FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: LNNQ9

Calculation Name: 4LLA-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 4LLA

Chain ID: A

ChEMBL ID:
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UniProt ID: Q8N423

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 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 196
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1989693.57618
FMO2-HF: Nuclear repulsion 1913890.491496
FMO2-HF: Total energy -75803.084683
FMO2-MP2: Total energy -76023.140209


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:4:SER)


Summations of interaction energy for fragment #1(A:4: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.
-9.033-3.7671.816-2.744-4.337-0.003
Interaction energy analysis for fragmet #1(A:4:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.057 / q_NPA : 0.013
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].
3A6LYS10.8640.9283.827-1.943-0.787-0.009-0.575-0.5720.003
4A7PRO0-0.031-0.0046.5870.1530.1530.0000.0000.0000.000
5A8SER0-0.018-0.0108.861-0.004-0.0040.0000.0000.0000.000
6A9LEU0-0.004-0.01712.621-0.005-0.0050.0000.0000.0000.000
7A10SER00.0100.01815.4850.0000.0000.0000.0000.0000.000
8A11VAL00.0350.01019.046-0.004-0.0040.0000.0000.0000.000
9A12GLN0-0.0350.01522.4280.0020.0020.0000.0000.0000.000
10A13PRO00.033-0.00925.296-0.002-0.0020.0000.0000.0000.000
11A14GLY00.0490.00626.5670.0020.0020.0000.0000.0000.000
12A15PRO00.0200.02524.864-0.002-0.0020.0000.0000.0000.000
13A16VAL0-0.048-0.02426.548-0.005-0.0050.0000.0000.0000.000
14A17MET00.0020.02228.4580.0030.0030.0000.0000.0000.000
15A18ALA0-0.018-0.01031.536-0.003-0.0030.0000.0000.0000.000
16A19PRO0-0.004-0.02434.1330.0010.0010.0000.0000.0000.000
17A20GLY0-0.043-0.00934.5770.0010.0010.0000.0000.0000.000
18A21GLU-1-0.859-0.91832.2110.0210.0210.0000.0000.0000.000
19A22SER0-0.058-0.03728.819-0.001-0.0010.0000.0000.0000.000
20A23LEU00.0280.01124.6320.0010.0010.0000.0000.0000.000
21A24THR00.001-0.00921.857-0.002-0.0020.0000.0000.0000.000
22A25LEU0-0.010-0.00418.6970.0020.0020.0000.0000.0000.000
23A26GLN0-0.042-0.02516.7280.0080.0080.0000.0000.0000.000
24A27CYS0-0.044-0.01611.7870.0140.0140.0000.0000.0000.000
25A28VAL00.0440.02212.1490.0010.0010.0000.0000.0000.000
26A29SER00.011-0.0116.418-0.051-0.0510.0000.0000.0000.000
27A30ASP-1-0.815-0.8936.2690.8750.8750.0000.0000.0000.000
28A31VAL0-0.0200.0032.291-0.6660.0060.553-0.381-0.844-0.002
29A32GLY00.0100.0035.6010.0240.0240.0000.0000.0000.000
30A33TYR0-0.062-0.0412.675-1.686-0.5691.030-0.898-1.249-0.009
31A34ASP-1-0.764-0.8658.2760.0980.0980.0000.0000.0000.000
32A35ARG10.8640.93710.459-0.138-0.1380.0000.0000.0000.000
33A36PHE00.0230.0009.1550.0560.0560.0000.0000.0000.000
34A37VAL0-0.003-0.00911.597-0.025-0.0250.0000.0000.0000.000
35A38LEU0-0.026-0.00313.0890.0010.0010.0000.0000.0000.000
36A39TYR00.000-0.02212.344-0.010-0.0100.0000.0000.0000.000
37A40LYS10.8890.94917.3190.0250.0250.0000.0000.0000.000
38A41GLU-1-0.812-0.91617.434-0.079-0.0790.0000.0000.0000.000
39A42GLY0-0.039-0.01620.1950.0050.0050.0000.0000.0000.000
40A43GLU-1-0.897-0.92721.407-0.028-0.0280.0000.0000.0000.000
41A44ARG10.9300.96320.8980.0430.0430.0000.0000.0000.000
42A45ASP-1-0.931-0.96020.956-0.028-0.0280.0000.0000.0000.000
43A46LEU0-0.004-0.00116.0810.0020.0020.0000.0000.0000.000
44A47ARG10.9450.97718.157-0.004-0.0040.0000.0000.0000.000
45A48GLN00.0280.01914.7140.0210.0210.0000.0000.0000.000
46A49LEU0-0.0010.00415.625-0.008-0.0080.0000.0000.0000.000
47A50PRO0-0.0280.00014.8310.0140.0140.0000.0000.0000.000
48A51GLY00.007-0.00113.227-0.002-0.0020.0000.0000.0000.000
49A52ARG10.9040.94914.156-0.066-0.0660.0000.0000.0000.000
50A53GLN00.0440.00713.0870.0000.0000.0000.0000.0000.000
51A54PRO0-0.0270.01016.249-0.001-0.0010.0000.0000.0000.000
52A55GLN00.0370.01216.586-0.001-0.0010.0000.0000.0000.000
53A56ALA00.0180.00315.7780.0050.0050.0000.0000.0000.000
54A57GLY0-0.008-0.00212.8580.0120.0120.0000.0000.0000.000
55A58LEU0-0.011-0.00911.3490.0390.0390.0000.0000.0000.000
56A59SER00.0070.0099.756-0.019-0.0190.0000.0000.0000.000
57A60GLN0-0.033-0.02411.577-0.005-0.0050.0000.0000.0000.000
58A61ALA00.0110.00913.817-0.004-0.0040.0000.0000.0000.000
59A62ASN00.0120.01015.9740.0010.0010.0000.0000.0000.000
60A63PHE00.018-0.00214.723-0.006-0.0060.0000.0000.0000.000
61A64THR00.0120.02620.1720.0000.0000.0000.0000.0000.000
62A65LEU0-0.052-0.02422.342-0.004-0.0040.0000.0000.0000.000
63A66GLY00.0440.01925.5980.0010.0010.0000.0000.0000.000
64A67PRO00.0220.00229.175-0.001-0.0010.0000.0000.0000.000
65A68VAL0-0.0010.02728.700-0.003-0.0030.0000.0000.0000.000
66A69SER0-0.012-0.01731.061-0.001-0.0010.0000.0000.0000.000
67A70ARG10.9240.94631.4630.0070.0070.0000.0000.0000.000
68A71SER00.007-0.00330.1760.0000.0000.0000.0000.0000.000
69A72TYR00.0160.01326.672-0.002-0.0020.0000.0000.0000.000
70A73GLY00.0280.03926.3320.0020.0020.0000.0000.0000.000
71A74GLY0-0.003-0.01425.146-0.005-0.0050.0000.0000.0000.000
72A75GLN0-0.051-0.02819.933-0.002-0.0020.0000.0000.0000.000
73A76TYR0-0.054-0.03518.637-0.007-0.0070.0000.0000.0000.000
74A77ARG10.8710.92213.6770.0690.0690.0000.0000.0000.000
75A79TYR00.0160.0137.990-0.051-0.0510.0000.0000.0000.000
76A80GLY00.0400.0216.811-0.081-0.0810.0000.0000.0000.000
77A81ALA00.0170.0026.4680.3560.3560.0000.0000.0000.000
78A82HIS00.017-0.0054.421-0.163-0.072-0.001-0.003-0.0860.000
79A83ASN0-0.080-0.0558.797-0.042-0.0420.0000.0000.0000.000
80A84LEU0-0.062-0.01212.219-0.020-0.0200.0000.0000.0000.000
81A85SER00.013-0.0167.514-0.092-0.0920.0000.0000.0000.000
82A86SER00.0160.0079.5430.0570.0570.0000.0000.0000.000
83A87GLU-1-0.913-0.9323.265-3.090-2.6620.026-0.139-0.3150.000
84A88CYS0-0.120-0.0625.3950.4920.4920.0000.0000.0000.000
85A89SER0-0.0110.0012.955-1.835-0.3490.216-0.705-0.9970.005
86A90ALA0-0.0010.0064.043-1.430-1.1140.001-0.043-0.2740.000
87A91PRO00.018-0.0016.0660.1010.1010.0000.0000.0000.000
88A92SER0-0.011-0.0089.551-0.028-0.0280.0000.0000.0000.000
89A93ASP-1-0.847-0.91311.4210.0280.0280.0000.0000.0000.000
90A94PRO0-0.032-0.01514.5760.0060.0060.0000.0000.0000.000
91A95LEU00.0110.00317.5090.0080.0080.0000.0000.0000.000
92A96ASP-1-0.820-0.91319.927-0.010-0.0100.0000.0000.0000.000
93A97ILE0-0.043-0.01322.9110.0060.0060.0000.0000.0000.000
94A98LEU0-0.021-0.02225.612-0.005-0.0050.0000.0000.0000.000
95A99ILE00.0120.01529.2670.0020.0020.0000.0000.0000.000
96A100THR0-0.016-0.00532.264-0.002-0.0020.0000.0000.0000.000
97A101GLY00.019-0.00535.6770.0000.0000.0000.0000.0000.000
98A102GLN0-0.036-0.00735.118-0.003-0.0030.0000.0000.0000.000
99A103ILE0-0.0310.00137.777-0.002-0.0020.0000.0000.0000.000
100A104ARG10.9300.96240.4010.0070.0070.0000.0000.0000.000
101A105GLY0-0.022-0.02943.1340.0000.0000.0000.0000.0000.000
102A106THR00.0380.00643.4500.0000.0000.0000.0000.0000.000
103A107PRO0-0.0340.00440.7880.0000.0000.0000.0000.0000.000
104A108PHE00.016-0.01844.0710.0010.0010.0000.0000.0000.000
105A109ILE0-0.0120.01140.425-0.001-0.0010.0000.0000.0000.000
106A110SER0-0.023-0.01344.3030.0000.0000.0000.0000.0000.000
107A111VAL00.0230.00243.5540.0000.0000.0000.0000.0000.000
108A112GLN0-0.0090.04345.386-0.001-0.0010.0000.0000.0000.000
109A113PRO00.040-0.00845.8540.0010.0010.0000.0000.0000.000
110A114GLY00.040-0.00747.888-0.001-0.0010.0000.0000.0000.000
111A115PRO0-0.0160.00346.0430.0010.0010.0000.0000.0000.000
112A116THR0-0.021-0.01246.4220.0010.0010.0000.0000.0000.000
113A117VAL00.0170.00343.449-0.001-0.0010.0000.0000.0000.000
114A118ALA00.0210.02745.9130.0010.0010.0000.0000.0000.000
115A119SER0-0.006-0.03341.3090.0010.0010.0000.0000.0000.000
116A120GLY0-0.040-0.01841.7700.0000.0000.0000.0000.0000.000
117A121GLU-1-0.890-0.92242.7800.0210.0210.0000.0000.0000.000
118A122ASN0-0.023-0.03442.5400.0020.0020.0000.0000.0000.000
119A123VAL00.0630.03041.694-0.001-0.0010.0000.0000.0000.000
120A124THR00.0030.01240.9490.0010.0010.0000.0000.0000.000
121A125LEU00.0130.00838.9370.0000.0000.0000.0000.0000.000
122A126LEU00.0010.00540.429-0.001-0.0010.0000.0000.0000.000
123A127CYS0-0.0250.01737.4130.0010.0010.0000.0000.0000.000
124A128GLN00.033-0.01142.151-0.001-0.0010.0000.0000.0000.000
125A129SER0-0.017-0.02043.9100.0000.0000.0000.0000.0000.000
126A130TRP00.0380.02845.948-0.001-0.0010.0000.0000.0000.000
127A131ARG10.9100.95145.8520.0000.0000.0000.0000.0000.000
128A132GLN00.0640.05242.6090.0000.0000.0000.0000.0000.000
129A133PHE0-0.0080.01439.5170.0000.0000.0000.0000.0000.000
130A134HIS00.0370.05336.8160.0000.0000.0000.0000.0000.000
131A135THR0-0.0100.00432.9010.0000.0000.0000.0000.0000.000
132A136PHE00.014-0.00236.0390.0000.0000.0000.0000.0000.000
133A137LEU0-0.018-0.02330.8650.0000.0000.0000.0000.0000.000
134A138LEU00.0020.02433.7210.0000.0000.0000.0000.0000.000
135A139THR0-0.030-0.02232.0710.0020.0020.0000.0000.0000.000
136A140LYS10.8780.92732.740-0.040-0.0400.0000.0000.0000.000
137A141ALA0-0.031-0.02533.0190.0010.0010.0000.0000.0000.000
138A142GLY00.017-0.00231.4980.0020.0020.0000.0000.0000.000
139A143ALA00.007-0.00528.157-0.001-0.0010.0000.0000.0000.000
140A144ALA0-0.0290.00129.044-0.001-0.0010.0000.0000.0000.000
141A145ASP-1-0.900-0.96823.0770.0660.0660.0000.0000.0000.000
142A146ALA0-0.1210.01725.050-0.001-0.0010.0000.0000.0000.000
143A147PRO00.0410.00925.7410.0010.0010.0000.0000.0000.000
144A148LEU00.043-0.01028.640-0.002-0.0020.0000.0000.0000.000
145A149ARG10.8680.93527.880-0.001-0.0010.0000.0000.0000.000
146A150LEU00.0080.01631.6650.0000.0000.0000.0000.0000.000
147A151ARG10.9390.96934.0910.0030.0030.0000.0000.0000.000
148A152SER0-0.067-0.08235.9180.0020.0020.0000.0000.0000.000
149A153ILE00.0290.00739.463-0.002-0.0020.0000.0000.0000.000
150A154HIS0-0.083-0.05642.2420.0000.0000.0000.0000.0000.000
151A155GLU-1-0.892-0.93145.4540.0000.0000.0000.0000.0000.000
152A156TYR0-0.0080.02248.3080.0010.0010.0000.0000.0000.000
153A157PRO0-0.016-0.01551.1880.0000.0000.0000.0000.0000.000
154A158LYS10.8600.91648.166-0.005-0.0050.0000.0000.0000.000
155A159TYR00.0130.01243.205-0.001-0.0010.0000.0000.0000.000
156A160GLN00.0840.02443.2830.0010.0010.0000.0000.0000.000
157A161ALA00.0050.00038.279-0.002-0.0020.0000.0000.0000.000
158A162GLU-1-0.904-0.95140.1520.0110.0110.0000.0000.0000.000
159A163PHE0-0.025-0.03434.0750.0000.0000.0000.0000.0000.000
160A164PRO0-0.008-0.00136.4920.0010.0010.0000.0000.0000.000
161A165MET0-0.039-0.01535.1380.0020.0020.0000.0000.0000.000
162A166SER00.002-0.01237.8690.0000.0000.0000.0000.0000.000
163A167PRO0-0.043-0.02238.0060.0010.0010.0000.0000.0000.000
164A168VAL00.0130.05837.7020.0020.0020.0000.0000.0000.000
165A169THR00.001-0.02835.5800.0020.0020.0000.0000.0000.000
166A170SER00.038-0.01537.984-0.001-0.0010.0000.0000.0000.000
167A171ALA00.0210.01933.029-0.001-0.0010.0000.0000.0000.000
168A172HIS00.0480.02234.8280.0010.0010.0000.0000.0000.000
169A173ALA00.0200.03536.372-0.002-0.0020.0000.0000.0000.000
170A174GLY00.0180.02337.1610.0030.0030.0000.0000.0000.000
171A175THR0-0.035-0.02738.160-0.002-0.0020.0000.0000.0000.000
172A176TYR0-0.030-0.02735.0690.0020.0020.0000.0000.0000.000
173A177ARG10.9580.98437.444-0.020-0.0200.0000.0000.0000.000
174A179TYR00.0270.00035.5060.0000.0000.0000.0000.0000.000
175A180GLY00.0570.02937.4530.0000.0000.0000.0000.0000.000
176A181SER0-0.011-0.02534.183-0.001-0.0010.0000.0000.0000.000
177A182LEU0-0.015-0.02136.1160.0000.0000.0000.0000.0000.000
178A183ASN00.041-0.01233.8610.0010.0010.0000.0000.0000.000
179A184SER0-0.055-0.02133.338-0.002-0.0020.0000.0000.0000.000
180A185ASP-1-0.799-0.90830.688-0.018-0.0180.0000.0000.0000.000
181A186PRO0-0.0130.01429.5200.0030.0030.0000.0000.0000.000
182A187TYR00.0030.02124.3160.0020.0020.0000.0000.0000.000
183A188LEU0-0.052-0.00329.8960.0030.0030.0000.0000.0000.000
184A189LEU0-0.007-0.00432.098-0.001-0.0010.0000.0000.0000.000
185A190SER0-0.036-0.02535.507-0.001-0.0010.0000.0000.0000.000
186A191HIS00.0340.01038.2400.0020.0020.0000.0000.0000.000
187A192PRO00.0010.01138.740-0.001-0.0010.0000.0000.0000.000
188A193SER0-0.0190.00040.278-0.001-0.0010.0000.0000.0000.000
189A194GLU-1-0.905-0.96642.5710.0130.0130.0000.0000.0000.000
190A195PRO0-0.062-0.02641.9240.0000.0000.0000.0000.0000.000
191A196LEU0-0.0010.00442.084-0.001-0.0010.0000.0000.0000.000
192A197GLU-1-0.850-0.92141.3180.0280.0280.0000.0000.0000.000
193A198LEU0-0.040-0.00939.778-0.001-0.0010.0000.0000.0000.000
194A199VAL00.0180.01141.7190.0020.0020.0000.0000.0000.000
195A200VAL0-0.0050.01040.6340.0000.0000.0000.0000.0000.000
196A201SER0-0.025-0.01143.8090.0000.0000.0000.0000.0000.000