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: G66K1

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 OptH
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 -2778719.813617
FMO2-HF: Nuclear repulsion 2688355.953142
FMO2-HF: Total energy -90363.860475
FMO2-MP2: Total energy -90630.240869


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.
-0.9710.274-0.002-0.612-0.6310.002
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 : -0.019 / q_NPA : -0.027
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].
3A4PRO0-0.013-0.0143.707-2.611-1.366-0.002-0.612-0.6310.002
4A5LEU00.0090.0175.1360.4300.4300.0000.0000.0000.000
5A6LEU00.004-0.0057.488-0.299-0.2990.0000.0000.0000.000
6A7ARG10.9290.95310.2090.3100.3100.0000.0000.0000.000
7A8PRO00.0660.03312.514-0.030-0.0300.0000.0000.0000.000
8A9PHE00.0270.01015.208-0.005-0.0050.0000.0000.0000.000
9A10GLU-1-0.977-0.99416.025-0.093-0.0930.0000.0000.0000.000
10A11THR0-0.018-0.01517.940-0.002-0.0020.0000.0000.0000.000
11A12VAL0-0.0390.01419.5140.0010.0010.0000.0000.0000.000
12A13SER00.0300.01421.464-0.015-0.0150.0000.0000.0000.000
13A14LEU00.0400.01523.5440.0110.0110.0000.0000.0000.000
14A15GLU-1-0.875-0.95325.1290.1170.1170.0000.0000.0000.000
15A16ASN00.016-0.00821.148-0.006-0.0060.0000.0000.0000.000
16A17ALA0-0.013-0.01520.3470.0240.0240.0000.0000.0000.000
17A18VAL00.0180.00420.8430.0150.0150.0000.0000.0000.000
18A19GLU-1-0.845-0.93921.9190.2350.2350.0000.0000.0000.000
19A20ASP-1-0.892-0.93215.7330.3720.3720.0000.0000.0000.000
20A21LEU0-0.030-0.03018.4480.0280.0280.0000.0000.0000.000
21A22VAL00.0450.03519.8900.0000.0000.0000.0000.0000.000
22A23VAL00.0050.00916.0720.0060.0060.0000.0000.0000.000
23A24ARG10.7600.88111.959-0.325-0.3250.0000.0000.0000.000
24A25PHE0-0.049-0.03717.4940.0050.0050.0000.0000.0000.000
25A26ILE0-0.060-0.02620.733-0.017-0.0170.0000.0000.0000.000
26A27LEU00.0290.00522.398-0.006-0.0060.0000.0000.0000.000
27A28ASN0-0.071-0.02318.9290.0050.0050.0000.0000.0000.000
28A29VAL00.0150.01020.7170.0070.0070.0000.0000.0000.000
29A30PRO00.0010.01023.4000.0010.0010.0000.0000.0000.000
30A31PRO00.0760.00926.073-0.013-0.0130.0000.0000.0000.000
31A32GLU-1-0.879-0.92929.3210.1380.1380.0000.0000.0000.000
32A33ASP-1-0.858-0.91726.5590.1440.1440.0000.0000.0000.000
33A34LEU0-0.007-0.03126.7540.0070.0070.0000.0000.0000.000
34A35SER0-0.053-0.00330.239-0.009-0.0090.0000.0000.0000.000
35A36THR0-0.013-0.01532.938-0.010-0.0100.0000.0000.0000.000
36A37VAL00.0460.02133.1210.0050.0050.0000.0000.0000.000
37A38GLU-1-0.923-0.97633.7500.0810.0810.0000.0000.0000.000
38A39ARG10.8480.93926.358-0.131-0.1310.0000.0000.0000.000
39A40VAL00.0630.03028.2150.0030.0030.0000.0000.0000.000
40A41LEU0-0.005-0.00729.1260.0000.0000.0000.0000.0000.000
41A42PHE0-0.056-0.01925.995-0.008-0.0080.0000.0000.0000.000
42A43HIS10.8650.92223.616-0.175-0.1750.0000.0000.0000.000
43A44PHE00.0170.01525.0410.0050.0050.0000.0000.0000.000
44A45GLU-1-0.925-0.96526.9100.0640.0640.0000.0000.0000.000
45A46GLU-1-0.943-0.99322.6290.1420.1420.0000.0000.0000.000
46A47ALA00.0150.02122.092-0.001-0.0010.0000.0000.0000.000
47A48SER00.0270.01723.064-0.007-0.0070.0000.0000.0000.000
48A49TRP0-0.018-0.01624.170-0.009-0.0090.0000.0000.0000.000
49A50PHE0-0.0150.00914.963-0.008-0.0080.0000.0000.0000.000
50A51TYR00.038-0.01820.358-0.004-0.0040.0000.0000.0000.000
51A52THR0-0.013-0.00722.600-0.012-0.0120.0000.0000.0000.000
52A53ASP-1-0.876-0.95721.7330.0110.0110.0000.0000.0000.000
53A54PHE0-0.118-0.07217.410-0.030-0.0300.0000.0000.0000.000
54A55VAL0-0.0020.01018.646-0.012-0.0120.0000.0000.0000.000
55A56LYS10.9160.97620.262-0.020-0.0200.0000.0000.0000.000
56A57LEU0-0.049-0.03121.429-0.010-0.0100.0000.0000.0000.000
57A58MET0-0.044-0.00315.933-0.022-0.0220.0000.0000.0000.000
58A59ASN00.0400.02819.705-0.021-0.0210.0000.0000.0000.000
59A60PRO0-0.015-0.00222.2340.0070.0070.0000.0000.0000.000
60A61TYR0-0.009-0.00824.7770.0000.0000.0000.0000.0000.000
61A62LEU0-0.0300.01522.6160.0070.0070.0000.0000.0000.000
62A63PRO00.0480.02527.084-0.009-0.0090.0000.0000.0000.000
63A64ASN00.0410.00428.7030.0010.0010.0000.0000.0000.000
64A65LEU0-0.0310.00027.8560.0010.0010.0000.0000.0000.000
65A66SER0-0.0130.00629.569-0.001-0.0010.0000.0000.0000.000
66A67ILE00.0670.01330.0470.0040.0040.0000.0000.0000.000
67A68LYS10.9200.97631.620-0.032-0.0320.0000.0000.0000.000
68A69SER00.0790.03233.7220.0030.0030.0000.0000.0000.000
69A70PHE00.0210.01124.1780.0020.0020.0000.0000.0000.000
70A71SER00.022-0.00129.7030.0080.0080.0000.0000.0000.000
71A72LYS10.9530.98131.350-0.055-0.0550.0000.0000.0000.000
72A73ILE00.0210.00828.6580.0010.0010.0000.0000.0000.000
73A74VAL00.001-0.00126.3720.0070.0070.0000.0000.0000.000
74A75ILE0-0.080-0.04528.9820.0070.0070.0000.0000.0000.000
75A76ASP-1-0.949-0.96432.1910.0930.0930.0000.0000.0000.000
76A77ILE00.0100.00826.7200.0040.0040.0000.0000.0000.000
77A78CYS0-0.051-0.01326.2470.0150.0150.0000.0000.0000.000
78A79PRO00.011-0.00128.9750.0020.0020.0000.0000.0000.000
79A80LEU0-0.046-0.01729.071-0.003-0.0030.0000.0000.0000.000
80A81ILE0-0.028-0.00726.9440.0010.0010.0000.0000.0000.000
81A82TRP0-0.058-0.03030.367-0.004-0.0040.0000.0000.0000.000
82A83ASN00.0240.01033.571-0.004-0.0040.0000.0000.0000.000
83A84TRP0-0.021-0.02233.732-0.006-0.0060.0000.0000.0000.000
84A85ASP-1-0.890-0.93739.1440.0710.0710.0000.0000.0000.000
85A86ILE0-0.057-0.00539.968-0.003-0.0030.0000.0000.0000.000
86A87THR00.0630.04139.2690.0030.0030.0000.0000.0000.000
87A88PRO00.1070.03634.683-0.002-0.0020.0000.0000.0000.000
88A89GLU-1-0.892-0.94636.6750.0640.0640.0000.0000.0000.000
89A90ASN0-0.058-0.05838.526-0.006-0.0060.0000.0000.0000.000
90A91ALA00.0320.02637.476-0.003-0.0030.0000.0000.0000.000
91A92LEU0-0.040-0.02233.659-0.002-0.0020.0000.0000.0000.000
92A93VAL0-0.034-0.02536.826-0.004-0.0040.0000.0000.0000.000
93A94LYS10.9330.96740.186-0.052-0.0520.0000.0000.0000.000
94A95PHE00.0370.01937.872-0.002-0.0020.0000.0000.0000.000
95A96SER00.0010.00333.6290.0000.0000.0000.0000.0000.000
96A97ASN0-0.045-0.02936.198-0.007-0.0070.0000.0000.0000.000
97A98TYR00.0200.03638.507-0.004-0.0040.0000.0000.0000.000
98A99LYS10.8810.95432.021-0.072-0.0720.0000.0000.0000.000
99A100LYS10.9580.96537.751-0.026-0.0260.0000.0000.0000.000
100A101THR0-0.019-0.00535.124-0.003-0.0030.0000.0000.0000.000
101A102ILE0-0.030-0.02138.195-0.002-0.0020.0000.0000.0000.000
102A103PRO0-0.009-0.00637.320-0.001-0.0010.0000.0000.0000.000
103A104VAL0-0.071-0.02636.157-0.003-0.0030.0000.0000.0000.000
104A105ARG10.8620.92635.619-0.012-0.0120.0000.0000.0000.000
105A106GLY00.1000.05236.072-0.002-0.0020.0000.0000.0000.000
106A107ALA00.0400.00733.9410.0020.0020.0000.0000.0000.000
107A108ALA0-0.039-0.01629.925-0.004-0.0040.0000.0000.0000.000
108A109ILE00.0270.01731.961-0.001-0.0010.0000.0000.0000.000
109A110PHE00.026-0.00627.031-0.009-0.0090.0000.0000.0000.000
110A111ASN00.1640.08132.5060.0020.0020.0000.0000.0000.000
111A112ASP-1-0.857-0.95433.363-0.051-0.0510.0000.0000.0000.000
112A113SER0-0.033-0.00333.720-0.004-0.0040.0000.0000.0000.000
113A114LEU00.0090.02827.076-0.009-0.0090.0000.0000.0000.000
114A115SER0-0.130-0.07428.964-0.010-0.0100.0000.0000.0000.000
115A116LYS10.8790.92029.7570.0650.0650.0000.0000.0000.000
116A117ILE00.0430.04329.0120.0020.0020.0000.0000.0000.000
117A118LEU00.0280.02431.692-0.002-0.0020.0000.0000.0000.000
118A119LEU0-0.042-0.02430.4460.0030.0030.0000.0000.0000.000
119A120LEU00.0400.02734.680-0.003-0.0030.0000.0000.0000.000
120A121ARG10.8980.94836.7700.0400.0400.0000.0000.0000.000
121A122GLY00.0570.03538.5290.0010.0010.0000.0000.0000.000
122A123ILE00.0220.01341.125-0.002-0.0020.0000.0000.0000.000
123A124ASN00.0270.01141.716-0.001-0.0010.0000.0000.0000.000
124A125SER00.0020.00637.741-0.001-0.0010.0000.0000.0000.000
125A126LYS10.8880.92737.4340.0300.0300.0000.0000.0000.000
126A127HIS0-0.004-0.00430.271-0.002-0.0020.0000.0000.0000.000
127A128TRP00.0160.00832.2570.0020.0020.0000.0000.0000.000
128A129SER0-0.083-0.06231.9250.0010.0010.0000.0000.0000.000
129A130PHE00.0460.03328.186-0.002-0.0020.0000.0000.0000.000
130A131PRO00.0270.01834.3550.0020.0020.0000.0000.0000.000
131A132ARG10.8650.96432.7700.0220.0220.0000.0000.0000.000
132A133GLY00.1260.07237.9900.0000.0000.0000.0000.0000.000
133A134LYS10.8230.89240.4940.0030.0030.0000.0000.0000.000
134A135ILE00.0380.02140.963-0.001-0.0010.0000.0000.0000.000
135A136GLY00.0280.01643.677-0.001-0.0010.0000.0000.0000.000
136A137LYS10.8490.92146.284-0.010-0.0100.0000.0000.0000.000
137A138ASP-1-0.921-0.97347.5330.0120.0120.0000.0000.0000.000
138A139GLU-1-0.821-0.91245.0130.0030.0030.0000.0000.0000.000
139A140ASP-1-0.874-0.93942.9520.0070.0070.0000.0000.0000.000
140A141ASP-1-0.904-0.97438.2420.0150.0150.0000.0000.0000.000
141A142VAL00.0170.00938.378-0.002-0.0020.0000.0000.0000.000
142A143ALA00.0220.02140.603-0.003-0.0030.0000.0000.0000.000
143A144CYS0-0.041-0.01241.904-0.001-0.0010.0000.0000.0000.000
144A145CYM-1-0.912-0.93637.848-0.011-0.0110.0000.0000.0000.000
145A146ILE0-0.012-0.02340.404-0.003-0.0030.0000.0000.0000.000
146A147ARG10.9230.97242.7780.0000.0000.0000.0000.0000.000
147A148GLU-1-0.828-0.92941.487-0.008-0.0080.0000.0000.0000.000
148A149VAL0-0.0180.00939.323-0.002-0.0020.0000.0000.0000.000
149A150LYS10.8440.93642.1470.0080.0080.0000.0000.0000.000
150A151GLU-1-0.973-0.98245.480-0.010-0.0100.0000.0000.0000.000
151A152GLU-1-0.880-0.96140.635-0.019-0.0190.0000.0000.0000.000
152A153THR0-0.191-0.10940.255-0.003-0.0030.0000.0000.0000.000
153A154GLY00.0260.02143.704-0.001-0.0010.0000.0000.0000.000
154A155PHE0-0.032-0.04041.938-0.001-0.0010.0000.0000.0000.000
155A156ASP-1-0.795-0.87642.904-0.014-0.0140.0000.0000.0000.000
156A157LEU0-0.001-0.00938.380-0.001-0.0010.0000.0000.0000.000
157A158THR0-0.019-0.01641.9630.0010.0010.0000.0000.0000.000
158A159GLY00.0280.01238.432-0.001-0.0010.0000.0000.0000.000
159A160PHE00.0320.00138.208-0.001-0.0010.0000.0000.0000.000
160A161ILE00.0390.01133.7810.0030.0030.0000.0000.0000.000
161A162ASH0-0.019-0.01334.0120.0020.0020.0000.0000.0000.000
162A163ALA0-0.0160.01434.3580.0010.0010.0000.0000.0000.000
163A164ASP-1-0.900-0.95833.0910.0180.0180.0000.0000.0000.000
164A165GLN0-0.062-0.01827.836-0.003-0.0030.0000.0000.0000.000
165A166TYR0-0.032-0.01430.621-0.004-0.0040.0000.0000.0000.000
166A167VAL0-0.023-0.02225.265-0.001-0.0010.0000.0000.0000.000
167A168GLU-1-0.941-0.96928.1010.0350.0350.0000.0000.0000.000
168A169ARG10.9970.99421.749-0.023-0.0230.0000.0000.0000.000
169A170ASN00.0130.03028.222-0.010-0.0100.0000.0000.0000.000
170A171MET0-0.065-0.03627.5890.0030.0030.0000.0000.0000.000
171A172ASN0-0.022-0.02430.6860.0010.0010.0000.0000.0000.000
172A173GLY00.0650.04133.028-0.003-0.0030.0000.0000.0000.000
173A174LYS10.9260.96434.229-0.007-0.0070.0000.0000.0000.000
174A175ASN00.0150.01432.478-0.002-0.0020.0000.0000.0000.000
175A176PHE00.001-0.01031.124-0.004-0.0040.0000.0000.0000.000
176A177LYS10.9190.96731.227-0.015-0.0150.0000.0000.0000.000
177A178ILE0-0.045-0.00430.577-0.001-0.0010.0000.0000.0000.000
178A179PHE00.0450.00830.9190.0020.0020.0000.0000.0000.000
179A180LEU0-0.042-0.01927.398-0.006-0.0060.0000.0000.0000.000
180A181VAL00.0420.01931.6500.0020.0020.0000.0000.0000.000
181A182LYS10.8990.95731.7180.0450.0450.0000.0000.0000.000
182A183GLY0-0.045-0.01533.8280.0030.0030.0000.0000.0000.000
183A184VAL00.0390.02037.0000.0040.0040.0000.0000.0000.000
184A185PRO0-0.026-0.00638.684-0.004-0.0040.0000.0000.0000.000
185A186GLU-1-0.974-1.01037.593-0.068-0.0680.0000.0000.0000.000
186A187ASP-1-0.949-0.97539.775-0.051-0.0510.0000.0000.0000.000
187A188PHE0-0.036-0.00243.3110.0010.0010.0000.0000.0000.000
188A189GLU-1-0.960-0.97543.820-0.038-0.0380.0000.0000.0000.000
189A190PHE0-0.007-0.00341.1300.0020.0020.0000.0000.0000.000
190A191LYS10.9250.93945.1080.0270.0270.0000.0000.0000.000
191A192PRO0-0.0080.01346.3020.0010.0010.0000.0000.0000.000
192A193GLU-1-0.890-0.93947.729-0.020-0.0200.0000.0000.0000.000
193A194HIS0-0.0030.00149.1220.0020.0020.0000.0000.0000.000
194A195LYS10.8990.95450.4900.0120.0120.0000.0000.0000.000
195A196ASN00.0220.00947.3040.0010.0010.0000.0000.0000.000
196A204LYN00.1150.06231.246-0.001-0.0010.0000.0000.0000.000
197A205ASP-1-0.945-0.98929.664-0.100-0.1000.0000.0000.0000.000
198A206PHE00.0360.01522.575-0.007-0.0070.0000.0000.0000.000
199A207LYS10.9050.94324.7560.1090.1090.0000.0000.0000.000
200A208LYS10.8970.94124.7190.0820.0820.0000.0000.0000.000
201A209LEU00.0480.02325.484-0.002-0.0020.0000.0000.0000.000
202A210SER0-0.050-0.01420.525-0.006-0.0060.0000.0000.0000.000
203A211LYS10.9560.96620.4000.1940.1940.0000.0000.0000.000
204A212ALA0-0.029-0.00921.674-0.006-0.0060.0000.0000.0000.000
205A213ILE00.0160.01019.8740.0050.0050.0000.0000.0000.000
206A214THR0-0.034-0.01216.3550.0020.0020.0000.0000.0000.000
207A215LYS10.9230.97517.7550.1570.1570.0000.0000.0000.000
208A216ASN00.0360.03017.9280.0160.0160.0000.0000.0000.000
209A224LEU00.012-0.01028.485-0.001-0.0010.0000.0000.0000.000
210A225VAL00.0690.05027.1240.0010.0010.0000.0000.0000.000
211A226ASN0-0.021-0.01224.857-0.003-0.0030.0000.0000.0000.000
212A227SER0-0.066-0.03622.613-0.002-0.0020.0000.0000.0000.000
213A228MET00.0280.01422.0500.0030.0030.0000.0000.0000.000
214A229ILE00.0430.02219.123-0.008-0.0080.0000.0000.0000.000
215A230ARG10.9370.96312.0100.1810.1810.0000.0000.0000.000
216A231PRO00.0870.05619.060-0.013-0.0130.0000.0000.0000.000
217A232LEU00.0550.01921.418-0.004-0.0040.0000.0000.0000.000
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