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: N64NQ

Calculation Name: 1RO5-A-Xray549

Preferred Name: Acyl-homoserine-lactone synthase

Target Type: SINGLE PROTEIN

Ligand Name: sulfate ion | zinc ion

Ligand 3-letter code: SO4 | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1RO5

Chain ID: A

ChEMBL ID: CHEMBL1795157

UniProt ID: P33883

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 197
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230712
Total energy (hartree)
FMO2-HF: Electronic energy -2296748.349078
FMO2-HF: Nuclear repulsion 2217611.395809
FMO2-HF: Total energy -79136.953269
FMO2-MP2: Total energy -79363.70333


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:397:GLY)


Summations of interaction energy for fragment #1(A:397:GLY)
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.
-91.072-88.8097.435-5.009-4.687-0.07
Interaction energy analysis for fragmet #1(A:397:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.776 / q_NPA : 0.872
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].
3A399HIS00.0620.0402.066-22.825-20.7767.438-4.928-4.558-0.070
4A1MET00.0410.0284.101-4.653-4.530-0.001-0.060-0.0620.000
5A2ILE0-0.049-0.0184.275-1.250-1.164-0.001-0.007-0.0770.000
62A59ASP-1-0.899-0.9604.578-48.707-48.702-0.001-0.0140.0100.000
6A3VAL00.002-0.0017.4942.2732.2730.0000.0000.0000.000
7A4GLN0-0.034-0.01511.1781.2501.2500.0000.0000.0000.000
8A5ILE0-0.022-0.02713.6780.7170.7170.0000.0000.0000.000
9A6GLY00.0510.04817.5040.0030.0030.0000.0000.0000.000
10A7ARG10.9760.97220.15412.22612.2260.0000.0000.0000.000
11A8ARG10.8650.91521.90312.23812.2380.0000.0000.0000.000
12A9GLU-1-0.989-1.00422.533-11.962-11.9620.0000.0000.0000.000
13A10GLU-1-0.898-0.93019.320-15.119-15.1190.0000.0000.0000.000
14A11PHE0-0.0210.00015.230-1.143-1.1430.0000.0000.0000.000
15A12ASP-1-0.884-0.94015.352-19.185-19.1850.0000.0000.0000.000
16A13LYS10.9480.94818.03713.30813.3080.0000.0000.0000.000
17A14LYS10.9640.98715.95718.50518.5050.0000.0000.0000.000
18A15LEU00.0700.04411.835-0.041-0.0410.0000.0000.0000.000
19A16LEU0-0.021-0.00315.8940.3040.3040.0000.0000.0000.000
20A17GLY00.0320.01719.3430.5400.5400.0000.0000.0000.000
21A18GLU-1-0.842-0.93312.769-23.723-23.7230.0000.0000.0000.000
22A19MET0-0.0080.00917.1810.6460.6460.0000.0000.0000.000
23A20HIS00.0240.01118.6210.4520.4520.0000.0000.0000.000
24A21LYS10.8730.94419.51514.36714.3670.0000.0000.0000.000
25A22LEU00.0130.01416.3350.5680.5680.0000.0000.0000.000
26A23ARG10.7740.83019.91913.39013.3900.0000.0000.0000.000
27A24ALA00.0050.00823.0060.6350.6350.0000.0000.0000.000
28A25GLN0-0.066-0.04619.5260.0570.0570.0000.0000.0000.000
29A26VAL0-0.0410.00122.1020.2800.2800.0000.0000.0000.000
30A27PHE0-0.026-0.03424.8640.6530.6530.0000.0000.0000.000
31A28LYS11.0011.01326.99912.07912.0790.0000.0000.0000.000
32A29GLU-1-0.962-0.98429.569-9.836-9.8360.0000.0000.0000.000
33A30ARG10.8280.92629.40911.06111.0610.0000.0000.0000.000
34A31LYS10.9860.98433.3698.1678.1670.0000.0000.0000.000
35A32GLY0-0.017-0.01536.327-0.088-0.0880.0000.0000.0000.000
36A33TRP0-0.008-0.01931.065-0.061-0.0610.0000.0000.0000.000
37A34ASP-1-0.838-0.90532.999-9.123-9.1230.0000.0000.0000.000
38A35VAL00.0040.02230.170-0.264-0.2640.0000.0000.0000.000
39A36SER0-0.018-0.00931.3150.4420.4420.0000.0000.0000.000
40A37VAL0-0.018-0.01527.969-0.373-0.3730.0000.0000.0000.000
41A38ILE00.0040.00229.2130.4070.4070.0000.0000.0000.000
42A39ASP-1-0.897-0.95227.367-11.891-11.8910.0000.0000.0000.000
43A40GLU-1-0.894-0.93724.864-13.135-13.1350.0000.0000.0000.000
44A41MET0-0.041-0.01623.131-0.831-0.8310.0000.0000.0000.000
45A42GLU-1-0.800-0.87824.969-11.112-11.1120.0000.0000.0000.000
46A43ILE0-0.029-0.00625.860-0.489-0.4890.0000.0000.0000.000
47A44ASP-1-0.732-0.84028.250-10.328-10.3280.0000.0000.0000.000
48A45GLY00.0310.00330.896-0.135-0.1350.0000.0000.0000.000
49A46TYR0-0.001-0.02730.6170.0680.0680.0000.0000.0000.000
50A47ASP-1-0.751-0.83226.392-12.447-12.4470.0000.0000.0000.000
51A48ALA0-0.028-0.01128.201-0.265-0.2650.0000.0000.0000.000
52A49LEU0-0.058-0.02230.9960.1880.1880.0000.0000.0000.000
53A50SER0-0.041-0.01928.910-0.028-0.0280.0000.0000.0000.000
54A51PRO00.0000.02425.665-0.067-0.0670.0000.0000.0000.000
55A52TYR0-0.040-0.04622.899-0.489-0.4890.0000.0000.0000.000
56A53TYR0-0.056-0.06419.8340.4320.4320.0000.0000.0000.000
57A54MET0-0.0120.01316.095-0.289-0.2890.0000.0000.0000.000
58A55LEU0-0.043-0.02013.5370.4620.4620.0000.0000.0000.000
59A56ILE00.0340.01011.090-0.756-0.7560.0000.0000.0000.000
60A57GLN00.0060.0008.2001.6841.6840.0000.0000.0000.000
61A58GLU-1-0.856-0.9446.245-37.400-37.4000.0000.0000.0000.000
63A60GLY0-0.054-0.0245.5143.4833.4830.0000.0000.0000.000
64A64GLN0-0.026-0.0026.7263.9383.9380.0000.0000.0000.000
65A65VAL0-0.028-0.0249.785-1.951-1.9510.0000.0000.0000.000
66A66PHE0-0.013-0.0129.8672.0972.0970.0000.0000.0000.000
67A67GLY00.0090.00313.4731.6561.6560.0000.0000.0000.000
68A68CYS0-0.094-0.02415.273-0.663-0.6630.0000.0000.0000.000
69A69TRP00.0750.02817.9740.5710.5710.0000.0000.0000.000
70A70ARG10.7870.84820.99911.02911.0290.0000.0000.0000.000
71A71ILE0-0.022-0.00421.6040.2200.2200.0000.0000.0000.000
72A72LEU0-0.0120.00125.7030.0160.0160.0000.0000.0000.000
73A73ASP-1-0.774-0.86429.257-10.587-10.5870.0000.0000.0000.000
74A74THR0-0.018-0.02331.7640.3230.3230.0000.0000.0000.000
75A75THR0-0.010-0.02334.8060.2350.2350.0000.0000.0000.000
76A76GLY00.0300.03235.1480.2300.2300.0000.0000.0000.000
77A77PRO0-0.025-0.02235.6310.1170.1170.0000.0000.0000.000
78A78TYR0-0.070-0.05632.759-0.312-0.3120.0000.0000.0000.000
79A79MET00.0050.01731.2220.1140.1140.0000.0000.0000.000
80A80LEU0-0.030-0.02634.3140.2730.2730.0000.0000.0000.000
81A81LYS10.8280.93336.2308.6318.6310.0000.0000.0000.000
82A82ASN0-0.034-0.03537.4620.1280.1280.0000.0000.0000.000
83A83THR0-0.0150.00935.4850.0500.0500.0000.0000.0000.000
84A84PHE0-0.034-0.01433.1860.0260.0260.0000.0000.0000.000
85A85PRO00.0720.04438.649-0.003-0.0030.0000.0000.0000.000
86A86GLU-1-0.871-0.95240.972-7.774-7.7740.0000.0000.0000.000
87A87LEU0-0.065-0.03336.9230.0900.0900.0000.0000.0000.000
88A88LEU00.0050.00139.689-0.114-0.1140.0000.0000.0000.000
89A89HIS0-0.091-0.06142.0170.2810.2810.0000.0000.0000.000
90A90GLY00.0080.00445.2930.1230.1230.0000.0000.0000.000
91A91LYS10.8270.92243.5857.3747.3740.0000.0000.0000.000
92A92GLU-1-0.890-0.94643.322-7.197-7.1970.0000.0000.0000.000
93A93ALA0-0.0030.00039.627-0.157-0.1570.0000.0000.0000.000
94A94PRO0-0.003-0.00337.0650.0640.0640.0000.0000.0000.000
95A95CYS00.0110.02338.357-0.201-0.2010.0000.0000.0000.000
96A96SER00.0320.01236.8370.1490.1490.0000.0000.0000.000
97A97PRO00.0240.00234.621-0.218-0.2180.0000.0000.0000.000
98A98HIS10.8220.92932.9958.9088.9080.0000.0000.0000.000
99A99ILE00.0030.00432.444-0.087-0.0870.0000.0000.0000.000
100A100TRP00.0390.02924.594-0.127-0.1270.0000.0000.0000.000
101A101GLU-1-0.758-0.88829.710-9.978-9.9780.0000.0000.0000.000
102A102LEU00.0090.01624.410-0.428-0.4280.0000.0000.0000.000
103A103SER0-0.016-0.00626.2510.3260.3260.0000.0000.0000.000
104A104ARG10.7750.85324.95910.48110.4810.0000.0000.0000.000
105A105PHE00.0220.01922.513-0.464-0.4640.0000.0000.0000.000
106A106ALA0-0.003-0.00821.0160.5300.5300.0000.0000.0000.000
107A107ILE00.0250.00716.916-0.858-0.8580.0000.0000.0000.000
108A108ASN0-0.021-0.00414.9071.9401.9400.0000.0000.0000.000
109A109SER0-0.007-0.00617.701-0.637-0.6370.0000.0000.0000.000
110A110GLY00.0100.01118.5600.4710.4710.0000.0000.0000.000
111A111GLN0-0.029-0.04617.525-0.653-0.6530.0000.0000.0000.000
112A112LYS10.9460.97912.50122.16422.1640.0000.0000.0000.000
113A113GLY00.0530.04512.120-1.970-1.9700.0000.0000.0000.000
114A114SER0-0.0130.0009.9972.3772.3770.0000.0000.0000.000
115A115LEU00.0090.01511.9880.2690.2690.0000.0000.0000.000
116A116GLY00.0050.01513.4651.5731.5730.0000.0000.0000.000
117A117PHE0-0.027-0.02816.474-0.371-0.3710.0000.0000.0000.000
118A118SER0-0.011-0.02319.1630.0780.0780.0000.0000.0000.000
119A119ASP-1-0.829-0.91716.859-16.230-16.2300.0000.0000.0000.000
120A120CYS0-0.0090.00915.236-0.741-0.7410.0000.0000.0000.000
121A121THR0-0.001-0.01816.1910.0040.0040.0000.0000.0000.000
122A122LEU0-0.032-0.00118.7450.4700.4700.0000.0000.0000.000
123A123GLU-1-0.831-0.92513.759-19.657-19.6570.0000.0000.0000.000
124A124ALA0-0.0150.00016.287-0.105-0.1050.0000.0000.0000.000
125A125MET00.012-0.00717.4890.4350.4350.0000.0000.0000.000
126A126ARG10.8390.91517.15917.22917.2290.0000.0000.0000.000
127A127ALA00.0230.02115.5890.5090.5090.0000.0000.0000.000
128A128LEU00.0180.00717.7200.4970.4970.0000.0000.0000.000
129A129ALA00.0190.02120.4950.6210.6210.0000.0000.0000.000
130A130ARG10.9500.97816.27317.48617.4860.0000.0000.0000.000
131A131TYR00.0130.00019.7600.5930.5930.0000.0000.0000.000
132A132SER00.006-0.01821.8770.5430.5430.0000.0000.0000.000
133A133LEU0-0.017-0.00725.3100.4260.4260.0000.0000.0000.000
134A134GLN0-0.023-0.00521.407-0.109-0.1090.0000.0000.0000.000
135A135ASN0-0.097-0.04923.9500.2660.2660.0000.0000.0000.000
136A136ASP-1-0.833-0.91227.555-9.153-9.1530.0000.0000.0000.000
137A137ILE0-0.0110.01528.1380.4080.4080.0000.0000.0000.000
138A138GLN0-0.044-0.03229.5710.0630.0630.0000.0000.0000.000
139A139THR0-0.065-0.04731.848-0.014-0.0140.0000.0000.0000.000
140A140LEU00.0050.00525.719-0.104-0.1040.0000.0000.0000.000
141A141VAL00.011-0.00230.0080.1690.1690.0000.0000.0000.000
142A142THR0-0.031-0.03228.838-0.388-0.3880.0000.0000.0000.000
143A143VAL00.0280.02531.0740.3780.3780.0000.0000.0000.000
144A144THR00.0180.01427.809-0.298-0.2980.0000.0000.0000.000
145A145THR00.0510.02230.1810.3980.3980.0000.0000.0000.000
146A146VAL00.010-0.00631.692-0.136-0.1360.0000.0000.0000.000
147A147GLY0-0.056-0.02931.0270.0780.0780.0000.0000.0000.000
148A148VAL00.0400.01526.369-0.181-0.1810.0000.0000.0000.000
149A149GLU-1-0.723-0.83828.735-9.090-9.0900.0000.0000.0000.000
150A150LYS10.9070.94631.1839.0849.0840.0000.0000.0000.000
151A151MET0-0.0380.00324.4300.0150.0150.0000.0000.0000.000
152A152MET00.0490.01526.316-0.231-0.2310.0000.0000.0000.000
153A153ILE0-0.024-0.00928.3290.0290.0290.0000.0000.0000.000
154A154ARG10.9030.95028.90810.64810.6480.0000.0000.0000.000
155A155ALA0-0.0080.01225.535-0.018-0.0180.0000.0000.0000.000
156A156GLY00.0370.01927.458-0.181-0.1810.0000.0000.0000.000
157A157LEU00.001-0.00425.5710.2080.2080.0000.0000.0000.000
158A158ASP-1-0.843-0.90129.718-8.689-8.6890.0000.0000.0000.000
159A159VAL00.0110.00130.635-0.178-0.1780.0000.0000.0000.000
160A160SER0-0.032-0.00533.5510.3550.3550.0000.0000.0000.000
161A161ARG10.7950.85936.0768.2098.2090.0000.0000.0000.000
162A162PHE0-0.009-0.00236.0920.2320.2320.0000.0000.0000.000
163A163GLY00.0230.00240.1710.2830.2830.0000.0000.0000.000
164A164PRO0-0.021-0.01340.765-0.226-0.2260.0000.0000.0000.000
165A165HIS00.0470.04638.578-0.200-0.2000.0000.0000.0000.000
166A166LEU00.0250.01039.3970.2320.2320.0000.0000.0000.000
167A167LYS10.8700.93139.0687.5517.5510.0000.0000.0000.000
168A168ILE00.0530.03836.2000.1610.1610.0000.0000.0000.000
169A169GLY00.0620.03236.536-0.264-0.2640.0000.0000.0000.000
170A170ILE0-0.029-0.02833.4880.3240.3240.0000.0000.0000.000
171A171GLU-1-0.861-0.90331.533-10.173-10.1730.0000.0000.0000.000
172A172ARG10.8970.94635.5768.7028.7020.0000.0000.0000.000
173A173ALA00.0280.01734.633-0.279-0.2790.0000.0000.0000.000
174A174VAL0-0.007-0.02434.2370.3680.3680.0000.0000.0000.000
175A175ALA00.0540.04934.349-0.301-0.3010.0000.0000.0000.000
176A176LEU0-0.064-0.03431.0360.2420.2420.0000.0000.0000.000
177A177ARG10.9380.97433.2108.2278.2270.0000.0000.0000.000
178A178ILE0-0.007-0.00427.9890.1350.1350.0000.0000.0000.000
179A179GLU-1-0.809-0.87831.042-9.244-9.2440.0000.0000.0000.000
180A180LEU0-0.0240.00026.576-0.210-0.2100.0000.0000.0000.000
181A181ASN00.008-0.02029.735-0.252-0.2520.0000.0000.0000.000
182A182ALA00.0600.01430.595-0.301-0.3010.0000.0000.0000.000
183A183LYS10.8460.93630.8759.0679.0670.0000.0000.0000.000
184A184THR00.030-0.00527.206-0.250-0.2500.0000.0000.0000.000
185A185GLN0-0.017-0.00326.314-0.491-0.4910.0000.0000.0000.000
186A186ILE0-0.0120.00026.025-0.424-0.4240.0000.0000.0000.000
187A187ALA0-0.048-0.01327.007-0.261-0.2610.0000.0000.0000.000
188A188LEU0-0.032-0.00522.071-0.425-0.4250.0000.0000.0000.000
189A189TYR0-0.059-0.06020.278-0.574-0.5740.0000.0000.0000.000
190A190GLY00.0170.02523.118-0.200-0.2000.0000.0000.0000.000
191A191GLY0-0.027-0.02125.9350.4510.4510.0000.0000.0000.000
192A192VAL0-0.019-0.01527.085-0.168-0.1680.0000.0000.0000.000
193A193LEU0-0.015-0.00422.720-0.286-0.2860.0000.0000.0000.000
194A194VAL0-0.023-0.01525.8200.4250.4250.0000.0000.0000.000
195A195GLU-1-0.833-0.90424.990-12.358-12.3580.0000.0000.0000.000
196A196GLN0-0.045-0.03224.8910.6340.6340.0000.0000.0000.000
197A197ARG0-0.065-0.03226.1420.1910.1910.0000.0000.0000.000