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: Z79YN

Calculation Name: 1DOV-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1DOV

Chain ID: A

ChEMBL ID:

UniProt ID: P26231

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 181
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1600006.171991
FMO2-HF: Nuclear repulsion 1530040.04508
FMO2-HF: Total energy -69966.126911
FMO2-MP2: Total energy -70168.693349


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:82:GLU)


Summations of interaction energy for fragment #1(A:82:GLU)
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.
-42.225-44.42819.507-9.055-8.2480.067
Interaction energy analysis for fragmet #1(A:82:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.026 / q_NPA : -0.006
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].
3A84GLN00.0400.0221.761-20.714-23.92518.823-8.475-7.1370.071
4A85PHE00.1020.0565.064-1.405-1.307-0.001-0.011-0.0850.000
67A148TYR0-0.025-0.0264.160-0.410-0.237-0.001-0.018-0.1530.000
71A152VAL0-0.050-0.0162.438-4.600-3.8630.686-0.551-0.873-0.004
5A86LEU00.0520.0327.6840.1840.1840.0000.0000.0000.000
6A87LYS10.8870.9415.552-19.204-19.2040.0000.0000.0000.000
7A88GLU-1-0.937-0.9698.6675.7115.7110.0000.0000.0000.000
8A89GLU-1-0.826-0.90011.0170.0860.0860.0000.0000.0000.000
9A90LEU0-0.006-0.00211.787-0.333-0.3330.0000.0000.0000.000
10A91VAL0-0.0010.00112.582-0.307-0.3070.0000.0000.0000.000
11A92VAL0-0.0020.00315.002-0.384-0.3840.0000.0000.0000.000
12A93ALA00.0090.00516.684-0.277-0.2770.0000.0000.0000.000
13A94VAL0-0.013-0.01217.047-0.229-0.2290.0000.0000.0000.000
14A95GLU-1-0.789-0.86919.1801.6961.6960.0000.0000.0000.000
15A96ASP-1-0.887-0.93521.1801.0611.0610.0000.0000.0000.000
16A97VAL0-0.028-0.01922.035-0.156-0.1560.0000.0000.0000.000
17A98ARG10.7640.86023.303-1.706-1.7060.0000.0000.0000.000
18A99LYS10.8860.94023.070-1.479-1.4790.0000.0000.0000.000
19A100GLN0-0.007-0.01126.919-0.147-0.1470.0000.0000.0000.000
20A101GLY00.0010.00827.871-0.081-0.0810.0000.0000.0000.000
21A102ASP-1-0.897-0.94629.0731.1201.1200.0000.0000.0000.000
22A103LEU0-0.014-0.01131.158-0.072-0.0720.0000.0000.0000.000
23A104MET0-0.044-0.00932.312-0.080-0.0800.0000.0000.0000.000
24A105LYS10.9510.97733.443-0.971-0.9710.0000.0000.0000.000
25A106SER00.0300.01235.323-0.019-0.0190.0000.0000.0000.000
26A107ALA0-0.012-0.00237.295-0.039-0.0390.0000.0000.0000.000
27A108ALA0-0.021-0.02537.614-0.041-0.0410.0000.0000.0000.000
28A109GLY00.0000.01339.428-0.021-0.0210.0000.0000.0000.000
29A110GLU-1-0.857-0.94441.2860.4400.4400.0000.0000.0000.000
30A111PHE0-0.063-0.03942.485-0.035-0.0350.0000.0000.0000.000
31A112ALA0-0.033-0.02143.014-0.023-0.0230.0000.0000.0000.000
32A113ASP-1-0.906-0.94344.9240.4690.4690.0000.0000.0000.000
33A114ASP-1-0.888-0.93647.2750.3080.3080.0000.0000.0000.000
34A115PRO00.0340.02347.470-0.012-0.0120.0000.0000.0000.000
35A116CYS0-0.043-0.03048.492-0.020-0.0200.0000.0000.0000.000
36A117SER0-0.0030.01548.391-0.018-0.0180.0000.0000.0000.000
37A118SER0-0.022-0.02347.9110.0130.0130.0000.0000.0000.000
38A119VAL00.0150.00246.1040.0040.0040.0000.0000.0000.000
39A120LYS10.8970.94744.320-0.376-0.3760.0000.0000.0000.000
40A121ARG11.0041.01742.927-0.245-0.2450.0000.0000.0000.000
41A122GLY00.0340.01642.2200.0080.0080.0000.0000.0000.000
42A123ASN0-0.060-0.02840.396-0.013-0.0130.0000.0000.0000.000
43A124MET00.0650.04238.4640.0230.0230.0000.0000.0000.000
44A125VAL0-0.022-0.01537.3370.0180.0180.0000.0000.0000.000
45A126ARG10.8460.90236.755-0.331-0.3310.0000.0000.0000.000
46A127ALA00.0580.03834.0960.0080.0080.0000.0000.0000.000
47A128ALA00.0460.01232.6320.0410.0410.0000.0000.0000.000
48A129ARG10.9170.96332.022-0.253-0.2530.0000.0000.0000.000
49A130ALA00.0370.03730.306-0.008-0.0080.0000.0000.0000.000
50A131LEU00.0360.01127.1600.0380.0380.0000.0000.0000.000
51A132LEU00.0010.00327.0970.0570.0570.0000.0000.0000.000
52A133SER0-0.025-0.01626.742-0.030-0.0300.0000.0000.0000.000
53A134ALA00.0070.00923.833-0.003-0.0030.0000.0000.0000.000
54A135VAL00.012-0.00622.4010.0940.0940.0000.0000.0000.000
55A136THR0-0.033-0.02922.2030.0360.0360.0000.0000.0000.000
56A137ARG10.8490.91516.565-0.932-0.9320.0000.0000.0000.000
57A138LEU00.001-0.00616.9640.0310.0310.0000.0000.0000.000
58A139LEU0-0.022-0.01817.2590.1310.1310.0000.0000.0000.000
59A140ILE00.0190.01217.7010.0040.0040.0000.0000.0000.000
60A141LEU0-0.0010.00612.280-0.169-0.1690.0000.0000.0000.000
61A142ALA0-0.011-0.00512.9960.1660.1660.0000.0000.0000.000
62A143ASP-1-0.800-0.87812.9890.2340.2340.0000.0000.0000.000
63A144MET00.0240.00812.335-0.252-0.2520.0000.0000.0000.000
64A145ALA0-0.020-0.0058.970-0.643-0.6430.0000.0000.0000.000
65A146ASP-1-0.835-0.9148.6522.5452.5450.0000.0000.0000.000
66A147VAL00.0350.02210.590-0.392-0.3920.0000.0000.0000.000
68A149LYS10.7690.8685.709-4.568-4.5680.0000.0000.0000.000
69A150LEU0-0.017-0.0126.774-1.234-1.2340.0000.0000.0000.000
70A151LEU00.0260.0039.025-0.963-0.9630.0000.0000.0000.000
72A153GLN0-0.064-0.0515.847-0.952-0.9520.0000.0000.0000.000
73A154LEU0-0.017-0.0127.8470.5560.5560.0000.0000.0000.000
74A155LYS10.9931.0007.3638.9338.9330.0000.0000.0000.000
75A156VAL0-0.0110.0126.1540.3870.3870.0000.0000.0000.000
76A157VAL0-0.006-0.0028.8181.2261.2260.0000.0000.0000.000
77A158GLU-1-0.878-0.92612.247-4.477-4.4770.0000.0000.0000.000
78A159ASP-1-0.897-0.95410.339-6.982-6.9820.0000.0000.0000.000
79A160GLY0-0.034-0.01912.8690.5450.5450.0000.0000.0000.000
80A161ILE00.000-0.01614.4350.5730.5730.0000.0000.0000.000
81A162LEU0-0.034-0.01716.6990.3760.3760.0000.0000.0000.000
82A163LYS10.9370.96411.5935.9525.9520.0000.0000.0000.000
83A164LEU0-0.037-0.01217.9890.2800.2800.0000.0000.0000.000
84A165ARG10.7820.87120.3291.9461.9460.0000.0000.0000.000
85A166ASN0-0.017-0.01420.5320.3280.3280.0000.0000.0000.000
86A167ALA00.0090.02522.1920.0010.0010.0000.0000.0000.000
87A168GLY00.0290.01223.4790.0990.0990.0000.0000.0000.000
88A169ASN0-0.021-0.01626.0930.1710.1710.0000.0000.0000.000
89A170GLU-1-0.792-0.90226.306-0.799-0.7990.0000.0000.0000.000
90A171GLN0-0.024-0.00626.815-0.029-0.0290.0000.0000.0000.000
91A172ASP-1-0.819-0.91122.302-1.475-1.4750.0000.0000.0000.000
92A173LEU0-0.0250.00521.873-0.131-0.1310.0000.0000.0000.000
93A174GLY00.0130.00622.559-0.036-0.0360.0000.0000.0000.000
94A175ILE0-0.046-0.02318.9900.0930.0930.0000.0000.0000.000
95A176GLN00.019-0.00716.634-0.312-0.3120.0000.0000.0000.000
96A177TYR00.0030.00117.689-0.072-0.0720.0000.0000.0000.000
97A178LYS10.9090.95519.0510.7010.7010.0000.0000.0000.000
98A179ALA00.0130.01814.2970.1690.1690.0000.0000.0000.000
99A180LEU0-0.0050.00514.299-0.102-0.1020.0000.0000.0000.000
100A181LYS10.8320.90915.3650.4510.4510.0000.0000.0000.000
101A182PRO00.0480.02014.3120.1340.1340.0000.0000.0000.000
102A183GLU-1-0.798-0.8839.844-2.513-2.5130.0000.0000.0000.000
103A184VAL00.007-0.00312.620-0.122-0.1220.0000.0000.0000.000
104A185ASP-1-0.814-0.89115.454-0.191-0.1910.0000.0000.0000.000
105A186LYS10.8470.9138.4200.8140.8140.0000.0000.0000.000
106A187LEU00.0360.02011.9210.3090.3090.0000.0000.0000.000
107A188ASN00.0400.03412.9440.1930.1930.0000.0000.0000.000
108A189ILE0-0.008-0.00613.9850.1740.1740.0000.0000.0000.000
109A190MET0-0.084-0.0377.6480.5280.5280.0000.0000.0000.000
110A191ALA00.0260.01013.0230.0260.0260.0000.0000.0000.000
111A192ALA0-0.029-0.02415.7180.0550.0550.0000.0000.0000.000
112A193LYS10.9510.98512.968-2.363-2.3630.0000.0000.0000.000
113A194ARG10.8620.92514.481-0.061-0.0610.0000.0000.0000.000
114A195GLN00.0160.02217.295-0.069-0.0690.0000.0000.0000.000
115A196GLN0-0.053-0.03520.2550.0500.0500.0000.0000.0000.000
116A197GLU-1-0.876-0.93816.9821.0261.0260.0000.0000.0000.000
117A198LEU0-0.039-0.00919.570-0.024-0.0240.0000.0000.0000.000
118A199LYS10.9610.97722.511-0.239-0.2390.0000.0000.0000.000
119A200ASP-1-0.838-0.92426.065-0.225-0.2250.0000.0000.0000.000
120A201VAL0-0.011-0.01526.789-0.014-0.0140.0000.0000.0000.000
121A202GLY00.0840.05927.994-0.028-0.0280.0000.0000.0000.000
122A203ASN0-0.003-0.02323.159-0.021-0.0210.0000.0000.0000.000
123A204ARG10.8380.93223.415-0.206-0.2060.0000.0000.0000.000
124A205ASP-1-0.866-0.93424.853-0.250-0.2500.0000.0000.0000.000
125A206GLN0-0.042-0.02223.731-0.012-0.0120.0000.0000.0000.000
126A207MET0-0.0220.00417.339-0.184-0.1840.0000.0000.0000.000
127A208ALA0-0.027-0.00522.016-0.038-0.0380.0000.0000.0000.000
128A209ALA00.0090.00324.483-0.025-0.0250.0000.0000.0000.000
129A210ALA0-0.021-0.00420.983-0.050-0.0500.0000.0000.0000.000
130A211ARG10.8720.91218.9050.1090.1090.0000.0000.0000.000
131A212GLY00.0050.01221.391-0.002-0.0020.0000.0000.0000.000
132A213ILE0-0.049-0.03124.362-0.001-0.0010.0000.0000.0000.000
133A214LEU00.0160.00116.884-0.029-0.0290.0000.0000.0000.000
134A215GLN0-0.045-0.02320.8750.0440.0440.0000.0000.0000.000
135A216LYS10.9510.98122.5640.7080.7080.0000.0000.0000.000
136A217ASN00.033-0.00324.1340.1120.1120.0000.0000.0000.000
137A218VAL00.0280.02819.188-0.048-0.0480.0000.0000.0000.000
138A219PRO0-0.020-0.01822.231-0.037-0.0370.0000.0000.0000.000
139A220ILE00.0290.02825.1550.0030.0030.0000.0000.0000.000
140A221LEU00.0390.02321.7440.0120.0120.0000.0000.0000.000
141A222TYR00.0220.03823.717-0.029-0.0290.0000.0000.0000.000
142A223THR0-0.007-0.01025.4350.0430.0430.0000.0000.0000.000
143A224ALA00.0110.00728.4300.0290.0290.0000.0000.0000.000
144A225SER0-0.023-0.05725.683-0.009-0.0090.0000.0000.0000.000
145A226GLN0-0.018-0.01227.834-0.005-0.0050.0000.0000.0000.000
146A227ALA00.0280.01829.6990.0260.0260.0000.0000.0000.000
147A228CYS0-0.124-0.05930.0240.0090.0090.0000.0000.0000.000
148A229LEU0-0.040-0.00827.4110.0060.0060.0000.0000.0000.000
149A230GLN0-0.043-0.02031.9740.0560.0560.0000.0000.0000.000
150A231HIS0-0.011-0.00735.0970.0280.0280.0000.0000.0000.000
151A232PRO00.0480.03334.880-0.016-0.0160.0000.0000.0000.000
152A233ASP-1-0.893-0.94835.996-0.752-0.7520.0000.0000.0000.000
153A234VAL0-0.022-0.00437.5300.0150.0150.0000.0000.0000.000
154A235ALA0-0.008-0.01535.948-0.044-0.0440.0000.0000.0000.000
155A236ALA00.0140.00435.410-0.047-0.0470.0000.0000.0000.000
156A237TYR00.0300.00633.617-0.018-0.0180.0000.0000.0000.000
157A238LYS10.9350.96531.1080.9010.9010.0000.0000.0000.000
158A239ALA00.0190.01530.604-0.078-0.0780.0000.0000.0000.000
159A240ASN00.0140.00531.472-0.036-0.0360.0000.0000.0000.000
160A241ARG10.8750.91926.2131.3501.3500.0000.0000.0000.000
161A242ASP-1-0.780-0.86126.843-1.543-1.5430.0000.0000.0000.000
162A243LEU0-0.0090.00127.084-0.098-0.0980.0000.0000.0000.000
163A244ILE00.0130.01025.368-0.055-0.0550.0000.0000.0000.000
164A245TYR00.0130.00219.0610.0220.0220.0000.0000.0000.000
165A246LYS10.9450.97222.7061.3931.3930.0000.0000.0000.000
166A247GLN0-0.001-0.00423.800-0.065-0.0650.0000.0000.0000.000
167A248LEU0-0.0350.00819.9930.0190.0190.0000.0000.0000.000
168A249GLN00.012-0.01316.176-0.119-0.1190.0000.0000.0000.000
169A250GLN0-0.030-0.00519.499-0.107-0.1070.0000.0000.0000.000
170A251ALA0-0.023-0.00821.5120.0220.0220.0000.0000.0000.000
171A252VAL00.0120.00015.0370.0830.0830.0000.0000.0000.000
172A253THR0-0.003-0.02216.834-0.201-0.2010.0000.0000.0000.000
173A254GLY0-0.0050.00018.3520.0620.0620.0000.0000.0000.000
174A255ILE00.001-0.01015.2370.1570.1570.0000.0000.0000.000
175A256SER0-0.017-0.00614.9630.1080.1080.0000.0000.0000.000
176A257ASN0-0.021-0.00315.9070.0500.0500.0000.0000.0000.000
177A258ALA0-0.014-0.00119.2320.1350.1350.0000.0000.0000.000
178A259ALA00.030-0.00115.4240.1840.1840.0000.0000.0000.000
179A260GLN0-0.083-0.06215.3920.0870.0870.0000.0000.0000.000
180A261ALA0-0.0170.00417.6660.0310.0310.0000.0000.0000.000
181A262THR-1-0.944-0.95220.463-0.115-0.1150.0000.0000.0000.000