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: GV3M1

Calculation Name: 4Y9A-B-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4Y9A

Chain ID: B

ChEMBL ID:

UniProt ID: Q9Z520

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 255
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -3225404.44914
FMO2-HF: Nuclear repulsion 3129116.76206
FMO2-HF: Total energy -96287.68708
FMO2-MP2: Total energy -96568.330101


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:6:THR)


Summations of interaction energy for fragment #1(A:6: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.
-231.196-228.2840.259-1.577-1.594-0.013
Interaction energy analysis for fragmet #1(A:6:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.834 / 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].
3A8THR00.0120.0142.836-6.707-3.8380.260-1.573-1.556-0.013
209A214LYS10.8110.9214.90922.12922.172-0.001-0.004-0.0380.000
4A9PRO00.0220.0224.9183.3403.3400.0000.0000.0000.000
5A10LEU0-0.030-0.0187.4271.2451.2450.0000.0000.0000.000
6A11MET0-0.0010.01511.0501.0711.0710.0000.0000.0000.000
7A12ALA00.0180.01214.0650.6210.6210.0000.0000.0000.000
8A13GLY00.016-0.01917.0870.4090.4090.0000.0000.0000.000
9A14ASN0-0.004-0.00220.4020.6270.6270.0000.0000.0000.000
10A15TRP00.0280.00323.1330.4320.4320.0000.0000.0000.000
11A16LYS10.8780.92425.79011.64411.6440.0000.0000.0000.000
12A17MET0-0.0150.00128.4960.0810.0810.0000.0000.0000.000
13A18ASN0-0.072-0.05330.1480.5720.5720.0000.0000.0000.000
14A19LEU0-0.0060.00528.722-0.264-0.2640.0000.0000.0000.000
15A20ASN00.0220.02132.6040.0600.0600.0000.0000.0000.000
16A21HIS00.0450.01432.976-0.216-0.2160.0000.0000.0000.000
17A22LEU0-0.021-0.01633.304-0.156-0.1560.0000.0000.0000.000
18A23GLU-1-0.870-0.93433.059-8.786-8.7860.0000.0000.0000.000
19A24ALA00.0180.00929.325-0.281-0.2810.0000.0000.0000.000
20A25ILE0-0.032-0.01128.796-0.358-0.3580.0000.0000.0000.000
21A26ALA00.0210.00429.725-0.236-0.2360.0000.0000.0000.000
22A27HIS0-0.076-0.03825.4050.1540.1540.0000.0000.0000.000
23A28VAL00.0250.00223.957-0.363-0.3630.0000.0000.0000.000
24A29GLN0-0.002-0.00825.197-0.153-0.1530.0000.0000.0000.000
25A30LYS10.9020.96727.1449.7489.7480.0000.0000.0000.000
26A31LEU00.0280.01021.510-0.220-0.2200.0000.0000.0000.000
27A32ALA0-0.026-0.01622.187-0.487-0.4870.0000.0000.0000.000
28A33PHE0-0.071-0.02523.667-0.048-0.0480.0000.0000.0000.000
29A34ALA00.0110.01223.6980.0570.0570.0000.0000.0000.000
30A35LEU0-0.034-0.00117.494-0.459-0.4590.0000.0000.0000.000
31A36ALA00.019-0.00118.8560.5860.5860.0000.0000.0000.000
32A37ASP-1-0.902-0.96817.449-16.114-16.1140.0000.0000.0000.000
33A38LYS10.9530.97014.04317.44417.4440.0000.0000.0000.000
34A39ASP-1-0.768-0.85413.091-18.106-18.1060.0000.0000.0000.000
35A40TYR00.012-0.01412.625-0.870-0.8700.0000.0000.0000.000
36A41ASP-1-1.000-0.97911.274-26.283-26.2830.0000.0000.0000.000
37A42ALA0-0.030-0.0118.365-2.831-2.8310.0000.0000.0000.000
38A43VAL0-0.027-0.0167.684-3.137-3.1370.0000.0000.0000.000
39A44GLU-1-0.765-0.8239.817-22.521-22.5210.0000.0000.0000.000
40A45VAL00.0150.00911.6480.5470.5470.0000.0000.0000.000
41A46ALA0-0.006-0.00815.1350.4660.4660.0000.0000.0000.000
42A47VAL0-0.0070.00617.5020.2810.2810.0000.0000.0000.000
43A48LEU0-0.015-0.01419.919-0.018-0.0180.0000.0000.0000.000
44A49ALA00.0180.02323.1290.3480.3480.0000.0000.0000.000
45A50PRO00.0600.02826.768-0.053-0.0530.0000.0000.0000.000
46A51PHE00.028-0.00929.449-0.013-0.0130.0000.0000.0000.000
47A52THR0-0.067-0.04231.6180.0160.0160.0000.0000.0000.000
48A53ASP-1-0.794-0.89830.332-9.385-9.3850.0000.0000.0000.000
49A54LEU0-0.0050.00526.513-0.122-0.1220.0000.0000.0000.000
50A55ARG10.9000.94429.0559.3119.3110.0000.0000.0000.000
51A56SER00.0210.00331.7430.1270.1270.0000.0000.0000.000
52A57VAL00.0290.01125.140-0.016-0.0160.0000.0000.0000.000
53A58GLN00.0320.03627.1630.1980.1980.0000.0000.0000.000
54A59THR0-0.074-0.04528.1920.0110.0110.0000.0000.0000.000
55A60LEU0-0.0160.01627.4610.1160.1160.0000.0000.0000.000
56A61VAL00.0020.00623.059-0.043-0.0430.0000.0000.0000.000
57A62ASP-1-0.819-0.90125.916-11.589-11.5890.0000.0000.0000.000
58A63GLY0-0.038-0.01028.0420.1490.1490.0000.0000.0000.000
59A64ASP-1-0.871-0.96127.669-10.266-10.2660.0000.0000.0000.000
60A65LYS10.7500.87524.77110.59710.5970.0000.0000.0000.000
61A66LEU0-0.0010.01422.691-0.528-0.5280.0000.0000.0000.000
62A67LYS10.9220.96317.24915.69715.6970.0000.0000.0000.000
63A68ILE0-0.0300.00717.448-0.970-0.9700.0000.0000.0000.000
64A69LYS10.8780.93114.69520.73720.7370.0000.0000.0000.000
65A70TYR0-0.006-0.03718.7780.2750.2750.0000.0000.0000.000
66A71GLY00.0320.00221.275-0.429-0.4290.0000.0000.0000.000
67A72ALA00.0050.01122.7410.4460.4460.0000.0000.0000.000
68A73GLN0-0.038-0.04924.078-0.206-0.2060.0000.0000.0000.000
69A74ASP-1-0.782-0.85826.296-10.353-10.3530.0000.0000.0000.000
70A75ILE0-0.044-0.02626.564-0.065-0.0650.0000.0000.0000.000
71A76SER0-0.046-0.04729.1640.1740.1740.0000.0000.0000.000
72A77ALA00.0180.01030.590-0.270-0.2700.0000.0000.0000.000
73A78HIS10.8600.92731.7289.0029.0020.0000.0000.0000.000
74A79ASP-1-0.776-0.88432.551-9.862-9.8620.0000.0000.0000.000
75A80GLY00.010-0.00434.098-0.041-0.0410.0000.0000.0000.000
76A81GLY00.000-0.00137.3990.0270.0270.0000.0000.0000.000
77A82ALA0-0.025-0.00940.952-0.012-0.0120.0000.0000.0000.000
78A83TYR0-0.0020.00138.3210.0580.0580.0000.0000.0000.000
79A84THR00.002-0.01139.552-0.160-0.1600.0000.0000.0000.000
80A85GLY00.0210.01739.2720.0410.0410.0000.0000.0000.000
81A86GLU-1-0.849-0.89535.189-9.106-9.1060.0000.0000.0000.000
82A87ILE0-0.007-0.00231.4410.1400.1400.0000.0000.0000.000
83A88SER00.027-0.00531.904-0.293-0.2930.0000.0000.0000.000
84A89GLY00.0950.04528.689-0.093-0.0930.0000.0000.0000.000
85A90PRO0-0.014-0.02128.976-0.210-0.2100.0000.0000.0000.000
86A91MET0-0.067-0.00631.1600.0350.0350.0000.0000.0000.000
87A92LEU00.0590.02226.538-0.009-0.0090.0000.0000.0000.000
88A93ALA00.0650.04626.615-0.287-0.2870.0000.0000.0000.000
89A94LYS10.8930.94127.6739.6509.6500.0000.0000.0000.000
90A95LEU0-0.018-0.00228.8260.1300.1300.0000.0000.0000.000
91A96LYS10.7820.88924.91111.49711.4970.0000.0000.0000.000
92A97CYS0-0.0350.01123.504-0.288-0.2880.0000.0000.0000.000
93A98THR0-0.019-0.01016.898-0.311-0.3110.0000.0000.0000.000
94A99TYR0-0.008-0.03513.587-0.348-0.3480.0000.0000.0000.000
95A100VAL0-0.025-0.01119.8900.8480.8480.0000.0000.0000.000
96A101ALA0-0.0040.02421.587-0.513-0.5130.0000.0000.0000.000
97A102VAL0-0.019-0.02022.6350.6530.6530.0000.0000.0000.000
98A103GLY00.0780.03523.482-0.415-0.4150.0000.0000.0000.000
99A104HIS0-0.044-0.02523.6170.1660.1660.0000.0000.0000.000
100A105SER0-0.008-0.03425.4850.6650.6650.0000.0000.0000.000
101A106GLU-1-0.817-0.89827.317-10.175-10.1750.0000.0000.0000.000
102A107ARG10.8230.91928.73810.41610.4160.0000.0000.0000.000
103A108ARG10.8070.88224.37012.02612.0260.0000.0000.0000.000
104A109GLN0-0.0140.00930.7740.4540.4540.0000.0000.0000.000
105A110TYR0-0.052-0.03433.3090.3290.3290.0000.0000.0000.000
106A111HIS0-0.046-0.03533.6120.0480.0480.0000.0000.0000.000
107A112ALA00.0000.01334.9210.0210.0210.0000.0000.0000.000
108A113GLU-1-0.848-0.91429.184-10.552-10.5520.0000.0000.0000.000
109A114THR00.009-0.02430.848-0.242-0.2420.0000.0000.0000.000
110A115ASP-1-0.768-0.88527.335-11.510-11.5100.0000.0000.0000.000
111A116GLU-1-0.861-0.91928.080-9.900-9.9000.0000.0000.0000.000
112A117ILE0-0.054-0.01630.314-0.093-0.0930.0000.0000.0000.000
113A118VAL00.0320.02324.938-0.188-0.1880.0000.0000.0000.000
114A119ASN0-0.073-0.04624.8600.0360.0360.0000.0000.0000.000
115A120ALA0-0.028-0.01426.504-0.206-0.2060.0000.0000.0000.000
116A121LYS10.7670.85827.26510.28910.2890.0000.0000.0000.000
117A122VAL00.0240.01821.361-0.250-0.2500.0000.0000.0000.000
118A123LYS10.8940.94923.56410.83910.8390.0000.0000.0000.000
119A124ALA0-0.045-0.01225.634-0.013-0.0130.0000.0000.0000.000
120A125ALA00.006-0.01423.1460.0040.0040.0000.0000.0000.000
121A126TYR00.0420.00816.4700.2030.2030.0000.0000.0000.000
122A127LYS10.7990.90323.02010.05010.0500.0000.0000.0000.000
123A128HIS0-0.069-0.04326.0700.2790.2790.0000.0000.0000.000
124A129GLY00.0000.00522.4310.1300.1300.0000.0000.0000.000
125A130LEU0-0.063-0.01721.584-0.370-0.3700.0000.0000.0000.000
126A131THR00.0180.00915.511-0.388-0.3880.0000.0000.0000.000
127A132PRO0-0.046-0.02018.8870.1690.1690.0000.0000.0000.000
128A133ILE00.008-0.00616.639-0.798-0.7980.0000.0000.0000.000
129A134LEU0-0.0070.01018.4540.9800.9800.0000.0000.0000.000
130A135CYS0-0.080-0.02519.095-0.661-0.6610.0000.0000.0000.000
131A136VAL00.0230.01119.3160.5920.5920.0000.0000.0000.000
132A137GLY00.0370.00821.503-0.479-0.4790.0000.0000.0000.000
133A138GLU-1-0.707-0.80223.657-11.927-11.9270.0000.0000.0000.000
134A139GLU-1-0.912-0.96826.382-9.533-9.5330.0000.0000.0000.000
135A140LEU0-0.015-0.03229.378-0.139-0.1390.0000.0000.0000.000
136A141ASP-1-0.864-0.92831.081-8.754-8.7540.0000.0000.0000.000
137A142VAL0-0.030-0.01828.1300.0700.0700.0000.0000.0000.000
138A143ARG10.8240.91221.71912.02412.0240.0000.0000.0000.000
139A144GLU-1-0.973-0.99528.434-8.672-8.6720.0000.0000.0000.000
140A145ALA0-0.072-0.03531.6840.1330.1330.0000.0000.0000.000
141A146GLY0-0.0230.00228.5140.0710.0710.0000.0000.0000.000
142A147ASN00.0130.01027.574-0.302-0.3020.0000.0000.0000.000
143A148HIS0-0.022-0.03022.4370.2100.2100.0000.0000.0000.000
144A149VAL00.0370.01620.989-0.341-0.3410.0000.0000.0000.000
145A150GLU-1-0.925-0.95422.657-10.853-10.8530.0000.0000.0000.000
146A151HIS0-0.009-0.00425.2530.1130.1130.0000.0000.0000.000
147A152THR0-0.008-0.01320.185-0.053-0.0530.0000.0000.0000.000
148A153LEU0-0.013-0.02018.815-0.433-0.4330.0000.0000.0000.000
149A154ALA0-0.0190.00521.717-0.141-0.1410.0000.0000.0000.000
150A155GLN00.0440.02223.587-0.387-0.3870.0000.0000.0000.000
151A156VAL0-0.031-0.01017.864-0.113-0.1130.0000.0000.0000.000
152A157GLU-1-0.826-0.91921.075-12.214-12.2140.0000.0000.0000.000
153A158GLY0-0.031-0.02122.7700.2500.2500.0000.0000.0000.000
154A159GLY00.018-0.00323.1090.2180.2180.0000.0000.0000.000
155A160LEU00.004-0.00217.353-0.088-0.0880.0000.0000.0000.000
156A161LYS10.8980.97421.91611.16711.1670.0000.0000.0000.000
157A162ASP-1-0.905-0.96725.257-10.889-10.8890.0000.0000.0000.000
158A163LEU0-0.0230.02319.3610.1880.1880.0000.0000.0000.000
159A164ALA00.0290.02321.333-0.281-0.2810.0000.0000.0000.000
160A165ALA00.0370.00316.656-0.461-0.4610.0000.0000.0000.000
161A166GLU-1-0.891-0.93916.047-16.355-16.3550.0000.0000.0000.000
162A167GLN0-0.045-0.01716.650-0.119-0.1190.0000.0000.0000.000
163A168ALA00.0250.01216.269-0.940-0.9400.0000.0000.0000.000
164A169GLU-1-0.876-0.94111.027-26.171-26.1710.0000.0000.0000.000
165A170SER0-0.070-0.04111.194-1.812-1.8120.0000.0000.0000.000
166A171VAL0-0.036-0.00313.3050.1360.1360.0000.0000.0000.000
167A172VAL0-0.011-0.01312.637-1.876-1.8760.0000.0000.0000.000
168A173ILE00.0120.01013.8011.5901.5900.0000.0000.0000.000
169A174ALA0-0.007-0.01014.683-0.994-0.9940.0000.0000.0000.000
170A175TYR00.000-0.04316.6130.7380.7380.0000.0000.0000.000
171A176GLU-1-0.786-0.87118.362-12.594-12.5940.0000.0000.0000.000
172A177PRO00.0290.02120.2110.4500.4500.0000.0000.0000.000
173A178VAL00.0360.00023.0030.3310.3310.0000.0000.0000.000
174A179TRP0-0.053-0.01723.3420.5360.5360.0000.0000.0000.000
175A180ALA0-0.055-0.03224.7210.3190.3190.0000.0000.0000.000
176A181ILE0-0.0120.01423.840-0.289-0.2890.0000.0000.0000.000
177A182GLY0-0.0050.00226.3960.1190.1190.0000.0000.0000.000
178A183THR0-0.052-0.04929.4460.4350.4350.0000.0000.0000.000
179A184GLY0-0.027-0.00329.409-0.235-0.2350.0000.0000.0000.000
180A185LYS10.9120.97128.7149.3219.3210.0000.0000.0000.000
181A186VAL00.0190.00023.263-0.095-0.0950.0000.0000.0000.000
182A187CYS00.0120.03320.0920.0180.0180.0000.0000.0000.000
183A188GLY00.0450.03220.711-0.417-0.4170.0000.0000.0000.000
184A189ALA00.0630.02115.239-0.394-0.3940.0000.0000.0000.000
185A190ASP-1-0.904-0.94815.622-16.293-16.2930.0000.0000.0000.000
186A191ASP-1-0.869-0.93317.697-12.848-12.8480.0000.0000.0000.000
187A192ALA0-0.019-0.01615.799-0.097-0.0970.0000.0000.0000.000
188A193GLN00.022-0.01210.898-1.258-1.2580.0000.0000.0000.000
189A194GLU-1-0.887-0.93314.313-13.736-13.7360.0000.0000.0000.000
190A195VAL00.0010.00116.852-0.229-0.2290.0000.0000.0000.000
191A196CYS0-0.043-0.02212.022-0.109-0.1090.0000.0000.0000.000
192A197ALA00.0310.01712.380-0.909-0.9090.0000.0000.0000.000
193A198ALA0-0.0140.00013.334-0.087-0.0870.0000.0000.0000.000
194A199ILE0-0.013-0.00714.3910.2990.2990.0000.0000.0000.000
195A200ARG10.7410.8348.00029.33129.3310.0000.0000.0000.000
196A201GLY00.0090.00212.986-0.161-0.1610.0000.0000.0000.000
197A202LYS10.9100.94115.81013.56213.5620.0000.0000.0000.000
198A203LEU0-0.016-0.01212.5910.4270.4270.0000.0000.0000.000
199A204ALA0-0.049-0.02613.497-0.108-0.1080.0000.0000.0000.000
200A205GLU-1-0.995-0.99815.115-13.485-13.4850.0000.0000.0000.000
201A206LEU0-0.077-0.03318.3860.6850.6850.0000.0000.0000.000
202A207TYR0-0.053-0.03915.5570.1430.1430.0000.0000.0000.000
203A208SER00.0370.01413.9880.1220.1220.0000.0000.0000.000
204A209GLN00.0260.00010.132-1.679-1.6790.0000.0000.0000.000
205A210GLU-1-0.912-0.9389.350-26.459-26.4590.0000.0000.0000.000
206A211LEU0-0.0070.0089.477-1.710-1.7100.0000.0000.0000.000
207A212ALA00.0040.0019.953-1.437-1.4370.0000.0000.0000.000
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