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: MZVKZ

Calculation Name: 4V8P-A-Xray547

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: 4V8P

Chain ID: A

ChEMBL ID:

UniProt ID: Q245F2

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 203
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1757131.327588
FMO2-HF: Nuclear repulsion 1678083.925961
FMO2-HF: Total energy -79047.401627
FMO2-MP2: Total energy -79282.766328


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
243.922249.2710.463-2.419-3.391-0.014
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.839 / q_NPA : 0.904
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].
3A3HIS00.1160.0653.8581.4035.564-0.031-2.120-2.010-0.013
4A4ASN00.0410.0124.883-3.082-2.943-0.001-0.003-0.1330.000
7A7LEU00.0330.0103.463-2.739-2.1320.437-0.173-0.871-0.001
8A8PRO0-0.024-0.0033.9391.8202.2620.058-0.123-0.3770.000
5A5ASN0-0.0210.0055.9733.8483.8480.0000.0000.0000.000
6A6GLN00.0110.0105.630-1.523-1.5230.0000.0000.0000.000
9A9VAL00.0320.0146.9900.5940.5940.0000.0000.0000.000
10A10ALA0-0.037-0.0199.940-0.101-0.1010.0000.0000.0000.000
11A11GLN00.0470.02311.1960.9400.9400.0000.0000.0000.000
12A12LEU0-0.029-0.02914.2911.1491.1490.0000.0000.0000.000
13A13ARG10.9670.9909.99423.56623.5660.0000.0000.0000.000
14A14LYS10.9810.99214.84814.73714.7370.0000.0000.0000.000
15A15HIS00.1230.06418.621-0.188-0.1880.0000.0000.0000.000
16A16GLN0-0.015-0.01819.4990.7870.7870.0000.0000.0000.000
17A17GLN00.0350.01821.644-0.032-0.0320.0000.0000.0000.000
18A18PHE00.0530.02823.7590.2860.2860.0000.0000.0000.000
19A19ARG10.8430.92022.34013.21013.2100.0000.0000.0000.000
20A20ILE00.0260.03222.443-0.262-0.2620.0000.0000.0000.000
21A21LYS10.9400.96725.96710.08210.0820.0000.0000.0000.000
22A22THR00.0360.01628.405-0.260-0.2600.0000.0000.0000.000
23A23PHE00.026-0.00429.2090.3270.3270.0000.0000.0000.000
24A24PHE00.0850.04730.8220.2720.2720.0000.0000.0000.000
25A25ASN00.0230.01135.4690.1460.1460.0000.0000.0000.000
26A26GLN00.0000.00334.6530.2470.2470.0000.0000.0000.000
27A27ALA00.0220.01338.0650.2000.2000.0000.0000.0000.000
28A28ALA00.0710.03040.4700.2010.2010.0000.0000.0000.000
29A29GLN00.0730.02540.4250.2790.2790.0000.0000.0000.000
30A30LYS10.9080.98141.4047.5747.5740.0000.0000.0000.000
31A31LYS11.0131.01143.3086.6086.6080.0000.0000.0000.000
32A32ALA00.0400.02045.8400.1690.1690.0000.0000.0000.000
33A33ARG10.8950.92139.7627.7567.7560.0000.0000.0000.000
34A34LEU0-0.041-0.01547.1990.1130.1130.0000.0000.0000.000
35A35HIS00.028-0.00149.5260.0490.0490.0000.0000.0000.000
36A36ALA00.0370.02849.8570.1200.1200.0000.0000.0000.000
37A37ARG10.9200.95745.6376.7246.7240.0000.0000.0000.000
38A38ARG10.9670.98652.3686.1036.1030.0000.0000.0000.000
39A39ALA00.0510.03455.1930.1060.1060.0000.0000.0000.000
40A40GLN0-0.0030.00354.5920.0860.0860.0000.0000.0000.000
41A41ALA0-0.006-0.01856.5800.0850.0850.0000.0000.0000.000
42A42ALA00.0060.00258.4190.0930.0930.0000.0000.0000.000
43A43ALA00.0130.00859.7340.0960.0960.0000.0000.0000.000
44A44VAL0-0.097-0.05258.6800.0670.0670.0000.0000.0000.000
45A45PHE00.0480.03961.6730.0330.0330.0000.0000.0000.000
46A46PRO00.0200.01663.764-0.006-0.0060.0000.0000.0000.000
47A47ARG10.9390.97862.0164.9304.9300.0000.0000.0000.000
48A48PRO00.0130.01258.699-0.061-0.0610.0000.0000.0000.000
49A49THR00.010-0.00153.824-0.048-0.0480.0000.0000.0000.000
50A50GLU-1-1.009-1.00050.372-6.261-6.2610.0000.0000.0000.000
51A51LYS10.9420.97054.5635.4545.4540.0000.0000.0000.000
52A52LEU00.0070.01754.818-0.120-0.1200.0000.0000.0000.000
53A53GLN00.0050.00050.179-0.072-0.0720.0000.0000.0000.000
54A54PRO0-0.0200.02352.4980.0400.0400.0000.0000.0000.000
55A55VAL0-0.001-0.01450.682-0.144-0.1440.0000.0000.0000.000
56A56VAL0-0.041-0.01848.6210.0930.0930.0000.0000.0000.000
57A57ARG10.9340.97046.9396.1316.1310.0000.0000.0000.000
58A58LYS10.9140.94941.1147.1697.1690.0000.0000.0000.000
59A59GLN00.0370.02841.0880.0500.0500.0000.0000.0000.000
60A60THR00.009-0.00736.805-0.179-0.1790.0000.0000.0000.000
61A61GLN00.0790.04838.5800.1370.1370.0000.0000.0000.000
62A62ARG10.9680.97431.6008.9048.9040.0000.0000.0000.000
63A63TYR00.0140.00235.271-0.019-0.0190.0000.0000.0000.000
64A64ASN00.0380.02140.9300.1040.1040.0000.0000.0000.000
65A65LYS10.9930.99941.6467.2557.2550.0000.0000.0000.000
66A66SER0-0.050-0.02142.8890.0580.0580.0000.0000.0000.000
67A67THR00.0570.03145.3850.0610.0610.0000.0000.0000.000
68A68LYS10.9300.95542.9106.7266.7260.0000.0000.0000.000
69A69LEU00.0690.05846.7930.1190.1190.0000.0000.0000.000
70A70GLY0-0.044-0.03147.444-0.154-0.1540.0000.0000.0000.000
71A71ARG10.9610.97348.0566.2536.2530.0000.0000.0000.000
72A72GLY00.026-0.00749.9330.0400.0400.0000.0000.0000.000
73A73PHE00.013-0.00153.684-0.064-0.0640.0000.0000.0000.000
74A74THR0-0.051-0.01956.030-0.030-0.0300.0000.0000.0000.000
75A75LEU00.0680.01957.2900.0720.0720.0000.0000.0000.000
76A76GLN00.0590.02358.2310.0490.0490.0000.0000.0000.000
77A77GLU-1-0.677-0.79856.516-5.463-5.4630.0000.0000.0000.000
78A78LEU0-0.010-0.00560.2320.0580.0580.0000.0000.0000.000
79A79LYS10.9790.99663.0954.6084.6080.0000.0000.0000.000
80A80ALA00.0030.00163.9830.0750.0750.0000.0000.0000.000
81A81ALA0-0.0050.00464.5640.0380.0380.0000.0000.0000.000
82A82GLY00.0310.03766.4670.0500.0500.0000.0000.0000.000
83A83ILE0-0.056-0.03264.3750.0550.0550.0000.0000.0000.000
84A84SER00.0600.02665.881-0.048-0.0480.0000.0000.0000.000
85A85ALA00.024-0.00461.086-0.019-0.0190.0000.0000.0000.000
86A86ALA00.0480.02462.632-0.046-0.0460.0000.0000.0000.000
87A87PHE00.0690.04664.533-0.034-0.0340.0000.0000.0000.000
88A88ALA00.0530.02662.164-0.019-0.0190.0000.0000.0000.000
89A89GLN0-0.040-0.02559.208-0.073-0.0730.0000.0000.0000.000
90A90SER0-0.069-0.04161.622-0.035-0.0350.0000.0000.0000.000
91A91ILE00.0660.04163.885-0.004-0.0040.0000.0000.0000.000
92A92GLY0-0.0180.00460.327-0.044-0.0440.0000.0000.0000.000
93A93ILE0-0.025-0.01558.853-0.108-0.1080.0000.0000.0000.000
94A94LYS10.9120.96551.2735.9715.9710.0000.0000.0000.000
95A95VAL00.0360.01656.1980.0180.0180.0000.0000.0000.000
96A96ASP-1-0.901-0.95050.934-6.165-6.1650.0000.0000.0000.000
97A97HIS00.0560.02953.6450.0450.0450.0000.0000.0000.000
98A98ARG10.8990.93749.2086.1906.1900.0000.0000.0000.000
99A99ARG10.7170.85350.6935.6595.6590.0000.0000.0000.000
100A100LYS10.9960.98651.8915.8375.8370.0000.0000.0000.000
101A101ASN0-0.039-0.03653.561-0.083-0.0830.0000.0000.0000.000
102A102ARG10.9650.97749.2336.0556.0550.0000.0000.0000.000
103A103CYS00.0160.01254.240-0.056-0.0560.0000.0000.0000.000
104A104GLN00.1540.09756.701-0.043-0.0430.0000.0000.0000.000
105A105GLU-1-0.832-0.92056.055-5.312-5.3120.0000.0000.0000.000
106A106SER0-0.123-0.07254.431-0.050-0.0500.0000.0000.0000.000
107A107LEU00.0250.01556.091-0.036-0.0360.0000.0000.0000.000
108A108GLU-1-0.870-0.94359.553-4.853-4.8530.0000.0000.0000.000
109A109LEU0-0.051-0.02654.2430.0210.0210.0000.0000.0000.000
110A110ASN0-0.020-0.01554.627-0.028-0.0280.0000.0000.0000.000
111A111LYS11.0141.01258.5594.6994.6990.0000.0000.0000.000
112A112LYS10.9670.98460.8185.0645.0640.0000.0000.0000.000
113A113ARG10.8210.89353.8505.6395.6390.0000.0000.0000.000
114A114LEU0-0.028-0.01160.2960.0240.0240.0000.0000.0000.000
115A115LEU00.0360.01262.6040.0420.0420.0000.0000.0000.000
116A116ALA00.0080.01162.5430.0510.0510.0000.0000.0000.000
117A117TYR0-0.057-0.04861.6330.0020.0020.0000.0000.0000.000
118A118VAL00.004-0.00463.7240.0280.0280.0000.0000.0000.000
119A119SER0-0.055-0.03366.8130.0500.0500.0000.0000.0000.000
120A120LYS10.8940.93863.4284.9394.9390.0000.0000.0000.000
121A121LEU0-0.0310.00266.006-0.050-0.0500.0000.0000.0000.000
122A122VAL00.0750.04968.1750.0660.0660.0000.0000.0000.000
123A123LEU0-0.068-0.03869.011-0.075-0.0750.0000.0000.0000.000
124A124PHE00.0510.01768.8170.0530.0530.0000.0000.0000.000
125A125PRO0-0.0270.00172.464-0.045-0.0450.0000.0000.0000.000
126A126ARG10.9650.97075.1813.9883.9880.0000.0000.0000.000
127A127HIS00.0450.00476.929-0.008-0.0080.0000.0000.0000.000
128A128GLN00.0490.05279.063-0.001-0.0010.0000.0000.0000.000
129A129GLY00.0470.04780.2470.0560.0560.0000.0000.0000.000
130A130LYS10.8780.91579.1413.9333.9330.0000.0000.0000.000
131A131ALA00.0010.00376.2610.0330.0330.0000.0000.0000.000
132A132LYS11.0401.00177.6953.8143.8140.0000.0000.0000.000
133A133LYS10.8860.93670.1434.4184.4180.0000.0000.0000.000
134A134GLY0-0.080-0.05171.133-0.044-0.0440.0000.0000.0000.000
135A135LEU0-0.0060.00971.911-0.017-0.0170.0000.0000.0000.000
136A136VAL0-0.0230.00773.431-0.055-0.0550.0000.0000.0000.000
137A137ASN0-0.019-0.00572.4080.0920.0920.0000.0000.0000.000
138A138ASP-1-0.792-0.88575.902-3.979-3.9790.0000.0000.0000.000
139A139THR0-0.015-0.03777.412-0.053-0.0530.0000.0000.0000.000
140A140ALA00.0710.05378.375-0.021-0.0210.0000.0000.0000.000
141A141ASP-1-0.832-0.91373.453-4.291-4.2910.0000.0000.0000.000
142A142THR0-0.109-0.06073.477-0.088-0.0880.0000.0000.0000.000
143A143SER0-0.065-0.04074.235-0.028-0.0280.0000.0000.0000.000
144A144SER0-0.057-0.04071.883-0.047-0.0470.0000.0000.0000.000
145A145ALA0-0.016-0.01169.829-0.052-0.0520.0000.0000.0000.000
146A146ALA00.0180.02566.500-0.061-0.0610.0000.0000.0000.000
147A147GLN0-0.005-0.00160.405-0.137-0.1370.0000.0000.0000.000
148A148ASN0-0.001-0.00461.147-0.003-0.0030.0000.0000.0000.000
149A149ALA00.0270.01255.854-0.055-0.0550.0000.0000.0000.000
150A150LEU00.030-0.00155.9710.0560.0560.0000.0000.0000.000
151A151GLN0-0.064-0.03051.0340.0430.0430.0000.0000.0000.000
152A152THR00.0510.02455.400-0.020-0.0200.0000.0000.0000.000
153A153SER00.0130.01858.5020.1020.1020.0000.0000.0000.000
154A154VAL0-0.037-0.00558.5890.0880.0880.0000.0000.0000.000
155A155PRO00.0490.03955.928-0.112-0.1120.0000.0000.0000.000
156A156LEU0-0.011-0.02052.7680.0610.0610.0000.0000.0000.000
157A157PRO00.0150.02553.808-0.126-0.1260.0000.0000.0000.000
158A158SER0-0.038-0.03451.4720.0060.0060.0000.0000.0000.000
159A159VAL00.0560.02552.606-0.093-0.0930.0000.0000.0000.000
160A160SER0-0.039-0.01349.8960.0240.0240.0000.0000.0000.000
161A161LYS11.0131.01451.9815.1475.1470.0000.0000.0000.000
162A162ARG10.9100.94853.5585.6645.6640.0000.0000.0000.000
163A163GLU-1-0.923-0.95655.685-4.976-4.9760.0000.0000.0000.000
164A164LYS10.9390.95455.9635.3765.3760.0000.0000.0000.000
165A165ALA00.0830.05059.9470.0700.0700.0000.0000.0000.000
166A166VAL00.0550.01661.713-0.069-0.0690.0000.0000.0000.000
167A167SER00.0510.03063.736-0.038-0.0380.0000.0000.0000.000
168A168ASN00.021-0.00560.751-0.012-0.0120.0000.0000.0000.000
169A169ILE0-0.042-0.01358.745-0.074-0.0740.0000.0000.0000.000
170A170ALA00.0210.01060.597-0.051-0.0510.0000.0000.0000.000
171A171GLU-1-0.887-0.92961.729-4.917-4.9170.0000.0000.0000.000
172A172LEU0-0.048-0.05256.690-0.066-0.0660.0000.0000.0000.000
173A173ARG10.9610.97557.1405.1605.1600.0000.0000.0000.000
174A174LYS10.9500.99958.4594.7084.7080.0000.0000.0000.000
175A175LYS10.9450.99755.4915.4285.4280.0000.0000.0000.000
176A176LYS11.0030.99152.8985.4265.4260.0000.0000.0000.000
177A177VAL00.0550.01448.764-0.049-0.0490.0000.0000.0000.000
178A178TYR00.0640.02443.315-0.068-0.0680.0000.0000.0000.000
179A179ARG11.0000.99247.9895.4595.4590.0000.0000.0000.000
180A180ILE00.0450.03250.513-0.004-0.0040.0000.0000.0000.000
181A181ILE00.0050.00244.645-0.052-0.0520.0000.0000.0000.000
182A182ARG10.9120.95641.1336.7566.7560.0000.0000.0000.000
183A183GLN00.0320.03546.769-0.106-0.1060.0000.0000.0000.000
184A184GLU-1-0.830-0.91248.514-5.826-5.8260.0000.0000.0000.000
185A185LYS10.8960.94540.1837.1207.1200.0000.0000.0000.000
186A186THR0-0.055-0.03045.132-0.100-0.1000.0000.0000.0000.000
187A187ASN0-0.012-0.03046.9770.0370.0370.0000.0000.0000.000
188A188GLN00.0290.01444.8650.1020.1020.0000.0000.0000.000
189A189LYS10.8980.96241.0306.9046.9040.0000.0000.0000.000
190A190TRP0-0.016-0.02645.004-0.056-0.0560.0000.0000.0000.000
191A191ASP-1-0.809-0.88048.027-5.676-5.6760.0000.0000.0000.000
192A192GLY00.0390.02348.7230.0880.0880.0000.0000.0000.000
193A193LYS10.9630.97443.9886.5416.5410.0000.0000.0000.000
194A194ARG10.8930.95450.2945.8455.8450.0000.0000.0000.000
195A195LYS10.9000.93352.4585.7195.7190.0000.0000.0000.000
196A196ALA00.0460.03352.0400.0710.0710.0000.0000.0000.000
197A197LYS10.9230.95552.7625.6065.6060.0000.0000.0000.000
198A198ALA0-0.018-0.01356.1030.0660.0660.0000.0000.0000.000
199A199GLN0-0.077-0.04156.491-0.019-0.0190.0000.0000.0000.000
200A200ALA00.0270.00257.0780.0600.0600.0000.0000.0000.000
201A201ALA0-0.071-0.03059.1200.0400.0400.0000.0000.0000.000
202A202ALA0-0.074-0.03861.8400.0680.0680.0000.0000.0000.000
203A203GLU-2-1.814-1.87260.269-9.627-9.6270.0000.0000.0000.000