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: QL4JY

Calculation Name: 3F5D-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3F5D

Chain ID: A

ChEMBL ID:

UniProt ID: P96658

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 193
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2207711.937141
FMO2-HF: Nuclear repulsion 2130734.87284
FMO2-HF: Total energy -76977.064301
FMO2-MP2: Total energy -77201.97866


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:3:LEU)


Summations of interaction energy for fragment #1(A:3:LEU)
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.
-154.745-145.1155.746-5.617-9.757-0.064
Interaction energy analysis for fragmet #1(A:3:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.824 / q_NPA : 0.916
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].
3A5LYS10.9720.9883.00237.37640.1820.241-1.268-1.780-0.006
4A6ALA00.0530.0255.1332.1802.226-0.001-0.004-0.0410.000
28A30GLU-1-0.868-0.9304.352-43.293-43.028-0.001-0.032-0.2320.000
29A31ASP-1-0.876-0.9272.504-59.494-57.3111.593-1.471-2.304-0.016
30A32TRP0-0.014-0.0342.841-12.944-10.6921.556-1.695-2.112-0.020
31A33SER00.0320.0312.553-4.266-2.2182.346-1.166-3.227-0.022
32A34VAL0-0.038-0.0203.6121.2411.2710.0120.019-0.0610.000
5A7LEU0-0.027-0.0158.5990.0830.0830.0000.0000.0000.000
6A8PHE00.0240.00010.9041.1301.1300.0000.0000.0000.000
7A9LEU0-0.043-0.02314.2070.3710.3710.0000.0000.0000.000
8A10ILE00.0280.01917.2800.5160.5160.0000.0000.0000.000
9A11LEU00.0030.01319.7740.0770.0770.0000.0000.0000.000
10A12ASP-1-0.738-0.86823.302-10.587-10.5870.0000.0000.0000.000
11A13GLN0-0.0460.00125.8970.2010.2010.0000.0000.0000.000
12A14TYR0-0.039-0.01920.2360.0280.0280.0000.0000.0000.000
13A15ALA00.0470.01124.0460.2420.2420.0000.0000.0000.000
14A16ASP-1-0.808-0.88122.344-11.834-11.8340.0000.0000.0000.000
15A17TRP0-0.019-0.02321.439-0.555-0.5550.0000.0000.0000.000
16A18GLU-1-0.800-0.92021.607-12.247-12.2470.0000.0000.0000.000
17A19GLY00.0220.00717.368-0.388-0.3880.0000.0000.0000.000
18A20VAL00.0150.00915.956-1.109-1.1090.0000.0000.0000.000
19A21TYR00.0440.02715.865-0.696-0.6960.0000.0000.0000.000
20A22LEU00.0290.02512.744-0.729-0.7290.0000.0000.0000.000
21A23ALA0-0.008-0.00811.527-1.625-1.6250.0000.0000.0000.000
22A24SER0-0.020-0.03310.776-1.492-1.4920.0000.0000.0000.000
23A25ALA00.0000.01311.774-0.856-0.8560.0000.0000.0000.000
24A26LEU0-0.023-0.0137.834-1.422-1.4220.0000.0000.0000.000
25A27ASN00.0350.0036.376-4.870-4.8700.0000.0000.0000.000
26A28GLN0-0.041-0.0207.2430.2350.2350.0000.0000.0000.000
27A29ARG10.7760.8865.97930.31230.3120.0000.0000.0000.000
33A35HIS0-0.013-0.0065.686-3.045-3.0450.0000.0000.0000.000
34A36THR0-0.016-0.0259.7390.9190.9190.0000.0000.0000.000
35A37VAL0-0.018-0.01713.386-0.260-0.2600.0000.0000.0000.000
36A38SER00.020-0.01415.5940.7050.7050.0000.0000.0000.000
37A39LEU0-0.063-0.03719.387-0.134-0.1340.0000.0000.0000.000
38A40ASP-1-0.874-0.92722.241-11.067-11.0670.0000.0000.0000.000
39A41PRO0-0.006-0.01920.132-0.522-0.5220.0000.0000.0000.000
40A42ILE0-0.019-0.02220.133-0.378-0.3780.0000.0000.0000.000
41A43VAL0-0.0110.01620.5110.3640.3640.0000.0000.0000.000
42A44SER0-0.045-0.03722.867-0.250-0.2500.0000.0000.0000.000
43A45SER0-0.067-0.04923.290-0.033-0.0330.0000.0000.0000.000
44A46ILE00.0210.00725.0300.3520.3520.0000.0000.0000.000
45A47GLY0-0.036-0.01826.8600.3770.3770.0000.0000.0000.000
46A48GLY0-0.022-0.00727.8540.1570.1570.0000.0000.0000.000
47A49PHE0-0.038-0.02422.3870.0290.0290.0000.0000.0000.000
48A50LYS10.9120.95223.58310.27310.2730.0000.0000.0000.000
49A51THR00.0210.02717.255-0.025-0.0250.0000.0000.0000.000
50A52SER00.0140.00117.7020.5150.5150.0000.0000.0000.000
51A53VAL0-0.054-0.02415.974-0.721-0.7210.0000.0000.0000.000
52A54ASP-1-0.849-0.88811.208-20.379-20.3790.0000.0000.0000.000
53A55TYR0-0.019-0.0227.809-0.274-0.2740.0000.0000.0000.000
54A56ILE00.0240.02114.7130.4140.4140.0000.0000.0000.000
55A57ILE0-0.021-0.01817.556-0.408-0.4080.0000.0000.0000.000
56A58GLY0-0.108-0.06218.5310.8900.8900.0000.0000.0000.000
57A59LEU0-0.056-0.02516.8090.3680.3680.0000.0000.0000.000
58A60GLU-1-0.824-0.89613.308-17.582-17.5820.0000.0000.0000.000
59A61PRO0-0.048-0.0148.9820.2000.2000.0000.0000.0000.000
60A62ALA00.0500.01511.553-0.095-0.0950.0000.0000.0000.000
61A63ASN0-0.072-0.04110.673-0.377-0.3770.0000.0000.0000.000
62A64PHE0-0.008-0.0057.834-1.591-1.5910.0000.0000.0000.000
63A65ASN0-0.002-0.0066.209-2.472-2.4720.0000.0000.0000.000
64A66LEU00.0490.0389.1411.0851.0850.0000.0000.0000.000
65A67LEU0-0.032-0.00211.147-0.527-0.5270.0000.0000.0000.000
66A68VAL00.0080.00513.1720.8430.8430.0000.0000.0000.000
67A69MET0-0.047-0.01915.8090.2450.2450.0000.0000.0000.000
68A70ILE00.0210.00817.8720.2830.2830.0000.0000.0000.000
69A71GLY00.0170.02020.6850.2700.2700.0000.0000.0000.000
70A72GLY00.0470.01123.987-0.285-0.2850.0000.0000.0000.000
71A73ASP-1-0.893-0.94426.676-9.553-9.5530.0000.0000.0000.000
72A74SER0-0.063-0.04827.0760.3800.3800.0000.0000.0000.000
73A75TRP0-0.011-0.02821.647-0.045-0.0450.0000.0000.0000.000
74A76SER0-0.058-0.02328.2660.0720.0720.0000.0000.0000.000
75A77ASN0-0.012-0.00827.8340.2560.2560.0000.0000.0000.000
76A78ASP-1-0.890-0.94929.257-9.283-9.2830.0000.0000.0000.000
77A79ASN00.0450.02926.773-0.181-0.1810.0000.0000.0000.000
78A80LYS10.9780.98025.95810.93610.9360.0000.0000.0000.000
79A81LYS10.9010.93923.37811.43911.4390.0000.0000.0000.000
80A82LEU00.0860.05321.828-0.494-0.4940.0000.0000.0000.000
81A83LEU00.0190.01022.564-0.449-0.4490.0000.0000.0000.000
82A84HIS0-0.029-0.01321.4110.2770.2770.0000.0000.0000.000
83A85PHE00.0290.03614.521-0.233-0.2330.0000.0000.0000.000
84A86VAL00.0610.02918.908-0.603-0.6030.0000.0000.0000.000
85A87LYS10.9510.98020.34910.67610.6760.0000.0000.0000.000
86A88THR00.009-0.02418.6210.0160.0160.0000.0000.0000.000
87A89ALA0-0.029-0.01116.570-0.604-0.6040.0000.0000.0000.000
88A90PHE00.0600.01317.821-0.461-0.4610.0000.0000.0000.000
89A91GLN0-0.061-0.02620.695-0.264-0.2640.0000.0000.0000.000
90A92LYS10.8280.91714.85318.83818.8380.0000.0000.0000.000
91A93ASN0-0.028-0.00717.021-0.515-0.5150.0000.0000.0000.000
92A94ILE0-0.0040.01612.971-0.531-0.5310.0000.0000.0000.000
93A95PRO00.0230.00813.0141.2471.2470.0000.0000.0000.000
94A96ILE0-0.0030.00314.590-0.732-0.7320.0000.0000.0000.000
95A97ALA00.0150.01617.2010.6160.6160.0000.0000.0000.000
96A98ALA0-0.033-0.01618.726-0.123-0.1230.0000.0000.0000.000
97A99ILE0-0.0200.00321.0260.3580.3580.0000.0000.0000.000
98A100CYS00.0210.02223.5480.2500.2500.0000.0000.0000.000
99A101GLY00.0240.00526.8060.0390.0390.0000.0000.0000.000
100A102ALA0-0.0190.00522.6450.1400.1400.0000.0000.0000.000
101A103VAL0-0.020-0.02024.708-0.072-0.0720.0000.0000.0000.000
102A104ASP-1-0.772-0.88126.470-9.726-9.7260.0000.0000.0000.000
103A105PHE0-0.001-0.00225.1170.2030.2030.0000.0000.0000.000
104A106LEU0-0.013-0.01022.8430.1300.1300.0000.0000.0000.000
105A107ALA00.0300.02526.9540.1640.1640.0000.0000.0000.000
106A108LYS10.9030.95530.6359.2399.2390.0000.0000.0000.000
107A109ASN0-0.074-0.06327.9160.3930.3930.0000.0000.0000.000
108A110GLY0-0.0070.00529.540-0.112-0.1120.0000.0000.0000.000
109A111LEU0-0.079-0.03723.981-0.028-0.0280.0000.0000.0000.000
110A112LEU00.0010.01026.330-0.319-0.3190.0000.0000.0000.000
111A113ASN0-0.028-0.01228.4870.1590.1590.0000.0000.0000.000
112A114ASN00.008-0.00828.2960.5420.5420.0000.0000.0000.000
113A115HIS0-0.023-0.00723.190-0.216-0.2160.0000.0000.0000.000
114A116SER00.0140.00928.2930.4600.4600.0000.0000.0000.000
115A117HIS0-0.008-0.00127.627-0.204-0.2040.0000.0000.0000.000
116A118THR00.019-0.00127.4390.4250.4250.0000.0000.0000.000
117A119GLY00.035-0.00728.655-0.314-0.3140.0000.0000.0000.000
118A120ASN00.0020.00229.4260.0290.0290.0000.0000.0000.000
119A121PHE00.0460.01031.8440.2040.2040.0000.0000.0000.000
120A122VAL00.0520.04235.3290.0570.0570.0000.0000.0000.000
121A123TYR00.002-0.01436.2250.1150.1150.0000.0000.0000.000
122A124LEU0-0.044-0.01133.8280.2050.2050.0000.0000.0000.000
123A125TRP0-0.034-0.05930.3040.0190.0190.0000.0000.0000.000
124A126LYS10.8640.92336.3717.2257.2250.0000.0000.0000.000
125A127ASP-1-0.839-0.88539.846-7.206-7.2060.0000.0000.0000.000
126A128TYR0-0.030-0.00832.884-0.075-0.0750.0000.0000.0000.000
127A129LYS10.9800.98337.2857.8787.8780.0000.0000.0000.000
128A130GLN0-0.073-0.03431.9860.0310.0310.0000.0000.0000.000
129A131TYR00.0170.01232.310-0.120-0.1200.0000.0000.0000.000
130A132LYS10.8240.88634.4898.5308.5300.0000.0000.0000.000
131A133PRO0-0.0130.01633.101-0.105-0.1050.0000.0000.0000.000
132A134ILE00.0000.00431.8830.2650.2650.0000.0000.0000.000
133A135SER0-0.065-0.01632.0790.0240.0240.0000.0000.0000.000
134A136SER0-0.013-0.02234.1840.0660.0660.0000.0000.0000.000
135A137PHE00.0230.02732.140-0.287-0.2870.0000.0000.0000.000
136A138VAL0-0.019-0.00931.5250.3020.3020.0000.0000.0000.000
137A139GLU-1-0.915-0.95032.404-8.470-8.4700.0000.0000.0000.000
138A140LYS10.8970.94130.3359.5489.5480.0000.0000.0000.000
139A141GLN00.0040.01327.8790.1570.1570.0000.0000.0000.000
140A142ALA00.005-0.00623.979-0.211-0.2110.0000.0000.0000.000
141A143VAL0-0.024-0.01225.3620.3280.3280.0000.0000.0000.000
142A144ARG10.9400.98818.45915.81615.8160.0000.0000.0000.000
143A145ASP-1-0.761-0.86723.644-11.413-11.4130.0000.0000.0000.000
144A146LYS10.8480.90622.20311.78111.7810.0000.0000.0000.000
145A147ASN00.0010.00616.657-0.348-0.3480.0000.0000.0000.000
146A148LEU00.0020.00918.932-0.422-0.4220.0000.0000.0000.000
147A149VAL00.0180.00019.0430.4820.4820.0000.0000.0000.000
148A150THR0-0.038-0.01521.4180.1740.1740.0000.0000.0000.000
149A151ALA00.0640.01823.8420.0870.0870.0000.0000.0000.000
150A152ASN00.0310.04625.5860.0090.0090.0000.0000.0000.000
151A153GLY00.0790.02026.421-0.311-0.3110.0000.0000.0000.000
152A154THR0-0.049-0.03227.219-0.016-0.0160.0000.0000.0000.000
153A155ALA0-0.0080.01626.0840.0260.0260.0000.0000.0000.000
154A156PRO00.0470.02621.610-0.455-0.4550.0000.0000.0000.000
155A157ILE00.0000.00920.719-0.786-0.7860.0000.0000.0000.000
156A158GLU-1-0.785-0.89121.440-11.896-11.8960.0000.0000.0000.000
157A159PHE00.014-0.00418.709-0.405-0.4050.0000.0000.0000.000
158A160THR0-0.007-0.02515.936-0.859-0.8590.0000.0000.0000.000
159A161ASN0-0.001-0.00917.173-0.882-0.8820.0000.0000.0000.000
160A162LEU0-0.004-0.00318.546-0.566-0.5660.0000.0000.0000.000
161A163ILE0-0.007-0.01013.897-0.493-0.4930.0000.0000.0000.000
162A164LEU0-0.026-0.01812.749-1.289-1.2890.0000.0000.0000.000
163A165GLU-1-0.871-0.93614.845-15.254-15.2540.0000.0000.0000.000
164A166MET0-0.132-0.04615.6040.2090.2090.0000.0000.0000.000
165A167ILE0-0.094-0.04610.206-0.462-0.4620.0000.0000.0000.000
166A168ASP-1-0.930-0.95311.443-22.230-22.2300.0000.0000.0000.000
167A169PHE0-0.026-0.0088.620-1.437-1.4370.0000.0000.0000.000
168A170ASP-1-0.827-0.91011.482-22.245-22.2450.0000.0000.0000.000
169A171THR0-0.016-0.02314.3590.3900.3900.0000.0000.0000.000
170A172PRO00.0700.02518.047-0.024-0.0240.0000.0000.0000.000
171A173GLU-1-0.888-0.92820.940-13.999-13.9990.0000.0000.0000.000
172A174ASN0-0.078-0.04217.0960.8500.8500.0000.0000.0000.000
173A175ILE00.0190.00415.8530.0740.0740.0000.0000.0000.000
174A176GLU-1-0.859-0.90618.673-11.376-11.3760.0000.0000.0000.000
175A177LYS10.9290.97421.07813.35513.3550.0000.0000.0000.000
176A178MET00.0070.00513.7790.1010.1010.0000.0000.0000.000
177A179MET0-0.040-0.02017.6680.3410.3410.0000.0000.0000.000
178A180TYR0-0.009-0.00621.6570.5380.5380.0000.0000.0000.000
179A181MET00.0090.01021.8660.6530.6530.0000.0000.0000.000
180A182ASN0-0.032-0.02318.4410.4270.4270.0000.0000.0000.000
181A183ARG10.8300.91522.92711.58611.5860.0000.0000.0000.000
182A184TYR0-0.043-0.02626.2880.3240.3240.0000.0000.0000.000
183A185GLY00.0280.03426.4620.3140.3140.0000.0000.0000.000
184A186PHE00.020-0.01526.2060.0930.0930.0000.0000.0000.000
185A187TYR00.0150.00627.922-0.014-0.0140.0000.0000.0000.000
186A188HIS00.0640.03330.787-0.072-0.0720.0000.0000.0000.000
187A189PHE0-0.046-0.01123.559-0.097-0.0970.0000.0000.0000.000
188A190CYS0-0.012-0.01228.454-0.024-0.0240.0000.0000.0000.000
189A191ASP-1-0.925-0.95930.503-8.717-8.7170.0000.0000.0000.000
190A192LYS10.8100.91628.25610.82410.8240.0000.0000.0000.000
191A193TYR0-0.083-0.08226.500-0.098-0.0980.0000.0000.0000.000
192A194GLY0-0.0390.00129.177-0.135-0.1350.0000.0000.0000.000
193A195ASN-1-0.933-0.96525.630-11.025-11.0250.0000.0000.0000.000