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: 5519Z

Calculation Name: 4OCM-B-Xray547

Preferred Name:

Target Type:

Ligand Name: zinc ion | potassium ion

Ligand 3-letter code: ZN | K

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4OCM

Chain ID: B

ChEMBL ID:

UniProt ID: P43588

Base Structure: X-ray

Registration Date: 2025-10-05

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 179
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1846736.346316
FMO2-HF: Nuclear repulsion 1775128.06481
FMO2-HF: Total energy -71608.281506
FMO2-MP2: Total energy -71811.128463


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:23:THR)


Summations of interaction energy for fragment #1(A:23:THR)
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.
-126.489-117.7643.3-5.165-6.859-0.063
Interaction energy analysis for fragmet #1(A:23:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.817 / q_NPA : 0.903
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].
3A25GLU00.026-0.0152.561-8.230-5.0480.873-1.741-2.314-0.019
4A26THR0-0.061-0.0314.0384.2024.297-0.001-0.008-0.0860.000
39A61TYR0-0.074-0.0532.756-19.771-14.4292.429-3.411-4.360-0.044
40A62THR0-0.013-0.0044.919-1.382-1.276-0.001-0.005-0.0990.000
5A27VAL00.0300.0226.5050.9110.9110.0000.0000.0000.000
6A28TYR00.002-0.0036.195-0.010-0.0100.0000.0000.0000.000
7A29ILE0-0.020-0.00911.5281.2771.2770.0000.0000.0000.000
8A30SER00.002-0.01915.2430.2300.2300.0000.0000.0000.000
9A31SER00.003-0.03418.0840.1670.1670.0000.0000.0000.000
10A32ILE0-0.026-0.01521.0840.4210.4210.0000.0000.0000.000
11A33ALA00.0280.03319.2680.4350.4350.0000.0000.0000.000
12A34LEU00.0320.01918.8940.3700.3700.0000.0000.0000.000
13A35LEU0-0.006-0.01321.0640.4520.4520.0000.0000.0000.000
14A36LYS10.8070.89624.55311.78611.7860.0000.0000.0000.000
15A37MET00.0160.02518.5950.3070.3070.0000.0000.0000.000
16A38LEU0-0.0010.00422.8060.3770.3770.0000.0000.0000.000
17A39LYS10.9290.96725.8499.6179.6170.0000.0000.0000.000
18A40HIS00.0130.01927.8160.0730.0730.0000.0000.0000.000
19A41GLY00.0600.02527.4920.2550.2550.0000.0000.0000.000
20A42ARG10.9030.93328.4559.2499.2490.0000.0000.0000.000
21A43ALA0-0.053-0.02530.9240.3130.3130.0000.0000.0000.000
22A44GLY00.0310.02232.2170.2580.2580.0000.0000.0000.000
23A45VAL0-0.0460.00332.0380.1190.1190.0000.0000.0000.000
24A46PRO0-0.026-0.02734.3160.2000.2000.0000.0000.0000.000
25A47MET00.000-0.00334.591-0.066-0.0660.0000.0000.0000.000
26A48GLU-1-0.905-0.95929.718-10.626-10.6260.0000.0000.0000.000
27A49VAL0-0.064-0.03228.6360.2750.2750.0000.0000.0000.000
28A50MET00.0070.00726.030-0.415-0.4150.0000.0000.0000.000
29A51GLY00.0230.00025.5040.4950.4950.0000.0000.0000.000
30A52LEU00.0150.02423.647-0.519-0.5190.0000.0000.0000.000
31A53MET0-0.057-0.02816.5910.1470.1470.0000.0000.0000.000
32A54LEU0-0.004-0.00120.603-0.099-0.0990.0000.0000.0000.000
33A55GLY0-0.031-0.04017.522-0.258-0.2580.0000.0000.0000.000
34A56GLU-1-0.882-0.92814.058-17.584-17.5840.0000.0000.0000.000
35A57PHE00.0230.01012.546-0.584-0.5840.0000.0000.0000.000
36A58VAL00.003-0.0119.5170.9790.9790.0000.0000.0000.000
37A59ASP-1-0.875-0.9285.372-39.253-39.2530.0000.0000.0000.000
38A60ASP-1-0.872-0.9196.523-30.565-30.5650.0000.0000.0000.000
41A63VAL00.0410.0397.4312.7002.7000.0000.0000.0000.000
42A64ASN0-0.060-0.03210.828-1.263-1.2630.0000.0000.0000.000
43A65VAL00.0260.00013.2001.1551.1550.0000.0000.0000.000
44A66VAL00.011-0.00316.0880.3030.3030.0000.0000.0000.000
45A67ASP-1-0.774-0.85118.667-11.300-11.3000.0000.0000.0000.000
46A68VAL0-0.018-0.00221.239-0.422-0.4220.0000.0000.0000.000
47A69PHE0-0.005-0.00923.6420.4500.4500.0000.0000.0000.000
48A70ALA00.0070.01226.829-0.258-0.2580.0000.0000.0000.000
49A71MET00.0150.01828.8030.1680.1680.0000.0000.0000.000
50A72PRO0-0.023-0.00931.1090.1040.1040.0000.0000.0000.000
51A73GLN0-0.015-0.00931.221-0.218-0.2180.0000.0000.0000.000
52A74SER0-0.014-0.01334.8150.0560.0560.0000.0000.0000.000
53A75GLY00.0200.02635.6810.1860.1860.0000.0000.0000.000
54A76THR0-0.028-0.05134.872-0.169-0.1690.0000.0000.0000.000
55A77GLY0-0.017-0.00134.124-0.184-0.1840.0000.0000.0000.000
56A78VAL0-0.014-0.01227.190-0.137-0.1370.0000.0000.0000.000
57A79SER00.0210.00830.074-0.044-0.0440.0000.0000.0000.000
58A80VAL00.0410.00028.572-0.073-0.0730.0000.0000.0000.000
59A81GLU-1-0.886-0.91030.688-8.337-8.3370.0000.0000.0000.000
60A82ALA0-0.034-0.00631.1820.2130.2130.0000.0000.0000.000
61A83VAL0-0.040-0.02528.060-0.122-0.1220.0000.0000.0000.000
62A84ASP-1-0.823-0.91430.999-8.470-8.4700.0000.0000.0000.000
63A85ASP-1-0.849-0.93832.425-9.624-9.6240.0000.0000.0000.000
64A86VAL00.0160.00933.489-0.011-0.0110.0000.0000.0000.000
65A87PHE0-0.067-0.03431.9900.0800.0800.0000.0000.0000.000
66A88GLN0-0.023-0.01528.029-0.474-0.4740.0000.0000.0000.000
67A89ALA00.0010.00631.457-0.126-0.1260.0000.0000.0000.000
68A90LYS10.9540.97633.2597.8787.8780.0000.0000.0000.000
69A91MET0-0.030-0.01130.2720.0880.0880.0000.0000.0000.000
70A92MET0-0.003-0.00826.382-0.209-0.2090.0000.0000.0000.000
71A93ASP-1-0.909-0.94730.408-8.835-8.8350.0000.0000.0000.000
72A94MET0-0.018-0.01433.3220.0870.0870.0000.0000.0000.000
73A95LEU0-0.022-0.00827.512-0.023-0.0230.0000.0000.0000.000
74A96LYS10.8720.94929.17610.10710.1070.0000.0000.0000.000
75A97GLN0-0.045-0.03330.4010.0080.0080.0000.0000.0000.000
76A98THR0-0.093-0.04631.8710.1090.1090.0000.0000.0000.000
77A99GLY00.0010.00629.083-0.095-0.0950.0000.0000.0000.000
78A100ARG10.7480.86423.50911.68911.6890.0000.0000.0000.000
79A101ASP-1-0.820-0.91325.796-10.840-10.8400.0000.0000.0000.000
80A102GLN0-0.025-0.00620.475-0.238-0.2380.0000.0000.0000.000
81A103MET00.0290.02819.5650.3110.3110.0000.0000.0000.000
82A104VAL00.030-0.00120.704-0.422-0.4220.0000.0000.0000.000
83A105VAL0-0.0080.00915.956-0.137-0.1370.0000.0000.0000.000
84A106GLY00.0370.01316.949-0.970-0.9700.0000.0000.0000.000
85A107TRP0-0.084-0.02619.3291.0751.0750.0000.0000.0000.000
86A108TYR00.010-0.00520.163-0.682-0.6820.0000.0000.0000.000
87A109HIS10.8600.91721.96813.21913.2190.0000.0000.0000.000
88A110SER00.005-0.00123.817-0.427-0.4270.0000.0000.0000.000
89A111HIS10.9080.96224.52012.24612.2460.0000.0000.0000.000
90A112PRO0-0.063-0.02727.718-0.218-0.2180.0000.0000.0000.000
91A113GLY0-0.0100.00129.2790.2770.2770.0000.0000.0000.000
92A114PHE0-0.027-0.00427.9640.0470.0470.0000.0000.0000.000
93A115GLY00.0240.00624.546-0.216-0.2160.0000.0000.0000.000
94A116CYS0-0.075-0.01519.6260.2180.2180.0000.0000.0000.000
95A117TRP00.0070.00020.879-0.309-0.3090.0000.0000.0000.000
96A118LEU00.0220.01819.4470.4750.4750.0000.0000.0000.000
97A119SER00.0290.00923.0180.1500.1500.0000.0000.0000.000
98A120SER00.0370.00225.898-0.332-0.3320.0000.0000.0000.000
99A121VAL00.0370.02128.165-0.082-0.0820.0000.0000.0000.000
100A122ASP-1-0.778-0.87523.847-12.250-12.2500.0000.0000.0000.000
101A123VAL00.0330.01222.583-0.343-0.3430.0000.0000.0000.000
102A124ASN0-0.008-0.01724.316-0.479-0.4790.0000.0000.0000.000
103A125THR0-0.004-0.01225.4290.2200.2200.0000.0000.0000.000
104A126GLN00.015-0.00518.0590.4610.4610.0000.0000.0000.000
105A127LYS10.9590.98022.33812.11712.1170.0000.0000.0000.000
106A128SER0-0.044-0.00623.9380.0080.0080.0000.0000.0000.000
107A129PHE00.004-0.01421.5590.1180.1180.0000.0000.0000.000
108A130GLU-1-0.907-0.95518.166-16.814-16.8140.0000.0000.0000.000
109A131GLN0-0.053-0.02721.1130.1390.1390.0000.0000.0000.000
110A132LEU0-0.051-0.01023.8650.2110.2110.0000.0000.0000.000
111A133ASN0-0.011-0.02917.666-0.785-0.7850.0000.0000.0000.000
112A134SER00.0480.03316.293-0.009-0.0090.0000.0000.0000.000
113A135ARG00.035-0.00310.124-1.126-1.1260.0000.0000.0000.000
114A136ALA0-0.026-0.00314.789-0.596-0.5960.0000.0000.0000.000
115A137VAL0-0.0020.00213.075-0.265-0.2650.0000.0000.0000.000
116A138ALA00.0180.01616.2001.1411.1410.0000.0000.0000.000
117A139VAL0-0.003-0.01816.233-0.597-0.5970.0000.0000.0000.000
118A140VAL0-0.065-0.02218.5370.9480.9480.0000.0000.0000.000
119A141VAL00.0400.00120.076-0.480-0.4800.0000.0000.0000.000
120A142ASP-1-0.693-0.83622.688-10.583-10.5830.0000.0000.0000.000
121A143PRO0-0.019-0.00625.466-0.041-0.0410.0000.0000.0000.000
122A144ILE0-0.021-0.00427.6190.2980.2980.0000.0000.0000.000
123A145GLN0-0.080-0.05725.640-0.088-0.0880.0000.0000.0000.000
124A146SER00.005-0.01524.617-0.250-0.2500.0000.0000.0000.000
125A147VAL0-0.065-0.02426.198-0.013-0.0130.0000.0000.0000.000
126A148LYS10.9080.95527.60410.43210.4320.0000.0000.0000.000
127A149GLY00.0220.02427.5390.0500.0500.0000.0000.0000.000
128A150LYS10.9190.96119.60214.32014.3200.0000.0000.0000.000
129A151VAL00.0250.00820.4770.2840.2840.0000.0000.0000.000
130A152VAL0-0.051-0.02520.676-0.590-0.5900.0000.0000.0000.000
131A153ILE00.008-0.01916.9580.6170.6170.0000.0000.0000.000
132A154ASP-1-0.848-0.92414.610-20.240-20.2400.0000.0000.0000.000
133A155ALA00.001-0.01112.8391.0741.0740.0000.0000.0000.000
134A156PHE0-0.011-0.01013.678-1.023-1.0230.0000.0000.0000.000
135A157ARG00.0410.08811.153-0.644-0.6440.0000.0000.0000.000
136A158LEU0-0.039-0.03315.6000.5330.5330.0000.0000.0000.000
137A159ILE0-0.050-0.02314.130-1.040-1.0400.0000.0000.0000.000
138A160ASP-1-0.920-0.92416.897-13.977-13.9770.0000.0000.0000.000
139A161THR-1-1.020-1.02617.020-18.848-18.8480.0000.0000.0000.000
140A178GLY00.0440.00714.6600.1110.1110.0000.0000.0000.000
141A179LEU0-0.026-0.00211.1170.3330.3330.0000.0000.0000.000
142A180LEU00.0510.02310.905-1.810-1.8100.0000.0000.0000.000
143A181ASN0-0.009-0.0058.8541.0551.0550.0000.0000.0000.000
144A182LYS11.0000.99410.74315.68815.6880.0000.0000.0000.000
145A183ALA00.0310.01911.8960.6310.6310.0000.0000.0000.000
146A184ASN00.0480.0156.4610.9430.9430.0000.0000.0000.000
147A185ILE00.0450.03110.5860.4220.4220.0000.0000.0000.000
148A186GLN0-0.011-0.01913.4570.7040.7040.0000.0000.0000.000
149A187ALA00.0000.00212.3091.0311.0310.0000.0000.0000.000
150A188LEU00.0560.03210.7050.7050.7050.0000.0000.0000.000
151A189ILE0-0.0030.00314.3601.0591.0590.0000.0000.0000.000
152A190HIS0-0.042-0.03717.6450.8680.8680.0000.0000.0000.000
153A191GLY00.0160.01716.7100.7120.7120.0000.0000.0000.000
154A192LEU00.0410.00917.1070.8080.8080.0000.0000.0000.000
155A193ASN0-0.082-0.03319.3631.0571.0570.0000.0000.0000.000
156A194ARG10.8450.93318.44616.96716.9670.0000.0000.0000.000
157A195HIS00.0090.00520.7650.0530.0530.0000.0000.0000.000
158A196TYR00.0110.01717.972-0.229-0.2290.0000.0000.0000.000
159A197TYR-1-0.936-0.97610.452-25.858-25.8580.0000.0000.0000.000
160A198SER0-0.024-0.01313.3050.7500.7500.0000.0000.0000.000
161A199LEU0-0.0100.0029.226-2.267-2.2670.0000.0000.0000.000
162A200ASN0-0.052-0.0355.8442.7032.7030.0000.0000.0000.000
163A201ILE00.0030.0098.7890.2720.2720.0000.0000.0000.000
164A202ASP-1-0.891-0.9379.129-24.624-24.6240.0000.0000.0000.000
165A203TYR0-0.051-0.03311.1370.9700.9700.0000.0000.0000.000
166A204HIS00.0300.02313.663-0.530-0.5300.0000.0000.0000.000
167A205LYS10.9310.94815.09115.53515.5350.0000.0000.0000.000
168A206THR00.003-0.01518.079-0.011-0.0110.0000.0000.0000.000
169A207ALA00.0230.01020.0880.3260.3260.0000.0000.0000.000
170A208LYS10.9170.95522.29311.43111.4310.0000.0000.0000.000
171A209GLU-1-0.691-0.81421.068-13.163-13.1630.0000.0000.0000.000
172A210THR0-0.031-0.01721.3110.0260.0260.0000.0000.0000.000
173A211LYS10.9740.98323.68211.07911.0790.0000.0000.0000.000
174A212MET0-0.0030.01127.0990.3880.3880.0000.0000.0000.000
175A213LEU00.022-0.00123.0140.2290.2290.0000.0000.0000.000
176A214MET0-0.054-0.03224.3810.1780.1780.0000.0000.0000.000
177A215ASN0-0.060-0.02928.6890.4850.4850.0000.0000.0000.000
178A216LEU0-0.052-0.01728.8590.2480.2480.0000.0000.0000.000
179A217HIS00.0130.02528.9240.6610.6610.0000.0000.0000.000