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: LQRZ9

Calculation Name: 1DU5-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1DU5

Chain ID: A

ChEMBL ID:

UniProt ID: P33679

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 198
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2243533.867416
FMO2-HF: Nuclear repulsion 2162747.080703
FMO2-HF: Total energy -80786.786712
FMO2-MP2: Total energy -81010.989713


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.
-46.599-38.97615.643-9.976-13.292-0.103
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 : 0.814 / q_NPA : 0.921
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].
3A3PHE00.0400.0192.451-1.7750.6630.731-1.221-1.949-0.005
35A35THR00.006-0.0033.941-6.840-6.709-0.001-0.047-0.0830.000
36A36ALA00.0350.0313.2917.6728.5650.019-0.357-0.5540.000
37A37PRO00.0190.0101.897-40.043-40.6397.316-3.948-2.773-0.054
38A38ALA00.0200.0044.320-0.852-0.675-0.001-0.017-0.1590.000
39A39GLY00.0250.0145.0114.8834.888-0.001-0.002-0.0020.000
85A87LEU0-0.052-0.0162.401-3.672-3.6942.855-0.761-2.072-0.006
92A94ASP-1-0.771-0.8683.666-57.737-57.1680.006-0.232-0.343-0.001
190A197GLY0-0.035-0.0184.0933.7153.756-0.001-0.015-0.0240.000
191A198THR0-0.058-0.0244.6862.8612.983-0.001-0.032-0.0890.000
192A199ASN0-0.006-0.0012.258-33.453-29.9243.228-2.977-3.781-0.031
193A200TYR00.020-0.0182.3338.7209.0821.494-0.366-1.491-0.006
194A201LYS10.8290.9105.09722.71622.690-0.001-0.0010.0280.000
4A4THR0-0.040-0.0295.5603.3663.3660.0000.0000.0000.000
5A5VAL00.0210.0208.8990.9280.9280.0000.0000.0000.000
6A6VAL00.020-0.00811.4240.9200.9200.0000.0000.0000.000
7A7ASN0-0.029-0.02314.7640.1780.1780.0000.0000.0000.000
8A8GLN0-0.050-0.02818.2630.2160.2160.0000.0000.0000.000
9A9CYS0-0.055-0.02117.6041.1091.1090.0000.0000.0000.000
10A10PRO0-0.035-0.03322.9040.0380.0380.0000.0000.0000.000
11A11PHE0-0.0010.00723.4170.4340.4340.0000.0000.0000.000
12A12THR0-0.022-0.00723.739-0.351-0.3510.0000.0000.0000.000
13A13VAL0-0.0200.00618.9240.3260.3260.0000.0000.0000.000
14A14TRP0-0.008-0.02720.198-0.242-0.2420.0000.0000.0000.000
15A15ALA00.0230.02714.682-0.055-0.0550.0000.0000.0000.000
16A16ALA0-0.003-0.01015.1890.4260.4260.0000.0000.0000.000
17A17SER0-0.043-0.0399.579-1.423-1.4230.0000.0000.0000.000
18A18VAL0-0.0190.03111.8220.3780.3780.0000.0000.0000.000
19A19PRO00.0520.0129.894-1.148-1.1480.0000.0000.0000.000
20A20VAL00.0070.0016.6610.6570.6570.0000.0000.0000.000
21A21GLY00.0300.0199.962-1.455-1.4550.0000.0000.0000.000
22A22GLY00.0350.02611.5741.5621.5620.0000.0000.0000.000
23A23GLY00.023-0.01115.0910.0440.0440.0000.0000.0000.000
24A24ARG10.8800.96116.11118.07718.0770.0000.0000.0000.000
25A25GLN0-0.008-0.00317.8880.1310.1310.0000.0000.0000.000
26A26LEU00.0030.00815.375-0.513-0.5130.0000.0000.0000.000
27A27ASN00.0420.01920.1060.2820.2820.0000.0000.0000.000
28A28ARG10.9580.98621.53910.90210.9020.0000.0000.0000.000
29A29GLY0-0.001-0.00420.9460.4690.4690.0000.0000.0000.000
30A30GLU-1-0.867-0.91819.362-14.604-14.6040.0000.0000.0000.000
31A31SER0-0.037-0.03813.846-0.844-0.8440.0000.0000.0000.000
32A32TRP0-0.0020.00413.1580.4570.4570.0000.0000.0000.000
33A33ARG10.9110.9509.41125.27425.2740.0000.0000.0000.000
34A34ILE00.0100.0217.4031.5801.5800.0000.0000.0000.000
40A40THR0-0.051-0.0355.6165.5485.5480.0000.0000.0000.000
41A41THR00.030-0.0097.758-1.160-1.1600.0000.0000.0000.000
42A42ALA00.0270.02410.5240.4730.4730.0000.0000.0000.000
43A43ALA00.0160.0318.2451.2321.2320.0000.0000.0000.000
44A44ARG10.8330.90010.34317.85617.8560.0000.0000.0000.000
45A45ILE0-0.026-0.0077.3770.0980.0980.0000.0000.0000.000
46A46TRP0-0.031-0.02011.6080.7860.7860.0000.0000.0000.000
47A47ALA00.0330.02015.159-0.375-0.3750.0000.0000.0000.000
48A48ARG10.8260.92518.01216.03216.0320.0000.0000.0000.000
49A49THR00.0570.02921.281-0.003-0.0030.0000.0000.0000.000
50A50GLY00.0420.00924.5390.2030.2030.0000.0000.0000.000
51A51CYS0-0.095-0.02524.249-0.040-0.0400.0000.0000.0000.000
52A52LYS10.9450.97227.03710.16910.1690.0000.0000.0000.000
53A53PHE00.0200.00223.628-0.089-0.0890.0000.0000.0000.000
54A54ASP-1-0.819-0.91028.382-10.350-10.3500.0000.0000.0000.000
55A55ALA0-0.002-0.01528.414-0.425-0.4250.0000.0000.0000.000
56A56SER0-0.0130.00728.336-0.155-0.1550.0000.0000.0000.000
57A57GLY0-0.043-0.00925.007-0.462-0.4620.0000.0000.0000.000
58A58ARG10.8390.90325.49110.84610.8460.0000.0000.0000.000
59A59GLY00.026-0.00828.2480.2160.2160.0000.0000.0000.000
60A60SER0-0.060-0.00827.6170.1160.1160.0000.0000.0000.000
61A62ARG10.8870.94126.71010.52510.5250.0000.0000.0000.000
62A63THR00.0730.04224.125-0.132-0.1320.0000.0000.0000.000
63A64GLY00.0880.04421.150-0.338-0.3380.0000.0000.0000.000
64A65ASP-1-0.832-0.91621.170-12.669-12.6690.0000.0000.0000.000
65A66CYS0-0.0110.01316.6740.6430.6430.0000.0000.0000.000
66A67GLY00.0490.03222.179-0.072-0.0720.0000.0000.0000.000
67A68GLY00.0430.01325.4720.2450.2450.0000.0000.0000.000
68A69VAL0-0.051-0.01221.9520.3860.3860.0000.0000.0000.000
69A70LEU0-0.0050.00320.230-0.429-0.4290.0000.0000.0000.000
70A71GLN0-0.014-0.02617.516-1.620-1.6200.0000.0000.0000.000
71A73THR00.0500.01116.703-1.018-1.0180.0000.0000.0000.000
72A74GLY00.0200.01217.951-0.309-0.3090.0000.0000.0000.000
73A75TYR0-0.057-0.05214.5070.3030.3030.0000.0000.0000.000
74A76GLY00.0160.01318.4390.6910.6910.0000.0000.0000.000
75A77ARG10.8790.94120.48711.18711.1870.0000.0000.0000.000
76A78ALA00.0310.04223.504-0.110-0.1100.0000.0000.0000.000
77A79PRO0-0.048-0.01224.3230.3630.3630.0000.0000.0000.000
78A80ASN0-0.042-0.07419.528-0.146-0.1460.0000.0000.0000.000
79A81THR00.0250.01617.6790.1290.1290.0000.0000.0000.000
80A82LEU0-0.049-0.00815.103-0.741-0.7410.0000.0000.0000.000
81A83ALA00.0340.00910.4640.3180.3180.0000.0000.0000.000
82A84GLU-1-0.832-0.91311.105-19.735-19.7350.0000.0000.0000.000
83A85TYR00.008-0.0245.059-3.709-3.7090.0000.0000.0000.000
84A86ALA0-0.0190.0008.1030.9190.9190.0000.0000.0000.000
86A88LYS10.8580.9125.86334.24834.2480.0000.0000.0000.000
87A89GLN0-0.0080.0107.5804.6454.6450.0000.0000.0000.000
88A90PHE00.0410.01111.1170.2990.2990.0000.0000.0000.000
89A91ASN0-0.001-0.00812.917-0.096-0.0960.0000.0000.0000.000
90A92ASN0-0.0090.00610.329-1.402-1.4020.0000.0000.0000.000
91A93LEU00.0260.0239.352-2.040-2.0400.0000.0000.0000.000
93A95PHE0-0.007-0.0206.9763.4503.4500.0000.0000.0000.000
94A96PHE0-0.041-0.0387.953-2.549-2.5490.0000.0000.0000.000
95A97ASP-1-0.799-0.90210.065-18.400-18.4000.0000.0000.0000.000
96A98ILE0-0.020-0.01712.464-1.108-1.1080.0000.0000.0000.000
97A99SER00.0160.02415.1401.3141.3140.0000.0000.0000.000
98A100LEU00.027-0.00817.6960.0140.0140.0000.0000.0000.000
99A101ILE00.0050.03320.0160.8390.8390.0000.0000.0000.000
100A102ASP-1-0.858-0.92620.321-13.639-13.6390.0000.0000.0000.000
101A103GLY00.020-0.00522.5500.1150.1150.0000.0000.0000.000
102A104PHE0-0.025-0.01821.867-0.599-0.5990.0000.0000.0000.000
103A105ASN0-0.022-0.03520.8760.1100.1100.0000.0000.0000.000
104A106VAL0-0.012-0.01119.1430.4670.4670.0000.0000.0000.000
105A107PRO00.0530.03820.579-0.475-0.4750.0000.0000.0000.000
106A108MET0-0.0150.00214.709-0.715-0.7150.0000.0000.0000.000
107A109SER00.002-0.00714.5250.7960.7960.0000.0000.0000.000
108A110PHE0-0.047-0.0116.644-1.111-1.1110.0000.0000.0000.000
109A111LEU00.0130.0109.9030.7420.7420.0000.0000.0000.000
110A112PRO00.0300.0216.869-3.064-3.0640.0000.0000.0000.000
111A113ASP-1-0.856-0.9316.711-24.198-24.1980.0000.0000.0000.000
112A114GLY00.0380.0308.070-0.548-0.5480.0000.0000.0000.000
113A115GLY0-0.022-0.0216.134-3.871-3.8710.0000.0000.0000.000
114A116SER0-0.030-0.0387.1932.1532.1530.0000.0000.0000.000
115A117GLY00.0210.0099.8370.5960.5960.0000.0000.0000.000
116A118CYS0-0.096-0.0187.1183.4873.4870.0000.0000.0000.000
117A119SER00.0350.00710.914-0.785-0.7850.0000.0000.0000.000
118A120ARG10.9390.97113.14717.60717.6070.0000.0000.0000.000
119A121GLY00.0260.00111.730-1.861-1.8610.0000.0000.0000.000
120A122PRO0-0.0130.02911.8201.1561.1560.0000.0000.0000.000
121A123ARG10.9210.93714.32015.25915.2590.0000.0000.0000.000
122A124CYS0-0.097-0.04417.0570.6070.6070.0000.0000.0000.000
123A125ALA00.0560.01419.898-0.024-0.0240.0000.0000.0000.000
124A126VAL00.0130.02521.3570.3770.3770.0000.0000.0000.000
125A127ASP-1-0.816-0.92624.669-10.755-10.7550.0000.0000.0000.000
126A128VAL0-0.013-0.01124.3660.4610.4610.0000.0000.0000.000
127A129ASN00.0360.02126.3430.2570.2570.0000.0000.0000.000
128A130ALA0-0.0070.01129.5830.3820.3820.0000.0000.0000.000
129A131ARG10.9430.96331.5599.2459.2450.0000.0000.0000.000
130A132CYS0-0.0260.03627.4840.5150.5150.0000.0000.0000.000
131A133PRO00.0530.01732.1820.2800.2800.0000.0000.0000.000
132A134ALA00.0240.00834.683-0.140-0.1400.0000.0000.0000.000
133A135GLU-1-0.842-0.90535.855-8.333-8.3330.0000.0000.0000.000
134A136LEU0-0.026-0.01130.563-0.092-0.0920.0000.0000.0000.000
135A137ARG10.7720.89631.3968.6318.6310.0000.0000.0000.000
136A138GLN0-0.009-0.00230.2610.2620.2620.0000.0000.0000.000
137A139ASP-1-0.865-0.93629.059-10.378-10.3780.0000.0000.0000.000
138A140GLY0-0.054-0.02029.965-0.194-0.1940.0000.0000.0000.000
139A141VAL0-0.085-0.02826.147-0.077-0.0770.0000.0000.0000.000
140A143ASN00.0430.00226.673-0.873-0.8730.0000.0000.0000.000
141A144ASN00.030-0.00224.8000.7310.7310.0000.0000.0000.000
142A145ALA00.026-0.00827.8770.1250.1250.0000.0000.0000.000
143A146CYS0-0.081-0.03126.973-0.176-0.1760.0000.0000.0000.000
144A147PRO0-0.007-0.01626.2660.3030.3030.0000.0000.0000.000
145A148VAL0-0.0250.00829.0280.2390.2390.0000.0000.0000.000
146A149PHE00.000-0.01132.2250.2920.2920.0000.0000.0000.000
147A150LYS10.8840.94431.8859.4139.4130.0000.0000.0000.000
148A151LYS10.9710.98132.4698.6138.6130.0000.0000.0000.000
149A152ASP-1-0.860-0.92132.107-9.340-9.3400.0000.0000.0000.000
150A153GLU-1-0.887-0.94531.610-8.866-8.8660.0000.0000.0000.000
151A154TYR0-0.060-0.03930.073-0.185-0.1850.0000.0000.0000.000
152A156CYS0-0.106-0.01326.977-0.410-0.4100.0000.0000.0000.000
153A157VAL00.0480.02626.786-0.280-0.2800.0000.0000.0000.000
154A158GLY00.0140.00627.6190.3850.3850.0000.0000.0000.000
155A159SER00.024-0.00229.403-0.100-0.1000.0000.0000.0000.000
156A160ALA00.0220.02331.1760.1680.1680.0000.0000.0000.000
157A161ALA0-0.020-0.01427.287-0.042-0.0420.0000.0000.0000.000
158A162ASN0-0.087-0.05629.081-0.166-0.1660.0000.0000.0000.000
159A163ASP-1-0.867-0.92831.879-8.517-8.5170.0000.0000.0000.000
160A165HIS00.0110.00530.047-0.183-0.1830.0000.0000.0000.000
161A166PRO0-0.049-0.02729.348-0.093-0.0930.0000.0000.0000.000
162A167THR00.0760.04130.9580.2890.2890.0000.0000.0000.000
163A168ASN0-0.009-0.01532.996-0.193-0.1930.0000.0000.0000.000
164A169TYR0-0.025-0.04331.217-0.152-0.1520.0000.0000.0000.000
165A170SER00.0360.03027.404-0.055-0.0550.0000.0000.0000.000
166A171ARG10.9530.96227.9508.6438.6430.0000.0000.0000.000
167A172TYR0-0.030-0.01029.2190.0540.0540.0000.0000.0000.000
168A173PHE00.016-0.00824.947-0.144-0.1440.0000.0000.0000.000
169A174LYS10.8070.91122.04313.02213.0220.0000.0000.0000.000
170A175GLY0-0.027-0.01026.123-0.107-0.1070.0000.0000.0000.000
171A176GLN0-0.081-0.03425.8900.1960.1960.0000.0000.0000.000
172A178PRO00.0700.03822.600-0.314-0.3140.0000.0000.0000.000
173A179ASP-1-0.859-0.92017.564-15.283-15.2830.0000.0000.0000.000
174A180ALA0-0.007-0.00318.126-0.791-0.7910.0000.0000.0000.000
175A181TYR0-0.028-0.03616.5280.6060.6060.0000.0000.0000.000
176A182SER0-0.075-0.05520.3110.2640.2640.0000.0000.0000.000
177A183TYR00.004-0.02723.8370.4980.4980.0000.0000.0000.000
178A184PRO00.033-0.00322.824-0.457-0.4570.0000.0000.0000.000
179A185LYS10.8910.94922.73711.99211.9920.0000.0000.0000.000
180A186ASP-1-0.766-0.85421.995-12.382-12.3820.0000.0000.0000.000
181A187ASP-1-0.770-0.86320.177-14.220-14.2200.0000.0000.0000.000
182A188ALA0-0.039-0.01919.889-0.629-0.6290.0000.0000.0000.000
183A189THR0-0.042-0.01521.6250.0160.0160.0000.0000.0000.000
184A190SER0-0.0050.00018.459-0.088-0.0880.0000.0000.0000.000
185A191THR0-0.025-0.00914.701-1.192-1.1920.0000.0000.0000.000
186A192PHE0-0.051-0.02412.2750.6320.6320.0000.0000.0000.000
187A193THR0-0.011-0.01210.188-0.961-0.9610.0000.0000.0000.000
188A195PRO00.0270.0218.218-1.128-1.1280.0000.0000.0000.000
189A196ALA00.0210.0345.198-3.644-3.6440.0000.0000.0000.000
195A202VAL00.0090.0088.5460.7470.7470.0000.0000.0000.000
196A203VAL0-0.005-0.00310.8980.2100.2100.0000.0000.0000.000
197A204PHE00.013-0.00714.2980.3020.3020.0000.0000.0000.000
198A206PRO-1-0.864-0.90917.166-13.739-13.7390.0000.0000.0000.000