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: R4YV8

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 -2269972.889456
FMO2-HF: Nuclear repulsion 2187421.188173
FMO2-HF: Total energy -82551.701283
FMO2-MP2: Total energy -82796.69789


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:GLY)


Summations of interaction energy for fragment #1(A:2:GLY)
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.
445.644447.730.052-0.819-1.317-0.004
Interaction energy analysis for fragmet #1(A:2:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.941 / q_NPA : 0.960
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].
3A4TYR00.033-0.0103.8476.7337.458-0.001-0.252-0.4720.000
4A5LYS10.9040.9433.44645.07245.4740.003-0.150-0.2540.000
5A6TYR00.1510.0762.7960.5301.4890.050-0.417-0.591-0.004
6A7LEU00.0150.0106.9126.1766.1760.0000.0000.0000.000
7A8GLU-1-0.852-0.8937.864-27.261-27.2610.0000.0000.0000.000
8A9GLU-1-0.923-0.9698.518-29.533-29.5330.0000.0000.0000.000
9A10LEU00.0200.02411.1412.4792.4790.0000.0000.0000.000
10A11TRP00.028-0.01712.5052.9612.9610.0000.0000.0000.000
11A12ARG10.8450.91011.12526.32626.3260.0000.0000.0000.000
12A13LYS10.9971.02012.30025.40525.4050.0000.0000.0000.000
13A14LYS10.8500.91917.10116.37516.3750.0000.0000.0000.000
14A15GLN00.0240.00619.7230.6360.6360.0000.0000.0000.000
15A16SER00.0500.04318.7800.3430.3430.0000.0000.0000.000
16A17ASP-1-0.806-0.89021.281-13.131-13.1310.0000.0000.0000.000
17A18LEU00.0470.02516.1640.1380.1380.0000.0000.0000.000
18A19MET0-0.061-0.01615.965-0.223-0.2230.0000.0000.0000.000
19A20SER00.0450.00919.8050.5960.5960.0000.0000.0000.000
20A21PHE00.0160.03523.1670.4940.4940.0000.0000.0000.000
21A22ILE00.0350.01617.9050.2940.2940.0000.0000.0000.000
22A23LEU0-0.067-0.04720.8570.3130.3130.0000.0000.0000.000
23A24ARG10.9130.95223.60612.43912.4390.0000.0000.0000.000
24A25LEU00.0580.04323.9020.3970.3970.0000.0000.0000.000
25A26ARG10.9040.94217.47016.83316.8330.0000.0000.0000.000
26A27THR0-0.099-0.08825.0510.3790.3790.0000.0000.0000.000
27A28TRP00.0410.02027.8490.2500.2500.0000.0000.0000.000
28A29GLU-1-0.811-0.89925.026-12.404-12.4040.0000.0000.0000.000
29A30TYR0-0.087-0.05722.4800.0670.0670.0000.0000.0000.000
30A31ARG10.8580.91329.28110.37910.3790.0000.0000.0000.000
31A32GLN00.0110.02032.3450.5120.5120.0000.0000.0000.000
32A33LEU00.0220.03628.6550.1790.1790.0000.0000.0000.000
33A34PRO00.0540.02832.7740.1300.1300.0000.0000.0000.000
34A35VAL0-0.048-0.03132.802-0.325-0.3250.0000.0000.0000.000
35A36ILE0-0.024-0.02931.405-0.284-0.2840.0000.0000.0000.000
36A37HIS00.0110.00328.335-0.100-0.1000.0000.0000.0000.000
37A38LYS11.0191.01726.79510.85410.8540.0000.0000.0000.000
38A39ALA0-0.026-0.01723.2870.0650.0650.0000.0000.0000.000
39A40SER00.0390.01523.917-0.137-0.1370.0000.0000.0000.000
40A41ARG11.0040.99517.54415.67615.6760.0000.0000.0000.000
41A42SER0-0.0050.00116.1680.2840.2840.0000.0000.0000.000
42A43SER00.0150.01116.846-1.232-1.2320.0000.0000.0000.000
43A44ARG10.7980.91114.69419.11019.1100.0000.0000.0000.000
44A45PRO00.0900.04711.4850.0930.0930.0000.0000.0000.000
45A46ASP-1-0.775-0.9019.149-27.462-27.4620.0000.0000.0000.000
46A47LYS10.8530.92610.51819.41919.4190.0000.0000.0000.000
47A48ALA00.0580.02013.8560.7790.7790.0000.0000.0000.000
48A49ARG10.9691.0018.80129.07929.0790.0000.0000.0000.000
49A50LYS10.7680.87510.35929.10629.1060.0000.0000.0000.000
50A51LEU0-0.111-0.04413.7641.1331.1330.0000.0000.0000.000
51A52GLY00.0710.03016.0051.1231.1230.0000.0000.0000.000
52A53TYR0-0.032-0.02815.1540.5920.5920.0000.0000.0000.000
53A54LYS10.9150.95313.60318.19318.1930.0000.0000.0000.000
54A55ASN00.0070.01514.6921.4031.4030.0000.0000.0000.000
55A56LYS10.9150.95617.29814.36114.3610.0000.0000.0000.000
56A57ASP-1-0.795-0.89120.320-12.456-12.4560.0000.0000.0000.000
57A58GLY00.0480.01524.0400.0310.0310.0000.0000.0000.000
58A59TYR0-0.030-0.01819.658-0.101-0.1010.0000.0000.0000.000
59A60ALA00.0060.00323.0340.1950.1950.0000.0000.0000.000
60A61ILE0-0.043-0.02119.428-0.363-0.3630.0000.0000.0000.000
61A62TRP00.0630.03623.3760.4530.4530.0000.0000.0000.000
62A63ARG10.8720.94522.26112.79412.7940.0000.0000.0000.000
63A64VAL00.0010.00026.8110.4820.4820.0000.0000.0000.000
64A65ARG10.8550.94528.6259.0689.0680.0000.0000.0000.000
65A66VAL0-0.062-0.03931.1570.3540.3540.0000.0000.0000.000
66A67ARG10.9911.00033.1858.0238.0230.0000.0000.0000.000
67A68ARG10.8570.93230.51110.00910.0090.0000.0000.0000.000
68A69GLY00.0440.01435.6140.2170.2170.0000.0000.0000.000
69A70GLY0-0.0060.00537.875-0.210-0.2100.0000.0000.0000.000
70A71ARG10.8840.94240.5067.2677.2670.0000.0000.0000.000
71A72LYS11.0361.02342.7226.6306.6300.0000.0000.0000.000
72A73ARG10.8630.94046.0866.1756.1750.0000.0000.0000.000
73A74PRO0-0.036-0.01447.3760.0700.0700.0000.0000.0000.000
74A75VAL00.0050.01149.9220.0430.0430.0000.0000.0000.000
75A76SER00.0700.02953.633-0.018-0.0180.0000.0000.0000.000
76A77LYS10.9960.98556.1345.3095.3090.0000.0000.0000.000
77A78GLY0-0.020-0.00254.6430.0210.0210.0000.0000.0000.000
78A79ILE00.0240.01255.635-0.004-0.0040.0000.0000.0000.000
79A80VAL0-0.073-0.04554.842-0.083-0.0830.0000.0000.0000.000
80A81TYR00.0890.04557.6120.0310.0310.0000.0000.0000.000
81A82GLY00.001-0.01458.737-0.074-0.0740.0000.0000.0000.000
82A83LYS11.0121.01658.6765.3735.3730.0000.0000.0000.000
83A84PRO00.1160.04457.875-0.112-0.1120.0000.0000.0000.000
84A85SER00.0010.00753.790-0.058-0.0580.0000.0000.0000.000
85A86SER0-0.056-0.03053.130-0.107-0.1070.0000.0000.0000.000
86A87VAL00.0170.02154.047-0.102-0.1020.0000.0000.0000.000
87A88GLY00.0540.03351.202-0.042-0.0420.0000.0000.0000.000
88A89ILE0-0.019-0.02149.946-0.092-0.0920.0000.0000.0000.000
89A90ASN00.0710.01647.580-0.183-0.1830.0000.0000.0000.000
90A91GLN00.0410.03144.839-0.252-0.2520.0000.0000.0000.000
91A92LEU00.0290.04143.760-0.198-0.1980.0000.0000.0000.000
92A93LYS10.9190.94238.8107.6567.6560.0000.0000.0000.000
93A94PHE0-0.004-0.00936.9340.1520.1520.0000.0000.0000.000
94A95ALA00.0310.01937.732-0.169-0.1690.0000.0000.0000.000
95A96ARG10.7740.86634.0138.8158.8150.0000.0000.0000.000
96A97ASN00.000-0.01429.2510.0930.0930.0000.0000.0000.000
97A98LEU00.0930.03030.613-0.088-0.0880.0000.0000.0000.000
98A99ARG10.8160.91222.48213.52113.5210.0000.0000.0000.000
99A100SER00.0400.03128.5350.0710.0710.0000.0000.0000.000
100A101CYS0-0.044-0.02130.7370.2880.2880.0000.0000.0000.000
101A102ALA00.0360.01228.6110.1560.1560.0000.0000.0000.000
102A103GLU-1-0.741-0.80226.101-11.802-11.8020.0000.0000.0000.000
103A104GLU-1-0.794-0.86729.723-8.552-8.5520.0000.0000.0000.000
104A105ARG10.9230.96932.7378.9308.9300.0000.0000.0000.000
105A106VAL00.0370.01628.3020.1140.1140.0000.0000.0000.000
106A107GLY00.004-0.00331.4890.1150.1150.0000.0000.0000.000
107A108LYS10.8910.92532.9178.4348.4340.0000.0000.0000.000
108A109ARG10.9340.98533.8499.0779.0770.0000.0000.0000.000
109A110VAL0-0.028-0.01530.9660.0200.0200.0000.0000.0000.000
110A111PRO0-0.0040.00332.897-0.268-0.2680.0000.0000.0000.000
111A112GLU-1-0.826-0.91133.944-8.886-8.8860.0000.0000.0000.000
112A113LEU0-0.041-0.01228.545-0.230-0.2300.0000.0000.0000.000
113A114ARG10.8510.92428.4309.7519.7510.0000.0000.0000.000
114A115VAL0-0.004-0.00526.545-0.498-0.4980.0000.0000.0000.000
115A116LEU00.0480.05320.5290.1450.1450.0000.0000.0000.000
116A117ASN0-0.034-0.03120.6230.3320.3320.0000.0000.0000.000
117A118SER00.0190.00122.6650.0460.0460.0000.0000.0000.000
118A119TYR0-0.064-0.06618.753-0.696-0.6960.0000.0000.0000.000
119A120TRP00.0010.00720.2610.0590.0590.0000.0000.0000.000
120A121VAL0-0.031-0.01819.937-1.098-1.0980.0000.0000.0000.000
121A122GLY00.1240.07221.890-0.194-0.1940.0000.0000.0000.000
122A123GLN0-0.050-0.02924.5970.3410.3410.0000.0000.0000.000
123A124ASP-1-0.669-0.80628.016-10.088-10.0880.0000.0000.0000.000
124A125GLY00.0480.02331.095-0.070-0.0700.0000.0000.0000.000
125A126THR0-0.011-0.01134.3210.2110.2110.0000.0000.0000.000
126A127TYR00.0200.00831.9590.1390.1390.0000.0000.0000.000
127A128LYS10.8240.90027.88911.02511.0250.0000.0000.0000.000
128A129PHE00.0270.02026.3260.2620.2620.0000.0000.0000.000
129A130TYR0-0.055-0.05324.302-0.700-0.7000.0000.0000.0000.000
130A131GLU-1-0.678-0.80920.332-15.004-15.0040.0000.0000.0000.000
131A132VAL0-0.039-0.03722.642-0.457-0.4570.0000.0000.0000.000
132A133ILE0-0.012-0.00318.441-0.068-0.0680.0000.0000.0000.000
133A134LEU0-0.009-0.01222.5330.2900.2900.0000.0000.0000.000
134A135ALA00.0110.00924.123-0.481-0.4810.0000.0000.0000.000
135A136ASP-1-0.760-0.86625.735-9.762-9.7620.0000.0000.0000.000
136A137PRO0-0.006-0.01928.751-0.107-0.1070.0000.0000.0000.000
137A138SER0-0.030-0.04131.1620.3100.3100.0000.0000.0000.000
138A139HIS00.0560.03626.4490.3550.3550.0000.0000.0000.000
139A140ASN00.0800.01829.332-0.212-0.2120.0000.0000.0000.000
140A141ALA0-0.0090.00424.467-0.132-0.1320.0000.0000.0000.000
141A142ILE0-0.092-0.04424.020-0.568-0.5680.0000.0000.0000.000
142A143ARG10.8870.93226.3249.1529.1520.0000.0000.0000.000
143A144ASN00.0640.02627.4990.2300.2300.0000.0000.0000.000
144A145ASP-1-0.827-0.89520.929-14.671-14.6710.0000.0000.0000.000
145A146PRO00.0600.01323.6960.0350.0350.0000.0000.0000.000
146A147ARG10.8920.96116.48216.09016.0900.0000.0000.0000.000
147A148ILE0-0.071-0.05320.749-0.198-0.1980.0000.0000.0000.000
148A149ASN00.0740.06024.3070.1180.1180.0000.0000.0000.000
149A150TRP00.0450.02724.0640.4940.4940.0000.0000.0000.000
150A151ILE0-0.110-0.05525.9500.3380.3380.0000.0000.0000.000
151A152CYS00.0000.02328.9050.2240.2240.0000.0000.0000.000
152A153GLU-1-0.884-0.91931.194-8.921-8.9210.0000.0000.0000.000
153A154SER00.010-0.02634.284-0.131-0.1310.0000.0000.0000.000
154A155ALA00.0370.03235.3440.0730.0730.0000.0000.0000.000
155A156HIS00.0100.00630.830-0.175-0.1750.0000.0000.0000.000
156A157LYS10.9891.00932.4017.7357.7350.0000.0000.0000.000
157A158HIS00.0280.01333.7360.2310.2310.0000.0000.0000.000
158A159ARG10.8760.93325.66011.67811.6780.0000.0000.0000.000
159A160GLU-1-0.834-0.94030.132-9.895-9.8950.0000.0000.0000.000
160A161LEU00.0010.00531.5520.0650.0650.0000.0000.0000.000
161A162ARG10.8320.91134.7569.0339.0330.0000.0000.0000.000
162A163GLY0-0.025-0.01532.5120.0060.0060.0000.0000.0000.000
163A164LEU0-0.0050.00030.938-0.147-0.1470.0000.0000.0000.000
164A165THR0-0.012-0.01527.229-0.552-0.5520.0000.0000.0000.000
165A166SER00.020-0.00823.4270.1910.1910.0000.0000.0000.000
166A167ALA0-0.0270.00025.7270.0110.0110.0000.0000.0000.000
167A168GLY00.0760.02527.6330.2860.2860.0000.0000.0000.000
168A169ARG10.9660.98126.75811.50711.5070.0000.0000.0000.000
169A170LYS10.9080.96026.98811.52411.5240.0000.0000.0000.000
170A171GLY00.0040.01129.7410.1990.1990.0000.0000.0000.000
171A172ARG10.8890.92932.9659.5639.5630.0000.0000.0000.000
172A173GLY00.0620.03032.6000.1670.1670.0000.0000.0000.000
173A174LEU0-0.035-0.01531.306-0.122-0.1220.0000.0000.0000.000
174A175ARG10.8580.92523.27712.64012.6400.0000.0000.0000.000
175A176VAL00.0390.03928.412-0.294-0.2940.0000.0000.0000.000
176A177LYS10.9760.99227.99911.41811.4180.0000.0000.0000.000
177A178GLY00.1170.05732.434-0.150-0.1500.0000.0000.0000.000
178A179HIS00.1040.05235.427-0.066-0.0660.0000.0000.0000.000
179A180ARG10.9880.98731.4449.8509.8500.0000.0000.0000.000
180A181ALA0-0.024-0.01534.9460.0140.0140.0000.0000.0000.000
181A182LYS10.9890.99937.0147.4007.4000.0000.0000.0000.000
182A183SER00.0130.01239.9440.1070.1070.0000.0000.0000.000
183A184LEU0-0.059-0.03835.8100.1110.1110.0000.0000.0000.000
184A185ARG10.8320.89331.4909.4949.4940.0000.0000.0000.000
185A186THR00.0860.03737.9020.0820.0820.0000.0000.0000.000
186A187SER0-0.020-0.00238.6750.2450.2450.0000.0000.0000.000
187A188ARG11.0191.01540.0617.7537.7530.0000.0000.0000.000
188A189LYS11.0000.99442.1907.3097.3090.0000.0000.0000.000
189A190GLY00.0280.04143.6210.1860.1860.0000.0000.0000.000
190A191ASN00.0470.02542.8480.1240.1240.0000.0000.0000.000
191A192TRP00.004-0.00144.8570.0300.0300.0000.0000.0000.000
192A193ARG10.9880.97245.5986.9356.9350.0000.0000.0000.000
193A194ALA00.0070.00047.0800.1060.1060.0000.0000.0000.000
194A195ARG10.8280.90444.6637.0077.0070.0000.0000.0000.000
195A196GLN00.0160.00850.5190.1540.1540.0000.0000.0000.000
196A197MET0-0.064-0.02152.0350.1090.1090.0000.0000.0000.000
197A198LEU00.0630.04754.552-0.033-0.0330.0000.0000.0000.000
198A199LYS10.9100.95052.0776.1876.1870.0000.0000.0000.000
199A200LEU00.0630.03857.9580.0120.0120.0000.0000.0000.000
200A201ARG10.9400.96255.5025.5765.5760.0000.0000.0000.000
201A202ARG10.9800.99362.3035.1265.1260.0000.0000.0000.000
202A203TYR00.002-0.00364.5550.0380.0380.0000.0000.0000.000
203A204ARG00.0800.05864.364-0.246-0.2460.0000.0000.0000.000