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: 855ZY

Calculation Name: 5LON-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5LON

Chain ID: A

ChEMBL ID:

UniProt ID: Q6CPV9

Base Structure: X-ray

Registration Date: 2023-06-21

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 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 225
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2781392.313703
FMO2-HF: Nuclear repulsion 2691026.491524
FMO2-HF: Total energy -90365.822179
FMO2-MP2: Total energy -90632.234348


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:2:SER)


Summations of interaction energy for fragment #1(A:2:SER)
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.
-1.812-0.251-0.007-0.837-0.7170.004
Interaction energy analysis for fragmet #1(A:2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / q_NPA : 0.010
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].
3A4PRO0-0.013-0.0123.798-2.759-1.198-0.007-0.837-0.7170.004
4A5LEU0-0.0070.0135.2290.7880.7880.0000.0000.0000.000
5A6LEU00.0180.0017.566-0.077-0.0770.0000.0000.0000.000
6A7ARG10.8220.88310.2560.4690.4690.0000.0000.0000.000
7A8PRO00.0560.02212.6090.0500.0500.0000.0000.0000.000
8A9PHE00.0380.01014.9910.0360.0360.0000.0000.0000.000
9A10GLU-1-0.846-0.91415.646-0.376-0.3760.0000.0000.0000.000
10A11THR0-0.029-0.01917.9670.0140.0140.0000.0000.0000.000
11A12VAL0-0.0400.01219.4510.0170.0170.0000.0000.0000.000
12A13SER00.0360.01321.5160.0090.0090.0000.0000.0000.000
13A14LEU00.0230.01323.596-0.007-0.0070.0000.0000.0000.000
14A15GLU-1-0.858-0.94825.179-0.077-0.0770.0000.0000.0000.000
15A16ASN0-0.003-0.03221.361-0.003-0.0030.0000.0000.0000.000
16A17ALA0-0.032-0.01520.375-0.008-0.0080.0000.0000.0000.000
17A18VAL00.0150.00520.890-0.001-0.0010.0000.0000.0000.000
18A19GLU-1-0.797-0.89722.001-0.098-0.0980.0000.0000.0000.000
19A20ASP-1-0.836-0.89215.939-0.230-0.2300.0000.0000.0000.000
20A21LEU0-0.030-0.02118.5060.0120.0120.0000.0000.0000.000
21A22VAL00.0410.02619.9340.0170.0170.0000.0000.0000.000
22A23VAL00.0010.00916.2360.0140.0140.0000.0000.0000.000
23A24ARG10.6950.83511.9730.2560.2560.0000.0000.0000.000
24A25PHE0-0.046-0.03717.5390.0160.0160.0000.0000.0000.000
25A26ILE0-0.062-0.03220.7690.0110.0110.0000.0000.0000.000
26A27LEU00.0240.00322.1540.0080.0080.0000.0000.0000.000
27A28ASN0-0.064-0.01618.619-0.003-0.0030.0000.0000.0000.000
28A29VAL00.0210.00920.3360.0060.0060.0000.0000.0000.000
29A30PRO0-0.0100.00822.9530.0000.0000.0000.0000.0000.000
30A31PRO00.0830.01425.547-0.005-0.0050.0000.0000.0000.000
31A32GLU-1-0.867-0.91828.8320.0410.0410.0000.0000.0000.000
32A33ASP-1-0.849-0.89526.4400.0220.0220.0000.0000.0000.000
33A34LEU0-0.010-0.03326.649-0.005-0.0050.0000.0000.0000.000
34A35SER0-0.041-0.00729.920-0.003-0.0030.0000.0000.0000.000
35A36THR0-0.018-0.01632.662-0.001-0.0010.0000.0000.0000.000
36A37VAL00.0410.02032.952-0.001-0.0010.0000.0000.0000.000
37A38GLU-1-0.904-0.97133.7400.0020.0020.0000.0000.0000.000
38A39ARG10.8390.92226.886-0.028-0.0280.0000.0000.0000.000
39A40VAL00.0570.03028.529-0.002-0.0020.0000.0000.0000.000
40A41LEU0-0.013-0.00529.156-0.005-0.0050.0000.0000.0000.000
41A42PHE0-0.038-0.01326.005-0.004-0.0040.0000.0000.0000.000
42A43HIS10.8340.88724.170-0.009-0.0090.0000.0000.0000.000
43A44PHE00.0080.01525.065-0.008-0.0080.0000.0000.0000.000
44A45GLU-1-0.816-0.90426.927-0.015-0.0150.0000.0000.0000.000
45A46GLU-1-0.898-0.95522.906-0.002-0.0020.0000.0000.0000.000
46A47ALA00.0080.02122.089-0.007-0.0070.0000.0000.0000.000
47A48SER00.0070.00823.078-0.011-0.0110.0000.0000.0000.000
48A49TRP0-0.015-0.01324.047-0.004-0.0040.0000.0000.0000.000
49A50PHE00.0090.01014.836-0.009-0.0090.0000.0000.0000.000
50A51TYR00.027-0.01520.356-0.022-0.0220.0000.0000.0000.000
51A52THR00.000-0.01022.607-0.013-0.0130.0000.0000.0000.000
52A53ASP-1-0.830-0.91221.635-0.061-0.0610.0000.0000.0000.000
53A54PHE0-0.102-0.06716.691-0.002-0.0020.0000.0000.0000.000
54A55VAL00.0160.01818.528-0.018-0.0180.0000.0000.0000.000
55A56LYS10.8490.94820.2690.0990.0990.0000.0000.0000.000
56A57LEU0-0.017-0.02221.426-0.002-0.0020.0000.0000.0000.000
57A58MET0-0.060-0.00315.646-0.030-0.0300.0000.0000.0000.000
58A59ASN00.0270.01819.699-0.003-0.0030.0000.0000.0000.000
59A60PRO0-0.004-0.00322.2450.0140.0140.0000.0000.0000.000
60A61TYR00.000-0.00425.0680.0160.0160.0000.0000.0000.000
61A62LEU0-0.0210.02022.7080.0100.0100.0000.0000.0000.000
62A63PRO00.0620.03527.1040.0030.0030.0000.0000.0000.000
63A64ASN00.0460.00928.716-0.009-0.0090.0000.0000.0000.000
64A65LEU0-0.0240.00727.9440.0060.0060.0000.0000.0000.000
65A66SER00.0050.00829.5750.0020.0020.0000.0000.0000.000
66A67ILE00.0560.01429.9930.0000.0000.0000.0000.0000.000
67A68LYS10.9240.97231.6310.0350.0350.0000.0000.0000.000
68A69SER00.0460.01233.5820.0020.0020.0000.0000.0000.000
69A70PHE00.0440.01924.2940.0000.0000.0000.0000.0000.000
70A71SER00.0150.00629.740-0.001-0.0010.0000.0000.0000.000
71A72LYS10.8920.93431.3840.0330.0330.0000.0000.0000.000
72A73ILE00.0330.01428.7310.0010.0010.0000.0000.0000.000
73A74VAL00.0080.00426.497-0.002-0.0020.0000.0000.0000.000
74A75ILE0-0.081-0.04629.0330.0020.0020.0000.0000.0000.000
75A76ASP-1-0.944-0.96132.234-0.039-0.0390.0000.0000.0000.000
76A77ILE00.0120.01526.8260.0000.0000.0000.0000.0000.000
77A78CYS0-0.067-0.02326.317-0.002-0.0020.0000.0000.0000.000
78A79PRO00.009-0.00229.0090.0050.0050.0000.0000.0000.000
79A80LEU0-0.034-0.01329.1620.0040.0040.0000.0000.0000.000
80A81ILE0-0.012-0.00426.8590.0050.0050.0000.0000.0000.000
81A82TRP0-0.041-0.02830.2060.0040.0040.0000.0000.0000.000
82A83ASN0-0.013-0.00232.8620.0010.0010.0000.0000.0000.000
83A84TRP0-0.028-0.02933.4120.0010.0010.0000.0000.0000.000
84A85ASP-1-0.897-0.94039.007-0.010-0.0100.0000.0000.0000.000
85A86ILE0-0.048-0.00239.839-0.001-0.0010.0000.0000.0000.000
86A87THR00.0370.00139.3100.0000.0000.0000.0000.0000.000
87A88PRO00.0970.03734.7210.0020.0020.0000.0000.0000.000
88A89GLU-1-0.811-0.88036.710-0.025-0.0250.0000.0000.0000.000
89A90ASN0-0.049-0.03938.5540.0030.0030.0000.0000.0000.000
90A91ALA00.0380.02937.5050.0020.0020.0000.0000.0000.000
91A92LEU0-0.041-0.01733.9660.0020.0020.0000.0000.0000.000
92A93VAL0-0.023-0.01636.8450.0000.0000.0000.0000.0000.000
93A94LYS10.9120.96140.1990.0100.0100.0000.0000.0000.000
94A95PHE00.0420.01437.9280.0010.0010.0000.0000.0000.000
95A96SER00.0220.00733.2590.0030.0030.0000.0000.0000.000
96A97ASN0-0.075-0.04936.2760.0020.0020.0000.0000.0000.000
97A98TYR00.0160.03438.5080.0010.0010.0000.0000.0000.000
98A99LYS10.7980.90932.2570.0030.0030.0000.0000.0000.000
99A100LYS10.9500.96137.740-0.001-0.0010.0000.0000.0000.000
100A101THR0-0.010-0.00235.1010.0010.0010.0000.0000.0000.000
101A102ILE0-0.020-0.01938.141-0.001-0.0010.0000.0000.0000.000
102A103PRO0-0.005-0.00437.2880.0000.0000.0000.0000.0000.000
103A104VAL0-0.054-0.01836.1440.0010.0010.0000.0000.0000.000
104A105ARG10.8150.88335.6830.0230.0230.0000.0000.0000.000
105A106GLY00.0980.04735.9940.0020.0020.0000.0000.0000.000
106A107ALA00.0390.01233.899-0.003-0.0030.0000.0000.0000.000
107A108ALA0-0.038-0.01929.8260.0030.0030.0000.0000.0000.000
108A109ILE00.0320.01731.898-0.004-0.0040.0000.0000.0000.000
109A110PHE00.020-0.00926.968-0.001-0.0010.0000.0000.0000.000
110A111ASN00.0930.03032.536-0.002-0.0020.0000.0000.0000.000
111A112ASP-1-0.829-0.93233.293-0.062-0.0620.0000.0000.0000.000
112A113SER0-0.0240.00532.628-0.003-0.0030.0000.0000.0000.000
113A114LEU00.0030.02527.456-0.006-0.0060.0000.0000.0000.000
114A115SER0-0.090-0.05328.879-0.005-0.0050.0000.0000.0000.000
115A116LYS10.8280.89229.6660.0440.0440.0000.0000.0000.000
116A117ILE00.0230.02828.985-0.002-0.0020.0000.0000.0000.000
117A118LEU00.0280.02531.6100.0040.0040.0000.0000.0000.000
118A119LEU0-0.058-0.02629.9910.0010.0010.0000.0000.0000.000
119A120LEU00.0380.02434.5980.0010.0010.0000.0000.0000.000
120A121ARG10.8460.91536.8100.0060.0060.0000.0000.0000.000
121A122GLY00.0660.04638.656-0.001-0.0010.0000.0000.0000.000
122A123ILE00.0480.02541.2840.0010.0010.0000.0000.0000.000
123A124ASN00.0300.00942.3240.0000.0000.0000.0000.0000.000
124A125SER00.0170.01938.0460.0020.0020.0000.0000.0000.000
125A126LYS10.9020.93137.978-0.006-0.0060.0000.0000.0000.000
126A127HIS00.0070.00630.2330.0010.0010.0000.0000.0000.000
127A128TRP00.0160.00932.337-0.001-0.0010.0000.0000.0000.000
128A129SER0-0.072-0.05832.0210.0010.0010.0000.0000.0000.000
129A130PHE00.0540.03628.1670.0000.0000.0000.0000.0000.000
130A131PRO00.0220.01534.2850.0030.0030.0000.0000.0000.000
131A132ARG10.8640.96232.8620.0070.0070.0000.0000.0000.000
132A133GLY00.0450.02337.9300.0030.0030.0000.0000.0000.000
133A134LYS10.8930.93240.4780.0080.0080.0000.0000.0000.000
134A135ILE00.0540.03340.872-0.001-0.0010.0000.0000.0000.000
135A136GLY00.0330.01843.6410.0020.0020.0000.0000.0000.000
136A137LYS10.7440.84946.2580.0130.0130.0000.0000.0000.000
137A138ASP-1-0.835-0.91147.488-0.015-0.0150.0000.0000.0000.000
138A139GLU-1-0.789-0.88844.770-0.019-0.0190.0000.0000.0000.000
139A140ASP-1-0.861-0.94042.983-0.029-0.0290.0000.0000.0000.000
140A141ASP-1-0.819-0.90738.112-0.030-0.0300.0000.0000.0000.000
141A142VAL00.0140.00238.2190.0000.0000.0000.0000.0000.000
142A143ALA00.0310.03240.5720.0000.0000.0000.0000.0000.000
143A144CYS0-0.043-0.03241.8390.0020.0020.0000.0000.0000.000
144A145CYM-1-0.925-0.93838.152-0.033-0.0330.0000.0000.0000.000
145A146ILE00.011-0.01740.3600.0010.0010.0000.0000.0000.000
146A147ARG10.7730.88342.7290.0190.0190.0000.0000.0000.000
147A148GLU-1-0.784-0.88341.324-0.015-0.0150.0000.0000.0000.000
148A149VAL0-0.0280.00039.5630.0010.0010.0000.0000.0000.000
149A150LYS10.8440.91642.0860.0230.0230.0000.0000.0000.000
150A151GLU-1-0.918-0.95045.492-0.012-0.0120.0000.0000.0000.000
151A152GLU-1-0.907-0.97540.408-0.014-0.0140.0000.0000.0000.000
152A153THR0-0.171-0.09840.1630.0000.0000.0000.0000.0000.000
153A154GLY00.0280.02243.6310.0000.0000.0000.0000.0000.000
154A155PHE0-0.025-0.03641.989-0.001-0.0010.0000.0000.0000.000
155A156ASP-1-0.804-0.86942.843-0.027-0.0270.0000.0000.0000.000
156A157LEU0-0.005-0.01238.147-0.001-0.0010.0000.0000.0000.000
157A158THR0-0.004-0.00141.8990.0000.0000.0000.0000.0000.000
158A159GLY00.0250.00538.317-0.002-0.0020.0000.0000.0000.000
159A160PHE00.0400.00338.051-0.003-0.0030.0000.0000.0000.000
160A161ILE00.0360.01133.6110.0010.0010.0000.0000.0000.000
161A162ASH0-0.073-0.06333.8710.0010.0010.0000.0000.0000.000
162A163ALA0-0.0160.01234.3680.0000.0000.0000.0000.0000.000
163A164ASP-1-0.896-0.95133.078-0.055-0.0550.0000.0000.0000.000
164A165GLN0-0.079-0.02627.698-0.008-0.0080.0000.0000.0000.000
165A166TYR0-0.022-0.01430.4410.0030.0030.0000.0000.0000.000
166A167VAL0-0.025-0.02225.374-0.007-0.0070.0000.0000.0000.000
167A168GLU-1-0.902-0.95128.069-0.031-0.0310.0000.0000.0000.000
168A169ARG10.8900.93321.8120.0290.0290.0000.0000.0000.000
169A170ASN0-0.0190.00628.1930.0000.0000.0000.0000.0000.000
170A171MET0-0.045-0.02927.1300.0040.0040.0000.0000.0000.000
171A172ASN0-0.028-0.02530.7140.0010.0010.0000.0000.0000.000
172A173GLY00.0610.03833.1800.0000.0000.0000.0000.0000.000
173A174LYS10.9430.97334.1970.0010.0010.0000.0000.0000.000
174A175ASN00.0090.01832.7460.0000.0000.0000.0000.0000.000
175A176PHE0-0.011-0.00931.1100.0000.0000.0000.0000.0000.000
176A177LYS10.8510.92131.1940.0370.0370.0000.0000.0000.000
177A178ILE0-0.050-0.01130.3990.0010.0010.0000.0000.0000.000
178A179PHE00.0660.02830.878-0.005-0.0050.0000.0000.0000.000
179A180LEU0-0.010-0.00227.2380.0010.0010.0000.0000.0000.000
180A181VAL00.0440.04731.604-0.002-0.0020.0000.0000.0000.000
181A182LYS10.8620.93831.4550.0700.0700.0000.0000.0000.000
182A183GLY0-0.048-0.01833.7720.0000.0000.0000.0000.0000.000
183A184VAL00.0330.01936.9400.0030.0030.0000.0000.0000.000
184A185PRO0-0.017-0.00438.612-0.002-0.0020.0000.0000.0000.000
185A186GLU-1-0.837-0.92236.598-0.047-0.0470.0000.0000.0000.000
186A187ASP-1-0.942-0.96439.692-0.034-0.0340.0000.0000.0000.000
187A188PHE0-0.041-0.01743.2250.0020.0020.0000.0000.0000.000
188A189GLU-1-0.887-0.93243.736-0.020-0.0200.0000.0000.0000.000
189A190PHE0-0.010-0.00240.8710.0000.0000.0000.0000.0000.000
190A191LYS10.8520.90245.0260.0190.0190.0000.0000.0000.000
191A192PRO0-0.0120.00746.3030.0000.0000.0000.0000.0000.000
192A193GLU-1-0.894-0.94147.652-0.016-0.0160.0000.0000.0000.000
193A194HIS0-0.028-0.00848.9690.0010.0010.0000.0000.0000.000
194A195LYS10.9010.95250.4270.0080.0080.0000.0000.0000.000
195A196ASN00.0100.00547.3350.0000.0000.0000.0000.0000.000
196A204LYN00.0820.04331.223-0.001-0.0010.0000.0000.0000.000
197A205ASP-1-0.845-0.91129.759-0.042-0.0420.0000.0000.0000.000
198A206PHE00.0500.01722.4930.0030.0030.0000.0000.0000.000
199A207LYS10.9060.93724.6630.0550.0550.0000.0000.0000.000
200A208LYS10.8410.89424.7090.0280.0280.0000.0000.0000.000
201A209LEU00.0490.02725.5060.0070.0070.0000.0000.0000.000
202A210SER0-0.040-0.00520.4210.0050.0050.0000.0000.0000.000
203A211LYS10.9550.97020.5430.0630.0630.0000.0000.0000.000
204A212ALA0-0.026-0.00522.0490.0110.0110.0000.0000.0000.000
205A213ILE00.0150.00920.1810.0080.0080.0000.0000.0000.000
206A214THR0-0.041-0.03016.5140.0100.0100.0000.0000.0000.000
207A215LYS10.9160.97918.355-0.004-0.0040.0000.0000.0000.000
208A216ASN00.0400.03218.7080.0080.0080.0000.0000.0000.000
209A224LEU00.022-0.00228.5720.0010.0010.0000.0000.0000.000
210A225VAL00.0710.04327.019-0.003-0.0030.0000.0000.0000.000
211A226ASN0-0.021-0.01924.988-0.008-0.0080.0000.0000.0000.000
212A227SER0-0.059-0.02422.6770.0040.0040.0000.0000.0000.000
213A228MET00.0180.01721.990-0.003-0.0030.0000.0000.0000.000
214A229ILE00.0370.01819.240-0.010-0.0100.0000.0000.0000.000
215A230ARG10.9420.96811.8190.0390.0390.0000.0000.0000.000
216A231PRO00.0820.04918.995-0.015-0.0150.0000.0000.0000.000
217A232LEU00.0570.02221.369-0.007-0.0070.0000.0000.0000.000
218A233SER0-0.101-0.03719.218-0.012-0.0120.0000.0000.0000.000
219A234LEU0-0.020-0.01817.514-0.014-0.0140.0000.0000.0000.000
220A235TYR00.0130.00020.588-0.005-0.0050.0000.0000.0000.000
221A236VAL0-0.045-0.02423.1680.0010.0010.0000.0000.0000.000
222A237LYS10.8490.90016.2180.1860.1860.0000.0000.0000.000
223A238ASN0-0.025-0.01521.561-0.022-0.0220.0000.0000.0000.000
224A239GLU-1-0.841-0.89923.589-0.094-0.0940.0000.0000.0000.000
225A240LYS10.8410.94224.8290.1090.1090.0000.0000.0000.000