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: 4G72N

Calculation Name: 1X82-A-Xray549

Preferred Name:

Target Type:

Ligand Name: 5-phosphoarabinonic acid

Ligand 3-letter code: PA5

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1X82

Chain ID: A

ChEMBL ID:

UniProt ID: P83194

Base Structure: X-ray

Registration Date: 2025-10-11

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 OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 190
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2122060.740206
FMO2-HF: Nuclear repulsion 2046880.788273
FMO2-HF: Total energy -75179.951934
FMO2-MP2: Total energy -75401.276947


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:0:MET)


Summations of interaction energy for fragment #1(A:0:MET)
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.
-95.348-89.8964.113-2.932-6.633-0.022
Interaction energy analysis for fragmet #1(A:0:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.835 / q_NPA : 0.917
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].
3A2TYR00.008-0.0032.941-12.883-7.6014.113-2.903-6.492-0.022
4A3LYS10.8280.8914.18627.03927.2090.000-0.029-0.1410.000
5A4GLU-1-0.876-0.9357.192-23.758-23.7580.0000.0000.0000.000
6A5PRO0-0.045-0.0189.8251.3811.3810.0000.0000.0000.000
7A6PHE0-0.0090.00212.2990.7700.7700.0000.0000.0000.000
8A7GLY00.0130.00915.8310.2150.2150.0000.0000.0000.000
9A8VAL0-0.015-0.00919.2600.0110.0110.0000.0000.0000.000
10A9LYS10.8330.90122.00910.49210.4920.0000.0000.0000.000
11A10VAL00.017-0.00324.700-0.085-0.0850.0000.0000.0000.000
12A11ASP-1-0.829-0.88727.397-8.657-8.6570.0000.0000.0000.000
13A12PHE0-0.003-0.02228.131-0.034-0.0340.0000.0000.0000.000
14A13GLU-1-0.858-0.90432.808-7.654-7.6540.0000.0000.0000.000
15A14THR0-0.051-0.05234.0500.1190.1190.0000.0000.0000.000
16A15GLY00.0430.01331.6010.0340.0340.0000.0000.0000.000
17A16ILE0-0.065-0.00529.700-0.332-0.3320.0000.0000.0000.000
18A17ILE00.0080.01223.291-0.082-0.0820.0000.0000.0000.000
19A18GLU-1-0.833-0.91325.880-10.629-10.6290.0000.0000.0000.000
20A19GLY0-0.021-0.01924.454-0.469-0.4690.0000.0000.0000.000
21A20ALA0-0.008-0.00123.325-0.160-0.1600.0000.0000.0000.000
22A21LYS10.9300.97024.35410.64810.6480.0000.0000.0000.000
23A22LYS10.8510.93627.2278.7148.7140.0000.0000.0000.000
24A23SER0-0.050-0.01728.6490.1260.1260.0000.0000.0000.000
25A24VAL0-0.005-0.02130.6090.1130.1130.0000.0000.0000.000
26A25ARG10.8400.93031.4298.9668.9660.0000.0000.0000.000
27A26ARG10.8920.94436.1957.4357.4350.0000.0000.0000.000
28A27LEU00.0470.02739.905-0.095-0.0950.0000.0000.0000.000
29A28SER0-0.019-0.03942.325-0.061-0.0610.0000.0000.0000.000
30A29ASP-1-0.868-0.91337.167-8.295-8.2950.0000.0000.0000.000
31A30MET0-0.078-0.05138.185-0.242-0.2420.0000.0000.0000.000
32A31GLU-1-0.851-0.92540.525-6.559-6.5590.0000.0000.0000.000
33A32GLY0-0.041-0.02842.053-0.128-0.1280.0000.0000.0000.000
34A33TYR0-0.007-0.01135.551-0.060-0.0600.0000.0000.0000.000
35A34PHE0-0.0070.00041.967-0.028-0.0280.0000.0000.0000.000
36A35VAL0-0.032-0.02545.0550.0970.0970.0000.0000.0000.000
37A36ASP-1-0.893-0.95348.221-5.687-5.6870.0000.0000.0000.000
38A37GLU-1-0.865-0.93649.042-6.087-6.0870.0000.0000.0000.000
39A38ARG10.9800.99150.1205.4525.4520.0000.0000.0000.000
40A39ALA00.0260.01151.2920.0040.0040.0000.0000.0000.000
41A40TRP0-0.057-0.02443.7380.0450.0450.0000.0000.0000.000
42A41LYS10.8730.93348.6106.1496.1490.0000.0000.0000.000
43A42GLU-1-0.982-0.99650.300-5.545-5.5450.0000.0000.0000.000
44A43LEU00.0380.01447.8010.0100.0100.0000.0000.0000.000
45A44VAL0-0.009-0.01645.551-0.090-0.0900.0000.0000.0000.000
46A45GLU-1-0.967-0.99548.131-5.980-5.9800.0000.0000.0000.000
47A46LYS10.7990.91451.4515.7735.7730.0000.0000.0000.000
48A47GLU-1-0.937-0.96747.339-6.401-6.4010.0000.0000.0000.000
49A48ASP-1-0.778-0.85843.681-7.290-7.2900.0000.0000.0000.000
50A49PRO00.0300.03744.226-0.175-0.1750.0000.0000.0000.000
51A50VAL0-0.035-0.02938.133-0.127-0.1270.0000.0000.0000.000
52A51VAL0-0.0010.01438.9560.0800.0800.0000.0000.0000.000
53A52TYR00.009-0.01231.9540.0230.0230.0000.0000.0000.000
54A53GLU-1-0.824-0.87433.483-8.499-8.4990.0000.0000.0000.000
55A54VAL0-0.011-0.00427.210-0.005-0.0050.0000.0000.0000.000
56A55TYR00.0310.00926.5500.0010.0010.0000.0000.0000.000
57A56ALA00.0440.01422.8440.0150.0150.0000.0000.0000.000
58A57VAL0-0.013-0.00417.552-0.213-0.2130.0000.0000.0000.000
59A58GLU-1-0.849-0.90117.711-13.596-13.5960.0000.0000.0000.000
60A59GLN0-0.0010.01112.349-2.101-2.1010.0000.0000.0000.000
61A60GLU-1-0.936-0.96810.720-20.392-20.3920.0000.0000.0000.000
62A61GLU-1-0.896-0.94412.052-17.265-17.2650.0000.0000.0000.000
63A62LYS10.9170.9347.49123.83723.8370.0000.0000.0000.000
64A63GLU-1-0.913-0.93811.361-17.311-17.3110.0000.0000.0000.000
65A64GLY0-0.043-0.02610.494-1.381-1.3810.0000.0000.0000.000
66A65ASP-1-0.844-0.9149.885-23.185-23.1850.0000.0000.0000.000
67A66LEU0-0.044-0.02111.5351.3871.3870.0000.0000.0000.000
68A67ASN00.0000.00114.848-1.382-1.3820.0000.0000.0000.000
69A68PHE00.000-0.00817.4940.4540.4540.0000.0000.0000.000
70A69ALA00.0160.01420.854-0.158-0.1580.0000.0000.0000.000
71A70THR00.007-0.00624.3270.1340.1340.0000.0000.0000.000
72A71THR0-0.057-0.04327.693-0.037-0.0370.0000.0000.0000.000
73A72VAL00.0100.02031.0150.0950.0950.0000.0000.0000.000
74A73LEU0-0.012-0.01034.5490.0080.0080.0000.0000.0000.000
75A74TYR0-0.024-0.03936.9330.2000.2000.0000.0000.0000.000
76A75PRO0-0.0200.00940.385-0.009-0.0090.0000.0000.0000.000
77A76GLY00.0390.00643.6800.0660.0660.0000.0000.0000.000
78A77LYS10.8500.90345.4265.9115.9110.0000.0000.0000.000
79A78VAL00.0050.02045.6200.0600.0600.0000.0000.0000.000
80A79GLY00.020-0.00148.2860.0440.0440.0000.0000.0000.000
81A80LYS10.8380.89751.1855.5365.5360.0000.0000.0000.000
82A81GLU-1-0.823-0.91144.605-6.713-6.7130.0000.0000.0000.000
83A82PHE00.0380.01543.5240.0060.0060.0000.0000.0000.000
84A83PHE00.0020.01241.195-0.090-0.0900.0000.0000.0000.000
85A84PHE00.001-0.01538.303-0.101-0.1010.0000.0000.0000.000
86A85THR00.016-0.00332.718-0.028-0.0280.0000.0000.0000.000
87A86LYS10.8740.93733.8688.5548.5540.0000.0000.0000.000
88A87GLY00.0340.02632.8600.2250.2250.0000.0000.0000.000
89A88HIS0-0.013-0.00226.108-0.037-0.0370.0000.0000.0000.000
90A89PHE00.0470.02129.3600.0840.0840.0000.0000.0000.000
91A90HIS10.7840.87523.75710.99610.9960.0000.0000.0000.000
92A91ALA00.0060.01023.4500.2650.2650.0000.0000.0000.000
93A92LYS10.8070.91016.70315.58115.5810.0000.0000.0000.000
94A93LEU00.025-0.00422.813-0.074-0.0740.0000.0000.0000.000
95A94ASP-1-0.874-0.91121.994-12.092-12.0920.0000.0000.0000.000
96A95ARG10.7840.85316.66013.97813.9780.0000.0000.0000.000
97A96ALA0-0.021-0.00221.7190.4390.4390.0000.0000.0000.000
98A97GLU-1-0.810-0.90722.088-11.507-11.5070.0000.0000.0000.000
99A98VAL0-0.055-0.02423.0840.3830.3830.0000.0000.0000.000
100A99TYR00.006-0.00924.888-0.147-0.1470.0000.0000.0000.000
101A100VAL0-0.013-0.01526.7010.1340.1340.0000.0000.0000.000
102A101ALA00.0070.00929.438-0.068-0.0680.0000.0000.0000.000
103A102LEU0-0.062-0.02829.361-0.010-0.0100.0000.0000.0000.000
104A103LYS10.8610.91633.6987.8267.8260.0000.0000.0000.000
105A104GLY00.0790.05737.185-0.084-0.0840.0000.0000.0000.000
106A105LYS10.9280.95039.6926.5736.5730.0000.0000.0000.000
107A106GLY00.0710.02638.7060.0900.0900.0000.0000.0000.000
108A107GLY0-0.022-0.01637.2370.1190.1190.0000.0000.0000.000
109A108MET0-0.036-0.01230.374-0.161-0.1610.0000.0000.0000.000
110A109LEU0-0.0080.01135.9720.1570.1570.0000.0000.0000.000
111A110LEU00.002-0.00931.522-0.249-0.2490.0000.0000.0000.000
112A111GLN00.0070.00734.2850.3930.3930.0000.0000.0000.000
113A112THR00.0590.04334.011-0.264-0.2640.0000.0000.0000.000
114A113PRO00.004-0.01632.3760.1260.1260.0000.0000.0000.000
115A114GLU-1-0.966-0.96435.189-7.455-7.4550.0000.0000.0000.000
116A115GLY00.0260.01438.3600.2210.2210.0000.0000.0000.000
117A116ASP-1-0.904-0.92739.115-6.996-6.9960.0000.0000.0000.000
118A117ALA00.0120.00238.389-0.220-0.2200.0000.0000.0000.000
119A118LYS10.8850.94736.8027.8147.8140.0000.0000.0000.000
120A119TRP00.0510.01538.206-0.131-0.1310.0000.0000.0000.000
121A120ILE0-0.043-0.02334.7690.0530.0530.0000.0000.0000.000
122A121SER00.0320.02137.648-0.059-0.0590.0000.0000.0000.000
123A122MET0-0.062-0.01932.039-0.156-0.1560.0000.0000.0000.000
124A123GLU-1-0.914-0.94137.387-7.009-7.0090.0000.0000.0000.000
125A124PRO00.0120.00235.908-0.210-0.2100.0000.0000.0000.000
126A125GLY00.0220.01633.3100.1170.1170.0000.0000.0000.000
127A126THR0-0.060-0.03233.324-0.054-0.0540.0000.0000.0000.000
128A127VAL0-0.0080.00028.073-0.195-0.1950.0000.0000.0000.000
129A128VAL0-0.019-0.01929.7560.2550.2550.0000.0000.0000.000
130A129TYR00.0050.00424.601-0.217-0.2170.0000.0000.0000.000
131A130VAL00.0220.01026.7780.3650.3650.0000.0000.0000.000
132A131PRO0-0.017-0.01026.434-0.385-0.3850.0000.0000.0000.000
133A132PRO00.0130.00624.3960.0500.0500.0000.0000.0000.000
134A133TYR0-0.021-0.02826.4510.3430.3430.0000.0000.0000.000
135A134TRP0-0.049-0.01628.8690.4250.4250.0000.0000.0000.000
136A135ALA0-0.0050.02029.416-0.296-0.2960.0000.0000.0000.000
137A136HIS0-0.028-0.02727.4360.1420.1420.0000.0000.0000.000
138A137ARG10.9110.96432.4187.5847.5840.0000.0000.0000.000
139A138THR0-0.0150.01932.4230.1680.1680.0000.0000.0000.000
140A139VAL0-0.006-0.02135.0770.0530.0530.0000.0000.0000.000
141A140ASN0-0.022-0.02438.6910.0130.0130.0000.0000.0000.000
142A141ILE0-0.060-0.03440.5810.1090.1090.0000.0000.0000.000
143A142GLY00.0140.00643.6930.1470.1470.0000.0000.0000.000
144A143ASP-1-0.912-0.95745.055-6.306-6.3060.0000.0000.0000.000
145A144GLU-1-0.917-0.95941.816-7.205-7.2050.0000.0000.0000.000
146A145PRO0-0.026-0.02438.633-0.028-0.0280.0000.0000.0000.000
147A146PHE0-0.0230.00635.185-0.065-0.0650.0000.0000.0000.000
148A147ILE0-0.0120.00132.484-0.194-0.1940.0000.0000.0000.000
149A148PHE00.012-0.00129.7290.0770.0770.0000.0000.0000.000
150A149LEU00.0120.00523.771-0.156-0.1560.0000.0000.0000.000
151A150ALA00.0120.01625.3680.2470.2470.0000.0000.0000.000
152A151ILE0-0.011-0.01619.331-0.410-0.4100.0000.0000.0000.000
153A152TYR0-0.028-0.04019.9400.4760.4760.0000.0000.0000.000
154A153PRO00.0250.00516.412-0.593-0.5930.0000.0000.0000.000
155A154ALA00.0030.00413.8780.5820.5820.0000.0000.0000.000
156A155ASP-1-0.787-0.86114.970-15.321-15.3210.0000.0000.0000.000
157A156ALA00.0100.00816.9440.5450.5450.0000.0000.0000.000
158A157GLY00.0440.02020.3840.4700.4700.0000.0000.0000.000
159A158HIS0-0.047-0.05022.3230.0160.0160.0000.0000.0000.000
160A159ASP-1-0.786-0.86326.129-9.157-9.1570.0000.0000.0000.000
161A160TYR00.008-0.00127.8490.2740.2740.0000.0000.0000.000
162A161GLY0-0.0070.00932.2140.2690.2690.0000.0000.0000.000
163A162THR0-0.035-0.05733.3900.3590.3590.0000.0000.0000.000
164A163ILE0-0.019-0.01233.9440.2230.2230.0000.0000.0000.000
165A164ALA0-0.0160.00236.4400.2130.2130.0000.0000.0000.000
166A165GLU-1-0.884-0.92838.294-7.359-7.3590.0000.0000.0000.000
167A166LYS10.8220.90638.4187.8387.8380.0000.0000.0000.000
168A167GLY00.0210.03040.1630.1700.1700.0000.0000.0000.000
169A168PHE0-0.029-0.02134.732-0.147-0.1470.0000.0000.0000.000
170A169SER00.009-0.01540.5400.1840.1840.0000.0000.0000.000
171A170LYS10.8490.91742.2526.7226.7220.0000.0000.0000.000
172A171ILE0-0.0110.00242.585-0.141-0.1410.0000.0000.0000.000
173A172VAL00.010-0.00141.8440.0650.0650.0000.0000.0000.000
174A173ILE0-0.013-0.00644.944-0.016-0.0160.0000.0000.0000.000
175A174GLU-1-0.822-0.89248.326-5.902-5.9020.0000.0000.0000.000
176A175GLU-1-0.870-0.91950.968-5.449-5.4490.0000.0000.0000.000
177A176ASN0-0.062-0.04254.6010.0210.0210.0000.0000.0000.000
178A177GLY00.0320.03154.5250.0640.0640.0000.0000.0000.000
179A178GLU-1-0.916-0.94152.634-5.680-5.6800.0000.0000.0000.000
180A179VAL0-0.013-0.01245.986-0.016-0.0160.0000.0000.0000.000
181A180LYS10.8460.90648.9865.6095.6090.0000.0000.0000.000
182A181VAL00.0080.00543.399-0.107-0.1070.0000.0000.0000.000
183A182VAL0-0.043-0.02246.4010.1240.1240.0000.0000.0000.000
184A183ASP-1-0.827-0.90646.573-6.376-6.3760.0000.0000.0000.000
185A184ASN0-0.007-0.01744.1940.2290.2290.0000.0000.0000.000
186A185PRO0-0.019-0.01347.4180.0160.0160.0000.0000.0000.000
187A186ARG10.9000.95247.8396.2686.2680.0000.0000.0000.000
188A187TRP00.0070.02040.065-0.161-0.1610.0000.0000.0000.000
189A188LYS10.8350.91443.9706.9256.9250.0000.0000.0000.000
190A189LYS0-0.0180.00042.1430.3580.3580.0000.0000.0000.000