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: JQ779

Calculation Name: 3L9D-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: 3L9D

Chain ID: A

ChEMBL ID:
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UniProt ID: Q8DU97

Base Structure: X-ray

Registration Date: 2023-09-23

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 199
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2410233.209396
FMO2-HF: Nuclear repulsion 2326790.562825
FMO2-HF: Total energy -83442.646572
FMO2-MP2: Total energy -83685.973022


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-11.584-5.70610.632-4.341-12.166-0.013
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.007 / 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].
3A3TRP00.036-0.0152.689-3.1022.4951.139-1.951-4.785-0.006
4A4GLU-1-0.926-0.9545.017-0.701-0.5930.000-0.004-0.1040.000
5A5GLU-1-0.891-0.9346.8270.2390.2390.0000.0000.0000.000
6A6PHE0-0.020-0.0143.214-2.482-0.9140.347-0.510-1.405-0.007
7A7LEU0-0.009-0.0445.115-0.301-0.245-0.001-0.002-0.0530.000
8A8ASP-1-0.908-0.9277.509-0.229-0.2290.0000.0000.0000.000
9A9PRO00.0660.0238.6720.0170.0170.0000.0000.0000.000
10A10TYR0-0.013-0.0236.8370.0900.0900.0000.0000.0000.000
11A11ILE0-0.010-0.01511.5300.0350.0350.0000.0000.0000.000
12A12GLN0-0.0140.00413.6930.0200.0200.0000.0000.0000.000
13A13ALA00.0570.03614.4110.0210.0210.0000.0000.0000.000
14A14VAL0-0.021-0.01014.9940.0240.0240.0000.0000.0000.000
15A15GLY0-0.016-0.00317.4170.0190.0190.0000.0000.0000.000
16A16GLU-1-0.834-0.90519.092-0.125-0.1250.0000.0000.0000.000
17A17LEU00.0140.00717.7400.0150.0150.0000.0000.0000.000
18A18LYS10.8610.95120.7760.1780.1780.0000.0000.0000.000
19A19ILE0-0.023-0.01523.3110.0110.0110.0000.0000.0000.000
20A20LYS10.8340.91322.7010.1100.1100.0000.0000.0000.000
21A21PHE00.0450.00722.2670.0090.0090.0000.0000.0000.000
22A22ARG10.8830.94125.4350.1220.1220.0000.0000.0000.000
23A23GLY0-0.010-0.01129.2350.0050.0050.0000.0000.0000.000
24A24ILE00.0460.02928.9620.0050.0050.0000.0000.0000.000
25A25ARG10.9560.98532.2460.0700.0700.0000.0000.0000.000
26A26LYS10.8950.93932.3980.0770.0770.0000.0000.0000.000
27A27GLN0-0.028-0.00532.9830.0070.0070.0000.0000.0000.000
28A28PHE00.0390.02434.7980.0030.0030.0000.0000.0000.000
29A29ARG10.9050.95937.8370.0570.0570.0000.0000.0000.000
30A30LYS10.9430.97838.8150.0520.0520.0000.0000.0000.000
31A31GLN0-0.0170.00740.0940.0030.0030.0000.0000.0000.000
32A32LYS10.9410.97743.1840.0390.0390.0000.0000.0000.000
33A33ARG10.9220.95740.5070.0430.0430.0000.0000.0000.000
34A34HIS00.0490.02238.744-0.001-0.0010.0000.0000.0000.000
35A35SER0-0.091-0.05435.251-0.001-0.0010.0000.0000.0000.000
36A36PRO00.0510.04133.915-0.001-0.0010.0000.0000.0000.000
37A37ILE00.0050.01029.122-0.003-0.0030.0000.0000.0000.000
38A38GLU-1-0.885-0.96232.524-0.062-0.0620.0000.0000.0000.000
39A39PHE0-0.068-0.05028.856-0.002-0.0020.0000.0000.0000.000
40A40VAL00.0380.03024.573-0.002-0.0020.0000.0000.0000.000
41A41THR0-0.041-0.01323.966-0.004-0.0040.0000.0000.0000.000
42A42GLY00.0550.01020.2020.0020.0020.0000.0000.0000.000
43A43ARG10.8820.94016.5420.2600.2600.0000.0000.0000.000
44A44VAL00.0830.05610.5720.0040.0040.0000.0000.0000.000
45A45LYS10.8610.95211.1740.3230.3230.0000.0000.0000.000
46A46PRO00.018-0.00310.956-0.040-0.0400.0000.0000.0000.000
47A47ILE00.1060.0386.082-0.001-0.0010.0000.0000.0000.000
48A48GLU-1-0.890-0.9437.989-0.495-0.4950.0000.0000.0000.000
49A49SER0-0.051-0.03010.4800.0640.0640.0000.0000.0000.000
50A50ILE0-0.011-0.0105.7500.0490.0490.0000.0000.0000.000
51A51LYS10.9770.9865.1350.8540.8540.0000.0000.0000.000
52A52GLU-1-0.862-0.9157.8780.0280.0280.0000.0000.0000.000
53A53LYS10.9000.94410.4530.2120.2120.0000.0000.0000.000
54A54MET0-0.047-0.0054.156-0.359-0.1750.000-0.023-0.1600.000
55A55VAL00.0160.0109.1930.1080.1080.0000.0000.0000.000
56A56LEU0-0.033-0.02411.7740.0190.0190.0000.0000.0000.000
57A57ARG10.8250.91511.6680.2200.2200.0000.0000.0000.000
58A58GLY00.0160.02712.2540.0130.0130.0000.0000.0000.000
59A59ILE0-0.048-0.0157.4260.0330.0330.0000.0000.0000.000
60A60LYS10.9680.9807.369-0.522-0.5220.0000.0000.0000.000
61A61LYS10.9550.9592.011-6.714-8.8947.684-1.464-4.0390.004
62A62GLU-1-0.860-0.9463.4700.6301.1590.037-0.143-0.423-0.002
63A63ASN00.0040.0115.386-0.158-0.125-0.0010.001-0.0320.000
64A64LEU0-0.006-0.0042.477-0.244-0.2611.427-0.245-1.165-0.002
65A65THR0-0.015-0.0116.0850.0260.0260.0000.0000.0000.000
66A66GLN0-0.023-0.0027.7700.0960.0960.0000.0000.0000.000
67A67ASP-1-0.832-0.9119.7070.0000.0000.0000.0000.0000.000
68A68MET0-0.136-0.0637.9700.0290.0290.0000.0000.0000.000
69A69GLN00.000-0.01910.547-0.018-0.0180.0000.0000.0000.000
70A70ASP-1-0.815-0.92012.959-0.271-0.2710.0000.0000.0000.000
71A71ILE0-0.0130.0066.7490.0020.0020.0000.0000.0000.000
72A72ALA00.0310.02010.9400.0300.0300.0000.0000.0000.000
73A73GLY00.0340.03113.5500.0160.0160.0000.0000.0000.000
74A74LEU0-0.057-0.06016.7590.0070.0070.0000.0000.0000.000
75A75ARG10.9380.98020.2770.1450.1450.0000.0000.0000.000
76A76ILE0-0.004-0.00523.7280.0010.0010.0000.0000.0000.000
77A77MET0-0.022-0.00426.4390.0020.0020.0000.0000.0000.000
78A78VAL00.0220.00829.9480.0010.0010.0000.0000.0000.000
79A79GLN00.0460.01733.0980.0000.0000.0000.0000.0000.000
80A80PHE00.0180.01036.6580.0010.0010.0000.0000.0000.000
81A81VAL00.0290.01035.648-0.002-0.0020.0000.0000.0000.000
82A82ASP-1-0.847-0.94035.795-0.041-0.0410.0000.0000.0000.000
83A83ASP-1-0.817-0.91035.327-0.052-0.0520.0000.0000.0000.000
84A84VAL0-0.024-0.01630.605-0.003-0.0030.0000.0000.0000.000
85A85ASN00.0440.00232.029-0.005-0.0050.0000.0000.0000.000
86A86ASP-1-0.880-0.92533.924-0.046-0.0460.0000.0000.0000.000
87A87VAL0-0.071-0.04728.892-0.002-0.0020.0000.0000.0000.000
88A88LEU0-0.024-0.01727.958-0.004-0.0040.0000.0000.0000.000
89A89GLU-1-0.917-0.94630.217-0.044-0.0440.0000.0000.0000.000
90A90LEU0-0.069-0.04331.1480.0000.0000.0000.0000.0000.000
91A91LEU0-0.029-0.02925.301-0.002-0.0020.0000.0000.0000.000
92A92ARG10.8340.86927.1130.0500.0500.0000.0000.0000.000
93A93GLN0-0.0340.01128.8350.0020.0020.0000.0000.0000.000
94A94ARG10.7730.87926.0120.0850.0850.0000.0000.0000.000
95A95LYS10.9740.96627.1950.0450.0450.0000.0000.0000.000
96A96ASP-1-0.756-0.85223.927-0.090-0.0900.0000.0000.0000.000
97A97MET0-0.0180.00521.005-0.013-0.0130.0000.0000.0000.000
98A98LYS10.9701.00421.1730.0690.0690.0000.0000.0000.000
99A99VAL00.0210.00521.309-0.013-0.0130.0000.0000.0000.000
100A100ILE0-0.048-0.03017.4900.0130.0130.0000.0000.0000.000
101A101GLN0-0.012-0.00619.8830.0120.0120.0000.0000.0000.000
102A102GLU-1-0.767-0.80922.677-0.067-0.0670.0000.0000.0000.000
103A103ARG10.9200.95819.9150.0830.0830.0000.0000.0000.000
104A104ASP-1-0.795-0.88026.106-0.055-0.0550.0000.0000.0000.000
105A105TYR0-0.039-0.04124.0840.0010.0010.0000.0000.0000.000
106A106ILE00.006-0.01229.610-0.001-0.0010.0000.0000.0000.000
107A107ASN00.0190.00132.7340.0000.0000.0000.0000.0000.000
108A108ASN0-0.0530.00131.3430.0070.0070.0000.0000.0000.000
109A109LEU0-0.022-0.03733.668-0.002-0.0020.0000.0000.0000.000
110A110LYS10.9210.96935.2270.0290.0290.0000.0000.0000.000
111A111PRO00.0570.04737.331-0.002-0.0020.0000.0000.0000.000
112A112SER0-0.023-0.03036.8740.0000.0000.0000.0000.0000.000
113A113GLY00.0030.01033.0360.0000.0000.0000.0000.0000.000
114A114TYR0-0.054-0.06124.315-0.003-0.0030.0000.0000.0000.000
115A115ARG10.9761.00129.8850.0520.0520.0000.0000.0000.000
116A116SER0-0.033-0.02125.383-0.005-0.0050.0000.0000.0000.000
117A117TYR00.0550.01526.7290.0050.0050.0000.0000.0000.000
118A118HIS0-0.0320.00921.334-0.003-0.0030.0000.0000.0000.000
119A119VAL00.0480.02322.5160.0090.0090.0000.0000.0000.000
120A120ILE0-0.0130.01416.801-0.013-0.0130.0000.0000.0000.000
121A121VAL0-0.026-0.02118.3600.0190.0190.0000.0000.0000.000
122A122GLU-1-0.887-0.93716.423-0.129-0.1290.0000.0000.0000.000
123A123TYR0-0.052-0.08816.1330.0280.0280.0000.0000.0000.000
124A124PRO0-0.003-0.00115.790-0.024-0.0240.0000.0000.0000.000
125A125VAL00.0020.01013.5270.0060.0060.0000.0000.0000.000
126A126ASP-1-0.906-0.96015.655-0.085-0.0850.0000.0000.0000.000
127A127THR0-0.006-0.03012.763-0.005-0.0050.0000.0000.0000.000
128A128ILE00.029-0.00716.0730.0160.0160.0000.0000.0000.000
129A129SER0-0.042-0.00913.6730.0200.0200.0000.0000.0000.000
130A130GLY00.0410.02315.9610.0220.0220.0000.0000.0000.000
131A131GLN0-0.0150.02415.563-0.016-0.0160.0000.0000.0000.000
132A132ARG10.8760.9439.8890.1040.1040.0000.0000.0000.000
133A133ILE00.0400.02613.260-0.003-0.0030.0000.0000.0000.000
134A134ILE0-0.0240.00510.186-0.046-0.0460.0000.0000.0000.000
135A135MET00.0190.01411.8030.0700.0700.0000.0000.0000.000
136A136ALA0-0.048-0.02113.010-0.043-0.0430.0000.0000.0000.000
137A137GLU-1-0.833-0.92715.639-0.139-0.1390.0000.0000.0000.000
138A138ILE0-0.046-0.01417.826-0.004-0.0040.0000.0000.0000.000
139A139GLN0-0.068-0.03820.2670.0210.0210.0000.0000.0000.000
140A140ILE0-0.0020.00423.658-0.002-0.0020.0000.0000.0000.000
141A141ARG10.8610.91323.9400.1100.1100.0000.0000.0000.000
142A142THR00.057-0.00829.653-0.003-0.0030.0000.0000.0000.000
143A143LEU0-0.014-0.01131.828-0.005-0.0050.0000.0000.0000.000
144A144ALA00.0430.02632.880-0.004-0.0040.0000.0000.0000.000
145A145MET0-0.0120.02430.481-0.003-0.0030.0000.0000.0000.000
146A146ASN0-0.010-0.01227.044-0.010-0.0100.0000.0000.0000.000
147A147PHE0-0.039-0.01428.984-0.006-0.0060.0000.0000.0000.000
148A148TRP00.0380.01528.841-0.004-0.0040.0000.0000.0000.000
149A149ALA0-0.005-0.00326.230-0.002-0.0020.0000.0000.0000.000
150A150THR0-0.076-0.03225.762-0.010-0.0100.0000.0000.0000.000
151A151ILE0-0.011-0.00726.480-0.005-0.0050.0000.0000.0000.000
152A152GLU-1-0.943-0.97726.203-0.077-0.0770.0000.0000.0000.000
153A153HIS00.0490.02619.2470.0060.0060.0000.0000.0000.000
154A154SER0-0.034-0.02023.428-0.008-0.0080.0000.0000.0000.000
155A155LEU0-0.042-0.01924.8310.0010.0010.0000.0000.0000.000
156A156ASN00.0460.00522.2150.0130.0130.0000.0000.0000.000
157A157TYR0-0.027-0.01117.0970.0040.0040.0000.0000.0000.000
158A158LYS10.9400.98122.0580.0740.0740.0000.0000.0000.000
159A159TYR0-0.054-0.04724.4510.0030.0030.0000.0000.0000.000
160A160HIS00.0270.02320.1500.0070.0070.0000.0000.0000.000
161A161GLY0-0.0020.01123.3900.0080.0080.0000.0000.0000.000
162A162GLU-1-0.994-0.98125.572-0.015-0.0150.0000.0000.0000.000
163A163PHE0-0.076-0.03327.417-0.001-0.0010.0000.0000.0000.000
164A164PRO00.0210.00231.0930.0040.0040.0000.0000.0000.000
165A165GLU-1-0.735-0.84034.375-0.026-0.0260.0000.0000.0000.000
166A166ASP-1-0.856-0.93537.469-0.037-0.0370.0000.0000.0000.000
167A167ILE00.0480.01431.787-0.001-0.0010.0000.0000.0000.000
168A168LYS10.9310.96834.0050.0260.0260.0000.0000.0000.000
169A169ARG10.8450.90034.9630.0270.0270.0000.0000.0000.000
170A170ARG10.9260.98136.5490.0410.0410.0000.0000.0000.000
171A171LEU00.0220.00530.854-0.002-0.0020.0000.0000.0000.000
172A172GLU-1-0.824-0.92434.755-0.032-0.0320.0000.0000.0000.000
173A173LEU0-0.051-0.01836.5900.0000.0000.0000.0000.0000.000
174A174THR00.004-0.01535.2100.0000.0000.0000.0000.0000.000
175A175SER0-0.0080.01534.197-0.001-0.0010.0000.0000.0000.000
176A176LYS10.8530.92236.0170.0320.0320.0000.0000.0000.000
177A177ILE0-0.0160.00139.3840.0010.0010.0000.0000.0000.000
178A178ALA0-0.028-0.01335.6350.0000.0000.0000.0000.0000.000
179A179PHE00.006-0.00737.2690.0000.0000.0000.0000.0000.000
180A180GLN00.0450.01738.6360.0010.0010.0000.0000.0000.000
181A181LEU00.0000.02539.3150.0010.0010.0000.0000.0000.000
182A182ASP-1-0.789-0.88536.354-0.055-0.0550.0000.0000.0000.000
183A183GLU-1-0.921-0.96640.001-0.037-0.0370.0000.0000.0000.000
184A184GLU-1-0.914-0.96342.408-0.030-0.0300.0000.0000.0000.000
185A185MET0-0.024-0.01342.2720.0010.0010.0000.0000.0000.000
186A186ARG10.7670.89339.6860.0390.0390.0000.0000.0000.000
187A187GLN00.0110.00843.1690.0010.0010.0000.0000.0000.000
188A188ILE00.0290.03346.7660.0010.0010.0000.0000.0000.000
189A189ARG10.8840.91941.8700.0350.0350.0000.0000.0000.000
190A190ASP-1-0.957-0.98245.233-0.034-0.0340.0000.0000.0000.000
191A191ASP-1-0.866-0.92147.380-0.030-0.0300.0000.0000.0000.000
192A192ILE0-0.013-0.00644.287-0.001-0.0010.0000.0000.0000.000
193A193LYS10.8480.92941.4110.0400.0400.0000.0000.0000.000
194A194GLU-1-0.909-0.94845.440-0.030-0.0300.0000.0000.0000.000
195A195ALA00.0240.00748.7320.0000.0000.0000.0000.0000.000
196A196GLN0-0.024-0.02241.839-0.001-0.0010.0000.0000.0000.000
197A197LEU0-0.105-0.04744.078-0.001-0.0010.0000.0000.0000.000
198A198LEU0-0.041-0.00447.1720.0010.0010.0000.0000.0000.000
199A199PHE0-0.007-0.00942.798-0.002-0.0020.0000.0000.0000.000