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: 2LLNR

Calculation Name: 3R1W-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3R1W

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-27

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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1840459.090347
FMO2-HF: Nuclear repulsion 1771419.764064
FMO2-HF: Total energy -69039.326283
FMO2-MP2: Total energy -69238.681466


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:10:THR)


Summations of interaction energy for fragment #1(A:10:THR)
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.
-5.205-1.1810.364-1.65-2.736-0.001
Interaction energy analysis for fragmet #1(A:10:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / q_NPA : -0.023
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].
3A12VAL00.0180.0243.321-2.316-0.168-0.001-0.961-1.1860.000
4A13ARG10.8660.9242.656-3.858-1.9810.367-0.679-1.565-0.001
5A14THR00.0560.0305.2590.2440.270-0.001-0.003-0.0210.000
6A15TYR0-0.030-0.0098.363-0.087-0.0870.0000.0000.0000.000
7A16GLN0-0.008-0.01210.7600.0370.0370.0000.0000.0000.000
8A17GLY00.0070.00412.8830.0160.0160.0000.0000.0000.000
9A18ILE00.0300.03213.4550.0120.0120.0000.0000.0000.000
10A19SER0-0.032-0.0439.893-0.041-0.0410.0000.0000.0000.000
11A20PRO0-0.0090.0098.3460.0230.0230.0000.0000.0000.000
12A21LYS10.8330.92711.260-0.056-0.0560.0000.0000.0000.000
13A22LEU0-0.017-0.0239.7410.0080.0080.0000.0000.0000.000
14A23GLY00.0340.03214.222-0.012-0.0120.0000.0000.0000.000
15A24GLU-1-0.931-0.98416.7150.1540.1540.0000.0000.0000.000
16A25ARG10.8060.85917.652-0.120-0.1200.0000.0000.0000.000
17A26VAL00.0290.03913.218-0.006-0.0060.0000.0000.0000.000
18A27PHE0-0.024-0.00211.9720.0420.0420.0000.0000.0000.000
19A28VAL00.0180.0038.004-0.044-0.0440.0000.0000.0000.000
20A29ASP-1-0.778-0.8878.9500.3190.3190.0000.0000.0000.000
21A30ARG10.9350.9605.3610.1080.1080.0000.0000.0000.000
22A31SER0-0.097-0.0564.830-0.355-0.382-0.001-0.0070.0360.000
23A32SER0-0.073-0.0237.3800.1330.1330.0000.0000.0000.000
24A33VAL0-0.023-0.0305.3770.1040.1040.0000.0000.0000.000
25A34ILE00.0100.0106.642-0.006-0.0060.0000.0000.0000.000
26A35ILE0-0.040-0.0276.759-0.209-0.2090.0000.0000.0000.000
27A36GLY00.016-0.0048.7820.0550.0550.0000.0000.0000.000
28A37ASP-1-0.889-0.93611.3320.0610.0610.0000.0000.0000.000
29A38VAL0-0.012-0.01412.1700.0130.0130.0000.0000.0000.000
30A39GLU-1-0.856-0.92313.7280.0870.0870.0000.0000.0000.000
31A40LEU0-0.026-0.02112.5470.0010.0010.0000.0000.0000.000
32A41GLY00.0640.02816.4460.0050.0050.0000.0000.0000.000
33A42ASP-1-0.839-0.92118.6230.1310.1310.0000.0000.0000.000
34A43ASP-1-0.816-0.88919.6740.1120.1120.0000.0000.0000.000
35A44CYS0-0.0220.02117.123-0.009-0.0090.0000.0000.0000.000
36A45SER0-0.012-0.01015.5090.0140.0140.0000.0000.0000.000
37A46VAL0-0.0050.00011.756-0.023-0.0230.0000.0000.0000.000
38A47TRP0-0.012-0.01712.3840.0300.0300.0000.0000.0000.000
39A48PRO00.015-0.00111.3690.0320.0320.0000.0000.0000.000
40A49LEU0-0.017-0.01910.154-0.017-0.0170.0000.0000.0000.000
41A50ALA0-0.0060.03111.796-0.011-0.0110.0000.0000.0000.000
42A51VAL0-0.027-0.02810.3780.0670.0670.0000.0000.0000.000
43A52ILE00.0090.00510.929-0.042-0.0420.0000.0000.0000.000
44A53ARG10.8520.91011.004-0.205-0.2050.0000.0000.0000.000
45A54GLY00.0650.03412.345-0.002-0.0020.0000.0000.0000.000
46A55ASP-1-0.775-0.87912.6610.0990.0990.0000.0000.0000.000
47A56MET0-0.069-0.04714.380-0.013-0.0130.0000.0000.0000.000
48A57HIS00.009-0.00117.549-0.003-0.0030.0000.0000.0000.000
49A58HIS00.0170.03217.4400.0080.0080.0000.0000.0000.000
50A59ILE0-0.018-0.01714.9680.0050.0050.0000.0000.0000.000
51A60ARG10.9560.97717.363-0.071-0.0710.0000.0000.0000.000
52A61ILE0-0.010-0.00616.557-0.002-0.0020.0000.0000.0000.000
53A62GLY00.0310.02519.7710.0040.0040.0000.0000.0000.000
54A63ALA00.001-0.01420.9470.0120.0120.0000.0000.0000.000
55A64ARG10.8020.87222.044-0.088-0.0880.0000.0000.0000.000
56A65THR00.0190.01020.151-0.009-0.0090.0000.0000.0000.000
57A66SER0-0.056-0.01118.8850.0130.0130.0000.0000.0000.000
58A67VAL00.0350.00915.727-0.011-0.0110.0000.0000.0000.000
59A68GLN0-0.009-0.01716.1710.0150.0150.0000.0000.0000.000
60A69ASP-1-0.762-0.89515.5880.1590.1590.0000.0000.0000.000
61A70GLY0-0.012-0.00215.085-0.021-0.0210.0000.0000.0000.000
62A71SER0-0.052-0.01316.217-0.013-0.0130.0000.0000.0000.000
63A72VAL0-0.012-0.00214.8900.0330.0330.0000.0000.0000.000
64A73LEU0-0.030-0.01115.438-0.025-0.0250.0000.0000.0000.000
65A74HIS0-0.054-0.03115.2240.0150.0150.0000.0000.0000.000
66A75ILE00.0170.01717.457-0.008-0.0080.0000.0000.0000.000
67A76THR0-0.056-0.05920.0250.0070.0070.0000.0000.0000.000
68A77HIS0-0.010-0.00621.175-0.008-0.0080.0000.0000.0000.000
69A78ALA00.0160.01422.7210.0000.0000.0000.0000.0000.000
70A79SER0-0.028-0.02026.018-0.003-0.0030.0000.0000.0000.000
71A80ASP-1-0.851-0.93528.4760.0260.0260.0000.0000.0000.000
72A81TYR0-0.080-0.03929.2900.0000.0000.0000.0000.0000.000
73A82ASN0-0.026-0.01427.4370.0020.0020.0000.0000.0000.000
74A83PRO00.0710.04628.5850.0010.0010.0000.0000.0000.000
75A84GLY00.0030.00328.5640.0010.0010.0000.0000.0000.000
76A85GLY0-0.011-0.01725.1860.0010.0010.0000.0000.0000.000
77A86TYR0-0.073-0.02824.286-0.002-0.0020.0000.0000.0000.000
78A87PRO00.0430.02921.7690.0060.0060.0000.0000.0000.000
79A88LEU0-0.031-0.01118.4270.0020.0020.0000.0000.0000.000
80A89ILE0-0.043-0.01520.9580.0020.0020.0000.0000.0000.000
81A90ILE00.002-0.01119.995-0.002-0.0020.0000.0000.0000.000
82A91GLY00.0480.04123.0390.0030.0030.0000.0000.0000.000
83A92ASP-1-0.841-0.93123.9470.0890.0890.0000.0000.0000.000
84A93ASP-1-0.863-0.91525.2890.0720.0720.0000.0000.0000.000
85A94VAL0-0.022-0.00823.832-0.005-0.0050.0000.0000.0000.000
86A95THR0-0.027-0.01023.4850.0070.0070.0000.0000.0000.000
87A96ILE0-0.007-0.00320.210-0.008-0.0080.0000.0000.0000.000
88A97GLY00.0130.00321.1420.0090.0090.0000.0000.0000.000
89A98HIS0-0.031-0.04519.883-0.002-0.0020.0000.0000.0000.000
90A99GLN0-0.026-0.01419.423-0.023-0.0230.0000.0000.0000.000
91A100ALA00.0120.03720.446-0.008-0.0080.0000.0000.0000.000
92A101MET0-0.013-0.00218.9820.0180.0180.0000.0000.0000.000
93A102LEU0-0.007-0.00920.310-0.013-0.0130.0000.0000.0000.000
94A103HIS10.8070.87420.235-0.091-0.0910.0000.0000.0000.000
95A104GLY00.0600.04021.619-0.007-0.0070.0000.0000.0000.000
96A105CYS0-0.0280.01123.494-0.005-0.0050.0000.0000.0000.000
97A106THR00.010-0.00424.9140.0020.0020.0000.0000.0000.000
98A107ILE0-0.059-0.03323.939-0.002-0.0020.0000.0000.0000.000
99A108GLY00.0540.03726.8600.0020.0020.0000.0000.0000.000
100A109ASN00.012-0.00627.7580.0090.0090.0000.0000.0000.000
101A110ARG10.8580.91428.824-0.060-0.0600.0000.0000.0000.000
102A111VAL00.0210.03228.028-0.004-0.0040.0000.0000.0000.000
103A112LEU0-0.025-0.00627.6820.0050.0050.0000.0000.0000.000
104A113ILE00.0190.00524.755-0.005-0.0050.0000.0000.0000.000
105A114GLY00.0210.01525.7890.0050.0050.0000.0000.0000.000
106A115MET00.0220.00824.5060.0050.0050.0000.0000.0000.000
107A116LYS10.8920.92023.537-0.114-0.1140.0000.0000.0000.000
108A117SER0-0.077-0.01325.124-0.005-0.0050.0000.0000.0000.000
109A118MET00.004-0.00624.8470.0100.0100.0000.0000.0000.000
110A119ILE0-0.019-0.01925.101-0.009-0.0090.0000.0000.0000.000
111A120MET00.0050.00325.1750.0070.0070.0000.0000.0000.000
112A121ASP-1-0.707-0.80424.7900.0760.0760.0000.0000.0000.000
113A122GLY00.019-0.01527.099-0.005-0.0050.0000.0000.0000.000
114A123ALA0-0.095-0.01928.916-0.003-0.0030.0000.0000.0000.000
115A124ILE00.017-0.00529.2770.0030.0030.0000.0000.0000.000
116A125VAL0-0.053-0.02729.269-0.003-0.0030.0000.0000.0000.000
117A126GLU-1-0.825-0.91430.8700.0460.0460.0000.0000.0000.000
118A127ASP-1-0.826-0.92632.2970.0580.0580.0000.0000.0000.000
119A128GLU-1-0.854-0.92232.7180.0440.0440.0000.0000.0000.000
120A129VAL0-0.0160.01232.581-0.003-0.0030.0000.0000.0000.000
121A130ILE0-0.023-0.01332.0460.0040.0040.0000.0000.0000.000
122A131VAL0-0.0080.00229.544-0.004-0.0040.0000.0000.0000.000
123A132ALA0-0.003-0.01730.5280.0030.0030.0000.0000.0000.000
124A133ALA00.020-0.00529.1040.0030.0030.0000.0000.0000.000
125A134GLY0-0.030-0.00228.545-0.005-0.0050.0000.0000.0000.000
126A135ALA0-0.071-0.01929.847-0.002-0.0020.0000.0000.0000.000
127A136THR00.0240.00329.4880.0060.0060.0000.0000.0000.000
128A137VAL0-0.024-0.01329.838-0.006-0.0060.0000.0000.0000.000
129A138SER00.013-0.01630.2230.0040.0040.0000.0000.0000.000
130A139PRO00.0720.02930.1740.0000.0000.0000.0000.0000.000
131A140GLY00.0010.01731.285-0.003-0.0030.0000.0000.0000.000
132A141LYS10.8840.95833.285-0.047-0.0470.0000.0000.0000.000
133A142VAL00.0490.02933.3640.0030.0030.0000.0000.0000.000
134A143LEU0-0.148-0.07832.291-0.002-0.0020.0000.0000.0000.000
135A144GLU-1-0.802-0.90835.6820.0370.0370.0000.0000.0000.000
136A145SER0-0.012-0.02636.6480.0000.0000.0000.0000.0000.000
137A146GLY00.0270.01737.154-0.002-0.0020.0000.0000.0000.000
138A147PHE0-0.051-0.02537.943-0.002-0.0020.0000.0000.0000.000
139A148VAL00.0140.00736.0290.0030.0030.0000.0000.0000.000
140A149TYR00.0210.01534.593-0.003-0.0030.0000.0000.0000.000
141A150MET00.0320.01634.6720.0030.0030.0000.0000.0000.000
142A151GLY0-0.007-0.00734.878-0.003-0.0030.0000.0000.0000.000
143A152THR0-0.0020.03232.3490.0030.0030.0000.0000.0000.000
144A153PRO00.0450.01134.822-0.002-0.0020.0000.0000.0000.000
145A154ALA0-0.023-0.01433.673-0.002-0.0020.0000.0000.0000.000
146A155LYS10.8810.93635.755-0.045-0.0450.0000.0000.0000.000
147A156LYS10.8760.92638.876-0.035-0.0350.0000.0000.0000.000
148A157VAL0-0.063-0.03339.767-0.002-0.0020.0000.0000.0000.000
149A158ARG10.8190.88337.984-0.046-0.0460.0000.0000.0000.000
150A159PRO00.0520.03540.9040.0020.0020.0000.0000.0000.000
151A160ILE0-0.060-0.02936.6480.0000.0000.0000.0000.0000.000
152A161THR00.0150.00539.738-0.002-0.0020.0000.0000.0000.000
153A162GLU-1-0.880-0.95539.7870.0370.0370.0000.0000.0000.000
154A163LYS10.9870.99138.267-0.038-0.0380.0000.0000.0000.000
155A164GLU-1-0.773-0.85536.0700.0490.0490.0000.0000.0000.000
156A165ARG10.9550.98635.102-0.039-0.0390.0000.0000.0000.000
157A166SER0-0.070-0.04435.2730.0020.0020.0000.0000.0000.000
158A167PHE00.004-0.01229.3180.0020.0020.0000.0000.0000.000
159A168PHE00.0440.04530.5520.0030.0030.0000.0000.0000.000
160A169THR00.0460.02429.4040.0040.0040.0000.0000.0000.000
161A170TYR0-0.042-0.01629.8670.0030.0030.0000.0000.0000.000
162A171GLY0-0.015-0.01328.4950.0020.0020.0000.0000.0000.000
163A172ALA00.0550.03925.2840.0050.0050.0000.0000.0000.000
164A173GLY00.0450.01724.9320.0060.0060.0000.0000.0000.000
165A174ASN0-0.110-0.07025.9920.0000.0000.0000.0000.0000.000
166A175TYR00.0350.00719.737-0.003-0.0030.0000.0000.0000.000
167A176VAL00.0180.03021.2050.0110.0110.0000.0000.0000.000
168A177ARG10.9740.97621.813-0.064-0.0640.0000.0000.0000.000
169A178LEU0-0.064-0.01620.164-0.001-0.0010.0000.0000.0000.000
170A179LYS10.7440.84616.914-0.154-0.1540.0000.0000.0000.000
171A180ASP-1-0.820-0.89317.4510.1470.1470.0000.0000.0000.000
172A181LYS10.9010.94619.402-0.071-0.0710.0000.0000.0000.000
173A182HIS00.0400.02115.0410.0010.0010.0000.0000.0000.000
174A183LEU0-0.026-0.00813.5140.0090.0090.0000.0000.0000.000
175A184ALA0-0.054-0.02715.5950.0050.0050.0000.0000.0000.000
176A185GLU-1-0.951-0.96316.1540.0370.0370.0000.0000.0000.000
177A186GLY0-0.065-0.02413.442-0.021-0.0210.0000.0000.0000.000
178A187TYR0-0.050-0.03511.2560.0070.0070.0000.0000.0000.000
179A188ASP-1-0.823-0.9078.6300.4240.4240.0000.0000.0000.000
180A189ARG10.8220.9367.336-0.042-0.0420.0000.0000.0000.000