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: 5RLJZ

Calculation Name: 2I9D-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2I9D

Chain ID: A

ChEMBL ID:

UniProt ID: Q8A336

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 214
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2666483.225938
FMO2-HF: Nuclear repulsion 2580550.565409
FMO2-HF: Total energy -85932.660529
FMO2-MP2: Total energy -86186.286199


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-233.411-227.8882.401-3.274-4.65-0.031
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.831 / q_NPA : 0.909
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].
3A3GLN00.0030.0193.8105.9807.687-0.027-0.698-0.982-0.002
80A80TYR00.006-0.0103.588-6.977-6.5720.002-0.119-0.288-0.001
81A81ASP-1-0.898-0.9582.453-64.367-61.1462.428-2.446-3.204-0.028
82A82THR0-0.097-0.0584.5278.0868.278-0.001-0.010-0.1810.000
140A140ASP-1-0.826-0.9025.084-57.198-57.200-0.001-0.0010.0050.000
4A4ILE00.009-0.0066.9880.6560.6560.0000.0000.0000.000
5A5ILE0-0.046-0.0089.7181.1761.1760.0000.0000.0000.000
6A6ASP-1-0.846-0.90912.851-15.369-15.3690.0000.0000.0000.000
7A7ILE0-0.057-0.04516.1850.1540.1540.0000.0000.0000.000
8A8GLU-1-0.867-0.91718.613-12.382-12.3820.0000.0000.0000.000
9A9ASN0-0.076-0.04418.5751.0541.0540.0000.0000.0000.000
10A10TRP00.0350.00016.724-0.112-0.1120.0000.0000.0000.000
11A11GLU-1-0.918-0.96218.605-15.117-15.1170.0000.0000.0000.000
12A12ARG10.7890.87418.83115.68515.6850.0000.0000.0000.000
13A13LYS10.8510.94220.94312.68712.6870.0000.0000.0000.000
14A14GLU-1-0.825-0.92421.775-11.896-11.8960.0000.0000.0000.000
15A15ASN0-0.012-0.00622.5750.2820.2820.0000.0000.0000.000
16A16PHE00.031-0.00117.7550.1410.1410.0000.0000.0000.000
17A17ASN0-0.024-0.01821.720-0.307-0.3070.0000.0000.0000.000
18A18PHE0-0.035-0.00124.3590.4340.4340.0000.0000.0000.000
19A19PHE00.004-0.01623.2510.3480.3480.0000.0000.0000.000
20A20ARG10.8780.95319.93814.74714.7470.0000.0000.0000.000
21A21HIS00.0500.02023.618-0.181-0.1810.0000.0000.0000.000
22A22PHE0-0.025-0.00125.9910.4940.4940.0000.0000.0000.000
23A23GLN0-0.040-0.02126.498-0.116-0.1160.0000.0000.0000.000
24A24ASN00.0860.03325.393-0.682-0.6820.0000.0000.0000.000
25A25PRO0-0.0170.01821.8220.3840.3840.0000.0000.0000.000
26A26GLN00.0060.00520.700-1.196-1.1960.0000.0000.0000.000
27A27LEU0-0.057-0.01723.4570.6980.6980.0000.0000.0000.000
28A28SER0-0.001-0.01123.867-0.497-0.4970.0000.0000.0000.000
29A29ILE0-0.017-0.00424.4900.4980.4980.0000.0000.0000.000
30A30THR0-0.030-0.03526.488-0.196-0.1960.0000.0000.0000.000
31A31SER00.0120.02127.9180.4220.4220.0000.0000.0000.000
32A32GLU-1-0.882-0.92928.831-9.374-9.3740.0000.0000.0000.000
33A33VAL00.0280.01826.327-0.149-0.1490.0000.0000.0000.000
34A34GLU-1-0.851-0.91629.676-8.929-8.9290.0000.0000.0000.000
35A35CYS0-0.016-0.01829.027-0.312-0.3120.0000.0000.0000.000
36A36GLY00.0320.02030.4070.0340.0340.0000.0000.0000.000
37A37GLY00.014-0.00231.9520.0950.0950.0000.0000.0000.000
38A38ALA00.0040.00427.560-0.034-0.0340.0000.0000.0000.000
39A39ARG10.9590.98729.3339.6399.6390.0000.0000.0000.000
40A40GLN0-0.044-0.02232.0650.1310.1310.0000.0000.0000.000
41A41ARG10.8570.93726.96911.36711.3670.0000.0000.0000.000
42A42ALA00.0090.01828.7600.0340.0340.0000.0000.0000.000
43A43LYS10.9390.96530.1848.4298.4290.0000.0000.0000.000
44A44ALA0-0.046-0.02633.7440.1940.1940.0000.0000.0000.000
45A45ALA00.0020.00529.9280.1580.1580.0000.0000.0000.000
46A46GLY0-0.0130.00831.255-0.112-0.1120.0000.0000.0000.000
47A47GLN0-0.0060.00726.242-0.244-0.2440.0000.0000.0000.000
48A48SER00.0360.00525.6510.3390.3390.0000.0000.0000.000
49A49PHE00.019-0.02525.951-0.400-0.4000.0000.0000.0000.000
50A50PHE00.0120.01021.462-0.080-0.0800.0000.0000.0000.000
51A51LEU00.0430.02220.392-0.440-0.4400.0000.0000.0000.000
52A52HIS0-0.027-0.01821.330-0.604-0.6040.0000.0000.0000.000
53A53TYR00.0460.01122.319-0.417-0.4170.0000.0000.0000.000
54A54LEU0-0.038-0.00417.873-0.380-0.3800.0000.0000.0000.000
55A55TYR00.0080.02116.742-0.595-0.5950.0000.0000.0000.000
56A56ALA0-0.013-0.00617.647-0.733-0.7330.0000.0000.0000.000
57A57VAL00.0150.00117.234-0.358-0.3580.0000.0000.0000.000
58A58LEU0-0.0110.01311.591-0.524-0.5240.0000.0000.0000.000
59A59ARG10.8480.92113.67215.54315.5430.0000.0000.0000.000
60A60ALA0-0.028-0.02115.343-0.538-0.5380.0000.0000.0000.000
61A61ALA0-0.022-0.01113.2490.0680.0680.0000.0000.0000.000
62A62ASN0-0.006-0.0139.367-4.483-4.4830.0000.0000.0000.000
63A63GLU-1-0.786-0.88112.062-17.972-17.9720.0000.0000.0000.000
64A64ILE0-0.028-0.00414.8601.2371.2370.0000.0000.0000.000
65A65PRO00.0270.02212.712-1.060-1.0600.0000.0000.0000.000
66A66GLU-1-0.810-0.92412.775-19.671-19.6710.0000.0000.0000.000
67A67PHE0-0.026-0.02114.1530.0280.0280.0000.0000.0000.000
68A68ARG10.8620.9408.24130.84630.8460.0000.0000.0000.000
69A69TYR0-0.0150.0089.435-3.444-3.4440.0000.0000.0000.000
70A70ARG10.7440.8548.88629.16129.1610.0000.0000.0000.000
71A71ILE0-0.036-0.01311.5460.3660.3660.0000.0000.0000.000
72A72ASP-1-0.705-0.8288.271-37.421-37.4210.0000.0000.0000.000
73A73PRO00.0230.02410.0682.3932.3930.0000.0000.0000.000
74A74ASP-1-0.847-0.90312.329-22.726-22.7260.0000.0000.0000.000
75A75GLY0-0.027-0.01414.6531.2641.2640.0000.0000.0000.000
76A76ARG10.8090.88910.24724.96524.9650.0000.0000.0000.000
77A77VAL0-0.0250.00012.919-0.900-0.9000.0000.0000.0000.000
78A78VAL0-0.008-0.0057.810-0.024-0.0240.0000.0000.0000.000
79A79LEU0-0.0040.0078.3811.6431.6430.0000.0000.0000.000
83A83ILE0-0.072-0.0135.250-5.918-5.9180.0000.0000.0000.000
84A84ASP-1-0.742-0.8507.887-34.330-34.3300.0000.0000.0000.000
85A85MET0-0.062-0.0369.6011.2221.2220.0000.0000.0000.000
86A86LEU00.0500.03112.8020.2580.2580.0000.0000.0000.000
87A87SER0-0.019-0.04815.3711.0041.0040.0000.0000.0000.000
88A88PRO0-0.0050.00919.123-0.027-0.0270.0000.0000.0000.000
89A89ILE0-0.0020.00521.2790.5740.5740.0000.0000.0000.000
90A90LYS10.8290.89924.1739.9239.9230.0000.0000.0000.000
91A91ILE00.0230.01526.7340.0280.0280.0000.0000.0000.000
92A92LYS10.8550.93029.48310.27510.2750.0000.0000.0000.000
93A93GLU-1-0.810-0.90933.057-9.457-9.4570.0000.0000.0000.000
94A94ASN0-0.063-0.03134.570-0.048-0.0480.0000.0000.0000.000
95A95GLY00.0130.00732.4580.0310.0310.0000.0000.0000.000
96A96LYS10.8230.92828.23910.83510.8350.0000.0000.0000.000
97A97PHE00.0170.00923.8000.1270.1270.0000.0000.0000.000
98A98PHE00.012-0.00320.8520.2650.2650.0000.0000.0000.000
99A99THR0-0.019-0.01717.865-0.050-0.0500.0000.0000.0000.000
100A100THR0-0.0100.00317.481-0.487-0.4870.0000.0000.0000.000
101A101ARG10.7680.8496.37637.87737.8770.0000.0000.0000.000
102A102PHE0-0.040-0.01913.5901.0491.0490.0000.0000.0000.000
103A103PRO00.0390.03210.414-1.284-1.2840.0000.0000.0000.000
104A104TYR00.030-0.0089.5702.8452.8450.0000.0000.0000.000
105A105HIS00.0230.00610.717-0.462-0.4620.0000.0000.0000.000
106A106ASN0-0.008-0.01813.3041.5941.5940.0000.0000.0000.000
107A107ASP-1-0.812-0.88215.014-14.411-14.4110.0000.0000.0000.000
108A108PHE0-0.036-0.01217.733-0.557-0.5570.0000.0000.0000.000
109A109ASP-1-0.887-0.94220.120-12.934-12.9340.0000.0000.0000.000
110A110THR0-0.063-0.05916.4490.0990.0990.0000.0000.0000.000
111A111PHE00.0120.01214.6930.2440.2440.0000.0000.0000.000
112A112TYR0-0.016-0.00117.5510.3870.3870.0000.0000.0000.000
113A113GLN0-0.050-0.04020.7380.1290.1290.0000.0000.0000.000
114A114GLU-1-0.867-0.94015.243-19.369-19.3690.0000.0000.0000.000
115A115ALA0-0.0010.00118.0290.2300.2300.0000.0000.0000.000
116A116ARG10.8730.93819.14712.27312.2730.0000.0000.0000.000
117A117LEU0-0.018-0.01020.9100.5670.5670.0000.0000.0000.000
118A118ILE0-0.0100.00015.8820.4140.4140.0000.0000.0000.000
119A119ILE0-0.046-0.03120.2620.3190.3190.0000.0000.0000.000
120A120ASP-1-0.908-0.96423.145-11.479-11.4790.0000.0000.0000.000
121A121ALA0-0.043-0.01022.2540.4540.4540.0000.0000.0000.000
122A122ILE0-0.053-0.01521.964-0.269-0.2690.0000.0000.0000.000
123A123PRO0-0.027-0.00323.8200.5340.5340.0000.0000.0000.000
124A124GLU-1-0.907-0.96326.788-10.040-10.0400.0000.0000.0000.000
125A125ASP-1-0.901-0.97829.149-9.950-9.9500.0000.0000.0000.000
126A126GLY00.0260.01826.061-0.316-0.3160.0000.0000.0000.000
127A127ASP-1-0.880-0.93623.597-13.062-13.0620.0000.0000.0000.000
128A128PRO0-0.041-0.02023.595-0.407-0.4070.0000.0000.0000.000
129A129TYR00.014-0.00620.9140.0200.0200.0000.0000.0000.000
130A130ALA00.0020.02319.713-0.683-0.6830.0000.0000.0000.000
131A131ALA00.0750.03715.729-0.545-0.5450.0000.0000.0000.000
132A132GLU-1-0.839-0.90315.064-18.407-18.4070.0000.0000.0000.000
133A133ASN0-0.030-0.03115.543-0.962-0.9620.0000.0000.0000.000
134A134GLU-1-0.970-0.96613.684-20.311-20.3110.0000.0000.0000.000
135A135GLU-1-0.762-0.8849.797-31.209-31.2090.0000.0000.0000.000
136A136VAL0-0.099-0.05511.214-1.615-1.6150.0000.0000.0000.000
137A137ALA0-0.074-0.03013.7460.1150.1150.0000.0000.0000.000
138A138ASP-1-0.951-0.9679.109-30.592-30.5920.0000.0000.0000.000
139A139GLY0-0.052-0.0279.744-1.401-1.4010.0000.0000.0000.000
141A141TYR00.006-0.0197.0094.1394.1390.0000.0000.0000.000
142A142GLY00.0190.0075.5222.4232.4230.0000.0000.0000.000
143A143LEU0-0.017-0.0136.4920.8620.8620.0000.0000.0000.000
144A144ILE0-0.026-0.01510.0531.0561.0560.0000.0000.0000.000
145A145LEU00.0280.03813.596-0.141-0.1410.0000.0000.0000.000
146A146LEU0-0.005-0.00616.7380.7790.7790.0000.0000.0000.000
147A147SER00.0240.02419.7270.1900.1900.0000.0000.0000.000
148A148ALA00.0170.00423.1230.1370.1370.0000.0000.0000.000
149A149THR00.009-0.00226.0120.2310.2310.0000.0000.0000.000
150A150PRO00.0100.00729.0730.2280.2280.0000.0000.0000.000
151A151ASP-1-0.899-0.95831.250-9.008-9.0080.0000.0000.0000.000
152A152LEU0-0.046-0.02932.6400.3560.3560.0000.0000.0000.000
153A153TYR0-0.054-0.03132.822-0.303-0.3030.0000.0000.0000.000
154A154PHE00.000-0.00227.6900.3150.3150.0000.0000.0000.000
155A155THR00.006-0.01232.878-0.160-0.1600.0000.0000.0000.000
156A156SER0-0.012-0.01631.208-0.233-0.2330.0000.0000.0000.000
157A157ILE00.0050.01227.3610.2160.2160.0000.0000.0000.000
158A158THR0-0.028-0.00727.633-0.163-0.1630.0000.0000.0000.000
159A159GLY00.0080.01323.8850.0380.0380.0000.0000.0000.000
160A160THR00.005-0.00123.3170.3040.3040.0000.0000.0000.000
161A161GLN0-0.068-0.05922.760-0.134-0.1340.0000.0000.0000.000
162A162GLU-1-0.807-0.88018.579-16.214-16.2140.0000.0000.0000.000
163A163LYS10.8580.91716.99417.89917.8990.0000.0000.0000.000
164A164ARG10.8930.94922.70211.11311.1130.0000.0000.0000.000
165A165SER00.0290.01218.7790.3430.3430.0000.0000.0000.000
166A166GLY0-0.023-0.01819.719-0.441-0.4410.0000.0000.0000.000
167A167ASN0-0.016-0.03317.7670.0990.0990.0000.0000.0000.000
168A168ASN00.0060.01613.136-0.023-0.0230.0000.0000.0000.000
169A169TYR0-0.006-0.03611.624-2.314-2.3140.0000.0000.0000.000
170A170PRO0-0.061-0.02413.5021.5391.5390.0000.0000.0000.000
171A171LEU00.0120.02416.148-0.481-0.4810.0000.0000.0000.000
172A172LEU0-0.005-0.01617.6730.5870.5870.0000.0000.0000.000
173A173ASN00.0020.00121.228-0.106-0.1060.0000.0000.0000.000
174A174ALA00.0290.02224.1780.0970.0970.0000.0000.0000.000
175A175GLY00.0120.00425.9000.1660.1660.0000.0000.0000.000
176A176LYS10.8830.94329.7018.4858.4850.0000.0000.0000.000
177A177ALA00.000-0.00831.1870.0510.0510.0000.0000.0000.000
178A178ILE0-0.070-0.04132.8960.2780.2780.0000.0000.0000.000
179A179ILE0-0.019-0.00636.405-0.102-0.1020.0000.0000.0000.000
180A180ARG10.9270.96936.8538.7448.7440.0000.0000.0000.000
181A181GLU-1-0.926-0.96140.063-7.603-7.6030.0000.0000.0000.000
182A182GLY0-0.019-0.00342.4360.0200.0200.0000.0000.0000.000
183A183ARG10.8500.91236.6158.4948.4940.0000.0000.0000.000
184A184LEU0-0.057-0.02633.1050.0740.0740.0000.0000.0000.000
185A185VAL00.0800.03732.668-0.195-0.1950.0000.0000.0000.000
186A186MET0-0.018-0.01526.2800.1420.1420.0000.0000.0000.000
187A187PRO0-0.0230.02529.844-0.168-0.1680.0000.0000.0000.000
188A188ILE00.0500.00323.129-0.247-0.2470.0000.0000.0000.000
189A189ALA00.0030.02425.7840.1670.1670.0000.0000.0000.000
190A190MET00.0140.00819.134-0.442-0.4420.0000.0000.0000.000
191A191THR0-0.0030.01121.2420.9240.9240.0000.0000.0000.000
192A192ILE00.0060.01418.440-0.964-0.9640.0000.0000.0000.000
193A193HIS00.1020.04917.7570.8310.8310.0000.0000.0000.000
194A194HIS10.8770.94019.64512.57912.5790.0000.0000.0000.000
195A195GLY00.0250.00920.6090.3320.3320.0000.0000.0000.000
196A196PHE0-0.016-0.00614.664-0.024-0.0240.0000.0000.0000.000
197A197ILE00.0250.02216.5100.0190.0190.0000.0000.0000.000
198A198ASP-1-0.810-0.88220.332-12.624-12.6240.0000.0000.0000.000
199A199GLY00.024-0.00823.687-0.222-0.2220.0000.0000.0000.000
200A200HIS00.0030.00223.2740.4520.4520.0000.0000.0000.000
201A201HIS00.0330.01420.0030.5110.5110.0000.0000.0000.000
202A202LEU00.0350.00921.548-0.304-0.3040.0000.0000.0000.000
203A203SER0-0.0260.00123.2710.0970.0970.0000.0000.0000.000
204A204LEU00.001-0.00422.0060.0820.0820.0000.0000.0000.000
205A205PHE00.0090.00016.9570.0160.0160.0000.0000.0000.000
206A206TYR0-0.003-0.03521.418-0.087-0.0870.0000.0000.0000.000
207A207LYS10.8640.93324.53711.20711.2070.0000.0000.0000.000
208A208LYS10.8720.93318.66116.19516.1950.0000.0000.0000.000
209A209VAL00.0130.00320.798-0.070-0.0700.0000.0000.0000.000
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