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: 6YMVZ

Calculation Name: 3APQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3APQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q9DC23

Base Structure: X-ray

Registration Date: 2023-09-24

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 -2414466.888941
FMO2-HF: Nuclear repulsion 2330102.313577
FMO2-HF: Total energy -84364.575364
FMO2-MP2: Total energy -84609.765348


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:33:ILE)


Summations of interaction energy for fragment #1(A:33:ILE)
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.
-1.4582.0960.196-1.884-1.865-0.002
Interaction energy analysis for fragmet #1(A:33:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.035 / q_NPA : 0.014
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].
3A35ASN00.0320.0152.939-2.5680.9860.196-1.884-1.865-0.002
4A36PHE00.048-0.0035.4070.2160.2160.0000.0000.0000.000
5A37TYR00.000-0.0078.9900.1950.1950.0000.0000.0000.000
6A38SER0-0.012-0.0176.337-0.063-0.0630.0000.0000.0000.000
7A39LEU0-0.092-0.0318.5450.2490.2490.0000.0000.0000.000
8A40LEU00.001-0.00910.0700.2180.2180.0000.0000.0000.000
9A41GLY0-0.0370.00111.4220.1350.1350.0000.0000.0000.000
10A42VAL0-0.031-0.02012.4560.1320.1320.0000.0000.0000.000
11A43SER00.0370.00911.872-0.189-0.1890.0000.0000.0000.000
12A44LYS10.8880.92510.6100.8350.8350.0000.0000.0000.000
13A45THR0-0.027-0.02213.1880.0420.0420.0000.0000.0000.000
14A46ALA0-0.0400.01216.1110.0550.0550.0000.0000.0000.000
15A47SER00.057-0.01717.991-0.001-0.0010.0000.0000.0000.000
16A48SER00.025-0.02120.291-0.040-0.0400.0000.0000.0000.000
17A49ARG10.8920.94221.6820.2160.2160.0000.0000.0000.000
18A50GLU-1-0.853-0.89519.516-0.350-0.3500.0000.0000.0000.000
19A51ILE00.0130.00316.312-0.022-0.0220.0000.0000.0000.000
20A52ARG10.7730.85418.8130.2360.2360.0000.0000.0000.000
21A53GLN00.0410.02221.6980.0140.0140.0000.0000.0000.000
22A54ALA0-0.050-0.01116.8700.0150.0150.0000.0000.0000.000
23A55PHE00.0240.00617.858-0.003-0.0030.0000.0000.0000.000
24A56LYS10.9150.95419.1670.2280.2280.0000.0000.0000.000
25A57LYS10.9480.98116.7520.4130.4130.0000.0000.0000.000
26A58LEU0-0.047-0.02714.8070.0290.0290.0000.0000.0000.000
27A59ALA00.0420.02219.4870.0280.0280.0000.0000.0000.000
28A60LEU0-0.043-0.02122.4160.0270.0270.0000.0000.0000.000
29A61LYS10.9230.97620.6310.1930.1930.0000.0000.0000.000
30A62LEU0-0.015-0.03517.6300.0190.0190.0000.0000.0000.000
31A63HIS0-0.0100.02622.0540.0090.0090.0000.0000.0000.000
32A64PRO00.0530.02222.6260.0150.0150.0000.0000.0000.000
33A65ASP-1-0.854-0.92725.048-0.115-0.1150.0000.0000.0000.000
34A66LYS10.7980.89827.3030.1280.1280.0000.0000.0000.000
35A67ASN0-0.086-0.04224.8620.0110.0110.0000.0000.0000.000
36A68PRO00.0520.02926.2910.0010.0010.0000.0000.0000.000
37A69ASN0-0.022-0.01828.6300.0070.0070.0000.0000.0000.000
38A70ASN0-0.0100.00220.6350.0200.0200.0000.0000.0000.000
39A71PRO00.0460.02123.209-0.012-0.0120.0000.0000.0000.000
40A72ASN00.0070.00517.5250.0060.0060.0000.0000.0000.000
41A73ALA0-0.0120.00519.298-0.029-0.0290.0000.0000.0000.000
42A74HIS00.0980.04820.419-0.032-0.0320.0000.0000.0000.000
43A75GLY00.0360.01318.374-0.021-0.0210.0000.0000.0000.000
44A76ASP-1-0.855-0.93514.812-0.289-0.2890.0000.0000.0000.000
45A77PHE0-0.003-0.00515.897-0.069-0.0690.0000.0000.0000.000
46A78LEU00.0270.02517.541-0.031-0.0310.0000.0000.0000.000
47A79LYS10.8370.92411.5550.3900.3900.0000.0000.0000.000
48A80ILE0-0.032-0.01113.257-0.084-0.0840.0000.0000.0000.000
49A81ASN0-0.042-0.03714.849-0.021-0.0210.0000.0000.0000.000
50A82ARG10.8410.91210.4160.4810.4810.0000.0000.0000.000
51A83ALA0-0.020-0.01011.584-0.013-0.0130.0000.0000.0000.000
52A84TYR00.0400.00813.2290.0030.0030.0000.0000.0000.000
53A85GLU-1-0.915-0.97916.561-0.252-0.2520.0000.0000.0000.000
54A86VAL0-0.042-0.00613.4020.0240.0240.0000.0000.0000.000
55A87LEU0-0.054-0.04212.1610.0200.0200.0000.0000.0000.000
56A88LYS10.8530.92815.9940.2910.2910.0000.0000.0000.000
57A89ASP-1-0.845-0.90919.033-0.234-0.2340.0000.0000.0000.000
58A90GLU-1-0.740-0.82919.346-0.256-0.2560.0000.0000.0000.000
59A91ASP-1-0.839-0.92219.891-0.244-0.2440.0000.0000.0000.000
60A92LEU0-0.036-0.01317.148-0.015-0.0150.0000.0000.0000.000
61A93ARG10.8410.92015.0740.4600.4600.0000.0000.0000.000
62A94LYS10.7830.88014.9710.2030.2030.0000.0000.0000.000
63A95LYS10.8680.92915.6040.2900.2900.0000.0000.0000.000
64A96TYR00.0420.0326.913-0.126-0.1260.0000.0000.0000.000
65A97ASP-1-0.827-0.89010.971-0.796-0.7960.0000.0000.0000.000
66A98LYS10.8900.95412.0720.2170.2170.0000.0000.0000.000
67A99TYR0-0.053-0.04612.0570.0490.0490.0000.0000.0000.000
68A100GLY00.0530.0478.6720.0170.0170.0000.0000.0000.000
69A101GLU-1-0.829-0.9188.029-0.738-0.7380.0000.0000.0000.000
70A102LYS10.9901.00210.6160.2950.2950.0000.0000.0000.000
71A103GLY0-0.077-0.05713.606-0.010-0.0100.0000.0000.0000.000
72A104LEU0-0.0340.00711.7920.0110.0110.0000.0000.0000.000
73A105GLU-1-0.878-0.93515.223-0.156-0.1560.0000.0000.0000.000
74A106ASP-1-0.921-0.96812.979-0.262-0.2620.0000.0000.0000.000
75A107ASN0-0.051-0.02914.777-0.017-0.0170.0000.0000.0000.000
76A108GLN00.0480.04716.1460.0200.0200.0000.0000.0000.000
77A109GLY0-0.002-0.00817.268-0.029-0.0290.0000.0000.0000.000
78A110GLY00.005-0.00418.846-0.011-0.0110.0000.0000.0000.000
79A111GLN0-0.051-0.02021.0630.0270.0270.0000.0000.0000.000
80A112TYR0-0.015-0.01521.806-0.011-0.0110.0000.0000.0000.000
81A113GLU-1-0.865-0.93224.242-0.137-0.1370.0000.0000.0000.000
82A114SER00.0600.02426.808-0.003-0.0030.0000.0000.0000.000
83A115TRP0-0.014-0.02626.985-0.003-0.0030.0000.0000.0000.000
84A116SER00.030-0.00128.896-0.003-0.0030.0000.0000.0000.000
85A117TYR00.0040.01826.423-0.005-0.0050.0000.0000.0000.000
86A118TYR00.0560.01523.326-0.002-0.0020.0000.0000.0000.000
87A119ARG10.8380.93027.6600.1310.1310.0000.0000.0000.000
88A120TYR0-0.032-0.03930.1670.0020.0020.0000.0000.0000.000
89A121ASP-1-0.791-0.87931.160-0.132-0.1320.0000.0000.0000.000
90A122PHE0-0.0110.01022.636-0.006-0.0060.0000.0000.0000.000
91A123GLY00.0050.00427.302-0.001-0.0010.0000.0000.0000.000
92A124ILE0-0.030-0.00328.0950.0030.0030.0000.0000.0000.000
93A125TYR00.019-0.00131.4160.0100.0100.0000.0000.0000.000
94A126ASP-1-0.745-0.83126.364-0.234-0.2340.0000.0000.0000.000
95A127ASP-1-0.931-0.96028.520-0.199-0.1990.0000.0000.0000.000
96A128ASP-1-0.827-0.90531.020-0.119-0.1190.0000.0000.0000.000
97A129PRO0-0.030-0.01132.419-0.005-0.0050.0000.0000.0000.000
98A130GLU-1-0.779-0.89033.495-0.117-0.1170.0000.0000.0000.000
99A131ILE0-0.049-0.01234.4190.0050.0050.0000.0000.0000.000
100A132ILE0-0.0120.00131.279-0.010-0.0100.0000.0000.0000.000
101A133THR0-0.034-0.02929.1260.0080.0080.0000.0000.0000.000
102A134LEU0-0.068-0.02229.412-0.012-0.0120.0000.0000.0000.000
103A135GLU-1-0.761-0.86225.110-0.245-0.2450.0000.0000.0000.000
104A136ARG10.8980.93028.4960.1480.1480.0000.0000.0000.000
105A137ARG10.8150.88225.6720.2100.2100.0000.0000.0000.000
106A138GLU-1-0.848-0.94227.250-0.196-0.1960.0000.0000.0000.000
107A139PHE00.0070.00130.6450.0120.0120.0000.0000.0000.000
108A140ASP-1-0.774-0.89332.989-0.117-0.1170.0000.0000.0000.000
109A141ALA0-0.0030.00432.7500.0080.0080.0000.0000.0000.000
110A142ALA00.0120.01134.6580.0080.0080.0000.0000.0000.000
111A143VAL0-0.032-0.01436.5470.0080.0080.0000.0000.0000.000
112A144ASN0-0.033-0.01737.7230.0100.0100.0000.0000.0000.000
113A145SER0-0.054-0.02637.9030.0060.0060.0000.0000.0000.000
114A146GLY00.015-0.00139.7590.0040.0040.0000.0000.0000.000
115A147GLU-1-0.881-0.91438.539-0.103-0.1030.0000.0000.0000.000
116A148LEU0-0.039-0.01442.473-0.001-0.0010.0000.0000.0000.000
117A149TRP00.0450.01534.911-0.005-0.0050.0000.0000.0000.000
118A150PHE00.002-0.00141.3040.0040.0040.0000.0000.0000.000
119A151VAL0-0.018-0.00136.763-0.005-0.0050.0000.0000.0000.000
120A152ASN00.0020.00438.2360.0050.0050.0000.0000.0000.000
121A153PHE0-0.002-0.00836.409-0.009-0.0090.0000.0000.0000.000
122A154TYR00.0590.00631.4250.0070.0070.0000.0000.0000.000
123A155SER0-0.003-0.01434.192-0.006-0.0060.0000.0000.0000.000
124A156PRO0-0.0050.02030.7720.0050.0050.0000.0000.0000.000
125A157GLY00.019-0.00233.4550.0060.0060.0000.0000.0000.000
126A158CYS0-0.121-0.03536.0290.0100.0100.0000.0000.0000.000
127A159SER00.0540.00438.911-0.002-0.0020.0000.0000.0000.000
128A160HIS00.0750.04641.600-0.001-0.0010.0000.0000.0000.000
129A162HIS0-0.052-0.04235.1120.0020.0020.0000.0000.0000.000
130A163ASP-1-0.913-0.94939.741-0.080-0.0800.0000.0000.0000.000
131A164LEU0-0.037-0.01641.6550.0020.0020.0000.0000.0000.000
132A165ALA0-0.009-0.00137.8790.0000.0000.0000.0000.0000.000
133A166PRO00.004-0.00639.877-0.002-0.0020.0000.0000.0000.000
134A167THR00.0720.04141.6560.0000.0000.0000.0000.0000.000
135A168TRP0-0.023-0.00938.0750.0040.0040.0000.0000.0000.000
136A169ARG10.8220.89834.6440.1230.1230.0000.0000.0000.000
137A170GLU-1-0.919-0.95840.284-0.073-0.0730.0000.0000.0000.000
138A171PHE00.017-0.01043.2730.0020.0020.0000.0000.0000.000
139A172ALA0-0.027-0.01539.7600.0020.0020.0000.0000.0000.000
140A173LYS10.8150.89637.7460.1080.1080.0000.0000.0000.000
141A174GLU-1-0.876-0.91442.371-0.065-0.0650.0000.0000.0000.000
142A175VAL0-0.040-0.03544.0630.0030.0030.0000.0000.0000.000
143A176ASP-1-0.889-0.93739.920-0.103-0.1030.0000.0000.0000.000
144A177GLY0-0.020-0.00141.6210.0040.0040.0000.0000.0000.000
145A178LEU0-0.097-0.04642.6600.0030.0030.0000.0000.0000.000
146A179LEU0-0.023-0.02143.6020.0030.0030.0000.0000.0000.000
147A180ARG10.8460.92635.2350.1140.1140.0000.0000.0000.000
148A181ILE00.0480.03338.8580.0020.0020.0000.0000.0000.000
149A182GLY00.0330.00735.749-0.008-0.0080.0000.0000.0000.000
150A183ALA0-0.020-0.01333.7510.0070.0070.0000.0000.0000.000
151A184VAL00.0140.00432.463-0.009-0.0090.0000.0000.0000.000
152A185ASN00.0320.01328.1650.0210.0210.0000.0000.0000.000
153A186CYS0-0.022-0.03030.7470.0000.0000.0000.0000.0000.000
154A187GLY0-0.049-0.03730.6980.0030.0030.0000.0000.0000.000
155A188ASP-1-0.839-0.90225.348-0.233-0.2330.0000.0000.0000.000
156A189ASP-1-0.846-0.91727.363-0.166-0.1660.0000.0000.0000.000
157A190ARG10.9210.95629.9810.1410.1410.0000.0000.0000.000
158A191MET00.0080.00632.2240.0130.0130.0000.0000.0000.000
159A192LEU00.0370.02931.8510.0090.0090.0000.0000.0000.000
160A194ARG10.9660.98736.4740.1000.1000.0000.0000.0000.000
161A195MET0-0.072-0.03835.4450.0040.0040.0000.0000.0000.000
162A196LYS10.8010.91936.6650.1160.1160.0000.0000.0000.000
163A197GLY00.0170.01940.3800.0030.0030.0000.0000.0000.000
164A198VAL0-0.041-0.01539.2440.0030.0030.0000.0000.0000.000
165A199ASN0-0.041-0.03539.942-0.004-0.0040.0000.0000.0000.000
166A200SER0-0.0210.00041.9290.0020.0020.0000.0000.0000.000
167A201TYR0-0.0020.00237.649-0.005-0.0050.0000.0000.0000.000
168A202PRO00.0500.00740.5020.0030.0030.0000.0000.0000.000
169A203SER0-0.069-0.03940.8160.0070.0070.0000.0000.0000.000
170A204LEU0-0.0210.00941.245-0.005-0.0050.0000.0000.0000.000
171A205PHE00.0340.01142.2680.0050.0050.0000.0000.0000.000
172A206ILE00.0040.01042.741-0.005-0.0050.0000.0000.0000.000
173A207PHE00.001-0.02340.7250.0020.0020.0000.0000.0000.000
174A208ARG10.9550.95943.7200.0680.0680.0000.0000.0000.000
175A209SER00.0180.02642.5410.0040.0040.0000.0000.0000.000
176A210GLY0-0.0020.00144.1980.0030.0030.0000.0000.0000.000
177A211MET0-0.0400.00046.8620.0050.0050.0000.0000.0000.000
178A212ALA0-0.015-0.00246.822-0.003-0.0030.0000.0000.0000.000
179A213ALA0-0.004-0.00244.3860.0000.0000.0000.0000.0000.000
180A214VAL00.0190.01846.3450.0030.0030.0000.0000.0000.000
181A215LYS10.8970.96445.8250.0730.0730.0000.0000.0000.000
182A216TYR0-0.016-0.01246.9260.0020.0020.0000.0000.0000.000
183A217ASN0-0.069-0.05948.509-0.003-0.0030.0000.0000.0000.000
184A218GLY00.0390.03550.8100.0020.0020.0000.0000.0000.000
185A219ASP-1-0.821-0.90651.240-0.062-0.0620.0000.0000.0000.000
186A220ARG10.8760.92146.0980.0750.0750.0000.0000.0000.000
187A221SER00.0080.00748.188-0.003-0.0030.0000.0000.0000.000
188A222LYS10.8680.90947.3550.0650.0650.0000.0000.0000.000
189A223GLU-1-0.849-0.92349.169-0.063-0.0630.0000.0000.0000.000
190A224SER0-0.0100.00151.5840.0000.0000.0000.0000.0000.000
191A225LEU0-0.038-0.01145.3310.0000.0000.0000.0000.0000.000
192A226VAL00.0460.02848.789-0.001-0.0010.0000.0000.0000.000
193A227ALA0-0.0050.00250.0700.0000.0000.0000.0000.0000.000
194A228PHE00.0040.00047.4660.0010.0010.0000.0000.0000.000
195A229ALA00.0210.00647.2000.0000.0000.0000.0000.0000.000
196A230MET00.0330.01148.9210.0000.0000.0000.0000.0000.000
197A231GLN0-0.051-0.01951.6100.0030.0030.0000.0000.0000.000
198A232HIS0-0.054-0.03549.3010.0020.0020.0000.0000.0000.000
199A233VAL0-0.007-0.00647.8700.0000.0000.0000.0000.0000.000
200A234ARG10.8850.94550.2760.0520.0520.0000.0000.0000.000
201A235SER0-0.0210.00952.9810.0020.0020.0000.0000.0000.000
202A236THR00.0450.03451.797-0.003-0.0030.0000.0000.0000.000
203A237VAL0-0.023-0.02551.443-0.001-0.0010.0000.0000.0000.000
204A238THR0-0.027-0.01853.3630.0010.0010.0000.0000.0000.000
205A239GLU-1-0.956-0.97956.787-0.047-0.0470.0000.0000.0000.000
206A240LEU0-0.014-0.00259.6520.0010.0010.0000.0000.0000.000