Manual

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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: PL7J9

Calculation Name: 3G3P-A-Xray28

Preferred Name:

Target Type:

Ligand Name: norleucine

ligand 3-letter code: NLE

PDB ID: 3G3P

Chain ID: A

ChEMBL ID:

UniProt ID: Q9A5I0

Base Structure: X-ray

Registration Date: 2018-07-26

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water Apo structure with with a 3 angstrom solvent shell.
Procedure Auto-FMO protocol ver. 1.20180227
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 202
LigandCharge MG2=2
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -829497.98374
FMO2-HF: Nuclear repulsion 786439.020306
FMO2-HF: Total energy -43058.963435
FMO2-MP2: Total energy -43179.429207


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:37:ACE)


Summations of interaction energy for fragment #1(A:37:ACE)
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.
1.9732.4590-0.213-0.2730.001
Interaction energy analysis for fragmet #1(A:37:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.030 / q_NPA : 0.003
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].
3A39SER0-0.0320.0113.8501.0061.4920.000-0.213-0.2730.001
4A40LEU00.0500.0336.3220.2900.2900.0000.0000.0000.000
5A41TYR00.0300.0138.650-0.228-0.2280.0000.0000.0000.000
6A42ARG10.8480.92812.5590.4430.4430.0000.0000.0000.000
7A43VAL00.0110.00215.936-0.006-0.0060.0000.0000.0000.000
8A44LEU0-0.034-0.01919.0280.0180.0180.0000.0000.0000.000
9A45ILE00.0340.01421.7620.0020.0020.0000.0000.0000.000
10A46LEU00.002-0.00224.0220.0000.0000.0000.0000.0000.000
11A47ASN00.0150.02327.4190.0050.0050.0000.0000.0000.000
12A48ASP-1-0.793-0.87631.056-0.101-0.1010.0000.0000.0000.000
13A49ASP-1-0.878-0.92233.918-0.075-0.0750.0000.0000.0000.000
14A50TYR0-0.041-0.01536.5840.0060.0060.0000.0000.0000.000
15A51THR0-0.054-0.04433.4280.0030.0030.0000.0000.0000.000
16A52PRO00.0050.02436.394-0.001-0.0010.0000.0000.0000.000
17A53ALA00.0960.03935.855-0.005-0.0050.0000.0000.0000.000
18A54GLU-1-0.859-0.92135.583-0.070-0.0700.0000.0000.0000.000
19A55PHE00.0190.01532.426-0.003-0.0030.0000.0000.0000.000
20A56VAL00.0250.01330.243-0.006-0.0060.0000.0000.0000.000
21A57VAL0-0.032-0.01231.234-0.007-0.0070.0000.0000.0000.000
22A58TYR00.0240.02032.459-0.005-0.0050.0000.0000.0000.000
23A59VAL0-0.027-0.00828.025-0.004-0.0040.0000.0000.0000.000
24A60LEU0-0.010-0.01226.381-0.009-0.0090.0000.0000.0000.000
25A61GLU-1-0.797-0.87028.162-0.085-0.0850.0000.0000.0000.000
26A62ARG10.8550.94229.9010.0920.0920.0000.0000.0000.000
27A63PHE0-0.035-0.02125.8750.0000.0000.0000.0000.0000.000
28A64PHE00.000-0.00721.562-0.016-0.0160.0000.0000.0000.000
29A65ASN0-0.044-0.00124.5190.0070.0070.0000.0000.0000.000
30A66LYS10.8430.95623.0500.1650.1650.0000.0000.0000.000
31A67SER00.0810.02928.6200.0040.0040.0000.0000.0000.000
32A68ARG11.0221.02031.9050.0560.0560.0000.0000.0000.000
33A69GLU-1-0.840-0.86833.998-0.068-0.0680.0000.0000.0000.000
34A70ASP-1-0.755-0.83928.690-0.102-0.1020.0000.0000.0000.000
35A71ALA0-0.011-0.00329.906-0.007-0.0070.0000.0000.0000.000
36A72THR00.016-0.00330.995-0.001-0.0010.0000.0000.0000.000
37A73ARG10.9210.98025.8990.1180.1180.0000.0000.0000.000
38A74ILE0-0.049-0.02825.640-0.003-0.0030.0000.0000.0000.000
39A75MET0-0.0080.01428.913-0.003-0.0030.0000.0000.0000.000
40A76LEU00.0330.00331.5400.0010.0010.0000.0000.0000.000
41A77HIS0-0.0120.01626.453-0.007-0.0070.0000.0000.0000.000
42A78VAL0-0.035-0.00227.834-0.003-0.0030.0000.0000.0000.000
43A79HIS00.0170.00529.766-0.003-0.0030.0000.0000.0000.000
44A80GLN0-0.019-0.00132.7020.0010.0010.0000.0000.0000.000
45A81ASN0-0.039-0.02828.1370.0030.0030.0000.0000.0000.000
46A82GLY00.0670.04828.713-0.004-0.0040.0000.0000.0000.000
47A83VAL0-0.007-0.00823.173-0.008-0.0080.0000.0000.0000.000
48A84GLY00.0420.03725.1370.0080.0080.0000.0000.0000.000
49A85VAL0-0.071-0.02519.434-0.014-0.0140.0000.0000.0000.000
50A86CYS00.0180.01521.6930.0190.0190.0000.0000.0000.000
51A87GLY00.0340.01119.8690.0210.0210.0000.0000.0000.000
52A88VAL0-0.074-0.01813.625-0.029-0.0290.0000.0000.0000.000
53A89TYR0-0.013-0.01114.6800.0500.0500.0000.0000.0000.000
54A90THR00.0660.02010.922-0.095-0.0950.0000.0000.0000.000
55A91TYR0-0.004-0.00710.6190.0330.0330.0000.0000.0000.000
56A92GLU-1-0.787-0.88212.498-0.409-0.4090.0000.0000.0000.000
57A93VAL0-0.0150.00615.2440.0550.0550.0000.0000.0000.000
58A94ALA0-0.011-0.01115.2060.0410.0410.0000.0000.0000.000
59A95GLU-1-0.754-0.88316.111-0.276-0.2760.0000.0000.0000.000
60A96THR0-0.021-0.00318.5050.0420.0420.0000.0000.0000.000
61A97LYS10.8200.90520.2770.2050.2050.0000.0000.0000.000
62A98VAL00.0270.00719.6540.0210.0210.0000.0000.0000.000
63A99ALA0-0.022-0.00622.4170.0200.0200.0000.0000.0000.000
64A100GLN00.0260.03724.5610.0140.0140.0000.0000.0000.000
65A101VAL00.0540.02925.3560.0150.0150.0000.0000.0000.000
66A102ILE0-0.0210.00125.9030.0120.0120.0000.0000.0000.000
67A103ASP-1-0.756-0.85328.437-0.089-0.0890.0000.0000.0000.000
68A104SER00.0030.00330.2790.0110.0110.0000.0000.0000.000
69A105ALA0-0.0020.00331.1820.0080.0080.0000.0000.0000.000
70A106ARG10.8600.93729.8300.1190.1190.0000.0000.0000.000
71A107ARG10.8350.91032.8810.0930.0930.0000.0000.0000.000
72A108HIS0-0.106-0.04835.3520.0080.0080.0000.0000.0000.000
73A109GLN0-0.055-0.01137.6230.0030.0030.0000.0000.0000.000
74A110HIS00.0370.02134.7260.0070.0070.0000.0000.0000.000
75A111PRO00.0160.01633.830-0.005-0.0050.0000.0000.0000.000
76A112LEU00.0160.02029.143-0.006-0.0060.0000.0000.0000.000
77A113GLN0-0.0050.02026.845-0.005-0.0050.0000.0000.0000.000
78A114CYS0-0.078-0.02523.471-0.006-0.0060.0000.0000.0000.000
79A115THR00.0660.02820.312-0.003-0.0030.0000.0000.0000.000
80A116MET00.0050.00914.4600.0080.0080.0000.0000.0000.000
81A117GLU-1-0.837-0.86414.940-0.309-0.3090.0000.0000.0000.000
82A118LYS10.9020.9558.2560.7880.7880.0000.0000.0000.000
83A119ASP-2-1.215-1.70710.603-1.021-1.0210.0000.0000.0000.000
84A1MG221.1961.82611.7581.0241.0240.0000.0000.0000.000
85A2HOH00.003-0.01330.059-0.002-0.0020.0000.0000.0000.000
86A3HOH0-0.021-0.01529.5490.0010.0010.0000.0000.0000.000
87A5HOH0-0.014-0.03128.145-0.001-0.0010.0000.0000.0000.000
88A6HOH00.0370.00833.5720.0000.0000.0000.0000.0000.000
89A8HOH00.0080.00438.807-0.002-0.0020.0000.0000.0000.000
90A9HOH0-0.017-0.01437.125-0.001-0.0010.0000.0000.0000.000
91A10HOH00.0160.01238.742-0.001-0.0010.0000.0000.0000.000
92A11HOH00.0420.02922.228-0.002-0.0020.0000.0000.0000.000
93A13HOH00.0140.01421.061-0.009-0.0090.0000.0000.0000.000
94A15HOH00.0070.0058.5120.1330.1330.0000.0000.0000.000
95A17HOH00.0290.01935.0570.0000.0000.0000.0000.0000.000
96A18HOH0-0.006-0.01532.816-0.003-0.0030.0000.0000.0000.000
97A20HOH00.0080.00537.9530.0000.0000.0000.0000.0000.000
98A22HOH0-0.002-0.01015.029-0.023-0.0230.0000.0000.0000.000
99A27HOH00.009-0.00324.6750.0040.0040.0000.0000.0000.000
100A28HOH0-0.035-0.03536.9160.0000.0000.0000.0000.0000.000
101A29HOH0-0.004-0.01524.432-0.005-0.0050.0000.0000.0000.000
102A33HOH0-0.010-0.00229.672-0.004-0.0040.0000.0000.0000.000
103A120HOH0-0.022-0.02321.2330.0090.0090.0000.0000.0000.000
104A122HOH0-0.051-0.03937.1480.0020.0020.0000.0000.0000.000
105A124HOH00.0500.02818.7370.0030.0030.0000.0000.0000.000
106A125HOH0-0.048-0.03432.1620.0010.0010.0000.0000.0000.000
107A126HOH0-0.039-0.02640.3170.0010.0010.0000.0000.0000.000
108A127HOH0-0.069-0.05219.0810.0040.0040.0000.0000.0000.000
109A128HOH0-0.025-0.01919.5650.0060.0060.0000.0000.0000.000
110A129HOH0-0.029-0.01714.9760.0170.0170.0000.0000.0000.000
111A130HOH00.0190.01130.6130.0030.0030.0000.0000.0000.000
112A131HOH0-0.004-0.01139.2300.0000.0000.0000.0000.0000.000
113A133HOH0-0.020-0.01540.4730.0010.0010.0000.0000.0000.000
114A134HOH00.0290.01436.580-0.002-0.0020.0000.0000.0000.000
115A135HOH00.0290.01434.6390.0000.0000.0000.0000.0000.000
116A136HOH0-0.032-0.02032.8300.0020.0020.0000.0000.0000.000
117A139HOH00.0020.00622.562-0.004-0.0040.0000.0000.0000.000
118A141HOH0-0.054-0.03439.2620.0000.0000.0000.0000.0000.000
119A142HOH00.0020.01716.2100.0180.0180.0000.0000.0000.000
120A143HOH0-0.019-0.01736.6620.0020.0020.0000.0000.0000.000
121A145HOH0-0.026-0.03917.764-0.003-0.0030.0000.0000.0000.000
122A146HOH00.084-0.0059.0740.0770.0770.0000.0000.0000.000
123A147HOH00.0290.00622.9940.0070.0070.0000.0000.0000.000
124A148HOH0-0.048-0.02717.9900.0120.0120.0000.0000.0000.000
125A149HOH00.0230.01125.669-0.004-0.0040.0000.0000.0000.000
126A150HOH0-0.038-0.02331.7990.0000.0000.0000.0000.0000.000
127A151HOH00.0190.00439.818-0.001-0.0010.0000.0000.0000.000
128A153HOH0-0.025-0.01529.6820.0030.0030.0000.0000.0000.000
129A154HOH0-0.007-0.00918.1710.0070.0070.0000.0000.0000.000
130A156HOH00.0090.00337.5230.0010.0010.0000.0000.0000.000
131A158HOH0-0.007-0.00614.506-0.035-0.0350.0000.0000.0000.000
132A159HOH0-0.0020.00136.523-0.001-0.0010.0000.0000.0000.000
133A160HOH0-0.013-0.01629.532-0.002-0.0020.0000.0000.0000.000
134A163HOH00.0280.01723.184-0.006-0.0060.0000.0000.0000.000
135A164HOH0-0.016-0.02135.9810.0000.0000.0000.0000.0000.000
136A165HOH00.0280.01524.844-0.004-0.0040.0000.0000.0000.000
137A166HOH0-0.031-0.01826.395-0.005-0.0050.0000.0000.0000.000
138A167HOH0-0.023-0.01324.594-0.003-0.0030.0000.0000.0000.000
139A168HOH00.0030.00812.780-0.025-0.0250.0000.0000.0000.000
140A171HOH0-0.031-0.02022.3180.0070.0070.0000.0000.0000.000
141A172HOH0-0.014-0.01719.732-0.008-0.0080.0000.0000.0000.000
142A173HOH0-0.032-0.03031.182-0.001-0.0010.0000.0000.0000.000
143A174HOH0-0.003-0.00838.1650.0000.0000.0000.0000.0000.000
144A175HOH00.0230.01629.000-0.001-0.0010.0000.0000.0000.000
145A176HOH0-0.018-0.01333.3510.0000.0000.0000.0000.0000.000
146A177HOH0-0.039-0.02514.6230.0160.0160.0000.0000.0000.000
147A178HOH0-0.018-0.02131.4810.0020.0020.0000.0000.0000.000
148A179HOH0-0.011-0.01532.0420.0030.0030.0000.0000.0000.000
149A180HOH00.0280.00413.559-0.043-0.0430.0000.0000.0000.000
150A181HOH00.0170.00941.3610.0000.0000.0000.0000.0000.000
151A184HOH0-0.047-0.04819.615-0.005-0.0050.0000.0000.0000.000
152A189HOH00.0120.00336.6870.0000.0000.0000.0000.0000.000
153A191HOH00.0160.00829.8900.0030.0030.0000.0000.0000.000
154A195HOH0-0.065-0.04232.9770.0010.0010.0000.0000.0000.000
155A197HOH0-0.055-0.04636.6920.0020.0020.0000.0000.0000.000
156A199HOH0-0.043-0.02810.405-0.014-0.0140.0000.0000.0000.000
157A203HOH0-0.019-0.00835.6340.0000.0000.0000.0000.0000.000
158A204HOH00.038-0.01313.266-0.004-0.0040.0000.0000.0000.000
159A205HOH0-0.0070.00131.6480.0030.0030.0000.0000.0000.000
160A206HOH0-0.035-0.03833.8140.0020.0020.0000.0000.0000.000
161A207HOH0-0.021-0.01521.5000.0020.0020.0000.0000.0000.000
162A208HOH0-0.028-0.02318.3330.0130.0130.0000.0000.0000.000
163A210HOH0-0.017-0.01818.944-0.010-0.0100.0000.0000.0000.000
164A211HOH0-0.029-0.02926.6090.0010.0010.0000.0000.0000.000
165A220HOH0-0.028-0.02137.9640.0010.0010.0000.0000.0000.000
166A227HOH0-0.084-0.07935.6210.0000.0000.0000.0000.0000.000
167A234HOH00.0130.00837.2990.0000.0000.0000.0000.0000.000
168A241HOH0-0.037-0.02429.0130.0020.0020.0000.0000.0000.000
169A242HOH0-0.012-0.01713.5060.0020.0020.0000.0000.0000.000
170A243HOH0-0.052-0.04027.672-0.003-0.0030.0000.0000.0000.000
171A244HOH00.0370.02627.543-0.001-0.0010.0000.0000.0000.000
172A247HOH00.0090.00416.1850.0030.0030.0000.0000.0000.000
173A249HOH00.0170.0047.4890.0770.0770.0000.0000.0000.000
174A251HOH0-0.003-0.0066.6470.1690.1690.0000.0000.0000.000
175A252HOH0-0.0070.00432.9660.0030.0030.0000.0000.0000.000
176A256HOH0-0.030-0.02226.9970.0010.0010.0000.0000.0000.000
177A261HOH00.0060.00125.489-0.002-0.0020.0000.0000.0000.000
178A264HOH0-0.026-0.02036.4760.0020.0020.0000.0000.0000.000
179A265HOH0-0.024-0.01035.2580.0020.0020.0000.0000.0000.000
180A266HOH0-0.048-0.04234.5940.0010.0010.0000.0000.0000.000
181A267HOH00.0280.03032.7790.0010.0010.0000.0000.0000.000
182A269HOH00.0360.01839.808-0.002-0.0020.0000.0000.0000.000
183A276HOH00.0470.03626.2180.0040.0040.0000.0000.0000.000
184A281HOH00.029-0.00225.430-0.002-0.0020.0000.0000.0000.000
185A287HOH0-0.034-0.0215.4540.2050.2050.0000.0000.0000.000
186A290HOH0-0.019-0.00117.345-0.010-0.0100.0000.0000.0000.000
187A294HOH0-0.038-0.04141.2190.0000.0000.0000.0000.0000.000
188A296HOH00.0340.01938.281-0.001-0.0010.0000.0000.0000.000
189A297HOH0-0.024-0.02537.2650.0010.0010.0000.0000.0000.000
190A302HOH00.0030.01122.7350.0030.0030.0000.0000.0000.000
191A304HOH00.0140.00519.525-0.001-0.0010.0000.0000.0000.000
192A305HOH00.003-0.0156.801-0.356-0.3560.0000.0000.0000.000
193B34HOH0-0.022-0.01528.573-0.002-0.0020.0000.0000.0000.000
194B144HOH00.068-0.00410.5280.0340.0340.0000.0000.0000.000
195B153HOH00.009-0.00432.177-0.003-0.0030.0000.0000.0000.000
196B169HOH0-0.016-0.00824.317-0.006-0.0060.0000.0000.0000.000
197B193HOH0-0.051-0.04424.8060.0020.0020.0000.0000.0000.000
198B198HOH0-0.034-0.02425.366-0.006-0.0060.0000.0000.0000.000
199B214HOH00.0300.01734.084-0.002-0.0020.0000.0000.0000.000
200B257HOH00.0260.02016.145-0.027-0.0270.0000.0000.0000.000
201B275HOH0-0.020-0.02327.0270.0030.0030.0000.0000.0000.000
202B306HOH00.0230.01220.787-0.002-0.0020.0000.0000.0000.000