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: 87GRY

Calculation Name: 3TR8-A-Xray547

Preferred Name:

Target Type:

Ligand Name: acetate ion | magnesium ion | manganese (ii) ion

Ligand 3-letter code: ACT | MG | MN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3TR8

Chain ID: A

ChEMBL ID:

UniProt ID: Q83C93

Base Structure: X-ray

Registration Date: 2025-10-04

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 184
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2035180.706303
FMO2-HF: Nuclear repulsion 1961217.166103
FMO2-HF: Total energy -73963.5402
FMO2-MP2: Total energy -74179.590487


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:SER)


Summations of interaction energy for fragment #1(A:-2: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.
-110.355-108.691-0.011-0.813-0.84-0.003
Interaction energy analysis for fragmet #1(A:-2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.854 / q_NPA : 0.911
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].
3A0ALA00.0480.0193.729-2.844-1.180-0.011-0.813-0.840-0.003
4A1MET00.0070.0196.4823.5123.5120.0000.0000.0000.000
5A2ASP-1-0.844-0.9227.882-25.683-25.6830.0000.0000.0000.000
6A3PHE0-0.078-0.0248.8761.3981.3980.0000.0000.0000.000
7A4SER00.000-0.0129.063-2.764-2.7640.0000.0000.0000.000
8A5ASP-1-0.805-0.88511.438-18.556-18.5560.0000.0000.0000.000
9A6ASP-1-0.920-0.94613.655-16.994-16.9940.0000.0000.0000.000
10A7ASN0-0.059-0.03312.6620.8350.8350.0000.0000.0000.000
11A8LEU0-0.037-0.01916.1130.7340.7340.0000.0000.0000.000
12A9ILE0-0.007-0.01519.791-0.185-0.1850.0000.0000.0000.000
13A10TRP0-0.014-0.02021.8010.9290.9290.0000.0000.0000.000
14A11LEU0-0.035-0.02824.855-0.274-0.2740.0000.0000.0000.000
15A12ASP-1-0.886-0.93127.826-9.197-9.1970.0000.0000.0000.000
16A13LEU0-0.044-0.02931.442-0.145-0.1450.0000.0000.0000.000
17A14GLU-1-0.785-0.88834.498-8.035-8.0350.0000.0000.0000.000
18A15MET0-0.026-0.02136.925-0.011-0.0110.0000.0000.0000.000
19A16THR0-0.044-0.05740.7440.0660.0660.0000.0000.0000.000
20A17GLY00.0320.00743.8650.2070.2070.0000.0000.0000.000
21A18LEU0-0.046-0.01943.473-0.159-0.1590.0000.0000.0000.000
22A19ASP-1-0.869-0.93144.539-6.797-6.7970.0000.0000.0000.000
23A20PRO00.0080.00640.5790.0110.0110.0000.0000.0000.000
24A21GLU-1-0.864-0.93042.518-7.284-7.2840.0000.0000.0000.000
25A22ARG10.8570.93645.0656.3476.3470.0000.0000.0000.000
26A23ASP-1-0.804-0.88143.779-6.850-6.8500.0000.0000.0000.000
27A24ARG10.8490.92441.3297.2257.2250.0000.0000.0000.000
28A25ILE00.0220.01934.7760.0670.0670.0000.0000.0000.000
29A26ILE0-0.023-0.01638.6130.1080.1080.0000.0000.0000.000
30A27GLU-1-0.781-0.87934.012-8.980-8.9800.0000.0000.0000.000
31A28ILE00.0160.01129.0210.0160.0160.0000.0000.0000.000
32A29ALA00.0020.01428.965-0.061-0.0610.0000.0000.0000.000
33A30THR00.028-0.01124.123-0.219-0.2190.0000.0000.0000.000
34A31ILE0-0.0010.01221.841-0.068-0.0680.0000.0000.0000.000
35A32VAL0-0.0100.00517.0470.1310.1310.0000.0000.0000.000
36A33THR00.0190.00718.0820.0550.0550.0000.0000.0000.000
37A34ASN00.0230.00813.9160.4840.4840.0000.0000.0000.000
38A35SER00.005-0.03015.9031.0621.0620.0000.0000.0000.000
39A36HIS0-0.098-0.05517.0441.4161.4160.0000.0000.0000.000
40A37LEU00.0150.01318.7000.7120.7120.0000.0000.0000.000
41A38ASP-1-0.792-0.85816.616-15.781-15.7810.0000.0000.0000.000
42A39ILE0-0.025-0.02717.886-0.442-0.4420.0000.0000.0000.000
43A40LEU0-0.069-0.01413.102-0.309-0.3090.0000.0000.0000.000
44A41ALA00.012-0.00316.306-0.175-0.1750.0000.0000.0000.000
45A42GLU-1-0.830-0.87918.909-11.603-11.6030.0000.0000.0000.000
46A43GLY00.0230.00122.311-0.428-0.4280.0000.0000.0000.000
47A44PRO0-0.072-0.02923.7450.3380.3380.0000.0000.0000.000
48A45ALA00.011-0.00626.8950.0660.0660.0000.0000.0000.000
49A46PHE0-0.028-0.01028.2060.1840.1840.0000.0000.0000.000
50A47ALA00.0420.02632.7630.0910.0910.0000.0000.0000.000
51A48ILE0-0.046-0.01234.212-0.076-0.0760.0000.0000.0000.000
52A49HIS0-0.019-0.00437.4900.3480.3480.0000.0000.0000.000
53A50GLN00.014-0.01640.1560.1950.1950.0000.0000.0000.000
54A51PRO00.0160.02243.7120.1200.1200.0000.0000.0000.000
55A52ASP-1-0.756-0.89347.384-6.465-6.4650.0000.0000.0000.000
56A53LYS10.8470.93150.0785.8535.8530.0000.0000.0000.000
57A54LEU0-0.0150.01445.5390.0980.0980.0000.0000.0000.000
58A55LEU00.0430.01644.7040.0410.0410.0000.0000.0000.000
59A56THR0-0.086-0.07248.6590.0780.0780.0000.0000.0000.000
60A57ALA0-0.065-0.02551.1460.1350.1350.0000.0000.0000.000
61A58MET00.0050.03146.661-0.100-0.1000.0000.0000.0000.000
62A59ASP-1-0.818-0.88549.937-6.324-6.3240.0000.0000.0000.000
63A60ASN00.013-0.01851.047-0.082-0.0820.0000.0000.0000.000
64A61TRP0-0.0040.01345.5270.0820.0820.0000.0000.0000.000
65A62ASN00.031-0.00245.155-0.230-0.2300.0000.0000.0000.000
66A63THR00.0160.00646.853-0.102-0.1020.0000.0000.0000.000
67A64SER0-0.060-0.01248.910-0.070-0.0700.0000.0000.0000.000
68A65HIS10.8610.92144.0146.8696.8690.0000.0000.0000.000
69A66HIS00.0670.03441.604-0.090-0.0900.0000.0000.0000.000
70A67THR0-0.060-0.03444.515-0.051-0.0510.0000.0000.0000.000
71A68ALA0-0.053-0.02646.099-0.037-0.0370.0000.0000.0000.000
72A69SER00.0400.02440.5450.0080.0080.0000.0000.0000.000
73A70GLY00.0120.00341.104-0.182-0.1820.0000.0000.0000.000
74A71LEU0-0.0120.00238.250-0.032-0.0320.0000.0000.0000.000
75A72LEU0-0.004-0.01641.392-0.018-0.0180.0000.0000.0000.000
76A73GLU-1-0.882-0.94444.473-6.768-6.7680.0000.0000.0000.000
77A74ARG10.8080.88135.1648.6408.6400.0000.0000.0000.000
78A75VAL0-0.0090.00540.253-0.111-0.1110.0000.0000.0000.000
79A76LYS10.8550.92641.6976.6206.6200.0000.0000.0000.000
80A77ASN0-0.102-0.05942.4890.1000.1000.0000.0000.0000.000
81A78SER0-0.035-0.01137.322-0.169-0.1690.0000.0000.0000.000
82A79SER0-0.033-0.03036.8140.1690.1690.0000.0000.0000.000
83A80VAL0-0.0300.00633.130-0.051-0.0510.0000.0000.0000.000
84A81ASP-1-0.816-0.90435.852-8.576-8.5760.0000.0000.0000.000
85A82GLU-1-0.827-0.94034.716-8.473-8.4730.0000.0000.0000.000
86A83VAL00.0030.00533.049-0.349-0.3490.0000.0000.0000.000
87A84GLU-1-0.867-0.93331.472-9.988-9.9880.0000.0000.0000.000
88A85ALA00.0310.01530.049-0.440-0.4400.0000.0000.0000.000
89A86GLU-1-0.756-0.85028.716-10.653-10.6530.0000.0000.0000.000
90A87THR0-0.058-0.04827.001-0.510-0.5100.0000.0000.0000.000
91A88LEU0-0.027-0.01525.503-0.638-0.6380.0000.0000.0000.000
92A89THR00.003-0.00524.499-0.515-0.5150.0000.0000.0000.000
93A90LEU0-0.043-0.01723.091-0.552-0.5520.0000.0000.0000.000
94A91ALA00.0220.01120.998-0.698-0.6980.0000.0000.0000.000
95A92PHE0-0.062-0.01619.614-0.777-0.7770.0000.0000.0000.000
96A93LEU00.0370.01018.374-0.983-0.9830.0000.0000.0000.000
97A94GLU-1-0.896-0.95917.355-15.708-15.7080.0000.0000.0000.000
98A95LYS10.8460.93314.22515.56815.5680.0000.0000.0000.000
99A96TYR0-0.030-0.01413.056-1.454-1.4540.0000.0000.0000.000
100A97VAL00.0290.02313.719-0.884-0.8840.0000.0000.0000.000
101A98SER0-0.047-0.04215.2000.9440.9440.0000.0000.0000.000
102A99ALA00.0260.01116.7510.4190.4190.0000.0000.0000.000
103A100GLY0-0.041-0.02720.245-0.321-0.3210.0000.0000.0000.000
104A101LYS10.7870.90716.70917.04417.0440.0000.0000.0000.000
105A102SER00.0870.04420.0180.2130.2130.0000.0000.0000.000
106A103PRO0-0.045-0.01421.3350.4930.4930.0000.0000.0000.000
107A104LEU00.0300.02724.463-0.364-0.3640.0000.0000.0000.000
108A105CYS0-0.0240.00424.1000.2800.2800.0000.0000.0000.000
109A106GLY00.1140.03926.723-0.048-0.0480.0000.0000.0000.000
110A107ASN0-0.041-0.02829.680-0.097-0.0970.0000.0000.0000.000
111A108SER00.000-0.01333.3520.1000.1000.0000.0000.0000.000
112A109VAL00.0320.03330.7050.1930.1930.0000.0000.0000.000
113A110CYS-1-0.892-0.92133.900-8.280-8.2800.0000.0000.0000.000
114A111GLN00.0430.00736.4080.0780.0780.0000.0000.0000.000
115A112ASP-1-0.755-0.89832.630-9.147-9.1470.0000.0000.0000.000
116A113ARG10.8220.89928.58310.25810.2580.0000.0000.0000.000
117A114ARG10.8230.89233.7287.7397.7390.0000.0000.0000.000
118A115PHE00.0400.01636.7320.0950.0950.0000.0000.0000.000
119A116LEU00.0250.00429.712-0.012-0.0120.0000.0000.0000.000
120A117SER0-0.078-0.05133.631-0.049-0.0490.0000.0000.0000.000
121A118ARG10.7170.88034.9457.4267.4260.0000.0000.0000.000
122A119TYR0-0.017-0.01636.5110.1480.1480.0000.0000.0000.000
123A120MET0-0.065-0.00431.030-0.184-0.1840.0000.0000.0000.000
124A121PRO00.0490.01631.297-0.294-0.2940.0000.0000.0000.000
125A122ARG10.7580.85527.52110.39510.3950.0000.0000.0000.000
126A123LEU00.0370.01025.517-0.401-0.4010.0000.0000.0000.000
127A124ASN0-0.0010.00827.003-0.331-0.3310.0000.0000.0000.000
128A125GLN0-0.042-0.02927.615-0.250-0.2500.0000.0000.0000.000
129A126PHE00.0000.01618.846-0.263-0.2630.0000.0000.0000.000
130A127PHE00.0020.01622.746-0.628-0.6280.0000.0000.0000.000
131A128HIS0-0.0130.00723.6050.5600.5600.0000.0000.0000.000
132A129TYR00.009-0.00225.2830.3200.3200.0000.0000.0000.000
133A130ARG10.9350.95627.20311.19411.1940.0000.0000.0000.000
134A131HIS00.0560.04128.042-0.311-0.3110.0000.0000.0000.000
135A132LEU0-0.024-0.01724.2970.0480.0480.0000.0000.0000.000
136A133ASP-1-0.767-0.87128.100-9.203-9.2030.0000.0000.0000.000
137A134VAL00.0550.02029.1440.2100.2100.0000.0000.0000.000
138A135THR0-0.037-0.03331.7930.1920.1920.0000.0000.0000.000
139A136THR0-0.026-0.00633.6820.3470.3470.0000.0000.0000.000
140A137LEU00.0050.00030.0630.2140.2140.0000.0000.0000.000
141A138LYS10.8720.94034.6288.6538.6530.0000.0000.0000.000
142A139ILE0-0.016-0.00437.1640.2720.2720.0000.0000.0000.000
143A140LEU0-0.017-0.01635.5500.2090.2090.0000.0000.0000.000
144A141ALA00.0350.02037.1840.1670.1670.0000.0000.0000.000
145A142GLN0-0.028-0.02439.1460.2080.2080.0000.0000.0000.000
146A143ARG10.8610.94142.1107.0837.0830.0000.0000.0000.000
147A144TRP0-0.020-0.01937.9700.1170.1170.0000.0000.0000.000
148A145ALA0-0.0050.01139.9220.0650.0650.0000.0000.0000.000
149A146PRO00.0440.03341.356-0.124-0.1240.0000.0000.0000.000
150A147GLN00.025-0.00242.2560.0240.0240.0000.0000.0000.000
151A148ILE0-0.0060.00336.712-0.028-0.0280.0000.0000.0000.000
152A149ALA00.0290.02038.439-0.173-0.1730.0000.0000.0000.000
153A150ALA0-0.053-0.02939.858-0.048-0.0480.0000.0000.0000.000
154A151ALA0-0.019-0.00639.2920.0650.0650.0000.0000.0000.000
155A152HIS0-0.0110.00133.357-0.348-0.3480.0000.0000.0000.000
156A153ILE0-0.027-0.01137.597-0.031-0.0310.0000.0000.0000.000
157A154LYS10.8720.95033.0139.0749.0740.0000.0000.0000.000
158A155GLU-1-0.981-0.99238.331-7.378-7.3780.0000.0000.0000.000
159A156SER0-0.039-0.04437.517-0.013-0.0130.0000.0000.0000.000
160A157GLN0-0.009-0.02136.5060.3060.3060.0000.0000.0000.000
161A158HIS0-0.128-0.04238.2180.3640.3640.0000.0000.0000.000
162A159LEU00.004-0.01135.6840.1170.1170.0000.0000.0000.000
163A160ALA00.0950.06832.160-0.212-0.2120.0000.0000.0000.000
164A161LEU0-0.050-0.03527.099-0.203-0.2030.0000.0000.0000.000
165A162GLN0-0.035-0.01729.764-0.403-0.4030.0000.0000.0000.000
166A163ASP-1-0.714-0.82731.787-8.802-8.8020.0000.0000.0000.000
167A164ILE00.0170.00926.332-0.164-0.1640.0000.0000.0000.000
168A165ARG10.7680.84627.12910.62610.6260.0000.0000.0000.000
169A166ASP-1-0.834-0.91928.571-9.310-9.3100.0000.0000.0000.000
170A167SER0-0.124-0.07928.9320.1160.1160.0000.0000.0000.000
171A168ILE0-0.0020.00423.468-0.076-0.0760.0000.0000.0000.000
172A169GLU-1-0.876-0.92626.638-11.145-11.1450.0000.0000.0000.000
173A170GLU-1-0.727-0.83828.638-8.731-8.7310.0000.0000.0000.000
174A171LEU0-0.036-0.01925.2860.1590.1590.0000.0000.0000.000
175A172ARG10.8180.89022.10712.41812.4180.0000.0000.0000.000
176A173TYR0-0.018-0.01827.0110.0620.0620.0000.0000.0000.000
177A174TYR0-0.015-0.04030.6950.2430.2430.0000.0000.0000.000
178A175ARG10.8470.91321.48712.96412.9640.0000.0000.0000.000
179A176ALA0-0.0020.00828.463-0.070-0.0700.0000.0000.0000.000
180A177HIS0-0.065-0.02929.9000.3210.3210.0000.0000.0000.000
181A178LEU0-0.059-0.03332.6200.3310.3310.0000.0000.0000.000
182A179LEU0-0.068-0.01927.8740.0890.0890.0000.0000.0000.000
183A180ASN0-0.051-0.02631.4130.1870.1870.0000.0000.0000.000
184A181LEU-1-0.934-0.95425.498-10.981-10.9810.0000.0000.0000.000