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: NNNRQ

Calculation Name: 3LYK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LYK

Chain ID: A

ChEMBL ID:

UniProt ID: P45207

Base Structure: X-ray

Registration Date: 2023-09-21

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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2237816.271697
FMO2-HF: Nuclear repulsion 2159485.801392
FMO2-HF: Total energy -78330.470305
FMO2-MP2: Total energy -78556.238242


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:10:VAL)


Summations of interaction energy for fragment #1(A:10:VAL)
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.
-7.369-2.5650.757-1.939-3.623-0.005
Interaction energy analysis for fragmet #1(A:10:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : 0.008
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].
3A12THR0-0.002-0.0162.728-2.5990.3240.596-1.402-2.118-0.005
4A13LEU0-0.035-0.0244.4540.2630.289-0.001-0.008-0.0170.000
5A14PHE00.0290.0247.4520.1340.1340.0000.0000.0000.000
6A15SER00.010-0.03910.3420.0990.0990.0000.0000.0000.000
7A16ASN00.063-0.00113.3650.0530.0530.0000.0000.0000.000
8A17LYS10.8080.88416.8510.2640.2640.0000.0000.0000.000
9A18ASP-1-0.865-0.91218.761-0.215-0.2150.0000.0000.0000.000
10A19ASP-1-0.736-0.85118.718-0.399-0.3990.0000.0000.0000.000
11A20ILE0-0.015-0.00220.095-0.016-0.0160.0000.0000.0000.000
12A21TYR0-0.072-0.06819.609-0.008-0.0080.0000.0000.0000.000
13A22CYS0-0.069-0.02015.861-0.074-0.0740.0000.0000.0000.000
14A23HIS0-0.0170.00916.480-0.027-0.0270.0000.0000.0000.000
15A24GLN00.0170.00518.826-0.029-0.0290.0000.0000.0000.000
16A25VAL00.0160.00113.0950.0040.0040.0000.0000.0000.000
17A26LYS10.8660.94813.5720.5350.5350.0000.0000.0000.000
18A27ILE0-0.009-0.00415.5440.0230.0230.0000.0000.0000.000
19A28VAL0-0.001-0.00416.1890.0220.0220.0000.0000.0000.000
20A29LEU0-0.016-0.01310.4090.0060.0060.0000.0000.0000.000
21A30ALA00.0080.02513.8140.0280.0280.0000.0000.0000.000
22A31GLU-1-0.837-0.87215.952-0.165-0.1650.0000.0000.0000.000
23A32LYS10.6930.83414.2950.3880.3880.0000.0000.0000.000
24A33GLY0-0.0030.01214.3290.0120.0120.0000.0000.0000.000
25A34VAL0-0.062-0.0209.3420.0550.0550.0000.0000.0000.000
26A35LEU0-0.011-0.0187.452-0.056-0.0560.0000.0000.0000.000
27A36TYR0-0.020-0.0176.079-0.289-0.2890.0000.0000.0000.000
28A37GLU-1-0.876-0.9124.238-2.129-1.7620.001-0.058-0.3100.000
29A38ASN0-0.015-0.0326.096-0.264-0.2640.0000.0000.0000.000
30A39ALA00.0360.0317.7340.1720.1720.0000.0000.0000.000
31A40GLU-1-0.820-0.9049.554-0.447-0.4470.0000.0000.0000.000
32A41VAL0-0.012-0.00413.0740.0190.0190.0000.0000.0000.000
33A42ASP-1-0.826-0.90415.615-0.241-0.2410.0000.0000.0000.000
34A43LEU00.000-0.01118.690-0.016-0.0160.0000.0000.0000.000
35A44GLN0-0.105-0.06120.7610.0120.0120.0000.0000.0000.000
36A45ALA0-0.068-0.03521.0300.0220.0220.0000.0000.0000.000
37A46LEU0-0.0080.01317.163-0.018-0.0180.0000.0000.0000.000
38A47PRO0-0.0060.00913.2700.0400.0400.0000.0000.0000.000
39A48GLU-1-0.886-0.96415.065-0.344-0.3440.0000.0000.0000.000
40A49ASP-1-0.850-0.9299.640-0.739-0.7390.0000.0000.0000.000
41A50LEU0-0.036-0.01711.460-0.107-0.1070.0000.0000.0000.000
42A51MET0-0.026-0.00412.453-0.009-0.0090.0000.0000.0000.000
43A52GLU-1-0.999-0.99912.863-0.389-0.3890.0000.0000.0000.000
44A53LEU0-0.064-0.0257.914-0.044-0.0440.0000.0000.0000.000
45A54ASN0-0.044-0.04212.0620.0540.0540.0000.0000.0000.000
46A55PRO00.0460.03514.7280.0340.0340.0000.0000.0000.000
47A56TYR0-0.079-0.04218.0940.0560.0560.0000.0000.0000.000
48A57GLY00.0250.00716.8200.0280.0280.0000.0000.0000.000
49A58THR0-0.042-0.00916.2430.0130.0130.0000.0000.0000.000
50A59VAL00.0030.02213.940-0.085-0.0850.0000.0000.0000.000
51A60PRO0-0.027-0.03013.7840.0620.0620.0000.0000.0000.000
52A61THR0-0.027-0.03210.3320.0840.0840.0000.0000.0000.000
53A62LEU0-0.041-0.0137.918-0.067-0.0670.0000.0000.0000.000
54A63VAL00.0380.0154.7210.1690.301-0.001-0.008-0.1230.000
55A64ASP-1-0.754-0.8625.070-3.119-3.037-0.001-0.016-0.0650.000
56A65ARG10.8230.8882.7261.0552.0960.160-0.432-0.7690.000
57A66ASP-1-0.830-0.8953.672-0.2220.0110.003-0.015-0.2210.000
58A67LEU0-0.064-0.0147.2520.3000.3000.0000.0000.0000.000
59A68VAL00.0400.0148.429-0.444-0.4440.0000.0000.0000.000
60A69LEU0-0.044-0.01810.4410.2330.2330.0000.0000.0000.000
61A70PHE00.0570.02112.270-0.076-0.0760.0000.0000.0000.000
62A71ASN00.0240.00615.0300.0600.0600.0000.0000.0000.000
63A72SER00.0420.00816.914-0.037-0.0370.0000.0000.0000.000
64A73ARG10.9340.96917.8730.3220.3220.0000.0000.0000.000
65A74ILE0-0.030-0.01216.7720.0110.0110.0000.0000.0000.000
66A75ILE00.0180.01912.807-0.022-0.0220.0000.0000.0000.000
67A76MET0-0.019-0.00415.171-0.018-0.0180.0000.0000.0000.000
68A77GLU-1-0.794-0.87617.466-0.291-0.2910.0000.0000.0000.000
69A78TYR0-0.047-0.0379.7410.1280.1280.0000.0000.0000.000
70A79LEU00.000-0.00911.543-0.002-0.0020.0000.0000.0000.000
71A80ASP-1-0.828-0.92014.796-0.257-0.2570.0000.0000.0000.000
72A81GLU-1-0.925-0.95717.596-0.267-0.2670.0000.0000.0000.000
73A82ARG10.8040.9087.0161.2161.2160.0000.0000.0000.000
74A83PHE0-0.012-0.0128.6190.0290.0290.0000.0000.0000.000
75A84PRO00.0060.00714.7660.0260.0260.0000.0000.0000.000
76A85HIS0-0.039-0.00517.7030.0210.0210.0000.0000.0000.000
77A86PRO00.0810.04317.636-0.017-0.0170.0000.0000.0000.000
78A87PRO0-0.0110.00920.421-0.033-0.0330.0000.0000.0000.000
79A88LEU00.0210.01119.6840.0110.0110.0000.0000.0000.000
80A89MET0-0.020-0.00123.2210.0020.0020.0000.0000.0000.000
81A90GLN00.0160.01325.5140.0170.0170.0000.0000.0000.000
82A91VAL00.0380.01827.672-0.010-0.0100.0000.0000.0000.000
83A92TYR0-0.0010.00129.055-0.001-0.0010.0000.0000.0000.000
84A93PRO00.0500.01330.737-0.007-0.0070.0000.0000.0000.000
85A94VAL00.0090.00431.790-0.007-0.0070.0000.0000.0000.000
86A95SER0-0.032-0.02531.9740.0010.0010.0000.0000.0000.000
87A96ARG10.8910.94922.8730.2300.2300.0000.0000.0000.000
88A97ALA0-0.007-0.00229.439-0.013-0.0130.0000.0000.0000.000
89A98LYS10.9330.96631.8670.1160.1160.0000.0000.0000.000
90A99ASP-1-0.779-0.89528.641-0.175-0.1750.0000.0000.0000.000
91A100ARG10.8410.88724.1260.2510.2510.0000.0000.0000.000
92A101LEU0-0.026-0.00528.884-0.005-0.0050.0000.0000.0000.000
93A102LEU0-0.028-0.01731.2890.0030.0030.0000.0000.0000.000
94A103MET00.0000.01125.134-0.006-0.0060.0000.0000.0000.000
95A104LEU0-0.0020.00428.354-0.005-0.0050.0000.0000.0000.000
96A105ARG10.8420.89829.4660.1430.1430.0000.0000.0000.000
97A106ILE0-0.0420.00228.5720.0050.0050.0000.0000.0000.000
98A107GLU-1-0.884-0.92825.784-0.258-0.2580.0000.0000.0000.000
99A108GLN0-0.048-0.04328.7590.0040.0040.0000.0000.0000.000
100A109ASP-1-0.811-0.88731.831-0.143-0.1430.0000.0000.0000.000
101A110TRP0-0.028-0.02031.9740.0070.0070.0000.0000.0000.000
102A111TYR00.0300.00524.271-0.004-0.0040.0000.0000.0000.000
103A112PRO00.0260.02329.8100.0000.0000.0000.0000.0000.000
104A113THR0-0.033-0.00832.0960.0050.0050.0000.0000.0000.000
105A114LEU00.023-0.00328.0150.0070.0070.0000.0000.0000.000
106A115ALA00.0420.02929.1580.0020.0020.0000.0000.0000.000
107A116LYS10.9080.95730.5400.1250.1250.0000.0000.0000.000
108A117ALA0-0.061-0.04333.3380.0080.0080.0000.0000.0000.000
109A118GLU-1-0.839-0.89627.846-0.206-0.2060.0000.0000.0000.000
110A119ASN0-0.064-0.04528.5780.0010.0010.0000.0000.0000.000
111A120GLY00.0160.03332.4170.0030.0030.0000.0000.0000.000
112A121THR0-0.018-0.05836.2030.0040.0040.0000.0000.0000.000
113A122GLU-1-0.803-0.90538.402-0.114-0.1140.0000.0000.0000.000
114A123LYS10.8430.93840.5530.0890.0890.0000.0000.0000.000
115A124GLU-1-0.803-0.86638.610-0.119-0.1190.0000.0000.0000.000
116A125LYS10.9100.96534.6350.1260.1260.0000.0000.0000.000
117A126THR0-0.009-0.03438.0530.0020.0020.0000.0000.0000.000
118A127SER0-0.068-0.02041.0550.0000.0000.0000.0000.0000.000
119A128ALA00.0270.00436.5400.0020.0020.0000.0000.0000.000
120A129LEU00.0370.02235.517-0.002-0.0020.0000.0000.0000.000
121A130LYS10.8040.89138.1760.0850.0850.0000.0000.0000.000
122A131GLN0-0.069-0.04438.3990.0030.0030.0000.0000.0000.000
123A132LEU00.0780.03033.4170.0010.0010.0000.0000.0000.000
124A133LYS10.8570.93537.6450.0890.0890.0000.0000.0000.000
125A134GLU-1-0.869-0.92339.655-0.082-0.0820.0000.0000.0000.000
126A135GLU-1-0.840-0.91937.221-0.127-0.1270.0000.0000.0000.000
127A136LEU00.0040.00334.3760.0000.0000.0000.0000.0000.000
128A137LEU0-0.043-0.03138.5450.0030.0030.0000.0000.0000.000
129A138GLY0-0.024-0.00641.9040.0040.0040.0000.0000.0000.000
130A139ILE0-0.017-0.00536.3170.0020.0020.0000.0000.0000.000
131A140ALA00.0020.01240.060-0.002-0.0020.0000.0000.0000.000
132A141PRO0-0.043-0.03641.3780.0010.0010.0000.0000.0000.000
133A142ILE00.0270.01437.3210.0020.0020.0000.0000.0000.000
134A143PHE0-0.009-0.00433.463-0.001-0.0010.0000.0000.0000.000
135A144GLN0-0.034-0.01838.0890.0040.0040.0000.0000.0000.000
136A145GLN0-0.042-0.01839.7320.0010.0010.0000.0000.0000.000
137A146MET0-0.0280.01436.2990.0030.0030.0000.0000.0000.000
138A147PRO0-0.0340.01634.075-0.002-0.0020.0000.0000.0000.000
139A148TYR00.0490.03429.445-0.006-0.0060.0000.0000.0000.000
140A149PHE00.004-0.00931.0570.0080.0080.0000.0000.0000.000
141A150MET0-0.087-0.04432.490-0.007-0.0070.0000.0000.0000.000
142A151ASN0-0.020-0.01231.3720.0040.0040.0000.0000.0000.000
143A152GLU-1-0.867-0.95833.463-0.090-0.0900.0000.0000.0000.000
144A153GLU-1-0.920-0.98028.513-0.119-0.1190.0000.0000.0000.000
145A154PHE0-0.052-0.01322.898-0.004-0.0040.0000.0000.0000.000
146A155GLY00.0590.02125.002-0.005-0.0050.0000.0000.0000.000
147A156LEU0-0.008-0.02520.406-0.007-0.0070.0000.0000.0000.000
148A157VAL0-0.004-0.00823.979-0.006-0.0060.0000.0000.0000.000
149A158ASP-1-0.692-0.82626.552-0.171-0.1710.0000.0000.0000.000
150A159CYS0-0.057-0.01221.526-0.004-0.0040.0000.0000.0000.000
151A160TYR00.0390.01723.029-0.024-0.0240.0000.0000.0000.000
152A161VAL0-0.0030.01225.4790.0060.0060.0000.0000.0000.000
153A162ALA00.0060.00425.3890.0070.0070.0000.0000.0000.000
154A163PRO00.0520.01422.7060.0150.0150.0000.0000.0000.000
155A164LEU00.0200.02725.1780.0090.0090.0000.0000.0000.000
156A165LEU0-0.006-0.01728.4320.0130.0130.0000.0000.0000.000
157A166TRP00.0230.01624.2700.0240.0240.0000.0000.0000.000
158A167LYS10.8090.88424.7880.2480.2480.0000.0000.0000.000
159A168LEU00.005-0.00228.7600.0120.0120.0000.0000.0000.000
160A169LYS10.9230.96330.6260.1330.1330.0000.0000.0000.000
161A170HIS0-0.041-0.02127.4950.0180.0180.0000.0000.0000.000
162A171LEU0-0.0200.00731.3050.0050.0050.0000.0000.0000.000
163A172GLY0-0.0060.00333.7010.0070.0070.0000.0000.0000.000
164A173VAL0-0.063-0.03735.7750.0080.0080.0000.0000.0000.000
165A174GLU-1-0.853-0.91637.218-0.085-0.0850.0000.0000.0000.000
166A175PHE0-0.0020.00835.4050.0050.0050.0000.0000.0000.000
167A176THR00.007-0.00740.4860.0030.0030.0000.0000.0000.000
168A177GLY00.0540.03044.216-0.001-0.0010.0000.0000.0000.000
169A178THR00.0240.00346.102-0.001-0.0010.0000.0000.0000.000
170A179GLY00.0320.02244.539-0.003-0.0030.0000.0000.0000.000
171A180SER0-0.003-0.02141.533-0.003-0.0030.0000.0000.0000.000
172A181LYS10.9140.95440.6350.0670.0670.0000.0000.0000.000
173A182ALA0-0.023-0.00340.1680.0000.0000.0000.0000.0000.000
174A183ILE00.0360.02436.103-0.003-0.0030.0000.0000.0000.000
175A184LYS10.8490.91635.8510.0800.0800.0000.0000.0000.000
176A185ALA00.0600.03235.926-0.004-0.0040.0000.0000.0000.000
177A186TYR0-0.086-0.06729.946-0.001-0.0010.0000.0000.0000.000
178A187MET0-0.017-0.01631.678-0.005-0.0050.0000.0000.0000.000
179A188GLU-1-0.935-0.97431.112-0.093-0.0930.0000.0000.0000.000
180A189ARG10.8510.93831.5180.1040.1040.0000.0000.0000.000
181A190VAL00.0270.01427.521-0.004-0.0040.0000.0000.0000.000
182A191PHE0-0.081-0.05026.778-0.008-0.0080.0000.0000.0000.000
183A192THR0-0.052-0.04526.711-0.001-0.0010.0000.0000.0000.000
184A193ARG10.8700.93423.6500.1860.1860.0000.0000.0000.000
185A194ASP-1-0.854-0.93821.683-0.120-0.1200.0000.0000.0000.000
186A195SER0-0.058-0.05019.254-0.004-0.0040.0000.0000.0000.000
187A196PHE00.0490.02119.656-0.034-0.0340.0000.0000.0000.000
188A197LEU0-0.0010.00621.577-0.011-0.0110.0000.0000.0000.000
189A198GLN0-0.041-0.02816.351-0.011-0.0110.0000.0000.0000.000
190A199SER0-0.081-0.05017.258-0.025-0.0250.0000.0000.0000.000
191A200VAL0-0.039-0.01618.335-0.023-0.0230.0000.0000.0000.000
192A201GLY0-0.036-0.00717.7900.0080.0080.0000.0000.0000.000