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: KK563

Calculation Name: 1VHZ-B-Xray547

Preferred Name:

Target Type:

Ligand Name: adenosine-5-diphosphoribose

Ligand 3-letter code: APR

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1VHZ

Chain ID: B

ChEMBL ID:

UniProt ID: P45799

Base Structure: X-ray

Registration Date: 2025-10-03

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 185
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1882526.984045
FMO2-HF: Nuclear repulsion 1808812.433937
FMO2-HF: Total energy -73714.550108
FMO2-MP2: Total energy -73929.449008


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:2:SER)


Summations of interaction energy for fragment #1(A:2:SER)
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.
-46.113-44.727-0.009-0.597-0.781-0.002
Interaction energy analysis for fragmet #1(A:2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.875 / q_NPA : 0.924
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].
3A4SER00.0500.0273.815-0.2501.136-0.009-0.597-0.781-0.002
4A5LEU00.0130.0066.3540.1320.1320.0000.0000.0000.000
5A6GLN00.006-0.0118.5511.0151.0150.0000.0000.0000.000
6A7LYS10.9610.97911.79716.51716.5170.0000.0000.0000.000
7A8PRO00.0180.01714.870-0.291-0.2910.0000.0000.0000.000
8A9THR0-0.018-0.00516.8650.8010.8010.0000.0000.0000.000
9A10ILE00.016-0.00719.8250.0430.0430.0000.0000.0000.000
10A11LEU0-0.048-0.02122.7450.2270.2270.0000.0000.0000.000
11A12ASN00.0130.00825.3360.5420.5420.0000.0000.0000.000
12A13VAL0-0.056-0.03327.616-0.405-0.4050.0000.0000.0000.000
13A14GLU-1-0.905-0.93430.085-8.817-8.8170.0000.0000.0000.000
14A15THR0-0.096-0.06133.115-0.034-0.0340.0000.0000.0000.000
15A16VAL00.0470.03333.2700.2230.2230.0000.0000.0000.000
16A17ALA00.0220.01736.0260.2320.2320.0000.0000.0000.000
17A18ARG10.9190.95237.5997.6927.6920.0000.0000.0000.000
18A19SER00.0120.01040.1910.1870.1870.0000.0000.0000.000
19A20ARG10.9790.97742.3496.6166.6160.0000.0000.0000.000
20A21LEU00.0160.01940.9310.0430.0430.0000.0000.0000.000
21A22PHE00.0320.02936.111-0.211-0.2110.0000.0000.0000.000
22A23THR00.012-0.02035.5770.2110.2110.0000.0000.0000.000
23A24VAL00.0280.02731.937-0.215-0.2150.0000.0000.0000.000
24A25GLU-1-0.824-0.93030.424-9.857-9.8570.0000.0000.0000.000
25A26SER00.0670.04129.632-0.425-0.4250.0000.0000.0000.000
26A27VAL0-0.027-0.02424.6370.0550.0550.0000.0000.0000.000
27A28ASP-1-0.816-0.89825.393-11.466-11.4660.0000.0000.0000.000
28A29LEU0-0.047-0.03520.018-0.382-0.3820.0000.0000.0000.000
29A30GLU-1-0.820-0.89918.046-15.202-15.2020.0000.0000.0000.000
30A31PHE00.0050.00213.865-0.729-0.7290.0000.0000.0000.000
31A32SER0-0.016-0.00610.385-1.145-1.1450.0000.0000.0000.000
32A33ASN0-0.031-0.03210.867-0.441-0.4410.0000.0000.0000.000
33A34GLY00.0630.04312.6170.4560.4560.0000.0000.0000.000
34A35VAL0-0.047-0.01215.2141.1281.1280.0000.0000.0000.000
35A36ARG10.8830.92017.26613.71013.7100.0000.0000.0000.000
36A37ARG10.8760.93418.86415.21615.2160.0000.0000.0000.000
37A38VAL00.0810.05822.307-0.070-0.0700.0000.0000.0000.000
38A39TYR0-0.070-0.04518.788-0.252-0.2520.0000.0000.0000.000
39A40GLU-1-0.878-0.93225.356-9.621-9.6210.0000.0000.0000.000
40A41ARG10.8130.89825.45010.94110.9410.0000.0000.0000.000
41A42MET00.0240.02128.5710.4570.4570.0000.0000.0000.000
42A43ARG10.8610.93430.0018.8178.8170.0000.0000.0000.000
43A44PRO0-0.060-0.02227.9160.0550.0550.0000.0000.0000.000
44A45THR00.003-0.00530.2140.3180.3180.0000.0000.0000.000
45A46ASN00.006-0.00731.059-0.508-0.5080.0000.0000.0000.000
46A47ARG10.8540.92432.8837.7167.7160.0000.0000.0000.000
47A48GLU-1-0.799-0.87831.123-9.982-9.9820.0000.0000.0000.000
48A49ALA00.0500.03034.3640.2470.2470.0000.0000.0000.000
49A50VAL0-0.008-0.01135.546-0.279-0.2790.0000.0000.0000.000
50A51MET0-0.0040.00235.744-0.062-0.0620.0000.0000.0000.000
51A52ILE00.0180.01738.644-0.159-0.1590.0000.0000.0000.000
52A53VAL0-0.026-0.00838.9300.0580.0580.0000.0000.0000.000
53A54PRO00.0280.01842.025-0.002-0.0020.0000.0000.0000.000
54A55ILE0-0.033-0.02342.6460.0120.0120.0000.0000.0000.000
55A56VAL00.007-0.00447.0150.0590.0590.0000.0000.0000.000
56A57ASP-1-0.901-0.94750.818-5.752-5.7520.0000.0000.0000.000
57A58ASP-1-0.890-0.92748.939-6.241-6.2410.0000.0000.0000.000
58A59HIS0-0.092-0.06548.404-0.036-0.0360.0000.0000.0000.000
59A60LEU00.0000.00642.585-0.044-0.0440.0000.0000.0000.000
60A61ILE0-0.014-0.01446.2470.1490.1490.0000.0000.0000.000
61A62LEU0-0.056-0.02543.287-0.169-0.1690.0000.0000.0000.000
62A63ILE00.0590.02844.8670.1950.1950.0000.0000.0000.000
63A64ARG10.9180.95246.2176.2796.2790.0000.0000.0000.000
64A65GLU-1-0.876-0.94344.401-6.870-6.8700.0000.0000.0000.000
65A66TYR00.0010.01446.004-0.135-0.1350.0000.0000.0000.000
66A67ALA00.0330.01941.940-0.079-0.0790.0000.0000.0000.000
67A68VAL00.025-0.00543.940-0.030-0.0300.0000.0000.0000.000
68A69GLY0-0.070-0.03340.7670.0040.0040.0000.0000.0000.000
69A70THR0-0.051-0.03539.926-0.171-0.1710.0000.0000.0000.000
70A71GLU-1-0.989-0.97142.595-6.562-6.5620.0000.0000.0000.000
71A72SER0-0.037-0.02244.4650.1000.1000.0000.0000.0000.000
72A73TYR0-0.095-0.07746.171-0.016-0.0160.0000.0000.0000.000
73A74GLU-1-0.857-0.91640.257-7.842-7.8420.0000.0000.0000.000
74A75LEU0-0.043-0.02943.4420.2300.2300.0000.0000.0000.000
75A76GLY0-0.008-0.02041.649-0.202-0.2020.0000.0000.0000.000
76A77PHE0-0.058-0.02738.3140.1320.1320.0000.0000.0000.000
77A78SER00.011-0.00841.741-0.089-0.0890.0000.0000.0000.000
78A79LYS10.7560.85137.9137.5067.5060.0000.0000.0000.000
79A80GLY00.1790.11640.5380.1030.1030.0000.0000.0000.000
80A81LEU0-0.141-0.08538.179-0.348-0.3480.0000.0000.0000.000
81A82ILE00.0020.00936.2140.1150.1150.0000.0000.0000.000
82A83ASP-1-0.825-0.89439.888-7.208-7.2080.0000.0000.0000.000
83A84PRO0-0.106-0.07940.805-0.119-0.1190.0000.0000.0000.000
84A85GLY0-0.011-0.00341.0160.1710.1710.0000.0000.0000.000
85A86GLU-1-0.775-0.83941.893-7.032-7.0320.0000.0000.0000.000
86A87SER0-0.084-0.07939.493-0.275-0.2750.0000.0000.0000.000
87A88VAL0-0.014-0.03135.4860.0760.0760.0000.0000.0000.000
88A89TYR00.001-0.00437.954-0.005-0.0050.0000.0000.0000.000
89A90GLU-1-0.822-0.87242.064-6.923-6.9230.0000.0000.0000.000
90A91ALA00.0420.03540.9320.1030.1030.0000.0000.0000.000
91A92ALA0-0.002-0.01041.1780.0820.0820.0000.0000.0000.000
92A93ASN00.002-0.01343.0250.1430.1430.0000.0000.0000.000
93A94ARG10.7230.83343.7687.0327.0320.0000.0000.0000.000
94A95GLU-1-0.763-0.89943.028-6.950-6.9500.0000.0000.0000.000
95A96LEU0-0.053-0.02246.2470.0630.0630.0000.0000.0000.000
96A97LYS10.8150.90247.8926.1606.1600.0000.0000.0000.000
97A98GLU-1-0.878-0.92248.799-6.343-6.3430.0000.0000.0000.000
98A99GLU-1-0.752-0.85045.153-6.871-6.8710.0000.0000.0000.000
99A100VAL0-0.075-0.05348.6920.0470.0470.0000.0000.0000.000
100A101GLY0-0.0160.01151.2950.1120.1120.0000.0000.0000.000
101A102PHE0-0.062-0.04451.1910.1250.1250.0000.0000.0000.000
102A103GLY00.0800.03050.417-0.099-0.0990.0000.0000.0000.000
103A104ALA0-0.039-0.02947.3870.0370.0370.0000.0000.0000.000
104A105ASN0-0.090-0.05349.389-0.006-0.0060.0000.0000.0000.000
105A106ASP-1-0.917-0.94144.931-7.023-7.0230.0000.0000.0000.000
106A107LEU00.0170.00742.950-0.064-0.0640.0000.0000.0000.000
107A108THR0-0.001-0.00138.655-0.137-0.1370.0000.0000.0000.000
108A109PHE0-0.032-0.01731.549-0.139-0.1390.0000.0000.0000.000
109A110LEU0-0.0210.00633.900-0.132-0.1320.0000.0000.0000.000
110A111LYS10.9130.94226.49310.52410.5240.0000.0000.0000.000
111A112LYS10.8420.92728.43110.15510.1550.0000.0000.0000.000
112A113LEU00.0060.00427.080-0.486-0.4860.0000.0000.0000.000
113A114SER0-0.026-0.02224.5960.0920.0920.0000.0000.0000.000
114A115MET00.0550.02526.730-0.243-0.2430.0000.0000.0000.000
115A116ALA00.0330.01825.452-0.068-0.0680.0000.0000.0000.000
116A117PRO00.0240.00321.6460.0360.0360.0000.0000.0000.000
117A118SER0-0.064-0.02621.852-0.305-0.3050.0000.0000.0000.000
118A119TYR0-0.0060.00623.105-0.038-0.0380.0000.0000.0000.000
119A120PHE00.0390.02226.6350.4160.4160.0000.0000.0000.000
120A121SER0-0.012-0.01326.529-0.316-0.3160.0000.0000.0000.000
121A122SER0-0.035-0.00927.604-0.089-0.0890.0000.0000.0000.000
122A123LYS10.8750.93324.89411.24411.2440.0000.0000.0000.000
123A124MET00.0320.03730.4130.2580.2580.0000.0000.0000.000
124A125ASN0-0.077-0.05431.679-0.493-0.4930.0000.0000.0000.000
125A126ILE00.0350.01632.0060.2070.2070.0000.0000.0000.000
126A127VAL0-0.004-0.00835.402-0.151-0.1510.0000.0000.0000.000
127A128VAL00.0000.01038.5580.0800.0800.0000.0000.0000.000
128A129ALA00.0010.00540.9300.0180.0180.0000.0000.0000.000
129A130GLN0-0.032-0.03244.6400.0530.0530.0000.0000.0000.000
130A131ASP-1-0.852-0.92447.430-5.923-5.9230.0000.0000.0000.000
131A132LEU00.0070.01148.196-0.019-0.0190.0000.0000.0000.000
132A133TYR0-0.0240.00351.4780.1280.1280.0000.0000.0000.000
133A134PRO0-0.038-0.02954.626-0.067-0.0670.0000.0000.0000.000
134A135GLU-1-0.857-0.91854.677-5.720-5.7200.0000.0000.0000.000
135A136SER0-0.0010.00054.730-0.054-0.0540.0000.0000.0000.000
136A137LEU0-0.078-0.03351.3290.0760.0760.0000.0000.0000.000
137A138GLU-1-0.949-0.97454.333-5.558-5.5580.0000.0000.0000.000
138A139GLY00.0480.03951.282-0.084-0.0840.0000.0000.0000.000
139A140ASP-1-1.019-1.01949.703-6.084-6.0840.0000.0000.0000.000
140A141GLU-1-0.909-0.94649.949-6.133-6.1330.0000.0000.0000.000
141A142PRO0-0.080-0.04350.5470.1240.1240.0000.0000.0000.000
142A143GLU-1-0.892-0.93551.948-5.850-5.8500.0000.0000.0000.000
143A144PRO00.001-0.00652.934-0.084-0.0840.0000.0000.0000.000
144A145LEU00.0860.05547.966-0.005-0.0050.0000.0000.0000.000
145A146PRO0-0.070-0.03051.1010.0510.0510.0000.0000.0000.000
146A147GLN00.0250.01150.653-0.114-0.1140.0000.0000.0000.000
147A148VAL0-0.048-0.02548.8730.1110.1110.0000.0000.0000.000
148A149ARG10.9160.97749.2645.8095.8090.0000.0000.0000.000
149A150TRP00.015-0.00745.3680.1040.1040.0000.0000.0000.000
150A151PRO00.0070.01447.292-0.104-0.1040.0000.0000.0000.000
151A152LEU00.0490.01043.701-0.133-0.1330.0000.0000.0000.000
152A153ALA0-0.001-0.00344.126-0.142-0.1420.0000.0000.0000.000
153A154HIS10.7900.87745.0156.5736.5730.0000.0000.0000.000
154A155MET00.0310.03739.204-0.036-0.0360.0000.0000.0000.000
155A156MET00.001-0.00136.056-0.107-0.1070.0000.0000.0000.000
156A157ASP-1-0.820-0.89640.425-7.007-7.0070.0000.0000.0000.000
157A158LEU0-0.0120.00141.2130.0520.0520.0000.0000.0000.000
158A159LEU0-0.024-0.01835.453-0.097-0.0970.0000.0000.0000.000
159A160GLU-1-0.967-0.96539.471-7.614-7.6140.0000.0000.0000.000
160A161ASP-1-0.892-0.94342.352-6.734-6.7340.0000.0000.0000.000
161A162PRO0-0.076-0.05740.994-0.196-0.1960.0000.0000.0000.000
162A163ASP-1-0.871-0.91841.029-6.969-6.9690.0000.0000.0000.000
163A164PHE00.0110.00537.936-0.102-0.1020.0000.0000.0000.000
164A165ASN0-0.069-0.03336.946-0.364-0.3640.0000.0000.0000.000
165A166GLU-1-0.752-0.85435.035-9.019-9.0190.0000.0000.0000.000
166A167ALA0-0.016-0.02130.151-0.063-0.0630.0000.0000.0000.000
167A168ARG10.8060.88431.8118.4468.4460.0000.0000.0000.000
168A169ASN00.0620.03933.5160.0180.0180.0000.0000.0000.000
169A170VAL00.0600.02532.6470.0160.0160.0000.0000.0000.000
170A171SER0-0.053-0.04830.204-0.195-0.1950.0000.0000.0000.000
171A172ALA0-0.002-0.00932.060-0.060-0.0600.0000.0000.0000.000
172A173LEU00.0260.02834.9390.0780.0780.0000.0000.0000.000
173A174PHE0-0.021-0.01732.0670.0720.0720.0000.0000.0000.000
174A175LEU0-0.045-0.02729.434-0.046-0.0460.0000.0000.0000.000
175A176VAL00.0590.02433.3590.0480.0480.0000.0000.0000.000
176A177ARG10.8670.93633.5948.8648.8640.0000.0000.0000.000
177A178GLU-1-0.912-0.96031.499-9.120-9.1200.0000.0000.0000.000
178A179TRP0-0.008-0.00934.9030.0750.0750.0000.0000.0000.000
179A180LEU00.0370.01036.8440.1290.1290.0000.0000.0000.000
180A181LYS10.7880.87336.8747.9427.9420.0000.0000.0000.000
181A182GLY0-0.028-0.00737.3690.0930.0930.0000.0000.0000.000
182A183GLN0-0.049-0.02137.9970.2140.2140.0000.0000.0000.000
183A184GLY0-0.035-0.01941.3600.1910.1910.0000.0000.0000.000
184A185ARG10.8490.92742.9306.8596.8590.0000.0000.0000.000
185A186VAL-1-0.852-0.88641.663-7.250-7.2500.0000.0000.0000.000