Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: KG3Q3

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:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
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
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2854748.306295
FMO2-HF: Nuclear repulsion 2766185.140705
FMO2-HF: Total energy -88563.16559
FMO2-MP2: Total energy -88824.530411


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.
-9.174-1.8537.887-5.092-10.112-0.017
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 : 0.038 / q_NPA : -0.001
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].
3A5HIS10.7640.8533.469-1.9931.234-0.023-1.766-1.4380.002
4A6ILE00.0190.0193.407-0.1400.3470.010-0.098-0.3990.000
5A7LEU0-0.019-0.0182.939-2.545-1.3490.254-0.574-0.876-0.005
6A8ALA00.0120.0374.9780.2650.332-0.001-0.006-0.0600.000
7A9LYS10.9330.9604.9250.2960.381-0.001-0.002-0.0810.000
8A10LYS10.9940.9836.3340.2970.2970.0000.0000.0000.000
9A11GLY0-0.013-0.0057.1570.1060.1060.0000.0000.0000.000
10A12GLU-1-0.893-0.9428.968-0.866-0.8660.0000.0000.0000.000
11A13VAL0-0.0210.0076.716-0.008-0.0080.0000.0000.0000.000
12A14ALA0-0.042-0.0179.5960.0610.0610.0000.0000.0000.000
13A15GLU-1-0.884-0.94711.531-0.019-0.0190.0000.0000.0000.000
14A16ARG10.9280.96813.5070.0920.0920.0000.0000.0000.000
15A17VAL00.018-0.00311.349-0.051-0.0510.0000.0000.0000.000
16A18LEU00.0170.02014.7620.0400.0400.0000.0000.0000.000
17A19VAL0-0.031-0.00612.641-0.039-0.0390.0000.0000.0000.000
18A20VAL00.012-0.00515.2530.0350.0350.0000.0000.0000.000
19A21GLY00.0450.02115.585-0.024-0.0240.0000.0000.0000.000
20A22ASP-1-0.859-0.93216.827-0.177-0.1770.0000.0000.0000.000
21A23PRO00.0560.01915.711-0.009-0.0090.0000.0000.0000.000
22A24GLY0-0.018-0.02117.291-0.016-0.0160.0000.0000.0000.000
23A25ARG10.9640.99420.2650.1060.1060.0000.0000.0000.000
24A26ALA00.0580.03216.2650.0070.0070.0000.0000.0000.000
25A27ARG10.9750.98818.2890.2360.2360.0000.0000.0000.000
26A28LEU00.0060.06319.9540.0040.0040.0000.0000.0000.000
27A29LEU00.020-0.01620.7810.0110.0110.0000.0000.0000.000
28A30SER0-0.088-0.07619.1470.0040.0040.0000.0000.0000.000
29A31THR0-0.044-0.03020.9330.0040.0040.0000.0000.0000.000
30A32LEU0-0.038-0.01623.8390.0120.0120.0000.0000.0000.000
31A33LEU0-0.0140.00218.3980.0080.0080.0000.0000.0000.000
32A34GLN0-0.021-0.02222.7980.0030.0030.0000.0000.0000.000
33A35ASN0-0.047-0.03521.975-0.017-0.0170.0000.0000.0000.000
34A36PRO00.0250.01719.385-0.021-0.0210.0000.0000.0000.000
35A37LYS10.9170.96016.2900.2910.2910.0000.0000.0000.000
36A38LEU00.0010.00413.985-0.013-0.0130.0000.0000.0000.000
37A39THR0-0.006-0.00610.187-0.020-0.0200.0000.0000.0000.000
38A40ASN00.017-0.0127.636-0.424-0.4240.0000.0000.0000.000
39A41GLU-1-0.902-0.95410.008-0.404-0.4040.0000.0000.0000.000
40A42ASN0-0.039-0.0196.9310.2900.2900.0000.0000.0000.000
41A43ARG10.9180.9388.5790.5120.5120.0000.0000.0000.000
42A44GLY00.0360.03411.4980.0900.0900.0000.0000.0000.000
43A45PHE0-0.045-0.0228.8530.0750.0750.0000.0000.0000.000
44A46LEU0-0.026-0.00210.312-0.120-0.1200.0000.0000.0000.000
45A47VAL00.0000.0048.5840.0660.0660.0000.0000.0000.000
46A48TYR00.0190.01511.940-0.026-0.0260.0000.0000.0000.000
47A49THR00.015-0.01512.0730.0290.0290.0000.0000.0000.000
48A50GLY00.0220.01915.106-0.001-0.0010.0000.0000.0000.000
49A51LYS10.9120.95918.3760.1530.1530.0000.0000.0000.000
50A52TYR00.0110.01121.091-0.005-0.0050.0000.0000.0000.000
51A53ASN00.0000.00223.5270.0020.0020.0000.0000.0000.000
52A54GLY0-0.0180.00125.0790.0060.0060.0000.0000.0000.000
53A55GLU-1-0.906-0.94420.225-0.065-0.0650.0000.0000.0000.000
54A56THR0-0.032-0.02815.344-0.009-0.0090.0000.0000.0000.000
55A57VAL0-0.012-0.00616.4540.0190.0190.0000.0000.0000.000
56A58SER00.0260.00712.324-0.035-0.0350.0000.0000.0000.000
57A59ILE0-0.015-0.00514.3340.0480.0480.0000.0000.0000.000
58A60ALA00.0140.00910.605-0.056-0.0560.0000.0000.0000.000
59A61THR0-0.0080.01012.0500.0810.0810.0000.0000.0000.000
60A62HIS00.009-0.00411.177-0.040-0.0400.0000.0000.0000.000
61A63GLY0-0.0010.00612.6000.0340.0340.0000.0000.0000.000
62A64ILE00.001-0.01014.9860.0160.0160.0000.0000.0000.000
63A65GLY00.0280.00617.1850.0040.0040.0000.0000.0000.000
64A66GLY00.0530.01915.6800.0010.0010.0000.0000.0000.000
65A67PRO00.016-0.02014.0830.0320.0320.0000.0000.0000.000
66A68SER0-0.0050.00011.8730.0400.0400.0000.0000.0000.000
67A69ILE00.0210.00210.575-0.008-0.0080.0000.0000.0000.000
68A70ALA00.0250.01510.7940.0140.0140.0000.0000.0000.000
69A71ILE0-0.027-0.0066.3700.1320.1320.0000.0000.0000.000
70A72VAL0-0.023-0.0116.2040.1090.1090.0000.0000.0000.000
71A73LEU0-0.032-0.0096.970-0.099-0.0990.0000.0000.0000.000
72A74GLU-1-0.799-0.9026.6061.1971.1970.0000.0000.0000.000
73A75GLU-1-0.730-0.8412.030-1.777-2.4436.154-1.844-3.643-0.011
74A76LEU0-0.012-0.0013.782-0.962-0.5110.011-0.108-0.354-0.001
75A77ALA00.0220.0146.435-0.080-0.0800.0000.0000.0000.000
76A78MET0-0.093-0.0272.597-1.743-0.1961.073-0.481-2.138-0.002
77A79LEU0-0.063-0.0332.602-1.146-0.2110.411-0.212-1.1330.000
78A80GLY0-0.059-0.0345.193-0.046-0.054-0.001-0.0010.0100.000
79A81ALA0-0.0150.0168.3770.0360.0360.0000.0000.0000.000
80A82ASN0-0.019-0.00910.2870.0880.0880.0000.0000.0000.000
81A83VAL00.0080.00513.0720.0200.0200.0000.0000.0000.000
82A84PHE00.0100.0039.903-0.050-0.0500.0000.0000.0000.000
83A85ILE0-0.011-0.00815.9350.0230.0230.0000.0000.0000.000
84A86ARG10.8790.93817.648-0.022-0.0220.0000.0000.0000.000
85A87TYR0-0.060-0.06318.6670.0120.0120.0000.0000.0000.000
86A88GLY00.019-0.00920.586-0.017-0.0170.0000.0000.0000.000
87A89THR0-0.0170.00222.585-0.002-0.0020.0000.0000.0000.000
88A90THR0-0.070-0.04825.0780.0060.0060.0000.0000.0000.000
89A91GLY00.0800.05527.714-0.005-0.0050.0000.0000.0000.000
90A92ALA0-0.012-0.02631.0090.0060.0060.0000.0000.0000.000
91A93LEU0-0.033-0.02331.9720.0000.0000.0000.0000.0000.000
92A94VAL0-0.0050.00535.3770.0020.0020.0000.0000.0000.000
93A95PRO00.0560.01538.095-0.003-0.0030.0000.0000.0000.000
94A96TYR0-0.074-0.03937.887-0.002-0.0020.0000.0000.0000.000
95A97ILE00.0070.03234.627-0.001-0.0010.0000.0000.0000.000
96A98ASN0-0.051-0.02538.0840.0000.0000.0000.0000.0000.000
97A99LEU00.0290.04134.8660.0000.0000.0000.0000.0000.000
98A100GLY0-0.0110.00633.132-0.001-0.0010.0000.0000.0000.000
99A101GLU-1-0.829-0.91133.439-0.014-0.0140.0000.0000.0000.000
100A102TYR0-0.068-0.10929.0810.0000.0000.0000.0000.0000.000
101A103ILE0-0.002-0.00528.9210.0040.0040.0000.0000.0000.000
102A104ILE0-0.0280.00227.445-0.002-0.0020.0000.0000.0000.000
103A105VAL0-0.011-0.01524.9630.0040.0040.0000.0000.0000.000
104A106THR0-0.002-0.01426.5120.0010.0010.0000.0000.0000.000
105A107GLY0-0.008-0.01326.5570.0090.0090.0000.0000.0000.000
106A108ALA0-0.0350.00224.011-0.010-0.0100.0000.0000.0000.000
107A109SER0-0.004-0.00326.0310.0120.0120.0000.0000.0000.000
108A110TYR0-0.025-0.03124.295-0.001-0.0010.0000.0000.0000.000
109A111ASN00.0030.00626.177-0.001-0.0010.0000.0000.0000.000
110A112GLN00.0480.01125.2790.0070.0070.0000.0000.0000.000
111A113GLY00.0590.03624.134-0.010-0.0100.0000.0000.0000.000
112A114GLY00.0170.00220.7580.0150.0150.0000.0000.0000.000
113A115LEU00.0320.03014.9280.0250.0250.0000.0000.0000.000
114A116PHE00.0480.00717.8600.0420.0420.0000.0000.0000.000
115A117TYR0-0.0140.01420.2220.0170.0170.0000.0000.0000.000
116A118GLN0-0.033-0.03015.418-0.015-0.0150.0000.0000.0000.000
117A119TYR0-0.107-0.05910.8600.0030.0030.0000.0000.0000.000
118A120LEU0-0.031-0.02517.3020.0170.0170.0000.0000.0000.000
119A121ARG10.8920.95317.434-0.451-0.4510.0000.0000.0000.000
120A122ASP-1-0.847-0.91522.0820.1840.1840.0000.0000.0000.000
121A123ASN0-0.039-0.03324.5770.0120.0120.0000.0000.0000.000
122A124ALA00.0130.01626.902-0.016-0.0160.0000.0000.0000.000
123A125CYS0-0.051-0.02926.2740.0090.0090.0000.0000.0000.000
124A126VAL00.0150.01922.981-0.009-0.0090.0000.0000.0000.000
125A127ALA00.003-0.00725.449-0.005-0.0050.0000.0000.0000.000
126A128SER00.0340.03722.6700.0150.0150.0000.0000.0000.000
127A129THR00.007-0.02023.834-0.013-0.0130.0000.0000.0000.000
128A130PRO0-0.0050.02122.0570.0170.0170.0000.0000.0000.000
129A131ASP-1-0.894-0.97621.3860.0980.0980.0000.0000.0000.000
130A132PHE00.0310.00523.310-0.014-0.0140.0000.0000.0000.000
131A133GLU-1-0.918-0.96025.4770.0540.0540.0000.0000.0000.000
132A134LEU0-0.014-0.00620.377-0.011-0.0110.0000.0000.0000.000
133A135THR00.0350.00524.694-0.012-0.0120.0000.0000.0000.000
134A136ASN00.0120.00926.625-0.010-0.0100.0000.0000.0000.000
135A137LYS10.9100.96025.186-0.023-0.0230.0000.0000.0000.000
136A138LEU00.0130.01323.887-0.008-0.0080.0000.0000.0000.000
137A139VAL00.0130.00727.870-0.007-0.0070.0000.0000.0000.000
138A140THR0-0.047-0.02531.440-0.004-0.0040.0000.0000.0000.000
139A141SER0-0.058-0.04228.121-0.005-0.0050.0000.0000.0000.000
140A142PHE00.015-0.00427.192-0.004-0.0040.0000.0000.0000.000
141A143SER00.0000.01932.228-0.003-0.0030.0000.0000.0000.000
142A144LYS10.9420.98232.8740.0170.0170.0000.0000.0000.000
143A145ARG10.7870.86930.0380.0500.0500.0000.0000.0000.000
144A146ASN0-0.053-0.02135.4390.0000.0000.0000.0000.0000.000
145A147LEU0-0.0060.00631.650-0.001-0.0010.0000.0000.0000.000
146A148LYS10.9500.98335.4590.0080.0080.0000.0000.0000.000
147A149TYR0-0.009-0.00832.382-0.002-0.0020.0000.0000.0000.000
148A150TYR0-0.041-0.02233.3740.0040.0040.0000.0000.0000.000
149A151VAL00.004-0.01031.702-0.001-0.0010.0000.0000.0000.000
150A152GLY00.0270.00231.2050.0000.0000.0000.0000.0000.000
151A153ASN00.0040.02629.2380.0010.0010.0000.0000.0000.000
152A154VAL00.0160.00825.311-0.008-0.0080.0000.0000.0000.000
153A155PHE0-0.002-0.00527.7680.0100.0100.0000.0000.0000.000
154A156SER0-0.035-0.04722.490-0.004-0.0040.0000.0000.0000.000
155A157SER0-0.015-0.00624.5890.0130.0130.0000.0000.0000.000
156A158ASP-1-0.892-0.95221.6460.1090.1090.0000.0000.0000.000
157A159ALA0-0.049-0.03323.548-0.006-0.0060.0000.0000.0000.000
158A160PHE0-0.031-0.02025.461-0.002-0.0020.0000.0000.0000.000
159A161TYR00.003-0.01427.244-0.003-0.0030.0000.0000.0000.000
160A162ALA0-0.0170.02129.6930.0000.0000.0000.0000.0000.000
161A163GLU-1-0.938-0.96831.3300.0100.0100.0000.0000.0000.000
162A164ASP-1-0.880-0.96734.5610.0420.0420.0000.0000.0000.000
163A165GLU-1-0.924-0.95236.4490.0200.0200.0000.0000.0000.000
164A166GLU-1-0.966-0.98038.9540.0300.0300.0000.0000.0000.000
165A167PHE0-0.020-0.00230.2400.0020.0020.0000.0000.0000.000
166A168VAL00.0440.00735.9620.0030.0030.0000.0000.0000.000
167A169LYS10.9771.00237.294-0.017-0.0170.0000.0000.0000.000
168A170LYS10.9600.99534.953-0.045-0.0450.0000.0000.0000.000
169A171TRP00.024-0.00530.9720.0070.0070.0000.0000.0000.000
170A172SER00.001-0.00834.8210.0020.0020.0000.0000.0000.000
171A173SER0-0.095-0.04436.8830.0020.0020.0000.0000.0000.000
172A174ARG10.8970.95033.828-0.057-0.0570.0000.0000.0000.000
173A175GLY00.0060.01134.8360.0050.0050.0000.0000.0000.000
174A176ASN0-0.082-0.02330.8980.0040.0040.0000.0000.0000.000
175A177ILE00.0490.02932.053-0.004-0.0040.0000.0000.0000.000
176A178ALA0-0.012-0.01329.678-0.006-0.0060.0000.0000.0000.000
177A179VAL00.0280.02727.6940.0080.0080.0000.0000.0000.000
178A180GLU-1-0.742-0.84521.8350.0350.0350.0000.0000.0000.000
179A181MET0-0.0070.00121.1990.0010.0010.0000.0000.0000.000
180A182GLU-1-0.816-0.89716.6460.0180.0180.0000.0000.0000.000
181A183CYS0-0.049-0.02118.4010.0190.0190.0000.0000.0000.000
182A184ALA00.0070.01820.3340.0170.0170.0000.0000.0000.000
183A185THR00.011-0.00115.0100.0250.0250.0000.0000.0000.000
184A186LEU0-0.0030.00115.2210.0380.0380.0000.0000.0000.000
185A187PHE00.012-0.00316.8170.0220.0220.0000.0000.0000.000
186A188THR00.0330.01219.1280.0120.0120.0000.0000.0000.000
187A189LEU0-0.0200.00411.6940.0140.0140.0000.0000.0000.000
188A190SER0-0.0210.02015.0870.0350.0350.0000.0000.0000.000
189A191LYS10.9290.96416.088-0.133-0.1330.0000.0000.0000.000
190A192VAL0-0.043-0.00315.8230.0000.0000.0000.0000.0000.000
191A193LYS10.8720.93810.256-0.999-0.9990.0000.0000.0000.000
192A194GLY0-0.0060.01714.2420.0100.0100.0000.0000.0000.000
193A195TRP0-0.010-0.0109.473-0.056-0.0560.0000.0000.0000.000
194A196LYS10.9130.96215.482-0.115-0.1150.0000.0000.0000.000
195A197SER00.027-0.04916.467-0.023-0.0230.0000.0000.0000.000
196A198ALA00.0060.01618.8540.0040.0040.0000.0000.0000.000
197A199THR0-0.011-0.02120.388-0.002-0.0020.0000.0000.0000.000
198A200VAL0-0.0150.01222.5460.0040.0040.0000.0000.0000.000
199A201LEU0-0.030-0.01823.323-0.008-0.0080.0000.0000.0000.000
200A202VAL00.0260.01026.2640.0020.0020.0000.0000.0000.000
201A203VAL0-0.0040.00028.5580.0000.0000.0000.0000.0000.000
202A204SER0-0.011-0.01629.436-0.004-0.0040.0000.0000.0000.000
203A205ASP-1-0.855-0.93131.382-0.017-0.0170.0000.0000.0000.000
204A206ASN0-0.079-0.05333.5820.0060.0060.0000.0000.0000.000
205A207LEU00.0440.02732.3030.0000.0000.0000.0000.0000.000
206A208ALA0-0.029-0.00736.5740.0020.0020.0000.0000.0000.000
207A209LYS10.8840.94939.6430.0070.0070.0000.0000.0000.000
208A210GLY00.0700.04540.383-0.001-0.0010.0000.0000.0000.000
209A211GLY0-0.049-0.04442.5960.0020.0020.0000.0000.0000.000
210A212ILE0-0.020-0.01641.948-0.001-0.0010.0000.0000.0000.000
211A213TRP00.011-0.00334.488-0.004-0.0040.0000.0000.0000.000
212A214ILE0-0.011-0.00534.2140.0000.0000.0000.0000.0000.000
213A215THR0-0.018-0.01037.101-0.001-0.0010.0000.0000.0000.000
214A216LYS10.9560.95631.9830.0720.0720.0000.0000.0000.000
215A217GLU-1-0.842-0.92632.985-0.065-0.0650.0000.0000.0000.000
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