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

tag_button

FMODB ID: YNZK2

Calculation Name: 1AN8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1AN8

Chain ID: A

ChEMBL ID:

UniProt ID: Q8NKX2

Base Structure: X-ray

Registration Date: 2023-09-27

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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2556118.199989
FMO2-HF: Nuclear repulsion 2472091.496322
FMO2-HF: Total energy -84026.703667
FMO2-MP2: Total energy -84274.861054


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(A:3:LYS)


Summations of interaction energy for fragment #1(A:3: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.
-116.694-110.9620.831-3.019-3.543-0.016
Interaction energy analysis for fragmet #1(A:3:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 1.003 / q_NPA : 1.003
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].
3A5ASP-1-0.782-0.8762.679-66.045-60.7900.834-2.979-3.110-0.016
4A6ILE00.0070.0023.9392.8623.201-0.001-0.036-0.3030.000
5A7SER0-0.049-0.0415.3206.2406.306-0.001-0.001-0.0630.000
6A8ASN0-0.011-0.0247.5615.5585.5580.0000.0000.0000.000
7A9VAL00.0060.0194.7403.3993.471-0.001-0.003-0.0670.000
8A10LYS10.8350.9227.98631.03431.0340.0000.0000.0000.000
9A11SER00.0330.02510.3383.1993.1990.0000.0000.0000.000
10A12ASP-1-0.773-0.85510.604-26.218-26.2180.0000.0000.0000.000
11A13LEU0-0.047-0.0239.5562.2842.2840.0000.0000.0000.000
12A14LEU00.0090.00813.4601.7671.7670.0000.0000.0000.000
13A15TYR00.0160.02215.8851.7221.7220.0000.0000.0000.000
14A16ALA0-0.029-0.01615.9291.2091.2090.0000.0000.0000.000
15A17TYR00.002-0.03614.5190.6980.6980.0000.0000.0000.000
16A18THR0-0.041-0.00918.8350.8330.8330.0000.0000.0000.000
17A19ILE0-0.080-0.04021.3470.2700.2700.0000.0000.0000.000
18A20THR0-0.023-0.01224.0510.0960.0960.0000.0000.0000.000
19A21PRO0-0.0120.00125.9860.0050.0050.0000.0000.0000.000
20A22TYR0-0.033-0.02027.4060.2130.2130.0000.0000.0000.000
21A23ASP-1-0.833-0.92530.282-9.799-9.7990.0000.0000.0000.000
22A24TYR0-0.079-0.05332.4500.3310.3310.0000.0000.0000.000
23A25LYS10.8760.92334.7488.9898.9890.0000.0000.0000.000
24A26ASP-1-0.829-0.89837.934-7.224-7.2240.0000.0000.0000.000
25A27CYS0-0.0320.00838.0560.1610.1610.0000.0000.0000.000
26A28ARG10.9160.96440.0097.1547.1540.0000.0000.0000.000
27A29VAL00.0100.01237.167-0.135-0.1350.0000.0000.0000.000
28A30ASN0-0.002-0.00939.2820.4140.4140.0000.0000.0000.000
29A31PHE0-0.043-0.03936.9910.2410.2410.0000.0000.0000.000
30A32SER00.0360.02035.521-0.166-0.1660.0000.0000.0000.000
31A33THR0-0.029-0.02232.5240.1590.1590.0000.0000.0000.000
32A34THR0-0.006-0.02230.4380.0770.0770.0000.0000.0000.000
33A35HIS00.0420.03227.285-0.045-0.0450.0000.0000.0000.000
34A36THR0-0.0180.01228.537-0.249-0.2490.0000.0000.0000.000
35A37LEU00.0290.02730.8130.3300.3300.0000.0000.0000.000
36A38ASN0-0.0140.00933.177-0.059-0.0590.0000.0000.0000.000
37A39ILE00.014-0.01233.6470.2340.2340.0000.0000.0000.000
38A40ASP-1-0.798-0.87737.153-7.538-7.5380.0000.0000.0000.000
39A41THR00.0340.00635.9640.0420.0420.0000.0000.0000.000
40A42GLN00.0200.01439.4000.0860.0860.0000.0000.0000.000
41A43LYS10.7890.90241.7137.6027.6020.0000.0000.0000.000
42A44TYR0-0.092-0.07438.7050.0630.0630.0000.0000.0000.000
43A45ARG10.8160.88733.2869.2099.2090.0000.0000.0000.000
44A46GLY00.0140.03039.9650.0350.0350.0000.0000.0000.000
45A47LYS10.8180.86042.7046.7306.7300.0000.0000.0000.000
46A48ASP-1-0.820-0.89742.392-7.116-7.1160.0000.0000.0000.000
47A49TYR0-0.030-0.00436.369-0.110-0.1100.0000.0000.0000.000
48A50TYR0-0.064-0.02533.8150.1610.1610.0000.0000.0000.000
49A51ILE0-0.0160.00631.348-0.226-0.2260.0000.0000.0000.000
50A52SER0-0.004-0.01130.0550.3330.3330.0000.0000.0000.000
51A53SER0-0.061-0.04028.717-0.377-0.3770.0000.0000.0000.000
52A54GLU-1-0.776-0.88023.294-12.310-12.3100.0000.0000.0000.000
53A55MET0-0.056-0.02825.785-0.349-0.3490.0000.0000.0000.000
54A56SER0-0.012-0.01924.7160.2060.2060.0000.0000.0000.000
55A57TYR00.0200.00526.4400.3260.3260.0000.0000.0000.000
56A58GLU-1-0.816-0.90626.623-10.835-10.8350.0000.0000.0000.000
57A59ALA0-0.032-0.00228.0980.2960.2960.0000.0000.0000.000
58A60SER0-0.008-0.02730.1270.3670.3670.0000.0000.0000.000
59A61GLN00.0140.00532.2670.2800.2800.0000.0000.0000.000
60A62LYS10.8410.93832.6079.3109.3100.0000.0000.0000.000
61A63PHE0-0.033-0.01332.1710.1100.1100.0000.0000.0000.000
62A64LYS10.8250.89237.2217.2807.2800.0000.0000.0000.000
63A65ARG10.9420.96840.1737.1467.1460.0000.0000.0000.000
64A66ASP-1-0.858-0.95342.261-6.831-6.8310.0000.0000.0000.000
65A67ASP-1-0.827-0.87139.953-7.605-7.6050.0000.0000.0000.000
66A68HIS0-0.081-0.05841.1940.0270.0270.0000.0000.0000.000
67A69VAL0-0.030-0.02635.359-0.071-0.0710.0000.0000.0000.000
68A70ASP-1-0.807-0.89434.729-8.487-8.4870.0000.0000.0000.000
69A71VAL0-0.028-0.03831.164-0.215-0.2150.0000.0000.0000.000
70A72PHE00.009-0.00725.5440.0490.0490.0000.0000.0000.000
71A73GLY0-0.0080.00525.964-0.285-0.2850.0000.0000.0000.000
72A74LEU0-0.0320.00120.8490.2940.2940.0000.0000.0000.000
73A75PHE0-0.0020.00324.194-0.261-0.2610.0000.0000.0000.000
74A76TYR0-0.019-0.02821.125-0.549-0.5490.0000.0000.0000.000
75A77ILE0-0.041-0.01422.650-0.242-0.2420.0000.0000.0000.000
76A78LEU00.0130.00825.3400.1840.1840.0000.0000.0000.000
77A79ASN0-0.051-0.02927.8710.2870.2870.0000.0000.0000.000
78A80SER00.0230.00429.906-0.077-0.0770.0000.0000.0000.000
79A81HIS00.011-0.00231.984-0.032-0.0320.0000.0000.0000.000
80A82THR00.0190.01335.755-0.062-0.0620.0000.0000.0000.000
81A83GLY00.0310.03333.8390.1000.1000.0000.0000.0000.000
82A84GLU-1-0.750-0.82831.161-9.838-9.8380.0000.0000.0000.000
83A85TYR00.0480.01327.2100.1530.1530.0000.0000.0000.000
84A86ILE00.0290.01525.511-0.410-0.4100.0000.0000.0000.000
85A87TYR0-0.016-0.01619.1340.4580.4580.0000.0000.0000.000
86A88GLY00.0340.02624.642-0.154-0.1540.0000.0000.0000.000
87A89GLY00.0280.00826.6110.2120.2120.0000.0000.0000.000
88A90ILE0-0.037-0.01027.9660.3410.3410.0000.0000.0000.000
89A91THR00.0300.01631.096-0.224-0.2240.0000.0000.0000.000
90A92PRO0-0.011-0.00933.5900.1390.1390.0000.0000.0000.000
91A93ALA0-0.0010.01737.057-0.101-0.1010.0000.0000.0000.000
92A94GLN0-0.026-0.01037.365-0.034-0.0340.0000.0000.0000.000
93A95ASN0-0.037-0.01739.3290.2760.2760.0000.0000.0000.000
94A96ASN0-0.050-0.00741.8210.1470.1470.0000.0000.0000.000
95A97LYS10.9910.97441.4096.7966.7960.0000.0000.0000.000
96A98VAL0-0.007-0.00437.0360.1260.1260.0000.0000.0000.000
97A99ASN0-0.029-0.01836.691-0.163-0.1630.0000.0000.0000.000
98A100HIS0-0.029-0.00633.3630.0570.0570.0000.0000.0000.000
99A101LYS10.9760.99432.8778.2718.2710.0000.0000.0000.000
100A102LEU00.0030.00026.9420.0640.0640.0000.0000.0000.000
101A103LEU00.0060.00129.6650.0220.0220.0000.0000.0000.000
102A104GLY00.0390.00325.618-0.257-0.2570.0000.0000.0000.000
103A105ASN0-0.083-0.03123.9820.7690.7690.0000.0000.0000.000
104A106LEU00.0040.00118.395-0.554-0.5540.0000.0000.0000.000
105A107PHE0-0.029-0.01018.6880.6770.6770.0000.0000.0000.000
106A108ILE00.0230.01916.218-1.287-1.2870.0000.0000.0000.000
107A109SER00.0430.00414.2790.4340.4340.0000.0000.0000.000
108A110GLY0-0.020-0.01116.4690.0960.0960.0000.0000.0000.000
109A111GLU-1-0.835-0.88719.503-14.988-14.9880.0000.0000.0000.000
110A112SER0-0.009-0.00421.7640.0180.0180.0000.0000.0000.000
111A113GLN0-0.023-0.01623.488-0.167-0.1670.0000.0000.0000.000
112A114GLN00.0140.02822.0320.7260.7260.0000.0000.0000.000
113A115ASN00.020-0.01025.294-0.033-0.0330.0000.0000.0000.000
114A116LEU0-0.003-0.01122.6640.1100.1100.0000.0000.0000.000
115A117ASN00.0240.02027.152-0.203-0.2030.0000.0000.0000.000
116A118ASN0-0.087-0.05530.1780.2620.2620.0000.0000.0000.000
117A119LYS10.9541.00427.52910.99910.9990.0000.0000.0000.000
118A120ILE00.0130.01724.1510.0090.0090.0000.0000.0000.000
119A121ILE00.001-0.00328.6660.2060.2060.0000.0000.0000.000
120A122LEU0-0.024-0.01627.856-0.203-0.2030.0000.0000.0000.000
121A123GLU-1-0.947-0.97831.989-8.828-8.8280.0000.0000.0000.000
122A124LYS10.9000.94331.34910.13510.1350.0000.0000.0000.000
123A125ASP-1-0.817-0.90634.027-8.594-8.5940.0000.0000.0000.000
124A126ILE0-0.061-0.03132.519-0.153-0.1530.0000.0000.0000.000
125A127VAL00.0490.02528.6070.0510.0510.0000.0000.0000.000
126A128THR00.0830.04826.156-0.308-0.3080.0000.0000.0000.000
127A129PHE00.031-0.00421.1210.0100.0100.0000.0000.0000.000
128A130GLN00.0230.02021.812-0.629-0.6290.0000.0000.0000.000
129A131GLU-1-0.801-0.87622.773-10.917-10.9170.0000.0000.0000.000
130A132ILE0-0.032-0.02622.720-0.063-0.0630.0000.0000.0000.000
131A133ASP-1-0.775-0.85517.488-18.298-18.2980.0000.0000.0000.000
132A134PHE00.0030.00219.959-0.306-0.3060.0000.0000.0000.000
133A135LYS10.8670.91821.55210.77010.7700.0000.0000.0000.000
134A136ILE00.0070.00819.2000.1480.1480.0000.0000.0000.000
135A137ARG10.8420.90312.76220.72820.7280.0000.0000.0000.000
136A138LYS10.8570.91218.72212.45712.4570.0000.0000.0000.000
137A139TYR00.0320.02721.4810.3970.3970.0000.0000.0000.000
138A140LEU00.0290.00216.6140.1730.1730.0000.0000.0000.000
139A141MET0-0.056-0.01217.158-0.491-0.4910.0000.0000.0000.000
140A142ASP-1-0.819-0.89619.193-12.929-12.9290.0000.0000.0000.000
141A143ASN0-0.122-0.07022.3610.7050.7050.0000.0000.0000.000
142A144TYR0-0.051-0.03918.4980.2830.2830.0000.0000.0000.000
143A145LYS10.8660.93118.00414.52614.5260.0000.0000.0000.000
144A146ILE0-0.003-0.01413.687-0.841-0.8410.0000.0000.0000.000
145A147TYR0-0.017-0.02711.416-0.994-0.9940.0000.0000.0000.000
146A148ASP-1-0.784-0.86313.913-17.006-17.0060.0000.0000.0000.000
147A149ALA00.0200.00613.465-1.360-1.3600.0000.0000.0000.000
148A150THR0-0.014-0.01913.357-1.103-1.1030.0000.0000.0000.000
149A151SER0-0.094-0.03013.011-0.013-0.0130.0000.0000.0000.000
150A152PRO00.020-0.00612.541-1.361-1.3610.0000.0000.0000.000
151A153TYR0-0.046-0.02310.948-0.864-0.8640.0000.0000.0000.000
152A154VAL00.002-0.0054.936-1.617-1.6170.0000.0000.0000.000
153A155SER0-0.026-0.0355.642-8.578-8.5780.0000.0000.0000.000
154A156GLY00.0700.0287.9213.5213.5210.0000.0000.0000.000
155A157ARG10.8010.90610.78419.99819.9980.0000.0000.0000.000
156A158ILE0-0.006-0.00213.4621.2441.2440.0000.0000.0000.000
157A159GLU-1-0.816-0.89517.122-17.842-17.8420.0000.0000.0000.000
158A160ILE0-0.017-0.01919.5530.7340.7340.0000.0000.0000.000
159A161GLY00.0750.04122.798-0.075-0.0750.0000.0000.0000.000
160A162THR0-0.042-0.05225.4970.2910.2910.0000.0000.0000.000
161A163LYS10.8350.89028.6649.2019.2010.0000.0000.0000.000
162A164ASP-1-0.844-0.87929.570-10.506-10.5060.0000.0000.0000.000
163A165GLY0-0.0050.00028.9710.0710.0710.0000.0000.0000.000
164A166LYS10.8510.92525.59210.45110.4510.0000.0000.0000.000
165A167HIS00.017-0.01121.2920.2160.2160.0000.0000.0000.000
166A168GLU-1-0.821-0.85520.842-13.985-13.9850.0000.0000.0000.000
167A169GLN0-0.041-0.03714.897-1.111-1.1110.0000.0000.0000.000
168A170ILE0-0.026-0.00915.2220.1590.1590.0000.0000.0000.000
169A171ASP-1-0.805-0.8988.754-33.914-33.9140.0000.0000.0000.000
170A172LEU0-0.033-0.01310.8671.5231.5230.0000.0000.0000.000
171A173PHE0-0.064-0.0316.7151.1581.1580.0000.0000.0000.000
172A174ASP-1-0.862-0.9256.399-35.977-35.9770.0000.0000.0000.000
173A175SER0-0.092-0.0807.5084.3104.3100.0000.0000.0000.000
174A176PRO00.0440.0257.930-2.410-2.4100.0000.0000.0000.000
175A177ASN0-0.064-0.0438.3810.7100.7100.0000.0000.0000.000
176A178GLU-1-0.911-0.9688.728-19.923-19.9230.0000.0000.0000.000
177A179GLY0-0.059-0.01111.152-0.297-0.2970.0000.0000.0000.000
178A180THR00.005-0.01411.9011.1261.1260.0000.0000.0000.000
179A181ARG10.8830.93115.62014.48614.4860.0000.0000.0000.000
180A182SER00.0050.01918.1270.0490.0490.0000.0000.0000.000
181A183ASP-1-0.762-0.85212.846-18.807-18.8070.0000.0000.0000.000
182A184ILE0-0.006-0.00612.701-0.249-0.2490.0000.0000.0000.000
183A185PHE0-0.019-0.02314.9030.0230.0230.0000.0000.0000.000
184A186ALA00.0410.03616.5420.7850.7850.0000.0000.0000.000
185A187LYS10.8670.92914.02021.23021.2300.0000.0000.0000.000
186A188TYR0-0.045-0.04617.7770.2340.2340.0000.0000.0000.000
187A189LYS10.8560.91920.28214.44414.4440.0000.0000.0000.000
188A190ASP-1-0.836-0.91821.931-13.327-13.3270.0000.0000.0000.000
189A191ASN0-0.049-0.03323.8840.4690.4690.0000.0000.0000.000
190A192ARG10.8290.89722.31113.92413.9240.0000.0000.0000.000
191A193ILE0-0.040-0.02325.842-0.036-0.0360.0000.0000.0000.000
192A194ILE0-0.016-0.00726.616-0.008-0.0080.0000.0000.0000.000
193A195ASN00.0060.00529.1740.3680.3680.0000.0000.0000.000
194A196MET00.1050.05330.192-0.221-0.2210.0000.0000.0000.000
195A197LYS10.8730.95232.9158.4698.4690.0000.0000.0000.000
196A198ASN00.030-0.00431.7150.3740.3740.0000.0000.0000.000
197A199PHE00.0150.02525.854-0.253-0.2530.0000.0000.0000.000
198A200SER0-0.043-0.01028.8800.2940.2940.0000.0000.0000.000
199A201HIS10.8100.87624.87312.46212.4620.0000.0000.0000.000
200A202PHE00.0190.01322.335-0.174-0.1740.0000.0000.0000.000
201A203ASP-1-0.792-0.87420.988-12.933-12.9330.0000.0000.0000.000
202A204ILE00.0140.00416.848-0.618-0.6180.0000.0000.0000.000
203A205TYR00.0060.00514.8030.6030.6030.0000.0000.0000.000
204A206LEU00.0150.02312.986-1.543-1.5430.0000.0000.0000.000
205A207GLU-1-0.839-0.9249.930-25.646-25.6460.0000.0000.0000.000
206A208LYS10.8240.90710.43715.86815.8680.0000.0000.0000.000