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: KV6M3

Calculation Name: 5ZBR-A-Xray547

Preferred Name:

Target Type:

Ligand Name: phosphoaminophosphonic acid-adenylate ester | phosphate ion | magnesium ion

Ligand 3-letter code: ANP | PO4 | MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5ZBR

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0G2

Base Structure: X-ray

Registration Date: 2025-10-06

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 354
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -5577647.254356
FMO2-HF: Nuclear repulsion 5439040.082005
FMO2-HF: Total energy -138607.17235
FMO2-MP2: Total energy -139008.814509


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:SER)


Summations of interaction energy for fragment #1(A:4: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.
35.62942.2722.301-4.508-4.437-0.04
Interaction energy analysis for fragmet #1(A:4:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.856 / q_NPA : 0.923
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].
3A6VAL00.0050.0253.525-6.306-4.3950.030-0.933-1.009-0.004
306A323LYS10.8880.9633.35335.95036.7010.012-0.356-0.4070.003
337A354ILE0-0.112-0.0833.294-5.387-4.9640.007-0.106-0.3240.000
338A355ASN00.0490.0173.18110.80211.6290.004-0.294-0.5370.000
339A356HIS10.8030.8772.25011.15713.7432.249-2.800-2.035-0.039
340A357ALA00.0080.0203.7697.2087.353-0.001-0.019-0.1250.000
4A7LYS10.8570.9366.10633.17833.1780.0000.0000.0000.000
5A8VAL0-0.022-0.0237.3402.2952.2950.0000.0000.0000.000
6A9ALA00.0180.01311.0680.3490.3490.0000.0000.0000.000
7A10VAL0-0.0130.00514.2040.2030.2030.0000.0000.0000.000
8A11ARG10.7840.87417.90513.27413.2740.0000.0000.0000.000
9A12VAL00.0090.00720.8400.1400.1400.0000.0000.0000.000
10A13ARG10.7450.85124.46510.32310.3230.0000.0000.0000.000
11A14PRO00.0910.03427.2310.0880.0880.0000.0000.0000.000
12A15MET0-0.0160.00830.735-0.188-0.1880.0000.0000.0000.000
13A16ASN0-0.037-0.03033.5470.3780.3780.0000.0000.0000.000
14A17ARG10.9750.97635.5077.4207.4200.0000.0000.0000.000
15A18ARG10.9430.98335.4868.6848.6840.0000.0000.0000.000
16A19GLU-1-0.740-0.84033.825-9.359-9.3590.0000.0000.0000.000
17A20ILE0-0.0030.00837.0250.0490.0490.0000.0000.0000.000
18A21ASP-1-0.834-0.92739.859-7.139-7.1390.0000.0000.0000.000
19A22LEU0-0.083-0.04341.5790.1780.1780.0000.0000.0000.000
20A23HIS0-0.0110.00041.628-0.088-0.0880.0000.0000.0000.000
21A24THR0-0.058-0.01336.489-0.080-0.0800.0000.0000.0000.000
22A25LYS10.9170.95234.7788.6948.6940.0000.0000.0000.000
23A26CYS00.0390.02431.571-0.266-0.2660.0000.0000.0000.000
24A27VAL0-0.086-0.05330.0230.1470.1470.0000.0000.0000.000
25A28VAL0-0.037-0.01425.033-0.319-0.3190.0000.0000.0000.000
26A29ASP-1-0.758-0.85826.907-10.661-10.6610.0000.0000.0000.000
27A30VAL0-0.059-0.04621.342-0.601-0.6010.0000.0000.0000.000
28A31GLU-1-0.811-0.89522.890-10.939-10.9390.0000.0000.0000.000
29A32ALA00.0250.01919.987-0.564-0.5640.0000.0000.0000.000
30A33ASN0-0.030-0.01814.4680.9190.9190.0000.0000.0000.000
31A34LYS10.8880.91516.99112.97312.9730.0000.0000.0000.000
32A35VAL00.0340.02619.4830.5150.5150.0000.0000.0000.000
33A36ILE0-0.012-0.01321.848-0.151-0.1510.0000.0000.0000.000
34A37LEU00.0130.01725.3260.2010.2010.0000.0000.0000.000
35A38ASN00.018-0.00627.1070.0530.0530.0000.0000.0000.000
36A39PRO0-0.040-0.01430.6890.0250.0250.0000.0000.0000.000
37A40ILE00.0480.03533.0860.2370.2370.0000.0000.0000.000
38A41ASN00.0400.01034.8590.0090.0090.0000.0000.0000.000
39A42THR00.0190.02231.524-0.473-0.4730.0000.0000.0000.000
40A43ASN0-0.062-0.04930.4770.0990.0990.0000.0000.0000.000
41A44LEU00.0420.03134.1620.1200.1200.0000.0000.0000.000
42A45SER0-0.011-0.00337.917-0.089-0.0890.0000.0000.0000.000
43A46LYS10.8780.93836.2848.8358.8350.0000.0000.0000.000
44A47GLY00.0380.02142.3140.1210.1210.0000.0000.0000.000
45A48ASP-1-0.783-0.87939.897-8.240-8.2400.0000.0000.0000.000
46A49ALA00.0230.02340.608-0.181-0.1810.0000.0000.0000.000
47A50ARG10.8220.87335.3168.3698.3690.0000.0000.0000.000
48A51GLY00.0230.01535.352-0.309-0.3090.0000.0000.0000.000
49A52GLN0-0.033-0.02431.3580.0320.0320.0000.0000.0000.000
50A53PRO00.0320.01229.180-0.120-0.1200.0000.0000.0000.000
51A54LYS10.8750.94925.21211.13811.1380.0000.0000.0000.000
52A55ILE00.0350.02721.869-0.033-0.0330.0000.0000.0000.000
53A56PHE0-0.025-0.00818.719-0.159-0.1590.0000.0000.0000.000
54A57ALA00.0350.02716.2810.2410.2410.0000.0000.0000.000
55A58TYR0-0.036-0.03113.203-0.700-0.7000.0000.0000.0000.000
56A59ASP-1-0.809-0.8878.277-31.316-31.3160.0000.0000.0000.000
57A60HIS00.0310.00311.482-0.715-0.7150.0000.0000.0000.000
58A61CYS0-0.080-0.02914.612-0.093-0.0930.0000.0000.0000.000
59A62PHE00.0450.01115.3110.2360.2360.0000.0000.0000.000
60A63TRP00.0840.02920.4940.1610.1610.0000.0000.0000.000
61A64SER0-0.034-0.02023.8570.0830.0830.0000.0000.0000.000
62A65MET0-0.068-0.03725.7270.2600.2600.0000.0000.0000.000
63A66ASP-1-0.820-0.89829.037-8.699-8.6990.0000.0000.0000.000
64A67GLU-1-0.860-0.93430.249-10.087-10.0870.0000.0000.0000.000
65A68SER0-0.065-0.04631.3710.0530.0530.0000.0000.0000.000
66A69VAL00.0040.00530.4740.0530.0530.0000.0000.0000.000
67A70ARG10.9590.96028.9509.6029.6020.0000.0000.0000.000
68A71GLU-1-0.967-0.97027.862-10.323-10.3230.0000.0000.0000.000
69A72LYS10.8090.88825.68410.53510.5350.0000.0000.0000.000
70A73TYR0-0.101-0.04024.995-0.573-0.5730.0000.0000.0000.000
71A74ALA0-0.0220.00321.422-0.287-0.2870.0000.0000.0000.000
72A75GLY00.0990.05823.5370.1310.1310.0000.0000.0000.000
73A76GLN0-0.035-0.03522.445-1.105-1.1050.0000.0000.0000.000
74A77ASP-1-0.873-0.94521.549-12.813-12.8130.0000.0000.0000.000
75A78ASP-1-0.809-0.89120.270-13.511-13.5110.0000.0000.0000.000
76A79VAL0-0.021-0.01217.288-1.003-1.0030.0000.0000.0000.000
77A80PHE00.000-0.00916.443-1.278-1.2780.0000.0000.0000.000
78A81LYS10.9210.95616.49412.95212.9520.0000.0000.0000.000
79A82CYS0-0.094-0.02513.876-0.806-0.8060.0000.0000.0000.000
80A83LEU0-0.053-0.03610.776-2.129-2.1290.0000.0000.0000.000
81A84GLY00.0100.00712.365-1.063-1.0630.0000.0000.0000.000
82A85GLU-1-0.831-0.92114.534-16.354-16.3540.0000.0000.0000.000
83A86ASN0-0.066-0.0359.521-0.611-0.6110.0000.0000.0000.000
84A87ILE0-0.038-0.0168.782-1.352-1.3520.0000.0000.0000.000
85A88LEU00.0270.01511.273-0.102-0.1020.0000.0000.0000.000
86A89GLN00.0170.01911.5881.5421.5420.0000.0000.0000.000
87A90ASN0-0.075-0.0547.777-2.632-2.6320.0000.0000.0000.000
88A91ALA00.0210.01310.705-0.298-0.2980.0000.0000.0000.000
89A92PHE00.0480.02413.7660.4120.4120.0000.0000.0000.000
90A93ASP-1-0.881-0.92911.094-22.541-22.5410.0000.0000.0000.000
91A94GLY00.0340.01413.087-0.229-0.2290.0000.0000.0000.000
92A95TYR0-0.047-0.0277.081-3.260-3.2600.0000.0000.0000.000
93A96ASN00.0120.01710.3503.3793.3790.0000.0000.0000.000
94A97ALA00.0090.0058.953-4.010-4.0100.0000.0000.0000.000
95A98CYS0-0.103-0.0579.5952.6542.6540.0000.0000.0000.000
96A99ILE00.0580.03410.444-1.792-1.7920.0000.0000.0000.000
97A100PHE00.009-0.00211.4141.2791.2790.0000.0000.0000.000
98A101ALA00.0340.03115.326-0.558-0.5580.0000.0000.0000.000
99A102TYR0-0.009-0.03017.7960.2840.2840.0000.0000.0000.000
100A103GLY00.0840.04919.498-0.043-0.0430.0000.0000.0000.000
101A104GLN00.0370.02222.7390.0500.0500.0000.0000.0000.000
102A105THR0-0.007-0.03626.474-0.277-0.2770.0000.0000.0000.000
103A106GLY0-0.0080.00128.8950.1470.1470.0000.0000.0000.000
104A107SER0-0.061-0.04125.054-0.034-0.0340.0000.0000.0000.000
105A108GLY00.0580.01024.998-0.031-0.0310.0000.0000.0000.000
106A109LYS10.7900.92721.64412.66312.6630.0000.0000.0000.000
107A110SER00.0800.00722.505-0.238-0.2380.0000.0000.0000.000
108A111TYR0-0.0180.00524.9230.0320.0320.0000.0000.0000.000
109A112THR00.0190.01019.306-0.042-0.0420.0000.0000.0000.000
110A113MET0-0.035-0.00616.835-0.494-0.4940.0000.0000.0000.000
111A114MET00.0160.02921.144-0.144-0.1440.0000.0000.0000.000
112A115GLY00.0030.00624.5830.1120.1120.0000.0000.0000.000
113A116THR0-0.047-0.03926.6470.1880.1880.0000.0000.0000.000
114A117ALA00.0200.00129.922-0.191-0.1910.0000.0000.0000.000
115A118ASP-1-0.871-0.92632.049-8.810-8.8100.0000.0000.0000.000
116A119GLN0-0.037-0.01428.492-0.469-0.4690.0000.0000.0000.000
117A120PRO00.0470.04126.408-0.423-0.4230.0000.0000.0000.000
118A121GLY00.0410.02023.308-0.211-0.2110.0000.0000.0000.000
119A122LEU0-0.018-0.02816.356-0.112-0.1120.0000.0000.0000.000
120A123ILE00.0060.00319.928-0.196-0.1960.0000.0000.0000.000
121A124PRO00.0250.01221.142-0.053-0.0530.0000.0000.0000.000
122A125ARG10.8900.94821.13312.49312.4930.0000.0000.0000.000
123A126LEU0-0.029-0.00915.597-0.152-0.1520.0000.0000.0000.000
124A127CYS0-0.043-0.02219.606-0.058-0.0580.0000.0000.0000.000
125A128SER0-0.026-0.00622.5030.3060.3060.0000.0000.0000.000
126A129GLY00.0770.03621.4400.2030.2030.0000.0000.0000.000
127A130LEU0-0.040-0.02318.838-0.197-0.1970.0000.0000.0000.000
128A131PHE00.012-0.00621.3710.0310.0310.0000.0000.0000.000
129A132GLU-1-0.979-0.97924.820-11.273-11.2730.0000.0000.0000.000
130A133ARG10.7980.87416.23216.12216.1220.0000.0000.0000.000
131A134THR0-0.014-0.01122.7690.0130.0130.0000.0000.0000.000
132A135GLN0-0.010-0.00224.6710.1170.1170.0000.0000.0000.000
133A136LYS10.8850.95525.46711.12011.1200.0000.0000.0000.000
134A137GLU-1-0.837-0.91420.681-14.409-14.4090.0000.0000.0000.000
135A138GLU-1-0.927-0.96925.451-10.781-10.7810.0000.0000.0000.000
136A139ASN0-0.045-0.03727.6450.4150.4150.0000.0000.0000.000
137A140GLU-1-0.913-0.95530.585-8.895-8.8950.0000.0000.0000.000
138A141GLU-1-0.946-0.95929.203-9.987-9.9870.0000.0000.0000.000
139A142GLN0-0.042-0.01823.768-0.914-0.9140.0000.0000.0000.000
140A143SER00.0380.02426.5250.3230.3230.0000.0000.0000.000
141A144PHE00.019-0.00120.848-0.594-0.5940.0000.0000.0000.000
142A145LYS10.8670.93824.47811.76811.7680.0000.0000.0000.000
143A146VAL00.0210.01422.527-0.727-0.7270.0000.0000.0000.000
144A147GLU-1-0.831-0.90523.179-11.766-11.7660.0000.0000.0000.000
145A148VAL00.0040.00122.826-0.742-0.7420.0000.0000.0000.000
146A149SER00.0040.00622.8730.3460.3460.0000.0000.0000.000
147A150TYR0-0.067-0.04523.446-0.765-0.7650.0000.0000.0000.000
148A151MET0-0.0020.01123.2180.2540.2540.0000.0000.0000.000
149A152GLU-1-0.694-0.80025.157-10.593-10.5930.0000.0000.0000.000
150A153ILE0-0.041-0.01522.6020.0930.0930.0000.0000.0000.000
151A154TYR00.0930.01726.661-0.056-0.0560.0000.0000.0000.000
152A155ASN0-0.008-0.00829.6560.1150.1150.0000.0000.0000.000
153A156GLU-1-0.809-0.88126.093-12.151-12.1510.0000.0000.0000.000
154A157LYS10.9040.96228.8599.5339.5330.0000.0000.0000.000
155A158VAL00.0290.01526.218-0.236-0.2360.0000.0000.0000.000
156A159ARG10.7560.85728.8159.9289.9280.0000.0000.0000.000
157A160ASP-1-0.705-0.83628.798-10.880-10.8800.0000.0000.0000.000
158A161LEU0-0.048-0.01727.2650.3570.3570.0000.0000.0000.000
159A162LEU0-0.032-0.02327.7130.2610.2610.0000.0000.0000.000
160A163ASP-1-0.780-0.85831.782-8.734-8.7340.0000.0000.0000.000
161A164PRO00.0140.00734.1030.0080.0080.0000.0000.0000.000
162A165LYS10.8980.96934.0599.3579.3570.0000.0000.0000.000
163A166GLY0-0.0010.00336.435-0.128-0.1280.0000.0000.0000.000
164A167SER0-0.065-0.06635.1600.1640.1640.0000.0000.0000.000
165A168ARG10.8620.91737.3207.9137.9130.0000.0000.0000.000
166A169GLN00.0620.04732.9950.0690.0690.0000.0000.0000.000
167A170THR00.000-0.01733.376-0.208-0.2080.0000.0000.0000.000
168A171LEU0-0.0570.00128.990-0.183-0.1830.0000.0000.0000.000
169A172LYS10.9290.95727.94110.27210.2720.0000.0000.0000.000
170A173VAL0-0.0060.00821.204-0.099-0.0990.0000.0000.0000.000
171A174ARG10.8570.92322.80312.01412.0140.0000.0000.0000.000
172A175GLU-1-0.830-0.91417.084-18.230-18.2300.0000.0000.0000.000
173A176HIS00.0720.03218.8690.1340.1340.0000.0000.0000.000
174A177SER0-0.021-0.01517.467-0.653-0.6530.0000.0000.0000.000
175A178VAL00.0060.00715.689-0.931-0.9310.0000.0000.0000.000
176A179LEU00.0050.00115.465-0.921-0.9210.0000.0000.0000.000
177A180GLY00.0710.05015.199-0.334-0.3340.0000.0000.0000.000
178A181PRO0-0.073-0.04415.0191.3191.3190.0000.0000.0000.000
179A182TYR0-0.056-0.02217.952-0.095-0.0950.0000.0000.0000.000
180A183VAL00.001-0.02121.1250.0560.0560.0000.0000.0000.000
181A184ASP-1-0.834-0.91924.594-10.978-10.9780.0000.0000.0000.000
182A185GLY00.0200.00327.7920.1240.1240.0000.0000.0000.000
183A186LEU0-0.085-0.03324.2740.2100.2100.0000.0000.0000.000
184A187SER0-0.019-0.03528.232-0.004-0.0040.0000.0000.0000.000
185A188LYS10.8480.91922.90612.76712.7670.0000.0000.0000.000
186A189LEU00.0090.00627.2930.3280.3280.0000.0000.0000.000
187A190ALA0-0.005-0.00327.593-0.416-0.4160.0000.0000.0000.000
188A191VAL0-0.061-0.03226.2960.3360.3360.0000.0000.0000.000
189A192THR0-0.030-0.03028.157-0.165-0.1650.0000.0000.0000.000
190A193SER00.0380.00329.6550.0130.0130.0000.0000.0000.000
191A194TYR00.0370.01325.992-0.277-0.2770.0000.0000.0000.000
192A195LYS10.9410.96128.5258.8988.8980.0000.0000.0000.000
193A196ASP-1-0.753-0.84030.095-9.521-9.5210.0000.0000.0000.000
194A197ILE00.010-0.00724.237-0.026-0.0260.0000.0000.0000.000
195A198GLU-1-0.909-0.95728.334-9.522-9.5220.0000.0000.0000.000
196A199SER0-0.008-0.00130.3170.1460.1460.0000.0000.0000.000
197A200LEU00.0080.00029.2330.0880.0880.0000.0000.0000.000
198A201MET0-0.022-0.01025.852-0.274-0.2740.0000.0000.0000.000
199A202SER0-0.0270.00528.9910.0460.0460.0000.0000.0000.000
200A203GLU-1-0.807-0.91032.549-8.363-8.3630.0000.0000.0000.000
201A204GLY00.0000.00230.1250.1290.1290.0000.0000.0000.000
202A205ASN00.012-0.02227.834-0.336-0.3360.0000.0000.0000.000
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