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

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FMODB ID: 988L2

Calculation Name: 4LLA-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4LLA

Chain ID: A

ChEMBL ID:

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 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 196
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1989679.442103
FMO2-HF: Nuclear repulsion 1913875.543237
FMO2-HF: Total energy -75803.898866
FMO2-MP2: Total energy -76023.951472


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.
-9.913-4.2963.115-3.422-5.305-0.019
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 : 0.053 / q_NPA : 0.017
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].
3A6LYS10.8720.9373.865-1.348-0.4500.001-0.396-0.5030.002
4A7PRO0-0.041-0.0096.2760.6060.6060.0000.0000.0000.000
5A8SER0-0.021-0.0178.488-0.028-0.0280.0000.0000.0000.000
6A9LEU0-0.018-0.03312.169-0.040-0.0400.0000.0000.0000.000
7A10SER00.0010.01714.9230.0460.0460.0000.0000.0000.000
8A11VAL00.0360.00418.572-0.022-0.0220.0000.0000.0000.000
9A12GLN0-0.0340.00421.9010.0330.0330.0000.0000.0000.000
10A13PRO00.0380.00524.940-0.010-0.0100.0000.0000.0000.000
11A14GLY00.0470.01125.9460.0110.0110.0000.0000.0000.000
12A15PRO00.0160.02524.165-0.009-0.0090.0000.0000.0000.000
13A16VAL0-0.059-0.03125.770-0.011-0.0110.0000.0000.0000.000
14A17MET00.0220.03128.1380.0080.0080.0000.0000.0000.000
15A18ALA0-0.0010.00431.132-0.002-0.0020.0000.0000.0000.000
16A19PRO0-0.038-0.04133.432-0.004-0.0040.0000.0000.0000.000
17A20GLY0-0.027-0.00434.1570.0070.0070.0000.0000.0000.000
18A21GLU-1-0.845-0.90631.830-0.083-0.0830.0000.0000.0000.000
19A22SER0-0.088-0.06528.060-0.006-0.0060.0000.0000.0000.000
20A23LEU00.0220.01224.0410.0070.0070.0000.0000.0000.000
21A24THR0-0.045-0.02421.509-0.017-0.0170.0000.0000.0000.000
22A25LEU00.0390.02018.1410.0060.0060.0000.0000.0000.000
23A26GLN0-0.045-0.02116.782-0.004-0.0040.0000.0000.0000.000
24A27CYS0-0.042-0.01411.5360.0200.0200.0000.0000.0000.000
25A28VAL00.0470.02012.1780.0360.0360.0000.0000.0000.000
26A29SER00.006-0.0026.552-0.031-0.0310.0000.0000.0000.000
27A30ASP-1-0.753-0.8626.8671.3951.3950.0000.0000.0000.000
28A31VAL0-0.040-0.0032.482-0.4130.3600.394-0.356-0.8100.000
29A32GLY00.0150.0065.535-0.332-0.3320.0000.0000.0000.000
30A33TYR0-0.053-0.0422.593-1.880-0.8101.627-1.172-1.524-0.012
31A34ASP-1-0.751-0.8538.0400.1760.1760.0000.0000.0000.000
32A35ARG10.8180.9139.9760.4450.4450.0000.0000.0000.000
33A36PHE00.0270.0128.597-0.093-0.0930.0000.0000.0000.000
34A37VAL0-0.013-0.01811.0160.1040.1040.0000.0000.0000.000
35A38LEU0-0.0050.01712.444-0.104-0.1040.0000.0000.0000.000
36A39TYR0-0.007-0.02211.751-0.036-0.0360.0000.0000.0000.000
37A40LYS10.8700.94216.7800.2860.2860.0000.0000.0000.000
38A41GLU-1-0.822-0.90216.619-0.627-0.6270.0000.0000.0000.000
39A42GLY0-0.027-0.01319.4010.0430.0430.0000.0000.0000.000
40A43GLU-1-0.901-0.93420.865-0.252-0.2520.0000.0000.0000.000
41A44ARG10.8750.92220.4390.2630.2630.0000.0000.0000.000
42A45ASP-1-0.885-0.92320.577-0.324-0.3240.0000.0000.0000.000
43A46LEU0-0.015-0.01115.698-0.021-0.0210.0000.0000.0000.000
44A47ARG10.9460.97017.3330.3300.3300.0000.0000.0000.000
45A48GLN00.0260.02313.823-0.091-0.0910.0000.0000.0000.000
46A49LEU0-0.009-0.00414.8840.0500.0500.0000.0000.0000.000
47A50PRO0-0.0210.00214.275-0.030-0.0300.0000.0000.0000.000
48A51GLY00.021-0.00312.941-0.004-0.0040.0000.0000.0000.000
49A52ARG10.8670.93313.9200.0720.0720.0000.0000.0000.000
50A53GLN00.0370.01012.756-0.015-0.0150.0000.0000.0000.000
51A54PRO0-0.029-0.00115.9840.0140.0140.0000.0000.0000.000
52A55GLN00.003-0.00616.699-0.018-0.0180.0000.0000.0000.000
53A56ALA00.0280.00915.9530.0190.0190.0000.0000.0000.000
54A57GLY0-0.006-0.00313.1400.0040.0040.0000.0000.0000.000
55A58LEU0-0.0060.00211.3930.0760.0760.0000.0000.0000.000
56A59SER0-0.021-0.0059.639-0.030-0.0300.0000.0000.0000.000
57A60GLN0-0.004-0.00811.161-0.072-0.0720.0000.0000.0000.000
58A61ALA00.0080.00713.3910.0160.0160.0000.0000.0000.000
59A62ASN00.0320.01715.361-0.010-0.0100.0000.0000.0000.000
60A63PHE00.0240.00213.9620.0100.0100.0000.0000.0000.000
61A64THR00.0100.00619.4680.0020.0020.0000.0000.0000.000
62A65LEU0-0.035-0.00221.958-0.009-0.0090.0000.0000.0000.000
63A66GLY00.0530.03524.8250.0150.0150.0000.0000.0000.000
64A67PRO00.021-0.00128.401-0.004-0.0040.0000.0000.0000.000
65A68VAL00.0400.03928.417-0.009-0.0090.0000.0000.0000.000
66A69SER0-0.013-0.01630.6350.0130.0130.0000.0000.0000.000
67A70ARG10.8950.94630.8970.1150.1150.0000.0000.0000.000
68A71SER00.0240.00829.294-0.004-0.0040.0000.0000.0000.000
69A72TYR0-0.0030.00326.337-0.022-0.0220.0000.0000.0000.000
70A73GLY00.0300.03425.929-0.011-0.0110.0000.0000.0000.000
71A74GLY0-0.010-0.02124.391-0.010-0.0100.0000.0000.0000.000
72A75GLN0-0.023-0.01119.301-0.016-0.0160.0000.0000.0000.000
73A76TYR0-0.060-0.05018.251-0.027-0.0270.0000.0000.0000.000
74A77ARG10.8420.89213.0530.6720.6720.0000.0000.0000.000
75A79TYR00.0240.0147.361-0.134-0.1340.0000.0000.0000.000
76A80GLY00.0570.0246.2590.3720.3720.0000.0000.0000.000
77A81ALA00.001-0.0075.642-0.473-0.4730.0000.0000.0000.000
78A82HIS00.0590.0144.304-0.428-0.326-0.001-0.007-0.0940.000
79A83ASN0-0.076-0.0608.935-0.232-0.2320.0000.0000.0000.000
80A84LEU0-0.0040.00211.739-0.049-0.0490.0000.0000.0000.000
81A85SER0-0.066-0.0255.8340.0400.0400.0000.0000.0000.000
82A86SER00.012-0.0068.754-0.014-0.0140.0000.0000.0000.000
83A87GLU-1-0.902-0.9262.690-5.339-4.7540.095-0.224-0.455-0.002
84A88CYS0-0.092-0.0514.7511.4541.551-0.001-0.013-0.0830.000
85A89SER0-0.030-0.0252.537-4.685-2.8760.974-1.338-1.444-0.006
86A90ALA00.0180.0143.2070.9871.2530.0270.085-0.378-0.001
87A91PRO00.0120.0095.1030.3000.317-0.001-0.001-0.0140.000
88A92SER0-0.007-0.0118.6930.0510.0510.0000.0000.0000.000
89A93ASP-1-0.828-0.89310.944-0.440-0.4400.0000.0000.0000.000
90A94PRO0-0.0190.00214.131-0.019-0.0190.0000.0000.0000.000
91A95LEU00.0210.00917.0490.0470.0470.0000.0000.0000.000
92A96ASP-1-0.801-0.89519.477-0.247-0.2470.0000.0000.0000.000
93A97ILE0-0.023-0.00222.2970.0190.0190.0000.0000.0000.000
94A98LEU0-0.028-0.01324.972-0.003-0.0030.0000.0000.0000.000
95A99ILE00.0000.00628.4830.0110.0110.0000.0000.0000.000
96A100THR0-0.016-0.02531.7270.0050.0050.0000.0000.0000.000
97A101GLY00.011-0.00735.1290.0000.0000.0000.0000.0000.000
98A102GLN0-0.059-0.02334.479-0.001-0.0010.0000.0000.0000.000
99A103ILE0-0.031-0.00336.834-0.002-0.0020.0000.0000.0000.000
100A104ARG10.9190.94739.5130.0910.0910.0000.0000.0000.000
101A105GLY00.005-0.01342.483-0.001-0.0010.0000.0000.0000.000
102A106THR0-0.022-0.00842.807-0.002-0.0020.0000.0000.0000.000
103A107PRO0-0.0280.00540.1250.0020.0020.0000.0000.0000.000
104A108PHE00.023-0.01243.4410.0020.0020.0000.0000.0000.000
105A109ILE0-0.032-0.00439.875-0.003-0.0030.0000.0000.0000.000
106A110SER0-0.017-0.01243.6910.0030.0030.0000.0000.0000.000
107A111VAL00.0240.00243.253-0.002-0.0020.0000.0000.0000.000
108A112GLN00.0100.03645.2500.0030.0030.0000.0000.0000.000
109A113PRO00.0480.01645.645-0.001-0.0010.0000.0000.0000.000
110A114GLY00.022-0.00747.5740.0000.0000.0000.0000.0000.000
111A115PRO0-0.0100.00245.8740.0000.0000.0000.0000.0000.000
112A116THR0-0.015-0.01546.1240.0010.0010.0000.0000.0000.000
113A117VAL0-0.0130.01243.7460.0000.0000.0000.0000.0000.000
114A118ALA00.0350.01646.5890.0020.0020.0000.0000.0000.000
115A119SER00.008-0.02341.884-0.001-0.0010.0000.0000.0000.000
116A120GLY0-0.027-0.01042.1120.0020.0020.0000.0000.0000.000
117A121GLU-1-0.875-0.92943.098-0.009-0.0090.0000.0000.0000.000
118A122ASN0-0.015-0.03942.7940.0010.0010.0000.0000.0000.000
119A123VAL00.0430.02541.877-0.001-0.0010.0000.0000.0000.000
120A124THR00.0010.00440.904-0.001-0.0010.0000.0000.0000.000
121A125LEU00.0360.02538.4450.0010.0010.0000.0000.0000.000
122A126LEU0-0.039-0.02040.640-0.004-0.0040.0000.0000.0000.000
123A127CYS0-0.0340.02036.906-0.004-0.0040.0000.0000.0000.000
124A128GLN00.0480.00441.5980.0010.0010.0000.0000.0000.000
125A129SER00.0210.01643.4810.0000.0000.0000.0000.0000.000
126A130TRP00.0650.03345.5120.0000.0000.0000.0000.0000.000
127A131ARG10.8410.91645.3690.0590.0590.0000.0000.0000.000
128A132GLN00.0540.03841.620-0.005-0.0050.0000.0000.0000.000
129A133PHE00.0140.02938.414-0.002-0.0020.0000.0000.0000.000
130A134HIS00.0000.01335.848-0.002-0.0020.0000.0000.0000.000
131A135THR0-0.004-0.00131.845-0.003-0.0030.0000.0000.0000.000
132A136PHE0-0.003-0.00835.1120.0020.0020.0000.0000.0000.000
133A137LEU0-0.009-0.01530.374-0.005-0.0050.0000.0000.0000.000
134A138LEU00.0060.02333.8780.0040.0040.0000.0000.0000.000
135A139THR0-0.056-0.04331.959-0.005-0.0050.0000.0000.0000.000
136A140LYS10.8980.94532.5190.0260.0260.0000.0000.0000.000
137A141ALA00.000-0.00133.002-0.005-0.0050.0000.0000.0000.000
138A142GLY0-0.0020.01031.3590.0010.0010.0000.0000.0000.000
139A143ALA0-0.006-0.00727.9720.0060.0060.0000.0000.0000.000
140A144ALA0-0.013-0.01228.6040.0020.0020.0000.0000.0000.000
141A145ASP-1-0.923-0.96822.736-0.103-0.1030.0000.0000.0000.000
142A146ALA00.0180.03224.8560.0010.0010.0000.0000.0000.000
143A147PRO0-0.041-0.02325.475-0.013-0.0130.0000.0000.0000.000
144A148LEU00.0350.00328.253-0.007-0.0070.0000.0000.0000.000
145A149ARG10.8150.90127.0580.1730.1730.0000.0000.0000.000
146A150LEU00.0070.01030.987-0.001-0.0010.0000.0000.0000.000
147A151ARG10.9350.96833.4310.0910.0910.0000.0000.0000.000
148A152SER0-0.061-0.05035.2270.0060.0060.0000.0000.0000.000
149A153ILE00.0440.02038.873-0.003-0.0030.0000.0000.0000.000
150A154HIS0-0.053-0.03841.9940.0010.0010.0000.0000.0000.000
151A155GLU-1-0.869-0.92845.128-0.050-0.0500.0000.0000.0000.000
152A156TYR0-0.0100.01347.7580.0010.0010.0000.0000.0000.000
153A157PRO0-0.016-0.00850.4910.0020.0020.0000.0000.0000.000
154A158LYS10.8330.90947.5090.0440.0440.0000.0000.0000.000
155A159TYR0-0.0020.00342.590-0.004-0.0040.0000.0000.0000.000
156A160GLN00.0340.00042.7350.0030.0030.0000.0000.0000.000
157A161ALA00.013-0.00137.781-0.005-0.0050.0000.0000.0000.000
158A162GLU-1-0.871-0.93139.645-0.041-0.0410.0000.0000.0000.000
159A163PHE0-0.018-0.03034.043-0.004-0.0040.0000.0000.0000.000
160A164PRO00.001-0.00136.6730.0040.0040.0000.0000.0000.000
161A165MET0-0.039-0.01835.008-0.001-0.0010.0000.0000.0000.000
162A166SER0-0.0440.00837.8260.0030.0030.0000.0000.0000.000
163A167PRO0-0.028-0.01538.174-0.002-0.0020.0000.0000.0000.000
164A168VAL0-0.0080.02138.2630.0010.0010.0000.0000.0000.000
165A169THR00.001-0.02836.2630.0060.0060.0000.0000.0000.000
166A170SER00.0410.00337.862-0.004-0.0040.0000.0000.0000.000
167A171ALA00.0110.01533.057-0.002-0.0020.0000.0000.0000.000
168A172HIS00.0340.01734.835-0.002-0.0020.0000.0000.0000.000
169A173ALA00.0170.03836.812-0.005-0.0050.0000.0000.0000.000
170A174GLY00.0210.01537.3330.0000.0000.0000.0000.0000.000
171A175THR0-0.031-0.04238.745-0.003-0.0030.0000.0000.0000.000
172A176TYR0-0.038-0.04134.850-0.005-0.0050.0000.0000.0000.000
173A177ARG10.9360.96737.1820.0510.0510.0000.0000.0000.000
174A179TYR00.0520.02135.1430.0020.0020.0000.0000.0000.000
175A180GLY00.0570.01637.0910.0010.0010.0000.0000.0000.000
176A181SER0-0.004-0.02033.190-0.005-0.0050.0000.0000.0000.000
177A182LEU0-0.009-0.02034.8130.0080.0080.0000.0000.0000.000
178A183ASN00.037-0.00532.822-0.009-0.0090.0000.0000.0000.000
179A184SER0-0.043-0.01832.736-0.006-0.0060.0000.0000.0000.000
180A185ASP-1-0.798-0.90929.932-0.196-0.1960.0000.0000.0000.000
181A186PRO0-0.0310.00228.4450.0090.0090.0000.0000.0000.000
182A187TYR0-0.0030.01823.6230.0030.0030.0000.0000.0000.000
183A188LEU0-0.038-0.00129.1590.0090.0090.0000.0000.0000.000
184A189LEU0-0.0070.00231.4500.0040.0040.0000.0000.0000.000
185A190SER0-0.045-0.03934.9980.0010.0010.0000.0000.0000.000
186A191HIS00.0500.03337.879-0.001-0.0010.0000.0000.0000.000
187A192PRO00.0240.02738.525-0.001-0.0010.0000.0000.0000.000
188A193SER0-0.0100.00139.9620.0010.0010.0000.0000.0000.000
189A194GLU-1-0.879-0.95841.999-0.043-0.0430.0000.0000.0000.000
190A195PRO0-0.061-0.01941.765-0.002-0.0020.0000.0000.0000.000
191A196LEU0-0.006-0.00241.7650.0020.0020.0000.0000.0000.000
192A197GLU-1-0.846-0.90641.572-0.021-0.0210.0000.0000.0000.000
193A198LEU0-0.0090.01339.6480.0010.0010.0000.0000.0000.000
194A199VAL0-0.014-0.00541.8930.0020.0020.0000.0000.0000.000
195A200VAL00.0260.00641.1150.0000.0000.0000.0000.0000.000
196A201SER0-0.030-0.00544.3320.0020.0020.0000.0000.0000.000