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: QL9GY

Calculation Name: 6J5Y-A-Xray547

Preferred Name:

Target Type:

Ligand Name: pyruvic acid | manganese (ii) ion

Ligand 3-letter code: PYR | MN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6J5Y

Chain ID: A

ChEMBL ID:

UniProt ID: Q9I111

Base Structure: X-ray

Registration Date: 2025-10-06

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 233
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2892879.617952
FMO2-HF: Nuclear repulsion 2802058.823127
FMO2-HF: Total energy -90820.794826
FMO2-MP2: Total energy -91084.349827


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:2:ASN)


Summations of interaction energy for fragment #1(A:2:ASN)
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.
-61.556-59.826-0.021-0.576-1.132-0.002
Interaction energy analysis for fragmet #1(A:2:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.818 / q_NPA : 0.897
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].
3A4LEU00.0300.0223.8025.3567.086-0.021-0.576-1.132-0.002
4A5PHE00.0160.0086.0723.3303.3300.0000.0000.0000.000
5A6ALA00.002-0.0037.521-4.062-4.0620.0000.0000.0000.000
6A7PRO0-0.019-0.0196.8781.6581.6580.0000.0000.0000.000
7A8GLU0-0.051-0.0499.6651.2681.2680.0000.0000.0000.000
8A9ALA0-0.013-0.00612.598-0.952-0.9520.0000.0000.0000.000
9A10PRO0-0.0080.00112.8710.7740.7740.0000.0000.0000.000
10A11VAL00.0510.02915.7200.3780.3780.0000.0000.0000.000
11A12SER0-0.012-0.01519.493-0.067-0.0670.0000.0000.0000.000
12A13LEU00.0190.02021.3310.2890.2890.0000.0000.0000.000
13A14THR00.0420.01425.117-0.201-0.2010.0000.0000.0000.000
14A15ILE00.0060.01725.4280.2480.2480.0000.0000.0000.000
15A16HIS0-0.038-0.02929.0420.2430.2430.0000.0000.0000.000
16A17GLY00.0000.00032.8540.0700.0700.0000.0000.0000.000
17A18SER0-0.069-0.03527.8280.0360.0360.0000.0000.0000.000
18A19ASP-1-0.886-0.93527.301-11.365-11.3650.0000.0000.0000.000
19A20GLN0-0.068-0.03023.970-0.816-0.8160.0000.0000.0000.000
20A21THR00.006-0.00921.0880.3640.3640.0000.0000.0000.000
21A22PHE00.0080.01022.398-0.412-0.4120.0000.0000.0000.000
22A23PRO0-0.048-0.02517.8060.0280.0280.0000.0000.0000.000
23A24VAL00.0200.00919.6740.3250.3250.0000.0000.0000.000
24A25ARG10.8050.88917.53714.40214.4020.0000.0000.0000.000
25A26ARG10.8680.93219.13414.11614.1160.0000.0000.0000.000
26A27VAL00.0470.02821.8780.2230.2230.0000.0000.0000.000
27A28TYR0-0.016-0.00524.906-0.197-0.1970.0000.0000.0000.000
28A29CYS0-0.0010.01628.0810.0560.0560.0000.0000.0000.000
29A30VAL0-0.015-0.00531.489-0.022-0.0220.0000.0000.0000.000
30A31GLY00.0100.01834.9750.1690.1690.0000.0000.0000.000
31A32ARG10.9260.94937.4417.5937.5930.0000.0000.0000.000
32A33ASN00.0070.00238.2050.3060.3060.0000.0000.0000.000
33A34TYR00.0950.06740.1090.1260.1260.0000.0000.0000.000
34A35ALA00.0340.01044.1660.0390.0390.0000.0000.0000.000
35A36ALA0-0.041-0.02547.5920.1080.1080.0000.0000.0000.000
36A37HIS00.012-0.01641.939-0.082-0.0820.0000.0000.0000.000
37A38ALA0-0.002-0.00445.277-0.011-0.0110.0000.0000.0000.000
38A39ARG10.9670.99246.1336.2176.2170.0000.0000.0000.000
39A40GLU-1-0.780-0.87045.982-6.772-6.7720.0000.0000.0000.000
40A41MET0-0.077-0.02743.349-0.068-0.0680.0000.0000.0000.000
41A42GLY0-0.045-0.01546.534-0.046-0.0460.0000.0000.0000.000
42A43PHE0-0.076-0.05244.962-0.048-0.0480.0000.0000.0000.000
43A44ASP-1-0.827-0.92448.100-6.133-6.1330.0000.0000.0000.000
44A45PRO0-0.040-0.02447.069-0.090-0.0900.0000.0000.0000.000
45A46GLU-1-0.949-0.96548.071-6.016-6.0160.0000.0000.0000.000
46A47ARG10.8260.92249.8456.0106.0100.0000.0000.0000.000
47A48GLU-1-0.943-0.97944.906-7.017-7.0170.0000.0000.0000.000
48A49PRO0-0.032-0.00141.5770.0300.0300.0000.0000.0000.000
49A50PRO00.0190.01639.174-0.057-0.0570.0000.0000.0000.000
50A51PHE0-0.039-0.01735.598-0.054-0.0540.0000.0000.0000.000
51A52PHE00.008-0.00631.584-0.098-0.0980.0000.0000.0000.000
52A53PHE0-0.024-0.01130.529-0.028-0.0280.0000.0000.0000.000
53A54CYS0-0.043-0.02825.346-0.154-0.1540.0000.0000.0000.000
54A55LYS10.8320.90025.80210.57910.5790.0000.0000.0000.000
55A56PRO00.0040.00920.693-0.303-0.3030.0000.0000.0000.000
56A57ALA00.0380.00018.5090.4120.4120.0000.0000.0000.000
57A58ASP-1-0.850-0.89618.535-15.648-15.6480.0000.0000.0000.000
58A59ALA0-0.019-0.00120.8970.4040.4040.0000.0000.0000.000
59A60VAL0-0.034-0.01123.5480.5920.5920.0000.0000.0000.000
60A61VAL0-0.040-0.02324.121-0.429-0.4290.0000.0000.0000.000
61A62PRO0-0.013-0.01424.4560.4350.4350.0000.0000.0000.000
62A63VAL0-0.031-0.00127.601-0.004-0.0040.0000.0000.0000.000
63A64ALA0-0.021-0.00730.9800.0270.0270.0000.0000.0000.000
64A65ALA00.1010.04032.3050.1850.1850.0000.0000.0000.000
65A66GLY0-0.020-0.00835.906-0.033-0.0330.0000.0000.0000.000
66A67SER0-0.070-0.02434.0200.0160.0160.0000.0000.0000.000
67A68THR0-0.020-0.00936.0040.2200.2200.0000.0000.0000.000
68A69LEU0-0.0230.00130.213-0.179-0.1790.0000.0000.0000.000
69A70GLU-1-0.781-0.85933.484-8.117-8.1170.0000.0000.0000.000
70A71LEU0-0.033-0.01631.019-0.356-0.3560.0000.0000.0000.000
71A72ALA00.0250.01031.7670.2700.2700.0000.0000.0000.000
72A73TYR0-0.0100.00733.660-0.082-0.0820.0000.0000.0000.000
73A74PRO0-0.0240.00432.396-0.178-0.1780.0000.0000.0000.000
74A75SER00.0580.01631.6970.2650.2650.0000.0000.0000.000
75A76GLN0-0.054-0.03934.0020.0770.0770.0000.0000.0000.000
76A77THR0-0.022-0.04536.3620.0230.0230.0000.0000.0000.000
77A78GLY00.0240.02238.6480.0280.0280.0000.0000.0000.000
78A79ASN0-0.062-0.02941.1600.1740.1740.0000.0000.0000.000
79A80TYR00.0340.01434.279-0.210-0.2100.0000.0000.0000.000
80A81HIS00.0470.01638.4480.1340.1340.0000.0000.0000.000
81A82TYR00.006-0.00437.712-0.282-0.2820.0000.0000.0000.000
82A83GLU-1-0.772-0.86736.989-8.239-8.2390.0000.0000.0000.000
83A84ILE0-0.0290.00737.002-0.302-0.3020.0000.0000.0000.000
84A85GLU-1-0.790-0.90434.785-8.820-8.8200.0000.0000.0000.000
85A86LEU00.0390.02935.998-0.074-0.0740.0000.0000.0000.000
86A87VAL0-0.0340.00729.558-0.141-0.1410.0000.0000.0000.000
87A88ALA00.0310.01731.6610.1480.1480.0000.0000.0000.000
88A89ALA00.0140.00726.725-0.343-0.3430.0000.0000.0000.000
89A90ILE0-0.007-0.00325.4220.2770.2770.0000.0000.0000.000
90A91GLY00.0050.00125.114-0.538-0.5380.0000.0000.0000.000
91A92LYS10.7720.85425.4759.6879.6870.0000.0000.0000.000
92A93GLY00.0320.01224.7110.2060.2060.0000.0000.0000.000
93A94GLY0-0.028-0.02125.6360.4480.4480.0000.0000.0000.000
94A95CYS0-0.007-0.00627.744-0.360-0.3600.0000.0000.0000.000
95A96ASP-1-0.885-0.95029.762-9.369-9.3690.0000.0000.0000.000
96A97ILE0-0.029-0.00329.5760.2420.2420.0000.0000.0000.000
97A98PRO00.0140.01433.9420.1630.1630.0000.0000.0000.000
98A99LEU00.0680.03537.323-0.132-0.1320.0000.0000.0000.000
99A100GLU-1-0.922-0.97039.455-7.721-7.7210.0000.0000.0000.000
100A101GLN0-0.0030.00534.198-0.286-0.2860.0000.0000.0000.000
101A102ALA0-0.0110.01434.523-0.274-0.2740.0000.0000.0000.000
102A103GLU-1-0.778-0.89633.666-8.345-8.3450.0000.0000.0000.000
103A104GLU-1-0.846-0.88333.006-9.830-9.8300.0000.0000.0000.000
104A105HIS10.7720.87429.02610.06710.0670.0000.0000.0000.000
105A106VAL0-0.0010.00829.231-0.520-0.5200.0000.0000.0000.000
106A107TRP00.013-0.00927.8170.1760.1760.0000.0000.0000.000
107A108GLY00.002-0.00429.8850.1920.1920.0000.0000.0000.000
108A109TYR0-0.028-0.03231.382-0.150-0.1500.0000.0000.0000.000
109A110ALA00.0330.01531.334-0.060-0.0600.0000.0000.0000.000
110A111VAL00.0440.03833.3170.1050.1050.0000.0000.0000.000
111A112GLY00.021-0.00332.875-0.334-0.3340.0000.0000.0000.000
112A113LEU00.002-0.00432.8040.3320.3320.0000.0000.0000.000
113A114ASP-1-0.767-0.86732.426-9.910-9.9100.0000.0000.0000.000
114A115MET0-0.0120.02732.7120.2970.2970.0000.0000.0000.000
115A116THR0-0.011-0.02233.091-0.305-0.3050.0000.0000.0000.000
116A117ARG10.8270.91830.32110.03510.0350.0000.0000.0000.000
117A118ARG10.8350.88736.5197.8767.8760.0000.0000.0000.000
118A119ASP-1-0.751-0.85739.279-7.925-7.9250.0000.0000.0000.000
119A120LEU0-0.057-0.02834.5060.0530.0530.0000.0000.0000.000
120A121GLN00.0350.02736.5180.0730.0730.0000.0000.0000.000
121A122MET0-0.028-0.01237.5970.0480.0480.0000.0000.0000.000
122A123ARG10.9560.98337.5958.2478.2470.0000.0000.0000.000
123A124MET0-0.062-0.03735.0260.0090.0090.0000.0000.0000.000
124A125ARG10.8630.94238.2847.1727.1720.0000.0000.0000.000
125A126GLU-1-0.846-0.91340.513-6.864-6.8640.0000.0000.0000.000
126A127MET0-0.095-0.04739.898-0.006-0.0060.0000.0000.0000.000
127A128GLY00.0070.02040.147-0.061-0.0610.0000.0000.0000.000
128A129ARG10.8750.93535.5438.3108.3100.0000.0000.0000.000
129A130PRO00.0510.02331.0650.1030.1030.0000.0000.0000.000
130A131TRP00.0550.00432.4660.1780.1780.0000.0000.0000.000
131A132GLU-1-0.856-0.92927.067-10.715-10.7150.0000.0000.0000.000
132A133ILE0-0.014-0.01129.762-0.088-0.0880.0000.0000.0000.000
133A134GLY00.0310.00831.3760.0930.0930.0000.0000.0000.000
134A135LYS10.7790.87331.5879.1109.1100.0000.0000.0000.000
135A136ALA0-0.0320.00426.442-0.098-0.0980.0000.0000.0000.000
136A137PHE0-0.0200.00226.150-0.471-0.4710.0000.0000.0000.000
137A138ASP-1-0.835-0.92825.262-12.159-12.1590.0000.0000.0000.000
138A139ARG10.9090.95125.00512.15312.1530.0000.0000.0000.000
139A140SER0-0.0020.00327.3800.3450.3450.0000.0000.0000.000
140A141ALA00.0240.01527.2560.2960.2960.0000.0000.0000.000
141A142PRO00.0100.00628.392-0.305-0.3050.0000.0000.0000.000
142A143ILE0-0.021-0.01027.4310.1430.1430.0000.0000.0000.000
143A144GLY00.0620.04030.499-0.102-0.1020.0000.0000.0000.000
144A145PRO0-0.044-0.01830.101-0.360-0.3600.0000.0000.0000.000
145A146LEU0-0.036-0.01626.9910.1910.1910.0000.0000.0000.000
146A147TYR00.0590.01930.442-0.082-0.0820.0000.0000.0000.000
147A148PRO0-0.016-0.00231.005-0.052-0.0520.0000.0000.0000.000
148A149ALA00.0580.02732.6900.3180.3180.0000.0000.0000.000
149A150SER0-0.083-0.04233.6250.2490.2490.0000.0000.0000.000
150A151GLN0-0.054-0.02334.2850.2910.2910.0000.0000.0000.000
151A152VAL00.0110.00036.2110.2350.2350.0000.0000.0000.000
152A153GLY0-0.0110.01038.3310.1840.1840.0000.0000.0000.000
153A154HIS00.0160.01434.384-0.179-0.1790.0000.0000.0000.000
154A155PRO00.0130.02038.2470.2220.2220.0000.0000.0000.000
155A156ARG10.8260.87740.6777.6217.6210.0000.0000.0000.000
156A157HIS10.8010.89043.8246.7346.7340.0000.0000.0000.000
157A158ALA00.0020.00642.624-0.082-0.0820.0000.0000.0000.000
158A159ALA00.0210.02544.532-0.041-0.0410.0000.0000.0000.000
159A160ILE0-0.019-0.00839.660-0.169-0.1690.0000.0000.0000.000
160A161SER0-0.059-0.03742.8340.2110.2110.0000.0000.0000.000
161A162LEU00.0170.00539.956-0.219-0.2190.0000.0000.0000.000
162A163GLN00.0120.01843.4440.1470.1470.0000.0000.0000.000
163A164VAL0-0.017-0.01943.246-0.231-0.2310.0000.0000.0000.000
164A165ASP-1-0.850-0.93145.398-6.795-6.7950.0000.0000.0000.000
165A166GLY0-0.040-0.01247.3630.1440.1440.0000.0000.0000.000
166A167GLU-1-0.940-0.95949.332-5.889-5.8890.0000.0000.0000.000
167A168ASP-1-0.825-0.91648.359-6.635-6.6350.0000.0000.0000.000
168A169ARG10.8250.92745.5756.8746.8740.0000.0000.0000.000
169A170GLN00.0080.00141.963-0.118-0.1180.0000.0000.0000.000
170A171ARG10.8260.88346.2796.5096.5090.0000.0000.0000.000
171A172SER00.0220.02745.6700.1260.1260.0000.0000.0000.000
172A173ASP-1-0.765-0.88845.913-6.904-6.9040.0000.0000.0000.000
173A174ILE00.0090.00140.583-0.048-0.0480.0000.0000.0000.000
174A175ASP-1-0.892-0.93043.271-6.638-6.6380.0000.0000.0000.000
175A176GLN0-0.095-0.05745.8730.1420.1420.0000.0000.0000.000
176A177LEU0-0.067-0.02339.542-0.038-0.0380.0000.0000.0000.000
177A178ILE0-0.055-0.02643.0470.1170.1170.0000.0000.0000.000
178A179TRP0-0.039-0.02137.741-0.063-0.0630.0000.0000.0000.000
179A180SER00.057-0.00839.896-0.206-0.2060.0000.0000.0000.000
180A181VAL00.0560.02934.882-0.203-0.2030.0000.0000.0000.000
181A182ALA00.0000.00235.854-0.246-0.2460.0000.0000.0000.000
182A183GLU-1-0.801-0.87536.766-7.718-7.7180.0000.0000.0000.000
183A184THR0-0.045-0.02934.688-0.243-0.2430.0000.0000.0000.000
184A185VAL0-0.002-0.00131.232-0.301-0.3010.0000.0000.0000.000
185A186SER0-0.008-0.02932.578-0.197-0.1970.0000.0000.0000.000
186A187TYR0-0.042-0.02634.402-0.160-0.1600.0000.0000.0000.000
187A188LEU00.0080.01928.974-0.125-0.1250.0000.0000.0000.000
188A189SER0-0.062-0.04029.713-0.268-0.2680.0000.0000.0000.000
189A190ARG10.9620.99630.7568.3528.3520.0000.0000.0000.000
190A191PHE0-0.069-0.02130.4420.0350.0350.0000.0000.0000.000
191A192PHE0-0.017-0.02425.364-0.530-0.5300.0000.0000.0000.000
192A193GLU-1-0.849-0.91122.677-13.755-13.7550.0000.0000.0000.000
193A194LEU0-0.0070.00923.860-0.597-0.5970.0000.0000.0000.000
194A195ARG10.7910.87019.48814.76914.7690.0000.0000.0000.000
195A196PRO0-0.012-0.01521.0560.2030.2030.0000.0000.0000.000
196A197GLY00.0600.03620.511-0.825-0.8250.0000.0000.0000.000
197A198ASP-1-0.807-0.88021.724-14.064-14.0640.0000.0000.0000.000
198A199LEU00.0040.00523.6150.4090.4090.0000.0000.0000.000
199A200VAL0-0.015-0.01926.476-0.143-0.1430.0000.0000.0000.000
200A201PHE00.0210.01228.0390.1440.1440.0000.0000.0000.000
201A202THR0-0.038-0.05332.0340.0970.0970.0000.0000.0000.000
202A203GLY00.0730.03835.3200.2290.2290.0000.0000.0000.000
203A204THR0-0.053-0.03737.4200.0990.0990.0000.0000.0000.000
204A205PRO0-0.017-0.00739.9390.1070.1070.0000.0000.0000.000
205A206GLU-1-0.894-0.97143.607-6.758-6.7580.0000.0000.0000.000
206A207GLY00.0200.00745.940-0.036-0.0360.0000.0000.0000.000
207A208VAL0-0.043-0.00841.787-0.065-0.0650.0000.0000.0000.000
208A209GLY0-0.017-0.01943.0650.1940.1940.0000.0000.0000.000
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