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: P4L9N

Calculation Name: 3K12-A-Xray28

Preferred Name:
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Target Type:
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Ligand Name: glycerol

ligand 3-letter code: GOL

PDB ID: 3K12

Chain ID: A

ChEMBL ID:
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UniProt ID: Q9I3E9

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 203
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1123457.873977
FMO2-HF: Nuclear repulsion 1070920.487853
FMO2-HF: Total energy -52537.386124
FMO2-MP2: Total energy -52688.923122


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:4:HIS)


Summations of interaction energy for fragment #1(A:4: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.
-10.551-5.5990.263-2.315-2.9-0.002
Interaction energy analysis for fragmet #1(A:4:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / q_NPA : 0.004
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].
3A6GLU-1-0.950-0.9652.963-9.784-4.9130.264-2.311-2.825-0.002
4A7ARG10.8580.9125.497-0.812-0.731-0.001-0.004-0.0750.000
5A8PHE00.0410.0277.334-0.220-0.2200.0000.0000.0000.000
6A9GLU-1-0.824-0.90711.688-0.067-0.0670.0000.0000.0000.000
7A10VAL0-0.0130.00815.177-0.078-0.0780.0000.0000.0000.000
8A11VAL00.0260.00117.1130.0520.0520.0000.0000.0000.000
9A12LYS10.9380.96920.0050.1510.1510.0000.0000.0000.000
10A13ARG10.9530.97623.1070.2390.2390.0000.0000.0000.000
11A14ARG10.8750.92325.0800.0740.0740.0000.0000.0000.000
12A15ALA0-0.003-0.00428.7640.0080.0080.0000.0000.0000.000
13A16GLU-1-0.760-0.84331.566-0.071-0.0710.0000.0000.0000.000
14A17MET00.0210.01233.2800.0060.0060.0000.0000.0000.000
15A18ALA0-0.027-0.00335.570-0.007-0.0070.0000.0000.0000.000
16A19LEU0-0.005-0.00138.2010.0050.0050.0000.0000.0000.000
17A20HIS0-0.0040.00241.139-0.004-0.0040.0000.0000.0000.000
18A21GLY00.0020.00143.9460.0030.0030.0000.0000.0000.000
19A22ASN00.008-0.01345.5210.0010.0010.0000.0000.0000.000
20A23THR0-0.032-0.00645.8480.0030.0030.0000.0000.0000.000
21A24VAL0-0.009-0.00241.050-0.004-0.0040.0000.0000.0000.000
22A25TYR0-0.012-0.00640.6130.0020.0020.0000.0000.0000.000
23A26ILE00.0050.00337.381-0.003-0.0030.0000.0000.0000.000
24A27GLY00.0190.01835.586-0.003-0.0030.0000.0000.0000.000
25A28GLY00.0240.01636.5960.0090.0090.0000.0000.0000.000
26A29GLN0-0.0280.01434.3810.0030.0030.0000.0000.0000.000
27A30VAL00.0660.01932.8820.0010.0010.0000.0000.0000.000
28A31ALA00.0460.02834.6680.0040.0040.0000.0000.0000.000
29A32ASP-1-0.720-0.80330.552-0.036-0.0360.0000.0000.0000.000
30A33ASP-1-0.809-0.86930.251-0.003-0.0030.0000.0000.0000.000
31A34PRO0-0.052-0.01231.3120.0040.0040.0000.0000.0000.000
32A35SER0-0.042-0.03933.466-0.003-0.0030.0000.0000.0000.000
33A36GLY00.0490.03535.2650.0020.0020.0000.0000.0000.000
34A37ASP-1-0.773-0.87238.741-0.016-0.0160.0000.0000.0000.000
35A38ILE0-0.024-0.01741.487-0.001-0.0010.0000.0000.0000.000
36A39GLN0-0.0030.00243.343-0.002-0.0020.0000.0000.0000.000
37A40ASP-1-0.836-0.89838.255-0.003-0.0030.0000.0000.0000.000
38A41GLN00.0440.03037.432-0.007-0.0070.0000.0000.0000.000
39A42THR0-0.018-0.02739.601-0.004-0.0040.0000.0000.0000.000
40A43ARG10.9540.97441.9870.0020.0020.0000.0000.0000.000
41A44GLN00.0130.01234.847-0.003-0.0030.0000.0000.0000.000
42A45ILE0-0.0020.00937.639-0.001-0.0010.0000.0000.0000.000
43A46LEU0-0.014-0.01438.953-0.002-0.0020.0000.0000.0000.000
44A47GLU-1-0.817-0.88539.1270.0030.0030.0000.0000.0000.000
45A48ASN0-0.061-0.05434.4480.0100.0100.0000.0000.0000.000
46A49ILE0-0.0010.00137.434-0.002-0.0020.0000.0000.0000.000
47A50ASP-1-0.732-0.83240.099-0.013-0.0130.0000.0000.0000.000
48A51ARG10.8500.93334.5560.0060.0060.0000.0000.0000.000
49A52LEU00.0120.00634.3810.0000.0000.0000.0000.0000.000
50A53LEU00.0350.02237.993-0.002-0.0020.0000.0000.0000.000
51A54GLN00.0330.04739.6340.0000.0000.0000.0000.0000.000
52A55SER0-0.096-0.05136.841-0.001-0.0010.0000.0000.0000.000
53A56VAL0-0.051-0.02438.697-0.002-0.0020.0000.0000.0000.000
54A57GLY0-0.033-0.01641.053-0.002-0.0020.0000.0000.0000.000
55A58SER0-0.044-0.03343.899-0.001-0.0010.0000.0000.0000.000
56A59ASP-1-0.850-0.94045.193-0.014-0.0140.0000.0000.0000.000
57A60ARG10.7980.85745.2250.0070.0070.0000.0000.0000.000
58A61GLY0-0.033-0.00947.458-0.002-0.0020.0000.0000.0000.000
59A62GLN00.0290.02548.380-0.003-0.0030.0000.0000.0000.000
60A63VAL00.007-0.00246.200-0.004-0.0040.0000.0000.0000.000
61A64LEU0-0.015-0.00148.3820.0010.0010.0000.0000.0000.000
62A65SER0-0.0040.02048.086-0.001-0.0010.0000.0000.0000.000
63A66VAL00.0200.01044.744-0.002-0.0020.0000.0000.0000.000
64A67ARG10.8700.93644.5280.0720.0720.0000.0000.0000.000
65A68ILE0-0.005-0.01644.256-0.001-0.0010.0000.0000.0000.000
66A69LEU0-0.022-0.01140.4080.0000.0000.0000.0000.0000.000
67A70LEU00.009-0.00442.3530.0010.0010.0000.0000.0000.000
68A71ALA00.0190.02140.380-0.002-0.0020.0000.0000.0000.000
69A72HIS00.0240.01940.226-0.001-0.0010.0000.0000.0000.000
70A73ARG10.9720.97745.1870.0500.0500.0000.0000.0000.000
71A74GLU-1-0.907-0.96747.657-0.041-0.0410.0000.0000.0000.000
72A75ASP-1-0.744-0.83844.038-0.032-0.0320.0000.0000.0000.000
73A76TYR00.0070.02147.5630.0010.0010.0000.0000.0000.000
74A77ALA00.0200.00850.0500.0010.0010.0000.0000.0000.000
75A78GLY00.0800.03148.4690.0020.0020.0000.0000.0000.000
76A79LEU00.020-0.00345.6150.0020.0020.0000.0000.0000.000
77A80ASN00.011-0.00347.8080.0000.0000.0000.0000.0000.000
78A81GLN00.0540.06549.8480.0000.0000.0000.0000.0000.000
79A82VAL00.0080.00845.4770.0020.0020.0000.0000.0000.000
80A83TRP00.0250.01146.3500.0000.0000.0000.0000.0000.000
81A84ASP-1-0.817-0.91149.418-0.023-0.0230.0000.0000.0000.000
82A85GLN0-0.116-0.04750.7130.0010.0010.0000.0000.0000.000
83A86TRP0-0.016-0.00343.9720.0040.0040.0000.0000.0000.000
84A87PHE00.0100.00047.4120.0010.0010.0000.0000.0000.000
85A88PRO00.0140.00551.0680.0010.0010.0000.0000.0000.000
86A89GLU-1-0.866-0.92054.312-0.012-0.0120.0000.0000.0000.000
87A90GLY00.0090.00257.9500.0000.0000.0000.0000.0000.000
88A91ARG10.9000.95053.7790.0160.0160.0000.0000.0000.000
89A92ALA0-0.0130.01252.706-0.001-0.0010.0000.0000.0000.000
90A93PRO00.0110.03349.063-0.001-0.0010.0000.0000.0000.000
91A94THR0-0.039-0.03052.001-0.001-0.0010.0000.0000.0000.000
92A95ARG10.8850.91850.0600.0350.0350.0000.0000.0000.000
93A96ALA0-0.0060.00049.7730.0000.0000.0000.0000.0000.000
94A97CYS0-0.0270.00048.311-0.004-0.0040.0000.0000.0000.000
95A98SER00.0160.01546.8570.0010.0010.0000.0000.0000.000
96A99LEU0-0.0090.00046.0810.0010.0010.0000.0000.0000.000
97A100ALA0-0.048-0.02541.988-0.002-0.0020.0000.0000.0000.000
98A101GLU-1-0.929-0.95437.847-0.104-0.1040.0000.0000.0000.000
99A102LEU0-0.105-0.05336.705-0.005-0.0050.0000.0000.0000.000
100A103ILE0-0.024-0.01630.743-0.004-0.0040.0000.0000.0000.000
101A104ASP-1-0.753-0.84330.146-0.105-0.1050.0000.0000.0000.000
102A105PRO00.0180.01431.9320.0100.0100.0000.0000.0000.000
103A106ARG10.8980.93429.5250.0560.0560.0000.0000.0000.000
104A107TRP00.0040.01330.9310.0030.0030.0000.0000.0000.000
105A108ARG10.8310.91336.4240.0320.0320.0000.0000.0000.000
106A109VAL0-0.028-0.01839.3470.0000.0000.0000.0000.0000.000
107A110GLU-1-0.764-0.84936.811-0.102-0.1020.0000.0000.0000.000
108A111MET0-0.034-0.01139.6330.0030.0030.0000.0000.0000.000
109A112ILE00.0020.01139.996-0.003-0.0030.0000.0000.0000.000
110A113VAL00.0350.02341.4780.0040.0040.0000.0000.0000.000
111A114VAL0-0.033-0.00442.669-0.005-0.0050.0000.0000.0000.000
112A115ALA00.0200.00744.7970.0040.0040.0000.0000.0000.000
113A116ALA00.0320.02546.538-0.004-0.0040.0000.0000.0000.000
114A117ARG10.8930.96443.6580.0430.0430.0000.0000.0000.000
115A118GLU-1-0.983-0.98147.510-0.028-0.0280.0000.0000.0000.000
116A0NME0-0.0070.00150.6800.0030.0030.0000.0000.0000.000
117A126HOH0-0.019-0.02032.7250.0000.0000.0000.0000.0000.000
118A127HOH0-0.003-0.01046.920-0.001-0.0010.0000.0000.0000.000
119A128HOH00.0200.00946.6360.0010.0010.0000.0000.0000.000
120A130HOH0-0.021-0.00811.540-0.024-0.0240.0000.0000.0000.000
121A131HOH0-0.025-0.02943.052-0.002-0.0020.0000.0000.0000.000
122A132HOH0-0.044-0.03551.812-0.001-0.0010.0000.0000.0000.000
123A133HOH0-0.015-0.02050.206-0.001-0.0010.0000.0000.0000.000
124A134HOH0-0.020-0.02051.646-0.001-0.0010.0000.0000.0000.000
125A135HOH0-0.045-0.04746.7100.0010.0010.0000.0000.0000.000
126A136HOH0-0.012-0.00837.077-0.001-0.0010.0000.0000.0000.000
127A137HOH0-0.002-0.00444.4400.0000.0000.0000.0000.0000.000
128A139HOH0-0.012-0.00811.9040.0560.0560.0000.0000.0000.000
129A140HOH00.0040.00241.754-0.003-0.0030.0000.0000.0000.000
130A142HOH0-0.017-0.01448.1260.0000.0000.0000.0000.0000.000
131A144HOH0-0.024-0.01852.383-0.001-0.0010.0000.0000.0000.000
132A145HOH00.0290.02412.344-0.001-0.0010.0000.0000.0000.000
133A147HOH0-0.005-0.01036.406-0.001-0.0010.0000.0000.0000.000
134A148HOH0-0.017-0.01849.1180.0000.0000.0000.0000.0000.000
135A149HOH0-0.014-0.00857.4680.0000.0000.0000.0000.0000.000
136A150HOH00.0280.02041.026-0.001-0.0010.0000.0000.0000.000
137A152HOH00.0290.02847.0930.0010.0010.0000.0000.0000.000
138A153HOH0-0.058-0.04115.4450.0130.0130.0000.0000.0000.000
139A154HOH0-0.049-0.03845.539-0.002-0.0020.0000.0000.0000.000
140A155HOH0-0.013-0.00844.741-0.001-0.0010.0000.0000.0000.000
141A158HOH0-0.011-0.00844.980-0.001-0.0010.0000.0000.0000.000
142A160HOH0-0.0050.00547.3410.0000.0000.0000.0000.0000.000
143A161HOH0-0.018-0.01634.379-0.003-0.0030.0000.0000.0000.000
144A162HOH0-0.052-0.03128.530-0.005-0.0050.0000.0000.0000.000
145A163HOH00.004-0.00135.2750.0030.0030.0000.0000.0000.000
146A164HOH0-0.060-0.05631.984-0.004-0.0040.0000.0000.0000.000
147A165HOH0-0.059-0.05342.468-0.001-0.0010.0000.0000.0000.000
148A166HOH0-0.039-0.02542.3430.0010.0010.0000.0000.0000.000
149A167HOH00.0340.01638.3730.0020.0020.0000.0000.0000.000
150A168HOH0-0.011-0.00543.503-0.001-0.0010.0000.0000.0000.000
151A169HOH00.0330.0196.4900.1950.1950.0000.0000.0000.000
152A170HOH0-0.037-0.02156.9950.0010.0010.0000.0000.0000.000
153A171HOH0-0.010-0.02438.8830.0020.0020.0000.0000.0000.000
154A172HOH0-0.0110.00138.676-0.002-0.0020.0000.0000.0000.000
155A173HOH0-0.049-0.04043.5830.0010.0010.0000.0000.0000.000
156A174HOH00.0320.0265.670-0.079-0.0790.0000.0000.0000.000
157A175HOH0-0.005-0.00330.287-0.005-0.0050.0000.0000.0000.000
158A178HOH0-0.015-0.00828.3600.0070.0070.0000.0000.0000.000
159A179HOH0-0.056-0.04340.624-0.001-0.0010.0000.0000.0000.000
160A180HOH00.0240.01359.2930.0000.0000.0000.0000.0000.000
161A182HOH0-0.050-0.02753.3370.0000.0000.0000.0000.0000.000
162A183HOH0-0.035-0.03633.2400.0040.0040.0000.0000.0000.000
163A184HOH00.0150.01612.4310.0460.0460.0000.0000.0000.000
164A185HOH0-0.051-0.04236.338-0.002-0.0020.0000.0000.0000.000
165A191HOH0-0.002-0.00453.4630.0000.0000.0000.0000.0000.000
166A193HOH0-0.014-0.01538.0470.0020.0020.0000.0000.0000.000
167A194HOH0-0.013-0.01350.4380.0000.0000.0000.0000.0000.000
168A195HOH0-0.044-0.03354.9300.0000.0000.0000.0000.0000.000
169A197HOH00.002-0.00154.4780.0000.0000.0000.0000.0000.000
170A198HOH0-0.030-0.02237.8520.0020.0020.0000.0000.0000.000
171A199HOH0-0.060-0.06137.9790.0020.0020.0000.0000.0000.000
172A201HOH0-0.044-0.03232.7020.0030.0030.0000.0000.0000.000
173A206HOH0-0.020-0.01529.409-0.005-0.0050.0000.0000.0000.000
174A207HOH0-0.047-0.03046.0940.0010.0010.0000.0000.0000.000
175A212HOH0-0.023-0.01521.362-0.002-0.0020.0000.0000.0000.000
176A216HOH0-0.039-0.02138.590-0.001-0.0010.0000.0000.0000.000
177A221HOH00.0250.01641.9400.0010.0010.0000.0000.0000.000
178A231HOH00.0280.01723.7590.0090.0090.0000.0000.0000.000
179A235HOH00.0030.01035.4420.0030.0030.0000.0000.0000.000
180A240HOH0-0.031-0.02314.0980.0060.0060.0000.0000.0000.000
181A245HOH0-0.016-0.01451.8070.0000.0000.0000.0000.0000.000
182A248HOH00.0330.02248.8400.0010.0010.0000.0000.0000.000
183A256HOH00.0320.02817.5450.0270.0270.0000.0000.0000.000
184A258HOH0-0.095-0.09131.853-0.001-0.0010.0000.0000.0000.000
185A290HOH00.000-0.00433.572-0.003-0.0030.0000.0000.0000.000
186A296HOH0-0.071-0.05634.714-0.004-0.0040.0000.0000.0000.000
187A305HOH0-0.004-0.00831.225-0.002-0.0020.0000.0000.0000.000
188A392HOH0-0.008-0.00353.6820.0010.0010.0000.0000.0000.000
189A406HOH0-0.046-0.03059.5210.0010.0010.0000.0000.0000.000
190A495HOH00.016-0.00253.0710.0000.0000.0000.0000.0000.000
191A500HOH0-0.058-0.05310.672-0.064-0.0640.0000.0000.0000.000
192A521HOH0-0.013-0.00332.0620.0030.0030.0000.0000.0000.000
193A533HOH0-0.055-0.03962.7840.0010.0010.0000.0000.0000.000
194A540HOH0-0.034-0.02645.2920.0000.0000.0000.0000.0000.000
195A545HOH0-0.037-0.02144.8630.0010.0010.0000.0000.0000.000
196B138HOH0-0.039-0.02829.6880.0030.0030.0000.0000.0000.000
197C126HOH00.0120.01155.0580.0000.0000.0000.0000.0000.000
198C318HOH0-0.022-0.01349.833-0.001-0.0010.0000.0000.0000.000
199C352HOH00.0210.01752.8030.0000.0000.0000.0000.0000.000
200D126HOH00.0170.01136.009-0.002-0.0020.0000.0000.0000.000
201D161HOH00.0280.01741.8900.0010.0010.0000.0000.0000.000
202D285HOH00.0220.01548.612-0.001-0.0010.0000.0000.0000.000
203D313HOH0-0.048-0.03039.311-0.003-0.0030.0000.0000.0000.000