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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: 5J3GZ

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 OptAll
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 -2863077.512319
FMO2-HF: Nuclear repulsion 2774513.029673
FMO2-HF: Total energy -88564.482645
FMO2-MP2: Total energy -88825.855918


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.
-10.578-1.6728.331-5.95-11.285-0.03
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 : 0.001 / q_NPA : -0.010
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].
3A5HIS10.7580.8543.497-0.7371.668-0.012-1.296-1.0960.001
4A6ILE00.002-0.0063.271-0.1350.3990.013-0.116-0.4310.000
5A7LEU0-0.016-0.0202.578-2.471-1.5721.832-1.047-1.684-0.012
6A8ALA00.0060.0264.5720.3200.408-0.001-0.009-0.0780.000
7A9LYS10.8520.8934.6510.2370.368-0.001-0.005-0.1250.000
8A10LYS10.8690.9186.2640.1270.1270.0000.0000.0000.000
9A11GLY00.0330.0207.0220.1410.1410.0000.0000.0000.000
10A12GLU-1-0.830-0.8858.759-0.867-0.8670.0000.0000.0000.000
11A13VAL0-0.0170.0006.636-0.039-0.0390.0000.0000.0000.000
12A14ALA0-0.0150.0069.4840.0550.0550.0000.0000.0000.000
13A15GLU-1-0.843-0.91511.4310.0070.0070.0000.0000.0000.000
14A16ARG10.8790.95313.2590.0870.0870.0000.0000.0000.000
15A17VAL00.013-0.01211.089-0.048-0.0480.0000.0000.0000.000
16A18LEU00.0270.02614.5570.0390.0390.0000.0000.0000.000
17A19VAL0-0.025-0.01012.760-0.040-0.0400.0000.0000.0000.000
18A20VAL00.0260.00715.0810.0320.0320.0000.0000.0000.000
19A21GLY00.0460.02415.380-0.026-0.0260.0000.0000.0000.000
20A22ASP-1-0.829-0.89217.227-0.164-0.1640.0000.0000.0000.000
21A23PRO00.0750.03115.405-0.002-0.0020.0000.0000.0000.000
22A24GLY0-0.011-0.00417.075-0.012-0.0120.0000.0000.0000.000
23A25ARG10.8610.89420.3510.1060.1060.0000.0000.0000.000
24A26ALA00.0340.01815.8870.0070.0070.0000.0000.0000.000
25A27ARG10.9690.98317.9930.2590.2590.0000.0000.0000.000
26A28LEU00.0020.02619.5600.0050.0050.0000.0000.0000.000
27A29LEU00.0250.00420.4980.0100.0100.0000.0000.0000.000
28A30SER0-0.077-0.04118.7650.0040.0040.0000.0000.0000.000
29A31THR0-0.051-0.04620.4240.0060.0060.0000.0000.0000.000
30A32LEU0-0.023-0.00823.4870.0120.0120.0000.0000.0000.000
31A33LEU0-0.038-0.00617.9840.0090.0090.0000.0000.0000.000
32A34GLN00.011-0.01622.3510.0010.0010.0000.0000.0000.000
33A35ASN00.008-0.00221.620-0.022-0.0220.0000.0000.0000.000
34A36PRO00.0580.04819.294-0.021-0.0210.0000.0000.0000.000
35A37LYS10.8320.90515.9460.2790.2790.0000.0000.0000.000
36A38LEU0-0.0070.01013.5390.0030.0030.0000.0000.0000.000
37A39THR0-0.048-0.03010.190-0.008-0.0080.0000.0000.0000.000
38A40ASN00.003-0.0047.419-0.441-0.4410.0000.0000.0000.000
39A41GLU-1-0.871-0.9439.548-0.407-0.4070.0000.0000.0000.000
40A42ASN00.0080.0136.6350.3670.3670.0000.0000.0000.000
41A43ARG10.9260.9458.8580.5900.5900.0000.0000.0000.000
42A44GLY00.0470.04511.4620.0920.0920.0000.0000.0000.000
43A45PHE0-0.041-0.0218.5590.0780.0780.0000.0000.0000.000
44A46LEU0-0.0210.00310.003-0.117-0.1170.0000.0000.0000.000
45A47VAL0-0.0120.0098.2290.0750.0750.0000.0000.0000.000
46A48TYR00.0660.02511.527-0.034-0.0340.0000.0000.0000.000
47A49THR00.005-0.01411.5900.0320.0320.0000.0000.0000.000
48A50GLY00.0260.01714.677-0.002-0.0020.0000.0000.0000.000
49A51LYS10.8430.92317.9200.1300.1300.0000.0000.0000.000
50A52TYR0-0.007-0.01820.694-0.006-0.0060.0000.0000.0000.000
51A53ASN0-0.023-0.00723.2460.0030.0030.0000.0000.0000.000
52A54GLY00.0360.03325.1010.0080.0080.0000.0000.0000.000
53A55GLU-1-0.818-0.89419.992-0.078-0.0780.0000.0000.0000.000
54A56THR0-0.042-0.03815.665-0.017-0.0170.0000.0000.0000.000
55A57VAL0-0.031-0.01716.3670.0200.0200.0000.0000.0000.000
56A58SER00.017-0.00812.435-0.026-0.0260.0000.0000.0000.000
57A59ILE0-0.025-0.00414.4040.0460.0460.0000.0000.0000.000
58A60ALA00.0090.00010.525-0.059-0.0590.0000.0000.0000.000
59A61THR0-0.020-0.01712.2560.0840.0840.0000.0000.0000.000
60A62HIS0-0.010-0.01910.916-0.052-0.0520.0000.0000.0000.000
61A63GLY00.0050.02312.2840.0340.0340.0000.0000.0000.000
62A64ILE00.010-0.00314.6360.0180.0180.0000.0000.0000.000
63A65GLY00.0520.03117.0320.0030.0030.0000.0000.0000.000
64A66GLY00.0600.01416.047-0.002-0.0020.0000.0000.0000.000
65A67PRO00.005-0.02214.1360.0270.0270.0000.0000.0000.000
66A68SER0-0.038-0.01612.1690.0240.0240.0000.0000.0000.000
67A69ILE0-0.008-0.00510.934-0.010-0.0100.0000.0000.0000.000
68A70ALA00.0380.01111.0810.0110.0110.0000.0000.0000.000
69A71ILE0-0.019-0.0096.4770.1160.1160.0000.0000.0000.000
70A72VAL0-0.009-0.0026.4200.1090.1090.0000.0000.0000.000
71A73LEU0-0.027-0.0057.043-0.081-0.0810.0000.0000.0000.000
72A74GLU-1-0.716-0.8346.5591.1071.1070.0000.0000.0000.000
73A75GLU-1-0.709-0.8252.252-3.968-1.7433.689-2.420-3.494-0.018
74A76LEU00.001-0.0043.453-1.173-0.5080.045-0.181-0.529-0.002
75A77ALA00.0220.0206.146-0.078-0.0780.0000.0000.0000.000
76A78MET0-0.076-0.0292.172-2.160-1.1172.121-0.611-2.5530.001
77A79LEU0-0.026-0.0132.476-1.118-0.2000.646-0.262-1.3010.000
78A80GLY0-0.021-0.0174.9840.0360.034-0.001-0.0030.0060.000
79A81ALA0-0.0290.0118.3550.0380.0380.0000.0000.0000.000
80A82ASN0-0.087-0.05910.3620.0960.0960.0000.0000.0000.000
81A83VAL0-0.0020.00313.2030.0170.0170.0000.0000.0000.000
82A84PHE00.0340.0139.521-0.055-0.0550.0000.0000.0000.000
83A85ILE0-0.033-0.01815.7020.0220.0220.0000.0000.0000.000
84A86ARG10.7810.87217.697-0.017-0.0170.0000.0000.0000.000
85A87TYR0-0.044-0.04518.6810.0110.0110.0000.0000.0000.000
86A88GLY00.0320.00520.149-0.014-0.0140.0000.0000.0000.000
87A89THR0-0.0310.00822.585-0.003-0.0030.0000.0000.0000.000
88A90THR0-0.053-0.02825.2190.0050.0050.0000.0000.0000.000
89A91GLY00.0650.04127.825-0.005-0.0050.0000.0000.0000.000
90A92ALA00.004-0.01931.1290.0060.0060.0000.0000.0000.000
91A93LEU0-0.027-0.00932.144-0.001-0.0010.0000.0000.0000.000
92A94VAL00.0200.00535.6780.0020.0020.0000.0000.0000.000
93A95PRO00.0380.02338.669-0.003-0.0030.0000.0000.0000.000
94A96TYR0-0.014-0.01637.830-0.002-0.0020.0000.0000.0000.000
95A97ILE0-0.0150.02434.828-0.001-0.0010.0000.0000.0000.000
96A98ASN0-0.028-0.02437.9390.0000.0000.0000.0000.0000.000
97A99LEU00.0280.02934.9660.0010.0010.0000.0000.0000.000
98A100GLY00.0100.00932.964-0.001-0.0010.0000.0000.0000.000
99A101GLU-1-0.786-0.83333.379-0.014-0.0140.0000.0000.0000.000
100A102TYR0-0.025-0.03928.9560.0000.0000.0000.0000.0000.000
101A103ILE0-0.010-0.01129.0600.0040.0040.0000.0000.0000.000
102A104ILE0-0.011-0.00327.529-0.002-0.0020.0000.0000.0000.000
103A105VAL0-0.007-0.00825.1400.0040.0040.0000.0000.0000.000
104A106THR0-0.022-0.03026.2480.0030.0030.0000.0000.0000.000
105A107GLY00.013-0.01025.9210.0090.0090.0000.0000.0000.000
106A108ALA0-0.055-0.01224.251-0.010-0.0100.0000.0000.0000.000
107A109SER00.011-0.00226.3370.0120.0120.0000.0000.0000.000
108A110TYR0-0.053-0.04124.615-0.002-0.0020.0000.0000.0000.000
109A111ASN00.0210.01226.135-0.004-0.0040.0000.0000.0000.000
110A112GLN0-0.004-0.01125.3560.0040.0040.0000.0000.0000.000
111A113GLY00.0670.02124.196-0.012-0.0120.0000.0000.0000.000
112A114GLY0-0.0050.00120.6720.0150.0150.0000.0000.0000.000
113A115LEU00.0400.03715.1420.0280.0280.0000.0000.0000.000
114A116PHE00.0310.00317.9720.0430.0430.0000.0000.0000.000
115A117TYR00.0310.02520.4630.0240.0240.0000.0000.0000.000
116A118GLN0-0.040-0.02115.905-0.017-0.0170.0000.0000.0000.000
117A119TYR0-0.056-0.05510.899-0.001-0.0010.0000.0000.0000.000
118A120LEU0-0.033-0.01217.4140.0220.0220.0000.0000.0000.000
119A121ARG10.8100.91018.133-0.397-0.3970.0000.0000.0000.000
120A122ASP-1-0.804-0.90422.4560.1550.1550.0000.0000.0000.000
121A123ASN0-0.036-0.03524.5270.0110.0110.0000.0000.0000.000
122A124ALA00.0040.02026.971-0.013-0.0130.0000.0000.0000.000
123A125CYS0-0.015-0.00826.3890.0110.0110.0000.0000.0000.000
124A126VAL00.0130.01522.942-0.009-0.0090.0000.0000.0000.000
125A127ALA00.0430.01925.744-0.006-0.0060.0000.0000.0000.000
126A128SER0-0.016-0.00122.2130.0010.0010.0000.0000.0000.000
127A129THR00.021-0.00923.546-0.016-0.0160.0000.0000.0000.000
128A130PRO00.0180.04121.9980.0180.0180.0000.0000.0000.000
129A131ASP-1-0.784-0.90621.3560.0920.0920.0000.0000.0000.000
130A132PHE00.0510.03423.250-0.014-0.0140.0000.0000.0000.000
131A133GLU-1-0.819-0.88925.1990.0490.0490.0000.0000.0000.000
132A134LEU0-0.016-0.00719.998-0.011-0.0110.0000.0000.0000.000
133A135THR00.029-0.00724.405-0.012-0.0120.0000.0000.0000.000
134A136ASN0-0.028-0.02226.599-0.011-0.0110.0000.0000.0000.000
135A137LYS10.8920.95425.387-0.036-0.0360.0000.0000.0000.000
136A138LEU00.0150.02823.700-0.008-0.0080.0000.0000.0000.000
137A139VAL00.0100.00427.755-0.006-0.0060.0000.0000.0000.000
138A140THR0-0.041-0.03031.151-0.004-0.0040.0000.0000.0000.000
139A141SER0-0.046-0.03128.611-0.004-0.0040.0000.0000.0000.000
140A142PHE00.000-0.01126.787-0.005-0.0050.0000.0000.0000.000
141A143SER0-0.0280.00131.919-0.003-0.0030.0000.0000.0000.000
142A144LYS10.9230.96832.5620.0150.0150.0000.0000.0000.000
143A145ARG10.8380.89329.6110.0500.0500.0000.0000.0000.000
144A146ASN0-0.051-0.02234.9610.0000.0000.0000.0000.0000.000
145A147LEU0-0.0150.01431.0660.0000.0000.0000.0000.0000.000
146A148LYS10.9250.96435.0040.0110.0110.0000.0000.0000.000
147A149TYR0-0.001-0.00132.4500.0000.0000.0000.0000.0000.000
148A150TYR0-0.058-0.06033.2490.0030.0030.0000.0000.0000.000
149A151VAL00.006-0.00431.628-0.001-0.0010.0000.0000.0000.000
150A152GLY00.0290.01631.3220.0000.0000.0000.0000.0000.000
151A153ASN00.0180.03629.4510.0010.0010.0000.0000.0000.000
152A154VAL00.0050.00025.676-0.007-0.0070.0000.0000.0000.000
153A155PHE00.0140.00427.9960.0090.0090.0000.0000.0000.000
154A156SER0-0.015-0.03522.831-0.005-0.0050.0000.0000.0000.000
155A157SER0-0.003-0.00324.8570.0120.0120.0000.0000.0000.000
156A158ASP-1-0.925-0.97421.4200.0960.0960.0000.0000.0000.000
157A159ALA0-0.037-0.02723.398-0.008-0.0080.0000.0000.0000.000
158A160PHE0-0.031-0.02825.379-0.001-0.0010.0000.0000.0000.000
159A161TYR0-0.001-0.00326.977-0.003-0.0030.0000.0000.0000.000
160A162ALA0-0.0100.00829.9500.0010.0010.0000.0000.0000.000
161A163GLU-1-0.932-0.95731.5490.0050.0050.0000.0000.0000.000
162A164ASP-1-0.813-0.91635.0710.0360.0360.0000.0000.0000.000
163A165GLU-1-0.915-0.95436.8340.0150.0150.0000.0000.0000.000
164A166GLU-1-0.863-0.92439.1940.0300.0300.0000.0000.0000.000
165A167PHE0-0.029-0.01030.2420.0000.0000.0000.0000.0000.000
166A168VAL00.0510.01835.9490.0030.0030.0000.0000.0000.000
167A169LYS10.9721.00637.275-0.013-0.0130.0000.0000.0000.000
168A170LYS10.7840.90135.871-0.032-0.0320.0000.0000.0000.000
169A171TRP00.0260.00831.1680.0080.0080.0000.0000.0000.000
170A172SER0-0.003-0.01734.9900.0030.0030.0000.0000.0000.000
171A173SER0-0.074-0.05537.1030.0020.0020.0000.0000.0000.000
172A174ARG10.8840.95333.918-0.049-0.0490.0000.0000.0000.000
173A175GLY00.0160.01834.9490.0040.0040.0000.0000.0000.000
174A176ASN0-0.093-0.03231.0050.0040.0040.0000.0000.0000.000
175A177ILE00.0420.01032.236-0.004-0.0040.0000.0000.0000.000
176A178ALA00.001-0.00729.821-0.006-0.0060.0000.0000.0000.000
177A179VAL00.0170.02028.0270.0080.0080.0000.0000.0000.000
178A180GLU-1-0.717-0.82322.0490.0260.0260.0000.0000.0000.000
179A181MET0-0.0120.02021.364-0.001-0.0010.0000.0000.0000.000
180A182GLU-1-0.764-0.89216.830-0.008-0.0080.0000.0000.0000.000
181A183CYS0-0.044-0.01218.7820.0190.0190.0000.0000.0000.000
182A184ALA00.0690.03420.5760.0160.0160.0000.0000.0000.000
183A185THR0-0.0270.00615.4340.0300.0300.0000.0000.0000.000
184A186LEU0-0.015-0.00615.3890.0340.0340.0000.0000.0000.000
185A187PHE00.015-0.00516.8910.0240.0240.0000.0000.0000.000
186A188THR00.006-0.00219.2870.0060.0060.0000.0000.0000.000
187A189LEU0-0.0390.00211.4950.0200.0200.0000.0000.0000.000
188A190SER00.006-0.03015.0640.0500.0500.0000.0000.0000.000
189A191LYS10.8240.91016.020-0.136-0.1360.0000.0000.0000.000
190A192VAL0-0.050-0.01915.7670.0040.0040.0000.0000.0000.000
191A193LYS10.7880.8919.969-0.940-0.9400.0000.0000.0000.000
192A194GLY00.0070.02314.4130.0110.0110.0000.0000.0000.000
193A195TRP00.0120.0039.390-0.052-0.0520.0000.0000.0000.000
194A196LYS10.8500.91315.520-0.103-0.1030.0000.0000.0000.000
195A197SER00.0260.01116.540-0.014-0.0140.0000.0000.0000.000
196A198ALA00.0010.00418.6540.0060.0060.0000.0000.0000.000
197A199THR0-0.014-0.02520.353-0.002-0.0020.0000.0000.0000.000
198A200VAL0-0.0170.00922.6210.0050.0050.0000.0000.0000.000
199A201LEU0-0.012-0.00423.103-0.009-0.0090.0000.0000.0000.000
200A202VAL00.0200.00926.1860.0040.0040.0000.0000.0000.000
201A203VAL0-0.003-0.01228.6720.0000.0000.0000.0000.0000.000
202A204SER0-0.003-0.00729.343-0.004-0.0040.0000.0000.0000.000
203A205ASP-1-0.806-0.90831.293-0.023-0.0230.0000.0000.0000.000
204A206ASN0-0.086-0.06733.6720.0050.0050.0000.0000.0000.000
205A207LEU00.0540.03532.4390.0000.0000.0000.0000.0000.000
206A208ALA0-0.032-0.00736.7540.0020.0020.0000.0000.0000.000
207A209LYS10.7620.87339.9290.0100.0100.0000.0000.0000.000
208A210GLY00.0720.04240.908-0.001-0.0010.0000.0000.0000.000
209A211GLY0-0.038-0.03142.8290.0010.0010.0000.0000.0000.000
210A212ILE0-0.026-0.02241.949-0.001-0.0010.0000.0000.0000.000
211A213TRP0-0.032-0.00733.499-0.004-0.0040.0000.0000.0000.000
212A214ILE0-0.020-0.01133.8960.0010.0010.0000.0000.0000.000
213A215THR00.014-0.00737.105-0.001-0.0010.0000.0000.0000.000
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215A217GLU-1-0.833-0.92432.751-0.064-0.0640.0000.0000.0000.000
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