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: G5RL1

Calculation Name: 3DLB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DLB

Chain ID: A

ChEMBL ID:

UniProt ID: Q746M7

Base Structure: X-ray

Registration Date: 2023-09-22

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 640
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -13947045.196093
FMO2-HF: Nuclear repulsion 13701681.579255
FMO2-HF: Total energy -245363.616838
FMO2-MP2: Total energy -246098.314669


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:3:HIS)


Summations of interaction energy for fragment #1(A:3:HIS)
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.
-43.087-44.97127.705-10.109-15.7120.047
Interaction energy analysis for fragmet #1(A:3:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.032 / q_NPA : -0.021
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].
3A5GLY0-0.0220.0023.159-1.9180.6470.000-1.297-1.2670.000
4A6LYS10.8810.9625.168-2.142-2.092-0.001-0.001-0.0470.000
5A7THR0-0.007-0.0288.2900.6040.6040.0000.0000.0000.000
6A8GLU-1-0.867-0.91610.1911.4481.4480.0000.0000.0000.000
7A9VAL0-0.019-0.01513.2110.1100.1100.0000.0000.0000.000
8A10PHE0-0.008-0.01115.208-0.116-0.1160.0000.0000.0000.000
9A11LEU00.0370.03117.0040.0110.0110.0000.0000.0000.000
10A12ASN0-0.056-0.02119.9480.0080.0080.0000.0000.0000.000
11A13ARG10.9880.99921.993-0.323-0.3230.0000.0000.0000.000
12A14PHE0-0.023-0.01024.8060.0400.0400.0000.0000.0000.000
13A15ALA00.0260.02527.105-0.025-0.0250.0000.0000.0000.000
14A16LEU0-0.038-0.01628.7520.0000.0000.0000.0000.0000.000
15A17ARG10.8150.90532.511-0.139-0.1390.0000.0000.0000.000
16A18PRO00.0700.00433.487-0.003-0.0030.0000.0000.0000.000
17A19LEU0-0.047-0.00934.622-0.004-0.0040.0000.0000.0000.000
18A20ASN00.0120.02737.550-0.005-0.0050.0000.0000.0000.000
19A21PRO00.0680.00540.933-0.003-0.0030.0000.0000.0000.000
20A22GLU-1-0.872-0.95442.9020.0880.0880.0000.0000.0000.000
21A23GLU-1-0.814-0.91640.1770.1150.1150.0000.0000.0000.000
22A24LEU00.0090.00336.913-0.003-0.0030.0000.0000.0000.000
23A25ARG10.8530.93940.717-0.083-0.0830.0000.0000.0000.000
24A26PRO00.0410.03042.066-0.001-0.0010.0000.0000.0000.000
25A27TRP00.0550.02844.840-0.005-0.0050.0000.0000.0000.000
26A28ARG10.9890.98646.957-0.026-0.0260.0000.0000.0000.000
27A29LEU0-0.071-0.04048.5730.0000.0000.0000.0000.0000.000
28A30GLU-1-0.876-0.91650.1920.0130.0130.0000.0000.0000.000
29A31VAL00.0050.00650.5820.0020.0020.0000.0000.0000.000
30A32VAL00.0350.01453.330-0.002-0.0020.0000.0000.0000.000
31A33LEU0-0.043-0.03751.8680.0020.0020.0000.0000.0000.000
32A34ASP-1-0.882-0.89856.4740.0010.0010.0000.0000.0000.000
33A35PRO00.0800.01559.6980.0020.0020.0000.0000.0000.000
34A36PRO0-0.022-0.02856.8430.0010.0010.0000.0000.0000.000
35A37PRO0-0.0160.01152.813-0.001-0.0010.0000.0000.0000.000
36A38GLY00.0910.05752.731-0.002-0.0020.0000.0000.0000.000
37A39ARG10.9770.97148.2140.0290.0290.0000.0000.0000.000
38A40GLU-1-0.949-0.98146.881-0.019-0.0190.0000.0000.0000.000
39A41GLU-1-0.876-0.95346.879-0.006-0.0060.0000.0000.0000.000
40A42VAL00.0400.02247.8460.0050.0050.0000.0000.0000.000
41A43TYR00.012-0.00641.2650.0050.0050.0000.0000.0000.000
42A44PRO0-0.070-0.04444.2550.0060.0060.0000.0000.0000.000
43A45LEU00.0410.01945.7230.0050.0050.0000.0000.0000.000
44A46LEU00.0480.03446.4590.0040.0040.0000.0000.0000.000
45A47ALA0-0.055-0.01343.7370.0050.0050.0000.0000.0000.000
46A48GLN0-0.060-0.05145.3530.0060.0060.0000.0000.0000.000
47A49VAL00.0630.03048.4580.0030.0030.0000.0000.0000.000
48A50ALA0-0.0080.00545.8210.0030.0030.0000.0000.0000.000
49A51ARG10.8110.90342.104-0.049-0.0490.0000.0000.0000.000
50A52ARG10.8900.96348.344-0.025-0.0250.0000.0000.0000.000
51A53ALA00.0440.03050.6710.0010.0010.0000.0000.0000.000
52A54GLY00.0130.01549.9110.0020.0020.0000.0000.0000.000
53A55GLY00.0440.01348.9250.0000.0000.0000.0000.0000.000
54A56VAL0-0.074-0.05342.7180.0010.0010.0000.0000.0000.000
55A57THR0-0.018-0.00745.2590.0000.0000.0000.0000.0000.000
56A58VAL00.001-0.00940.0700.0000.0000.0000.0000.0000.000
57A59ARG10.9550.98539.746-0.017-0.0170.0000.0000.0000.000
58A60MET0-0.040-0.03341.7240.0040.0040.0000.0000.0000.000
59A61GLY0-0.013-0.00442.152-0.002-0.0020.0000.0000.0000.000
60A62ASP-1-0.871-0.94143.731-0.002-0.0020.0000.0000.0000.000
61A63GLY0-0.008-0.00746.4890.0000.0000.0000.0000.0000.000
62A64LEU0-0.034-0.00346.2150.0010.0010.0000.0000.0000.000
63A65ALA00.0470.00743.331-0.001-0.0010.0000.0000.0000.000
64A66SER0-0.014-0.00645.1470.0030.0030.0000.0000.0000.000
65A67TRP00.0270.00437.9510.0020.0020.0000.0000.0000.000
66A68SER0-0.0300.01245.5950.0040.0040.0000.0000.0000.000
67A69PRO0-0.006-0.01148.685-0.002-0.0020.0000.0000.0000.000
68A70PRO00.030-0.00951.667-0.001-0.0010.0000.0000.0000.000
69A71GLU-1-0.899-0.93853.6460.0420.0420.0000.0000.0000.000
70A72VAL0-0.072-0.03452.5820.0000.0000.0000.0000.0000.000
71A73LEU0-0.068-0.01850.4470.0000.0000.0000.0000.0000.000
72A74VAL00.0070.03054.152-0.001-0.0010.0000.0000.0000.000
73A75LEU00.030-0.03855.449-0.002-0.0020.0000.0000.0000.000
74A76GLU-1-0.907-0.95357.0000.0200.0200.0000.0000.0000.000
75A77GLY00.0140.01457.5980.0020.0020.0000.0000.0000.000
76A78THR0-0.022-0.00558.096-0.001-0.0010.0000.0000.0000.000
77A79LEU0-0.025-0.02452.0350.0030.0030.0000.0000.0000.000
78A80ALA00.0150.00153.827-0.002-0.0020.0000.0000.0000.000
79A81ARG10.9010.95845.5510.0050.0050.0000.0000.0000.000
80A82MET00.0030.00050.648-0.002-0.0020.0000.0000.0000.000
81A83GLY00.0140.03152.838-0.002-0.0020.0000.0000.0000.000
82A84GLN00.012-0.00454.5430.0010.0010.0000.0000.0000.000
83A85THR0-0.034-0.01655.9030.0020.0020.0000.0000.0000.000
84A86TYR0-0.0060.00553.992-0.002-0.0020.0000.0000.0000.000
85A87ALA00.0150.00658.0500.0030.0030.0000.0000.0000.000
86A88TYR0-0.039-0.02155.005-0.002-0.0020.0000.0000.0000.000
87A89ARG11.0001.00356.977-0.017-0.0170.0000.0000.0000.000
88A90LEU0-0.064-0.02252.408-0.001-0.0010.0000.0000.0000.000
89A91TYR00.003-0.00254.8870.0000.0000.0000.0000.0000.000
90A92PRO00.005-0.00853.9440.0000.0000.0000.0000.0000.000
91A93LYS10.8740.93852.412-0.019-0.0190.0000.0000.0000.000
92A94GLY00.0390.02952.3650.0000.0000.0000.0000.0000.000
93A95ARG10.8310.94346.670-0.068-0.0680.0000.0000.0000.000
94A96ARG10.9610.97641.579-0.036-0.0360.0000.0000.0000.000
95A97PRO0-0.057-0.02642.4510.0030.0030.0000.0000.0000.000
96A98LEU0-0.018-0.00738.203-0.006-0.0060.0000.0000.0000.000
97A99ASP-1-0.837-0.94435.8890.0630.0630.0000.0000.0000.000
98A100PRO0-0.031-0.02032.256-0.004-0.0040.0000.0000.0000.000
99A101LYS10.9160.96230.470-0.086-0.0860.0000.0000.0000.000
100A102ASP-1-0.787-0.86230.7450.0150.0150.0000.0000.0000.000
101A103PRO0-0.031-0.03129.1400.0070.0070.0000.0000.0000.000
102A104GLY00.0250.02031.2300.0030.0030.0000.0000.0000.000
103A105GLU-1-0.846-0.93034.6400.0450.0450.0000.0000.0000.000
104A106ARG10.8100.89526.091-0.116-0.1160.0000.0000.0000.000
105A107SER0-0.096-0.04932.8290.0090.0090.0000.0000.0000.000
106A108VAL00.0290.01133.6500.0030.0030.0000.0000.0000.000
107A109LEU00.0050.00235.4960.0050.0050.0000.0000.0000.000
108A110SER00.0280.01632.1630.0140.0140.0000.0000.0000.000
109A111ALA0-0.0210.01334.5110.0050.0050.0000.0000.0000.000
110A112LEU0-0.016-0.00237.0660.0010.0010.0000.0000.0000.000
111A113ALA00.0350.01835.0800.0020.0020.0000.0000.0000.000
112A114ARG10.9771.00134.527-0.073-0.0730.0000.0000.0000.000
113A115ARG10.8460.89036.556-0.065-0.0650.0000.0000.0000.000
114A116LEU00.0140.01438.979-0.002-0.0020.0000.0000.0000.000
115A117LEU00.0020.00134.7070.0010.0010.0000.0000.0000.000
116A118GLN00.002-0.00938.737-0.005-0.0050.0000.0000.0000.000
117A119GLU-1-0.855-0.90440.9900.0720.0720.0000.0000.0000.000
118A120ARG10.9270.96541.252-0.120-0.1200.0000.0000.0000.000
119A121LEU0-0.004-0.00437.7950.0010.0010.0000.0000.0000.000
120A122ARG10.9020.95542.230-0.073-0.0730.0000.0000.0000.000
121A123ARG10.8900.95045.473-0.084-0.0840.0000.0000.0000.000
122A124LEU0-0.033-0.00541.5630.0030.0030.0000.0000.0000.000
123A125GLU-1-0.912-0.94946.0380.1040.1040.0000.0000.0000.000
124A126GLY0-0.021-0.00546.9320.0050.0050.0000.0000.0000.000
125A127VAL0-0.026-0.02241.9830.0080.0080.0000.0000.0000.000
126A128TRP00.0280.01841.816-0.006-0.0060.0000.0000.0000.000
127A129VAL00.0210.01140.8660.0060.0060.0000.0000.0000.000
128A130GLU-1-0.907-0.94539.7580.0660.0660.0000.0000.0000.000
129A131GLY0-0.014-0.00939.329-0.001-0.0010.0000.0000.0000.000
130A132LEU00.007-0.01134.363-0.002-0.0020.0000.0000.0000.000
131A133ALA0-0.0140.00935.6330.0120.0120.0000.0000.0000.000
132A134VAL00.0170.01536.607-0.007-0.0070.0000.0000.0000.000
133A135TYR0-0.027-0.00536.4810.0110.0110.0000.0000.0000.000
134A136ARG10.9110.94636.927-0.187-0.1870.0000.0000.0000.000
135A137ARG10.9870.99539.175-0.162-0.1620.0000.0000.0000.000
136A138GLU-1-0.756-0.88740.9650.0930.0930.0000.0000.0000.000
137A139HIS0-0.093-0.04537.8540.0190.0190.0000.0000.0000.000
138A140ALA00.0620.03641.7800.0000.0000.0000.0000.0000.000
139A141ARG10.8290.90144.474-0.076-0.0760.0000.0000.0000.000
140A142GLY00.1170.07247.514-0.002-0.0020.0000.0000.0000.000
141A143PRO00.015-0.00650.4590.0010.0010.0000.0000.0000.000
142A144GLY00.0510.00751.910-0.002-0.0020.0000.0000.0000.000
143A145TRP00.0200.03844.1050.0020.0020.0000.0000.0000.000
144A146ARG10.9310.96045.597-0.077-0.0770.0000.0000.0000.000
145A147VAL0-0.0050.02239.5450.0010.0010.0000.0000.0000.000
146A148LEU0-0.030-0.01240.9190.0050.0050.0000.0000.0000.000
147A149GLY00.0230.01736.9670.0010.0010.0000.0000.0000.000
148A150GLY0-0.032-0.05635.795-0.001-0.0010.0000.0000.0000.000
149A151ALA0-0.040-0.00731.6070.0150.0150.0000.0000.0000.000
150A152VAL0-0.0330.00630.321-0.013-0.0130.0000.0000.0000.000
151A153LEU0-0.010-0.01931.1220.0180.0180.0000.0000.0000.000
152A154ASP-1-0.846-0.94229.7110.1170.1170.0000.0000.0000.000
153A155LEU0-0.075-0.01731.2080.0190.0190.0000.0000.0000.000
154A156TRP0-0.041-0.02124.885-0.008-0.0080.0000.0000.0000.000
155A157VAL00.0230.01231.4220.0130.0130.0000.0000.0000.000
156A158SER00.0000.00227.038-0.010-0.0100.0000.0000.0000.000
157A159ASP-1-0.816-0.91725.4260.1500.1500.0000.0000.0000.000
158A160SER0-0.026-0.01927.0700.0020.0020.0000.0000.0000.000
159A161GLY0-0.039-0.01929.508-0.003-0.0030.0000.0000.0000.000
160A162ALA0-0.002-0.00130.589-0.004-0.0040.0000.0000.0000.000
161A163PHE0-0.029-0.01231.068-0.002-0.0020.0000.0000.0000.000
162A164LEU00.0170.01025.3220.0230.0230.0000.0000.0000.000
163A165LEU0-0.014-0.01129.221-0.019-0.0190.0000.0000.0000.000
164A166GLU-1-0.988-1.00225.7410.2390.2390.0000.0000.0000.000
165A167VAL00.041-0.00227.186-0.019-0.0190.0000.0000.0000.000
166A168ASP-1-0.815-0.91926.3150.2920.2920.0000.0000.0000.000
167A169PRO0-0.020-0.00827.735-0.024-0.0240.0000.0000.0000.000
168A170ALA0-0.033-0.01029.9640.0010.0010.0000.0000.0000.000
169A171TYR00.0220.00632.6970.0090.0090.0000.0000.0000.000
170A172ARG10.9190.95436.016-0.082-0.0820.0000.0000.0000.000
171A173ILE00.0400.03339.0180.0050.0050.0000.0000.0000.000
172A174LEU0-0.049-0.02241.870-0.005-0.0050.0000.0000.0000.000
173A175CYS0-0.0060.00145.053-0.001-0.0010.0000.0000.0000.000
174A176GLU-1-0.977-0.99948.3610.0630.0630.0000.0000.0000.000
175A177MET0-0.0230.02351.409-0.002-0.0020.0000.0000.0000.000
176A178SER00.0200.02252.6200.0000.0000.0000.0000.0000.000
177A179LEU00.014-0.01451.8520.0010.0010.0000.0000.0000.000
178A180GLU-1-0.820-0.88953.9570.0120.0120.0000.0000.0000.000
179A181ALA0-0.006-0.00756.439-0.001-0.0010.0000.0000.0000.000
180A182TRP00.008-0.03248.073-0.001-0.0010.0000.0000.0000.000
181A183LEU0-0.012-0.01453.2440.0000.0000.0000.0000.0000.000
182A184ALA00.0250.03855.838-0.001-0.0010.0000.0000.0000.000
183A185GLN0-0.087-0.06556.4670.0010.0010.0000.0000.0000.000
184A186GLY00.0370.02156.6460.0020.0020.0000.0000.0000.000
185A187HIS10.8250.94050.790-0.032-0.0320.0000.0000.0000.000
186A188PRO00.0670.03248.897-0.002-0.0020.0000.0000.0000.000
187A189LEU00.0400.00450.3340.0030.0030.0000.0000.0000.000
188A190PRO00.0130.02846.516-0.001-0.0010.0000.0000.0000.000
189A191LYS10.8900.94242.1630.0110.0110.0000.0000.0000.000
190A192ARG10.9300.95040.774-0.004-0.0040.0000.0000.0000.000
191A193VAL00.0380.03245.0450.0040.0040.0000.0000.0000.000
192A194ARG10.8680.95545.505-0.043-0.0430.0000.0000.0000.000
193A195ASN00.0450.05047.798-0.003-0.0030.0000.0000.0000.000
194A196ALA00.0250.00250.0990.0040.0040.0000.0000.0000.000
195A197TYR0-0.007-0.01452.5090.0030.0030.0000.0000.0000.000
196A198ASP-1-0.834-0.91449.5460.0270.0270.0000.0000.0000.000
197A199ARG10.8560.89043.817-0.063-0.0630.0000.0000.0000.000
198A200ARG10.9100.98945.071-0.004-0.0040.0000.0000.0000.000
199A201THR0-0.044-0.02642.7020.0000.0000.0000.0000.0000.000
200A202TRP0-0.004-0.02345.462-0.004-0.0040.0000.0000.0000.000
201A203GLU-1-0.929-0.94244.433-0.018-0.0180.0000.0000.0000.000
202A204LEU00.035-0.00146.127-0.002-0.0020.0000.0000.0000.000
203A205LEU0-0.063-0.02048.489-0.002-0.0020.0000.0000.0000.000
204A206ARG10.9520.97350.6600.0130.0130.0000.0000.0000.000
205A207LEU00.0560.02553.9080.0020.0020.0000.0000.0000.000
206A208GLY0-0.071-0.03857.036-0.003-0.0030.0000.0000.0000.000
207A209GLU-1-0.957-0.98360.236-0.007-0.0070.0000.0000.0000.000
208A210GLU-1-0.759-0.87961.829-0.009-0.0090.0000.0000.0000.000
209A211ASP-1-0.850-0.93664.591-0.001-0.0010.0000.0000.0000.000
210A212PRO0-0.019-0.01563.3740.0000.0000.0000.0000.0000.000
211A213LYS10.8670.90765.013-0.004-0.0040.0000.0000.0000.000
212A214GLU-1-0.895-0.93668.171-0.001-0.0010.0000.0000.0000.000
213A215LEU0-0.0220.02061.546-0.002-0.0020.0000.0000.0000.000
214A216PRO0-0.001-0.00465.3770.0010.0010.0000.0000.0000.000
215A217LEU0-0.049-0.03360.449-0.001-0.0010.0000.0000.0000.000
216A218PRO0-0.014-0.02359.6790.0000.0000.0000.0000.0000.000
217A219GLY0-0.002-0.00562.932-0.001-0.0010.0000.0000.0000.000
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