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: 5GN8Z

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 212
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2303845.356975
FMO2-HF: Nuclear repulsion 2220525.056655
FMO2-HF: Total energy -83320.300319
FMO2-MP2: Total energy -83566.507319


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.
365.606366.294-0.003-0.264-0.4210
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 : 0.929 / q_NPA : 0.955
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].
3A4ARG10.9940.9933.84632.17132.859-0.003-0.264-0.4210.000
4A5PRO00.0440.0146.6612.6242.6240.0000.0000.0000.000
5A6ALA00.0720.0308.8121.3971.3970.0000.0000.0000.000
6A7ARG11.0050.99511.94924.66624.6660.0000.0000.0000.000
7A8CYS0-0.070-0.02710.8800.7990.7990.0000.0000.0000.000
8A9TYR0-0.006-0.03310.408-0.262-0.2620.0000.0000.0000.000
9A10ARG10.8160.92915.35916.17716.1770.0000.0000.0000.000
10A11GLN00.1120.04417.5370.7750.7750.0000.0000.0000.000
11A12PRO0-0.0030.00320.335-0.606-0.6060.0000.0000.0000.000
12A13LYS10.9620.97420.27515.66715.6670.0000.0000.0000.000
13A14GLY00.0120.03222.3380.2800.2800.0000.0000.0000.000
14A15LYS11.0301.01523.44310.95710.9570.0000.0000.0000.000
15A16PRO00.004-0.01423.978-0.673-0.6730.0000.0000.0000.000
16A17TYR00.0180.00619.2600.4340.4340.0000.0000.0000.000
17A18PRO00.0820.04721.352-0.864-0.8640.0000.0000.0000.000
18A19LYS10.9550.97720.24014.88114.8810.0000.0000.0000.000
19A20SER00.0080.00622.7800.5970.5970.0000.0000.0000.000
20A21ARG11.0110.99724.9769.4219.4210.0000.0000.0000.000
21A22TYR00.0700.04526.0360.1700.1700.0000.0000.0000.000
22A23ASN0-0.097-0.04820.953-0.812-0.8120.0000.0000.0000.000
23A24ARG11.0411.02120.57214.18914.1890.0000.0000.0000.000
24A25GLY00.0240.00418.006-0.594-0.5940.0000.0000.0000.000
25A26VAL0-0.045-0.01516.390-1.261-1.2610.0000.0000.0000.000
26A27PRO00.0410.03012.9230.9660.9660.0000.0000.0000.000
27A28ASP-1-0.816-0.90215.431-15.284-15.2840.0000.0000.0000.000
28A29ALA0-0.032-0.01914.916-1.175-1.1750.0000.0000.0000.000
29A30ARG10.9680.9658.44128.13628.1360.0000.0000.0000.000
30A31ILE0-0.0060.02015.2450.4610.4610.0000.0000.0000.000
31A32ARG10.9030.92818.65815.83215.8320.0000.0000.0000.000
32A33ILE0-0.024-0.00820.9030.6750.6750.0000.0000.0000.000
33A34TYR00.0390.01121.418-0.151-0.1510.0000.0000.0000.000
34A35ASP-1-0.818-0.89625.686-10.092-10.0920.0000.0000.0000.000
35A36SER0-0.088-0.06226.931-0.346-0.3460.0000.0000.0000.000
36A37GLY00.0900.05429.0520.1670.1670.0000.0000.0000.000
37A38ARG10.8510.92132.0237.5717.5710.0000.0000.0000.000
38A39LYS10.8680.91628.55010.68410.6840.0000.0000.0000.000
39A40LYS10.9610.97435.0718.1848.1840.0000.0000.0000.000
40A41ALA00.0310.05038.4230.1840.1840.0000.0000.0000.000
41A42THR00.0420.02140.370-0.102-0.1020.0000.0000.0000.000
42A43VAL0-0.014-0.02141.971-0.110-0.1100.0000.0000.0000.000
43A44GLU-1-0.744-0.81643.322-6.537-6.5370.0000.0000.0000.000
44A45GLU-1-0.821-0.88542.631-7.236-7.2360.0000.0000.0000.000
45A46PHE0-0.059-0.03938.559-0.043-0.0430.0000.0000.0000.000
46A47PRO00.0430.03340.887-0.127-0.1270.0000.0000.0000.000
47A48TYR0-0.033-0.04640.485-0.050-0.0500.0000.0000.0000.000
48A49VAL0-0.022-0.01035.952-0.210-0.2100.0000.0000.0000.000
49A50VAL0-0.022-0.01233.3450.1210.1210.0000.0000.0000.000
50A51HIS00.0140.02631.792-0.418-0.4180.0000.0000.0000.000
51A52ILE0-0.0010.01125.3830.0310.0310.0000.0000.0000.000
52A53VAL00.005-0.00328.950-0.036-0.0360.0000.0000.0000.000
53A54SER00.0350.01925.544-0.120-0.1200.0000.0000.0000.000
54A55ASP-1-0.812-0.90627.165-9.733-9.7330.0000.0000.0000.000
55A56GLU-1-0.809-0.88923.475-13.260-13.2600.0000.0000.0000.000
56A57LYS10.8430.91525.80911.15311.1530.0000.0000.0000.000
57A58GLU-1-0.821-0.90620.362-15.446-15.4460.0000.0000.0000.000
58A59GLN0-0.058-0.03718.1191.0741.0740.0000.0000.0000.000
59A60ILE00.0280.02417.552-1.187-1.1870.0000.0000.0000.000
60A61THR00.010-0.00611.9180.0280.0280.0000.0000.0000.000
61A62SER00.002-0.01213.5840.7870.7870.0000.0000.0000.000
62A63GLU-1-0.815-0.90610.147-25.215-25.2150.0000.0000.0000.000
63A64ALA00.0090.02013.3660.3030.3030.0000.0000.0000.000
64A65LEU00.0200.01815.3670.9530.9530.0000.0000.0000.000
65A66GLU-1-0.769-0.88815.850-14.637-14.6370.0000.0000.0000.000
66A67ALA0-0.023-0.01014.9030.6410.6410.0000.0000.0000.000
67A68ALA00.0210.01116.9880.7240.7240.0000.0000.0000.000
68A69ARG10.8680.92920.30514.35114.3510.0000.0000.0000.000
69A70ILE0-0.041-0.02617.3890.7200.7200.0000.0000.0000.000
70A71ALA0-0.036-0.01220.7380.4790.4790.0000.0000.0000.000
71A72ALA00.0840.03922.3620.5130.5130.0000.0000.0000.000
72A73ASN00.002-0.01024.5880.8720.8720.0000.0000.0000.000
73A74LYS10.9400.96520.22314.66214.6620.0000.0000.0000.000
74A75ASN0-0.006-0.00525.9130.0620.0620.0000.0000.0000.000
75A76LEU00.0180.01128.2630.3340.3340.0000.0000.0000.000
76A77ILE0-0.078-0.04927.6600.3190.3190.0000.0000.0000.000
77A78LYS10.9310.97826.76311.42511.4250.0000.0000.0000.000
78A79PHE00.0140.00728.9780.0670.0670.0000.0000.0000.000
79A80ILE0-0.0040.01233.9320.2230.2230.0000.0000.0000.000
80A81SER00.1130.05335.0620.1020.1020.0000.0000.0000.000
81A82LYS10.9130.94729.26910.08910.0890.0000.0000.0000.000
82A83ASP-1-0.899-0.93934.082-7.914-7.9140.0000.0000.0000.000
83A84ALA00.0490.00937.1150.0450.0450.0000.0000.0000.000
84A85PHE00.0330.01629.930-0.045-0.0450.0000.0000.0000.000
85A86HIS0-0.0210.00532.7020.1260.1260.0000.0000.0000.000
86A87LEU0-0.0160.00026.1800.0930.0930.0000.0000.0000.000
87A88ARG10.9120.95028.7329.4459.4450.0000.0000.0000.000
88A89CYS0-0.039-0.00723.918-0.091-0.0910.0000.0000.0000.000
89A90ARG10.9030.93726.3839.7369.7360.0000.0000.0000.000
90A91VAL00.0010.02122.9970.0400.0400.0000.0000.0000.000
91A92HIS00.0380.01723.034-0.073-0.0730.0000.0000.0000.000
92A93PRO0-0.053-0.03418.1070.0110.0110.0000.0000.0000.000
93A94TRP00.0550.01319.840-0.720-0.7200.0000.0000.0000.000
94A95HIS0-0.0130.01318.6030.6170.6170.0000.0000.0000.000
95A96VAL0-0.007-0.00716.454-1.104-1.1040.0000.0000.0000.000
96A97LEU0-0.040-0.01312.9110.4310.4310.0000.0000.0000.000
97A98ARG10.8890.96414.15416.03016.0300.0000.0000.0000.000
98A99ILE0-0.017-0.0017.339-1.082-1.0820.0000.0000.0000.000
99A100ASN00.005-0.01211.7060.1150.1150.0000.0000.0000.000
100A101LYS10.8820.9167.81628.80128.8010.0000.0000.0000.000
101A102MET00.0790.06811.226-1.403-1.4030.0000.0000.0000.000
102A103LEU00.0440.0247.124-1.176-1.1760.0000.0000.0000.000
103A104SER0-0.012-0.0239.204-1.728-1.7280.0000.0000.0000.000
104A105CYS00.0580.02111.6420.7050.7050.0000.0000.0000.000
105A106ALA00.0410.04414.7310.9780.9780.0000.0000.0000.000
106A107GLY0-0.076-0.04215.6010.7450.7450.0000.0000.0000.000
107A108ALA00.0700.02717.079-0.306-0.3060.0000.0000.0000.000
108A109ASP-1-0.804-0.89719.081-15.312-15.3120.0000.0000.0000.000
109A110ARG10.9370.94219.76712.28912.2890.0000.0000.0000.000
110A111LEU0-0.070-0.02617.8550.1870.1870.0000.0000.0000.000
111A112GLN0-0.0070.00813.656-2.613-2.6130.0000.0000.0000.000
112A113SER00.0520.01816.153-0.604-0.6040.0000.0000.0000.000
113A114GLY0-0.019-0.00217.3310.2730.2730.0000.0000.0000.000
114A115MET0-0.0080.00017.9650.4780.4780.0000.0000.0000.000
115A116ARG10.9850.99621.32613.18113.1810.0000.0000.0000.000
116A117GLY00.0570.02521.1480.7510.7510.0000.0000.0000.000
117A118ALA00.0190.02018.401-0.756-0.7560.0000.0000.0000.000
118A119PHE00.0260.00217.746-0.974-0.9740.0000.0000.0000.000
119A120GLY0-0.019-0.00415.053-0.227-0.2270.0000.0000.0000.000
120A121LYS10.9050.96512.15924.98924.9890.0000.0000.0000.000
121A122ALA00.0170.00213.684-0.833-0.8330.0000.0000.0000.000
122A123LEU0-0.050-0.0197.544-1.608-1.6080.0000.0000.0000.000
123A124GLY00.0350.00410.491-1.947-1.9470.0000.0000.0000.000
124A125LYS10.8390.92812.58518.14118.1410.0000.0000.0000.000
125A126ALA00.013-0.00115.023-1.050-1.0500.0000.0000.0000.000
126A127ALA00.0060.01817.3900.7020.7020.0000.0000.0000.000
127A128ARG10.7830.88120.80113.44413.4440.0000.0000.0000.000
128A129VAL00.0000.00623.1460.4080.4080.0000.0000.0000.000
129A130ASP-1-0.757-0.86424.946-11.023-11.0230.0000.0000.0000.000
130A131ILE00.0180.01028.057-0.067-0.0670.0000.0000.0000.000
131A132GLY00.0300.01930.2170.2990.2990.0000.0000.0000.000
132A133SER0-0.056-0.03028.0900.0610.0610.0000.0000.0000.000
133A134ILE0-0.014-0.01628.900-0.233-0.2330.0000.0000.0000.000
134A135LEU00.003-0.00423.308-0.167-0.1670.0000.0000.0000.000
135A136PHE00.005-0.01222.294-0.204-0.2040.0000.0000.0000.000
136A137SER0-0.016-0.01527.9020.2960.2960.0000.0000.0000.000
137A138VAL00.0080.00630.587-0.169-0.1690.0000.0000.0000.000
138A139ARG10.7730.90933.0048.4498.4490.0000.0000.0000.000
139A140VAL00.0550.00935.667-0.141-0.1410.0000.0000.0000.000
140A141LYS10.9420.97438.4727.2047.2040.0000.0000.0000.000
141A142GLU-1-0.797-0.88241.006-6.984-6.9840.0000.0000.0000.000
142A143PRO00.0080.01342.055-0.131-0.1310.0000.0000.0000.000
143A144HIS00.0550.01637.807-0.146-0.1460.0000.0000.0000.000
144A145VAL0-0.0070.00337.145-0.312-0.3120.0000.0000.0000.000
145A146LYS10.9820.97936.4557.7607.7600.0000.0000.0000.000
146A147TYR00.0870.04934.377-0.323-0.3230.0000.0000.0000.000
147A148ALA0-0.010-0.00632.534-0.370-0.3700.0000.0000.0000.000
148A149ILE0-0.001-0.00931.506-0.350-0.3500.0000.0000.0000.000
149A150ASP-1-0.796-0.84130.798-10.381-10.3810.0000.0000.0000.000
150A151ALA00.0220.01128.202-0.434-0.4340.0000.0000.0000.000
151A152LEU0-0.048-0.02826.730-0.602-0.6020.0000.0000.0000.000
152A153THR0-0.021-0.02826.500-0.429-0.4290.0000.0000.0000.000
153A154ARG10.8370.89424.83910.17610.1760.0000.0000.0000.000
154A155ALA0-0.029-0.01622.425-0.670-0.6700.0000.0000.0000.000
155A156LYS10.9010.94121.66410.66610.6660.0000.0000.0000.000
156A157ALA00.0240.01821.317-0.312-0.3120.0000.0000.0000.000
157A158LYS10.8610.94016.98615.88415.8840.0000.0000.0000.000
158A159PHE0-0.033-0.01616.900-1.045-1.0450.0000.0000.0000.000
159A160PRO0-0.050-0.02616.240-0.260-0.2600.0000.0000.0000.000
160A161GLY00.0830.03618.4220.5970.5970.0000.0000.0000.000
161A162ARG10.8610.94521.69910.99810.9980.0000.0000.0000.000
162A163GLN00.023-0.00321.926-0.092-0.0920.0000.0000.0000.000
163A164LYS10.8680.92126.3449.8109.8100.0000.0000.0000.000
164A165VAL00.0130.00529.183-0.230-0.2300.0000.0000.0000.000
165A166VAL00.0120.01231.5190.2430.2430.0000.0000.0000.000
166A167THR00.0330.02434.997-0.109-0.1090.0000.0000.0000.000
167A168SER0-0.020-0.01237.8730.2080.2080.0000.0000.0000.000
168A169GLN00.0480.02139.8570.1260.1260.0000.0000.0000.000
169A170LYS10.8660.93441.0817.6797.6790.0000.0000.0000.000
170A171TRP00.0670.03642.418-0.059-0.0590.0000.0000.0000.000
171A172GLY00.0480.02339.550-0.028-0.0280.0000.0000.0000.000
172A173PHE0-0.082-0.06432.996-0.142-0.1420.0000.0000.0000.000
173A174THR00.0000.00838.272-0.054-0.0540.0000.0000.0000.000
174A175LYS10.9530.96440.3557.7277.7270.0000.0000.0000.000
175A176LEU00.0670.05342.8590.0220.0220.0000.0000.0000.000
176A177THR00.0250.00244.830-0.135-0.1350.0000.0000.0000.000
177A178ARG10.9350.96043.2527.2637.2630.0000.0000.0000.000
178A179ALA00.0510.04447.7450.0960.0960.0000.0000.0000.000
179A180GLN00.0350.01748.7970.0030.0030.0000.0000.0000.000
180A181TYR0-0.006-0.04347.1090.0450.0450.0000.0000.0000.000
181A182SER0-0.039-0.02649.9890.1100.1100.0000.0000.0000.000
182A183ARG10.9960.99252.6835.7145.7140.0000.0000.0000.000
183A184LEU00.015-0.00151.0960.0770.0770.0000.0000.0000.000
184A185ARG10.8370.89850.4256.3016.3010.0000.0000.0000.000
185A186ASN00.0010.00454.1440.0350.0350.0000.0000.0000.000
186A187GLN0-0.024-0.01657.4130.0140.0140.0000.0000.0000.000
187A188LYS10.9951.01256.4395.3065.3060.0000.0000.0000.000
188A189LYS10.9490.99154.3405.7245.7240.0000.0000.0000.000
189A190LEU0-0.055-0.03049.508-0.127-0.1270.0000.0000.0000.000
190A191VAL00.0750.04449.8440.0510.0510.0000.0000.0000.000
191A192THR0-0.015-0.01845.825-0.152-0.1520.0000.0000.0000.000
192A193ASP-1-0.800-0.89543.260-7.207-7.2070.0000.0000.0000.000
193A194GLY00.0410.03140.883-0.193-0.1930.0000.0000.0000.000
194A195SER0-0.039-0.03736.7460.1140.1140.0000.0000.0000.000
195A196ASN0-0.076-0.03339.599-0.218-0.2180.0000.0000.0000.000
196A197VAL0-0.008-0.01741.9720.1090.1090.0000.0000.0000.000
197A198LYS10.8630.94045.6256.8296.8290.0000.0000.0000.000
198A199VAL00.0150.00048.1810.0840.0840.0000.0000.0000.000
199A200ILE00.0120.00851.079-0.034-0.0340.0000.0000.0000.000
200A201GLY0-0.0050.00154.3340.0640.0640.0000.0000.0000.000
201A202GLU-1-0.830-0.93155.916-5.542-5.5420.0000.0000.0000.000
202A203ARG10.9370.96256.7375.4215.4210.0000.0000.0000.000
203A204GLY0-0.0210.00357.119-0.006-0.0060.0000.0000.0000.000
204A205PRO00.0590.01157.7410.0650.0650.0000.0000.0000.000
205A206LEU00.0750.02660.255-0.075-0.0750.0000.0000.0000.000
206A207SER00.0340.01761.064-0.004-0.0040.0000.0000.0000.000
207A208ARG10.7840.91955.4095.5815.5810.0000.0000.0000.000
208A209LEU0-0.072-0.03258.460-0.077-0.0770.0000.0000.0000.000
209A210GLU-1-0.928-0.98057.818-5.441-5.4410.0000.0000.0000.000
210A211LEU0-0.029-0.01661.1080.0380.0380.0000.0000.0000.000
211A212PHE0-0.043-0.01663.9530.0760.0760.0000.0000.0000.000
212A213ARG00.0550.05160.6670.2530.2530.0000.0000.0000.000