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: 7Y4ZK

Calculation Name: 1F3B-A-Xray547

Preferred Name:

Target Type:

Ligand Name: 2-amino-4-[1-(carboxymethyl-carbamoyl)-2-(9-hydroxy-7,8-dioxo-7,8,9,10-tetrahydro-benzo[def]chrysen-10-ylsulfanyl)-ethylcarbamoyl]-butyric acid | s-hydroxycysteine

Ligand 3-letter code: GBX | CSO

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1F3B

Chain ID: A

ChEMBL ID:

UniProt ID: P13745

Base Structure: X-ray

Registration Date: 2025-09-02

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 222
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2777220.36374
FMO2-HF: Nuclear repulsion 2687679.27492
FMO2-HF: Total energy -89541.08882
FMO2-MP2: Total energy -89800.764251


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:1:ALA)


Summations of interaction energy for fragment #1(A:1: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.
17.12919.5760.283-1.065-1.666-0.005
Interaction energy analysis for fragmet #1(A:1:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.843 / q_NPA : 0.904
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].
3A3LYS10.9320.9863.84332.21333.507-0.014-0.578-0.703-0.001
4A4PRO0-0.016-0.0064.603-5.803-5.714-0.001-0.011-0.0770.000
59A59ILE00.000-0.0123.893-4.286-4.2020.000-0.034-0.0500.000
60A60ASP-1-0.786-0.8582.687-42.193-41.4460.277-0.385-0.639-0.003
61A61GLY0-0.0040.0063.3882.6092.8590.022-0.041-0.231-0.001
62A62MET0-0.041-0.0054.6105.5835.566-0.001-0.0160.0340.000
5A5VAL0-0.0040.0035.5513.5033.5030.0000.0000.0000.000
6A6LEU00.007-0.0108.0740.9730.9730.0000.0000.0000.000
7A7HIS0-0.019-0.0199.7132.3862.3860.0000.0000.0000.000
8A8TYR00.012-0.01513.8641.1091.1090.0000.0000.0000.000
9A9PHE00.0550.05217.462-0.144-0.1440.0000.0000.0000.000
10A10ASN0-0.004-0.00220.049-0.586-0.5860.0000.0000.0000.000
11A11ALA00.0180.00121.4670.6950.6950.0000.0000.0000.000
12A12ARG10.7580.85221.59510.68810.6880.0000.0000.0000.000
13A13GLY00.003-0.00521.786-0.564-0.5640.0000.0000.0000.000
14A14ARG10.8710.91521.09312.23612.2360.0000.0000.0000.000
15A15MET00.0380.03114.337-0.543-0.5430.0000.0000.0000.000
16A16GLU-1-0.769-0.86617.823-15.031-15.0310.0000.0000.0000.000
17A17CYS00.0380.02919.500-0.563-0.5630.0000.0000.0000.000
18A18ILE0-0.022-0.01713.411-0.294-0.2940.0000.0000.0000.000
19A19ARG10.7270.84715.06015.36815.3680.0000.0000.0000.000
20A20TRP00.0290.00916.427-0.334-0.3340.0000.0000.0000.000
21A21LEU0-0.039-0.00915.4460.0950.0950.0000.0000.0000.000
22A22LEU0-0.008-0.00210.386-0.410-0.4100.0000.0000.0000.000
23A23ALA00.0300.02114.005-0.274-0.2740.0000.0000.0000.000
24A24ALA0-0.005-0.01316.7030.3470.3470.0000.0000.0000.000
25A25ALA0-0.028-0.00714.2260.5330.5330.0000.0000.0000.000
26A26GLY0-0.0190.00115.289-0.370-0.3700.0000.0000.0000.000
27A27VAL0-0.061-0.0279.356-1.119-1.1190.0000.0000.0000.000
28A28GLU-1-0.882-0.94511.178-23.642-23.6420.0000.0000.0000.000
29A29PHE0-0.003-0.0149.396-2.998-2.9980.0000.0000.0000.000
30A30GLU-1-0.890-0.9467.997-34.556-34.5560.0000.0000.0000.000
31A31GLU-1-0.763-0.87310.549-17.636-17.6360.0000.0000.0000.000
32A32LYS10.8980.9609.14829.22129.2210.0000.0000.0000.000
33A33PHE0-0.028-0.02313.8220.4830.4830.0000.0000.0000.000
34A34ILE0-0.0130.00217.4310.3140.3140.0000.0000.0000.000
35A35GLN0-0.074-0.06019.5980.7960.7960.0000.0000.0000.000
36A36SER0-0.021-0.00622.7510.6510.6510.0000.0000.0000.000
37A37PRO00.025-0.00723.342-0.555-0.5550.0000.0000.0000.000
38A38GLU-1-0.854-0.93924.123-11.834-11.8340.0000.0000.0000.000
39A39ASP-1-0.794-0.87619.132-15.124-15.1240.0000.0000.0000.000
40A40LEU0-0.030-0.01919.307-0.727-0.7270.0000.0000.0000.000
41A41GLU-1-0.831-0.93220.672-12.355-12.3550.0000.0000.0000.000
42A42LYS10.8210.91417.00817.14217.1420.0000.0000.0000.000
43A43LEU0-0.016-0.01014.365-0.511-0.5110.0000.0000.0000.000
44A44LYS10.8610.93917.44811.96711.9670.0000.0000.0000.000
45A45LYS10.9040.96420.15912.06212.0620.0000.0000.0000.000
46A46ASP-1-0.875-0.92816.116-17.299-17.2990.0000.0000.0000.000
47A47GLY00.0080.00916.475-0.857-0.8570.0000.0000.0000.000
48A48ASN0-0.064-0.03412.770-2.327-2.3270.0000.0000.0000.000
49A49LEU0-0.008-0.00714.312-0.901-0.9010.0000.0000.0000.000
50A50MET0-0.015-0.00216.6020.5390.5390.0000.0000.0000.000
51A51PHE00.009-0.00918.3080.5510.5510.0000.0000.0000.000
52A52ASP-1-0.844-0.92420.798-12.973-12.9730.0000.0000.0000.000
53A53GLN0-0.049-0.02720.4060.0290.0290.0000.0000.0000.000
54A54VAL00.0140.01716.493-0.887-0.8870.0000.0000.0000.000
55A55PRO0-0.080-0.06315.9830.8940.8940.0000.0000.0000.000
56A56MET0-0.0290.01511.599-0.438-0.4380.0000.0000.0000.000
57A57VAL00.0070.0027.9170.0200.0200.0000.0000.0000.000
58A58GLU-1-0.817-0.8946.028-32.802-32.8020.0000.0000.0000.000
63A63LYS10.9100.9447.18025.88525.8850.0000.0000.0000.000
64A64LEU0-0.0030.0129.6012.2892.2890.0000.0000.0000.000
65A65ALA00.0530.01511.4170.0490.0490.0000.0000.0000.000
66A66GLN00.0370.01514.9470.2010.2010.0000.0000.0000.000
67A67THR00.0210.00216.799-0.382-0.3820.0000.0000.0000.000
68A68ARG10.8530.89717.47411.62311.6230.0000.0000.0000.000
69A69ALA00.0390.02515.729-0.112-0.1120.0000.0000.0000.000
70A70ILE0-0.0140.00011.936-0.662-0.6620.0000.0000.0000.000
71A71LEU0-0.001-0.00713.423-0.799-0.7990.0000.0000.0000.000
72A72ASN00.0210.02015.965-0.063-0.0630.0000.0000.0000.000
73A73TYR0-0.026-0.0257.4091.3921.3920.0000.0000.0000.000
74A74ILE00.0200.00110.377-0.557-0.5570.0000.0000.0000.000
75A75ALA0-0.004-0.00912.4450.0510.0510.0000.0000.0000.000
76A76THR0-0.069-0.05114.3440.9090.9090.0000.0000.0000.000
77A77LYS10.8160.9085.62838.01838.0180.0000.0000.0000.000
78A78TYR00.008-0.0038.365-1.633-1.6330.0000.0000.0000.000
79A79ASP-1-0.880-0.92214.347-15.655-15.6550.0000.0000.0000.000
80A80LEU0-0.006-0.00316.5961.0801.0800.0000.0000.0000.000
81A81TYR0-0.092-0.08817.9850.5210.5210.0000.0000.0000.000
82A82GLY00.001-0.00220.4140.5060.5060.0000.0000.0000.000
83A83LYS10.8350.89522.2949.9629.9620.0000.0000.0000.000
84A84ASP-1-0.829-0.91224.543-10.477-10.4770.0000.0000.0000.000
85A85MET00.006-0.00625.854-0.103-0.1030.0000.0000.0000.000
86A86LYS10.9560.97527.4358.8228.8220.0000.0000.0000.000
87A87GLU-1-0.794-0.88226.579-10.961-10.9610.0000.0000.0000.000
88A88ARG10.9800.99721.38112.83412.8340.0000.0000.0000.000
89A89ALA00.0170.01725.5450.0030.0030.0000.0000.0000.000
90A90LEU0-0.026-0.01028.7280.1790.1790.0000.0000.0000.000
91A91ILE00.0240.00823.0130.0020.0020.0000.0000.0000.000
92A92ASP-1-0.811-0.86523.217-12.770-12.7700.0000.0000.0000.000
93A93MET0-0.032-0.00625.7870.1970.1970.0000.0000.0000.000
94A94TYR0-0.029-0.03128.2300.2150.2150.0000.0000.0000.000
95A95SER00.011-0.02223.931-0.114-0.1140.0000.0000.0000.000
96A96GLU-1-0.813-0.87624.655-11.846-11.8460.0000.0000.0000.000
97A97GLY00.0260.02227.5050.1420.1420.0000.0000.0000.000
98A98ILE0-0.011-0.01326.2940.2330.2330.0000.0000.0000.000
99A99LEU0-0.0210.00022.925-0.095-0.0950.0000.0000.0000.000
100A100ASP-1-0.864-0.92727.098-9.562-9.5620.0000.0000.0000.000
101A101LEU0-0.064-0.03130.7070.2180.2180.0000.0000.0000.000
102A102THR00.000-0.01926.0100.0900.0900.0000.0000.0000.000
103A103GLU-1-0.892-0.93326.717-11.000-11.0000.0000.0000.0000.000
104A104MET0-0.075-0.02530.0630.3350.3350.0000.0000.0000.000
105A105ILE0-0.007-0.00432.5030.2610.2610.0000.0000.0000.000
106A106GLY00.0200.01430.3570.1020.1020.0000.0000.0000.000
107A107GLN00.000-0.02530.379-0.120-0.1200.0000.0000.0000.000
108A108LEU00.0030.00533.1570.2490.2490.0000.0000.0000.000
109A109VAL0-0.066-0.03832.2100.2430.2430.0000.0000.0000.000
110A110LEU0-0.023-0.01330.9910.0450.0450.0000.0000.0000.000
111A111CYS0-0.082-0.01635.6180.1580.1580.0000.0000.0000.000
112A112PRO00.0400.02338.8680.0290.0290.0000.0000.0000.000
113A113PRO00.017-0.00942.0490.0420.0420.0000.0000.0000.000
114A114ASP-1-0.850-0.92444.349-6.827-6.8270.0000.0000.0000.000
115A115GLN00.0160.00243.093-0.059-0.0590.0000.0000.0000.000
116A116ARG10.8920.96437.7918.0298.0290.0000.0000.0000.000
117A117GLU-1-0.876-0.91842.627-6.636-6.6360.0000.0000.0000.000
118A118ALA00.0350.01744.951-0.035-0.0350.0000.0000.0000.000
119A119LYS10.9080.95239.7537.4767.4760.0000.0000.0000.000
120A120THR00.008-0.01040.507-0.195-0.1950.0000.0000.0000.000
121A121ALA00.0060.00041.565-0.057-0.0570.0000.0000.0000.000
122A122LEU0-0.014-0.00441.018-0.006-0.0060.0000.0000.0000.000
123A123ALA00.0610.02537.639-0.053-0.0530.0000.0000.0000.000
124A124LYS10.8930.94239.2137.3447.3440.0000.0000.0000.000
125A125ASP-1-0.929-0.94041.452-6.950-6.9500.0000.0000.0000.000
126A126ARG10.9200.94838.5617.2987.2980.0000.0000.0000.000
127A127THR00.020-0.00236.549-0.164-0.1640.0000.0000.0000.000
128A128LYS10.9250.96538.3786.9456.9450.0000.0000.0000.000
129A129ASN0-0.018-0.02741.3400.0930.0930.0000.0000.0000.000
130A130ARG10.8960.95537.9547.8497.8490.0000.0000.0000.000
131A131TYR0-0.012-0.01333.6150.0970.0970.0000.0000.0000.000
132A132LEU00.0130.02035.428-0.136-0.1360.0000.0000.0000.000
133A133PRO00.0130.00037.559-0.033-0.0330.0000.0000.0000.000
134A134ALA0-0.031-0.00236.2800.0550.0550.0000.0000.0000.000
135A135PHE00.0390.01431.200-0.029-0.0290.0000.0000.0000.000
136A136GLU-1-0.754-0.87535.337-7.895-7.8950.0000.0000.0000.000
137A137LYS10.9290.96238.3607.4587.4580.0000.0000.0000.000
138A138VAL0-0.0230.00032.9600.0920.0920.0000.0000.0000.000
139A139LEU00.0200.02033.1280.0530.0530.0000.0000.0000.000
140A140LYS10.9390.96136.7097.0027.0020.0000.0000.0000.000
141A141SER0-0.134-0.06737.7960.1340.1340.0000.0000.0000.000
142A142HIS0-0.005-0.01033.2800.2960.2960.0000.0000.0000.000
143A143GLY00.0060.01338.5600.0530.0530.0000.0000.0000.000
144A144GLN0-0.026-0.01233.702-0.237-0.2370.0000.0000.0000.000
145A145ASP-1-0.874-0.95432.176-9.074-9.0740.0000.0000.0000.000
146A146TYR0-0.032-0.01427.259-0.198-0.1980.0000.0000.0000.000
147A147LEU0-0.012-0.01628.0620.3190.3190.0000.0000.0000.000
148A148VAL00.008-0.00127.6360.3070.3070.0000.0000.0000.000
149A149GLY00.0390.01628.611-0.223-0.2230.0000.0000.0000.000
150A150ASN0-0.033-0.00829.809-0.062-0.0620.0000.0000.0000.000
151A151ARG10.8840.95321.88212.93412.9340.0000.0000.0000.000
152A152LEU00.0120.01122.0040.0020.0020.0000.0000.0000.000
153A153THR0-0.030-0.03422.238-0.403-0.4030.0000.0000.0000.000
154A154ARG10.9070.91819.36014.17814.1780.0000.0000.0000.000
155A155VAL0-0.0120.00221.0600.0780.0780.0000.0000.0000.000
156A156ASP-1-0.741-0.85624.556-10.887-10.8870.0000.0000.0000.000
157A157ILE00.0010.00220.4360.2640.2640.0000.0000.0000.000
158A158HIS00.0340.01819.5260.0400.0400.0000.0000.0000.000
159A159LEU00.0290.02124.3190.3330.3330.0000.0000.0000.000
160A160LEU0-0.006-0.00625.8150.3660.3660.0000.0000.0000.000
161A161GLU-1-0.809-0.89722.684-13.065-13.0650.0000.0000.0000.000
162A162VAL00.0100.00026.2370.3140.3140.0000.0000.0000.000
163A163LEU0-0.011-0.01328.9580.4270.4270.0000.0000.0000.000
164A164LEU0-0.031-0.00627.1760.3070.3070.0000.0000.0000.000
165A165TYR0-0.053-0.04824.2080.2510.2510.0000.0000.0000.000
166A166VAL0-0.010-0.01231.2510.3120.3120.0000.0000.0000.000
167A167GLU-1-0.838-0.90533.832-8.876-8.8760.0000.0000.0000.000
168A168GLU-1-0.795-0.86630.643-10.158-10.1580.0000.0000.0000.000
169A169PHE0-0.054-0.01534.9720.2360.2360.0000.0000.0000.000
170A170ASP-1-0.810-0.89136.780-7.118-7.1180.0000.0000.0000.000
171A171ALA00.0690.04138.8270.0030.0030.0000.0000.0000.000
172A172SER0-0.058-0.04039.7830.0810.0810.0000.0000.0000.000
173A173LEU00.008-0.00138.9770.1090.1090.0000.0000.0000.000
174A174LEU00.0440.01335.7780.0010.0010.0000.0000.0000.000
175A175THR0-0.059-0.03639.7330.0190.0190.0000.0000.0000.000
176A176PRO00.001-0.00942.7320.0720.0720.0000.0000.0000.000
177A177PHE0-0.0160.01239.4430.0750.0750.0000.0000.0000.000
178A178PRO00.0040.00639.871-0.182-0.1820.0000.0000.0000.000
179A179LEU00.004-0.00638.161-0.136-0.1360.0000.0000.0000.000
180A180LEU00.012-0.00134.091-0.270-0.2700.0000.0000.0000.000
181A181LYS10.8640.94735.0667.1947.1940.0000.0000.0000.000
182A182ALA00.0090.01736.073-0.177-0.1770.0000.0000.0000.000
183A183PHE0-0.0130.00128.474-0.173-0.1730.0000.0000.0000.000
184A184LYS10.8320.90431.4439.0819.0810.0000.0000.0000.000
185A185SER0-0.038-0.01931.406-0.267-0.2670.0000.0000.0000.000
186A186ARG10.8680.95231.3538.9558.9550.0000.0000.0000.000
187A187ILE00.0060.01825.880-0.328-0.3280.0000.0000.0000.000
188A188SER0-0.012-0.03627.086-0.481-0.4810.0000.0000.0000.000
189A189SER0-0.114-0.06328.753-0.082-0.0820.0000.0000.0000.000
190A190LEU00.0150.01824.938-0.091-0.0910.0000.0000.0000.000
191A191PRO00.011-0.00423.730-0.222-0.2220.0000.0000.0000.000
192A192ASN0-0.008-0.01218.8240.2340.2340.0000.0000.0000.000
193A193VAL00.0220.03021.458-0.346-0.3460.0000.0000.0000.000
194A194LYS10.9700.98423.54610.64710.6470.0000.0000.0000.000
195A195LYS10.9450.97220.92514.92314.9230.0000.0000.0000.000
196A196PHE00.0600.02218.678-0.214-0.2140.0000.0000.0000.000
197A197LEU0-0.0170.00022.4380.2030.2030.0000.0000.0000.000
198A198GLN0-0.017-0.00225.6050.0350.0350.0000.0000.0000.000
199A199PRO00.0190.00125.362-0.385-0.3850.0000.0000.0000.000
200A200GLY00.0060.00623.973-0.062-0.0620.0000.0000.0000.000
201A201SER0-0.045-0.00920.818-0.788-0.7880.0000.0000.0000.000
202A202GLN0-0.023-0.02413.5600.3430.3430.0000.0000.0000.000
203A203ARG10.8440.93419.06711.79711.7970.0000.0000.0000.000
204A204LYS10.7820.87618.37016.05516.0550.0000.0000.0000.000
205A205PRO00.0050.01023.7860.2670.2670.0000.0000.0000.000
206A206PRO0-0.004-0.01227.041-0.266-0.2660.0000.0000.0000.000
207A207MET0-0.040-0.01127.810-0.245-0.2450.0000.0000.0000.000
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