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: 7KMRK

Calculation Name: 2DCY-A-Xray547

Preferred Name:

Target Type:

Ligand Name: d(-)-tartaric acid | l(+)-tartaric acid | 1,4-diethylene dioxide

Ligand 3-letter code: TAR | TLA | DIO

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2DCY

Chain ID: A

ChEMBL ID:

UniProt ID: P18429

Base Structure: X-ray

Registration Date: 2025-10-05

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 185
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2029378.900459
FMO2-HF: Nuclear repulsion 1958420.073148
FMO2-HF: Total energy -70958.82731
FMO2-MP2: Total energy -71169.460313


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:1:ALA)


Summations of interaction energy for fragment #1(A:1:ALA)
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.
-48.235-49.55720.876-11.378-8.176-0.114
Interaction energy analysis for fragmet #1(A:1:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.767 / q_NPA : 0.866
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].
3A3THR0-0.0050.0173.511-2.092-0.6220.026-0.693-0.802-0.001
42A42TRP0-0.078-0.0482.6220.3681.0660.208-0.218-0.688-0.001
49A49ARG10.8310.9464.69735.80035.861-0.001-0.002-0.0580.000
52A52ASN0-0.011-0.0144.28011.63211.737-0.001-0.005-0.0990.000
185A185TRP-1-0.792-0.8751.708-118.873-122.52920.644-10.460-6.529-0.112
4A4ASP-1-0.824-0.8996.072-28.540-28.5400.0000.0000.0000.000
5A5TYR0-0.010-0.0078.6502.8412.8410.0000.0000.0000.000
6A6TRP0-0.018-0.03110.912-1.928-1.9280.0000.0000.0000.000
7A7GLN00.0440.03513.7890.7590.7590.0000.0000.0000.000
8A8ASN0-0.003-0.02116.079-0.007-0.0070.0000.0000.0000.000
9A9TRP00.0230.02019.4340.3290.3290.0000.0000.0000.000
10A10THR00.039-0.00122.444-0.082-0.0820.0000.0000.0000.000
11A11ASP-1-0.799-0.87825.842-10.402-10.4020.0000.0000.0000.000
12A12GLY0-0.014-0.00129.0430.3450.3450.0000.0000.0000.000
13A13GLY0-0.013-0.00430.7920.3180.3180.0000.0000.0000.000
14A14GLY00.002-0.00130.585-0.343-0.3430.0000.0000.0000.000
15A15ILE0-0.027-0.01328.953-0.040-0.0400.0000.0000.0000.000
16A16VAL00.026-0.00423.521-0.176-0.1760.0000.0000.0000.000
17A17ASN0-0.0220.00024.467-0.386-0.3860.0000.0000.0000.000
18A18ALA00.0140.00819.821-0.397-0.3970.0000.0000.0000.000
19A19VAL00.0030.00018.7760.0220.0220.0000.0000.0000.000
20A20ASN00.001-0.00414.488-2.212-2.2120.0000.0000.0000.000
21A21GLY00.0650.03314.7910.8420.8420.0000.0000.0000.000
22A22SER00.000-0.01012.988-1.519-1.5190.0000.0000.0000.000
23A23GLY00.0390.0158.907-1.373-1.3730.0000.0000.0000.000
24A24GLY00.0630.0347.0500.5860.5860.0000.0000.0000.000
25A25ASN0-0.092-0.0557.9502.4742.4740.0000.0000.0000.000
26A26TYR0-0.011-0.00811.3751.3021.3020.0000.0000.0000.000
27A27SER0-0.017-0.00514.3730.3190.3190.0000.0000.0000.000
28A28VAL00.0110.00917.7260.1700.1700.0000.0000.0000.000
29A29ASN0-0.013-0.00520.7780.4670.4670.0000.0000.0000.000
30A30TRP0-0.010-0.00222.118-0.116-0.1160.0000.0000.0000.000
31A31SER0-0.001-0.01726.7790.3200.3200.0000.0000.0000.000
32A32ASN0-0.001-0.00530.4830.1540.1540.0000.0000.0000.000
33A33THR0-0.046-0.00527.7590.1320.1320.0000.0000.0000.000
34A34GLY00.0460.03430.6700.3190.3190.0000.0000.0000.000
35A35ASN0-0.111-0.08425.404-0.218-0.2180.0000.0000.0000.000
36A36PHE0-0.0070.00622.2600.0110.0110.0000.0000.0000.000
37A37VAL00.0110.00118.195-0.286-0.2860.0000.0000.0000.000
38A38VAL00.0030.00616.965-0.027-0.0270.0000.0000.0000.000
39A39GLY00.006-0.00314.092-0.107-0.1070.0000.0000.0000.000
40A40LYS10.8160.9299.34127.60027.6000.0000.0000.0000.000
41A41GLY00.0200.0017.018-0.752-0.7520.0000.0000.0000.000
43A43THR00.007-0.0208.4212.6082.6080.0000.0000.0000.000
44A44THR0-0.0270.00310.5881.7281.7280.0000.0000.0000.000
45A45GLY0-0.003-0.00910.104-2.590-2.5900.0000.0000.0000.000
46A46SER00.005-0.01210.0371.1221.1220.0000.0000.0000.000
47A47PRO00.0330.02011.743-1.077-1.0770.0000.0000.0000.000
48A48PHE0-0.001-0.01711.5770.4610.4610.0000.0000.0000.000
50A50THR00.0050.0007.3993.2643.2640.0000.0000.0000.000
51A51ILE0-0.043-0.0146.008-6.002-6.0020.0000.0000.0000.000
53A53TYR0-0.028-0.0546.645-1.918-1.9180.0000.0000.0000.000
54A54ASN0-0.006-0.0088.7612.5022.5020.0000.0000.0000.000
55A55ALA00.0030.01011.601-0.385-0.3850.0000.0000.0000.000
56A56GLY00.0570.03014.6921.0991.0990.0000.0000.0000.000
57A57VAL0-0.004-0.00416.7351.1141.1140.0000.0000.0000.000
58A58TRP0-0.028-0.02418.630-0.961-0.9610.0000.0000.0000.000
59A59ALA0-0.0010.01120.7140.4860.4860.0000.0000.0000.000
60A60PRO0-0.0180.00723.0780.3270.3270.0000.0000.0000.000
61A61ASN0-0.024-0.01325.7460.3830.3830.0000.0000.0000.000
62A62GLY00.0890.03329.5760.2170.2170.0000.0000.0000.000
63A63ASN00.014-0.00127.855-0.620-0.6200.0000.0000.0000.000
64A64GLY00.0880.05424.681-0.012-0.0120.0000.0000.0000.000
65A65TYR0-0.046-0.02821.0380.2940.2940.0000.0000.0000.000
66A66LEU00.0200.02714.903-0.373-0.3730.0000.0000.0000.000
67A67THR0-0.014-0.04816.7420.5850.5850.0000.0000.0000.000
68A68LEU00.0100.01310.653-1.084-1.0840.0000.0000.0000.000
69A69TYR0-0.016-0.01713.7911.1821.1820.0000.0000.0000.000
70A70GLY00.0490.01813.976-1.736-1.7360.0000.0000.0000.000
71A71TRP00.0390.01615.7191.3231.3230.0000.0000.0000.000
72A72THR0-0.035-0.00517.204-0.785-0.7850.0000.0000.0000.000
73A73ARG10.8650.89919.64513.61713.6170.0000.0000.0000.000
74A74SER0-0.0080.00422.553-0.186-0.1860.0000.0000.0000.000
75A75PRO00.0440.01924.735-0.139-0.1390.0000.0000.0000.000
76A76LEU0-0.013-0.01123.593-0.527-0.5270.0000.0000.0000.000
77A77ILE0-0.077-0.03421.7260.4370.4370.0000.0000.0000.000
78A78GLU-1-0.731-0.82420.649-13.881-13.8810.0000.0000.0000.000
79A79TYR0-0.038-0.03713.944-0.136-0.1360.0000.0000.0000.000
80A80TYR0-0.025-0.03017.819-0.891-0.8910.0000.0000.0000.000
81A81VAL0-0.061-0.03415.6200.4680.4680.0000.0000.0000.000
82A82VAL00.0480.03116.913-0.897-0.8970.0000.0000.0000.000
83A83ASP-1-0.711-0.81015.313-19.228-19.2280.0000.0000.0000.000
84A84SER0-0.023-0.01818.6990.9790.9790.0000.0000.0000.000
85A85TRP00.0770.03021.046-0.429-0.4290.0000.0000.0000.000
86A86GLY00.0390.03223.8260.1000.1000.0000.0000.0000.000
87A87THR0-0.046-0.03726.762-0.004-0.0040.0000.0000.0000.000
88A88TYR0-0.0020.01028.6390.2320.2320.0000.0000.0000.000
89A89ARG10.7720.88625.98111.21711.2170.0000.0000.0000.000
90A90PRO00.0380.02224.1370.3710.3710.0000.0000.0000.000
91A91THR0-0.043-0.02927.172-0.019-0.0190.0000.0000.0000.000
92A92GLY00.0330.00529.2010.0130.0130.0000.0000.0000.000
93A93THR0-0.037-0.01130.6830.3290.3290.0000.0000.0000.000
94A94TYR0-0.012-0.00929.924-0.270-0.2700.0000.0000.0000.000
95A95LYS10.8690.94728.03110.39510.3950.0000.0000.0000.000
96A96GLY00.0920.04929.2840.2480.2480.0000.0000.0000.000
97A97THR0-0.089-0.03526.502-0.201-0.2010.0000.0000.0000.000
98A98VAL00.0370.01920.9100.0260.0260.0000.0000.0000.000
99A99LYS10.9100.94522.56711.96811.9680.0000.0000.0000.000
100A100SER00.044-0.00916.257-0.133-0.1330.0000.0000.0000.000
101A101ASP-1-0.786-0.83013.888-21.592-21.5920.0000.0000.0000.000
102A102GLY00.0420.02316.459-0.169-0.1690.0000.0000.0000.000
103A103GLY0-0.058-0.03119.5210.6060.6060.0000.0000.0000.000
104A104THR0-0.037-0.01221.0300.1840.1840.0000.0000.0000.000
105A105TYR0-0.057-0.04717.4040.0950.0950.0000.0000.0000.000
106A106ASP-1-0.740-0.84023.647-10.901-10.9010.0000.0000.0000.000
107A107ILE0-0.028-0.01023.660-0.535-0.5350.0000.0000.0000.000
108A108TYR00.024-0.00425.4350.5250.5250.0000.0000.0000.000
109A109THR00.0240.00925.870-0.423-0.4230.0000.0000.0000.000
110A110THR0-0.007-0.01627.6360.3490.3490.0000.0000.0000.000
111A111THR00.0120.01028.547-0.358-0.3580.0000.0000.0000.000
112A112ARG10.8840.95627.67410.47810.4780.0000.0000.0000.000
113A113TYR00.0590.00830.836-0.002-0.0020.0000.0000.0000.000
114A114ASN0-0.0180.00533.851-0.008-0.0080.0000.0000.0000.000
115A115ALA0-0.010-0.00130.3950.1540.1540.0000.0000.0000.000
116A116PRO00.0650.04227.840-0.003-0.0030.0000.0000.0000.000
117A117SER0-0.022-0.02525.253-0.341-0.3410.0000.0000.0000.000
118A118ILE0-0.029-0.01720.2670.0160.0160.0000.0000.0000.000
119A119ASP-1-0.808-0.88623.717-11.980-11.9800.0000.0000.0000.000
120A120GLY00.0090.01227.0040.4140.4140.0000.0000.0000.000
121A121ASP-1-0.890-0.95229.391-9.970-9.9700.0000.0000.0000.000
122A122ARG10.8150.89931.4808.8618.8610.0000.0000.0000.000
123A123THR00.0230.03529.4300.0060.0060.0000.0000.0000.000
124A124THR0-0.004-0.01731.6850.0440.0440.0000.0000.0000.000
125A125PHE0-0.0140.00725.322-0.072-0.0720.0000.0000.0000.000
126A126THR0-0.022-0.01026.8550.3620.3620.0000.0000.0000.000
127A127GLN00.0450.03024.0970.0680.0680.0000.0000.0000.000
128A128TYR0-0.037-0.05421.6270.6240.6240.0000.0000.0000.000
129A129TRP00.019-0.00121.635-0.828-0.8280.0000.0000.0000.000
130A130SER0-0.012-0.00519.6410.7180.7180.0000.0000.0000.000
131A131VAL0-0.002-0.00121.004-0.612-0.6120.0000.0000.0000.000
132A132ARG10.8860.96219.28715.81615.8160.0000.0000.0000.000
133A133GLN0-0.051-0.05822.8150.2920.2920.0000.0000.0000.000
134A134SER0-0.018-0.00624.8590.4290.4290.0000.0000.0000.000
135A135LYS10.8650.95122.84811.41711.4170.0000.0000.0000.000
136A136ARG10.7730.86214.06420.75420.7540.0000.0000.0000.000
137A137PRO0-0.010-0.00619.5560.0770.0770.0000.0000.0000.000
138A138THR0-0.0100.00117.176-0.759-0.7590.0000.0000.0000.000
139A139GLY00.0120.01316.8750.5890.5890.0000.0000.0000.000
140A140SER0-0.0210.00315.579-0.174-0.1740.0000.0000.0000.000
141A141ASN0-0.010-0.01910.482-0.202-0.2020.0000.0000.0000.000
142A142ALA0-0.0060.01011.0221.7311.7310.0000.0000.0000.000
143A143THR00.0200.0039.009-2.413-2.4130.0000.0000.0000.000
144A144ILE0-0.0030.00310.2603.0483.0480.0000.0000.0000.000
145A145THR00.023-0.02210.843-2.705-2.7050.0000.0000.0000.000
146A146PHE0-0.026-0.01511.7652.1542.1540.0000.0000.0000.000
147A147SER00.0580.03613.4271.4091.4090.0000.0000.0000.000
148A148ASN0-0.014-0.02015.3381.5691.5690.0000.0000.0000.000
149A149HIS00.0220.02515.9451.8081.8080.0000.0000.0000.000
150A150VAL00.0240.02016.1250.9530.9530.0000.0000.0000.000
151A151ASN0-0.030-0.01818.8301.2531.2530.0000.0000.0000.000
152A152ALA00.0430.02821.2230.7510.7510.0000.0000.0000.000
153A153TRP00.0160.00118.1890.5330.5330.0000.0000.0000.000
154A154LYS10.9760.99522.94413.29813.2980.0000.0000.0000.000
155A155SER0-0.087-0.05124.7860.5580.5580.0000.0000.0000.000
156A156HIS00.000-0.01326.2630.7170.7170.0000.0000.0000.000
157A157GLY0-0.010-0.01028.3040.2750.2750.0000.0000.0000.000
158A158MET0-0.083-0.01923.7450.2120.2120.0000.0000.0000.000
159A159ASN00.003-0.00223.812-0.785-0.7850.0000.0000.0000.000
160A160LEU0-0.0020.01517.7430.1160.1160.0000.0000.0000.000
161A161GLY00.0020.00921.2610.3710.3710.0000.0000.0000.000
162A162SER0-0.015-0.01720.154-0.698-0.6980.0000.0000.0000.000
163A163ASN0-0.025-0.00619.693-0.979-0.9790.0000.0000.0000.000
164A164TRP00.0100.00414.153-0.402-0.4020.0000.0000.0000.000
165A165ALA00.0220.02016.033-0.210-0.2100.0000.0000.0000.000
166A166TYR00.0570.02712.796-1.098-1.0980.0000.0000.0000.000
167A167GLN0-0.0030.0009.735-0.631-0.6310.0000.0000.0000.000
168A168VAL0-0.020-0.0089.608-2.885-2.8850.0000.0000.0000.000
169A169MET0-0.0130.01310.1531.1561.1560.0000.0000.0000.000
170A170ALA0-0.016-0.01811.711-0.362-0.3620.0000.0000.0000.000
171A171THR0-0.0040.01215.1860.4730.4730.0000.0000.0000.000
172A172GLU-1-0.794-0.88018.448-13.555-13.5550.0000.0000.0000.000
173A173GLY00.021-0.00621.5310.0710.0710.0000.0000.0000.000
174A174TYR0-0.036-0.02025.2220.0380.0380.0000.0000.0000.000
175A175GLN00.0010.00628.7240.1790.1790.0000.0000.0000.000
176A176SER0-0.044-0.01127.8140.1660.1660.0000.0000.0000.000
177A177SER0-0.005-0.01229.0890.1420.1420.0000.0000.0000.000
178A178GLY00.0200.00626.113-0.001-0.0010.0000.0000.0000.000
179A179SER0-0.0120.00923.129-0.101-0.1010.0000.0000.0000.000
180A180SER0-0.021-0.02918.304-0.001-0.0010.0000.0000.0000.000
181A181ASN00.0070.00515.644-0.963-0.9630.0000.0000.0000.000
182A182VAL00.0240.00911.3190.0710.0710.0000.0000.0000.000
183A183THR00.0000.0127.8790.1510.1510.0000.0000.0000.000
184A184VAL0-0.023-0.0116.2430.5570.5570.0000.0000.0000.000