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: 64M3Z

Calculation Name: 4Z1O-A-Xray547

Preferred Name:

Target Type:

Ligand Name: 1-o-pyrophosphono-5-o-phosphono-alpha-d-ribofuranose

Ligand 3-letter code: PRP

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4Z1O

Chain ID: A

ChEMBL ID:

UniProt ID: D0KMY9

Base Structure: X-ray

Registration Date: 2025-10-05

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 176
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1871897.335319
FMO2-HF: Nuclear repulsion 1802409.395018
FMO2-HF: Total energy -69487.940301
FMO2-MP2: Total energy -69695.900057


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:4:TYR)


Summations of interaction energy for fragment #1(A:4:TYR)
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.
-26.009-11.16815.292-10.362-19.768-0.062
Interaction energy analysis for fragmet #1(A:4:TYR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.791 / q_NPA : 0.886
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].
3A6ILE0-0.008-0.0112.629-4.021-1.3420.999-1.147-2.530-0.006
4A7PRO00.0020.0434.8692.6512.705-0.001-0.009-0.0430.000
138A141LYS10.8810.9452.66644.44045.3000.522-0.267-1.114-0.004
139A142TRP00.0120.0062.1720.7533.1173.458-1.945-3.877-0.006
140A143ILE00.0400.0122.213-28.698-24.8545.286-4.941-4.189-0.058
141A144ILE0-0.060-0.0222.7010.4682.0472.265-0.651-3.1930.002
142A145PHE00.0930.0415.179-0.185-0.160-0.001-0.002-0.0220.000
149A152VAL00.0440.0174.069-0.0220.2380.002-0.038-0.2240.000
153A156ASN00.0360.0133.5260.6331.0080.004-0.113-0.2660.000
156A159VAL0-0.0180.0132.627-4.391-2.8492.104-0.814-2.8330.007
157A160PRO0-0.0180.0022.7442.9694.2280.654-0.435-1.4770.003
5A8SER00.0430.0158.5690.9150.9150.0000.0000.0000.000
6A9TRP00.016-0.03311.3510.0400.0400.0000.0000.0000.000
7A10ASP-1-0.875-0.92114.524-17.228-17.2280.0000.0000.0000.000
8A11GLU-1-0.728-0.83510.148-29.473-29.4730.0000.0000.0000.000
9A12ILE0-0.081-0.04711.1700.2320.2320.0000.0000.0000.000
10A13GLU-1-0.924-0.95814.554-13.993-13.9930.0000.0000.0000.000
11A14ASP-1-0.837-0.91316.477-16.073-16.0730.0000.0000.0000.000
12A15ALA0-0.097-0.03814.7100.5440.5440.0000.0000.0000.000
13A16VAL0-0.009-0.02216.8710.6660.6660.0000.0000.0000.000
14A17PHE00.0210.00519.7150.8210.8210.0000.0000.0000.000
15A18SER0-0.011-0.01019.3540.4960.4960.0000.0000.0000.000
16A19ILE0-0.072-0.02418.8920.4680.4680.0000.0000.0000.000
17A20GLY00.0460.01522.0870.5800.5800.0000.0000.0000.000
18A21GLU-1-0.915-0.96424.656-12.300-12.3000.0000.0000.0000.000
19A22ALA0-0.027-0.01223.8750.5100.5100.0000.0000.0000.000
20A23LEU0-0.0070.00325.2270.4470.4470.0000.0000.0000.000
21A24VAL00.0070.00627.9120.4910.4910.0000.0000.0000.000
22A25LYS10.9000.95728.78410.35310.3530.0000.0000.0000.000
23A26SER0-0.050-0.03928.3340.2610.2610.0000.0000.0000.000
24A27ASN0-0.078-0.02831.0610.2520.2520.0000.0000.0000.000
25A28TYR0-0.023-0.04628.9810.3790.3790.0000.0000.0000.000
26A29ILE00.0570.03430.416-0.330-0.3300.0000.0000.0000.000
27A30PRO0-0.024-0.01428.7570.3270.3270.0000.0000.0000.000
28A31ASP-1-0.806-0.89932.075-8.492-8.4920.0000.0000.0000.000
29A32VAL0-0.056-0.04030.5260.1520.1520.0000.0000.0000.000
30A33LEU00.0050.02125.256-0.223-0.2230.0000.0000.0000.000
31A34ILE0-0.022-0.02125.5360.1940.1940.0000.0000.0000.000
32A35ALA00.0260.01122.922-0.472-0.4720.0000.0000.0000.000
33A36VAL0-0.016-0.01819.4060.5470.5470.0000.0000.0000.000
34A37LEU0-0.068-0.01720.062-0.495-0.4950.0000.0000.0000.000
35A38THR0-0.016-0.03617.290-0.114-0.1140.0000.0000.0000.000
36A39GLY00.0530.02815.3160.0520.0520.0000.0000.0000.000
37A40GLY00.0670.02615.950-0.270-0.2700.0000.0000.0000.000
38A41ILE0-0.055-0.01718.6970.6270.6270.0000.0000.0000.000
39A42ILE0-0.0130.00116.4020.5900.5900.0000.0000.0000.000
40A43PRO00.0220.00716.1700.4430.4430.0000.0000.0000.000
41A44ALA00.0250.02118.9160.5240.5240.0000.0000.0000.000
42A45LYS10.9450.97222.33011.60911.6090.0000.0000.0000.000
43A46LEU00.008-0.00118.4350.4320.4320.0000.0000.0000.000
44A47LEU00.0250.01322.4030.3520.3520.0000.0000.0000.000
45A48SER0-0.085-0.05923.9470.4650.4650.0000.0000.0000.000
46A49ASP-1-0.981-0.98725.789-10.540-10.5400.0000.0000.0000.000
47A50LEU00.0040.01523.6090.3480.3480.0000.0000.0000.000
48A51LEU0-0.039-0.02226.8720.2400.2400.0000.0000.0000.000
49A52ASP-1-0.794-0.86129.411-8.604-8.6040.0000.0000.0000.000
50A53LEU0-0.0110.00928.0180.3010.3010.0000.0000.0000.000
51A54LYS10.7780.86130.5198.4708.4700.0000.0000.0000.000
52A55VAL0-0.053-0.01232.5700.1150.1150.0000.0000.0000.000
53A56ILE00.0260.02526.447-0.222-0.2220.0000.0000.0000.000
54A57ARG10.7640.85028.9139.3939.3930.0000.0000.0000.000
55A58TYR00.0290.01125.221-0.493-0.4930.0000.0000.0000.000
56A59ILE00.0110.00824.0310.4130.4130.0000.0000.0000.000
57A60ASP-1-0.808-0.86523.480-12.527-12.5270.0000.0000.0000.000
58A61ILE00.0200.00421.2800.4300.4300.0000.0000.0000.000
59A62LYS10.8980.96116.69814.37914.3790.0000.0000.0000.000
60A63PHE00.0350.02716.5290.4500.4500.0000.0000.0000.000
61A64TYR0-0.008-0.01316.281-0.808-0.8080.0000.0000.0000.000
62A65ARG00.0240.0728.256-2.170-2.1700.0000.0000.0000.000
63A66SER00.013-0.00212.9070.7800.7800.0000.0000.0000.000
64A67VAL00.0360.01414.586-0.468-0.4680.0000.0000.0000.000
65A68GLY00.0800.04516.0380.6310.6310.0000.0000.0000.000
66A69LYS10.8890.92418.32112.39512.3950.0000.0000.0000.000
67A70THR0-0.052-0.01218.4590.4800.4800.0000.0000.0000.000
68A71GLU-1-0.821-0.91420.084-11.696-11.6960.0000.0000.0000.000
69A72SER0-0.103-0.06520.292-0.387-0.3870.0000.0000.0000.000
70A73LYS10.8890.94021.51511.84011.8400.0000.0000.0000.000
71A74PRO0-0.0280.00920.582-0.306-0.3060.0000.0000.0000.000
72A75VAL00.014-0.00121.6310.5650.5650.0000.0000.0000.000
73A76ILE0-0.003-0.01323.831-0.297-0.2970.0000.0000.0000.000
74A77ARG10.7650.85221.52112.43012.4300.0000.0000.0000.000
75A78SER00.0090.00427.6060.4540.4540.0000.0000.0000.000
76A79VAL00.0240.00528.151-0.434-0.4340.0000.0000.0000.000
77A80TYR0-0.031-0.00227.4000.4390.4390.0000.0000.0000.000
78A81THR00.006-0.02731.225-0.275-0.2750.0000.0000.0000.000
79A82ASP-1-0.799-0.84133.426-8.292-8.2920.0000.0000.0000.000
80A83SER00.0200.00236.025-0.238-0.2380.0000.0000.0000.000
81A84LEU0-0.011-0.01632.124-0.052-0.0520.0000.0000.0000.000
82A85GLU-1-0.851-0.90336.342-7.415-7.4150.0000.0000.0000.000
83A86GLY0-0.018-0.01439.4290.0800.0800.0000.0000.0000.000
84A87LYS10.9000.96335.8728.3458.3450.0000.0000.0000.000
85A88LYS10.8180.90633.5888.6598.6590.0000.0000.0000.000
86A89VAL00.0290.01329.171-0.108-0.1080.0000.0000.0000.000
87A90LEU0-0.0160.01124.798-0.077-0.0770.0000.0000.0000.000
88A91VAL0-0.012-0.00622.725-0.014-0.0140.0000.0000.0000.000
89A92VAL00.004-0.00420.382-0.316-0.3160.0000.0000.0000.000
90A93ASP-1-0.807-0.93217.099-16.370-16.3700.0000.0000.0000.000
91A94ASP-1-0.846-0.90813.166-20.757-20.7570.0000.0000.0000.000
92A95VAL0-0.049-0.03810.003-1.263-1.2630.0000.0000.0000.000
93A96ALA00.0190.02013.0480.9640.9640.0000.0000.0000.000
94A97ASP-1-0.825-0.91610.151-26.675-26.6750.0000.0000.0000.000
95A98THR00.0810.02013.1550.4260.4260.0000.0000.0000.000
96A99GLY00.0490.03216.2970.8050.8050.0000.0000.0000.000
97A100GLU-1-0.846-0.92018.747-12.189-12.1890.0000.0000.0000.000
98A101THR00.0120.00517.5490.7770.7770.0000.0000.0000.000
99A102LEU00.0980.04419.1750.6810.6810.0000.0000.0000.000
100A103GLU-1-0.885-0.91521.662-11.411-11.4110.0000.0000.0000.000
101A104ALA00.0080.00323.8050.5470.5470.0000.0000.0000.000
102A105VAL00.0150.00622.9450.4970.4970.0000.0000.0000.000
103A106SER00.0340.00325.3230.3710.3710.0000.0000.0000.000
104A107ASN0-0.031-0.00327.5090.4560.4560.0000.0000.0000.000
105A108VAL00.0120.00328.3770.3530.3530.0000.0000.0000.000
106A109ILE0-0.004-0.00528.3110.3010.3010.0000.0000.0000.000
107A110THR0-0.002-0.01831.1610.2830.2830.0000.0000.0000.000
108A111MET0-0.060-0.02933.5230.2150.2150.0000.0000.0000.000
109A112PHE0-0.055-0.02332.9640.2180.2180.0000.0000.0000.000
110A113ASN0-0.042-0.02736.6250.0080.0080.0000.0000.0000.000
111A114PRO00.0020.01733.5080.1510.1510.0000.0000.0000.000
112A115ALA0-0.0050.00136.5150.0440.0440.0000.0000.0000.000
113A116LYS10.8880.93631.4499.6379.6370.0000.0000.0000.000
114A117VAL00.0230.02728.358-0.078-0.0780.0000.0000.0000.000
115A118MET0-0.060-0.00727.2450.1840.1840.0000.0000.0000.000
116A119THR0-0.064-0.06022.630-0.232-0.2320.0000.0000.0000.000
117A120ALA00.0470.01721.036-0.013-0.0130.0000.0000.0000.000
118A121ALA0-0.027-0.00515.8450.0350.0350.0000.0000.0000.000
119A122LEU00.0320.02713.7940.0090.0090.0000.0000.0000.000
120A123TYR0-0.057-0.06810.662-0.499-0.4990.0000.0000.0000.000
121A124LEU0-0.0060.01112.6681.0281.0280.0000.0000.0000.000
122A125LYS10.8460.9387.23131.26231.2620.0000.0000.0000.000
123A126PRO0-0.012-0.01410.9721.7031.7030.0000.0000.0000.000
124A127TRP0-0.061-0.0348.4780.4960.4960.0000.0000.0000.000
125A128SER0-0.038-0.00415.5001.0121.0120.0000.0000.0000.000
126A129LYS10.8420.90816.89013.09613.0960.0000.0000.0000.000
127A130ARG10.8410.91119.70413.17013.1700.0000.0000.0000.000
128A131ILE00.0200.01819.113-0.779-0.7790.0000.0000.0000.000
129A132PRO0-0.019-0.00817.6730.5890.5890.0000.0000.0000.000
130A133ASP-1-0.836-0.89220.868-12.209-12.2090.0000.0000.0000.000
131A134PHE00.003-0.00421.8590.1950.1950.0000.0000.0000.000
132A135TYR00.010-0.01715.699-0.770-0.7700.0000.0000.0000.000
133A136TYR00.0420.03913.427-0.085-0.0850.0000.0000.0000.000
134A137LYS10.8930.94012.23820.52220.5220.0000.0000.0000.000
135A138GLN00.0150.01012.595-0.636-0.6360.0000.0000.0000.000
136A139ILE0-0.050-0.0286.178-1.596-1.5960.0000.0000.0000.000
137A140ASP-1-0.834-0.9287.006-37.270-37.2700.0000.0000.0000.000
143A146PRO0-0.018-0.0178.6040.4640.4640.0000.0000.0000.000
144A147TRP0-0.030-0.03611.1271.1191.1190.0000.0000.0000.000
145A148ASP-1-0.834-0.9058.353-28.025-28.0250.0000.0000.0000.000
146A149LYS10.9270.9548.15723.63023.6300.0000.0000.0000.000
147A150TRP0-0.026-0.0259.219-0.544-0.5440.0000.0000.0000.000
148A151ASP-1-0.830-0.89010.343-18.425-18.4250.0000.0000.0000.000
150A153VAL0-0.035-0.0227.0760.1460.1460.0000.0000.0000.000
151A154ARG10.8240.9098.88018.75118.7510.0000.0000.0000.000
152A155GLU0-0.052-0.0668.0261.7431.7430.0000.0000.0000.000
154A157SER00.0230.0035.897-1.805-1.8050.0000.0000.0000.000
155A158ASN0-0.033-0.0195.1071.4901.4900.0000.0000.0000.000
158A161VAL00.0200.0075.589-1.695-1.6950.0000.0000.0000.000
159A162ASP-1-0.836-0.9138.125-22.388-22.3880.0000.0000.0000.000
160A163LYS10.9410.95611.61417.32417.3240.0000.0000.0000.000
161A164LYS10.8760.9367.74127.48127.4810.0000.0000.0000.000
162A165GLU-1-0.844-0.92813.304-18.324-18.3240.0000.0000.0000.000
163A166ARG10.9720.98216.10214.21914.2190.0000.0000.0000.000
164A167PHE0-0.0040.00613.5070.7100.7100.0000.0000.0000.000
165A168LEU00.0410.00612.2960.6320.6320.0000.0000.0000.000
166A169ASN0-0.046-0.00616.3591.0371.0370.0000.0000.0000.000
167A170LEU00.0560.02520.1360.4540.4540.0000.0000.0000.000
168A171TYR00.005-0.00614.6940.3040.3040.0000.0000.0000.000
169A172ASN0-0.007-0.02018.2260.7550.7550.0000.0000.0000.000
170A173GLN0-0.017-0.01020.4600.2250.2250.0000.0000.0000.000
171A174LEU00.006-0.00120.3240.3660.3660.0000.0000.0000.000
172A175LEU00.0110.00317.8210.3640.3640.0000.0000.0000.000
173A176LYS10.8480.94122.22712.05712.0570.0000.0000.0000.000
174A177ILE0-0.025-0.01325.9150.3450.3450.0000.0000.0000.000
175A178ARG10.9000.94925.34610.38310.3830.0000.0000.0000.000
176A179LYS00.0530.05524.779-0.806-0.8060.0000.0000.0000.000