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: 7232K

Calculation Name: 3LH9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LH9

Chain ID: A

ChEMBL ID:

UniProt ID: Q8C0E2

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 289
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4019590.376629
FMO2-HF: Nuclear repulsion 3901848.042786
FMO2-HF: Total energy -117742.333844
FMO2-MP2: Total energy -118090.480906


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:9:SER)


Summations of interaction energy for fragment #1(A:9: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.
-24.88-21.6858.445-4.776-6.8630.037
Interaction energy analysis for fragmet #1(A:9:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : -0.006
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].
3A11GLU-1-0.803-0.8773.841-1.0131.155-0.024-1.052-1.091-0.002
4A12VAL00.0070.0075.8950.4420.4420.0000.0000.0000.000
5A13GLU-1-0.850-0.9089.138-0.301-0.3010.0000.0000.0000.000
6A14ILE0-0.036-0.01812.3960.0380.0380.0000.0000.0000.000
7A15LEU00.0000.00115.8380.0180.0180.0000.0000.0000.000
8A16LEU0-0.014-0.00318.5630.0040.0040.0000.0000.0000.000
9A17ASN0-0.001-0.02122.2360.0240.0240.0000.0000.0000.000
10A18ASP-1-0.873-0.94325.019-0.023-0.0230.0000.0000.0000.000
11A19ALA0-0.021-0.00522.659-0.009-0.0090.0000.0000.0000.000
12A20GLU-1-0.959-0.98924.690-0.010-0.0100.0000.0000.0000.000
13A21SER0-0.0240.00026.8010.0020.0020.0000.0000.0000.000
14A22ARG10.8260.91626.3580.0790.0790.0000.0000.0000.000
15A23LYS10.8250.90329.1910.0640.0640.0000.0000.0000.000
16A24ARG10.8980.94922.1100.1110.1110.0000.0000.0000.000
17A25ALA0-0.020-0.02128.6290.0070.0070.0000.0000.0000.000
18A26GLU-1-0.891-0.93628.779-0.097-0.0970.0000.0000.0000.000
19A27HIS0-0.009-0.00827.5120.0130.0130.0000.0000.0000.000
20A28LYS10.9430.98428.1880.1460.1460.0000.0000.0000.000
21A29THR00.0450.01923.989-0.005-0.0050.0000.0000.0000.000
22A30GLU-1-0.785-0.88625.094-0.257-0.2570.0000.0000.0000.000
23A31ASP-1-0.802-0.88026.381-0.181-0.1810.0000.0000.0000.000
24A32GLY0-0.042-0.02428.3630.0120.0120.0000.0000.0000.000
25A33LYS10.8530.92626.6290.1810.1810.0000.0000.0000.000
26A34LYS10.8210.90428.2560.0850.0850.0000.0000.0000.000
27A35GLU-1-0.826-0.89123.000-0.147-0.1470.0000.0000.0000.000
28A36LYS10.8290.88025.5040.0860.0860.0000.0000.0000.000
29A37TYR00.0170.01921.986-0.017-0.0170.0000.0000.0000.000
30A38PHE00.014-0.00321.0410.0160.0160.0000.0000.0000.000
31A39LEU0-0.0080.01126.119-0.012-0.0120.0000.0000.0000.000
32A40PHE0-0.004-0.00825.6290.0080.0080.0000.0000.0000.000
33A41TYR00.0290.00830.772-0.003-0.0030.0000.0000.0000.000
34A42ASP-1-0.758-0.88033.391-0.097-0.0970.0000.0000.0000.000
35A43GLY00.0080.01634.5870.0070.0070.0000.0000.0000.000
36A44GLU-1-0.845-0.90831.819-0.076-0.0760.0000.0000.0000.000
37A45THR00.0730.02229.049-0.010-0.0100.0000.0000.0000.000
38A46VAL0-0.038-0.01024.3000.0000.0000.0000.0000.0000.000
39A47SER0-0.003-0.00624.590-0.006-0.0060.0000.0000.0000.000
40A48GLY00.0430.01821.6190.0000.0000.0000.0000.0000.000
41A49LYS10.8160.90118.1150.0080.0080.0000.0000.0000.000
42A50VAL00.0020.00712.942-0.034-0.0340.0000.0000.0000.000
43A51SER00.000-0.00713.2450.0690.0690.0000.0000.0000.000
44A52LEU00.0030.0008.717-0.135-0.1350.0000.0000.0000.000
45A53SER00.0120.0067.8090.2240.2240.0000.0000.0000.000
46A54LEU0-0.030-0.0175.377-0.250-0.2500.0000.0000.0000.000
47A55LYS10.8100.8902.278-3.475-3.2773.064-1.052-2.2090.004
48A56ASN00.014-0.0044.395-1.358-1.192-0.001-0.021-0.1440.000
49A57PRO00.0340.0156.3240.2200.2200.0000.0000.0000.000
50A58ASN0-0.044-0.0069.088-0.300-0.3000.0000.0000.0000.000
51A59LYS10.8680.9272.008-20.842-20.7835.394-2.459-2.9940.034
52A60ARG10.8380.9347.229-0.347-0.3470.0000.0000.0000.000
53A61LEU0-0.037-0.0253.4860.3420.7650.014-0.155-0.2820.001
54A62GLU-1-0.813-0.8716.119-0.376-0.3760.0000.0000.0000.000
55A63HIS00.0240.0227.620-0.500-0.5000.0000.0000.0000.000
56A64GLN0-0.022-0.0429.9230.0890.0890.0000.0000.0000.000
57A65GLY00.0510.02912.7460.0210.0210.0000.0000.0000.000
58A66ILE0-0.026-0.01411.093-0.108-0.1080.0000.0000.0000.000
59A67LYS10.8950.95413.8880.4680.4680.0000.0000.0000.000
60A68ILE00.0130.00315.529-0.070-0.0700.0000.0000.0000.000
61A69GLU-1-0.783-0.87818.053-0.349-0.3490.0000.0000.0000.000
62A70PHE0-0.011-0.01020.597-0.016-0.0160.0000.0000.0000.000
63A71ILE00.0300.01621.1760.0110.0110.0000.0000.0000.000
64A72GLY00.0240.01724.5510.0000.0000.0000.0000.0000.000
65A73GLN0-0.001-0.00523.7700.0000.0000.0000.0000.0000.000
66A74ILE0-0.028-0.03128.2110.0050.0050.0000.0000.0000.000
67A75GLU-1-0.749-0.86525.011-0.300-0.3000.0000.0000.0000.000
68A76LEU00.021-0.00129.3000.0110.0110.0000.0000.0000.000
69A77TYR0-0.011-0.02229.226-0.016-0.0160.0000.0000.0000.000
70A78TYR0-0.031-0.01131.687-0.005-0.0050.0000.0000.0000.000
71A79ASP-1-0.907-0.94831.807-0.198-0.1980.0000.0000.0000.000
72A80ARG10.7510.86025.3180.2580.2580.0000.0000.0000.000
73A81GLY0-0.027-0.02225.257-0.009-0.0090.0000.0000.0000.000
74A82ASN0-0.082-0.03925.441-0.024-0.0240.0000.0000.0000.000
75A83HIS00.0050.00122.4150.0370.0370.0000.0000.0000.000
76A84HIS00.0180.01227.3680.0150.0150.0000.0000.0000.000
77A85GLU-1-0.859-0.91824.025-0.272-0.2720.0000.0000.0000.000
78A86PHE0-0.068-0.04228.7300.0110.0110.0000.0000.0000.000
79A87VAL0-0.0260.00428.4480.0120.0120.0000.0000.0000.000
80A88SER00.037-0.01025.475-0.010-0.0100.0000.0000.0000.000
81A89LEU0-0.065-0.01725.2540.0150.0150.0000.0000.0000.000
82A90VAL00.0280.01120.841-0.022-0.0220.0000.0000.0000.000
83A91LYS10.8820.93921.4180.1300.1300.0000.0000.0000.000
84A92ASP-1-0.888-0.95219.037-0.249-0.2490.0000.0000.0000.000
85A93LEU0-0.054-0.03716.2680.0310.0310.0000.0000.0000.000
86A94ALA0-0.024-0.00914.8820.0530.0530.0000.0000.0000.000
87A95ARG10.9640.98116.645-0.005-0.0050.0000.0000.0000.000
88A96PRO00.003-0.00414.4180.0180.0180.0000.0000.0000.000
89A97GLY00.0100.01113.1540.0360.0360.0000.0000.0000.000
90A98GLU-1-0.897-0.9579.9780.5590.5590.0000.0000.0000.000
91A99ILE0-0.045-0.0058.310-0.008-0.0080.0000.0000.0000.000
92A100THR00.029-0.0058.7430.3770.3770.0000.0000.0000.000
93A101GLN00.018-0.01010.186-0.051-0.0510.0000.0000.0000.000
94A102SER00.0090.01110.0850.0480.0480.0000.0000.0000.000
95A103GLN00.0020.01411.2820.0170.0170.0000.0000.0000.000
96A104ALA00.0260.01613.113-0.050-0.0500.0000.0000.0000.000
97A105PHE0-0.027-0.00812.9300.0290.0290.0000.0000.0000.000
98A106ASP-1-0.775-0.87417.844-0.017-0.0170.0000.0000.0000.000
99A107PHE0-0.045-0.01918.850-0.017-0.0170.0000.0000.0000.000
100A108GLU-1-0.838-0.93822.439-0.046-0.0460.0000.0000.0000.000
101A109PHE0-0.050-0.01322.0310.0010.0010.0000.0000.0000.000
102A110THR00.0490.02327.3230.0020.0020.0000.0000.0000.000
103A111HIS0-0.022-0.00731.071-0.008-0.0080.0000.0000.0000.000
104A112VAL0-0.0060.00928.237-0.007-0.0070.0000.0000.0000.000
105A113GLU-1-0.921-0.95331.287-0.103-0.1030.0000.0000.0000.000
106A114LYS10.7120.82629.6140.0980.0980.0000.0000.0000.000
107A115PRO00.0440.03133.1510.0050.0050.0000.0000.0000.000
108A116TYR0-0.023-0.00834.0240.0080.0080.0000.0000.0000.000
109A117GLU-1-0.754-0.83433.578-0.101-0.1010.0000.0000.0000.000
110A118SER00.0320.01128.667-0.004-0.0040.0000.0000.0000.000
111A119TYR0-0.073-0.05931.0580.0140.0140.0000.0000.0000.000
112A120THR0-0.027-0.01628.951-0.016-0.0160.0000.0000.0000.000
113A121GLY0-0.006-0.00831.2340.0100.0100.0000.0000.0000.000
114A122GLN0-0.078-0.04732.889-0.015-0.0150.0000.0000.0000.000
115A123ASN0-0.060-0.04934.112-0.008-0.0080.0000.0000.0000.000
116A124VAL0-0.0130.00032.471-0.004-0.0040.0000.0000.0000.000
117A125LYS10.8260.91724.1990.2810.2810.0000.0000.0000.000
118A126LEU0-0.067-0.01630.114-0.004-0.0040.0000.0000.0000.000
119A127ARG10.7620.83619.7110.3620.3620.0000.0000.0000.000
120A128TYR00.005-0.03025.945-0.002-0.0020.0000.0000.0000.000
121A129PHE0-0.036-0.01619.668-0.003-0.0030.0000.0000.0000.000
122A130LEU0-0.0160.00519.2620.0130.0130.0000.0000.0000.000
123A131ARG10.8560.91515.5270.4060.4060.0000.0000.0000.000
124A132ALA0-0.017-0.00713.2520.0460.0460.0000.0000.0000.000
125A133THR0-0.016-0.01111.910-0.142-0.1420.0000.0000.0000.000
126A134ILE0-0.036-0.0176.8420.1390.1390.0000.0000.0000.000
127A135SER00.0330.0039.560-0.215-0.2150.0000.0000.0000.000
128A136ARG10.7910.8803.9222.2582.379-0.001-0.033-0.0880.000
129A137ARG10.8680.9368.6830.4860.4860.0000.0000.0000.000
130A138LEU0-0.0140.0069.4890.0730.0730.0000.0000.0000.000
131A139ASN00.019-0.0017.5440.3270.3270.0000.0000.0000.000
132A140ASP-1-0.771-0.8768.158-1.309-1.3090.0000.0000.0000.000
133A141VAL0-0.056-0.0234.746-0.372-0.312-0.001-0.004-0.0550.000
134A142VAL00.0150.0097.7790.3230.3230.0000.0000.0000.000
135A143LYS10.8310.90610.5420.4820.4820.0000.0000.0000.000
136A144GLU-1-0.762-0.87312.331-0.381-0.3810.0000.0000.0000.000
137A145MET0-0.036-0.01515.7130.0020.0020.0000.0000.0000.000
138A146ASP-1-0.791-0.85918.100-0.293-0.2930.0000.0000.0000.000
139A147ILE0-0.062-0.02521.6560.0190.0190.0000.0000.0000.000
140A148VAL0-0.015-0.01024.680-0.006-0.0060.0000.0000.0000.000
141A149VAL00.0250.01428.1900.0090.0090.0000.0000.0000.000
142A150HIS00.0060.00231.330-0.002-0.0020.0000.0000.0000.000
143A151THR00.025-0.00434.8740.0010.0010.0000.0000.0000.000
144A152LEU0-0.025-0.00838.0790.0020.0020.0000.0000.0000.000
145A153SER0-0.044-0.02241.117-0.001-0.0010.0000.0000.0000.000
146A154THR00.010-0.00244.7080.0020.0020.0000.0000.0000.000
147A155TYR00.002-0.01847.460-0.001-0.0010.0000.0000.0000.000
148A156PRO00.0110.00651.4580.0010.0010.0000.0000.0000.000
149A157GLU-1-0.886-0.93252.174-0.039-0.0390.0000.0000.0000.000
150A158LEU0-0.0060.00655.3000.0020.0020.0000.0000.0000.000
151A159ASN0-0.078-0.04558.3140.0000.0000.0000.0000.0000.000
152A160SER00.004-0.00760.5610.0000.0000.0000.0000.0000.000
153A161SER0-0.053-0.03061.1670.0000.0000.0000.0000.0000.000
154A162ILE0-0.0140.00257.6400.0000.0000.0000.0000.0000.000
155A163LYS10.9050.95660.9640.0340.0340.0000.0000.0000.000
156A164MET0-0.083-0.01457.065-0.002-0.0020.0000.0000.0000.000
157A165GLU-1-0.821-0.89661.974-0.037-0.0370.0000.0000.0000.000
158A166VAL0-0.068-0.02861.665-0.002-0.0020.0000.0000.0000.000
159A167GLY00.0330.01964.1170.0010.0010.0000.0000.0000.000
160A168ILE0-0.044-0.02567.075-0.001-0.0010.0000.0000.0000.000
161A169GLU-1-0.897-0.94970.609-0.032-0.0320.0000.0000.0000.000
162A170ASP-1-0.907-0.95673.257-0.028-0.0280.0000.0000.0000.000
163A171CYS0-0.077-0.03273.2310.0010.0010.0000.0000.0000.000
164A172LEU0-0.028-0.00867.7240.0000.0000.0000.0000.0000.000
165A173HIS0-0.043-0.03468.6440.0000.0000.0000.0000.0000.000
166A174ILE0-0.005-0.01864.6830.0010.0010.0000.0000.0000.000
167A175GLU-1-0.823-0.92565.077-0.036-0.0360.0000.0000.0000.000
168A176PHE0-0.025-0.01556.6430.0000.0000.0000.0000.0000.000
169A177GLU-1-0.775-0.84562.030-0.034-0.0340.0000.0000.0000.000
170A178TYR0-0.046-0.05255.633-0.001-0.0010.0000.0000.0000.000
171A179ASN00.0820.04556.142-0.001-0.0010.0000.0000.0000.000
172A180LYS10.8340.93452.3630.0440.0440.0000.0000.0000.000
173A181SER00.0680.03354.698-0.001-0.0010.0000.0000.0000.000
174A182LYS10.8940.94850.0540.0510.0510.0000.0000.0000.000
175A183TYR00.000-0.00849.2070.0030.0030.0000.0000.0000.000
176A184HIS00.0210.02545.725-0.005-0.0050.0000.0000.0000.000
177A185LEU00.036-0.00440.0460.0020.0020.0000.0000.0000.000
178A186LYS10.9240.95340.7590.0570.0570.0000.0000.0000.000
179A187ASP-1-0.820-0.89345.787-0.042-0.0420.0000.0000.0000.000
180A188VAL0-0.018-0.01649.305-0.001-0.0010.0000.0000.0000.000
181A189ILE0-0.009-0.00150.5860.0010.0010.0000.0000.0000.000
182A190VAL0-0.029-0.01953.9110.0010.0010.0000.0000.0000.000
183A191GLY00.0350.00057.5690.0000.0000.0000.0000.0000.000
184A192LYS10.8490.93960.2220.0310.0310.0000.0000.0000.000
185A193ILE00.0310.02060.929-0.001-0.0010.0000.0000.0000.000
186A194TYR0-0.020-0.04464.2370.0020.0020.0000.0000.0000.000
187A195PHE00.029-0.00366.077-0.001-0.0010.0000.0000.0000.000
188A196LEU00.0050.00669.4880.0010.0010.0000.0000.0000.000
189A197SER00.002-0.02771.7160.0010.0010.0000.0000.0000.000
190A198VAL0-0.049-0.00971.158-0.001-0.0010.0000.0000.0000.000
191A199GLU-1-0.813-0.88373.353-0.028-0.0280.0000.0000.0000.000
192A200ILE0-0.063-0.02171.5750.0000.0000.0000.0000.0000.000
193A201LYS10.8830.94271.5560.0290.0290.0000.0000.0000.000
194A202ILE00.019-0.00165.579-0.001-0.0010.0000.0000.0000.000
195A203LYS10.8660.93262.6910.0410.0410.0000.0000.0000.000
196A204HIS0-0.041-0.04057.1500.0010.0010.0000.0000.0000.000
197A205MET00.0360.02461.0330.0000.0000.0000.0000.0000.000
198A206GLU-1-0.762-0.80853.986-0.054-0.0540.0000.0000.0000.000
199A207ILE00.0010.01554.5950.0000.0000.0000.0000.0000.000
200A208ASH0-0.074-0.08750.836-0.001-0.0010.0000.0000.0000.000
201A209ILE0-0.0100.00347.0370.0010.0010.0000.0000.0000.000
202A210ILE0-0.042-0.03047.004-0.002-0.0020.0000.0000.0000.000
203A211LYS10.9530.98837.9210.1110.1110.0000.0000.0000.000
204A212ARG10.8270.88643.9580.0720.0720.0000.0000.0000.000
205A213GLU-1-0.727-0.83136.995-0.134-0.1340.0000.0000.0000.000
206A214THR0-0.022-0.00741.2760.0010.0010.0000.0000.0000.000
207A215THR0-0.010-0.01036.247-0.004-0.0040.0000.0000.0000.000
208A216GLY00.0170.01839.2820.0030.0030.0000.0000.0000.000
209A217THR00.007-0.02235.226-0.009-0.0090.0000.0000.0000.000
210A218GLY00.0480.03137.8640.0020.0020.0000.0000.0000.000
211A219PRO0-0.058-0.02539.2670.0040.0040.0000.0000.0000.000
212A220ASN0-0.0040.00540.5370.0110.0110.0000.0000.0000.000
213A221VAL0-0.006-0.01241.458-0.003-0.0030.0000.0000.0000.000
214A222TYR0-0.0070.00539.1010.0010.0010.0000.0000.0000.000
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