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: J3Y29

Calculation Name: 2AP3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2AP3

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H3

Base Structure: X-ray

Registration Date: 2023-03-13

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 196
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2034858.746943
FMO2-HF: Nuclear repulsion 1956440.373579
FMO2-HF: Total energy -78418.373364
FMO2-MP2: Total energy -78652.402893


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:1:ALA)


Summations of interaction energy for fragment #1(A:1:ALA)
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.
-1.3563.6571.077-2.508-3.583-0.005
Interaction energy analysis for fragmet #1(A:1:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.053 / q_NPA : 0.031
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].
3A3MET0-0.019-0.0213.806-1.4810.5050.002-1.007-0.9810.006
4A4GLY00.0340.0322.9500.3481.1400.076-0.356-0.5130.001
5A5ILE0-0.053-0.0203.1030.7781.7260.209-0.289-0.868-0.002
6A6GLN00.0000.0032.691-0.8730.4140.790-0.856-1.221-0.010
7A7ARG10.9080.9395.4280.1950.1950.0000.0000.0000.000
8A8PRO00.0160.0048.1460.1670.1670.0000.0000.0000.000
9A9THR00.0970.0678.7430.0140.0140.0000.0000.0000.000
10A10SER00.0720.03010.919-0.081-0.0810.0000.0000.0000.000
11A11THR00.0380.01713.817-0.044-0.0440.0000.0000.0000.000
12A12THR0-0.038-0.03012.519-0.082-0.0820.0000.0000.0000.000
13A13THR0-0.014-0.01714.246-0.074-0.0740.0000.0000.0000.000
14A14ASP-1-0.735-0.86316.6560.2480.2480.0000.0000.0000.000
15A15LYS10.9810.99216.838-0.279-0.2790.0000.0000.0000.000
16A16LYS10.8320.92618.800-0.174-0.1740.0000.0000.0000.000
17A17GLU-1-0.794-0.87420.7220.1150.1150.0000.0000.0000.000
18A18ILE00.0730.02822.684-0.014-0.0140.0000.0000.0000.000
19A19LYS10.8920.94020.335-0.130-0.1300.0000.0000.0000.000
20A20ALA0-0.032-0.01025.177-0.013-0.0130.0000.0000.0000.000
21A21TYR0-0.023-0.04227.046-0.008-0.0080.0000.0000.0000.000
22A22LEU00.0290.00627.724-0.009-0.0090.0000.0000.0000.000
23A23LYS10.9500.98329.507-0.043-0.0430.0000.0000.0000.000
24A24GLN0-0.021-0.01830.274-0.004-0.0040.0000.0000.0000.000
25A25VAL00.0260.01133.140-0.005-0.0050.0000.0000.0000.000
26A26ASP-1-0.788-0.89134.0010.0510.0510.0000.0000.0000.000
27A27LYS10.8170.92035.421-0.035-0.0350.0000.0000.0000.000
28A28ILE00.0150.00837.191-0.004-0.0040.0000.0000.0000.000
29A29LYS10.8110.91037.879-0.043-0.0430.0000.0000.0000.000
30A30ASP-1-0.917-0.97138.2010.0310.0310.0000.0000.0000.000
31A31ASP-1-0.864-0.91741.2560.0270.0270.0000.0000.0000.000
32A32GLU-1-0.801-0.85743.4650.0410.0410.0000.0000.0000.000
33A33GLU-1-0.906-0.95345.3010.0190.0190.0000.0000.0000.000
34A34PRO00.016-0.00546.889-0.001-0.0010.0000.0000.0000.000
35A35ILE00.0330.02047.851-0.001-0.0010.0000.0000.0000.000
36A36LYS10.9350.96647.498-0.030-0.0300.0000.0000.0000.000
37A37THR0-0.024-0.01451.315-0.001-0.0010.0000.0000.0000.000
38A38VAL00.0390.03153.771-0.001-0.0010.0000.0000.0000.000
39A39GLY00.0260.01854.415-0.001-0.0010.0000.0000.0000.000
40A40LYS10.8750.93751.450-0.018-0.0180.0000.0000.0000.000
41A41LYS10.9330.97657.488-0.015-0.0150.0000.0000.0000.000
42A42ILE00.0310.01158.053-0.001-0.0010.0000.0000.0000.000
43A43ALA00.0280.02059.4600.0000.0000.0000.0000.0000.000
44A44GLU-1-0.888-0.94861.3570.0120.0120.0000.0000.0000.000
45A45LEU0-0.044-0.01963.296-0.001-0.0010.0000.0000.0000.000
46A46ASP-1-0.828-0.92063.0750.0190.0190.0000.0000.0000.000
47A47GLU-1-0.852-0.91465.1020.0140.0140.0000.0000.0000.000
48A48LYS10.8380.91466.093-0.013-0.0130.0000.0000.0000.000
49A49LYS10.8700.94167.801-0.018-0.0180.0000.0000.0000.000
50A50LYS10.8740.93065.272-0.017-0.0170.0000.0000.0000.000
51A51LYS10.8770.94268.917-0.013-0.0130.0000.0000.0000.000
52A52LEU00.0290.02873.7830.0000.0000.0000.0000.0000.000
53A53THR0-0.069-0.05274.4470.0000.0000.0000.0000.0000.000
54A54GLU-1-0.934-0.96376.9970.0100.0100.0000.0000.0000.000
55A55ASP-1-0.843-0.93679.7130.0100.0100.0000.0000.0000.000
56A56VAL0-0.075-0.03278.3400.0000.0000.0000.0000.0000.000
57A57ASN0-0.052-0.02880.6190.0000.0000.0000.0000.0000.000
58A58SER00.0490.02983.7990.0000.0000.0000.0000.0000.000
59A59LYS10.9550.96685.874-0.009-0.0090.0000.0000.0000.000
60A60ASP-1-0.815-0.87988.0650.0080.0080.0000.0000.0000.000
61A61THR00.039-0.00787.6300.0000.0000.0000.0000.0000.000
62A62ALA0-0.020-0.00287.2270.0000.0000.0000.0000.0000.000
63A63VAL0-0.0130.00583.3320.0000.0000.0000.0000.0000.000
64A64ARG10.9020.94582.921-0.011-0.0110.0000.0000.0000.000
65A65GLY0-0.007-0.00382.4260.0000.0000.0000.0000.0000.000
66A66LYS10.8340.89477.799-0.010-0.0100.0000.0000.0000.000
67A67ALA00.0680.04878.5750.0000.0000.0000.0000.0000.000
68A68VAL0-0.002-0.00577.5280.0010.0010.0000.0000.0000.000
69A69LYS10.8870.92277.333-0.011-0.0110.0000.0000.0000.000
70A70ASP-1-0.812-0.88875.0770.0110.0110.0000.0000.0000.000
71A71LEU0-0.031-0.01773.0870.0010.0010.0000.0000.0000.000
72A72ILE0-0.070-0.02972.3630.0010.0010.0000.0000.0000.000
73A73LYS10.8630.92069.867-0.012-0.0120.0000.0000.0000.000
74A74ASN00.0210.01468.3380.0010.0010.0000.0000.0000.000
75A75ALA0-0.012-0.01267.6980.0010.0010.0000.0000.0000.000
76A76ASP-1-0.790-0.87566.7570.0170.0170.0000.0000.0000.000
77A77ASP-1-0.841-0.90265.9590.0150.0150.0000.0000.0000.000
78A78ARG10.7900.88263.272-0.018-0.0180.0000.0000.0000.000
79A79LEU0-0.029-0.01361.9010.0010.0010.0000.0000.0000.000
80A80LYS10.8400.89861.389-0.018-0.0180.0000.0000.0000.000
81A81GLU-1-0.849-0.91958.5460.0180.0180.0000.0000.0000.000
82A82PHE0-0.012-0.01655.6190.0010.0010.0000.0000.0000.000
83A83GLU-1-0.775-0.85456.5070.0220.0220.0000.0000.0000.000
84A84LYS10.8600.91854.740-0.016-0.0160.0000.0000.0000.000
85A85GLU-1-0.857-0.91851.7580.0300.0300.0000.0000.0000.000
86A86GLU-1-0.793-0.89451.5710.0300.0300.0000.0000.0000.000
87A87ASP-1-0.901-0.95451.7440.0270.0270.0000.0000.0000.000
88A88ALA0-0.060-0.02048.6380.0010.0010.0000.0000.0000.000
89A89ILE00.000-0.00746.8520.0020.0020.0000.0000.0000.000
90A90LYS10.9430.97546.868-0.031-0.0310.0000.0000.0000.000
91A91LYS10.8730.92643.121-0.030-0.0300.0000.0000.0000.000
92A92SER0-0.012-0.03443.1650.0030.0030.0000.0000.0000.000
93A93GLU-1-0.849-0.91842.1110.0510.0510.0000.0000.0000.000
94A94GLN0-0.052-0.03142.4310.0020.0020.0000.0000.0000.000
95A95ASP-1-0.861-0.92539.8020.0400.0400.0000.0000.0000.000
96A96PHE0-0.040-0.01236.5520.0030.0030.0000.0000.0000.000
97A97LYS10.8630.92137.268-0.048-0.0480.0000.0000.0000.000
98A98LYS10.8960.96336.847-0.046-0.0460.0000.0000.0000.000
99A99ALA00.0130.03033.3690.0020.0020.0000.0000.0000.000
100A100LYS10.8270.87730.862-0.102-0.1020.0000.0000.0000.000
101A101SER00.0370.03229.7290.0080.0080.0000.0000.0000.000
102A102HIS0-0.062-0.04725.7730.0000.0000.0000.0000.0000.000
103A103VAL0-0.028-0.01626.6860.0070.0070.0000.0000.0000.000
104A104ASP-1-0.891-0.93627.2030.1250.1250.0000.0000.0000.000
105A105ASN0-0.048-0.03223.2560.0110.0110.0000.0000.0000.000
106A106ILE0-0.066-0.00721.8090.0140.0140.0000.0000.0000.000
107A107ASP-1-0.861-0.93617.5170.3900.3900.0000.0000.0000.000
108A108ASN00.0280.00919.211-0.025-0.0250.0000.0000.0000.000
109A109ASP-1-0.805-0.90121.1070.2320.2320.0000.0000.0000.000
110A110VAL0-0.041-0.01923.862-0.022-0.0220.0000.0000.0000.000
111A111LYS10.8110.88322.129-0.191-0.1910.0000.0000.0000.000
112A112ARG10.8030.88423.518-0.236-0.2360.0000.0000.0000.000
113A113LYS10.9110.94826.566-0.174-0.1740.0000.0000.0000.000
114A114GLU-1-0.798-0.87927.1210.1570.1570.0000.0000.0000.000
115A115VAL00.003-0.00127.126-0.012-0.0120.0000.0000.0000.000
116A116LYS10.9410.97330.126-0.141-0.1410.0000.0000.0000.000
117A117GLN0-0.0100.00132.760-0.008-0.0080.0000.0000.0000.000
118A118LEU00.008-0.00231.867-0.009-0.0090.0000.0000.0000.000
119A119ASP-1-0.813-0.90333.4860.0880.0880.0000.0000.0000.000
120A120ASP-1-0.850-0.91835.9760.0830.0830.0000.0000.0000.000
121A121VAL0-0.062-0.02238.056-0.006-0.0060.0000.0000.0000.000
122A122LEU0-0.016-0.00236.191-0.006-0.0060.0000.0000.0000.000
123A123LYS10.8350.90236.872-0.088-0.0880.0000.0000.0000.000
124A124GLU-1-0.819-0.89642.0610.0520.0520.0000.0000.0000.000
125A125LYS10.8280.90942.737-0.049-0.0490.0000.0000.0000.000
126A126TYR0-0.016-0.03241.041-0.002-0.0020.0000.0000.0000.000
127A127LYS10.8500.92146.209-0.055-0.0550.0000.0000.0000.000
128A128LEU00.004-0.01547.267-0.003-0.0030.0000.0000.0000.000
129A129HIS0-0.067-0.03948.776-0.001-0.0010.0000.0000.0000.000
130A130SER00.0340.02850.495-0.003-0.0030.0000.0000.0000.000
131A131ASP-1-0.946-0.96952.6080.0400.0400.0000.0000.0000.000
132A132TYR0-0.026-0.02653.020-0.002-0.0020.0000.0000.0000.000
133A133ALA00.0210.01354.470-0.002-0.0020.0000.0000.0000.000
134A134LYS10.9200.96556.233-0.033-0.0330.0000.0000.0000.000
135A135ALA0-0.031-0.02258.137-0.002-0.0020.0000.0000.0000.000
136A136TYR00.0440.02158.430-0.002-0.0020.0000.0000.0000.000
137A137LYS10.8500.90158.254-0.029-0.0290.0000.0000.0000.000
138A138LYS10.8840.96262.238-0.027-0.0270.0000.0000.0000.000
139A139ALA00.0410.02263.577-0.001-0.0010.0000.0000.0000.000
140A140VAL00.0490.04563.579-0.001-0.0010.0000.0000.0000.000
141A141ASN0-0.027-0.02865.200-0.002-0.0020.0000.0000.0000.000
142A142SER0-0.070-0.04068.0240.0000.0000.0000.0000.0000.000
143A143GLU-1-0.729-0.84268.0670.0190.0190.0000.0000.0000.000
144A144LYS10.8600.90870.355-0.018-0.0180.0000.0000.0000.000
145A145THR0-0.090-0.05071.999-0.001-0.0010.0000.0000.0000.000
146A146LEU00.0050.01074.0650.0000.0000.0000.0000.0000.000
147A147PHE00.0480.00471.457-0.001-0.0010.0000.0000.0000.000
148A148LYS10.9550.96675.107-0.017-0.0170.0000.0000.0000.000
149A149TYR0-0.0170.00478.1040.0000.0000.0000.0000.0000.000
150A150LEU00.0300.00878.7060.0000.0000.0000.0000.0000.000
151A151ASN0-0.0500.00380.267-0.001-0.0010.0000.0000.0000.000
152A152GLN0-0.065-0.02782.3020.0000.0000.0000.0000.0000.000
153A153ASN00.0240.00985.1630.0000.0000.0000.0000.0000.000
154A154ASP-1-0.875-0.93888.0590.0120.0120.0000.0000.0000.000
155A155ALA0-0.050-0.00884.1920.0000.0000.0000.0000.0000.000
156A156THR00.0590.01985.5590.0000.0000.0000.0000.0000.000
157A157GLN00.032-0.00882.1720.0000.0000.0000.0000.0000.000
158A158GLN00.0290.02183.1380.0000.0000.0000.0000.0000.000
159A159GLY00.0260.01482.3480.0010.0010.0000.0000.0000.000
160A160VAL00.0510.01379.2250.0010.0010.0000.0000.0000.000
161A161ASN00.0210.02678.4570.0000.0000.0000.0000.0000.000
162A162GLU-1-0.932-0.95177.7160.0180.0180.0000.0000.0000.000
163A163LYS10.8850.91575.868-0.016-0.0160.0000.0000.0000.000
164A164SER00.012-0.00374.1090.0010.0010.0000.0000.0000.000
165A165LYS10.9540.99772.928-0.019-0.0190.0000.0000.0000.000
166A166ALA0-0.028-0.01071.4190.0010.0010.0000.0000.0000.000
167A167ILE00.0160.01869.0450.0010.0010.0000.0000.0000.000
168A168GLU-1-0.813-0.90068.1000.0220.0220.0000.0000.0000.000
169A169GLN0-0.042-0.02266.4160.0020.0020.0000.0000.0000.000
170A170ASN0-0.013-0.04065.2410.0020.0020.0000.0000.0000.000
171A171TYR00.024-0.00363.2500.0010.0010.0000.0000.0000.000
172A172LYS10.8310.91962.621-0.023-0.0230.0000.0000.0000.000
173A173LYS10.9100.95761.309-0.026-0.0260.0000.0000.0000.000
174A174LEU00.0080.01157.9940.0010.0010.0000.0000.0000.000
175A175LYS10.8490.90757.223-0.031-0.0310.0000.0000.0000.000
176A176GLU-1-0.857-0.91956.8820.0370.0370.0000.0000.0000.000
177A177VAL0-0.033-0.02053.9780.0020.0020.0000.0000.0000.000
178A178SER00.0620.03153.2340.0010.0010.0000.0000.0000.000
179A179ASP-1-0.849-0.90052.4110.0350.0350.0000.0000.0000.000
180A180LYS10.8280.90750.632-0.038-0.0380.0000.0000.0000.000
181A181TYR00.0490.03047.2730.0030.0030.0000.0000.0000.000
182A182THR00.019-0.00747.5980.0010.0010.0000.0000.0000.000
183A183LYS10.9380.96946.697-0.045-0.0450.0000.0000.0000.000
184A184VAL00.0110.02343.3410.0030.0030.0000.0000.0000.000
185A185LEU00.0010.00642.7870.0030.0030.0000.0000.0000.000
186A186ASN0-0.061-0.04341.9310.0020.0020.0000.0000.0000.000
187A187LYS10.9140.97439.669-0.073-0.0730.0000.0000.0000.000
188A188VAL00.015-0.00137.9140.0050.0050.0000.0000.0000.000
189A189GLN00.0210.00736.0170.0070.0070.0000.0000.0000.000
190A190LYS10.8170.89135.085-0.093-0.0930.0000.0000.0000.000
191A191GLU-1-0.749-0.87134.2840.0980.0980.0000.0000.0000.000
192A192LYS10.8600.92632.289-0.055-0.0550.0000.0000.0000.000
193A193GLN0-0.039-0.01130.8810.0020.0020.0000.0000.0000.000
194A194ASP-1-0.847-0.90229.9360.1130.1130.0000.0000.0000.000
195A195VAL0-0.019-0.00927.7270.0120.0120.0000.0000.0000.000
196A196ASP-1-1.047-1.01026.2050.1210.1210.0000.0000.0000.000