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: JYYR9

Calculation Name: 4BAS-A-Xray547

Preferred Name:

Target Type:

Ligand Name: phosphoaminophosphonic acid-guanylate ester | sulfate ion | magnesium ion

Ligand 3-letter code: GNP | SO4 | MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4BAS

Chain ID: A

ChEMBL ID:

UniProt ID: C9ZVV9

Base Structure: X-ray

Registration Date: 2025-10-04

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 -1844391.974311
FMO2-HF: Nuclear repulsion 1776245.782256
FMO2-HF: Total energy -68146.192055
FMO2-MP2: Total energy -68343.804203


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:6:THR)


Summations of interaction energy for fragment #1(A:6:THR)
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.
-101.976-93.3964.712-5.497-7.794-0.065
Interaction energy analysis for fragmet #1(A:6:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.837 / q_NPA : 0.910
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].
3A8LEU00.0370.0292.692-4.790-1.8890.809-1.430-2.280-0.015
4A9GLN00.0090.0074.8274.0894.101-0.001-0.008-0.0030.000
47A52ARG10.9660.9773.63747.23947.8620.010-0.161-0.4720.000
48A53VAL0-0.025-0.0232.188-37.135-32.7453.885-3.786-4.487-0.049
49A54ALA00.0210.0273.57711.52012.0150.011-0.095-0.412-0.001
173A178SER0-0.049-0.0234.068-2.968-2.832-0.001-0.016-0.1200.000
174A179ARG10.9140.9715.07621.88521.908-0.001-0.001-0.0200.000
5A10VAL0-0.007-0.0098.3240.6620.6620.0000.0000.0000.000
6A11VAL00.0390.02910.8490.9280.9280.0000.0000.0000.000
7A12MET0-0.0280.00114.6780.0390.0390.0000.0000.0000.000
8A13CYS00.0120.02316.8390.6360.6360.0000.0000.0000.000
9A14GLY00.0990.04420.168-0.166-0.1660.0000.0000.0000.000
10A15LEU0-0.0070.00923.3180.0340.0340.0000.0000.0000.000
11A16ASP-1-0.832-0.89626.105-10.342-10.3420.0000.0000.0000.000
12A17ASN00.024-0.00628.447-0.019-0.0190.0000.0000.0000.000
13A18SER0-0.003-0.00524.625-0.124-0.1240.0000.0000.0000.000
14A19GLY00.0530.02424.471-0.107-0.1070.0000.0000.0000.000
15A20LYS10.8080.92320.11012.71012.7100.0000.0000.0000.000
16A21THR00.058-0.00619.674-0.434-0.4340.0000.0000.0000.000
17A22THR0-0.044-0.01220.911-0.219-0.2190.0000.0000.0000.000
18A23ILE00.0080.00417.122-0.314-0.3140.0000.0000.0000.000
19A24ILE00.0020.00113.133-0.675-0.6750.0000.0000.0000.000
20A25ASN0-0.011-0.03016.223-1.031-1.0310.0000.0000.0000.000
21A26GLN0-0.057-0.01518.399-0.251-0.2510.0000.0000.0000.000
22A27VAL0-0.053-0.02212.683-0.363-0.3630.0000.0000.0000.000
23A28LYS10.8030.91312.85715.67815.6780.0000.0000.0000.000
24A29PRO00.0380.01613.3150.8550.8550.0000.0000.0000.000
25A30ALA00.0500.02515.8750.7880.7880.0000.0000.0000.000
26A31GLN0-0.041-0.02119.533-0.280-0.2800.0000.0000.0000.000
27A32SER0-0.0210.01016.902-0.082-0.0820.0000.0000.0000.000
28A33SER0-0.014-0.01318.9840.2960.2960.0000.0000.0000.000
29A34SER0-0.028-0.03220.3940.5990.5990.0000.0000.0000.000
30A35LYS10.9590.97224.13010.18610.1860.0000.0000.0000.000
31A36HIS0-0.005-0.00227.0070.1820.1820.0000.0000.0000.000
32A37ILE00.0170.02122.943-0.341-0.3410.0000.0000.0000.000
33A38THR0-0.011-0.00326.9070.2940.2940.0000.0000.0000.000
34A39ALA0-0.006-0.00926.586-0.365-0.3650.0000.0000.0000.000
35A40THR00.0060.01322.4080.4180.4180.0000.0000.0000.000
36A41VAL0-0.037-0.01925.6680.2750.2750.0000.0000.0000.000
37A42GLY00.0170.00426.099-0.196-0.1960.0000.0000.0000.000
38A43TYR0-0.012-0.02619.4900.0890.0890.0000.0000.0000.000
39A44ASN00.0070.01719.8930.5450.5450.0000.0000.0000.000
40A45VAL0-0.004-0.00915.018-0.438-0.4380.0000.0000.0000.000
41A46GLU-1-0.825-0.89414.807-17.265-17.2650.0000.0000.0000.000
42A47THR0-0.017-0.00912.103-1.293-1.2930.0000.0000.0000.000
43A48PHE0-0.029-0.01711.0471.3111.3110.0000.0000.0000.000
44A49GLU-1-0.925-0.9577.287-39.369-39.3690.0000.0000.0000.000
45A50LYS10.8920.9457.32431.53731.5370.0000.0000.0000.000
46A51GLY00.0110.0076.986-2.425-2.4250.0000.0000.0000.000
50A55PHE00.023-0.0055.567-4.244-4.2440.0000.0000.0000.000
51A56THR0-0.0010.0007.6892.9572.9570.0000.0000.0000.000
52A57VAL0-0.024-0.01010.395-0.018-0.0180.0000.0000.0000.000
53A58PHE00.0420.02212.6051.2591.2590.0000.0000.0000.000
54A59ASP-1-0.777-0.87415.935-14.355-14.3550.0000.0000.0000.000
55A60MET0-0.0020.01618.3760.4780.4780.0000.0000.0000.000
56A61GLY00.0340.00921.1630.3150.3150.0000.0000.0000.000
57A62GLY00.001-0.00724.8940.0290.0290.0000.0000.0000.000
58A63ALA00.0160.01126.3060.2910.2910.0000.0000.0000.000
59A64LYS10.8910.92329.2169.6619.6610.0000.0000.0000.000
60A65LYS10.9430.96830.4779.1059.1050.0000.0000.0000.000
61A66PHE00.0170.00726.3930.1130.1130.0000.0000.0000.000
62A67ARG10.8000.90425.71410.11710.1170.0000.0000.0000.000
63A68GLY00.0180.01525.574-0.266-0.2660.0000.0000.0000.000
64A69LEU00.0140.00523.992-0.038-0.0380.0000.0000.0000.000
65A70TRP0-0.045-0.04221.254-0.535-0.5350.0000.0000.0000.000
66A71GLU-1-0.863-0.94820.182-12.263-12.2630.0000.0000.0000.000
67A72THR0-0.052-0.01820.930-0.082-0.0820.0000.0000.0000.000
68A73TYR0-0.020-0.01816.514-0.156-0.1560.0000.0000.0000.000
69A74TYR00.0380.00515.902-0.526-0.5260.0000.0000.0000.000
70A75ASP-1-0.785-0.87215.791-18.245-18.2450.0000.0000.0000.000
71A76ASN0-0.099-0.06512.136-1.335-1.3350.0000.0000.0000.000
72A77ILE0-0.112-0.02411.070-2.003-2.0030.0000.0000.0000.000
73A78ASP-1-0.779-0.8936.582-34.247-34.2470.0000.0000.0000.000
74A79ALA0-0.033-0.0309.0610.5470.5470.0000.0000.0000.000
75A80VAL00.0060.01411.1160.3500.3500.0000.0000.0000.000
76A81ILE0-0.013-0.00112.273-0.142-0.1420.0000.0000.0000.000
77A82PHE00.011-0.00715.6780.7420.7420.0000.0000.0000.000
78A83VAL0-0.050-0.01819.5060.1690.1690.0000.0000.0000.000
79A84VAL0-0.011-0.01721.7240.4460.4460.0000.0000.0000.000
80A85ASP-1-0.805-0.87925.327-10.227-10.2270.0000.0000.0000.000
81A86SER0-0.029-0.03228.0290.3580.3580.0000.0000.0000.000
82A87SER0-0.026-0.02329.5990.2970.2970.0000.0000.0000.000
83A88ASP-1-0.819-0.88731.405-8.985-8.9850.0000.0000.0000.000
84A89HIS00.019-0.01333.140-0.220-0.2200.0000.0000.0000.000
85A90LEU0-0.031-0.00635.1970.1090.1090.0000.0000.0000.000
86A91ARG10.7670.84030.9049.5939.5930.0000.0000.0000.000
87A92LEU00.0640.03730.013-0.272-0.2720.0000.0000.0000.000
88A93CYS00.0130.01231.312-0.216-0.2160.0000.0000.0000.000
89A94VAL00.0150.01130.413-0.068-0.0680.0000.0000.0000.000
90A95VAL0-0.019-0.00526.095-0.254-0.2540.0000.0000.0000.000
91A96LYS10.9310.97127.3698.9958.9950.0000.0000.0000.000
92A97SER0-0.011-0.01528.873-0.159-0.1590.0000.0000.0000.000
93A98GLU-1-0.806-0.89526.087-10.467-10.4670.0000.0000.0000.000
94A99ILE00.0120.01523.425-0.350-0.3500.0000.0000.0000.000
95A100GLN0-0.011-0.01724.968-0.063-0.0630.0000.0000.0000.000
96A101ALA0-0.061-0.01927.2740.0430.0430.0000.0000.0000.000
97A102MET00.0010.00319.0120.0010.0010.0000.0000.0000.000
98A103LEU00.003-0.00421.648-0.339-0.3390.0000.0000.0000.000
99A104LYS10.8770.94523.6589.6949.6940.0000.0000.0000.000
100A105HIS00.0260.02922.117-0.019-0.0190.0000.0000.0000.000
101A106GLU-1-0.857-0.93622.429-12.802-12.8020.0000.0000.0000.000
102A107ASP-1-0.867-0.93917.982-15.403-15.4030.0000.0000.0000.000
103A108ILE0-0.083-0.03817.319-0.954-0.9540.0000.0000.0000.000
104A109ARG10.8720.93519.12511.11411.1140.0000.0000.0000.000
105A110ARG10.8890.95913.29718.41418.4140.0000.0000.0000.000
106A111GLU-1-0.941-0.96817.733-14.421-14.4210.0000.0000.0000.000
107A112LEU0-0.033-0.02111.329-0.262-0.2620.0000.0000.0000.000
108A113PRO00.013-0.01311.8020.7070.7070.0000.0000.0000.000
109A114GLY00.0210.02512.7660.6580.6580.0000.0000.0000.000
110A115GLY00.0030.00713.8660.3670.3670.0000.0000.0000.000
111A116GLY0-0.0230.00014.1430.4760.4760.0000.0000.0000.000
112A117ARG10.8360.91415.21313.88213.8820.0000.0000.0000.000
113A118VAL00.0710.03413.400-0.804-0.8040.0000.0000.0000.000
114A119PRO00.0150.03310.6741.4161.4160.0000.0000.0000.000
115A120PHE0-0.004-0.01613.962-0.132-0.1320.0000.0000.0000.000
116A121LEU0-0.0250.00313.3150.2830.2830.0000.0000.0000.000
117A122PHE00.015-0.00815.9720.2800.2800.0000.0000.0000.000
118A123PHE0-0.007-0.00815.960-0.067-0.0670.0000.0000.0000.000
119A124ALA00.0290.01421.0240.4050.4050.0000.0000.0000.000
120A125ASN00.0370.00323.4310.0430.0430.0000.0000.0000.000
121A126LYS10.8140.91125.18610.81710.8170.0000.0000.0000.000
122A127MET0-0.0020.01226.5070.2110.2110.0000.0000.0000.000
123A128ASP-1-0.895-0.95929.167-10.236-10.2360.0000.0000.0000.000
124A129ALA0-0.0150.00331.8140.3140.3140.0000.0000.0000.000
125A130ALA00.010-0.00933.7300.0720.0720.0000.0000.0000.000
126A131GLY0-0.004-0.00936.583-0.003-0.0030.0000.0000.0000.000
127A132ALA0-0.042-0.00531.352-0.052-0.0520.0000.0000.0000.000
128A133LYS10.9180.97331.3168.8768.8760.0000.0000.0000.000
129A134THR0-0.021-0.04629.514-0.443-0.4430.0000.0000.0000.000
130A135ALA00.016-0.01324.9130.0380.0380.0000.0000.0000.000
131A136ALA00.0310.01726.863-0.086-0.0860.0000.0000.0000.000
132A137GLU-1-0.804-0.87629.125-8.903-8.9030.0000.0000.0000.000
133A138LEU0-0.027-0.01826.9960.1210.1210.0000.0000.0000.000
134A139VAL0-0.004-0.00125.587-0.083-0.0830.0000.0000.0000.000
135A140GLU-1-0.898-0.94228.219-8.892-8.8920.0000.0000.0000.000
136A141ILE0-0.053-0.03331.9860.1600.1600.0000.0000.0000.000
137A142LEU0-0.049-0.03126.6890.1110.1110.0000.0000.0000.000
138A143ASP-1-0.852-0.90130.374-9.383-9.3830.0000.0000.0000.000
139A144LEU0-0.015-0.00623.269-0.115-0.1150.0000.0000.0000.000
140A145THR00.027-0.00525.247-0.461-0.4610.0000.0000.0000.000
141A146THR0-0.028-0.02626.067-0.255-0.2550.0000.0000.0000.000
142A147LEU0-0.099-0.03926.0650.0080.0080.0000.0000.0000.000
143A148MET0-0.048-0.00621.164-0.514-0.5140.0000.0000.0000.000
144A149GLY00.0250.01422.699-0.292-0.2920.0000.0000.0000.000
145A150ASP-1-0.872-0.93821.277-12.383-12.3830.0000.0000.0000.000
146A151HIS10.7790.88917.60414.01314.0130.0000.0000.0000.000
147A152PRO00.0020.01814.5820.3860.3860.0000.0000.0000.000
148A153PHE00.005-0.02716.111-0.708-0.7080.0000.0000.0000.000
149A154VAL0-0.0010.01916.0390.3000.3000.0000.0000.0000.000
150A155ILE0-0.008-0.00918.471-0.101-0.1010.0000.0000.0000.000
151A156PHE00.0120.00916.4950.3060.3060.0000.0000.0000.000
152A157ALA0-0.0010.00721.6770.0480.0480.0000.0000.0000.000
153A158SER00.0350.00221.655-0.365-0.3650.0000.0000.0000.000
154A159ASN0-0.010-0.00523.6370.2920.2920.0000.0000.0000.000
155A160GLY00.0250.00422.391-0.361-0.3610.0000.0000.0000.000
156A161LEU0-0.007-0.00423.293-0.328-0.3280.0000.0000.0000.000
157A162LYS10.9230.95324.70610.96010.9600.0000.0000.0000.000
158A163GLY00.0550.04620.549-0.218-0.2180.0000.0000.0000.000
159A164THR0-0.001-0.01020.045-0.614-0.6140.0000.0000.0000.000
160A165GLY00.0800.03920.2250.2670.2670.0000.0000.0000.000
161A166VAL0-0.019-0.01016.159-0.588-0.5880.0000.0000.0000.000
162A167HIS00.0290.01414.573-2.191-2.1910.0000.0000.0000.000
163A168GLU-1-0.854-0.91213.953-17.250-17.2500.0000.0000.0000.000
164A169GLY00.017-0.00414.450-0.652-0.6520.0000.0000.0000.000
165A170PHE00.014-0.0209.881-0.796-0.7960.0000.0000.0000.000
166A171SER0-0.065-0.0369.763-2.827-2.8270.0000.0000.0000.000
167A172TRP00.0040.0079.996-1.852-1.8520.0000.0000.0000.000
168A173LEU00.0170.0147.706-0.542-0.5420.0000.0000.0000.000
169A174GLN00.010-0.0035.7701.1291.1290.0000.0000.0000.000
170A175GLU-1-0.929-0.9525.473-30.592-30.5920.0000.0000.0000.000
171A176THR0-0.065-0.0437.9360.3460.3460.0000.0000.0000.000
172A177ALA00.0250.0055.6530.7550.7550.0000.0000.0000.000
175A180GLN0-0.094-0.0608.1591.7631.7630.0000.0000.0000.000
176A181SER-1-0.943-0.9495.228-31.761-31.7610.0000.0000.0000.000