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: LL889

Calculation Name: 2AP3-A-Xray307

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 197
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2034728.795421
FMO2-HF: Nuclear repulsion 1956292.766208
FMO2-HF: Total energy -78436.029213
FMO2-MP2: Total energy -78670.101992


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.
93.6398.5270.916-2.351-3.463-0.018
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 : 1 / q_Mulliken : 0.875 / q_NPA : 0.930
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].
3A3MET 00.0290.0063.763-1.1600.0100.010-0.485-0.6960.000
4A4GLY 00.0150.0202.9554.2485.0050.061-0.325-0.494-0.001
5A5ILE 0-0.045-0.0183.1246.6007.7410.203-0.412-0.932-0.004
6A6GLN 00.0100.0092.704-7.798-5.9690.642-1.129-1.341-0.013
7A7ARG 10.9160.9445.45033.83333.8330.0000.0000.0000.000
8A8PRO 00.0080.0008.157-1.442-1.4420.0000.0000.0000.000
9A9THR 00.0870.0568.7030.2460.2460.0000.0000.0000.000
10A10SER 00.1120.04310.9410.9030.9030.0000.0000.0000.000
11A11THR 00.0350.02113.8101.0111.0110.0000.0000.0000.000
12A12THR 0-0.030-0.02612.7741.2531.2530.0000.0000.0000.000
13A13THR 0-0.006-0.00914.2161.1351.1350.0000.0000.0000.000
14A14ASP -1-0.740-0.86716.671-14.503-14.5030.0000.0000.0000.000
15A15LYS 10.9760.98916.68418.16818.1680.0000.0000.0000.000
16A16LYS 10.8490.92718.63015.38415.3840.0000.0000.0000.000
17A17GLU -1-0.814-0.89620.739-12.080-12.0800.0000.0000.0000.000
18A18ILE 00.0660.02222.3540.5920.5920.0000.0000.0000.000
19A19LYS 10.9190.96419.88714.99914.9990.0000.0000.0000.000
20A20ALA 0-0.029-0.01225.1960.4690.4690.0000.0000.0000.000
21A21TYR 0-0.030-0.05027.0630.3910.3910.0000.0000.0000.000
22A22LEU 00.0300.00127.7030.4610.4610.0000.0000.0000.000
23A23LYS 10.9490.98929.18710.68510.6850.0000.0000.0000.000
24A24GLN 0-0.023-0.03030.1400.4080.4080.0000.0000.0000.000
25A25VAL 00.0010.00033.1600.3370.3370.0000.0000.0000.000
26A26ASP -1-0.880-0.95533.975-8.741-8.7410.0000.0000.0000.000
27A27LYS 10.8500.94335.4338.2268.2260.0000.0000.0000.000
28A28ILE 00.0120.01337.2110.2410.2410.0000.0000.0000.000
29A29LYS 10.9130.96038.8058.0508.0500.0000.0000.0000.000
30A30ASP -1-0.932-0.96838.213-8.003-8.0030.0000.0000.0000.000
31A31ASP -1-0.904-0.94741.277-7.403-7.4030.0000.0000.0000.000
32A32GLU -1-0.822-0.85743.482-7.021-7.0210.0000.0000.0000.000
33A33GLU -1-0.964-0.96845.315-6.378-6.3780.0000.0000.0000.000
34A34PRO 00.020-0.00746.9110.1700.1700.0000.0000.0000.000
35A35ILE 00.0340.02047.8840.1670.1670.0000.0000.0000.000
36A36LYS 10.9240.95747.7676.6816.6810.0000.0000.0000.000
37A37THR 0-0.029-0.00951.3420.1590.1590.0000.0000.0000.000
38A38VAL 00.0230.01953.7940.1390.1390.0000.0000.0000.000
39A39GLY 00.0160.01254.4400.1200.1200.0000.0000.0000.000
40A40LYS 10.9400.96352.8576.0836.0830.0000.0000.0000.000
41A41LYS 10.9350.97857.5165.5925.5920.0000.0000.0000.000
42A42ILE 00.0270.00658.2150.1170.1170.0000.0000.0000.000
43A43ALA 00.0380.02859.5320.0940.0940.0000.0000.0000.000
44A44GLU -1-0.944-0.97861.387-5.005-5.0050.0000.0000.0000.000
45A45LEU 0-0.079-0.03563.1470.1210.1210.0000.0000.0000.000
46A46ASP -1-0.872-0.93962.759-4.987-4.9870.0000.0000.0000.000
47A47GLU -1-0.864-0.92164.890-4.778-4.7780.0000.0000.0000.000
48A48LYS 10.9080.94366.8164.8764.8760.0000.0000.0000.000
49A49LYS 10.9420.99068.7834.6914.6910.0000.0000.0000.000
50A50LYS 10.8480.90765.7674.9364.9360.0000.0000.0000.000
51A51LYS 10.9460.97570.8384.6004.6000.0000.0000.0000.000
52A52LEU 00.0220.02173.7360.0540.0540.0000.0000.0000.000
53A53THR 0-0.075-0.04474.3780.0440.0440.0000.0000.0000.000
54A54GLU -1-0.941-0.96377.029-3.932-3.9320.0000.0000.0000.000
55A55ASP -1-0.847-0.93879.723-3.956-3.9560.0000.0000.0000.000
56A56VAL 0-0.075-0.03078.3630.0500.0500.0000.0000.0000.000
57A57ASN 0-0.008-0.00880.7770.0340.0340.0000.0000.0000.000
58A58SER 00.0270.01783.8300.0770.0770.0000.0000.0000.000
59A59LYS 10.9580.96085.9043.5413.5410.0000.0000.0000.000
60A60ASP -1-0.820-0.88788.060-3.598-3.5980.0000.0000.0000.000
61A61THR 00.046-0.00687.658-0.037-0.0370.0000.0000.0000.000
62A62ALA 0-0.022-0.00387.253-0.040-0.0400.0000.0000.0000.000
63A63VAL 0-0.0210.00983.317-0.051-0.0510.0000.0000.0000.000
64A64ARG 10.8980.94682.9483.6983.6980.0000.0000.0000.000
65A65GLY 00.0080.00482.453-0.051-0.0510.0000.0000.0000.000
66A66LYS 10.8540.89877.9344.0724.0720.0000.0000.0000.000
67A67ALA 00.0610.04578.604-0.066-0.0660.0000.0000.0000.000
68A68VAL 0-0.007-0.00577.554-0.075-0.0750.0000.0000.0000.000
69A69LYS 10.8880.92677.3573.8723.8720.0000.0000.0000.000
70A70ASP -1-0.812-0.88375.208-4.264-4.2640.0000.0000.0000.000
71A71LEU 0-0.040-0.02173.155-0.099-0.0990.0000.0000.0000.000
72A72ILE 0-0.078-0.03272.388-0.070-0.0700.0000.0000.0000.000
73A73LYS 10.9160.96370.4374.4804.4800.0000.0000.0000.000
74A74ASN 00.0070.00568.334-0.101-0.1010.0000.0000.0000.000
75A75ALA 0-0.017-0.01067.722-0.090-0.0900.0000.0000.0000.000
76A76ASP -1-0.810-0.89266.779-4.648-4.6480.0000.0000.0000.000
77A77ASP -1-0.875-0.93665.979-4.784-4.7840.0000.0000.0000.000
78A78ARG 10.8200.90963.3014.7554.7550.0000.0000.0000.000
79A79LEU 0-0.038-0.01761.924-0.110-0.1100.0000.0000.0000.000
80A80LYS 10.8430.90861.4084.9674.9670.0000.0000.0000.000
81A81GLU -1-0.832-0.92358.084-5.553-5.5530.0000.0000.0000.000
82A82PHE 0-0.019-0.02155.536-0.111-0.1110.0000.0000.0000.000
83A83GLU -1-0.774-0.85656.528-5.317-5.3170.0000.0000.0000.000
84A84LYS 10.8700.93554.6735.3775.3770.0000.0000.0000.000
85A85GLU -1-0.856-0.91851.708-6.166-6.1660.0000.0000.0000.000
86A86GLU -1-0.846-0.92751.591-5.691-5.6910.0000.0000.0000.000
87A87ASP -1-0.908-0.95851.761-5.904-5.9040.0000.0000.0000.000
88A88ALA 0-0.045-0.01848.609-0.145-0.1450.0000.0000.0000.000
89A89ILE 00.010-0.00146.850-0.212-0.2120.0000.0000.0000.000
90A90LYS 10.9650.99346.8856.0946.0940.0000.0000.0000.000
91A91LYS 10.9400.96744.6846.8786.8780.0000.0000.0000.000
92A92SER 0-0.007-0.05743.162-0.223-0.2230.0000.0000.0000.000
93A93GLU -1-0.902-0.95842.126-7.059-7.0590.0000.0000.0000.000
94A94GLN 0-0.083-0.05742.443-0.005-0.0050.0000.0000.0000.000
95A95ASP -1-0.905-0.95139.761-7.631-7.6310.0000.0000.0000.000
96A96PHE 0-0.036-0.01736.884-0.227-0.2270.0000.0000.0000.000
97A97LYS 10.8900.94837.2816.9076.9070.0000.0000.0000.000
98A98LYS 10.8980.96136.8568.0048.0040.0000.0000.0000.000
99A99ALA 00.0190.03433.376-0.266-0.2660.0000.0000.0000.000
100A100LYS 10.8660.90130.6779.5889.5880.0000.0000.0000.000
101A101SER 00.0320.01929.5200.0140.0140.0000.0000.0000.000
102A102HIS 0-0.094-0.04126.0170.1010.1010.0000.0000.0000.000
103A103VAL 0-0.022-0.01326.894-0.170-0.1700.0000.0000.0000.000
104A104ASP -1-0.914-0.94626.920-10.174-10.1740.0000.0000.0000.000
105A105ASN 0-0.032-0.01823.165-0.095-0.0950.0000.0000.0000.000
106A106ILE 0-0.076-0.01421.818-0.631-0.6310.0000.0000.0000.000
107A107ASP -1-0.919-0.95718.339-15.721-15.7210.0000.0000.0000.000
108A108ASN 00.0380.02019.5020.9030.9030.0000.0000.0000.000
109A109ASP -1-0.780-0.88921.135-12.174-12.1740.0000.0000.0000.000
110A110VAL 0-0.028-0.01323.8850.6050.6050.0000.0000.0000.000
111A111LYS 10.7900.86722.14212.62312.6230.0000.0000.0000.000
112A112ARG 10.7870.87323.92212.61612.6160.0000.0000.0000.000
113A113LYS 10.9030.94326.59210.64410.6440.0000.0000.0000.000
114A114GLU -1-0.790-0.88627.181-11.010-11.0100.0000.0000.0000.000
115A115VAL 00.0070.00427.1630.3340.3340.0000.0000.0000.000
116A116LYS 10.9220.95630.18810.23210.2320.0000.0000.0000.000
117A117GLN 00.0160.02832.7930.3620.3620.0000.0000.0000.000
118A118LEU 00.010-0.00232.0130.3300.3300.0000.0000.0000.000
119A119ASP -1-0.820-0.90533.704-8.892-8.8920.0000.0000.0000.000
120A120ASP -1-0.948-0.97236.000-8.060-8.0600.0000.0000.0000.000
121A121VAL 0-0.069-0.03038.0870.3210.3210.0000.0000.0000.000
122A122LEU 0-0.017-0.00836.2360.2510.2510.0000.0000.0000.000
123A123LYS 10.9260.96637.5248.4188.4180.0000.0000.0000.000
124A124GLU -1-0.909-0.95642.084-6.585-6.5850.0000.0000.0000.000
125A125LYS 10.8380.91742.5617.5377.5370.0000.0000.0000.000
126A126TYR 0-0.002-0.01641.1510.1240.1240.0000.0000.0000.000
127A127LYS 10.9560.99346.2336.5686.5680.0000.0000.0000.000
128A128LEU 0-0.011-0.02047.2910.1830.1830.0000.0000.0000.000
129A129HIS 0-0.065-0.03948.7890.1280.1280.0000.0000.0000.000
130A130SER 00.0410.03150.5210.1730.1730.0000.0000.0000.000
131A131ASP -1-0.957-0.97352.639-5.836-5.8360.0000.0000.0000.000
132A132TYR 0-0.026-0.02753.0170.1880.1880.0000.0000.0000.000
133A133ALA 00.0450.02254.4910.1380.1380.0000.0000.0000.000
134A134LYS 10.9060.95856.2585.4155.4150.0000.0000.0000.000
135A135ALA 0-0.044-0.03058.1630.1370.1370.0000.0000.0000.000
136A136TYR 00.0490.02558.4760.1260.1260.0000.0000.0000.000
137A137LYS 10.9030.93058.6225.5505.5500.0000.0000.0000.000
138A138LYS 10.8560.94562.2624.9694.9690.0000.0000.0000.000
139A139ALA 00.0420.02363.6050.1040.1040.0000.0000.0000.000
140A140VAL 00.0500.05863.5340.1090.1090.0000.0000.0000.000
141A141ASN 0-0.007-0.01965.1960.1630.1630.0000.0000.0000.000
142A142SER 0-0.089-0.05768.0510.0910.0910.0000.0000.0000.000
143A143GLU -1-0.761-0.88167.839-4.693-4.6930.0000.0000.0000.000
144A144LYS 10.8840.92870.3824.6094.6090.0000.0000.0000.000
145A145THR 0-0.087-0.04372.1090.0850.0850.0000.0000.0000.000
146A146LEU 0-0.0010.00674.0900.0750.0750.0000.0000.0000.000
147A147PHE 00.0520.00671.6270.0580.0580.0000.0000.0000.000
148A148LYS 10.9510.96175.2884.2814.2810.0000.0000.0000.000
149A149TYR 0-0.0150.00878.1280.0490.0490.0000.0000.0000.000
150A150LEU 00.0230.00678.7800.0550.0550.0000.0000.0000.000
151A151ASN 0-0.0390.00180.3140.0630.0630.0000.0000.0000.000
152A152GLN 0-0.045-0.01682.326-0.011-0.0110.0000.0000.0000.000
153A153ASN 00.009-0.00385.186-0.022-0.0220.0000.0000.0000.000
154A154ASP -1-0.888-0.94188.084-3.545-3.5450.0000.0000.0000.000
155A155ALA 0-0.050-0.00584.216-0.019-0.0190.0000.0000.0000.000
156A156THR 00.0640.01685.5830.0160.0160.0000.0000.0000.000
157A157GLN 00.028-0.00982.131-0.022-0.0220.0000.0000.0000.000
158A158GLN 00.0190.01683.171-0.027-0.0270.0000.0000.0000.000
159A159GLY 00.0490.02282.377-0.052-0.0520.0000.0000.0000.000
160A160VAL 00.0210.00179.200-0.073-0.0730.0000.0000.0000.000
161A161ASN 00.0240.01278.489-0.094-0.0940.0000.0000.0000.000
162A162GLU -1-0.978-0.99277.749-4.095-4.0950.0000.0000.0000.000
163A163LYS 10.9240.94875.9044.0234.0230.0000.0000.0000.000
164A164SER 00.0190.01174.139-0.086-0.0860.0000.0000.0000.000
165A165LYS 10.9661.01072.9624.1024.1020.0000.0000.0000.000
166A166ALA 0-0.027-0.01071.448-0.076-0.0760.0000.0000.0000.000
167A167ILE 00.0040.01569.064-0.091-0.0910.0000.0000.0000.000
168A168GLU -1-0.903-0.95468.133-4.572-4.5720.0000.0000.0000.000
169A169GLN 0-0.046-0.02566.266-0.169-0.1690.0000.0000.0000.000
170A170ASN 0-0.038-0.04565.284-0.122-0.1220.0000.0000.0000.000
171A171TYR 00.017-0.00863.227-0.143-0.1430.0000.0000.0000.000
172A172LYS 10.9170.97462.6574.6764.6760.0000.0000.0000.000
173A173LYS 10.9680.98361.3564.9554.9550.0000.0000.0000.000
174A174LEU 00.0020.00757.981-0.106-0.1060.0000.0000.0000.000
175A175LYS 10.8910.94657.7785.4315.4310.0000.0000.0000.000
176A176GLU -1-0.957-0.96956.919-5.450-5.4500.0000.0000.0000.000
177A177VAL 0-0.017-0.01553.994-0.129-0.1290.0000.0000.0000.000
178A178SER 00.0260.01453.268-0.186-0.1860.0000.0000.0000.000
179A179ASP -1-0.837-0.91752.447-5.931-5.9310.0000.0000.0000.000
180A180LYS 10.8800.93450.6775.7495.7490.0000.0000.0000.000
181A181TYR 00.0520.02647.418-0.213-0.2130.0000.0000.0000.000
182A182THR 00.0270.00247.633-0.176-0.1760.0000.0000.0000.000
183A183LYS 10.9160.95246.7356.2936.2930.0000.0000.0000.000
184A184VAL 00.0070.02343.473-0.192-0.1920.0000.0000.0000.000
185A185LEU 0-0.018-0.00242.822-0.238-0.2380.0000.0000.0000.000
186A186ASN 0-0.002-0.00441.967-0.250-0.2500.0000.0000.0000.000
187A187LYS 10.8980.96339.8577.4587.4580.0000.0000.0000.000
188A188VAL 00.0380.00837.936-0.245-0.2450.0000.0000.0000.000
189A189GLN 0-0.012-0.01135.390-0.425-0.4250.0000.0000.0000.000
190A190LYS 10.9660.98435.7898.0518.0510.0000.0000.0000.000
191A191GLU -1-0.807-0.91534.308-9.004-9.0040.0000.0000.0000.000
192A192LYS 10.8820.95232.3248.4038.4030.0000.0000.0000.000
193A193GLN 0-0.033-0.01130.919-0.163-0.1630.0000.0000.0000.000
194A194ASP -1-0.885-0.92229.980-10.090-10.0900.0000.0000.0000.000
195A195VAL 0-0.032-0.01827.721-0.504-0.5040.0000.0000.0000.000
196A196ASP -1-1.010-0.99326.419-12.221-12.2210.0000.0000.0000.000
197A197NME 0-0.047-0.00425.655-0.373-0.3730.0000.0000.0000.000