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: 5YQ4Z

Calculation Name: 4WP3-B-Xray547

Preferred Name:

Target Type:

Ligand Name: chloride ion

Ligand 3-letter code: CL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4WP3

Chain ID: B

ChEMBL ID:

UniProt ID: Q5UFR5

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 189
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2083661.362686
FMO2-HF: Nuclear repulsion 2009969.811628
FMO2-HF: Total energy -73691.551058
FMO2-MP2: Total energy -73908.655223


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:29:ARG)


Summations of interaction energy for fragment #1(A:29:ARG)
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.
-318.993-311.40429.168-18.008-18.747-0.197
Interaction energy analysis for fragmet #1(A:29:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.629 / q_NPA : 1.796
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].
3A31SER00.0660.0002.880-13.886-11.2940.232-1.306-1.518-0.010
5A33GLU-1-0.831-0.8942.607-116.048-112.0961.815-2.056-3.710-0.016
6A34GLU-1-0.927-0.9572.347-125.877-121.1072.891-2.828-4.834-0.026
7A35LEU0-0.031-0.0103.2789.1979.2500.0170.171-0.2410.000
9A37ASP-1-0.793-0.8781.728-157.856-161.85524.215-11.915-8.301-0.145
10A38TRP0-0.031-0.0144.3589.2749.372-0.001-0.027-0.0690.000
38A66THR0-0.028-0.0104.144-5.481-5.358-0.001-0.047-0.0740.000
4A32ILE0-0.019-0.0015.4213.1713.1710.0000.0000.0000.000
8A36ALA0-0.013-0.0044.9397.0387.0380.0000.0000.0000.000
11A39ALA00.003-0.0077.1635.7995.7990.0000.0000.0000.000
12A40GLU-1-0.917-0.9487.561-38.582-38.5820.0000.0000.0000.000
13A41VAL0-0.021-0.0167.8613.7443.7440.0000.0000.0000.000
14A42GLU-1-0.935-0.96110.196-33.868-33.8680.0000.0000.0000.000
15A43ARG10.7390.85412.06440.94140.9410.0000.0000.0000.000
16A44PRO00.0310.01912.8552.3592.3590.0000.0000.0000.000
17A45ASP-1-0.758-0.87215.838-27.460-27.4600.0000.0000.0000.000
18A46LEU0-0.030-0.00618.7910.9460.9460.0000.0000.0000.000
19A47ALA0-0.020-0.02015.7260.0380.0380.0000.0000.0000.000
20A48ARG10.7600.86417.12329.52429.5240.0000.0000.0000.000
21A49VAL00.0040.01720.3001.2311.2310.0000.0000.0000.000
22A50THR0-0.041-0.03722.481-1.021-1.0210.0000.0000.0000.000
23A51PRO0-0.0200.02324.8150.7100.7100.0000.0000.0000.000
24A52ASP-1-0.850-0.94027.925-20.267-20.2670.0000.0000.0000.000
25A53GLY00.0320.01726.846-0.712-0.7120.0000.0000.0000.000
26A54ARG10.7950.88923.95421.82921.8290.0000.0000.0000.000
27A55VAL00.0230.00919.912-0.132-0.1320.0000.0000.0000.000
28A56VAL0-0.024-0.00520.735-0.858-0.8580.0000.0000.0000.000
29A57ILE0-0.022-0.01614.251-0.444-0.4440.0000.0000.0000.000
30A58LEU0-0.010-0.00315.8600.2680.2680.0000.0000.0000.000
31A59PHE00.021-0.0028.941-0.893-0.8930.0000.0000.0000.000
32A60THR0-0.018-0.03212.3072.5002.5000.0000.0000.0000.000
33A61ASP-1-0.760-0.8527.624-67.824-67.8240.0000.0000.0000.000
34A62ILE0-0.028-0.01710.7843.9223.9220.0000.0000.0000.000
35A63GLU-1-0.811-0.90310.063-41.345-41.3450.0000.0000.0000.000
36A64GLU-1-0.913-0.9658.869-51.647-51.6470.0000.0000.0000.000
37A65SER0-0.036-0.0147.321-1.142-1.1420.0000.0000.0000.000
39A67ALA00.1050.0566.4644.0494.0490.0000.0000.0000.000
40A68LEU0-0.073-0.0289.5284.5594.5590.0000.0000.0000.000
41A69ASN0-0.018-0.0238.9917.0707.0700.0000.0000.0000.000
42A70GLU-1-0.909-0.9658.238-51.424-51.4240.0000.0000.0000.000
43A71ARG10.8030.88811.37535.80735.8070.0000.0000.0000.000
44A72ILE0-0.090-0.04214.2442.6432.6430.0000.0000.0000.000
45A73GLY00.0390.02814.4182.0482.0480.0000.0000.0000.000
46A74ASP-1-0.808-0.92012.175-41.723-41.7230.0000.0000.0000.000
47A75ARG10.9100.94114.76227.86827.8680.0000.0000.0000.000
48A76ALA0-0.033-0.01317.5371.3811.3810.0000.0000.0000.000
49A77TRP00.0760.0489.5532.3562.3560.0000.0000.0000.000
50A78VAL00.0330.00614.9520.1190.1190.0000.0000.0000.000
51A79LYS10.8990.95416.60426.49026.4900.0000.0000.0000.000
52A80LEU0-0.0090.01014.5941.1081.1080.0000.0000.0000.000
53A81ILE00.0460.02212.2030.9390.9390.0000.0000.0000.000
54A82SER0-0.034-0.00616.1440.8110.8110.0000.0000.0000.000
55A83SER0-0.017-0.02019.4521.4281.4280.0000.0000.0000.000
56A84HIS00.0090.01614.8882.7492.7490.0000.0000.0000.000
57A85ASP-1-0.809-0.90717.204-31.141-31.1410.0000.0000.0000.000
58A86LYS10.7990.89518.49629.49329.4930.0000.0000.0000.000
59A87LEU0-0.0160.00721.1501.2561.2560.0000.0000.0000.000
60A88VAL00.0110.00216.7571.0981.0980.0000.0000.0000.000
61A89SER00.020-0.00620.0400.6960.6960.0000.0000.0000.000
62A90ASP-1-0.866-0.90621.784-21.146-21.1460.0000.0000.0000.000
63A91LEU0-0.031-0.01022.6740.9720.9720.0000.0000.0000.000
64A92VAL00.0270.00619.7880.6250.6250.0000.0000.0000.000
65A93ARG10.8840.93923.22123.77823.7780.0000.0000.0000.000
66A94ARG10.8510.91726.27322.33922.3390.0000.0000.0000.000
67A95GLN0-0.034-0.01725.5520.9350.9350.0000.0000.0000.000
68A96SER0-0.050-0.02327.5990.3650.3650.0000.0000.0000.000
69A97GLY00.0070.00823.3100.0870.0870.0000.0000.0000.000
70A98HIS0-0.011-0.01519.5601.3911.3910.0000.0000.0000.000
71A99VAL00.011-0.00316.578-1.129-1.1290.0000.0000.0000.000
72A100VAL0-0.026-0.01014.4590.6310.6310.0000.0000.0000.000
73A101LYS10.9160.96411.23140.53540.5350.0000.0000.0000.000
74A102SER00.0040.01012.691-0.420-0.4200.0000.0000.0000.000
75A103GLN0-0.001-0.0126.6967.0457.0450.0000.0000.0000.000
76A104GLY00.0090.0099.328-3.777-3.7770.0000.0000.0000.000
77A105ASP-1-0.753-0.8808.985-58.438-58.4380.0000.0000.0000.000
78A106GLY0-0.006-0.0058.9801.7881.7880.0000.0000.0000.000
79A107PHE0-0.029-0.0309.9812.5242.5240.0000.0000.0000.000
80A108MET0-0.0070.01811.385-1.829-1.8290.0000.0000.0000.000
81A109VAL0-0.027-0.02713.2761.8941.8940.0000.0000.0000.000
82A110ALA00.0180.01717.074-0.611-0.6110.0000.0000.0000.000
83A111PHE00.007-0.01219.3520.8200.8200.0000.0000.0000.000
84A112ALA00.0030.00622.951-0.318-0.3180.0000.0000.0000.000
85A113ARG10.9370.94425.92619.50519.5050.0000.0000.0000.000
86A114PRO00.028-0.00424.560-0.457-0.4570.0000.0000.0000.000
87A115GLU-1-0.788-0.85425.423-20.058-20.0580.0000.0000.0000.000
88A116GLN00.0310.02525.901-0.493-0.4930.0000.0000.0000.000
89A117ALA00.0260.02621.344-0.400-0.4000.0000.0000.0000.000
90A118VAL00.0560.02222.430-0.801-0.8010.0000.0000.0000.000
91A119ARG10.8250.90524.28621.29721.2970.0000.0000.0000.000
92A120CYS00.0020.00221.7250.2220.2220.0000.0000.0000.000
93A121GLY00.0340.01520.830-0.425-0.4250.0000.0000.0000.000
94A122ILE00.0310.00721.676-0.137-0.1370.0000.0000.0000.000
95A123GLU-1-0.813-0.88424.869-21.056-21.0560.0000.0000.0000.000
96A124LEU00.0150.01017.5910.3290.3290.0000.0000.0000.000
97A125GLN00.0460.01217.7380.2890.2890.0000.0000.0000.000
98A126ARG10.8370.92922.22821.76321.7630.0000.0000.0000.000
99A127ALA0-0.017-0.01524.1150.5590.5590.0000.0000.0000.000
100A128LEU00.0050.01718.5460.4910.4910.0000.0000.0000.000
101A129ARG10.8430.91521.37026.50426.5040.0000.0000.0000.000
102A130ARG0-0.022-0.02124.6071.0741.0740.0000.0000.0000.000
103A131ASN0-0.052-0.02823.7190.8170.8170.0000.0000.0000.000
104A132ALA00.0650.02521.7750.7590.7590.0000.0000.0000.000
105A133ASN00.0050.01023.657-0.450-0.4500.0000.0000.0000.000
106A134ARG10.8540.91926.87320.79620.7960.0000.0000.0000.000
107A135LYS10.9020.96622.72725.91125.9110.0000.0000.0000.000
108A136ARG10.9230.95724.13622.58022.5800.0000.0000.0000.000
109A137HIS0-0.017-0.03120.1820.9160.9160.0000.0000.0000.000
110A138GLU-1-0.773-0.84217.118-30.427-30.4270.0000.0000.0000.000
111A139GLU-1-0.771-0.86119.539-27.728-27.7280.0000.0000.0000.000
112A140ILE0-0.031-0.02015.738-0.660-0.6600.0000.0000.0000.000
113A141ARG10.8520.92016.19233.12633.1260.0000.0000.0000.000
114A142VAL00.002-0.00614.249-2.013-2.0130.0000.0000.0000.000
115A143ARG10.8810.9576.91763.92363.9230.0000.0000.0000.000
116A144ILE0-0.027-0.01314.027-0.365-0.3650.0000.0000.0000.000
117A145GLY00.0220.02015.1540.9330.9330.0000.0000.0000.000
118A146ILE0-0.028-0.01316.075-0.700-0.7000.0000.0000.0000.000
119A147HIS00.0230.02216.6850.5970.5970.0000.0000.0000.000
120A148MET00.0100.01618.6650.2570.2570.0000.0000.0000.000
121A149GLY0-0.0020.01520.715-0.021-0.0210.0000.0000.0000.000
122A150ARG10.9970.99021.57822.78122.7810.0000.0000.0000.000
123A151SER0-0.027-0.01423.171-0.592-0.5920.0000.0000.0000.000
124A152VAL00.0390.03420.7370.5020.5020.0000.0000.0000.000
125A153ARG10.9820.98724.23820.78420.7840.0000.0000.0000.000
126A154ARG10.9860.97322.55622.48722.4870.0000.0000.0000.000
127A155GLY0-0.019-0.01021.242-0.666-0.6660.0000.0000.0000.000
128A156ASP-1-0.864-0.92220.064-26.807-26.8070.0000.0000.0000.000
129A157ASP-1-0.755-0.85515.655-32.139-32.1390.0000.0000.0000.000
130A158LEU00.0170.00315.398-2.147-2.1470.0000.0000.0000.000
131A159PHE0-0.030-0.00617.1620.0510.0510.0000.0000.0000.000
132A160GLY0-0.0130.00016.917-0.921-0.9210.0000.0000.0000.000
133A161ARG10.8480.90910.47338.96638.9660.0000.0000.0000.000
134A162ASN00.0460.01313.428-1.461-1.4610.0000.0000.0000.000
135A163VAL00.0500.03010.514-0.063-0.0630.0000.0000.0000.000
136A164ALA00.0640.0309.022-1.977-1.9770.0000.0000.0000.000
137A165MET0-0.0050.01510.146-2.408-2.4080.0000.0000.0000.000
138A166ALA00.001-0.00713.016-0.522-0.5220.0000.0000.0000.000
139A167ALA00.0100.0108.424-0.267-0.2670.0000.0000.0000.000
140A168ARG00.0140.0178.357-4.048-4.0480.0000.0000.0000.000
141A169VAL0-0.035-0.01810.9080.9390.9390.0000.0000.0000.000
142A170ALA0-0.0050.00211.6391.0711.0710.0000.0000.0000.000
143A171ALA0-0.049-0.0368.415-0.547-0.5470.0000.0000.0000.000
144A172GLN0-0.026-0.03310.0152.0362.0360.0000.0000.0000.000
145A173ALA0-0.0340.00813.1472.5462.5460.0000.0000.0000.000
146A174ALA00.0420.01413.288-2.669-2.6690.0000.0000.0000.000
147A175GLY0-0.004-0.01914.906-0.084-0.0840.0000.0000.0000.000
148A176GLY0-0.098-0.05315.6581.8281.8280.0000.0000.0000.000
149A177GLU-1-0.801-0.85617.591-30.175-30.1750.0000.0000.0000.000
150A178ILE0-0.019-0.02018.239-1.385-1.3850.0000.0000.0000.000
151A179LEU0-0.0090.01916.1521.5751.5750.0000.0000.0000.000
152A180VAL0-0.018-0.01919.145-0.717-0.7170.0000.0000.0000.000
153A181SER00.044-0.00318.7760.6480.6480.0000.0000.0000.000
154A182GLN00.001-0.02020.7400.4630.4630.0000.0000.0000.000
155A183PRO0-0.013-0.01022.1230.9120.9120.0000.0000.0000.000
156A184VAL0-0.0080.00321.7380.8850.8850.0000.0000.0000.000
157A185ARG10.9010.96024.79722.21022.2100.0000.0000.0000.000
158A186ASP-1-0.868-0.91526.802-20.745-20.7450.0000.0000.0000.000
159A187ALA0-0.051-0.03027.9190.7740.7740.0000.0000.0000.000
160A188LEU0-0.023-0.01026.6860.5870.5870.0000.0000.0000.000
161A189SER00.004-0.00730.3520.3400.3400.0000.0000.0000.000
162A190ARG10.8450.91032.75217.47517.4750.0000.0000.0000.000
163A191SER0-0.009-0.00732.3050.3790.3790.0000.0000.0000.000
164A192ASP-1-0.803-0.88934.361-16.753-16.7530.0000.0000.0000.000
165A193GLY0-0.062-0.01533.791-0.380-0.3800.0000.0000.0000.000
166A194ILE0-0.027-0.02528.197-0.383-0.3830.0000.0000.0000.000
167A195ARG10.7920.88329.52319.07619.0760.0000.0000.0000.000
168A196PHE00.033-0.00825.307-0.759-0.7590.0000.0000.0000.000
169A197ASP-1-0.762-0.86924.530-24.360-24.3600.0000.0000.0000.000
170A198ASP-1-0.895-0.94927.905-19.962-19.9620.0000.0000.0000.000
171A199GLY0-0.037-0.02124.4720.0590.0590.0000.0000.0000.000
172A200ARG10.7970.87017.87031.30531.3050.0000.0000.0000.000
173A201GLU-1-0.854-0.91221.378-24.548-24.5480.0000.0000.0000.000
174A202VAL0-0.022-0.00715.408-0.188-0.1880.0000.0000.0000.000
175A203GLU-1-0.859-0.91715.474-31.231-31.2310.0000.0000.0000.000
176A204LEU0-0.068-0.03611.912-2.563-2.5630.0000.0000.0000.000
177A205LYS10.9270.9364.84881.12381.1230.0000.0000.0000.000
178A206GLY00.0210.0189.069-2.660-2.6600.0000.0000.0000.000
179A207PHE0-0.054-0.02910.3851.3851.3850.0000.0000.0000.000
180A208SER0-0.013-0.01613.893-0.187-0.1870.0000.0000.0000.000
181A209GLY0-0.0140.00217.2380.8890.8890.0000.0000.0000.000
182A210THR0-0.041-0.03517.923-1.574-1.5740.0000.0000.0000.000
183A211TYR0-0.004-0.01416.9510.5160.5160.0000.0000.0000.000
184A212ARG10.8470.92320.04723.28623.2860.0000.0000.0000.000
185A213LEU0-0.038-0.02116.219-0.610-0.6100.0000.0000.0000.000
186A214PHE0-0.031-0.01420.9090.6190.6190.0000.0000.0000.000
187A215ALA00.0330.01722.061-1.143-1.1430.0000.0000.0000.000
188A216VAL0-0.085-0.05422.9761.1641.1640.0000.0000.0000.000
189A217LEU-1-0.943-0.95824.831-22.359-22.3590.0000.0000.0000.000