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: QM2RY

Calculation Name: 6JEX-A-Xray547

Preferred Name:

Target Type:

Ligand Name: l-[(n-hydroxyamino)carbonyl]phenylalanine | zinc ion

Ligand 3-letter code: LHY | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6JEX

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2025-10-04

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 172
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1809252.186782
FMO2-HF: Nuclear repulsion 1740357.206498
FMO2-HF: Total energy -68894.980284
FMO2-MP2: Total energy -69094.650012


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.
-165.585-162.8020.124-1.718-1.188-0.011
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 : 0.804 / q_NPA : 0.889
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].
3A4LEU00.0220.0163.046-18.184-15.4010.124-1.718-1.188-0.011
4A5PRO0-0.048-0.0205.7961.8661.8660.0000.0000.0000.000
5A6ILE00.0460.0207.6682.3562.3560.0000.0000.0000.000
6A7LEU0-0.065-0.01811.0150.5410.5410.0000.0000.0000.000
7A8SER00.0240.01014.0810.4640.4640.0000.0000.0000.000
8A9PHE00.0120.01716.4770.7810.7810.0000.0000.0000.000
9A10PRO0-0.089-0.06220.233-0.037-0.0370.0000.0000.0000.000
10A11ASP-1-0.740-0.86216.914-17.538-17.5380.0000.0000.0000.000
11A12PRO0-0.001-0.00819.7990.2120.2120.0000.0000.0000.000
12A13ARG10.7900.86614.04820.57220.5720.0000.0000.0000.000
13A14LEU0-0.0030.00517.2470.0310.0310.0000.0000.0000.000
14A15ARG10.6710.79920.40312.91512.9150.0000.0000.0000.000
15A16THR0-0.060-0.02920.8330.7880.7880.0000.0000.0000.000
16A17ILE0-0.025-0.00323.133-0.163-0.1630.0000.0000.0000.000
17A18ALA00.0020.00921.881-0.107-0.1070.0000.0000.0000.000
18A19LYS10.8170.90622.87613.63513.6350.0000.0000.0000.000
19A20PRO00.000-0.01323.371-0.567-0.5670.0000.0000.0000.000
20A21VAL0-0.0040.00220.963-0.269-0.2690.0000.0000.0000.000
21A22GLU-1-0.858-0.91623.636-12.011-12.0110.0000.0000.0000.000
22A23GLU-1-0.912-0.96024.664-10.835-10.8350.0000.0000.0000.000
23A24VAL0-0.050-0.01421.856-0.658-0.6580.0000.0000.0000.000
24A25THR00.019-0.01320.4620.0920.0920.0000.0000.0000.000
25A26ASP-1-0.825-0.92517.937-16.032-16.0320.0000.0000.0000.000
26A27GLU-1-0.871-0.91215.153-17.768-17.7680.0000.0000.0000.000
27A28ILE0-0.074-0.03614.856-1.414-1.4140.0000.0000.0000.000
28A29ARG10.8510.92216.12213.84613.8460.0000.0000.0000.000
29A30GLN0-0.058-0.0278.9711.5051.5050.0000.0000.0000.000
30A31LEU0-0.024-0.00611.498-1.848-1.8480.0000.0000.0000.000
31A32ALA00.0450.01012.373-1.139-1.1390.0000.0000.0000.000
32A33ALA00.0260.02311.619-0.136-0.1360.0000.0000.0000.000
33A34ASP-1-0.855-0.9247.401-38.867-38.8670.0000.0000.0000.000
34A35MET0-0.081-0.0188.811-2.447-2.4470.0000.0000.0000.000
35A36PHE00.0320.01911.5060.2400.2400.0000.0000.0000.000
36A37GLU-1-0.910-0.9567.058-29.993-29.9930.0000.0000.0000.000
37A38THR0-0.068-0.0617.663-3.045-3.0450.0000.0000.0000.000
38A39MET0-0.052-0.0028.8471.2611.2610.0000.0000.0000.000
39A40TYR0-0.046-0.07611.1840.6830.6830.0000.0000.0000.000
40A41ALA0-0.037-0.0167.8121.0381.0380.0000.0000.0000.000
41A42ALA0-0.070-0.0039.7570.5920.5920.0000.0000.0000.000
42A43PRO0-0.031-0.00811.5060.7430.7430.0000.0000.0000.000
43A44GLY0-0.034-0.04313.9120.9410.9410.0000.0000.0000.000
44A45ILE00.0370.02216.500-0.360-0.3600.0000.0000.0000.000
45A46GLY00.0260.00118.2390.6840.6840.0000.0000.0000.000
46A47LEU0-0.038-0.01612.179-1.089-1.0890.0000.0000.0000.000
47A48ALA00.0690.04416.7180.0560.0560.0000.0000.0000.000
48A49ALA00.014-0.00515.150-1.000-1.0000.0000.0000.0000.000
49A50SER00.009-0.01915.173-1.101-1.1010.0000.0000.0000.000
50A51GLN00.024-0.00814.919-0.120-0.1200.0000.0000.0000.000
51A52VAL0-0.033-0.01110.277-1.291-1.2910.0000.0000.0000.000
52A53ASP-1-0.819-0.89411.737-21.035-21.0350.0000.0000.0000.000
53A54ARG10.9220.97912.27022.85322.8530.0000.0000.0000.000
54A55HIS00.020-0.00715.2440.9410.9410.0000.0000.0000.000
55A56ILE0-0.020-0.00918.1140.9410.9410.0000.0000.0000.000
56A57GLN0-0.029-0.02220.027-0.208-0.2080.0000.0000.0000.000
57A58LEU00.0260.00516.2850.4700.4700.0000.0000.0000.000
58A59ILE0-0.010-0.00518.857-0.670-0.6700.0000.0000.0000.000
59A60VAL0-0.0140.00414.6950.5070.5070.0000.0000.0000.000
60A61MET0-0.003-0.02018.1640.2600.2600.0000.0000.0000.000
61A62ASP-1-0.739-0.81218.267-15.722-15.7220.0000.0000.0000.000
62A63LEU0-0.025-0.02420.139-0.109-0.1090.0000.0000.0000.000
63A64SER0-0.049-0.02620.9440.4840.4840.0000.0000.0000.000
64A65GLU-1-0.980-0.99521.457-12.147-12.1470.0000.0000.0000.000
65A66SER0-0.056-0.03420.697-0.235-0.2350.0000.0000.0000.000
66A67LYS10.8130.93111.30022.74322.7430.0000.0000.0000.000
67A68ASP-1-0.874-0.95617.679-14.004-14.0040.0000.0000.0000.000
68A69GLU-1-0.922-0.94920.453-11.669-11.6690.0000.0000.0000.000
69A70PRO0-0.056-0.01717.825-0.204-0.2040.0000.0000.0000.000
70A71MET0-0.016-0.01519.7810.6990.6990.0000.0000.0000.000
71A72VAL0-0.019-0.02718.983-0.880-0.8800.0000.0000.0000.000
72A73PHE0-0.004-0.00921.5800.8260.8260.0000.0000.0000.000
73A74ILE00.001-0.00220.774-0.636-0.6360.0000.0000.0000.000
74A75ASN0-0.022-0.01723.9810.2220.2220.0000.0000.0000.000
75A76PRO00.0050.01124.9960.4540.4540.0000.0000.0000.000
76A77LYS10.9290.96327.9449.8019.8010.0000.0000.0000.000
77A78VAL00.0240.01030.502-0.087-0.0870.0000.0000.0000.000
78A79THR0-0.010-0.01232.4430.1990.1990.0000.0000.0000.000
79A80PRO0-0.0080.00936.140-0.031-0.0310.0000.0000.0000.000
80A81LEU0-0.033-0.01637.7160.2100.2100.0000.0000.0000.000
81A82THR0-0.022-0.01839.8450.2810.2810.0000.0000.0000.000
82A83GLU-1-0.951-0.97140.688-7.324-7.3240.0000.0000.0000.000
83A84GLU-1-0.972-0.97441.193-7.722-7.7220.0000.0000.0000.000
84A85THR0-0.046-0.03337.516-0.136-0.1360.0000.0000.0000.000
85A86GLN0-0.026-0.02332.9080.0990.0990.0000.0000.0000.000
86A87PRO00.0070.01134.886-0.256-0.2560.0000.0000.0000.000
87A88TYR0-0.012-0.01326.661-0.159-0.1590.0000.0000.0000.000
88A89GLU-1-0.797-0.87827.892-10.473-10.4730.0000.0000.0000.000
89A90GLU-1-0.725-0.82825.838-12.252-12.2520.0000.0000.0000.000
90A91GLY00.0410.00422.8370.2150.2150.0000.0000.0000.000
91A92CYS-1-0.935-0.84419.555-16.483-16.4830.0000.0000.0000.000
92A93LEU00.0450.02913.582-0.168-0.1680.0000.0000.0000.000
93A94SER00.034-0.01915.278-0.966-0.9660.0000.0000.0000.000
94A95VAL0-0.101-0.05317.0670.7050.7050.0000.0000.0000.000
95A96PRO00.0490.03216.0690.5740.5740.0000.0000.0000.000
96A97GLN00.001-0.01517.7561.1151.1150.0000.0000.0000.000
97A98ILE0-0.089-0.03420.8980.9560.9560.0000.0000.0000.000
98A99TYR00.0430.01921.301-0.521-0.5210.0000.0000.0000.000
99A100ASP-1-0.900-0.94826.272-9.635-9.6350.0000.0000.0000.000
100A101LYS10.7720.86429.5269.8379.8370.0000.0000.0000.000
101A102VAL0-0.045-0.02029.0560.1050.1050.0000.0000.0000.000
102A103ASP-1-0.810-0.89032.162-8.745-8.7450.0000.0000.0000.000
103A104ARG10.7810.84927.34311.17211.1720.0000.0000.0000.000
104A105PRO0-0.003-0.00234.4440.1320.1320.0000.0000.0000.000
105A106SER00.0190.00035.035-0.270-0.2700.0000.0000.0000.000
106A107ARG10.8400.91535.8207.9237.9230.0000.0000.0000.000
107A108VAL0-0.026-0.01532.1420.1520.1520.0000.0000.0000.000
108A109LYS10.8290.89635.2348.6858.6850.0000.0000.0000.000
109A110ILE0-0.016-0.02028.822-0.171-0.1710.0000.0000.0000.000
110A111GLU-1-0.848-0.91031.940-8.976-8.9760.0000.0000.0000.000
111A112ALA0-0.024-0.00926.863-0.318-0.3180.0000.0000.0000.000
112A113ILE0-0.0070.00925.7550.4070.4070.0000.0000.0000.000
113A114ASN00.0770.03324.481-0.533-0.5330.0000.0000.0000.000
114A115LEU00.031-0.01018.6210.0100.0100.0000.0000.0000.000
115A116GLU-1-0.899-0.94022.457-13.038-13.0380.0000.0000.0000.000
116A117GLY0-0.044-0.01725.5840.4210.4210.0000.0000.0000.000
117A118GLN0-0.054-0.02327.4110.6310.6310.0000.0000.0000.000
118A119ALA00.0130.00029.018-0.338-0.3380.0000.0000.0000.000
119A120PHE0-0.038-0.02026.5730.2650.2650.0000.0000.0000.000
120A121GLU-1-0.849-0.92532.122-8.764-8.7640.0000.0000.0000.000
121A122ILE0-0.020-0.00229.7720.0930.0930.0000.0000.0000.000
122A123GLU-1-0.863-0.92434.210-8.248-8.2480.0000.0000.0000.000
123A124ALA0-0.004-0.00531.618-0.156-0.1560.0000.0000.0000.000
124A125ASP-1-0.854-0.92933.644-9.014-9.0140.0000.0000.0000.000
125A126GLY00.0330.02132.164-0.342-0.3420.0000.0000.0000.000
126A127LEU00.0160.00025.141-0.024-0.0240.0000.0000.0000.000
127A128LEU00.0480.02926.611-0.393-0.3930.0000.0000.0000.000
128A129ALA00.0220.02528.563-0.245-0.2450.0000.0000.0000.000
129A130VAL00.0040.01027.359-0.109-0.1090.0000.0000.0000.000
130A131CYS0-0.031-0.00522.945-0.413-0.4130.0000.0000.0000.000
131A132ILE00.0450.01524.858-0.422-0.4220.0000.0000.0000.000
132A133GLN0-0.046-0.04526.5900.0850.0850.0000.0000.0000.000
133A134HIS10.7650.82820.95514.16514.1650.0000.0000.0000.000
134A135GLU-1-0.817-0.93919.962-16.308-16.3080.0000.0000.0000.000
135A136MET00.0050.00422.971-0.269-0.2690.0000.0000.0000.000
136A137ASP-1-0.780-0.83625.939-11.037-11.0370.0000.0000.0000.000
137A138HIS00.027-0.01119.7770.2160.2160.0000.0000.0000.000
138A139LEU0-0.0400.00521.078-0.268-0.2680.0000.0000.0000.000
139A140ASN0-0.069-0.04423.4960.5430.5430.0000.0000.0000.000
140A141GLY00.0330.04923.7670.4420.4420.0000.0000.0000.000
141A142LYS10.8090.88024.82711.01211.0120.0000.0000.0000.000
142A143LEU00.0500.01221.362-0.542-0.5420.0000.0000.0000.000
143A144PHE00.0540.02822.6860.5210.5210.0000.0000.0000.000
144A145VAL00.002-0.00824.9330.5180.5180.0000.0000.0000.000
145A146ASP-1-0.803-0.86327.444-11.393-11.3930.0000.0000.0000.000
146A147TYR0-0.034-0.02929.1160.5580.5580.0000.0000.0000.000
147A148LEU0-0.0080.02528.7650.3380.3380.0000.0000.0000.000
148A149SER00.0300.01032.6120.0240.0240.0000.0000.0000.000
149A150PRO00.0430.00333.191-0.287-0.2870.0000.0000.0000.000
150A151LEU00.0360.01832.571-0.301-0.3010.0000.0000.0000.000
151A152LYS10.8970.95831.0349.3499.3490.0000.0000.0000.000
152A153ARG10.9230.95727.8529.9259.9250.0000.0000.0000.000
153A154GLN0-0.030-0.01727.929-0.280-0.2800.0000.0000.0000.000
154A155ARG10.9720.97428.1539.8839.8830.0000.0000.0000.000
155A156ALA00.0190.01125.101-0.302-0.3020.0000.0000.0000.000
156A157ARG10.9490.98223.78710.86610.8660.0000.0000.0000.000
157A158GLU-1-0.892-0.93223.602-11.317-11.3170.0000.0000.0000.000
158A159LYS10.8930.95422.69213.10613.1060.0000.0000.0000.000
159A160VAL00.0170.01718.488-0.441-0.4410.0000.0000.0000.000
160A161GLU-1-0.785-0.87419.173-16.293-16.2930.0000.0000.0000.000
161A162LYS10.8220.89220.02511.51911.5190.0000.0000.0000.000
162A163ILE0-0.018-0.00716.459-0.251-0.2510.0000.0000.0000.000
163A164VAL00.0230.01514.777-0.953-0.9530.0000.0000.0000.000
164A165ARG10.8880.91215.48713.53413.5340.0000.0000.0000.000
165A166GLN0-0.040-0.00417.8690.6820.6820.0000.0000.0000.000
166A167ARG10.9980.99612.20821.91621.9160.0000.0000.0000.000
167A168GLU-1-0.866-0.91712.151-27.109-27.1090.0000.0000.0000.000
168A169ARG10.8740.92914.09515.16315.1630.0000.0000.0000.000
169A170GLU-1-0.918-0.96712.439-19.703-19.7030.0000.0000.0000.000
170A171LYS10.7640.8727.76027.51627.5160.0000.0000.0000.000
171A172VAL0-0.095-0.04411.969-0.441-0.4410.0000.0000.0000.000
172A173ALA-1-0.942-0.94414.432-18.931-18.9310.0000.0000.0000.000