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: 871LY

Calculation Name: 1EM2-A-Xray547

Preferred Name:

Target Type:

Ligand Name: d(-)-tartaric acid

Ligand 3-letter code: TAR

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1EM2

Chain ID: A

ChEMBL ID:

UniProt ID: Q14849

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 214
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2631833.78393
FMO2-HF: Nuclear repulsion 2546946.283415
FMO2-HF: Total energy -84887.500516
FMO2-MP2: Total energy -85136.806482


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:230:SER)


Summations of interaction energy for fragment #1(A:230:SER)
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.
48.66949.959-0.019-0.523-0.748-0.001
Interaction energy analysis for fragmet #1(A:230:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.836 / q_NPA : 0.907
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].
3A232SER00.007-0.0173.8495.2486.538-0.019-0.523-0.748-0.001
4A233ALA0-0.007-0.0216.490-0.551-0.5510.0000.0000.0000.000
5A234GLN00.0330.0319.6391.2721.2720.0000.0000.0000.000
6A235GLU-1-0.775-0.8596.700-42.082-42.0820.0000.0000.0000.000
7A236ARG10.9050.9265.46837.23437.2340.0000.0000.0000.000
8A237GLU-1-0.939-0.9599.127-17.637-17.6370.0000.0000.0000.000
9A238TYR00.020-0.00812.1600.6280.6280.0000.0000.0000.000
10A239ILE0-0.004-0.0117.3421.1971.1970.0000.0000.0000.000
11A240ARG10.8770.96011.52822.72222.7220.0000.0000.0000.000
12A241GLN00.1020.06614.0950.3240.3240.0000.0000.0000.000
13A242GLY00.0400.02415.5191.0581.0580.0000.0000.0000.000
14A243LYS10.8990.95410.33827.19927.1990.0000.0000.0000.000
15A244GLU-1-0.893-0.95316.689-16.333-16.3330.0000.0000.0000.000
16A245ALA00.0190.00519.4590.8520.8520.0000.0000.0000.000
17A246THR0-0.047-0.03818.8250.6870.6870.0000.0000.0000.000
18A247ALA00.0060.01120.7490.6010.6010.0000.0000.0000.000
19A248VAL00.0230.01222.4830.6340.6340.0000.0000.0000.000
20A249VAL0-0.0070.00024.1130.6090.6090.0000.0000.0000.000
21A250ASP-1-0.800-0.88423.136-12.824-12.8240.0000.0000.0000.000
22A251GLN0-0.042-0.00826.2850.1260.1260.0000.0000.0000.000
23A252ILE00.008-0.00628.4790.4540.4540.0000.0000.0000.000
24A253LEU0-0.021-0.01427.6380.4000.4000.0000.0000.0000.000
25A254ALA0-0.030-0.00730.2060.3140.3140.0000.0000.0000.000
26A255GLN0-0.044-0.03731.9210.1310.1310.0000.0000.0000.000
27A256GLU-1-0.825-0.88734.682-8.508-8.5080.0000.0000.0000.000
28A257GLU-1-0.947-0.97636.607-7.627-7.6270.0000.0000.0000.000
29A258ASN0-0.056-0.02737.3800.3600.3600.0000.0000.0000.000
30A259TRP0-0.090-0.03733.266-0.022-0.0220.0000.0000.0000.000
31A260LYS10.8440.91439.0718.2688.2680.0000.0000.0000.000
32A261PHE00.0190.00641.491-0.166-0.1660.0000.0000.0000.000
33A262GLU-1-0.908-0.91041.441-7.461-7.4610.0000.0000.0000.000
34A263LYS10.9220.95443.8406.9846.9840.0000.0000.0000.000
35A264ASN00.0300.01443.864-0.117-0.1170.0000.0000.0000.000
36A265ASN0-0.028-0.02943.9040.1420.1420.0000.0000.0000.000
37A266GLU-1-0.897-0.95547.261-6.258-6.2580.0000.0000.0000.000
38A267TYR0-0.035-0.01544.9470.0330.0330.0000.0000.0000.000
39A268GLY00.0020.01345.094-0.098-0.0980.0000.0000.0000.000
40A269ASP-1-0.797-0.85441.120-7.974-7.9740.0000.0000.0000.000
41A270THR0-0.035-0.03540.8600.2480.2480.0000.0000.0000.000
42A271VAL0-0.020-0.00838.868-0.272-0.2720.0000.0000.0000.000
43A272TYR00.0310.01238.1550.2240.2240.0000.0000.0000.000
44A273THR0-0.052-0.06537.454-0.212-0.2120.0000.0000.0000.000
45A274ILE00.0080.01233.3850.1800.1800.0000.0000.0000.000
46A275GLU-1-0.811-0.89535.901-8.308-8.3080.0000.0000.0000.000
47A276VAL00.0160.00229.453-0.038-0.0380.0000.0000.0000.000
48A277PRO00.000-0.01430.6390.0140.0140.0000.0000.0000.000
49A278PHE00.0060.01028.8000.1100.1100.0000.0000.0000.000
50A279HIS00.0090.00226.2650.1640.1640.0000.0000.0000.000
51A280GLY00.0140.03131.2610.1660.1660.0000.0000.0000.000
52A281LYS10.8490.91834.2747.7657.7650.0000.0000.0000.000
53A282THR0-0.0090.01030.977-0.225-0.2250.0000.0000.0000.000
54A283PHE00.012-0.00534.0550.2670.2670.0000.0000.0000.000
55A284ILE00.000-0.00233.272-0.397-0.3970.0000.0000.0000.000
56A285LEU00.0170.02634.7880.3110.3110.0000.0000.0000.000
57A286LYS10.8440.90534.9938.1378.1370.0000.0000.0000.000
58A287THR00.0350.00636.7000.2110.2110.0000.0000.0000.000
59A288PHE0-0.0040.00237.248-0.256-0.2560.0000.0000.0000.000
60A289LEU00.0280.00535.0080.1150.1150.0000.0000.0000.000
61A290PRO0-0.0010.00738.779-0.095-0.0950.0000.0000.0000.000
62A291CYS00.0490.02035.2890.0430.0430.0000.0000.0000.000
63A292PRO00.0370.02334.085-0.126-0.1260.0000.0000.0000.000
64A293ALA00.021-0.01130.751-0.137-0.1370.0000.0000.0000.000
65A294GLU-1-0.833-0.89527.042-12.210-12.2100.0000.0000.0000.000
66A295LEU00.0390.03029.172-0.320-0.3200.0000.0000.0000.000
67A296VAL00.0790.02330.827-0.152-0.1520.0000.0000.0000.000
68A297TYR0-0.016-0.00920.966-0.525-0.5250.0000.0000.0000.000
69A298GLN0-0.015-0.03326.158-0.259-0.2590.0000.0000.0000.000
70A299GLU-1-0.807-0.88527.242-10.441-10.4410.0000.0000.0000.000
71A300VAL0-0.038-0.01928.2780.0210.0210.0000.0000.0000.000
72A301ILE0-0.071-0.03022.785-0.346-0.3460.0000.0000.0000.000
73A302LEU0-0.017-0.01220.686-0.746-0.7460.0000.0000.0000.000
74A303GLN0-0.064-0.03122.972-0.350-0.3500.0000.0000.0000.000
75A304PRO00.001-0.00222.2960.4770.4770.0000.0000.0000.000
76A305GLU-1-0.843-0.93723.047-13.545-13.5450.0000.0000.0000.000
77A306ARG10.9180.96126.44911.62511.6250.0000.0000.0000.000
78A307MET00.0190.03327.8340.5250.5250.0000.0000.0000.000
79A308VAL0-0.027-0.01029.6900.3420.3420.0000.0000.0000.000
80A309LEU0-0.041-0.01332.3280.3060.3060.0000.0000.0000.000
81A310TRP00.0390.01931.5250.3600.3600.0000.0000.0000.000
82A311ASN00.0340.03632.0970.5600.5600.0000.0000.0000.000
83A312LYS10.9750.98334.9827.6327.6320.0000.0000.0000.000
84A313THR0-0.049-0.03135.0630.0020.0020.0000.0000.0000.000
85A314VAL0-0.055-0.02530.805-0.105-0.1050.0000.0000.0000.000
86A315THR0-0.022-0.01533.6120.0950.0950.0000.0000.0000.000
87A316ALA0-0.018-0.00729.9990.0290.0290.0000.0000.0000.000
88A317CYS0-0.053-0.02625.529-0.277-0.2770.0000.0000.0000.000
89A318GLN00.0310.03123.6320.5580.5580.0000.0000.0000.000
90A319ILE0-0.008-0.02117.917-0.336-0.3360.0000.0000.0000.000
91A320LEU0-0.080-0.03018.8230.1270.1270.0000.0000.0000.000
92A321GLN00.0290.01210.9901.0381.0380.0000.0000.0000.000
93A322ARG10.9620.98912.84719.57819.5780.0000.0000.0000.000
94A323VAL00.0180.0048.036-1.955-1.9550.0000.0000.0000.000
95A324GLU-1-0.835-0.9017.771-28.758-28.7580.0000.0000.0000.000
96A325ASP-1-0.872-0.9298.832-25.476-25.4760.0000.0000.0000.000
97A326ASN0-0.096-0.05011.8903.6483.6480.0000.0000.0000.000
98A327THR0-0.059-0.02711.7061.6511.6510.0000.0000.0000.000
99A328LEU00.008-0.00113.475-0.835-0.8350.0000.0000.0000.000
100A329ILE0-0.0110.00215.0000.6140.6140.0000.0000.0000.000
101A330SER0-0.027-0.04117.711-0.150-0.1500.0000.0000.0000.000
102A331TYR0-0.035-0.04821.3190.1380.1380.0000.0000.0000.000
103A332ASP-1-0.737-0.83724.617-13.085-13.0850.0000.0000.0000.000
104A333VAL00.008-0.00527.4390.1170.1170.0000.0000.0000.000
105A334SER00.0380.01431.2400.0370.0370.0000.0000.0000.000
106A335ALA00.0270.01234.0970.1010.1010.0000.0000.0000.000
107A336GLY0-0.028-0.01537.585-0.089-0.0890.0000.0000.0000.000
108A337ALA00.0550.03039.4970.0710.0710.0000.0000.0000.000
109A338ALA00.012-0.01641.5330.1350.1350.0000.0000.0000.000
110A339GLY00.0220.01144.7710.1300.1300.0000.0000.0000.000
111A340GLY0-0.0020.00744.6630.1260.1260.0000.0000.0000.000
112A341VAL0-0.035-0.00845.636-0.007-0.0070.0000.0000.0000.000
113A342VAL0-0.051-0.02639.469-0.064-0.0640.0000.0000.0000.000
114A343SER00.0450.01740.496-0.060-0.0600.0000.0000.0000.000
115A344PRO00.0060.02136.612-0.115-0.1150.0000.0000.0000.000
116A345ARG10.7920.88133.0948.7118.7110.0000.0000.0000.000
117A346ASP-1-0.763-0.82530.049-10.795-10.7950.0000.0000.0000.000
118A347PHE00.011-0.00227.0030.1120.1120.0000.0000.0000.000
119A348VAL0-0.0010.00121.446-0.136-0.1360.0000.0000.0000.000
120A349ASN0-0.037-0.01222.1700.2740.2740.0000.0000.0000.000
121A350VAL00.0020.00915.735-0.725-0.7250.0000.0000.0000.000
122A351ARG10.8750.93717.96215.11215.1120.0000.0000.0000.000
123A352ARG10.7870.86812.21020.22720.2270.0000.0000.0000.000
124A353ILE0-0.033-0.00716.9501.0631.0630.0000.0000.0000.000
125A354GLU-1-0.814-0.89517.078-18.440-18.4400.0000.0000.0000.000
126A355ARG10.9190.95816.29518.66518.6650.0000.0000.0000.000
127A356ARG10.7810.85720.46413.90713.9070.0000.0000.0000.000
128A357ARG10.9770.98523.61310.80010.8000.0000.0000.0000.000
129A358ASP-1-0.811-0.88826.791-10.763-10.7630.0000.0000.0000.000
130A359ARG10.8750.92825.62211.31611.3160.0000.0000.0000.000
131A360TYR0-0.048-0.03824.215-0.390-0.3900.0000.0000.0000.000
132A361LEU00.0170.00722.0480.5020.5020.0000.0000.0000.000
133A362SER0-0.012-0.01021.546-0.715-0.7150.0000.0000.0000.000
134A363SER00.0570.02720.4510.9330.9330.0000.0000.0000.000
135A364GLY0-0.019-0.02020.520-0.938-0.9380.0000.0000.0000.000
136A365ILE0-0.0160.00520.2870.5700.5700.0000.0000.0000.000
137A366ALA00.0230.02121.807-0.530-0.5300.0000.0000.0000.000
138A367THR0-0.033-0.04818.150-0.516-0.5160.0000.0000.0000.000
139A368SER00.0250.02419.9530.8570.8570.0000.0000.0000.000
140A369HIS00.0550.00815.6930.0060.0060.0000.0000.0000.000
141A370SER00.0080.00717.9590.6710.6710.0000.0000.0000.000
142A371ALA00.0040.01020.1220.6660.6660.0000.0000.0000.000
143A372LYS10.7960.91421.78312.88612.8860.0000.0000.0000.000
144A373PRO00.0840.05624.517-0.025-0.0250.0000.0000.0000.000
145A374PRO00.0130.01426.2860.1560.1560.0000.0000.0000.000
146A375THR0-0.012-0.01729.6720.1610.1610.0000.0000.0000.000
147A376HIS00.0450.01332.594-0.080-0.0800.0000.0000.0000.000
148A377LYS10.8970.97233.2359.5269.5260.0000.0000.0000.000
149A378TYR00.019-0.00632.6230.1090.1090.0000.0000.0000.000
150A379VAL0-0.0060.01134.667-0.054-0.0540.0000.0000.0000.000
151A380ARG10.7810.85726.44311.37111.3710.0000.0000.0000.000
152A381GLY0-0.0070.00331.3480.1980.1980.0000.0000.0000.000
153A382GLU-1-0.874-0.94727.606-11.306-11.3060.0000.0000.0000.000
154A383ASN0-0.010-0.00426.1680.7780.7780.0000.0000.0000.000
155A384GLY00.0620.03426.064-0.462-0.4620.0000.0000.0000.000
156A385PRO0-0.044-0.02324.198-0.289-0.2890.0000.0000.0000.000
157A386GLY00.0140.00224.9750.6190.6190.0000.0000.0000.000
158A387GLY00.010-0.00824.690-0.749-0.7490.0000.0000.0000.000
159A388MET0-0.0520.00325.7580.4830.4830.0000.0000.0000.000
160A389ILE0-0.014-0.01226.019-0.599-0.5990.0000.0000.0000.000
161A390VAL0-0.0020.01027.8370.4620.4620.0000.0000.0000.000
162A391LEU00.001-0.00528.926-0.380-0.3800.0000.0000.0000.000
163A392LYS10.8880.92927.67211.55211.5520.0000.0000.0000.000
164A393SER00.0220.02132.6230.0970.0970.0000.0000.0000.000
165A394ALA0-0.004-0.01135.700-0.040-0.0400.0000.0000.0000.000
166A395SER0-0.0020.00636.8740.0520.0520.0000.0000.0000.000
167A396ASN00.0330.01339.5280.1540.1540.0000.0000.0000.000
168A397PRO00.0520.02236.480-0.054-0.0540.0000.0000.0000.000
169A398ARG10.8950.93036.7807.3087.3080.0000.0000.0000.000
170A399VAL0-0.0180.01638.6520.0900.0900.0000.0000.0000.000
171A400CYS0-0.069-0.01733.889-0.254-0.2540.0000.0000.0000.000
172A401THR00.0110.00634.7000.3490.3490.0000.0000.0000.000
173A402PHE0-0.002-0.00130.079-0.392-0.3920.0000.0000.0000.000
174A403VAL00.0360.00731.2090.3240.3240.0000.0000.0000.000
175A404TRP0-0.033-0.01129.874-0.301-0.3010.0000.0000.0000.000
176A405ILE00.0260.02428.4040.3370.3370.0000.0000.0000.000
177A406LEU0-0.005-0.00429.378-0.420-0.4200.0000.0000.0000.000
178A407ASN00.006-0.01829.1490.1930.1930.0000.0000.0000.000
179A408THR0-0.020-0.03629.682-0.267-0.2670.0000.0000.0000.000
180A409ASP-1-0.801-0.87031.558-9.012-9.0120.0000.0000.0000.000
181A410LEU00.0210.00132.783-0.191-0.1910.0000.0000.0000.000
182A411LYS10.8300.91131.14010.30110.3010.0000.0000.0000.000
183A412GLY0-0.009-0.00236.6510.1790.1790.0000.0000.0000.000
184A413ARG10.9490.95740.0847.0687.0680.0000.0000.0000.000
185A414LEU00.0280.03142.2650.1900.1900.0000.0000.0000.000
186A415PRO00.0250.02043.463-0.125-0.1250.0000.0000.0000.000
187A416ARG11.0100.98439.4168.0658.0650.0000.0000.0000.000
188A417TYR00.0470.01842.494-0.147-0.1470.0000.0000.0000.000
189A418LEU00.0340.02444.751-0.036-0.0360.0000.0000.0000.000
190A419ILE00.0110.01138.311-0.072-0.0720.0000.0000.0000.000
191A420HIS00.001-0.01438.637-0.050-0.0500.0000.0000.0000.000
192A421GLN00.0220.00941.271-0.040-0.0400.0000.0000.0000.000
193A422SER00.0170.01341.043-0.020-0.0200.0000.0000.0000.000
194A423LEU0-0.0100.01235.549-0.096-0.0960.0000.0000.0000.000
195A424ALA00.0350.00838.623-0.107-0.1070.0000.0000.0000.000
196A425ALA0-0.037-0.01140.9000.0200.0200.0000.0000.0000.000
197A426THR00.0570.00636.288-0.062-0.0620.0000.0000.0000.000
198A427MET0-0.049-0.01934.903-0.129-0.1290.0000.0000.0000.000
199A428PHE0-0.014-0.01138.163-0.025-0.0250.0000.0000.0000.000
200A429GLU-1-0.945-0.96739.897-7.845-7.8450.0000.0000.0000.000
201A430PHE0-0.009-0.01031.898-0.068-0.0680.0000.0000.0000.000
202A431ALA0-0.004-0.00237.271-0.087-0.0870.0000.0000.0000.000
203A432PHE0-0.033-0.00438.8540.0540.0540.0000.0000.0000.000
204A433HIS00.0450.00937.5780.0830.0830.0000.0000.0000.000
205A434LEU00.0050.00633.764-0.083-0.0830.0000.0000.0000.000
206A435ARG10.8230.88536.9667.6737.6730.0000.0000.0000.000
207A436GLN0-0.0120.00040.2710.0420.0420.0000.0000.0000.000
208A437ARG10.8110.88933.3909.2709.2700.0000.0000.0000.000
209A438ILE00.000-0.02135.568-0.096-0.0960.0000.0000.0000.000
210A439SER0-0.108-0.05338.3290.1180.1180.0000.0000.0000.000
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212A441LEU0-0.055-0.03034.301-0.099-0.0990.0000.0000.0000.000
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