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: Z792N

Calculation Name: 1DIX-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1DIX

Chain ID: A

ChEMBL ID:

UniProt ID: P80022

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 203
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2370503.475924
FMO2-HF: Nuclear repulsion 2288381.886424
FMO2-HF: Total energy -82121.5895
FMO2-MP2: Total energy -82355.91254


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.
-224.79-218.75521.524-13.206-14.353-0.137
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 : 0.803 / q_NPA : 0.914
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].
3A3GLY00.0090.0083.8594.1725.573-0.018-0.687-0.6960.000
5A4LYS10.8170.9332.61754.61355.4650.355-0.275-0.9320.001
6A4ASP-1-0.805-0.8802.567-46.423-45.5422.027-1.410-1.498-0.017
7A4PHE0-0.028-0.0012.585-5.411-4.6600.742-0.516-0.978-0.004
8A5ASP-1-0.813-0.9321.764-120.664-122.00017.978-8.633-8.008-0.104
9A6PHE0-0.036-0.0283.6305.9065.9730.022-0.022-0.0670.000
47A45ASN00.0210.0002.984-16.806-14.8490.305-0.886-1.376-0.007
48A46ASN0-0.026-0.0302.8930.0111.4480.114-0.773-0.779-0.006
49A47ASP-1-0.827-0.8834.541-46.300-46.275-0.001-0.004-0.0190.000
4A4SER0-0.012-0.0076.187-1.838-1.8380.0000.0000.0000.000
10A7PHE00.0340.0127.246-1.462-1.4620.0000.0000.0000.000
11A8TYR0-0.009-0.03610.1060.9140.9140.0000.0000.0000.000
12A9PHE00.004-0.00212.9390.1350.1350.0000.0000.0000.000
13A10VAL00.0090.00716.1300.2620.2620.0000.0000.0000.000
14A11GLN0-0.006-0.00818.7220.8600.8600.0000.0000.0000.000
15A12GLN00.0370.01822.542-0.309-0.3090.0000.0000.0000.000
16A13TRP0-0.033-0.01425.3020.1940.1940.0000.0000.0000.000
17A14PRO00.0060.00328.959-0.043-0.0430.0000.0000.0000.000
18A15GLY00.0400.01731.3540.1780.1780.0000.0000.0000.000
19A16SER00.014-0.01729.8770.2480.2480.0000.0000.0000.000
20A17TYR0-0.040-0.01527.817-0.217-0.2170.0000.0000.0000.000
21A18CYS0-0.114-0.04131.394-0.110-0.1100.0000.0000.0000.000
22A19ASP-1-0.763-0.85734.392-9.013-9.0130.0000.0000.0000.000
23A20THR00.0210.01031.5010.1120.1120.0000.0000.0000.000
24A21LYS10.8610.91734.7778.6518.6510.0000.0000.0000.000
25A22GLN0-0.100-0.03430.919-0.127-0.1270.0000.0000.0000.000
26A23SER00.0110.00035.6380.1240.1240.0000.0000.0000.000
27A25CYS0-0.084-0.03030.9840.6640.6640.0000.0000.0000.000
28A26TYR00.0480.01934.426-0.152-0.1520.0000.0000.0000.000
29A27PRO00.0410.03933.0820.0800.0800.0000.0000.0000.000
30A28THR0-0.017-0.02435.1390.1570.1570.0000.0000.0000.000
31A29THR0-0.047-0.01935.1620.1870.1870.0000.0000.0000.000
32A30GLY00.0090.01737.9730.1600.1600.0000.0000.0000.000
33A31LYS10.8130.88637.2267.8067.8060.0000.0000.0000.000
34A32PRO00.0030.00133.0310.0750.0750.0000.0000.0000.000
35A33ALA00.0260.01333.9740.2150.2150.0000.0000.0000.000
36A34ALA0-0.0100.00334.115-0.208-0.2080.0000.0000.0000.000
37A35ASP-1-0.829-0.91830.477-10.277-10.2770.0000.0000.0000.000
38A36PHE0-0.018-0.02226.420-0.043-0.0430.0000.0000.0000.000
39A37GLY00.0080.01326.8570.0930.0930.0000.0000.0000.000
40A38ILE0-0.033-0.03120.746-0.398-0.3980.0000.0000.0000.000
41A39HIS0-0.063-0.03320.3270.1900.1900.0000.0000.0000.000
42A40GLY00.028-0.00218.0480.1550.1550.0000.0000.0000.000
43A41LEU0-0.043-0.00113.753-0.107-0.1070.0000.0000.0000.000
44A42TRP0-0.057-0.04312.280-0.682-0.6820.0000.0000.0000.000
45A43PRO00.0410.0317.583-0.755-0.7550.0000.0000.0000.000
46A44ASN0-0.006-0.0126.8933.7483.7480.0000.0000.0000.000
50A48GLY0-0.0160.0016.5085.2985.2980.0000.0000.0000.000
51A49THR0-0.076-0.0505.6942.9362.9360.0000.0000.0000.000
52A50TYR0-0.018-0.0207.113-2.211-2.2110.0000.0000.0000.000
53A51PRO0-0.0220.0106.1592.3132.3130.0000.0000.0000.000
54A52SER0-0.010-0.0598.7402.2992.2990.0000.0000.0000.000
55A53ASN0-0.056-0.03712.4940.7970.7970.0000.0000.0000.000
56A54CYS0-0.125-0.0129.480-0.885-0.8850.0000.0000.0000.000
57A55ASP-1-0.762-0.88013.228-16.039-16.0390.0000.0000.0000.000
58A56PRO0-0.053-0.02716.3670.6210.6210.0000.0000.0000.000
59A57ASN0-0.094-0.05019.5541.4021.4020.0000.0000.0000.000
60A58SER0-0.0050.01918.5360.8370.8370.0000.0000.0000.000
61A59PRO00.0280.02320.285-0.412-0.4120.0000.0000.0000.000
62A60TYR0-0.026-0.03322.7270.0830.0830.0000.0000.0000.000
63A61ASP-1-0.810-0.87623.892-10.176-10.1760.0000.0000.0000.000
64A62GLN00.0450.04826.625-0.274-0.2740.0000.0000.0000.000
65A63SER0-0.080-0.06428.5100.2160.2160.0000.0000.0000.000
66A64GLN0-0.037-0.02524.311-0.216-0.2160.0000.0000.0000.000
67A65ILE0-0.006-0.01123.856-0.275-0.2750.0000.0000.0000.000
68A66SER00.0010.01027.1560.1640.1640.0000.0000.0000.000
69A67ASP-1-0.858-0.90828.801-10.523-10.5230.0000.0000.0000.000
70A68LEU0-0.013-0.00824.3650.0190.0190.0000.0000.0000.000
71A69ILE00.0130.01028.243-0.009-0.0090.0000.0000.0000.000
72A70SER00.0160.01830.229-0.086-0.0860.0000.0000.0000.000
73A71SER00.0420.01928.2120.0210.0210.0000.0000.0000.000
74A72MET0-0.0080.00124.665-0.168-0.1680.0000.0000.0000.000
75A73GLN0-0.023-0.01927.9660.0610.0610.0000.0000.0000.000
76A74GLN0-0.063-0.02431.2570.1790.1790.0000.0000.0000.000
77A75ASN0-0.004-0.00126.6870.0670.0670.0000.0000.0000.000
78A76TRP0-0.020-0.00119.223-0.471-0.4710.0000.0000.0000.000
79A77PRO00.0420.03426.346-0.024-0.0240.0000.0000.0000.000
80A78THR00.003-0.00528.294-0.375-0.3750.0000.0000.0000.000
81A79LEU00.0440.00829.2940.3570.3570.0000.0000.0000.000
82A80ALA00.0320.03028.8850.2060.2060.0000.0000.0000.000
83A82PRO0-0.002-0.01632.867-0.176-0.1760.0000.0000.0000.000
84A83SER00.013-0.01234.208-0.158-0.1580.0000.0000.0000.000
85A84GLY00.011-0.00534.0240.1190.1190.0000.0000.0000.000
86A85SER0-0.014-0.01632.283-0.005-0.0050.0000.0000.0000.000
87A86GLY00.0480.02729.544-0.033-0.0330.0000.0000.0000.000
88A87SER0-0.032-0.04127.759-0.264-0.2640.0000.0000.0000.000
89A88THR00.0190.00726.923-0.275-0.2750.0000.0000.0000.000
90A89PHE0-0.0150.01222.395-0.343-0.3430.0000.0000.0000.000
91A90TRP0-0.021-0.01922.992-0.392-0.3920.0000.0000.0000.000
92A91SER0-0.011-0.00922.107-0.520-0.5200.0000.0000.0000.000
93A92HIS00.0270.01520.432-0.379-0.3790.0000.0000.0000.000
94A93GLU-1-0.831-0.92018.138-17.408-17.4080.0000.0000.0000.000
95A94TRP0-0.040-0.02316.940-1.236-1.2360.0000.0000.0000.000
96A95GLU-1-0.810-0.90017.146-14.189-14.1890.0000.0000.0000.000
97A96LYS10.9290.97115.73016.79516.7950.0000.0000.0000.000
98A97HIS10.8750.92112.65818.81118.8110.0000.0000.0000.000
99A98GLY00.0290.01412.744-1.360-1.3600.0000.0000.0000.000
100A99THR00.0230.00614.112-1.316-1.3160.0000.0000.0000.000
101A101ALA00.0270.0079.140-2.886-2.8860.0000.0000.0000.000
102A102GLU-1-0.829-0.91611.115-17.573-17.5730.0000.0000.0000.000
103A103SER0-0.077-0.0658.0851.3051.3050.0000.0000.0000.000
104A104VAL0-0.088-0.0338.6780.3160.3160.0000.0000.0000.000
105A105LEU0-0.070-0.04111.6861.7191.7190.0000.0000.0000.000
106A106THR0-0.008-0.00314.7610.4440.4440.0000.0000.0000.000
107A107ASN00.0150.00916.2290.7150.7150.0000.0000.0000.000
108A108GLN00.0970.04918.9040.0180.0180.0000.0000.0000.000
109A109HIS10.8340.89820.66411.75511.7550.0000.0000.0000.000
110A110ALA0-0.033-0.01318.2040.2330.2330.0000.0000.0000.000
111A111TYR00.013-0.01014.1530.2540.2540.0000.0000.0000.000
112A112PHE00.019-0.00617.795-0.067-0.0670.0000.0000.0000.000
113A113LYS10.8580.91621.03512.41012.4100.0000.0000.0000.000
114A114LYS10.8910.95116.04817.11317.1130.0000.0000.0000.000
115A115ALA00.0400.01418.624-0.045-0.0450.0000.0000.0000.000
116A116LEU0-0.018-0.01219.7070.3770.3770.0000.0000.0000.000
117A117ASP-1-0.874-0.92121.700-12.174-12.1740.0000.0000.0000.000
118A118LEU0-0.001-0.00516.5170.1330.1330.0000.0000.0000.000
119A119LYS10.8540.93521.15811.27411.2740.0000.0000.0000.000
120A120ASN0-0.047-0.02524.0090.5620.5620.0000.0000.0000.000
121A121GLN0-0.061-0.02121.6960.1440.1440.0000.0000.0000.000
122A122ILE0-0.046-0.01319.9960.0160.0160.0000.0000.0000.000
123A123ASP-1-0.745-0.84024.556-10.126-10.1260.0000.0000.0000.000
124A124LEU00.008-0.01423.5760.1540.1540.0000.0000.0000.000
125A125LEU00.0400.03327.6870.1900.1900.0000.0000.0000.000
126A126SER0-0.030-0.05131.3270.3760.3760.0000.0000.0000.000
127A127ILE0-0.054-0.01926.7140.1670.1670.0000.0000.0000.000
128A128LEU0-0.028-0.01028.9640.1200.1200.0000.0000.0000.000
129A129GLN0-0.041-0.01532.2280.5260.5260.0000.0000.0000.000
130A130GLY0-0.011-0.00334.6340.2700.2700.0000.0000.0000.000
131A131ALA0-0.058-0.03333.2310.0940.0940.0000.0000.0000.000
132A132ASP-1-0.887-0.92635.259-7.820-7.8200.0000.0000.0000.000
133A133ILE0-0.046-0.00632.2700.0310.0310.0000.0000.0000.000
134A134HIS10.8330.87635.0498.0648.0640.0000.0000.0000.000
135A135PRO0-0.0070.02134.5350.0100.0100.0000.0000.0000.000
136A136ASP0-0.063-0.10136.3050.1000.1000.0000.0000.0000.000
137A137GLY0-0.008-0.00438.2140.2160.2160.0000.0000.0000.000
138A138GLU-1-0.870-0.87438.906-7.760-7.7600.0000.0000.0000.000
139A139SER0-0.046-0.03136.085-0.291-0.2910.0000.0000.0000.000
140A140TYR00.0430.01333.4840.1000.1000.0000.0000.0000.000
141A141ASP-1-0.876-0.94232.943-9.303-9.3030.0000.0000.0000.000
142A142LEU00.000-0.00425.295-0.201-0.2010.0000.0000.0000.000
143A143VAL0-0.038-0.03827.958-0.398-0.3980.0000.0000.0000.000
144A144ASN00.0230.01428.956-0.267-0.2670.0000.0000.0000.000
145A145ILE00.0640.04027.261-0.104-0.1040.0000.0000.0000.000
146A146ARG10.9290.97422.82812.37312.3730.0000.0000.0000.000
147A147ASN00.006-0.01325.720-0.706-0.7060.0000.0000.0000.000
148A148ALA00.0210.03927.953-0.001-0.0010.0000.0000.0000.000
149A149ILE00.0370.01023.824-0.077-0.0770.0000.0000.0000.000
150A150LYS10.7990.89021.20414.24114.2410.0000.0000.0000.000
151A151SER0-0.075-0.05224.951-0.061-0.0610.0000.0000.0000.000
152A152ALA0-0.0280.00327.5520.1960.1960.0000.0000.0000.000
153A153ILE0-0.014-0.01021.022-0.036-0.0360.0000.0000.0000.000
154A154GLY00.0060.02222.825-0.443-0.4430.0000.0000.0000.000
155A155TYR0-0.024-0.01618.315-0.126-0.1260.0000.0000.0000.000
156A156THR0-0.064-0.07018.7891.0741.0740.0000.0000.0000.000
157A157PRO0-0.0130.01218.355-0.933-0.9330.0000.0000.0000.000
158A158TRP0-0.021-0.01317.5470.2420.2420.0000.0000.0000.000
159A159ILE0-0.004-0.00819.4000.1110.1110.0000.0000.0000.000
160A160GLN00.0380.03820.784-0.447-0.4470.0000.0000.0000.000
161A161CYS00.0240.03822.6380.3600.3600.0000.0000.0000.000
162A162ASN0-0.021-0.01825.427-0.414-0.4140.0000.0000.0000.000
163A163VAL0-0.026-0.01628.0410.1310.1310.0000.0000.0000.000
164A164ASP-1-0.698-0.81031.732-8.671-8.6710.0000.0000.0000.000
165A165GLN0-0.063-0.03934.8200.0240.0240.0000.0000.0000.000
166A166SER0-0.066-0.05637.7430.2410.2410.0000.0000.0000.000
167A167GLY0-0.060-0.02835.9280.1370.1370.0000.0000.0000.000
168A168ASN0-0.064-0.02835.515-0.102-0.1020.0000.0000.0000.000
169A169SER0-0.056-0.04629.963-0.334-0.3340.0000.0000.0000.000
170A170GLN0-0.024-0.03130.5780.0210.0210.0000.0000.0000.000
171A171LEU00.013-0.00426.945-0.534-0.5340.0000.0000.0000.000
172A172TYR0-0.0520.00224.3110.0240.0240.0000.0000.0000.000
173A173GLN00.014-0.01321.0390.1730.1730.0000.0000.0000.000
174A174VAL0-0.023-0.00221.414-0.069-0.0690.0000.0000.0000.000
175A175TYR0-0.029-0.01715.510-0.548-0.5480.0000.0000.0000.000
176A176ILE00.0280.00217.3220.1420.1420.0000.0000.0000.000
177A177CYS0-0.091-0.02512.303-1.955-1.9550.0000.0000.0000.000
178A178VAL00.0420.02112.3451.4081.4080.0000.0000.0000.000
179A179ASP-1-0.735-0.84610.257-25.777-25.7770.0000.0000.0000.000
180A180GLY00.0140.0077.2110.4890.4890.0000.0000.0000.000
181A181SER0-0.032-0.0408.0250.0110.0110.0000.0000.0000.000
182A182GLY0-0.013-0.00310.9821.4971.4970.0000.0000.0000.000
183A183SER0-0.051-0.02613.1721.7021.7020.0000.0000.0000.000
184A184SER0-0.055-0.03214.6371.2471.2470.0000.0000.0000.000
185A185LEU00.0040.00614.692-1.264-1.2640.0000.0000.0000.000
186A186ILE0-0.015-0.00710.643-0.119-0.1190.0000.0000.0000.000
187A187GLU-1-0.757-0.86215.202-15.942-15.9420.0000.0000.0000.000
188A189PRO0-0.026-0.0087.9700.5590.5590.0000.0000.0000.000
189A190ILE00.0290.0198.3220.2880.2880.0000.0000.0000.000
190A191PHE0-0.0020.01810.9550.0560.0560.0000.0000.0000.000
191A192PRO00.0250.01813.632-0.668-0.6680.0000.0000.0000.000
192A193GLY00.0170.02114.9580.8190.8190.0000.0000.0000.000
193A194GLY00.000-0.01517.7070.1890.1890.0000.0000.0000.000
194A195LYS10.9010.94021.32011.56911.5690.0000.0000.0000.000
195A197GLY00.0230.02127.2310.4320.4320.0000.0000.0000.000
196A198THR0-0.002-0.01629.579-0.188-0.1880.0000.0000.0000.000
197A199SER0-0.015-0.00631.774-0.024-0.0240.0000.0000.0000.000
198A200ILE0-0.032-0.01028.536-0.077-0.0770.0000.0000.0000.000
199A201GLU-1-0.792-0.88732.751-8.703-8.7030.0000.0000.0000.000
200A202PHE0-0.012-0.00531.602-0.450-0.4500.0000.0000.0000.000
201A203PRO00.0380.03333.0910.3060.3060.0000.0000.0000.000
202A204THR00.0300.01835.652-0.080-0.0800.0000.0000.0000.000
203A205PHE-1-0.877-0.92435.296-8.262-8.2620.0000.0000.0000.000