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: NL7KQ

Calculation Name: 3FSS-A-Xray547

Preferred Name:

Target Type:

Ligand Name: malonic acid | glycerol

Ligand 3-letter code: MLA | GOL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3FSS

Chain ID: A

ChEMBL ID:

UniProt ID: P40161

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 232
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2959305.706271
FMO2-HF: Nuclear repulsion 2866659.516669
FMO2-HF: Total energy -92646.189602
FMO2-MP2: Total energy -92917.813401


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:70:THR)


Summations of interaction energy for fragment #1(A:70:THR)
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.
-56.653-53.79416.875-9.223-10.508-0.044
Interaction energy analysis for fragmet #1(A:70:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.859 / q_NPA : 0.921
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].
3A72THR0-0.015-0.0173.3472.9794.7260.037-0.679-1.105-0.004
4A73ILE0-0.0160.0085.0551.6951.728-0.001-0.004-0.0280.000
25A94TYR0-0.024-0.0272.467-2.914-2.3042.215-0.821-2.004-0.009
26A95LEU00.0220.0223.4044.2024.5080.006-0.085-0.2270.000
27A96SER0-0.028-0.0312.660-16.461-14.7121.006-1.179-1.575-0.014
28A97ASN0-0.036-0.0521.987-22.668-24.29813.613-6.436-5.545-0.017
29A98VAL0-0.0260.0024.7152.5302.574-0.001-0.019-0.0240.000
5A74PHE00.0390.0148.2522.1622.1620.0000.0000.0000.000
6A75LYS10.9340.9587.61629.88629.8860.0000.0000.0000.000
7A76LEU0-0.0070.00311.5731.2811.2810.0000.0000.0000.000
8A77GLU-1-0.930-0.96615.070-15.407-15.4070.0000.0000.0000.000
9A78GLY00.0670.03416.7450.7000.7000.0000.0000.0000.000
10A79VAL00.0020.00516.7611.1131.1130.0000.0000.0000.000
11A80SER0-0.035-0.02919.3770.2350.2350.0000.0000.0000.000
12A81VAL00.0110.01417.8920.2970.2970.0000.0000.0000.000
13A82LEU0-0.074-0.04021.2370.5480.5480.0000.0000.0000.000
14A83SER00.007-0.00522.8350.5540.5540.0000.0000.0000.000
15A84PRO00.0090.02319.449-0.461-0.4610.0000.0000.0000.000
16A85LEU0-0.028-0.01718.3230.4690.4690.0000.0000.0000.000
17A86ARG10.9470.98122.07410.14210.1420.0000.0000.0000.000
18A87LYS10.8050.87920.19713.98613.9860.0000.0000.0000.000
19A88LYS10.8420.93320.80612.83612.8360.0000.0000.0000.000
20A89LEU0-0.043-0.02415.8590.1390.1390.0000.0000.0000.000
21A90ASP-1-0.848-0.92313.613-17.594-17.5940.0000.0000.0000.000
22A91LEU0-0.0190.00111.909-1.015-1.0150.0000.0000.0000.000
23A92VAL0-0.027-0.0276.319-0.957-0.9570.0000.0000.0000.000
24A93PHE00.0380.0337.952-0.140-0.1400.0000.0000.0000.000
30A99ASP-1-0.785-0.8757.967-25.266-25.2660.0000.0000.0000.000
31A100GLY0-0.0060.0127.2421.6941.6940.0000.0000.0000.000
32A101SER0-0.058-0.0348.1360.2080.2080.0000.0000.0000.000
33A102PRO00.0030.0087.239-3.854-3.8540.0000.0000.0000.000
34A103VAL0-0.045-0.0185.8872.1502.1500.0000.0000.0000.000
35A104ILE00.0090.0177.499-1.469-1.4690.0000.0000.0000.000
36A105THR0-0.037-0.0397.2900.3350.3350.0000.0000.0000.000
37A106LEU00.0140.0049.6790.0510.0510.0000.0000.0000.000
38A107LEU00.0240.0058.9000.0960.0960.0000.0000.0000.000
39A108LYS10.9870.99113.05515.52315.5230.0000.0000.0000.000
40A109GLY00.0110.00915.5140.3870.3870.0000.0000.0000.000
41A110ASN0-0.007-0.01812.148-2.152-2.1520.0000.0000.0000.000
42A111ASP-1-0.914-0.93412.014-18.323-18.3230.0000.0000.0000.000
43A112ARG10.8320.8796.00629.15329.1530.0000.0000.0000.000
44A113GLU-1-0.824-0.88812.320-13.825-13.8250.0000.0000.0000.000
45A114LEU0-0.004-0.00914.2260.8180.8180.0000.0000.0000.000
46A115SER0-0.017-0.0209.446-1.478-1.4780.0000.0000.0000.000
47A116ILE0-0.022-0.00310.9461.3401.3400.0000.0000.0000.000
48A117TYR00.023-0.0227.081-2.429-2.4290.0000.0000.0000.000
49A118GLN00.0390.0039.8841.3571.3570.0000.0000.0000.000
50A119LEU00.0330.00711.0591.7531.7530.0000.0000.0000.000
51A120ASN00.0090.00013.2160.6340.6340.0000.0000.0000.000
52A121LYS10.8880.94814.97817.46217.4620.0000.0000.0000.000
53A122ASN00.0130.01414.3731.5331.5330.0000.0000.0000.000
54A123ILE0-0.034-0.00215.5030.4320.4320.0000.0000.0000.000
55A124LYS10.8780.94418.22012.40012.4000.0000.0000.0000.000
56A125MET00.0380.03221.7580.5570.5570.0000.0000.0000.000
57A126ALA0-0.035-0.02818.947-0.358-0.3580.0000.0000.0000.000
58A127SER0-0.061-0.04020.9660.3060.3060.0000.0000.0000.000
59A128PHE0-0.022-0.02219.018-0.369-0.3690.0000.0000.0000.000
60A129LEU00.0300.01224.0070.4580.4580.0000.0000.0000.000
61A130PRO0-0.0060.01627.200-0.250-0.2500.0000.0000.0000.000
62A131VAL0-0.0030.00328.1550.0800.0800.0000.0000.0000.000
63A132PRO00.0190.00730.6560.1630.1630.0000.0000.0000.000
64A133GLU-1-0.937-0.97134.479-7.925-7.9250.0000.0000.0000.000
65A134LYS10.8880.95231.9828.8258.8250.0000.0000.0000.000
66A135PRO00.0880.04831.301-0.351-0.3510.0000.0000.0000.000
67A136ASN00.018-0.00130.554-0.129-0.1290.0000.0000.0000.000
68A137LEU0-0.061-0.03327.169-0.409-0.4090.0000.0000.0000.000
69A138ILE00.0050.00623.4400.2730.2730.0000.0000.0000.000
70A139TYR00.001-0.00324.109-0.206-0.2060.0000.0000.0000.000
71A140LEU00.0090.00916.805-0.038-0.0380.0000.0000.0000.000
72A141PHE00.007-0.00521.259-0.095-0.0950.0000.0000.0000.000
73A142MET00.018-0.00615.082-0.575-0.5750.0000.0000.0000.000
74A143THR0-0.0070.00820.4730.0820.0820.0000.0000.0000.000
75A144TYR00.012-0.01617.779-0.488-0.4880.0000.0000.0000.000
76A145THR0-0.025-0.01218.5970.5550.5550.0000.0000.0000.000
77A146SER0-0.0100.00617.4250.2840.2840.0000.0000.0000.000
78A147CYS0-0.070-0.01614.995-0.518-0.5180.0000.0000.0000.000
79A148GLU-1-0.725-0.80610.256-24.069-24.0690.0000.0000.0000.000
80A149ASP-1-0.900-0.96114.064-16.809-16.8090.0000.0000.0000.000
81A150ASN0-0.058-0.03117.0760.6210.6210.0000.0000.0000.000
82A151LYS10.8930.96715.09017.85617.8560.0000.0000.0000.000
83A152PHE0-0.016-0.03118.0550.5970.5970.0000.0000.0000.000
84A153SER00.0500.01220.755-0.237-0.2370.0000.0000.0000.000
85A154GLU-1-0.807-0.90622.933-10.269-10.2690.0000.0000.0000.000
86A155PRO00.0620.03422.217-0.629-0.6290.0000.0000.0000.000
87A156VAL00.0090.01517.1080.1140.1140.0000.0000.0000.000
88A157VAL0-0.0160.00120.4310.2940.2940.0000.0000.0000.000
89A158MET0-0.0030.01115.679-0.159-0.1590.0000.0000.0000.000
90A159THR0-0.016-0.01321.2400.4000.4000.0000.0000.0000.000
91A160LEU00.0150.01218.687-0.380-0.3800.0000.0000.0000.000
92A161ASN00.0190.00422.5870.4760.4760.0000.0000.0000.000
93A162LYS10.9190.98123.74810.09510.0950.0000.0000.0000.000
94A163GLU-1-0.796-0.89724.557-11.457-11.4570.0000.0000.0000.000
95A164ASN0-0.042-0.00721.415-0.674-0.6740.0000.0000.0000.000
96A165THR00.025-0.01119.069-0.628-0.6280.0000.0000.0000.000
97A166LEU00.0330.01620.376-0.722-0.7220.0000.0000.0000.000
98A167ASN0-0.109-0.06322.242-0.325-0.3250.0000.0000.0000.000
99A168GLN0-0.038-0.02417.187-1.282-1.2820.0000.0000.0000.000
100A169PHE00.0480.00315.581-0.790-0.7900.0000.0000.0000.000
101A170LYS10.8130.92818.61711.43311.4330.0000.0000.0000.000
102A171LYS10.9060.95319.07913.56213.5620.0000.0000.0000.000
103A172LEU0-0.044-0.01113.000-0.740-0.7400.0000.0000.0000.000
104A173GLY0-0.0020.00815.955-0.851-0.8510.0000.0000.0000.000
105A174LEU0-0.054-0.02213.9180.1310.1310.0000.0000.0000.000
106A175LEU0-0.029-0.02218.0620.6110.6110.0000.0000.0000.000
107A176ASP-1-0.760-0.88721.826-11.696-11.6960.0000.0000.0000.000
108A177SER0-0.023-0.01325.0720.2140.2140.0000.0000.0000.000
109A178ASN0-0.041-0.02826.9870.3940.3940.0000.0000.0000.000
110A179VAL0-0.034-0.00525.1520.3180.3180.0000.0000.0000.000
111A180THR00.023-0.00227.507-0.250-0.2500.0000.0000.0000.000
112A181ASP-1-0.838-0.90728.433-10.514-10.5140.0000.0000.0000.000
113A182PHE00.033-0.00122.312-0.454-0.4540.0000.0000.0000.000
114A183GLU-1-0.786-0.88324.004-11.800-11.8000.0000.0000.0000.000
115A184LYS10.8620.93023.56011.12111.1210.0000.0000.0000.000
116A185CYS0-0.049-0.01820.005-0.522-0.5220.0000.0000.0000.000
117A186VAL00.0160.02319.313-0.881-0.8810.0000.0000.0000.000
118A187GLU-1-0.805-0.90320.366-13.123-13.1230.0000.0000.0000.000
119A188TYR00.0050.00412.826-0.566-0.5660.0000.0000.0000.000
120A189ILE00.000-0.00415.505-0.933-0.9330.0000.0000.0000.000
121A190ARG00.014-0.00916.049-0.475-0.4750.0000.0000.0000.000
122A191LYS10.8960.94217.84914.07314.0730.0000.0000.0000.000
123A192GLN0-0.043-0.02512.133-1.699-1.6990.0000.0000.0000.000
124A193ALA0-0.0160.01413.214-1.188-1.1880.0000.0000.0000.000
125A194ILE00.0520.03015.149-0.398-0.3980.0000.0000.0000.000
126A195LEU0-0.058-0.03014.143-0.008-0.0080.0000.0000.0000.000
127A196THR0-0.085-0.0599.967-1.182-1.1820.0000.0000.0000.000
128A197GLY00.0100.00612.939-0.390-0.3900.0000.0000.0000.000
129A198PHE0-0.034-0.03712.6680.3530.3530.0000.0000.0000.000
130A199LYS00.0200.01117.284-0.124-0.1240.0000.0000.0000.000
131A200ILE0-0.076-0.03315.844-0.242-0.2420.0000.0000.0000.000
132A201SER-1-0.585-0.76620.178-11.798-11.7980.0000.0000.0000.000
133A202ASN0-0.046-0.05723.594-0.645-0.6450.0000.0000.0000.000
134A203PRO0-0.0070.00926.0810.3360.3360.0000.0000.0000.000
135A204PHE0-0.023-0.01329.2180.4280.4280.0000.0000.0000.000
136A205VAL00.0550.02130.167-0.238-0.2380.0000.0000.0000.000
137A206ASN0-0.113-0.07427.3790.3450.3450.0000.0000.0000.000
138A207SER00.0230.00326.5100.0350.0350.0000.0000.0000.000
139A208THR0-0.059-0.03425.3450.2800.2800.0000.0000.0000.000
140A209LEU0-0.021-0.00722.790-0.205-0.2050.0000.0000.0000.000
141A210VAL0-0.0120.00026.6580.0350.0350.0000.0000.0000.000
142A211ASP-1-0.806-0.89825.129-11.677-11.6770.0000.0000.0000.000
143A212THR0-0.0170.01926.0680.0590.0590.0000.0000.0000.000
144A213ASP-1-0.831-0.91728.140-9.756-9.7560.0000.0000.0000.000
145A214ALA0-0.058-0.05130.9790.3560.3560.0000.0000.0000.000
146A215GLU-1-0.984-0.98930.867-9.554-9.5540.0000.0000.0000.000
147A216LYS10.8790.93833.5198.2548.2540.0000.0000.0000.000
148A217ILE0-0.032-0.00435.0050.2770.2770.0000.0000.0000.000
149A218ASN00.001-0.00735.325-0.354-0.3540.0000.0000.0000.000
150A219SER00.0230.02533.7100.1570.1570.0000.0000.0000.000
151A220PHE0-0.024-0.01235.7920.0420.0420.0000.0000.0000.000
152A221HIS00.004-0.01034.347-0.262-0.2620.0000.0000.0000.000
153A222LEU0-0.0050.01836.4790.1620.1620.0000.0000.0000.000
154A223GLN00.0190.01336.939-0.405-0.4050.0000.0000.0000.000
155A224CYS0-0.0170.01039.1720.1490.1490.0000.0000.0000.000
156A225HIS00.0410.00939.826-0.220-0.2200.0000.0000.0000.000
157A226ARG10.9580.99735.4588.1258.1250.0000.0000.0000.000
158A227GLY00.0250.01540.515-0.048-0.0480.0000.0000.0000.000
159A228THR0-0.006-0.01743.0560.0260.0260.0000.0000.0000.000
160A229LYS10.8620.94234.9558.3588.3580.0000.0000.0000.000
161A230GLU-1-0.824-0.90139.054-7.611-7.6110.0000.0000.0000.000
162A231GLY0-0.078-0.05535.592-0.228-0.2280.0000.0000.0000.000
163A232THR0-0.028-0.02133.2600.1470.1470.0000.0000.0000.000
164A233LEU0-0.013-0.01234.100-0.227-0.2270.0000.0000.0000.000
165A234TYR0-0.009-0.04130.7640.1050.1050.0000.0000.0000.000
166A235PHE00.0260.00134.006-0.045-0.0450.0000.0000.0000.000
167A236LEU00.0180.00728.7940.0280.0280.0000.0000.0000.000
168A237PRO0-0.026-0.00930.9070.2300.2300.0000.0000.0000.000
169A238ASP-1-0.800-0.88730.285-9.380-9.3800.0000.0000.0000.000
170A239HIS10.7970.89128.04910.16310.1630.0000.0000.0000.000
171A240ILE00.0190.03031.9990.0860.0860.0000.0000.0000.000
172A241ILE0-0.006-0.00727.640-0.225-0.2250.0000.0000.0000.000
173A242PHE0-0.0190.00831.8490.1920.1920.0000.0000.0000.000
174A243GLY00.0280.02230.485-0.249-0.2490.0000.0000.0000.000
175A244PHE0-0.011-0.01227.7990.2410.2410.0000.0000.0000.000
176A245LYS10.9010.94429.1758.3508.3500.0000.0000.0000.000
177A246LYS10.9801.02728.31510.14210.1420.0000.0000.0000.000
178A247PRO0-0.065-0.05530.4560.3160.3160.0000.0000.0000.000
179A248ILE0-0.037-0.02026.2100.2300.2300.0000.0000.0000.000
180A249LEU0-0.040-0.00429.384-0.147-0.1470.0000.0000.0000.000
181A250LEU0-0.017-0.01726.524-0.149-0.1490.0000.0000.0000.000
182A251LEU0-0.0010.00230.3210.0910.0910.0000.0000.0000.000
183A252ASP-1-0.805-0.89930.536-10.028-10.0280.0000.0000.0000.000
184A253ALA0-0.012-0.01733.1750.2670.2670.0000.0000.0000.000
185A254SER0-0.016-0.01035.2390.1590.1590.0000.0000.0000.000
186A255ASP-1-0.877-0.94835.034-8.382-8.3820.0000.0000.0000.000
187A256ILE0-0.070-0.03337.7000.1690.1690.0000.0000.0000.000
188A257GLU-1-0.908-0.94540.198-6.866-6.8660.0000.0000.0000.000
189A258SER0-0.046-0.02943.7150.2010.2010.0000.0000.0000.000
190A259ILE0-0.0010.00443.773-0.149-0.1490.0000.0000.0000.000
191A260THR0-0.0200.00146.2450.1930.1930.0000.0000.0000.000
192A261TYR0-0.028-0.03946.887-0.108-0.1080.0000.0000.0000.000
193A262SER00.000-0.00949.9140.1310.1310.0000.0000.0000.000
194A263SER0-0.014-0.02151.488-0.049-0.0490.0000.0000.0000.000
195A264ILE00.0250.02552.720-0.050-0.0500.0000.0000.0000.000
196A265THR0-0.033-0.02253.4160.1360.1360.0000.0000.0000.000
197A266ARG10.9410.94754.6515.1845.1840.0000.0000.0000.000
198A267LEU0-0.0110.01252.196-0.004-0.0040.0000.0000.0000.000
199A268THR00.0140.02048.657-0.104-0.1040.0000.0000.0000.000
200A269PHE0-0.0100.00846.3930.1790.1790.0000.0000.0000.000
201A270ASN00.0370.02347.148-0.193-0.1930.0000.0000.0000.000
202A271ALA00.001-0.00644.5770.1240.1240.0000.0000.0000.000
203A272SER0-0.012-0.00644.538-0.179-0.1790.0000.0000.0000.000
204A273LEU00.0270.01339.3810.1020.1020.0000.0000.0000.000
205A274VAL0-0.0030.00642.127-0.075-0.0750.0000.0000.0000.000
206A275THR00.015-0.02637.766-0.027-0.0270.0000.0000.0000.000
207A276LYS10.8740.93239.5527.5617.5610.0000.0000.0000.000
208A277ASP-1-0.863-0.89437.865-7.760-7.7600.0000.0000.0000.000
209A278GLY0-0.029-0.00940.9300.1170.1170.0000.0000.0000.000
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