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: 1VN5Z

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 180
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1691912.937467
FMO2-HF: Nuclear repulsion 1621451.313815
FMO2-HF: Total energy -70461.623652
FMO2-MP2: Total energy -70670.535307


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:ALA)


Summations of interaction energy for fragment #1(A:2:ALA)
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.
197.658198.979-0.013-0.604-0.703-0.001
Interaction energy analysis for fragmet #1(A:2:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.850 / q_NPA : 0.917
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].
3A4ASP-1-0.849-0.9143.869-34.208-32.887-0.013-0.604-0.703-0.001
4A5LEU00.0300.0276.3225.4255.4250.0000.0000.0000.000
5A6HIS00.0740.0268.835-0.550-0.5500.0000.0000.0000.000
6A7LYS10.8830.92111.59919.15019.1500.0000.0000.0000.000
7A8GLN00.0320.0204.949-1.000-1.0000.0000.0000.0000.000
8A9GLY00.0360.0288.477-0.419-0.4190.0000.0000.0000.000
9A10ARG10.9180.9689.43628.45628.4560.0000.0000.0000.000
10A11VAL0-0.024-0.01013.1381.2931.2930.0000.0000.0000.000
11A12VAL00.0270.01215.6720.7670.7670.0000.0000.0000.000
12A13LYS11.0011.01519.01613.07913.0790.0000.0000.0000.000
13A14ARG10.9620.97021.68213.53413.5340.0000.0000.0000.000
14A15SER0-0.037-0.02724.5410.4030.4030.0000.0000.0000.000
15A16VAL0-0.014-0.00225.0910.2230.2230.0000.0000.0000.000
16A17VAL00.0070.00428.0120.2030.2030.0000.0000.0000.000
17A18ARG10.8840.95330.2788.6218.6210.0000.0000.0000.000
18A19GLN00.0850.03229.1050.5940.5940.0000.0000.0000.000
19A20THR0-0.036-0.01932.069-0.060-0.0600.0000.0000.0000.000
20A21LYS11.0041.02732.0939.5329.5320.0000.0000.0000.000
21A22SER0-0.055-0.06136.4390.1310.1310.0000.0000.0000.000
22A23THR00.0910.03640.279-0.109-0.1090.0000.0000.0000.000
23A24ASN00.0040.02642.874-0.011-0.0110.0000.0000.0000.000
24A25VAL00.0970.04144.123-0.104-0.1040.0000.0000.0000.000
25A26TYR00.0840.03144.379-0.173-0.1730.0000.0000.0000.000
26A27HIS0-0.027-0.00540.9430.1120.1120.0000.0000.0000.000
27A28LYS00.0600.03535.332-0.191-0.1910.0000.0000.0000.000
28A29LEU00.005-0.00440.918-0.164-0.1640.0000.0000.0000.000
29A30LEU00.0270.02643.436-0.043-0.0430.0000.0000.0000.000
30A31ILE00.003-0.01537.269-0.125-0.1250.0000.0000.0000.000
31A32LYS10.9130.96038.8677.7957.7950.0000.0000.0000.000
32A33LEU00.0450.03640.217-0.108-0.1080.0000.0000.0000.000
33A34TYR00.020-0.02740.500-0.108-0.1080.0000.0000.0000.000
34A35LYS10.8280.91133.8988.9778.9770.0000.0000.0000.000
35A36PHE0-0.0060.00237.173-0.228-0.2280.0000.0000.0000.000
36A37LEU00.011-0.00639.550-0.077-0.0770.0000.0000.0000.000
37A38VAL0-0.039-0.01034.964-0.017-0.0170.0000.0000.0000.000
38A39ARG10.9240.96234.6308.6248.6240.0000.0000.0000.000
39A40ARG10.9710.98836.0477.7357.7350.0000.0000.0000.000
40A41THR0-0.0100.00339.3330.2810.2810.0000.0000.0000.000
41A42ASP-1-0.878-0.91638.219-8.475-8.4750.0000.0000.0000.000
42A43SER0-0.043-0.02139.3820.0430.0430.0000.0000.0000.000
43A44LYS11.0180.98838.4247.9657.9650.0000.0000.0000.000
44A45PHE00.0400.03039.884-0.132-0.1320.0000.0000.0000.000
45A46ASN00.0750.01940.8960.0460.0460.0000.0000.0000.000
46A47GLN00.0200.01935.994-0.169-0.1690.0000.0000.0000.000
47A48ASN0-0.010-0.00937.213-0.092-0.0920.0000.0000.0000.000
48A49ILE00.0160.01739.204-0.058-0.0580.0000.0000.0000.000
49A50LEU00.0410.02335.396-0.030-0.0300.0000.0000.0000.000
50A51LYS10.9420.98334.4528.7858.7850.0000.0000.0000.000
51A52ARG10.7930.87536.4157.4447.4440.0000.0000.0000.000
52A53LEU00.0700.04839.5160.1350.1350.0000.0000.0000.000
53A54SER0-0.035-0.01735.4770.0660.0660.0000.0000.0000.000
54A55SER0-0.010-0.00436.212-0.366-0.3660.0000.0000.0000.000
55A56SER0-0.004-0.01635.6120.0130.0130.0000.0000.0000.000
56A57ARG11.0041.00237.8707.0837.0830.0000.0000.0000.000
57A58LEU00.0310.00440.4210.1520.1520.0000.0000.0000.000
58A59ASN0-0.070-0.03836.6580.1340.1340.0000.0000.0000.000
59A60LYS0-0.0260.00540.676-0.112-0.1120.0000.0000.0000.000
60A61PHE00.0220.01741.3140.0510.0510.0000.0000.0000.000
61A62PRO00.0370.03445.9780.0190.0190.0000.0000.0000.000
62A63LEU00.0330.02249.797-0.012-0.0120.0000.0000.0000.000
63A64SER00.0140.01251.7510.0190.0190.0000.0000.0000.000
64A65LEU00.0440.01455.448-0.041-0.0410.0000.0000.0000.000
65A66SER00.014-0.01958.192-0.031-0.0310.0000.0000.0000.000
66A67ARG10.8760.93752.3606.0026.0020.0000.0000.0000.000
67A68ILE0-0.008-0.01054.441-0.067-0.0670.0000.0000.0000.000
68A69VAL00.0250.00856.081-0.006-0.0060.0000.0000.0000.000
69A70LYS10.9630.98955.1755.7715.7710.0000.0000.0000.000
70A71ASN0-0.096-0.04251.9360.0180.0180.0000.0000.0000.000
71A72LEU0-0.015-0.01755.397-0.059-0.0590.0000.0000.0000.000
72A73ASN00.0740.04656.3270.1120.1120.0000.0000.0000.000
73A74GLU-1-0.873-0.94358.300-5.335-5.3350.0000.0000.0000.000
74A75THR00.0500.01756.708-0.001-0.0010.0000.0000.0000.000
75A76ASN0-0.087-0.04353.567-0.023-0.0230.0000.0000.0000.000
76A77LYS10.9470.97856.8004.9224.9220.0000.0000.0000.000
77A78GLU-1-0.953-0.97159.290-5.232-5.2320.0000.0000.0000.000
78A79GLN0-0.027-0.00154.082-0.078-0.0780.0000.0000.0000.000
79A80VAL0-0.027-0.01053.2300.0500.0500.0000.0000.0000.000
80A81ILE00.0240.02052.752-0.162-0.1620.0000.0000.0000.000
81A82VAL0-0.028-0.01547.6690.0130.0130.0000.0000.0000.000
82A83SER00.0340.01848.545-0.144-0.1440.0000.0000.0000.000
83A84THR0-0.033-0.03642.468-0.018-0.0180.0000.0000.0000.000
84A85SER0-0.009-0.03344.707-0.152-0.1520.0000.0000.0000.000
85A86THR0-0.018-0.01147.2190.1040.1040.0000.0000.0000.000
86A87VAL0-0.0030.00650.647-0.041-0.0410.0000.0000.0000.000
87A88THR0-0.033-0.03353.4260.0800.0800.0000.0000.0000.000
88A89ASN00.0740.02456.0770.0060.0060.0000.0000.0000.000
89A90ASP-1-0.789-0.84558.937-5.414-5.4140.0000.0000.0000.000
90A91GLU-1-0.905-0.96860.525-5.119-5.1190.0000.0000.0000.000
91A92ARG10.9290.95958.6215.3905.3900.0000.0000.0000.000
92A93LEU0-0.036-0.00161.2190.0090.0090.0000.0000.0000.000
93A94LEU00.0600.04964.8420.0160.0160.0000.0000.0000.000
94A95THR00.0370.01567.4470.0180.0180.0000.0000.0000.000
95A96VAL0-0.052-0.03662.978-0.088-0.0880.0000.0000.0000.000
96A97PRO00.0160.00862.7520.0600.0600.0000.0000.0000.000
97A98LYS11.0311.03064.0164.8844.8840.0000.0000.0000.000
98A99LEU00.010-0.01258.835-0.070-0.0700.0000.0000.0000.000
99A100THR00.0010.01157.0000.0610.0610.0000.0000.0000.000
100A101VAL00.0120.01254.284-0.097-0.0970.0000.0000.0000.000
101A102CYS0-0.0190.02250.3000.0380.0380.0000.0000.0000.000
102A103ALA0-0.026-0.00850.181-0.092-0.0920.0000.0000.0000.000
103A104LEU0-0.030-0.00744.521-0.012-0.0120.0000.0000.0000.000
104A105LYS10.9360.97249.1706.1176.1170.0000.0000.0000.000
105A106PHE00.0510.02452.277-0.023-0.0230.0000.0000.0000.000
106A107THR0-0.026-0.02155.5690.0430.0430.0000.0000.0000.000
107A108GLU-1-0.850-0.93057.511-5.209-5.2090.0000.0000.0000.000
108A109THR00.0190.00760.9520.0540.0540.0000.0000.0000.000
109A110ALA0-0.005-0.00558.4020.0550.0550.0000.0000.0000.000
110A111ARG10.9720.98257.4035.5075.5070.0000.0000.0000.000
111A112LYS11.0231.01161.0254.7124.7120.0000.0000.0000.000
112A113ARG10.8130.88963.3424.9924.9920.0000.0000.0000.000
113A114ILE00.005-0.01158.9150.0330.0330.0000.0000.0000.000
114A115LEU0-0.041-0.01462.4220.0040.0040.0000.0000.0000.000
115A116ALA00.0130.00765.0020.0530.0530.0000.0000.0000.000
116A117ALA0-0.0170.00865.4830.0670.0670.0000.0000.0000.000
117A118GLY00.0190.01667.4730.0080.0080.0000.0000.0000.000
118A119GLY0-0.026-0.01863.062-0.034-0.0340.0000.0000.0000.000
119A120LYS10.9140.94860.7755.0675.0670.0000.0000.0000.000
120A121CYS0-0.047-0.00657.708-0.074-0.0740.0000.0000.0000.000
121A122LEU00.018-0.00253.9720.0350.0350.0000.0000.0000.000
122A123THR00.010-0.02551.466-0.099-0.0990.0000.0000.0000.000
123A124PHE00.057-0.01445.972-0.014-0.0140.0000.0000.0000.000
124A125ASP-1-0.827-0.88948.593-6.291-6.2910.0000.0000.0000.000
125A126GLN00.0680.02650.0140.0330.0330.0000.0000.0000.000
126A127LEU0-0.023-0.01848.7490.0480.0480.0000.0000.0000.000
127A128ALA0-0.042-0.00947.435-0.012-0.0120.0000.0000.0000.000
128A129LEU00.0100.00048.999-0.005-0.0050.0000.0000.0000.000
129A130LYS10.9350.97652.4175.6585.6580.0000.0000.0000.000
130A131ALA00.0180.00651.0450.0610.0610.0000.0000.0000.000
131A132PRO00.0530.03846.637-0.135-0.1350.0000.0000.0000.000
132A133THR00.0110.00645.553-0.149-0.1490.0000.0000.0000.000
133A134GLY0-0.008-0.01945.875-0.134-0.1340.0000.0000.0000.000
134A135THR00.022-0.00147.784-0.010-0.0100.0000.0000.0000.000
135A136ASN00.0330.02350.8320.0030.0030.0000.0000.0000.000
136A137CYS0-0.046-0.00349.3780.0970.0970.0000.0000.0000.000
137A138PHE00.0520.02350.053-0.113-0.1130.0000.0000.0000.000
138A139LEU0-0.077-0.03443.172-0.002-0.0020.0000.0000.0000.000
139A140LEU00.0060.01946.843-0.122-0.1220.0000.0000.0000.000
140A141ARG10.8770.93039.4467.6387.6380.0000.0000.0000.000
141A142ALA00.0350.03246.2250.0870.0870.0000.0000.0000.000
142A143PRO0-0.011-0.00546.028-0.167-0.1670.0000.0000.0000.000
143A144LYS10.9010.95239.1337.9037.9030.0000.0000.0000.000
144A145SER00.0230.01645.5370.0030.0030.0000.0000.0000.000
145A146ARG10.9850.97240.9157.3557.3550.0000.0000.0000.000
146A147GLU-1-0.753-0.84846.646-6.603-6.6030.0000.0000.0000.000
147A148ALA00.0100.00042.253-0.019-0.0190.0000.0000.0000.000
148A149TYR00.007-0.00339.974-0.041-0.0410.0000.0000.0000.000
149A150ARG10.9200.96142.9506.1896.1890.0000.0000.0000.000
150A151HIS10.8180.90243.2426.8626.8620.0000.0000.0000.000
151A152TRP0-0.045-0.01738.677-0.171-0.1710.0000.0000.0000.000
152A153GLY00.0210.01238.5340.1560.1560.0000.0000.0000.000
153A154LYS10.9150.95738.1797.1977.1970.0000.0000.0000.000
154A155ALA00.0250.02939.3250.0820.0820.0000.0000.0000.000
155A156PRO0-0.002-0.01541.1230.0610.0610.0000.0000.0000.000
156A157GLY00.0650.03644.9640.0100.0100.0000.0000.0000.000
157A158GLN00.0200.02138.337-0.023-0.0230.0000.0000.0000.000
158A159ARG11.0301.00943.9066.6856.6850.0000.0000.0000.000
159A160GLY00.0470.02044.319-0.145-0.1450.0000.0000.0000.000
160A161SER0-0.067-0.02444.205-0.103-0.1030.0000.0000.0000.000
161A162HIS00.0170.00545.5190.2280.2280.0000.0000.0000.000
162A163SER0-0.052-0.03043.0830.1270.1270.0000.0000.0000.000
163A164ALA0-0.012-0.01145.9720.0800.0800.0000.0000.0000.000
164A165PRO00.0850.05146.404-0.188-0.1880.0000.0000.0000.000
165A166TYR0-0.062-0.05042.343-0.024-0.0240.0000.0000.0000.000
166A167VAL00.0380.03847.6230.0160.0160.0000.0000.0000.000
167A168ARG10.9640.97951.3375.6475.6470.0000.0000.0000.000
168A169SER0-0.008-0.01753.3800.0950.0950.0000.0000.0000.000
169A170GLU-1-0.884-0.92256.564-5.395-5.3950.0000.0000.0000.000
170A171GLY00.0670.01757.9260.1000.1000.0000.0000.0000.000
171A172ARG10.9640.96759.2684.7044.7040.0000.0000.0000.000
172A173LYS10.9600.98659.9484.9524.9520.0000.0000.0000.000
173A174PHE0-0.0160.00155.462-0.040-0.0400.0000.0000.0000.000
174A175GLU-1-0.900-0.96950.033-6.269-6.2690.0000.0000.0000.000
175A176ARG10.8690.93053.9375.3905.3900.0000.0000.0000.000
176A177ALA00.0030.01856.7410.0800.0800.0000.0000.0000.000
177A178HIS0-0.007-0.01055.799-0.110-0.1100.0000.0000.0000.000
178A179GLY00.003-0.00252.6060.0100.0100.0000.0000.0000.000
179A180LEU0-0.040-0.03950.4570.0660.0660.0000.0000.0000.000
180A181LYS00.0500.06351.586-0.009-0.0090.0000.0000.0000.000