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

tag_button

FMODB ID: 8Q38Y

Calculation Name: 5HVQ-D-Xray547

Preferred Name:

Target Type:

Ligand Name: zinc ion

Ligand 3-letter code: ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5HVQ

Chain ID: D

ChEMBL ID:

UniProt ID: Q8WV22

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 203
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2110550.135232
FMO2-HF: Nuclear repulsion 2027619.318537
FMO2-HF: Total energy -82930.816696
FMO2-MP2: Total energy -83175.467568


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:78:GLY)


Summations of interaction energy for fragment #1(A:78: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.
57.23758.3130.001-0.345-0.732-0.001
Interaction energy analysis for fragmet #1(A:78:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.884 / q_NPA : 0.932
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].
3A80ARG10.8690.9303.45660.00061.0760.001-0.345-0.732-0.001
4A81SER00.0250.0135.8833.4453.4450.0000.0000.0000.000
5A82GLN00.020-0.0079.680-0.857-0.8570.0000.0000.0000.000
6A83LYS11.0411.01712.64118.87218.8720.0000.0000.0000.000
7A84GLN00.0050.0066.252-3.121-3.1210.0000.0000.0000.000
8A85LEU00.0050.0018.2360.3970.3970.0000.0000.0000.000
9A86GLU-1-0.853-0.91911.273-17.779-17.7790.0000.0000.0000.000
10A87LEU0-0.011-0.01012.6671.2511.2510.0000.0000.0000.000
11A88LYS10.8360.9169.62227.19327.1930.0000.0000.0000.000
12A89VAL0-0.003-0.00512.7890.8770.8770.0000.0000.0000.000
13A90SER0-0.0170.00115.9551.4721.4720.0000.0000.0000.000
14A91GLU-1-0.833-0.91713.398-21.857-21.8570.0000.0000.0000.000
15A92LEU0-0.045-0.00916.3800.8930.8930.0000.0000.0000.000
16A93VAL00.0330.00718.1520.7920.7920.0000.0000.0000.000
17A94GLN00.0090.01820.7341.0041.0040.0000.0000.0000.000
18A95PHE0-0.031-0.02019.8790.6950.6950.0000.0000.0000.000
19A96LEU0-0.025-0.02721.5410.5660.5660.0000.0000.0000.000
20A97LEU00.0360.02523.9870.5420.5420.0000.0000.0000.000
21A98ILE0-0.016-0.00925.2140.4910.4910.0000.0000.0000.000
22A99LYS10.8880.96224.12312.82212.8220.0000.0000.0000.000
23A100ASP-1-0.762-0.88827.535-9.787-9.7870.0000.0000.0000.000
24A101GLN00.0240.02929.9240.4750.4750.0000.0000.0000.000
25A102LYS10.8930.94131.5929.1829.1820.0000.0000.0000.000
26A103LYS10.8620.91132.5899.4509.4500.0000.0000.0000.000
27A104ILE0-0.072-0.01128.0440.0190.0190.0000.0000.0000.000
28A105PRO00.0720.05429.7570.1590.1590.0000.0000.0000.000
29A106ILE0-0.009-0.02023.216-0.296-0.2960.0000.0000.0000.000
30A107LYS10.9730.99924.57111.85511.8550.0000.0000.0000.000
31A108ARG10.9430.97018.18115.14315.1430.0000.0000.0000.000
32A109ALA0-0.0130.00119.482-0.894-0.8940.0000.0000.0000.000
33A110ASP-1-0.856-0.94219.582-13.898-13.8980.0000.0000.0000.000
34A111ILE00.0240.01517.005-0.605-0.6050.0000.0000.0000.000
35A112LEU0-0.018-0.02814.385-1.177-1.1770.0000.0000.0000.000
36A113LYS10.9090.96414.72413.23913.2390.0000.0000.0000.000
37A114HIS0-0.037-0.02116.264-0.806-0.8060.0000.0000.0000.000
38A115VAL00.0370.03815.0650.0930.0930.0000.0000.0000.000
39A116ILE0-0.064-0.01411.203-1.641-1.6410.0000.0000.0000.000
40A117GLY00.0840.04210.231-2.954-2.9540.0000.0000.0000.000
41A118ASP-1-0.948-0.9765.479-45.410-45.4100.0000.0000.0000.000
42A119TYR0-0.042-0.0226.030-4.942-4.9420.0000.0000.0000.000
43A120LYS10.8880.9197.90532.01132.0110.0000.0000.0000.000
44A121ASP-1-0.796-0.8916.174-42.762-42.7620.0000.0000.0000.000
45A122ILE00.0060.0037.8432.2052.2050.0000.0000.0000.000
46A123PHE00.0260.01510.5441.9731.9730.0000.0000.0000.000
47A124PRO00.016-0.00713.3451.1361.1360.0000.0000.0000.000
48A125ASP-1-0.847-0.89713.333-20.370-20.3700.0000.0000.0000.000
49A126LEU00.0090.00010.2300.8160.8160.0000.0000.0000.000
50A127PHE00.0120.00614.7791.0231.0230.0000.0000.0000.000
51A128LYS10.9730.98918.03915.79815.7980.0000.0000.0000.000
52A129ARG10.8710.91112.79922.53222.5320.0000.0000.0000.000
53A130ALA00.0130.01218.1370.5200.5200.0000.0000.0000.000
54A131ALA00.0060.00019.7650.7490.7490.0000.0000.0000.000
55A132GLU-1-0.877-0.92321.853-13.266-13.2660.0000.0000.0000.000
56A133ARG10.8470.91820.70714.41714.4170.0000.0000.0000.000
57A134LEU00.009-0.00223.5680.3980.3980.0000.0000.0000.000
58A135GLN0-0.018-0.02025.4240.4900.4900.0000.0000.0000.000
59A136TYR0-0.049-0.03026.6760.4660.4660.0000.0000.0000.000
60A137VAL0-0.045-0.01925.2820.2250.2250.0000.0000.0000.000
61A138PHE0-0.019-0.02224.2730.1630.1630.0000.0000.0000.000
62A139GLY00.0860.06929.3970.2750.2750.0000.0000.0000.000
63A140TYR00.0050.01228.8070.2110.2110.0000.0000.0000.000
64A141LYS10.9590.98728.5489.1989.1980.0000.0000.0000.000
65A142LEU0-0.024-0.00623.0250.1320.1320.0000.0000.0000.000
66A143VAL0-0.012-0.01527.387-0.044-0.0440.0000.0000.0000.000
67A144GLU-1-0.852-0.92827.863-11.542-11.5420.0000.0000.0000.000
68A145LEU0-0.033-0.01429.3650.2400.2400.0000.0000.0000.000
69A146GLU-1-0.882-0.93132.017-8.747-8.7470.0000.0000.0000.000
70A147PRO0-0.012-0.00431.401-0.398-0.3980.0000.0000.0000.000
71A148LYS10.8900.94228.07211.23911.2390.0000.0000.0000.000
72A149SER00.0570.03129.598-0.055-0.0550.0000.0000.0000.000
73A150ASN0-0.095-0.06424.356-0.462-0.4620.0000.0000.0000.000
74A151THR00.003-0.01425.271-0.464-0.4640.0000.0000.0000.000
75A152TYR0-0.018-0.02322.704-0.119-0.1190.0000.0000.0000.000
76A153ILE00.0160.01127.6620.0070.0070.0000.0000.0000.000
77A154LEU0-0.040-0.01326.170-0.313-0.3130.0000.0000.0000.000
78A155ILE0-0.022-0.00930.1120.3250.3250.0000.0000.0000.000
79A156ASN00.0500.01932.818-0.355-0.3550.0000.0000.0000.000
80A157THR0-0.091-0.06433.3040.1050.1050.0000.0000.0000.000
81A158LEU00.0120.01834.6530.0570.0570.0000.0000.0000.000
82A159GLU-1-0.898-0.95337.702-7.435-7.4350.0000.0000.0000.000
83A160PRO0-0.046-0.00941.264-0.065-0.0650.0000.0000.0000.000
84A161VAL0-0.056-0.03042.5380.1700.1700.0000.0000.0000.000
85A162GLU-1-0.872-0.94738.568-8.417-8.4170.0000.0000.0000.000
86A163GLU-1-0.809-0.90943.470-7.190-7.1900.0000.0000.0000.000
87A164ASP-1-0.987-0.97539.219-8.108-8.1080.0000.0000.0000.000
88A165ALA00.0070.00141.4680.0550.0550.0000.0000.0000.000
89A166GLU-1-0.870-0.94243.070-6.760-6.7600.0000.0000.0000.000
90A167MET0-0.062-0.04546.3870.1520.1520.0000.0000.0000.000
91A168ARG10.7880.91340.7587.6977.6970.0000.0000.0000.000
92A169GLY00.0310.00646.482-0.082-0.0820.0000.0000.0000.000
93A170ASP-1-0.938-0.94249.568-6.266-6.2660.0000.0000.0000.000
94A171GLN00.010-0.01550.814-0.027-0.0270.0000.0000.0000.000
95A172GLY00.0100.02553.4000.1090.1090.0000.0000.0000.000
96A173THR0-0.004-0.01256.305-0.008-0.0080.0000.0000.0000.000
97A174PRO00.0490.01558.116-0.034-0.0340.0000.0000.0000.000
98A175THR0-0.007-0.01959.162-0.031-0.0310.0000.0000.0000.000
99A176THR00.0390.02857.6430.0290.0290.0000.0000.0000.000
100A177GLY00.0530.03256.553-0.031-0.0310.0000.0000.0000.000
101A178LEU0-0.022-0.02157.289-0.004-0.0040.0000.0000.0000.000
102A179LEU0-0.006-0.00660.1630.0290.0290.0000.0000.0000.000
103A180MET00.0120.01255.7170.0650.0650.0000.0000.0000.000
104A181ILE0-0.0050.00556.765-0.026-0.0260.0000.0000.0000.000
105A182VAL0-0.029-0.00658.8130.0350.0350.0000.0000.0000.000
106A183LEU00.0020.00060.7330.0430.0430.0000.0000.0000.000
107A184GLY00.0570.01858.1800.0080.0080.0000.0000.0000.000
108A185LEU0-0.027-0.01559.0370.0000.0000.0000.0000.0000.000
109A186ILE0-0.034-0.01961.0300.0480.0480.0000.0000.0000.000
110A187PHE0-0.042-0.00857.2240.0180.0180.0000.0000.0000.000
111A188MET00.006-0.00655.6110.0150.0150.0000.0000.0000.000
112A189LYS10.8080.90259.7664.8794.8790.0000.0000.0000.000
113A190GLY00.0020.01562.8680.0730.0730.0000.0000.0000.000
114A191ASN0-0.078-0.04863.8450.0570.0570.0000.0000.0000.000
115A192THR0-0.011-0.01865.7040.1090.1090.0000.0000.0000.000
116A193LEU0-0.037-0.00564.686-0.052-0.0520.0000.0000.0000.000
117A194LYS10.8980.94568.3684.4814.4810.0000.0000.0000.000
118A195GLU-1-0.804-0.91669.632-4.576-4.5760.0000.0000.0000.000
119A196THR00.015-0.01070.180-0.070-0.0700.0000.0000.0000.000
120A197GLU-1-0.747-0.86066.639-4.853-4.8530.0000.0000.0000.000
121A198ALA00.0550.01865.297-0.078-0.0780.0000.0000.0000.000
122A199TRP0-0.076-0.06265.629-0.073-0.0730.0000.0000.0000.000
123A200ASP-1-0.889-0.94065.905-4.812-4.8120.0000.0000.0000.000
124A201PHE0-0.049-0.03659.686-0.104-0.1040.0000.0000.0000.000
125A202LEU0-0.030-0.00361.486-0.051-0.0510.0000.0000.0000.000
126A203ARG10.8460.91062.1924.8924.8920.0000.0000.0000.000
127A204ARG00.0340.05958.529-0.149-0.1490.0000.0000.0000.000
128A219PRO10.8970.92266.9094.8124.8120.0000.0000.0000.000
129A220LYS10.9711.02766.7904.7684.7680.0000.0000.0000.000
130A221LYS10.8400.93668.3834.4304.4300.0000.0000.0000.000
131A222LEU00.0460.02971.7330.0260.0260.0000.0000.0000.000
132A223ILE00.0450.02065.9520.0140.0140.0000.0000.0000.000
133A224THR0-0.037-0.03067.967-0.038-0.0380.0000.0000.0000.000
134A225GLU-1-0.877-0.90770.019-4.193-4.1930.0000.0000.0000.000
135A226ASP-1-0.850-0.94970.708-4.603-4.6030.0000.0000.0000.000
136A227PHE00.0480.01564.313-0.006-0.0060.0000.0000.0000.000
137A228VAL0-0.0230.00369.969-0.011-0.0110.0000.0000.0000.000
138A229ARG10.8120.89272.8854.2274.2270.0000.0000.0000.000
139A230GLN0-0.042-0.02768.361-0.027-0.0270.0000.0000.0000.000
140A231ARG10.8660.93870.7654.3254.3250.0000.0000.0000.000
141A232TYR0-0.047-0.04964.256-0.012-0.0120.0000.0000.0000.000
142A233LEU0-0.0040.00366.459-0.057-0.0570.0000.0000.0000.000
143A234GLU-1-0.873-0.93069.866-4.345-4.3450.0000.0000.0000.000
144A235TYR00.0400.00472.485-0.055-0.0550.0000.0000.0000.000
145A236ARG10.8090.89873.8284.4184.4180.0000.0000.0000.000
146A237ARG10.8460.90677.1363.9213.9210.0000.0000.0000.000
147A238ILE00.0280.02879.237-0.017-0.0170.0000.0000.0000.000
148A239PRO00.015-0.01077.585-0.033-0.0330.0000.0000.0000.000
149A240HIS0-0.064-0.01876.2120.0760.0760.0000.0000.0000.000
150A241THR00.017-0.00881.4410.0370.0370.0000.0000.0000.000
151A242ASP-1-0.832-0.89181.772-3.892-3.8920.0000.0000.0000.000
152A243PRO0-0.025-0.02281.826-0.052-0.0520.0000.0000.0000.000
153A244VAL0-0.004-0.00378.844-0.026-0.0260.0000.0000.0000.000
154A245ASP-1-0.781-0.87574.462-4.453-4.4530.0000.0000.0000.000
155A246TYR0-0.052-0.04074.8310.0670.0670.0000.0000.0000.000
156A247GLU-1-0.826-0.89472.665-4.454-4.4540.0000.0000.0000.000
157A248PHE0-0.047-0.02768.8270.0160.0160.0000.0000.0000.000
158A249GLN00.0530.02368.736-0.028-0.0280.0000.0000.0000.000
159A250TRP00.033-0.01260.2580.0080.0080.0000.0000.0000.000
160A251GLY00.0220.04367.571-0.010-0.0100.0000.0000.0000.000
161A252PRO0-0.012-0.02369.045-0.050-0.0500.0000.0000.0000.000
162A253ARG10.8580.93166.4094.7254.7250.0000.0000.0000.000
163A254THR00.005-0.01164.179-0.070-0.0700.0000.0000.0000.000
164A255ASN0-0.032-0.01363.420-0.143-0.1430.0000.0000.0000.000
165A256LEU0-0.023-0.00164.239-0.034-0.0340.0000.0000.0000.000
166A257GLU-1-0.796-0.86162.026-5.096-5.0960.0000.0000.0000.000
167A258LEU0-0.084-0.03957.351-0.143-0.1430.0000.0000.0000.000
168A259SER00.0460.01657.4280.0430.0430.0000.0000.0000.000
169A260LYS10.9100.95858.3385.1045.1040.0000.0000.0000.000
170A261MET00.0460.03353.103-0.124-0.1240.0000.0000.0000.000
171A262LYS10.8880.95253.7585.5695.5690.0000.0000.0000.000
172A263VAL00.0300.01854.053-0.093-0.0930.0000.0000.0000.000
173A264LEU0-0.0170.00252.633-0.080-0.0800.0000.0000.0000.000
174A265LYS10.9550.96448.9776.4066.4060.0000.0000.0000.000
175A266PHE00.0240.02149.896-0.123-0.1230.0000.0000.0000.000
176A267VAL0-0.021-0.03151.306-0.079-0.0790.0000.0000.0000.000
177A268ALA0-0.038-0.01047.915-0.038-0.0380.0000.0000.0000.000
178A269LYS10.8200.89745.2756.9086.9080.0000.0000.0000.000
179A270VAL0-0.050-0.01147.417-0.070-0.0700.0000.0000.0000.000
180A271HIS10.8730.93147.0656.4516.4510.0000.0000.0000.000
181A272ASN0-0.0140.00541.4940.1360.1360.0000.0000.0000.000
182A273GLN0-0.049-0.01044.6020.1470.1470.0000.0000.0000.000
183A274ASP-1-0.824-0.88143.518-7.475-7.4750.0000.0000.0000.000
184A275PRO0-0.049-0.05246.3390.1280.1280.0000.0000.0000.000
185A276LYS10.9280.95045.9356.9926.9920.0000.0000.0000.000
186A277ASP-1-0.815-0.91246.543-6.896-6.8960.0000.0000.0000.000
187A278TRP0-0.031-0.00249.3060.1860.1860.0000.0000.0000.000
188A279PRO00.0320.01252.0380.1120.1120.0000.0000.0000.000
189A280ALA0-0.017-0.01354.2860.0780.0780.0000.0000.0000.000
190A281GLN00.0430.01955.0030.1330.1330.0000.0000.0000.000
191A282TYR00.011-0.01750.381-0.031-0.0310.0000.0000.0000.000
192A283CYS0-0.028-0.01155.1880.0190.0190.0000.0000.0000.000
193A284GLU-1-0.742-0.87057.684-5.149-5.1490.0000.0000.0000.000
194A285ALA0-0.008-0.01255.8860.0450.0450.0000.0000.0000.000
195A286LEU0-0.020-0.00853.122-0.027-0.0270.0000.0000.0000.000
196A287ALA00.0210.01657.0740.0280.0280.0000.0000.0000.000
197A288ASP-1-0.830-0.91659.922-5.237-5.2370.0000.0000.0000.000
198A289GLU-1-0.991-1.00753.444-6.043-6.0430.0000.0000.0000.000
199A290GLU-1-0.945-0.97258.213-5.432-5.4320.0000.0000.0000.000
200A291ASN0-0.053-0.02459.6230.0740.0740.0000.0000.0000.000
201A292ARG10.7600.87359.7425.2975.2970.0000.0000.0000.000
202A293ALA0-0.047-0.01060.003-0.009-0.0090.0000.0000.0000.000
203A294ARG00.0470.03361.921-0.114-0.1140.0000.0000.0000.000