FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: 4J3GN

Calculation Name: 1JDU-A-Xray372

Preferred Name: Purine nucleoside phosphorylase

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1JDU

Chain ID: A

ChEMBL ID: CHEMBL3751658

UniProt ID: P50389

Base Structure: X-ray

Registration Date: 2023-09-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 234
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2857393.937904
FMO2-HF: Nuclear repulsion 2768829.782752
FMO2-HF: Total energy -88564.155152
FMO2-MP2: Total energy -88825.539196


3D Structure
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:PRO)


Summations of interaction energy for fragment #1(A:3:PRO)
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.
-10.351-0.9026.405-5.3-10.553-0.02
Interaction energy analysis for fragmet #1(A:3:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : -0.007
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].
3A5HIS10.7650.8623.475-1.4851.496-0.023-1.611-1.3470.001
4A6ILE00.008-0.0023.434-0.2030.2310.007-0.086-0.3550.000
5A7LEU0-0.025-0.0182.947-2.364-1.1910.250-0.552-0.871-0.005
6A8ALA00.0070.0364.9710.2390.312-0.001-0.006-0.0650.000
7A9LYS10.8500.8995.0080.2650.344-0.001-0.002-0.0750.000
8A10LYS10.9850.9776.2640.2320.2320.0000.0000.0000.000
9A11GLY00.0000.0047.1630.1070.1070.0000.0000.0000.000
10A12GLU-1-0.818-0.8838.965-0.874-0.8740.0000.0000.0000.000
11A13VAL0-0.029-0.0026.581-0.005-0.0050.0000.0000.0000.000
12A14ALA0-0.032-0.0089.5560.0590.0590.0000.0000.0000.000
13A15GLU-1-0.839-0.91111.450-0.004-0.0040.0000.0000.0000.000
14A16ARG10.8770.94313.4150.0870.0870.0000.0000.0000.000
15A17VAL00.004-0.01411.206-0.049-0.0490.0000.0000.0000.000
16A18LEU00.0140.01614.6760.0390.0390.0000.0000.0000.000
17A19VAL0-0.030-0.01012.640-0.037-0.0370.0000.0000.0000.000
18A20VAL00.0140.00115.2940.0330.0330.0000.0000.0000.000
19A21GLY00.0590.02915.622-0.024-0.0240.0000.0000.0000.000
20A22ASP-1-0.837-0.92016.859-0.171-0.1710.0000.0000.0000.000
21A23PRO00.0730.02216.044-0.005-0.0050.0000.0000.0000.000
22A24GLY0-0.006-0.00517.324-0.014-0.0140.0000.0000.0000.000
23A25ARG10.8860.94020.2530.1120.1120.0000.0000.0000.000
24A26ALA00.0600.03516.2680.0070.0070.0000.0000.0000.000
25A27ARG10.9670.98618.3270.2460.2460.0000.0000.0000.000
26A28LEU00.0020.02819.9900.0050.0050.0000.0000.0000.000
27A29LEU00.023-0.00620.8890.0110.0110.0000.0000.0000.000
28A30SER0-0.077-0.03619.2280.0020.0020.0000.0000.0000.000
29A31THR0-0.052-0.04320.9350.0030.0030.0000.0000.0000.000
30A32LEU0-0.038-0.01123.8160.0120.0120.0000.0000.0000.000
31A33LEU0-0.019-0.00318.4050.0080.0080.0000.0000.0000.000
32A34GLN0-0.020-0.01922.7720.0020.0020.0000.0000.0000.000
33A35ASN0-0.003-0.01121.963-0.021-0.0210.0000.0000.0000.000
34A36PRO00.0510.03419.378-0.020-0.0200.0000.0000.0000.000
35A37LYS10.8440.91416.3700.2830.2830.0000.0000.0000.000
36A38LEU0-0.019-0.00213.896-0.009-0.0090.0000.0000.0000.000
37A39THR0-0.016-0.01110.392-0.027-0.0270.0000.0000.0000.000
38A40ASN00.030-0.0017.730-0.399-0.3990.0000.0000.0000.000
39A41GLU-1-0.892-0.95410.009-0.401-0.4010.0000.0000.0000.000
40A42ASN0-0.0090.0036.8740.3240.3240.0000.0000.0000.000
41A43ARG10.9160.9428.7070.5690.5690.0000.0000.0000.000
42A44GLY00.0360.03311.5090.0890.0890.0000.0000.0000.000
43A45PHE0-0.046-0.0238.8670.0760.0760.0000.0000.0000.000
44A46LEU0-0.0230.00110.344-0.112-0.1120.0000.0000.0000.000
45A47VAL00.0000.0058.5920.0670.0670.0000.0000.0000.000
46A48TYR00.0280.01711.978-0.026-0.0260.0000.0000.0000.000
47A49THR00.018-0.00112.0320.0290.0290.0000.0000.0000.000
48A50GLY00.0320.02415.092-0.001-0.0010.0000.0000.0000.000
49A51LYS10.8950.95518.3440.1440.1440.0000.0000.0000.000
50A52TYR0-0.006-0.01721.058-0.004-0.0040.0000.0000.0000.000
51A53ASN0-0.013-0.00123.4790.0030.0030.0000.0000.0000.000
52A54GLY0-0.0030.00525.0340.0060.0060.0000.0000.0000.000
53A55GLU-1-0.839-0.91219.893-0.076-0.0760.0000.0000.0000.000
54A56THR0-0.041-0.03315.773-0.018-0.0180.0000.0000.0000.000
55A57VAL0-0.017-0.01116.3740.0180.0180.0000.0000.0000.000
56A58SER00.0310.00012.295-0.031-0.0310.0000.0000.0000.000
57A59ILE0-0.019-0.00914.2850.0460.0460.0000.0000.0000.000
58A60ALA00.0170.01110.640-0.055-0.0550.0000.0000.0000.000
59A61THR0-0.0070.00712.0880.0750.0750.0000.0000.0000.000
60A62HIS0-0.012-0.02111.213-0.037-0.0370.0000.0000.0000.000
61A63GLY00.0040.01912.6330.0300.0300.0000.0000.0000.000
62A64ILE0-0.003-0.01015.0130.0170.0170.0000.0000.0000.000
63A65GLY00.0440.02017.2040.0030.0030.0000.0000.0000.000
64A66GLY00.0540.02215.701-0.001-0.0010.0000.0000.0000.000
65A67PRO00.025-0.01814.0840.0270.0270.0000.0000.0000.000
66A68SER0-0.019-0.01011.8920.0290.0290.0000.0000.0000.000
67A69ILE00.0220.00210.596-0.010-0.0100.0000.0000.0000.000
68A70ALA00.0280.01810.8200.0150.0150.0000.0000.0000.000
69A71ILE0-0.033-0.0136.4940.1270.1270.0000.0000.0000.000
70A72VAL0-0.019-0.0126.2240.0950.0950.0000.0000.0000.000
71A73LEU0-0.025-0.0027.005-0.083-0.0830.0000.0000.0000.000
72A74GLU-1-0.732-0.8436.5441.0981.0980.0000.0000.0000.000
73A75GLU-1-0.717-0.8352.262-3.081-1.0303.425-2.066-3.410-0.015
74A76LEU00.0010.0013.755-0.994-0.5120.015-0.118-0.379-0.001
75A77ALA00.0210.0136.330-0.083-0.0830.0000.0000.0000.000
76A78MET0-0.079-0.0202.290-2.184-0.9602.042-0.585-2.6820.000
77A79LEU0-0.065-0.0352.477-1.129-0.1720.692-0.272-1.3780.000
78A80GLY0-0.069-0.0415.109-0.026-0.031-0.001-0.0020.0090.000
79A81ALA0-0.0120.0198.2700.0380.0380.0000.0000.0000.000
80A82ASN0-0.040-0.03610.2560.0840.0840.0000.0000.0000.000
81A83VAL00.0090.01013.0390.0200.0200.0000.0000.0000.000
82A84PHE0-0.011-0.0099.799-0.047-0.0470.0000.0000.0000.000
83A85ILE0-0.010-0.01115.8860.0230.0230.0000.0000.0000.000
84A86ARG10.7870.88717.567-0.015-0.0150.0000.0000.0000.000
85A87TYR0-0.048-0.04918.7050.0120.0120.0000.0000.0000.000
86A88GLY00.0430.00620.625-0.016-0.0160.0000.0000.0000.000
87A89THR0-0.0210.00422.622-0.001-0.0010.0000.0000.0000.000
88A90THR0-0.061-0.03825.1110.0060.0060.0000.0000.0000.000
89A91GLY00.0760.05227.747-0.005-0.0050.0000.0000.0000.000
90A92ALA0-0.007-0.02431.0400.0060.0060.0000.0000.0000.000
91A93LEU0-0.028-0.02132.0390.0000.0000.0000.0000.0000.000
92A94VAL00.0090.00935.4060.0020.0020.0000.0000.0000.000
93A95PRO00.0610.02838.128-0.003-0.0030.0000.0000.0000.000
94A96TYR0-0.055-0.03838.117-0.002-0.0020.0000.0000.0000.000
95A97ILE0-0.0010.02534.713-0.001-0.0010.0000.0000.0000.000
96A98ASN0-0.047-0.03938.1190.0000.0000.0000.0000.0000.000
97A99LEU00.0240.02034.8810.0000.0000.0000.0000.0000.000
98A100GLY00.0030.01133.170-0.001-0.0010.0000.0000.0000.000
99A101GLU-1-0.796-0.84933.479-0.015-0.0150.0000.0000.0000.000
100A102TYR0-0.030-0.05929.1090.0010.0010.0000.0000.0000.000
101A103ILE0-0.011-0.01329.2090.0040.0040.0000.0000.0000.000
102A104ILE0-0.0230.00427.416-0.002-0.0020.0000.0000.0000.000
103A105VAL0-0.013-0.01325.0410.0040.0040.0000.0000.0000.000
104A106THR0-0.005-0.01726.5450.0010.0010.0000.0000.0000.000
105A107GLY0-0.002-0.01326.5310.0090.0090.0000.0000.0000.000
106A108ALA0-0.043-0.00124.031-0.010-0.0100.0000.0000.0000.000
107A109SER00.001-0.00726.0560.0120.0120.0000.0000.0000.000
108A110TYR0-0.037-0.03424.525-0.002-0.0020.0000.0000.0000.000
109A111ASN00.0060.00726.222-0.001-0.0010.0000.0000.0000.000
110A112GLN00.028-0.00625.2810.0070.0070.0000.0000.0000.000
111A113GLY00.0720.03624.137-0.010-0.0100.0000.0000.0000.000
112A114GLY00.0170.00220.7620.0140.0140.0000.0000.0000.000
113A115LEU00.0380.03015.1030.0250.0250.0000.0000.0000.000
114A116PHE00.0450.00817.8600.0410.0410.0000.0000.0000.000
115A117TYR0-0.0060.01720.2210.0200.0200.0000.0000.0000.000
116A118GLN0-0.035-0.02615.706-0.013-0.0130.0000.0000.0000.000
117A119TYR0-0.096-0.06410.7710.0030.0030.0000.0000.0000.000
118A120LEU0-0.031-0.03017.2980.0210.0210.0000.0000.0000.000
119A121ARG10.8540.93717.913-0.410-0.4100.0000.0000.0000.000
120A122ASP-1-0.813-0.91622.0780.1630.1630.0000.0000.0000.000
121A123ASN0-0.075-0.04124.5740.0110.0110.0000.0000.0000.000
122A124ALA00.0150.03026.929-0.014-0.0140.0000.0000.0000.000
123A125CYS0-0.042-0.01526.2700.0080.0080.0000.0000.0000.000
124A126VAL00.0180.01922.905-0.008-0.0080.0000.0000.0000.000
125A127ALA00.011-0.00525.348-0.005-0.0050.0000.0000.0000.000
126A128SER00.0050.00622.1480.0080.0080.0000.0000.0000.000
127A129THR00.034-0.00323.711-0.014-0.0140.0000.0000.0000.000
128A130PRO00.0170.04321.9800.0180.0180.0000.0000.0000.000
129A131ASP-1-0.816-0.92921.3370.0900.0900.0000.0000.0000.000
130A132PHE00.0690.03423.246-0.013-0.0130.0000.0000.0000.000
131A133GLU-1-0.820-0.89325.3890.0500.0500.0000.0000.0000.000
132A134LEU0-0.016-0.01020.341-0.011-0.0110.0000.0000.0000.000
133A135THR00.034-0.00624.647-0.011-0.0110.0000.0000.0000.000
134A136ASN0-0.040-0.02426.569-0.011-0.0110.0000.0000.0000.000
135A137LYS10.8830.93925.352-0.035-0.0350.0000.0000.0000.000
136A138LEU00.0110.01523.791-0.007-0.0070.0000.0000.0000.000
137A139VAL00.0150.00427.802-0.007-0.0070.0000.0000.0000.000
138A140THR0-0.045-0.02331.398-0.004-0.0040.0000.0000.0000.000
139A141SER0-0.058-0.04428.030-0.003-0.0030.0000.0000.0000.000
140A142PHE00.0210.00427.134-0.004-0.0040.0000.0000.0000.000
141A143SER0-0.0010.01732.264-0.002-0.0020.0000.0000.0000.000
142A144LYS10.9230.97732.8180.0170.0170.0000.0000.0000.000
143A145ARG10.8180.88529.9920.0510.0510.0000.0000.0000.000
144A146ASN0-0.059-0.02535.3590.0000.0000.0000.0000.0000.000
145A147LEU0-0.0080.00931.648-0.002-0.0020.0000.0000.0000.000
146A148LYS10.9380.97935.5000.0110.0110.0000.0000.0000.000
147A149TYR00.003-0.00532.407-0.001-0.0010.0000.0000.0000.000
148A150TYR0-0.071-0.06233.3980.0040.0040.0000.0000.0000.000
149A151VAL00.005-0.00931.634-0.001-0.0010.0000.0000.0000.000
150A152GLY00.0350.01631.2380.0000.0000.0000.0000.0000.000
151A153ASN00.0020.02529.2630.0010.0010.0000.0000.0000.000
152A154VAL00.0160.00525.482-0.007-0.0070.0000.0000.0000.000
153A155PHE00.0090.00127.7940.0090.0090.0000.0000.0000.000
154A156SER0-0.023-0.04122.507-0.004-0.0040.0000.0000.0000.000
155A157SER0-0.0030.00024.6120.0120.0120.0000.0000.0000.000
156A158ASP-1-0.906-0.96221.4420.0920.0920.0000.0000.0000.000
157A159ALA0-0.047-0.03323.563-0.007-0.0070.0000.0000.0000.000
158A160PHE0-0.030-0.01825.431-0.001-0.0010.0000.0000.0000.000
159A161TYR00.003-0.01427.264-0.002-0.0020.0000.0000.0000.000
160A162ALA0-0.0190.01829.6850.0000.0000.0000.0000.0000.000
161A163GLU-1-0.934-0.96231.3440.0040.0040.0000.0000.0000.000
162A164ASP-1-0.837-0.93134.6540.0350.0350.0000.0000.0000.000
163A165GLU-1-0.921-0.95336.4660.0150.0150.0000.0000.0000.000
164A166GLU-1-0.899-0.94738.9190.0280.0280.0000.0000.0000.000
165A167PHE0-0.017-0.00230.1360.0020.0020.0000.0000.0000.000
166A168VAL00.0530.01435.9850.0030.0030.0000.0000.0000.000
167A169LYS10.9801.01237.319-0.013-0.0130.0000.0000.0000.000
168A170LYS10.8270.92835.700-0.031-0.0310.0000.0000.0000.000
169A171TRP00.0370.00831.1970.0070.0070.0000.0000.0000.000
170A172SER0-0.002-0.01934.8450.0020.0020.0000.0000.0000.000
171A173SER0-0.105-0.06236.9090.0020.0020.0000.0000.0000.000
172A174ARG10.8920.94933.909-0.049-0.0490.0000.0000.0000.000
173A175GLY00.0070.01234.8590.0050.0050.0000.0000.0000.000
174A176ASN0-0.073-0.01430.8540.0040.0040.0000.0000.0000.000
175A177ILE00.0470.01732.146-0.004-0.0040.0000.0000.0000.000
176A178ALA0-0.014-0.01029.704-0.006-0.0060.0000.0000.0000.000
177A179VAL00.0190.02227.8640.0080.0080.0000.0000.0000.000
178A180GLU-1-0.719-0.83221.9280.0230.0230.0000.0000.0000.000
179A181MET0-0.0080.01021.1960.0010.0010.0000.0000.0000.000
180A182GLU-1-0.767-0.87816.673-0.005-0.0050.0000.0000.0000.000
181A183CYS0-0.044-0.01518.4270.0170.0170.0000.0000.0000.000
182A184ALA00.0660.04320.3600.0150.0150.0000.0000.0000.000
183A185THR0-0.0050.00715.0330.0290.0290.0000.0000.0000.000
184A186LEU0-0.012-0.00615.2850.0340.0340.0000.0000.0000.000
185A187PHE00.005-0.01216.8430.0200.0200.0000.0000.0000.000
186A188THR00.0210.00219.1520.0080.0080.0000.0000.0000.000
187A189LEU0-0.0230.00711.5180.0210.0210.0000.0000.0000.000
188A190SER0-0.008-0.02714.9980.0550.0550.0000.0000.0000.000
189A191LYS10.8420.91116.004-0.120-0.1200.0000.0000.0000.000
190A192VAL0-0.058-0.01515.7680.0020.0020.0000.0000.0000.000
191A193LYS10.7910.8879.661-0.977-0.9770.0000.0000.0000.000
192A194GLY0-0.0030.01914.1770.0120.0120.0000.0000.0000.000
193A195TRP0-0.012-0.0119.222-0.051-0.0510.0000.0000.0000.000
194A196LYS10.8350.90515.422-0.100-0.1000.0000.0000.0000.000
195A197SER00.0360.01816.378-0.004-0.0040.0000.0000.0000.000
196A198ALA00.0100.01718.7900.0050.0050.0000.0000.0000.000
197A199THR0-0.020-0.02620.424-0.001-0.0010.0000.0000.0000.000
198A200VAL0-0.0040.01322.5820.0050.0050.0000.0000.0000.000
199A201LEU0-0.026-0.01023.309-0.008-0.0080.0000.0000.0000.000
200A202VAL00.0280.00826.3010.0030.0030.0000.0000.0000.000
201A203VAL0-0.003-0.00228.596-0.001-0.0010.0000.0000.0000.000
202A204SER00.004-0.01129.446-0.004-0.0040.0000.0000.0000.000
203A205ASP-1-0.839-0.93231.416-0.023-0.0230.0000.0000.0000.000
204A206ASN0-0.083-0.05633.6150.0050.0050.0000.0000.0000.000
205A207LEU00.0480.03132.2760.0000.0000.0000.0000.0000.000
206A208ALA0-0.028-0.00936.6030.0020.0020.0000.0000.0000.000
207A209LYS10.8190.92039.6720.0100.0100.0000.0000.0000.000
208A210GLY00.0640.03940.414-0.001-0.0010.0000.0000.0000.000
209A211GLY0-0.042-0.03542.5150.0020.0020.0000.0000.0000.000
210A212ILE0-0.020-0.01741.915-0.001-0.0010.0000.0000.0000.000
211A213TRP0-0.0040.01034.066-0.004-0.0040.0000.0000.0000.000
212A214ILE0-0.019-0.00933.8980.0000.0000.0000.0000.0000.000
213A215THR0-0.011-0.02037.136-0.001-0.0010.0000.0000.0000.000
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215A217GLU-1-0.842-0.92633.022-0.065-0.0650.0000.0000.0000.000
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