FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: 2456R

Calculation Name: 1J2R-A-Xray547

Preferred Name:

Target Type:

Ligand Name: (4s)-2-methyl-2,4-pentanediol

Ligand 3-letter code: MPD

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1J2R

Chain ID: A

ChEMBL ID:

UniProt ID: P0ADI7

Base Structure: X-ray

Registration Date: 2025-10-03

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 188
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2000985.607653
FMO2-HF: Nuclear repulsion 1929983.250304
FMO2-HF: Total energy -71002.35735
FMO2-MP2: Total energy -71212.787916


3D Structure Molmil
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:12:MET)


Summations of interaction energy for fragment #1(A:12: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.
-127.003-124.6110.029-0.916-1.504-0.002
Interaction energy analysis for fragmet #1(A:12:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.850 / q_NPA : 0.913
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].
3A14GLU-1-0.850-0.9293.462-51.638-49.3460.030-0.907-1.415-0.002
183A194GLU-1-0.827-0.9034.687-42.040-41.940-0.001-0.009-0.0890.000
4A15LEU0-0.037-0.0246.0853.1503.1500.0000.0000.0000.000
5A16ASN00.0480.0389.740-0.372-0.3720.0000.0000.0000.000
6A17ALA00.0380.02012.4981.8221.8220.0000.0000.0000.000
7A18LYS10.9160.95314.04917.84817.8480.0000.0000.0000.000
8A19THR0-0.0200.00116.7490.6580.6580.0000.0000.0000.000
9A20THR00.008-0.00913.459-0.418-0.4180.0000.0000.0000.000
10A21ALA0-0.002-0.00416.4910.7180.7180.0000.0000.0000.000
11A22LEU0-0.0210.00916.262-0.892-0.8920.0000.0000.0000.000
12A23VAL0-0.015-0.01718.4280.9820.9820.0000.0000.0000.000
13A24VAL00.0330.00520.345-0.585-0.5850.0000.0000.0000.000
14A25ILE0-0.046-0.03222.5190.5600.5600.0000.0000.0000.000
15A26ASP-1-0.749-0.87025.126-10.754-10.7540.0000.0000.0000.000
16A27LEU0-0.0270.00422.6530.1660.1660.0000.0000.0000.000
17A28GLN00.013-0.01527.246-0.203-0.2030.0000.0000.0000.000
18A29GLU-1-0.882-0.96730.915-9.561-9.5610.0000.0000.0000.000
19A30GLY0-0.061-0.01433.3070.1490.1490.0000.0000.0000.000
20A31ILE0-0.057-0.02929.8190.1490.1490.0000.0000.0000.000
21A32LEU00.0190.00527.900-0.219-0.2190.0000.0000.0000.000
22A33PRO0-0.025-0.01830.671-0.164-0.1640.0000.0000.0000.000
23A34PHE0-0.038-0.00631.3450.1810.1810.0000.0000.0000.000
24A35ALA0-0.058-0.01726.952-0.198-0.1980.0000.0000.0000.000
25A36GLY00.001-0.00228.1600.2940.2940.0000.0000.0000.000
26A37GLY0-0.0230.00725.3720.1220.1220.0000.0000.0000.000
27A38PRO0-0.040-0.04120.5570.0410.0410.0000.0000.0000.000
28A39HIS0-0.019-0.00317.5610.5010.5010.0000.0000.0000.000
29A40THR0-0.021-0.02922.4490.5300.5300.0000.0000.0000.000
30A41ALA00.0660.02124.279-0.452-0.4520.0000.0000.0000.000
31A42ASP-1-0.857-0.92325.187-10.929-10.9290.0000.0000.0000.000
32A43GLU-1-0.870-0.90121.209-13.456-13.4560.0000.0000.0000.000
33A44VAL0-0.010-0.00320.555-0.671-0.6710.0000.0000.0000.000
34A45VAL00.0290.01020.930-0.500-0.5000.0000.0000.0000.000
35A46ASN0-0.063-0.05121.353-0.315-0.3150.0000.0000.0000.000
36A47ARG10.7920.91416.26616.34316.3430.0000.0000.0000.000
37A48ALA00.0530.02317.504-0.666-0.6660.0000.0000.0000.000
38A49GLY00.0410.02819.468-0.146-0.1460.0000.0000.0000.000
39A50LYS10.8780.94716.40714.55614.5560.0000.0000.0000.000
40A51LEU00.0100.00912.998-0.570-0.5700.0000.0000.0000.000
41A52ALA00.0320.00616.097-0.233-0.2330.0000.0000.0000.000
42A53ALA0-0.027-0.01118.7960.2030.2030.0000.0000.0000.000
43A54LYS10.8590.92711.42722.36822.3680.0000.0000.0000.000
44A55PHE00.0130.01313.995-0.362-0.3620.0000.0000.0000.000
45A56ARG10.8010.87217.38712.78112.7810.0000.0000.0000.000
46A57ALA0-0.035-0.01417.8500.3480.3480.0000.0000.0000.000
47A58SER0-0.062-0.04115.403-0.487-0.4870.0000.0000.0000.000
48A59GLY0-0.057-0.02917.659-0.082-0.0820.0000.0000.0000.000
49A60GLN0-0.068-0.03016.8710.7680.7680.0000.0000.0000.000
50A61PRO0-0.016-0.01519.9380.2940.2940.0000.0000.0000.000
51A62VAL00.0320.02520.082-0.803-0.8030.0000.0000.0000.000
52A63PHE0-0.022-0.01522.1130.7100.7100.0000.0000.0000.000
53A64LEU0-0.013-0.00223.699-0.457-0.4570.0000.0000.0000.000
54A65VAL0-0.019-0.01525.3950.4300.4300.0000.0000.0000.000
55A66ARG10.8530.91327.8639.4999.4990.0000.0000.0000.000
56A67VAL0-0.011-0.00331.0070.1520.1520.0000.0000.0000.000
57A68GLY00.0550.04033.6480.0880.0880.0000.0000.0000.000
58A69TRP0-0.056-0.03837.013-0.015-0.0150.0000.0000.0000.000
59A70SER00.007-0.02041.0320.0170.0170.0000.0000.0000.000
60A71ALA0-0.011-0.01544.316-0.011-0.0110.0000.0000.0000.000
61A72ASP-1-0.863-0.92946.840-6.637-6.6370.0000.0000.0000.000
62A73TYR0-0.039-0.04441.775-0.038-0.0380.0000.0000.0000.000
63A74ALA0-0.0040.01645.207-0.077-0.0770.0000.0000.0000.000
64A75GLU-1-0.820-0.90641.361-7.482-7.4820.0000.0000.0000.000
65A76ALA0-0.0150.01140.832-0.208-0.2080.0000.0000.0000.000
66A77LEU0-0.026-0.00737.5130.1600.1600.0000.0000.0000.000
67A78LYS10.8470.89741.6397.1347.1340.0000.0000.0000.000
68A79GLN0-0.0030.00640.5910.2230.2230.0000.0000.0000.000
69A80PRO0-0.0070.00743.965-0.069-0.0690.0000.0000.0000.000
70A81VAL00.004-0.01140.229-0.111-0.1110.0000.0000.0000.000
71A82ASP-1-0.897-0.94741.832-7.272-7.2720.0000.0000.0000.000
72A83ALA0-0.045-0.01939.2370.0850.0850.0000.0000.0000.000
73A84PRO0-0.026-0.00240.217-0.179-0.1790.0000.0000.0000.000
74A85SER00.010-0.00138.980-0.085-0.0850.0000.0000.0000.000
75A86PRO0-0.028-0.01041.3450.1270.1270.0000.0000.0000.000
76A87ALA00.0320.02043.528-0.110-0.1100.0000.0000.0000.000
77A88LYS0-0.0190.01544.4140.1490.1490.0000.0000.0000.000
78A89VAL00.016-0.00644.832-0.126-0.1260.0000.0000.0000.000
79A90LEU00.0070.00839.972-0.079-0.0790.0000.0000.0000.000
80A91PRO0-0.0010.00839.5630.1460.1460.0000.0000.0000.000
81A92GLU-1-0.893-0.96041.024-7.027-7.0270.0000.0000.0000.000
82A93ASN0-0.016-0.01036.8170.0330.0330.0000.0000.0000.000
83A94TRP00.016-0.01736.303-0.228-0.2280.0000.0000.0000.000
84A95TRP00.0260.01734.817-0.328-0.3280.0000.0000.0000.000
85A96GLN0-0.057-0.01133.467-0.009-0.0090.0000.0000.0000.000
86A97HIS00.009-0.02429.405-0.299-0.2990.0000.0000.0000.000
87A98PRO00.0480.04127.9140.2130.2130.0000.0000.0000.000
88A99ALA00.002-0.00328.280-0.328-0.3280.0000.0000.0000.000
89A100ALA0-0.023-0.00824.937-0.157-0.1570.0000.0000.0000.000
90A101LEU00.0200.00623.448-0.631-0.6310.0000.0000.0000.000
91A102GLY0-0.030-0.01724.146-0.373-0.3730.0000.0000.0000.000
92A103THR0-0.024-0.01826.120-0.206-0.2060.0000.0000.0000.000
93A104THR0-0.057-0.03226.2020.3690.3690.0000.0000.0000.000
94A105ASP-1-0.913-0.96228.813-9.175-9.1750.0000.0000.0000.000
95A106SER0-0.077-0.03826.836-0.050-0.0500.0000.0000.0000.000
96A107ASP-1-0.747-0.82325.470-12.258-12.2580.0000.0000.0000.000
97A108ILE0-0.032-0.03025.3980.4390.4390.0000.0000.0000.000
98A109GLU-1-0.753-0.85327.683-10.338-10.3380.0000.0000.0000.000
99A110ILE0-0.040-0.00927.7110.2270.2270.0000.0000.0000.000
100A111ILE00.0060.00530.563-0.053-0.0530.0000.0000.0000.000
101A112LYS10.7580.87128.80310.62810.6280.0000.0000.0000.000
102A113ARG10.8760.93033.9128.1788.1780.0000.0000.0000.000
103A114GLN0-0.006-0.01232.7640.4730.4730.0000.0000.0000.000
104A115TRP00.0270.00730.316-0.285-0.2850.0000.0000.0000.000
105A116GLY00.0680.03228.400-0.296-0.2960.0000.0000.0000.000
106A117ALA0-0.002-0.01326.9290.4010.4010.0000.0000.0000.000
107A118PHE00.0200.02124.3070.1760.1760.0000.0000.0000.000
108A119TYR0-0.0250.00230.0510.2720.2720.0000.0000.0000.000
109A120GLY00.0240.01033.6300.0420.0420.0000.0000.0000.000
110A121THR0-0.041-0.01830.8480.0870.0870.0000.0000.0000.000
111A122ASP-1-0.830-0.91232.311-9.899-9.8990.0000.0000.0000.000
112A123LEU00.0270.02024.899-0.212-0.2120.0000.0000.0000.000
113A124GLU-1-0.760-0.88327.425-11.421-11.4210.0000.0000.0000.000
114A125LEU0-0.053-0.01728.435-0.129-0.1290.0000.0000.0000.000
115A126GLN00.016-0.00827.623-0.352-0.3520.0000.0000.0000.000
116A127LEU00.0040.00722.211-0.225-0.2250.0000.0000.0000.000
117A128ARG10.8150.87924.95611.82911.8290.0000.0000.0000.000
118A129ARG10.8900.94126.9509.5229.5220.0000.0000.0000.000
119A130ARG10.8520.93524.59811.60411.6040.0000.0000.0000.000
120A131GLY0-0.0050.01023.849-0.391-0.3910.0000.0000.0000.000
121A132ILE0-0.074-0.03219.413-0.599-0.5990.0000.0000.0000.000
122A133ASP-1-0.823-0.88617.325-18.103-18.1030.0000.0000.0000.000
123A134THR0-0.061-0.04513.459-0.853-0.8530.0000.0000.0000.000
124A135ILE0-0.018-0.01116.9460.5340.5340.0000.0000.0000.000
125A136VAL00.0190.01212.704-0.948-0.9480.0000.0000.0000.000
126A137LEU0-0.036-0.01515.4201.2671.2670.0000.0000.0000.000
127A138CYS0-0.045-0.01516.994-0.720-0.7200.0000.0000.0000.000
128A139GLY00.0670.02419.2770.6120.6120.0000.0000.0000.000
129A140ILE00.0120.02122.853-0.264-0.2640.0000.0000.0000.000
130A141SER00.0100.00525.7060.1860.1860.0000.0000.0000.000
131A142THR00.001-0.05120.6820.1320.1320.0000.0000.0000.000
132A143ASN00.0480.02723.258-0.459-0.4590.0000.0000.0000.000
133A144ILE0-0.0230.00425.7260.3350.3350.0000.0000.0000.000
134A145GLY00.0410.02827.691-0.043-0.0430.0000.0000.0000.000
135A146VAL00.0210.02820.779-0.130-0.1300.0000.0000.0000.000
136A147GLU-1-0.729-0.83323.141-12.773-12.7730.0000.0000.0000.000
137A148SER0-0.024-0.02724.1560.0620.0620.0000.0000.0000.000
138A149THR0-0.011-0.01723.6830.3430.3430.0000.0000.0000.000
139A150ALA00.0020.01020.545-0.176-0.1760.0000.0000.0000.000
140A151ARG10.8590.90822.26811.73711.7370.0000.0000.0000.000
141A152ASN00.0300.01424.792-0.017-0.0170.0000.0000.0000.000
142A153ALA00.0160.00421.7550.0590.0590.0000.0000.0000.000
143A154TRP00.0040.00519.6620.1140.1140.0000.0000.0000.000
144A155GLU-1-0.964-0.98022.441-11.357-11.3570.0000.0000.0000.000
145A156LEU0-0.076-0.02525.7560.3160.3160.0000.0000.0000.000
146A157GLY0-0.0030.00522.8590.1320.1320.0000.0000.0000.000
147A158PHE0-0.056-0.02320.338-0.231-0.2310.0000.0000.0000.000
148A159ASN0-0.055-0.02715.091-0.676-0.6760.0000.0000.0000.000
149A160LEU00.0080.00416.121-0.099-0.0990.0000.0000.0000.000
150A161VAL0-0.039-0.02010.538-1.824-1.8240.0000.0000.0000.000
151A162ILE00.0010.00213.1181.4181.4180.0000.0000.0000.000
152A163ALA00.0610.02412.923-1.560-1.5600.0000.0000.0000.000
153A164GLU-1-0.826-0.89113.348-16.546-16.5460.0000.0000.0000.000
154A165ASP-1-0.735-0.87413.751-19.453-19.4530.0000.0000.0000.000
155A166ALA0-0.058-0.03116.3390.9340.9340.0000.0000.0000.000
156A167CYS0-0.062-0.02017.7470.5880.5880.0000.0000.0000.000
157A168SER00.008-0.01620.1360.0820.0820.0000.0000.0000.000
158A169ALA00.0200.00223.2970.1780.1780.0000.0000.0000.000
159A170ALA00.0500.03726.1430.1020.1020.0000.0000.0000.000
160A171SER0-0.033-0.04328.2520.2970.2970.0000.0000.0000.000
161A172ALA00.0680.03524.470-0.348-0.3480.0000.0000.0000.000
162A173GLU-1-0.839-0.90924.121-11.248-11.2480.0000.0000.0000.000
163A174GLN0-0.034-0.01425.578-0.250-0.2500.0000.0000.0000.000
164A175HIS0-0.0010.01218.5280.4050.4050.0000.0000.0000.000
165A176ASN00.0370.00120.666-0.977-0.9770.0000.0000.0000.000
166A177ASN0-0.0080.01321.278-0.481-0.4810.0000.0000.0000.000
167A178SER0-0.003-0.02322.361-0.129-0.1290.0000.0000.0000.000
168A179ILE0-0.028-0.01816.255-0.578-0.5780.0000.0000.0000.000
169A180ASN0-0.012-0.00117.300-1.668-1.6680.0000.0000.0000.000
170A181HIS0-0.066-0.04619.308-0.470-0.4700.0000.0000.0000.000
171A182ILE0-0.071-0.02621.2650.2510.2510.0000.0000.0000.000
172A183TYR00.028-0.01916.824-0.430-0.4300.0000.0000.0000.000
173A184PRO00.0000.00115.177-0.672-0.6720.0000.0000.0000.000
174A185ARG10.8810.94815.98913.33213.3320.0000.0000.0000.000
175A186ILE0-0.029-0.00418.1730.3980.3980.0000.0000.0000.000
176A187ALA0-0.0110.00015.429-0.004-0.0040.0000.0000.0000.000
177A188ARG10.9150.9638.77429.68129.6810.0000.0000.0000.000
178A189VAL00.0310.02211.687-0.147-0.1470.0000.0000.0000.000
179A190ARG10.8530.9295.41437.42737.4270.0000.0000.0000.000
180A191SER00.0420.0088.2362.9522.9520.0000.0000.0000.000
181A192VAL00.004-0.0309.704-1.616-1.6160.0000.0000.0000.000
182A193GLU-1-0.908-0.9376.269-35.929-35.9290.0000.0000.0000.000
184A195ILE0-0.024-0.0205.683-2.780-2.7800.0000.0000.0000.000
185A196LEU0-0.054-0.0278.4760.7140.7140.0000.0000.0000.000
186A197ASN0-0.086-0.0634.9253.3263.3260.0000.0000.0000.000
187A198ALA0-0.0360.0085.104-2.602-2.6020.0000.0000.0000.000
188A199LEU-1-0.869-0.9146.367-22.360-22.3600.0000.0000.0000.000