FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

tag_button

FMODB ID: 2LLJR

Calculation Name: 3LYP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LYP

Chain ID: A

ChEMBL ID:

UniProt ID: Q4K6H7

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 OptAll
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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2375352.683868
FMO2-HF: Nuclear repulsion 2295271.975911
FMO2-HF: Total energy -80080.707957
FMO2-MP2: Total energy -80315.046732


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:8:ARG)


Summations of interaction energy for fragment #1(A:8:ARG)
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.
-213.86-207.83127.505-16.752-16.779-0.169
Interaction energy analysis for fragmet #1(A:8:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.835 / q_NPA : 0.898
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].
3A10ALA00.0360.0253.335-14.081-11.0300.116-1.531-1.636-0.002
4A11CYS0-0.023-0.0245.3515.3745.456-0.001-0.006-0.0750.000
5A12TYR00.0090.0248.7961.0571.0570.0000.0000.0000.000
6A13SER00.0370.00111.8020.6080.6080.0000.0000.0000.000
7A14ASP-1-0.787-0.86614.306-15.496-15.4960.0000.0000.0000.000
8A15PRO00.003-0.00116.823-0.730-0.7300.0000.0000.0000.000
9A16ALA00.0630.04117.7650.2670.2670.0000.0000.0000.000
10A17ASP-1-0.750-0.85619.623-15.201-15.2010.0000.0000.0000.000
11A18HIS0-0.077-0.05219.639-1.080-1.0800.0000.0000.0000.000
12A19TYR0-0.057-0.05919.930-0.526-0.5260.0000.0000.0000.000
13A20SER0-0.015-0.05415.737-1.210-1.2100.0000.0000.0000.000
14A21HIS00.0110.03015.106-0.640-0.6400.0000.0000.0000.000
15A22ARG10.8660.92216.10313.63313.6330.0000.0000.0000.000
16A23VAL00.0020.00111.679-0.498-0.4980.0000.0000.0000.000
17A24ARG10.7780.84111.35318.34418.3440.0000.0000.0000.000
18A25ILE0-0.0070.00512.050-0.952-0.9520.0000.0000.0000.000
19A26VAL00.0070.00111.801-0.719-0.7190.0000.0000.0000.000
20A27LEU0-0.036-0.0296.892-1.189-1.1890.0000.0000.0000.000
21A28ALA0-0.0070.0168.375-2.823-2.8230.0000.0000.0000.000
22A29GLU-1-0.765-0.86910.767-17.629-17.6290.0000.0000.0000.000
23A30LYS10.7150.8469.48921.50021.5000.0000.0000.0000.000
24A31GLY00.0170.0228.454-1.183-1.1830.0000.0000.0000.000
25A32VAL0-0.038-0.0234.647-2.884-2.792-0.001-0.012-0.0770.000
26A33SER0-0.038-0.0242.654-16.958-14.2270.428-1.528-1.631-0.016
27A34ALA0-0.0170.0111.830-29.421-32.03111.664-4.752-4.302-0.047
28A35GLU-1-0.835-0.9091.733-99.778-99.56813.735-7.453-6.492-0.090
29A36ILE0-0.010-0.0074.9325.7275.768-0.001-0.003-0.0360.000
30A37ILE0-0.020-0.0037.2672.1812.1810.0000.0000.0000.000
31A38SER00.002-0.00910.6571.4631.4630.0000.0000.0000.000
32A39VAL0-0.073-0.04114.2910.2510.2510.0000.0000.0000.000
33A40GLU-1-0.868-0.93916.791-13.705-13.7050.0000.0000.0000.000
34A41ALA0-0.025-0.01119.8110.7380.7380.0000.0000.0000.000
35A42GLY00.0620.03020.912-0.267-0.2670.0000.0000.0000.000
36A43ARG10.8280.92218.52314.14814.1480.0000.0000.0000.000
37A44GLN00.0740.02217.994-0.309-0.3090.0000.0000.0000.000
38A45PRO00.0400.02113.4220.5690.5690.0000.0000.0000.000
39A46PRO0-0.016-0.01814.470-0.044-0.0440.0000.0000.0000.000
40A47LYS10.8750.9167.82722.20922.2090.0000.0000.0000.000
41A48LEU00.0040.02110.875-0.940-0.9400.0000.0000.0000.000
42A49ILE00.002-0.00812.7460.3040.3040.0000.0000.0000.000
43A50GLU-1-0.910-0.92511.108-19.088-19.0880.0000.0000.0000.000
44A51VAL0-0.021-0.0119.3790.2040.2040.0000.0000.0000.000
45A52ASN00.006-0.00912.7240.9780.9780.0000.0000.0000.000
46A53PRO0-0.0030.00515.4010.1580.1580.0000.0000.0000.000
47A54TYR0-0.033-0.01418.6890.7290.7290.0000.0000.0000.000
48A55GLY0-0.0070.00117.4310.2820.2820.0000.0000.0000.000
49A56SER00.0000.01517.7430.0450.0450.0000.0000.0000.000
50A57LEU0-0.0400.00015.699-1.254-1.2540.0000.0000.0000.000
51A58PRO00.0210.01114.2050.8240.8240.0000.0000.0000.000
52A59THR0-0.043-0.04511.4571.4451.4450.0000.0000.0000.000
53A60LEU0-0.0020.0127.934-1.632-1.6320.0000.0000.0000.000
54A61VAL0-0.001-0.0205.4303.0543.0540.0000.0000.0000.000
55A62ASP-1-0.753-0.8582.551-57.590-56.2121.451-1.206-1.622-0.014
56A63ARG10.6990.7822.92138.34839.3630.115-0.259-0.8720.000
57A64ASP-1-0.855-0.8895.230-25.830-25.791-0.001-0.002-0.0360.000
58A65LEU0-0.064-0.0147.5931.9351.9350.0000.0000.0000.000
59A66ALA00.0470.0178.165-1.919-1.9190.0000.0000.0000.000
60A67LEU0-0.0150.00110.7951.5381.5380.0000.0000.0000.000
61A68TRP00.015-0.00713.403-1.371-1.3710.0000.0000.0000.000
62A69GLU-1-0.707-0.80916.177-14.443-14.4430.0000.0000.0000.000
63A70SER0-0.035-0.02317.191-0.679-0.6790.0000.0000.0000.000
64A71THR0-0.039-0.05717.184-0.690-0.6900.0000.0000.0000.000
65A72VAL00.0150.01216.937-0.392-0.3920.0000.0000.0000.000
66A73VAL00.0040.00412.220-0.851-0.8510.0000.0000.0000.000
67A74MET0-0.030-0.01613.516-1.172-1.1720.0000.0000.0000.000
68A75GLU-1-0.768-0.85115.128-15.031-15.0310.0000.0000.0000.000
69A76TYR00.0140.0099.4710.1580.1580.0000.0000.0000.000
70A77LEU0-0.010-0.0238.588-1.098-1.0980.0000.0000.0000.000
71A78ASP-1-0.794-0.90011.932-17.969-17.9690.0000.0000.0000.000
72A79GLU-1-0.881-0.93514.837-15.341-15.3410.0000.0000.0000.000
73A80ARG10.8690.9487.75929.69029.6900.0000.0000.0000.000
74A81TYR0-0.012-0.0146.078-2.713-2.7130.0000.0000.0000.000
75A82PRO00.0300.01811.4820.5360.5360.0000.0000.0000.000
76A83HIS0-0.0160.01913.5201.5721.5720.0000.0000.0000.000
77A84PRO00.0640.03012.789-1.552-1.5520.0000.0000.0000.000
78A85PRO00.0030.00915.723-0.745-0.7450.0000.0000.0000.000
79A86LEU00.0190.00914.5650.4750.4750.0000.0000.0000.000
80A87LEU0-0.023-0.01018.6190.7780.7780.0000.0000.0000.000
81A88PRO00.0040.00121.470-0.094-0.0940.0000.0000.0000.000
82A89VAL00.0420.02823.785-0.230-0.2300.0000.0000.0000.000
83A90TYR00.0230.01125.0870.0140.0140.0000.0000.0000.000
84A91PRO00.0440.00928.217-0.067-0.0670.0000.0000.0000.000
85A92VAL00.0340.01729.319-0.123-0.1230.0000.0000.0000.000
86A93ALA00.0110.01528.5040.0240.0240.0000.0000.0000.000
87A94ARG10.8400.91619.79514.22614.2260.0000.0000.0000.000
88A95ALA00.0030.00326.389-0.210-0.2100.0000.0000.0000.000
89A96ASN00.011-0.00229.0490.1140.1140.0000.0000.0000.000
90A97SER00.0240.01024.6170.0200.0200.0000.0000.0000.000
91A98ARG10.8350.87621.60213.42213.4220.0000.0000.0000.000
92A99LEU0-0.019-0.00226.2480.0350.0350.0000.0000.0000.000
93A100LEU0-0.008-0.00827.9160.1940.1940.0000.0000.0000.000
94A101ILE00.0260.01222.1040.0830.0830.0000.0000.0000.000
95A102HIS00.0030.00426.029-0.194-0.1940.0000.0000.0000.000
96A103ARG10.8560.90828.5239.3669.3660.0000.0000.0000.000
97A104ILE00.0190.02525.9000.2380.2380.0000.0000.0000.000
98A105GLN00.0510.01725.510-0.393-0.3930.0000.0000.0000.000
99A106ARG10.8530.90928.1608.9828.9820.0000.0000.0000.000
100A107ASP-1-0.826-0.89731.971-8.987-8.9870.0000.0000.0000.000
101A108TRP0-0.016-0.02729.3530.0950.0950.0000.0000.0000.000
102A109CYS0-0.030-0.00426.722-0.187-0.1870.0000.0000.0000.000
103A110GLY00.0400.03728.895-0.016-0.0160.0000.0000.0000.000
104A111GLN0-0.022-0.02631.9150.1400.1400.0000.0000.0000.000
105A112VAL0-0.005-0.00726.9000.1260.1260.0000.0000.0000.000
106A113ASP-1-0.750-0.84027.380-11.873-11.8730.0000.0000.0000.000
107A114LEU0-0.033-0.00729.9710.1600.1600.0000.0000.0000.000
108A115ILE0-0.028-0.01232.4630.2960.2960.0000.0000.0000.000
109A116LEU00.0220.00526.8010.1090.1090.0000.0000.0000.000
110A117ASP-1-0.790-0.83830.868-9.850-9.8500.0000.0000.0000.000
111A118PRO00.0440.02131.6750.3640.3640.0000.0000.0000.000
112A119ARG10.7990.85633.3139.7939.7930.0000.0000.0000.000
113A120THR0-0.056-0.02735.7390.3450.3450.0000.0000.0000.000
114A121LYS10.9660.97438.3337.2627.2620.0000.0000.0000.000
115A122GLU-1-0.701-0.83039.120-8.428-8.4280.0000.0000.0000.000
116A123ALA0-0.005-0.00741.382-0.041-0.0410.0000.0000.0000.000
117A124ALA0-0.0060.00140.6720.0300.0300.0000.0000.0000.000
118A125ARG10.8300.91035.1868.8018.8010.0000.0000.0000.000
119A126VAL0-0.030-0.01638.455-0.101-0.1010.0000.0000.0000.000
120A127GLN0-0.051-0.04040.9910.0780.0780.0000.0000.0000.000
121A128ALA00.0580.02936.164-0.013-0.0130.0000.0000.0000.000
122A129ARG10.8000.87836.0828.4988.4980.0000.0000.0000.000
123A130LYS10.8070.90237.5287.2157.2150.0000.0000.0000.000
124A131GLU-1-0.837-0.90438.853-7.933-7.9330.0000.0000.0000.000
125A132LEU00.0060.01231.371-0.041-0.0410.0000.0000.0000.000
126A133ARG10.9090.94735.6117.6687.6680.0000.0000.0000.000
127A134GLU-1-0.814-0.87237.260-7.406-7.4060.0000.0000.0000.000
128A135SER0-0.0220.00636.159-0.034-0.0340.0000.0000.0000.000
129A136LEU00.0220.00631.236-0.043-0.0430.0000.0000.0000.000
130A137THR0-0.019-0.03535.177-0.004-0.0040.0000.0000.0000.000
131A138GLY0-0.0290.00038.3240.0750.0750.0000.0000.0000.000
132A139VAL0-0.025-0.00533.4750.0860.0860.0000.0000.0000.000
133A140SER0-0.017-0.02435.064-0.071-0.0710.0000.0000.0000.000
134A141PRO0-0.010-0.01535.927-0.117-0.1170.0000.0000.0000.000
135A142LEU00.0190.01534.344-0.024-0.0240.0000.0000.0000.000
136A143PHE0-0.046-0.02228.768-0.252-0.2520.0000.0000.0000.000
137A144ALA0-0.044-0.02433.250-0.114-0.1140.0000.0000.0000.000
138A145ASP-1-0.919-0.95535.181-8.396-8.3960.0000.0000.0000.000
139A146LYS10.7950.89030.6559.4469.4460.0000.0000.0000.000
140A147PRO0-0.0100.02327.920-0.004-0.0040.0000.0000.0000.000
141A148PHE00.0240.01322.656-0.293-0.2930.0000.0000.0000.000
142A149PHE00.015-0.00926.4460.5250.5250.0000.0000.0000.000
143A150LEU0-0.039-0.01628.032-0.093-0.0930.0000.0000.0000.000
144A151SER0-0.050-0.04224.9830.1440.1440.0000.0000.0000.000
145A152GLU-1-0.810-0.91527.786-9.846-9.8460.0000.0000.0000.000
146A153GLU-1-0.943-0.97122.398-13.454-13.4540.0000.0000.0000.000
147A154GLN00.0050.03118.4690.9630.9630.0000.0000.0000.000
148A155SER00.007-0.02320.333-0.365-0.3650.0000.0000.0000.000
149A156LEU00.0580.00416.375-0.235-0.2350.0000.0000.0000.000
150A157VAL0-0.0070.00019.9900.1240.1240.0000.0000.0000.000
151A158ASP-1-0.715-0.80721.656-12.528-12.5280.0000.0000.0000.000
152A159CYS0-0.067-0.02017.725-0.284-0.2840.0000.0000.0000.000
153A160CYS0-0.028-0.01519.714-0.287-0.2870.0000.0000.0000.000
154A161LEU0-0.0110.00522.2840.3780.3780.0000.0000.0000.000
155A162LEU00.001-0.00420.4550.3270.3270.0000.0000.0000.000
156A163PRO00.0190.01119.7380.3790.3790.0000.0000.0000.000
157A164ILE00.0120.01122.3560.3390.3390.0000.0000.0000.000
158A165LEU00.021-0.01026.1190.3670.3670.0000.0000.0000.000
159A166TRP0-0.025-0.02523.3400.4320.4320.0000.0000.0000.000
160A167ARG10.7930.85920.18914.78914.7890.0000.0000.0000.000
161A168LEU0-0.0330.00027.0140.3420.3420.0000.0000.0000.000
162A169PRO00.0470.01829.2750.3260.3260.0000.0000.0000.000
163A170VAL00.0220.01627.5230.3050.3050.0000.0000.0000.000
164A171LEU0-0.0290.00128.9030.1460.1460.0000.0000.0000.000
165A172GLY0-0.0010.01032.1430.3130.3130.0000.0000.0000.000
166A173ILE0-0.075-0.04933.1070.3220.3220.0000.0000.0000.000
167A174GLU-1-0.910-0.93534.344-8.541-8.5410.0000.0000.0000.000
168A175LEU0-0.016-0.01933.2840.1630.1630.0000.0000.0000.000
169A176PRO00.0090.01037.3090.1090.1090.0000.0000.0000.000
170A177ARG11.0010.97339.5597.4327.4320.0000.0000.0000.000
171A178GLN0-0.017-0.00640.921-0.095-0.0950.0000.0000.0000.000
172A179ALA00.0250.01736.6320.0050.0050.0000.0000.0000.000
173A180LYS10.8290.89436.3428.2758.2750.0000.0000.0000.000
174A181PRO00.0450.02335.477-0.202-0.2020.0000.0000.0000.000
175A182LEU00.0210.01830.592-0.295-0.2950.0000.0000.0000.000
176A183LEU0-0.007-0.01331.245-0.354-0.3540.0000.0000.0000.000
177A184ASP-1-0.774-0.86931.514-9.138-9.1380.0000.0000.0000.000
178A185TYR0-0.112-0.08025.132-0.332-0.3320.0000.0000.0000.000
179A186MET0-0.037-0.01127.224-0.332-0.3320.0000.0000.0000.000
180A187GLU-1-0.978-0.97326.764-10.240-10.2400.0000.0000.0000.000
181A188ARG10.8380.91527.06710.13410.1340.0000.0000.0000.000
182A189GLN00.003-0.01722.409-0.895-0.8950.0000.0000.0000.000
183A190PHE0-0.029-0.02822.190-0.612-0.6120.0000.0000.0000.000
184A191ALA00.0090.01722.388-0.445-0.4450.0000.0000.0000.000
185A192ARG10.7630.86317.96815.49215.4920.0000.0000.0000.000
186A193GLU-1-0.896-0.95015.307-18.722-18.7220.0000.0000.0000.000
187A194ALA00.0270.01814.194-0.728-0.7280.0000.0000.0000.000
188A195PHE00.0240.01714.762-0.742-0.7420.0000.0000.0000.000
189A196GLN00.0300.02317.162-0.383-0.3830.0000.0000.0000.000
190A197ALA00.0200.00511.862-0.134-0.1340.0000.0000.0000.000
191A198SER0-0.072-0.04012.689-0.978-0.9780.0000.0000.0000.000
192A199LEU0-0.054-0.00314.068-0.032-0.0320.0000.0000.0000.000
193A200SER00.010-0.03316.110-0.206-0.2060.0000.0000.0000.000
194A201GLY00.006-0.01016.9610.7540.7540.0000.0000.0000.000
195A202VAL00.0720.03619.8390.5610.5610.0000.0000.0000.000
196A203GLU-1-0.718-0.82517.926-16.795-16.7950.0000.0000.0000.000
197A204ARG10.7860.90117.40217.00417.0040.0000.0000.0000.000
198A205ASP-1-0.878-0.93822.769-12.523-12.5230.0000.0000.0000.000
199A206MET0-0.124-0.03623.2850.5320.5320.0000.0000.0000.000
200A207ARG10.8040.90726.06511.70911.7090.0000.0000.0000.000