.01131.363-0.001-0.0010.0000.0000.0000.000
95D119VAL0-0.030-0.01933.8240.0010.0010.0000.0000.0000.000
96D120LEU0-0.011-0.00428.111-0.003-0.0030.0000.0000.0000.000
97D121GLN00.016-0.00429.894-0.001-0.0010.0000.0000.0000.000
98D122VAL00.0190.01625.812-0.007-0.0070.0000.0000.0000.000
99D123VAL0-0.034-0.00626.2510.0040.0040.0000.0000.0000.000
100D124SER0-0.056-0.04621.9980.0060.0060.0000.0000.0000.000
101D125ASP-1-0.815-0.89921.754-0.212-0.2120.0000.0000.0000.000
102D126ALA00.001-0.01418.163-0.003-0.0030.0000.0000.0000.000
103D127GLY00.0050.02316.230-0.050-0.0500.0000.0000.0000.000
104D128SER0-0.019-0.05714.3530.0030.0030.0000.0000.0000.000
105D129LEU00.0120.01817.1520.0320.0320.0000.0000.0000.000
106D130LEU00.010-0.01720.8920.0120.0120.0000.0000.0000.000
107D131ALA0-0.012-0.00217.7470.0170.0170.0000.0000.0000.000
108D132CYS00.0280.04419.6530.0190.0190.0000.0000.0000.000
109D133CYS0-0.036-0.01220.8920.0190.0190.0000.0000.0000.000
110D134LEU0-0.0060.01821.4350.0150.0150.0000.0000.0000.000
111D135ASN00.1120.04218.8410.0280.0280.0000.0000.0000.000
112D136ALA00.0180.03022.7760.0090.0090.0000.0000.0000.000
113D137ALA00.042-0.00625.1570.0100.0100.0000.0000.0000.000
114D138CYS0-0.086-0.01924.8400.0120.0120.0000.0000.0000.000
115D139MET0-0.002-0.00923.7480.0100.0100.0000.0000.0000.000
116D140ALA00.0040.00427.2370.0050.0050.0000.0000.0000.000
117D141LEU0-0.031-0.03129.9510.0050.0050.0000.0000.0000.000
118D142VAL0-0.018-0.02927.1380.0040.0040.0000.0000.0000.000
119D143ASP-1-0.790-0.89130.404-0.044-0.0440.0000.0000.0000.000
120D144ALA0-0.032-0.00132.2540.0030.0030.0000.0000.0000.000
121D145GLY0-0.034-0.03034.0280.0030.0030.0000.0000.0000.000
122D146VAL0-0.062-0.01634.8130.0040.0040.0000.0000.0000.000
123D147PRO0-0.0200.00034.4180.0010.0010.0000.0000.0000.000
124D148MET00.0320.01629.872-0.002-0.0020.0000.0000.0000.000
125D149ARG10.8090.90731.292-0.002-0.0020.0000.0000.0000.000
126D150ALA0-0.022-0.01427.0500.0050.0050.0000.0000.0000.000
127D151LEU00.018-0.00524.414-0.007-0.0070.0000.0000.0000.000
128D152PHE00.0500.00123.2770.0090.0090.0000.0000.0000.000
129D153CYS0-0.079-0.01318.261-0.008-0.0080.0000.0000.0000.000
130D154GLY00.0430.01819.1350.0160.0160.0000.0000.0000.000
131D155VAL0-0.050-0.02313.770-0.027-0.0270.0000.0000.0000.000
132D156ALA00.0280.00414.2250.0370.0370.0000.0000.0000.000
133D157CYS0-0.051-0.02911.726-0.052-0.0520.0000.0000.0000.000
134D158ALA00.006-0.00411.7730.0720.0720.0000.0000.0000.000
135D159LEU00.0490.03311.484-0.074-0.0740.0000.0000.0000.000
136D160ASP-1-0.657-0.83311.841-0.259-0.2590.0000.0000.0000.000
137D161SER0-0.097-0.05614.3690.0340.0340.0000.0000.0000.000
138D162ASP-1-0.864-0.92613.544-0.091-0.0910.0000.0000.0000.000
139D163GLY0-0.123-0.04613.4050.0310.0310.0000.0000.0000.000
140D164THR0-0.016-0.0167.7910.0500.0500.0000.0000.0000.000
141D165LEU0-0.036-0.0067.758-0.036-0.0360.0000.0000.0000.000
142D166VAL0-0.008-0.0186.606-0.245-0.2450.0000.0000.0000.000
143D167LEU0-0.011-0.0177.1800.3920.3920.0000.0000.0000.000
144D168ASP-1-0.832-0.8468.931-0.638-0.6380.0000.0000.0000.000
145D169PRO0-0.0110.00811.176-0.089-0.0890.0000.0000.0000.000
146D170THR0-0.018-0.01212.347-0.033-0.0330.0000.0000.0000.000
147D171SER00.1000.05114.4410.0280.0280.0000.0000.0000.000
148D172LYS10.7820.88913.7380.4290.4290.0000.0000.0000.000
149D173GLN00.0820.0089.4980.1460.1460.0000.0000.0000.000
150D174GLU-1-0.863-0.94313.993-0.247-0.2470.0000.0000.0000.000
151D175LYS10.8550.92616.8780.2050.2050.0000.0000.0000.000
152D176GLU-1-0.831-0.88715.092-0.332-0.3320.0000.0000.0000.000
153D177ALA0-0.0270.01414.6620.0110.0110.0000.0000.0000.000
154D178ARG10.7970.89016.3650.1040.1040.0000.0000.0000.000
155D179ALA0-0.056-0.04216.6140.0290.0290.0000.0000.0000.000
156D180VAL00.0440.03516.074-0.040-0.0400.0000.0000.0000.000
157D181LEU0-0.033-0.02115.8300.0380.0380.0000.0000.0000.000
158D182THR0-0.0010.00216.756-0.041-0.0410.0000.0000.0000.000
159D183PHE0-0.026-0.02216.1620.0210.0210.0000.0000.0000.000
160D184ALA00.0080.00619.721-0.010-0.0100.0000.0000.0000.000
161D185LEU0-0.049-0.02717.9410.0180.0180.0000.0000.0000.000
162D186ASP-1-0.754-0.88621.7610.0200.0200.0000.0000.0000.000
163D187SER00.0470.03322.0230.0080.0080.0000.0000.0000.000
164D188VAL0-0.110-0.04722.9280.0120.0120.0000.0000.0000.000
165D189GLU-1-0.794-0.89124.5300.0620.0620.0000.0000.0000.000
166D190ARG10.8420.94718.111-0.116-0.1160.0000.0000.0000.000
167D191LYS10.8370.84921.540-0.050-0.0500.0000.0000.0000.000
168D192LEU00.0020.00520.487-0.011-0.0110.0000.0000.0000.000
169D193LEU0-0.0540.00323.096-0.002-0.0020.0000.0000.0000.000
170D194MET00.0120.01124.361-0.009-0.0090.0000.0000.0000.000
171D195SER00.0070.01522.084-0.008-0.0080.0000.0000.0000.000
172D196SER0-0.007-0.00622.5540.0050.0050.0000.0000.0000.000
173D197THR00.0090.01120.115-0.011-0.0110.0000.0000.0000.000
174D198LYS10.9090.95921.9510.0900.0900.0000.0000.0000.000
175D199GLY00.0570.01520.697-0.020-0.0200.0000.0000.0000.000
176D200LEU0-0.052-0.01720.6750.0130.0130.0000.0000.0000.000
177D201TYR0-0.0030.01518.6310.0000.0000.0000.0000.0000.000
178D202SER00.0550.01720.3430.0060.0060.0000.0000.0000.000
179D203ASP-1-0.831-0.93120.7840.0710.0710.0000.0000.0000.000
180D204THR00.0450.01419.2440.0060.0060.0000.0000.0000.000
181D205GLU-1-0.960-0.97716.744-0.017-0.0170.0000.0000.0000.000
182D206LEU0-0.018-0.01316.6970.0100.0100.0000.0000.0000.000
183D207GLN0-0.0080.01117.3500.0260.0260.0000.0000.0000.000
184D208GLN00.0590.03512.506-0.004-0.0040.0000.0000.0000.000
185D209CYS00.0380.01612.4390.0210.0210.0000.0000.0000.000
186D210LEU00.0710.04313.492-0.010-0.0100.0000.0000.0000.000
187D211ALA00.0810.03215.2080.0030.0030.0000.0000.0000.000
188D212ALA0-0.072-0.02710.1260.0510.0510.0000.0000.0000.000
189D213ALA0-0.046-0.03312.135-0.009-0.0090.0000.0000.0000.000
190D214GLN0-0.024-0.01013.768-0.011-0.0110.0000.0000.0000.000
191D215ALA00.0390.04110.807-0.033-0.0330.0000.0000.0000.000
192D216ALA00.0150.00510.709-0.021-0.0210.0000.0000.0000.000
193D217SER00.013-0.02611.557-0.038-0.0380.0000.0000.0000.000
194D218GLN00.0380.00014.108-0.018-0.0180.0000.0000.0000.000
195D219HIS0-0.0120.0138.746-0.048-0.0480.0000.0000.0000.000
196D220VAL00.0230.04813.649-0.015-0.0150.0000.0000.0000.000
197D221PHE00.0250.00715.926-0.001-0.0010.0000.0000.0000.000
198D222ARG10.8230.88412.002-0.198-0.1980.0000.0000.0000.000
199D223PHE0-0.004-0.00515.993-0.003-0.0030.0000.0000.0000.000
200D224TYR0-0.018-0.01617.786-0.003-0.0030.0000.0000.0000.000
201D225ARG10.9850.99921.217-0.034-0.0340.0000.0000.0000.000
202D226GLU-1-0.784-0.87019.235-0.040-0.0400.0000.0000.0000.000
203D227SER00.0370.01120.827-0.005-0.0050.0000.0000.0000.000
204D228LEU0-0.049-0.03223.2390.0010.0010.0000.0000.0000.000
205D229GLN0-0.029-0.02424.412-0.001-0.0010.0000.0000.0000.000
206D230ARG10.7990.89022.2980.0430.0430.0000.0000.0000.000
207D231ARG10.8840.97224.7090.0770.0770.0000.0000.0000.000
208D232TYR00.0380.01229.8180.0020.0020.0000.0000.0000.000
209D233SER0-0.048-0.02729.2860.0040.0040.0000.0000.0000.000
210D234LYS10.8710.95031.2790.0320.0320.0000.0000.0000.000