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: RLV58

Calculation Name: 3J80-F-Other547

Preferred Name:

Target Type:

Ligand Name: magnesium ion | zinc ion

Ligand 3-letter code: MG | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3J80

Chain ID: F

ChEMBL ID:

UniProt ID: P38912

Base Structure: ElectronMicroscopy

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 206
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2214647.269504
FMO2-HF: Nuclear repulsion 2135545.437361
FMO2-HF: Total energy -79101.832143
FMO2-MP2: Total energy -79336.110175


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:22:PHE)


Summations of interaction energy for fragment #1(A:22:PHE)
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.
-57.886-56.69313.182-8.639-5.735-0.098
Interaction energy analysis for fragmet #1(A:22:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.789 / 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].
3A24PRO00.0360.0453.885-0.8910.469-0.006-0.618-0.736-0.002
16A37GLN0-0.016-0.0103.685-3.179-2.9700.000-0.042-0.1670.000
17A38ALA0-0.045-0.0114.830-3.552-3.486-0.001-0.001-0.0630.000
20A41GLU-1-0.870-0.9231.743-113.174-113.61613.189-7.978-4.769-0.096
4A25VAL0-0.003-0.0046.2264.1054.1050.0000.0000.0000.000
5A26GLU-1-0.939-0.9609.486-23.075-23.0750.0000.0000.0000.000
6A27LEU0-0.030-0.02212.3501.1291.1290.0000.0000.0000.000
7A28ALA00.0140.00415.7870.2060.2060.0000.0000.0000.000
8A29THR0-0.041-0.01217.6580.7740.7740.0000.0000.0000.000
9A30THR00.0460.02315.631-0.690-0.6900.0000.0000.0000.000
10A31ILE00.0080.00012.1610.7960.7960.0000.0000.0000.000
11A32PRO00.0180.00212.173-1.509-1.5090.0000.0000.0000.000
12A33VAL00.0970.0457.646-1.274-1.2740.0000.0000.0000.000
13A34GLU-1-0.864-0.9317.729-31.106-31.1060.0000.0000.0000.000
14A35ILE0-0.118-0.0639.208-0.328-0.3280.0000.0000.0000.000
15A36GLN00.006-0.0046.927-2.879-2.8790.0000.0000.0000.000
18A39GLN0-0.012-0.0216.6003.8993.8990.0000.0000.0000.000
19A40GLN00.0290.0206.4584.2464.2460.0000.0000.0000.000
21A42ILE00.0130.0085.9744.6674.6670.0000.0000.0000.000
22A43LYS10.8980.9558.96728.33528.3350.0000.0000.0000.000
23A44LEU0-0.017-0.0048.5881.6641.6640.0000.0000.0000.000
24A45PHE00.0070.00912.7421.9741.9740.0000.0000.0000.000
25A46ASN0-0.071-0.05515.189-0.474-0.4740.0000.0000.0000.000
26A47LYS10.8500.91110.86626.73726.7370.0000.0000.0000.000
27A48TRP00.0940.06211.992-1.970-1.9700.0000.0000.0000.000
28A49SER00.0550.02012.861-0.284-0.2840.0000.0000.0000.000
29A50PHE0-0.082-0.04513.9351.5861.5860.0000.0000.0000.000
30A51GLU-1-0.877-0.93712.461-23.561-23.5610.0000.0000.0000.000
31A52ASP-1-0.882-0.93315.189-19.287-19.2870.0000.0000.0000.000
32A53VAL0-0.076-0.03917.8230.4430.4430.0000.0000.0000.000
33A54GLU-1-0.843-0.92920.850-14.297-14.2970.0000.0000.0000.000
34A55VAL0-0.082-0.04523.8960.2080.2080.0000.0000.0000.000
35A56LYS10.8870.92526.21411.51011.5100.0000.0000.0000.000
36A57ASP-1-0.880-0.92929.186-8.694-8.6940.0000.0000.0000.000
37A58ALA00.0240.02232.197-0.198-0.1980.0000.0000.0000.000
38A59SER0-0.044-0.03334.7070.2840.2840.0000.0000.0000.000
39A60LEU00.016-0.01033.491-0.188-0.1880.0000.0000.0000.000
40A61VAL00.0850.02928.550-0.210-0.2100.0000.0000.0000.000
41A62ASP-1-0.897-0.92529.416-10.267-10.2670.0000.0000.0000.000
42A63TYR0-0.120-0.09430.5120.0760.0760.0000.0000.0000.000
43A64ILE0-0.045-0.01128.4840.0750.0750.0000.0000.0000.000
44A65GLN0-0.069-0.02825.232-0.499-0.4990.0000.0000.0000.000
45A66ILE00.0820.04822.048-0.019-0.0190.0000.0000.0000.000
46A67SER00.0620.02822.6190.0400.0400.0000.0000.0000.000
47A68LYS10.8700.93021.58012.53412.5340.0000.0000.0000.000
48A69PRO00.0450.02316.6080.3260.3260.0000.0000.0000.000
49A70ILE0-0.038-0.02218.7540.4420.4420.0000.0000.0000.000
50A71TYR00.0580.03512.700-0.126-0.1260.0000.0000.0000.000
51A72VAL0-0.006-0.00517.4670.0160.0160.0000.0000.0000.000
52A73ALA0-0.0020.00720.7790.3820.3820.0000.0000.0000.000
53A74HIS0-0.049-0.05924.0080.6510.6510.0000.0000.0000.000
54A75THR0-0.001-0.01024.684-0.257-0.2570.0000.0000.0000.000
55A76ALA0-0.004-0.00127.1210.3750.3750.0000.0000.0000.000
56A77GLY00.0240.01629.3800.2960.2960.0000.0000.0000.000
57A78ARG10.9350.96230.4428.7458.7450.0000.0000.0000.000
58A79TYR00.0480.01628.0640.1050.1050.0000.0000.0000.000
59A80ALA0-0.054-0.02334.6940.1740.1740.0000.0000.0000.000
60A81ASN00.018-0.00536.9420.2010.2010.0000.0000.0000.000
61A82LYS10.9810.98239.7537.9987.9980.0000.0000.0000.000
62A83ARG10.9950.99439.9517.2867.2860.0000.0000.0000.000
63A84PHE00.0880.02937.216-0.070-0.0700.0000.0000.0000.000
64A85ARG10.9981.02434.0809.1209.1200.0000.0000.0000.000
65A86LYS10.9200.96433.7147.9547.9540.0000.0000.0000.000
66A87ALA0-0.017-0.00533.460-0.125-0.1250.0000.0000.0000.000
67A88GLN00.0580.03330.0230.1150.1150.0000.0000.0000.000
68A89CYS0-0.054-0.00628.856-0.262-0.2620.0000.0000.0000.000
69A90PRO00.0690.03924.7600.2230.2230.0000.0000.0000.000
70A91ILE00.0510.02224.7640.3770.3770.0000.0000.0000.000
71A92VAL00.0710.04023.3170.4150.4150.0000.0000.0000.000
72A93GLU-1-0.739-0.83726.153-11.296-11.2960.0000.0000.0000.000
73A94ARG10.8110.89828.3709.9459.9450.0000.0000.0000.000
74A95LEU00.0860.05428.5320.3750.3750.0000.0000.0000.000
75A96THR0-0.059-0.03627.9240.2930.2930.0000.0000.0000.000
76A97ASN00.022-0.02230.9830.1880.1880.0000.0000.0000.000
77A98SER0-0.022-0.01333.8540.3020.3020.0000.0000.0000.000
78A99LEU00.0770.02031.6830.2740.2740.0000.0000.0000.000
79A100MET0-0.097-0.02034.8440.1280.1280.0000.0000.0000.000
80A101MET00.0150.02637.3360.1950.1950.0000.0000.0000.000
81A102ASN00.0450.02040.746-0.141-0.1410.0000.0000.0000.000
82A103GLY00.0650.03342.591-0.128-0.1280.0000.0000.0000.000
83A104ARG10.9470.97942.0347.3697.3690.0000.0000.0000.000
84A105ASN0-0.075-0.05435.880-0.158-0.1580.0000.0000.0000.000
85A106ASN00.0670.06038.373-0.299-0.2990.0000.0000.0000.000
86A107GLY00.0230.01537.5760.0350.0350.0000.0000.0000.000
87A108LYS10.8770.91634.8937.9377.9370.0000.0000.0000.000
88A109LYS10.9200.95629.14510.70310.7030.0000.0000.0000.000
89A110LEU00.0000.00728.572-0.245-0.2450.0000.0000.0000.000
90A111LYS10.9560.97929.1268.5828.5820.0000.0000.0000.000
91A112ALA00.0250.02730.516-0.171-0.1710.0000.0000.0000.000
92A113VAL00.0300.00924.969-0.154-0.1540.0000.0000.0000.000
93A114ARG10.9430.97725.17711.63911.6390.0000.0000.0000.000
94A115ILE0-0.0100.00326.970-0.163-0.1630.0000.0000.0000.000
95A116VAL00.0360.01325.117-0.084-0.0840.0000.0000.0000.000
96A117LYS10.9030.96418.52316.24516.2450.0000.0000.0000.000
97A118HIS00.0540.02323.642-0.508-0.5080.0000.0000.0000.000
98A119THR0-0.066-0.03525.9870.0540.0540.0000.0000.0000.000
99A120LEU0-0.031-0.01321.876-0.016-0.0160.0000.0000.0000.000
100A121GLU-1-0.859-0.93319.517-16.461-16.4610.0000.0000.0000.000
101A122ILE0-0.023-0.00422.757-0.092-0.0920.0000.0000.0000.000
102A123ILE0-0.038-0.03324.1790.1400.1400.0000.0000.0000.000
103A124ASN0-0.012-0.01719.313-0.046-0.0460.0000.0000.0000.000
104A125VAL00.0030.01421.872-0.215-0.2150.0000.0000.0000.000
105A126LEU0-0.071-0.01624.0630.4280.4280.0000.0000.0000.000
106A127THR0-0.093-0.06224.9360.3240.3240.0000.0000.0000.000
107A128ASP-1-0.870-0.92519.724-14.890-14.8900.0000.0000.0000.000
108A129GLN0-0.027-0.01620.4270.5300.5300.0000.0000.0000.000
109A130ASN00.0550.03517.518-0.704-0.7040.0000.0000.0000.000
110A131PRO00.0290.01419.4690.8710.8710.0000.0000.0000.000
111A132LEU0-0.038-0.03219.2560.8340.8340.0000.0000.0000.000
112A133GLN00.006-0.00722.6900.1570.1570.0000.0000.0000.000
113A134VAL00.0520.02924.5360.5870.5870.0000.0000.0000.000
114A135VAL0-0.033-0.01926.4580.5570.5570.0000.0000.0000.000
115A136VAL0-0.016-0.00925.7900.4930.4930.0000.0000.0000.000
116A137ASP-1-0.772-0.87828.050-10.742-10.7420.0000.0000.0000.000
117A138ALA0-0.0030.00330.5420.4450.4450.0000.0000.0000.000
118A139ILE0-0.077-0.03930.0860.4010.4010.0000.0000.0000.000
119A140ILE0-0.037-0.01030.6650.2980.2980.0000.0000.0000.000
120A141ASN0-0.045-0.02934.5090.3340.3340.0000.0000.0000.000
121A142SER0-0.037-0.03136.3600.2920.2920.0000.0000.0000.000
122A143GLY0-0.016-0.00438.3760.1790.1790.0000.0000.0000.000
123A144PRO00.0030.00540.002-0.003-0.0030.0000.0000.0000.000
124A145ARG10.8220.88840.0847.5147.5140.0000.0000.0000.000
125A146GLU-1-0.860-0.92644.696-6.397-6.3970.0000.0000.0000.000
126A147ASP-1-0.795-0.90847.405-6.842-6.8420.0000.0000.0000.000
127A148THR0-0.0320.00449.8070.1240.1240.0000.0000.0000.000
128A149THR0-0.0140.00552.195-0.005-0.0050.0000.0000.0000.000
129A150ARG10.9350.96254.5705.4695.4690.0000.0000.0000.000
130A151VAL00.0060.00157.954-0.010-0.0100.0000.0000.0000.000
131A152GLY00.0170.00460.5700.0540.0540.0000.0000.0000.000
132A153GLY0-0.002-0.01563.8120.0490.0490.0000.0000.0000.000
133A154GLY00.0370.02966.2690.0650.0650.0000.0000.0000.000
134A155GLY0-0.003-0.00767.4190.0460.0460.0000.0000.0000.000
135A156ALA00.0100.02266.691-0.043-0.0430.0000.0000.0000.000
136A157ALA0-0.027-0.01561.872-0.061-0.0610.0000.0000.0000.000
137A158ARG10.9410.98461.1055.1475.1470.0000.0000.0000.000
138A159ARG10.8850.89953.8595.8465.8460.0000.0000.0000.000
139A160GLN00.0430.01957.3210.1600.1600.0000.0000.0000.000
140A161ALA00.0170.02052.713-0.082-0.0820.0000.0000.0000.000
141A162VAL0-0.033-0.01850.1630.0780.0780.0000.0000.0000.000
142A163ASP-1-0.841-0.90747.321-6.625-6.6250.0000.0000.0000.000
143A164VAL0-0.067-0.02643.597-0.026-0.0260.0000.0000.0000.000
144A165SER00.016-0.00342.722-0.245-0.2450.0000.0000.0000.000
145A166PRO00.1090.04437.721-0.050-0.0500.0000.0000.0000.000
146A167LEU0-0.014-0.00537.483-0.126-0.1260.0000.0000.0000.000
147A168ARG10.8620.94038.7786.9756.9750.0000.0000.0000.000
148A169ARG10.9020.95337.8288.1338.1330.0000.0000.0000.000
149A170VAL00.0670.04733.808-0.021-0.0210.0000.0000.0000.000
150A171ASN0-0.062-0.04536.676-0.277-0.2770.0000.0000.0000.000
151A172GLN0-0.008-0.00438.3930.0450.0450.0000.0000.0000.000
152A173SER00.0590.03836.207-0.051-0.0510.0000.0000.0000.000
153A174ILE00.0280.00432.738-0.019-0.0190.0000.0000.0000.000
154A175ALA0-0.027-0.00735.881-0.036-0.0360.0000.0000.0000.000
155A176LEU0-0.017-0.00339.1270.0800.0800.0000.0000.0000.000
156A177LEU00.0590.03133.5140.0790.0790.0000.0000.0000.000
157A178THR0-0.033-0.02734.8710.0850.0850.0000.0000.0000.000
158A179ILE0-0.078-0.03937.3920.1270.1270.0000.0000.0000.000
159A180GLY00.0620.03240.1500.1540.1540.0000.0000.0000.000
160A181ALA00.0240.01236.2110.0800.0800.0000.0000.0000.000
161A182ARG10.7350.86038.1478.2368.2360.0000.0000.0000.000
162A183GLU-1-0.900-0.92640.477-6.844-6.8440.0000.0000.0000.000
163A184ALA00.0380.02539.7070.0930.0930.0000.0000.0000.000
164A185ALA00.0090.00538.4860.0260.0260.0000.0000.0000.000
165A186PHE0-0.069-0.04540.3960.0910.0910.0000.0000.0000.000
166A187ARG10.9120.96244.0056.8096.8090.0000.0000.0000.000
167A188ASN00.0430.02340.8560.0470.0470.0000.0000.0000.000
168A189ILE00.0480.02638.753-0.093-0.0930.0000.0000.0000.000
169A190LYS10.8610.94435.8838.5398.5390.0000.0000.0000.000
170A191THR00.0280.00533.5210.0090.0090.0000.0000.0000.000
171A192ILE00.030-0.00934.397-0.129-0.1290.0000.0000.0000.000
172A193ALA0-0.0100.00629.4980.0070.0070.0000.0000.0000.000
173A194GLU-1-0.822-0.90931.189-10.451-10.4510.0000.0000.0000.000
174A195THR0-0.057-0.03932.6590.1610.1610.0000.0000.0000.000
175A196LEU0-0.025-0.01631.2420.1040.1040.0000.0000.0000.000
176A197ALA00.0410.01729.651-0.058-0.0580.0000.0000.0000.000
177A198GLU-1-0.856-0.91431.223-9.126-9.1260.0000.0000.0000.000
178A199GLU-1-0.783-0.87434.391-8.158-8.1580.0000.0000.0000.000
179A200LEU0-0.020-0.01629.0780.0690.0690.0000.0000.0000.000
180A201ILE00.0340.01928.852-0.067-0.0670.0000.0000.0000.000
181A202ASN0-0.048-0.03032.4940.2230.2230.0000.0000.0000.000
182A203ALA0-0.0010.00034.5400.1760.1760.0000.0000.0000.000
183A204ALA00.0050.01030.3890.1020.1020.0000.0000.0000.000
184A205LYS10.9260.96529.53410.32910.3290.0000.0000.0000.000
185A206GLY00.0180.01134.1180.2200.2200.0000.0000.0000.000
186A207SER0-0.003-0.00237.2910.1820.1820.0000.0000.0000.000
187A208SER0-0.030-0.03840.2050.1070.1070.0000.0000.0000.000
188A209THR00.0140.01539.9500.1520.1520.0000.0000.0000.000
189A210SER0-0.018-0.02838.5690.1440.1440.0000.0000.0000.000
190A211TYR0-0.048-0.06840.6770.2010.2010.0000.0000.0000.000
191A212ALA0-0.053-0.02439.0950.1670.1670.0000.0000.0000.000
192A213ILE0-0.0050.01138.4290.0960.0960.0000.0000.0000.000
193A214LYS10.8720.95841.8847.3447.3440.0000.0000.0000.000
194A215LYS11.0011.00144.5487.2957.2950.0000.0000.0000.000
195A216LYS00.0260.06241.2090.1570.1570.0000.0000.0000.000
196A217ASP-1-0.782-0.88244.901-7.006-7.0060.0000.0000.0000.000
197A218GLU-1-0.969-0.99146.882-6.468-6.4680.0000.0000.0000.000
198A219LEU0-0.054-0.01746.3030.1630.1630.0000.0000.0000.000
199A220GLU-1-0.724-0.86845.125-7.015-7.0150.0000.0000.0000.000
200A221ARG10.7710.87647.2096.7446.7440.0000.0000.0000.000
201A222VAL00.0070.00752.3240.1320.1320.0000.0000.0000.000
202A223ALA0-0.024-0.00651.3000.1360.1360.0000.0000.0000.000
203A224LYS10.9750.98249.2496.4856.4850.0000.0000.0000.000
204A225SER0-0.074-0.03254.5070.1040.1040.0000.0000.0000.000
205A226ASN0-0.116-0.07556.8510.1790.1790.0000.0000.0000.000
206A227ARG0-0.0170.00752.4130.4440.4440.0000.0000.0000.000