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: 2GNKR

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 226
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2722483.062422
FMO2-HF: Nuclear repulsion 2635390.827483
FMO2-HF: Total energy -87092.234938
FMO2-MP2: Total energy -87342.835846


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:0:SER)


Summations of interaction energy for fragment #1(A:0: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.
-277.868-272.615.717-10.886-10.099-0.116
Interaction energy analysis for fragmet #1(A:0:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.738 / q_NPA : 0.857
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].
3A2ALA0-0.0010.0093.8553.5475.098-0.010-0.751-0.790-0.001
42A41GLU-1-0.839-0.9054.850-40.754-40.728-0.001-0.002-0.0230.000
203A202TRP0-0.027-0.0143.685-2.165-1.5050.002-0.283-0.379-0.001
204A203ALA00.0290.0291.773-27.124-29.3369.011-3.997-2.802-0.043
205A204ALA00.0270.0073.8714.9675.0870.000-0.044-0.0750.000
225A224LEU0-0.0070.0132.250-0.2710.3701.026-0.635-1.033-0.002
226A225ASN-1-0.935-0.9612.020-118.034-113.5525.689-5.174-4.997-0.069
4A3ARG10.7920.8916.34834.44534.4450.0000.0000.0000.000
5A4ARG10.8600.9278.76122.79422.7940.0000.0000.0000.000
6A5CYS0-0.021-0.01212.559-0.210-0.2100.0000.0000.0000.000
7A6GLN0-0.001-0.01414.8420.5380.5380.0000.0000.0000.000
8A7PHE0-0.0090.00118.5110.0530.0530.0000.0000.0000.000
9A8GLU-1-0.860-0.91720.463-10.523-10.5230.0000.0000.0000.000
10A9ASN0-0.009-0.00823.211-0.260-0.2600.0000.0000.0000.000
11A10SER0-0.0040.01122.731-0.204-0.2040.0000.0000.0000.000
12A11ASN00.0280.00119.242-0.884-0.8840.0000.0000.0000.000
13A12ASP-1-0.856-0.91518.192-14.333-14.3330.0000.0000.0000.000
14A13ILE00.0210.00414.0000.5530.5530.0000.0000.0000.000
15A14GLY00.0570.05216.491-0.009-0.0090.0000.0000.0000.000
16A15VAL0-0.046-0.02317.1950.6380.6380.0000.0000.0000.000
17A16PHE0-0.027-0.01119.3370.5350.5350.0000.0000.0000.000
18A17CYS0-0.057-0.03014.991-0.211-0.2110.0000.0000.0000.000
19A18LYS10.8990.95116.08914.82814.8280.0000.0000.0000.000
20A19LEU0-0.0160.0098.2400.3850.3850.0000.0000.0000.000
21A20THR00.0530.04012.968-0.198-0.1980.0000.0000.0000.000
22A21SER0-0.016-0.03810.712-1.018-1.0180.0000.0000.0000.000
23A22ALA00.007-0.00211.793-0.313-0.3130.0000.0000.0000.000
24A23TYR0-0.017-0.02814.2170.6730.6730.0000.0000.0000.000
25A24CYS0-0.0010.01012.484-0.759-0.7590.0000.0000.0000.000
26A25LEU0-0.0160.00714.4930.8640.8640.0000.0000.0000.000
27A26VAL00.0370.00615.800-0.517-0.5170.0000.0000.0000.000
28A27SER00.0050.01218.4900.7760.7760.0000.0000.0000.000
29A28VAL0-0.018-0.01121.794-0.247-0.2470.0000.0000.0000.000
30A29GLY0-0.0180.00224.4040.1780.1780.0000.0000.0000.000
31A30ALA0-0.0100.01520.4910.1140.1140.0000.0000.0000.000
32A31SER00.0280.01121.5860.0480.0480.0000.0000.0000.000
33A32GLU-1-0.816-0.92920.199-13.192-13.1920.0000.0000.0000.000
34A33ASN0-0.053-0.01318.449-0.708-0.7080.0000.0000.0000.000
35A34PHE0-0.0020.00516.556-1.064-1.0640.0000.0000.0000.000
36A35TYR00.018-0.02615.235-0.901-0.9010.0000.0000.0000.000
37A36SER00.0160.00414.632-0.853-0.8530.0000.0000.0000.000
38A37VAL0-0.049-0.01510.374-1.271-1.2710.0000.0000.0000.000
39A38PHE00.0200.00810.138-1.846-1.8460.0000.0000.0000.000
40A39GLU-1-0.879-0.96510.317-17.064-17.0640.0000.0000.0000.000
41A40SER0-0.079-0.06010.912-1.088-1.0880.0000.0000.0000.000
43A42LEU0-0.028-0.0257.121-0.885-0.8850.0000.0000.0000.000
44A43VAL0-0.0010.0099.4880.7450.7450.0000.0000.0000.000
45A44PRO0-0.069-0.03511.0160.9360.9360.0000.0000.0000.000
46A45HIS0-0.022-0.0028.7431.4891.4890.0000.0000.0000.000
47A46ILE0-0.0310.0089.9070.4250.4250.0000.0000.0000.000
48A47PRO0-0.0090.02213.1380.0610.0610.0000.0000.0000.000
49A48VAL00.0410.00713.512-0.220-0.2200.0000.0000.0000.000
50A49ILE0-0.0080.00716.1190.8350.8350.0000.0000.0000.000
51A50HIS10.8410.93418.44913.86513.8650.0000.0000.0000.000
52A51THR00.020-0.00721.5410.6810.6810.0000.0000.0000.000
53A52SER0-0.057-0.03423.678-0.277-0.2770.0000.0000.0000.000
54A53ILE00.018-0.00223.765-0.031-0.0310.0000.0000.0000.000
55A54GLY00.0090.01527.615-0.001-0.0010.0000.0000.0000.000
56A55GLY0-0.073-0.03230.6680.2180.2180.0000.0000.0000.000
57A56THR0-0.080-0.04927.922-0.108-0.1080.0000.0000.0000.000
58A57ARG10.8910.89724.32710.74710.7470.0000.0000.0000.000
59A58ILE00.0110.01023.310-0.484-0.4840.0000.0000.0000.000
60A59VAL00.0360.00419.990-0.028-0.0280.0000.0000.0000.000
61A60GLY00.0300.03919.469-0.003-0.0030.0000.0000.0000.000
62A61ARG10.7980.86218.76414.04414.0440.0000.0000.0000.000
63A62VAL0-0.039-0.01123.1510.3250.3250.0000.0000.0000.000
64A63THR0-0.024-0.00521.5410.1470.1470.0000.0000.0000.000
65A64CYS0-0.029-0.00220.543-0.429-0.4290.0000.0000.0000.000
66A65GLY00.0670.01819.7030.5660.5660.0000.0000.0000.000
67A66ASN0-0.004-0.00116.774-0.491-0.4910.0000.0000.0000.000
68A67LYS10.8210.89615.55417.89217.8920.0000.0000.0000.000
69A68ASN0-0.008-0.00617.423-0.014-0.0140.0000.0000.0000.000
70A69GLY00.0640.02520.8430.6750.6750.0000.0000.0000.000
71A70LEU0-0.042-0.01020.322-0.570-0.5700.0000.0000.0000.000
72A71LEU0-0.0010.00122.5990.6330.6330.0000.0000.0000.000
73A72VAL00.005-0.01024.699-0.272-0.2720.0000.0000.0000.000
74A73PRO00.0580.03426.9790.2910.2910.0000.0000.0000.000
75A74ASN00.029-0.00429.948-0.111-0.1110.0000.0000.0000.000
76A75THR00.0060.00930.6920.0820.0820.0000.0000.0000.000
77A76CYS0-0.056-0.00728.992-0.075-0.0750.0000.0000.0000.000
78A77ASN00.0810.03130.8270.3590.3590.0000.0000.0000.000
79A78ASP-1-0.811-0.89531.767-8.453-8.4530.0000.0000.0000.000
80A79ASN0-0.043-0.04132.575-0.113-0.1130.0000.0000.0000.000
81A80GLU-1-0.724-0.82228.089-9.900-9.9000.0000.0000.0000.000
82A81LEU00.0420.01427.648-0.319-0.3190.0000.0000.0000.000
83A82ARG10.8900.94628.4278.1548.1540.0000.0000.0000.000
84A83ASN0-0.019-0.00624.980-0.088-0.0880.0000.0000.0000.000
85A84ILE00.0080.01022.828-0.314-0.3140.0000.0000.0000.000
86A85ARG10.8660.92824.1199.5149.5140.0000.0000.0000.000
87A86ASN0-0.017-0.01426.041-0.048-0.0480.0000.0000.0000.000
88A87SER0-0.050-0.01721.985-0.016-0.0160.0000.0000.0000.000
89A88LEU0-0.017-0.01019.447-0.740-0.7400.0000.0000.0000.000
90A89PRO00.0070.01418.5130.4050.4050.0000.0000.0000.000
91A90ASP-1-0.892-0.96521.837-11.322-11.3220.0000.0000.0000.000
92A91ASN0-0.078-0.03020.1670.6400.6400.0000.0000.0000.000
93A92VAL0-0.0090.02619.9920.0990.0990.0000.0000.0000.000
94A93ARG10.9450.97522.43210.24410.2440.0000.0000.0000.000
95A94VAL00.0030.00224.097-0.152-0.1520.0000.0000.0000.000
96A95ARG10.9390.96526.3439.6379.6370.0000.0000.0000.000
97A96ARG10.8180.89628.3368.4718.4710.0000.0000.0000.000
98A97ILE00.0200.00628.2170.2120.2120.0000.0000.0000.000
99A98GLU-1-0.984-0.99931.957-7.910-7.9100.0000.0000.0000.000
100A99GLU-1-0.743-0.83631.119-8.884-8.8840.0000.0000.0000.000
101A100LYS10.9270.95333.7317.5897.5890.0000.0000.0000.000
102A101LEU0-0.0080.00231.3700.0370.0370.0000.0000.0000.000
103A102SER00.026-0.00230.597-0.222-0.2220.0000.0000.0000.000
104A103ALA0-0.017-0.00127.208-0.204-0.2040.0000.0000.0000.000
105A104LEU00.0820.02825.315-0.211-0.2110.0000.0000.0000.000
106A105GLY0-0.020-0.00322.108-0.284-0.2840.0000.0000.0000.000
107A106ASN0-0.002-0.01221.975-0.940-0.9400.0000.0000.0000.000
108A107CYS0-0.053-0.02024.6550.0680.0680.0000.0000.0000.000
109A108VAL00.0390.01722.6070.2670.2670.0000.0000.0000.000
110A109VAL0-0.0150.00018.254-0.455-0.4550.0000.0000.0000.000
111A110ALA0-0.020-0.01618.7500.5750.5750.0000.0000.0000.000
112A111ASN00.0300.02515.186-0.112-0.1120.0000.0000.0000.000
113A112ASP-1-0.781-0.87314.594-18.257-18.2570.0000.0000.0000.000
114A113TYR0-0.036-0.01416.2630.0390.0390.0000.0000.0000.000
115A114VAL00.0300.02119.8620.7380.7380.0000.0000.0000.000
116A115ALA0-0.001-0.01020.386-0.665-0.6650.0000.0000.0000.000
117A116LEU00.0040.01922.5790.4320.4320.0000.0000.0000.000
118A117ILE0-0.031-0.02824.342-0.210-0.2100.0000.0000.0000.000
119A118HIS00.015-0.01127.1470.0960.0960.0000.0000.0000.000
120A119PRO0-0.0020.00629.6750.1120.1120.0000.0000.0000.000
121A120ASP-1-0.917-0.95832.814-8.337-8.3370.0000.0000.0000.000
122A121LEU0-0.0180.00229.399-0.119-0.1190.0000.0000.0000.000
123A122ASP-1-0.825-0.91433.430-7.914-7.9140.0000.0000.0000.000
124A123ARG10.9470.95933.9558.1638.1630.0000.0000.0000.000
125A124GLU-1-0.900-0.94634.641-8.050-8.0500.0000.0000.0000.000
126A125SER0-0.050-0.07031.035-0.207-0.2070.0000.0000.0000.000
127A126GLU-1-0.862-0.91230.148-9.677-9.6770.0000.0000.0000.000
128A127GLU-1-0.940-0.96729.944-8.763-8.7630.0000.0000.0000.000
129A128ILE0-0.040-0.02328.935-0.160-0.1600.0000.0000.0000.000
130A129ILE0-0.028-0.02324.789-0.351-0.3510.0000.0000.0000.000
131A130ALA00.0170.01325.974-0.388-0.3880.0000.0000.0000.000
132A131ASP-1-0.946-0.97127.281-9.989-9.9890.0000.0000.0000.000
133A132THR0-0.090-0.05225.378-0.153-0.1530.0000.0000.0000.000
134A133LEU0-0.027-0.00221.322-0.322-0.3220.0000.0000.0000.000
135A134GLY00.0060.03222.497-0.592-0.5920.0000.0000.0000.000
136A135VAL0-0.072-0.03421.559-0.461-0.4610.0000.0000.0000.000
137A136GLU-1-0.916-0.95124.377-11.024-11.0240.0000.0000.0000.000
138A137VAL0-0.023-0.02024.992-0.473-0.4730.0000.0000.0000.000
139A138PHE00.0330.01725.6070.4930.4930.0000.0000.0000.000
140A139ARG10.7240.84927.7718.8968.8960.0000.0000.0000.000
141A140THR0-0.012-0.01927.1870.0070.0070.0000.0000.0000.000
142A141THR0-0.022-0.00728.6650.1360.1360.0000.0000.0000.000
143A142ILE00.0050.00722.953-0.094-0.0940.0000.0000.0000.000
144A143ALA00.0320.01526.1680.1030.1030.0000.0000.0000.000
145A144ASN0-0.067-0.02427.7920.1980.1980.0000.0000.0000.000
146A145ASN0-0.0030.00227.9620.5890.5890.0000.0000.0000.000
147A146VAL00.0650.02028.709-0.277-0.2770.0000.0000.0000.000
148A147LEU0-0.056-0.01626.548-0.124-0.1240.0000.0000.0000.000
149A148VAL00.0640.02124.133-0.451-0.4510.0000.0000.0000.000
150A149GLY00.0230.02321.066-0.580-0.5800.0000.0000.0000.000
151A150THR0-0.067-0.04520.657-0.377-0.3770.0000.0000.0000.000
152A151TYR0-0.015-0.00821.644-0.218-0.2180.0000.0000.0000.000
153A152CYS0-0.0140.01619.301-0.375-0.3750.0000.0000.0000.000
154A153VAL0-0.0220.00913.4100.0750.0750.0000.0000.0000.000
155A154ILE00.0300.00814.543-0.617-0.6170.0000.0000.0000.000
156A155ASN0-0.0050.0018.3391.4751.4750.0000.0000.0000.000
157A156ASN0-0.039-0.05411.9402.5492.5490.0000.0000.0000.000
158A157ARG10.8620.9498.14532.97832.9780.0000.0000.0000.000
159A158GLY00.1000.03612.3860.7550.7550.0000.0000.0000.000
160A159GLY00.0240.00713.348-0.378-0.3780.0000.0000.0000.000
161A160LEU0-0.062-0.01713.7210.1230.1230.0000.0000.0000.000
162A161VAL00.019-0.00615.8420.4160.4160.0000.0000.0000.000
163A162HIS00.035-0.00519.593-0.269-0.2690.0000.0000.0000.000
164A163PRO0-0.027-0.01122.2370.0780.0780.0000.0000.0000.000
165A164LEU0-0.068-0.04023.3910.2620.2620.0000.0000.0000.000
166A165ALA0-0.0010.01623.9710.4150.4150.0000.0000.0000.000
167A166SER0-0.037-0.03625.813-0.219-0.2190.0000.0000.0000.000
168A167VAL0-0.008-0.02426.109-0.302-0.3020.0000.0000.0000.000
169A168GLU-1-0.902-0.93926.773-9.781-9.7810.0000.0000.0000.000
170A169GLU-1-0.795-0.88626.635-11.130-11.1300.0000.0000.0000.000
171A170LEU0-0.046-0.02621.139-0.351-0.3510.0000.0000.0000.000
172A171ASP-1-0.889-0.94723.392-12.559-12.5590.0000.0000.0000.000
173A172GLU-1-0.948-0.96625.586-10.713-10.7130.0000.0000.0000.000
174A173LEU0-0.028-0.03022.918-0.152-0.1520.0000.0000.0000.000
175A174ALA0-0.006-0.00721.173-0.422-0.4220.0000.0000.0000.000
176A175ASN0-0.051-0.02922.123-0.410-0.4100.0000.0000.0000.000
177A176LEU0-0.044-0.01424.882-0.074-0.0740.0000.0000.0000.000
178A177LEU0-0.027-0.02519.308-0.072-0.0720.0000.0000.0000.000
179A178GLN0-0.036-0.00120.246-0.783-0.7830.0000.0000.0000.000
180A179ILE0-0.051-0.00915.512-0.955-0.9550.0000.0000.0000.000
181A180PRO0-0.046-0.03015.5830.5270.5270.0000.0000.0000.000
182A181LEU00.0110.01516.245-0.966-0.9660.0000.0000.0000.000
183A182CYS0-0.058-0.03316.1760.2570.2570.0000.0000.0000.000
184A183ALA00.0660.04918.136-0.168-0.1680.0000.0000.0000.000
185A184GLY0-0.012-0.01718.331-0.474-0.4740.0000.0000.0000.000
186A185THR0-0.044-0.03818.4120.6680.6680.0000.0000.0000.000
187A186ILE0-0.0100.00013.323-1.271-1.2710.0000.0000.0000.000
188A187ASN0-0.019-0.01916.9660.2410.2410.0000.0000.0000.000
189A188ARG10.8930.94918.94014.40814.4080.0000.0000.0000.000
190A189GLY00.014-0.00320.4340.7650.7650.0000.0000.0000.000
191A190SER0-0.026-0.00121.1720.7330.7330.0000.0000.0000.000
192A191ASP-1-0.787-0.90921.066-12.691-12.6910.0000.0000.0000.000
193A192VAL0-0.022-0.00222.436-0.147-0.1470.0000.0000.0000.000
194A193ILE00.0230.00316.422-0.366-0.3660.0000.0000.0000.000
195A194GLY00.0140.00417.277-0.892-0.8920.0000.0000.0000.000
196A195ALA0-0.048-0.03418.117-0.098-0.0980.0000.0000.0000.000
197A196GLY00.000-0.00417.399-0.108-0.1080.0000.0000.0000.000
198A197LEU0-0.049-0.02010.464-1.007-1.0070.0000.0000.0000.000
199A198VAL0-0.023-0.00710.9071.1401.1400.0000.0000.0000.000
200A199VAL0-0.018-0.0177.381-1.991-1.9910.0000.0000.0000.000
201A200ASN00.0240.0096.711-0.666-0.6660.0000.0000.0000.000
202A201ASP-1-0.797-0.9067.143-28.431-28.4310.0000.0000.0000.000
206A205PHE0-0.0010.0006.715-1.000-1.0000.0000.0000.0000.000
207A206CYS0-0.0140.0049.7161.4211.4210.0000.0000.0000.000
208A207GLY00.0900.03612.8870.1000.1000.0000.0000.0000.000
209A208LEU0-0.0080.00615.875-0.807-0.8070.0000.0000.0000.000
210A209ASP-1-0.889-0.94517.211-14.912-14.9120.0000.0000.0000.000
211A210THR0-0.036-0.01113.8230.6040.6040.0000.0000.0000.000
212A211THR0-0.036-0.03416.082-0.656-0.6560.0000.0000.0000.000
213A212SER00.0280.00314.302-0.829-0.8290.0000.0000.0000.000
214A213THR00.0060.01013.932-1.692-1.6920.0000.0000.0000.000
215A214GLU-1-0.690-0.81914.690-17.674-17.6740.0000.0000.0000.000
216A215ILE00.0210.0119.164-0.345-0.3450.0000.0000.0000.000
217A216SER00.002-0.0069.928-2.638-2.6380.0000.0000.0000.000
218A217VAL0-0.039-0.01511.052-1.104-1.1040.0000.0000.0000.000
219A218VAL00.0020.0018.110-0.513-0.5130.0000.0000.0000.000
220A219GLU-1-0.843-0.9295.626-45.073-45.0730.0000.0000.0000.000
221A220ASN0-0.051-0.0286.990-3.976-3.9760.0000.0000.0000.000
222A221ILE0-0.041-0.0049.4370.1840.1840.0000.0000.0000.000
223A222PHE0-0.018-0.0097.6160.9780.9780.0000.0000.0000.000
224A223LYS10.8620.9307.58123.11123.1110.0000.0000.0000.000