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: GVN71

Calculation Name: 1QWJ-A-Xray547

Preferred Name:

Target Type:

Ligand Name: cytidine-5'-monophosphate-5-n-acetylneuraminic acid

Ligand 3-letter code: NCC

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1QWJ

Chain ID: A

ChEMBL ID:

UniProt ID: Q99KK2

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 228
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2750053.425032
FMO2-HF: Nuclear repulsion 2659870.001383
FMO2-HF: Total energy -90183.423649
FMO2-MP2: Total energy -90449.520066


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:40:PRO)


Summations of interaction energy for fragment #1(A:40:PRO)
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.
-77.594-74.6440.192-1.422-1.721-0.011
Interaction energy analysis for fragmet #1(A:40:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.817 / q_NPA : 0.885
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].
3A42HIS00.0090.0012.893-9.926-7.2360.192-1.383-1.500-0.011
45A84GLN0-0.017-0.0103.947-3.430-3.1700.000-0.039-0.2210.000
4A43LEU00.0200.0045.0906.8056.8050.0000.0000.0000.000
5A44ALA00.0070.0116.9940.5430.5430.0000.0000.0000.000
6A45ALA00.0010.01010.3241.2561.2560.0000.0000.0000.000
7A46LEU00.002-0.01113.3910.3010.3010.0000.0000.0000.000
8A47VAL00.0180.01416.6220.5540.5540.0000.0000.0000.000
9A48LEU00.0120.00620.2150.2990.2990.0000.0000.0000.000
10A49ALA0-0.0180.00223.0220.5310.5310.0000.0000.0000.000
11A50ARG10.8230.90825.7869.7469.7460.0000.0000.0000.000
12A51GLY00.026-0.00228.7890.1230.1230.0000.0000.0000.000
13A52GLY0-0.0210.00132.1670.3180.3180.0000.0000.0000.000
14A53SER0-0.045-0.05132.457-0.346-0.3460.0000.0000.0000.000
15A54LYS10.9140.95333.9799.1259.1250.0000.0000.0000.000
16A55GLY00.0250.02537.0900.0290.0290.0000.0000.0000.000
17A56ILE00.0040.00337.9760.0680.0680.0000.0000.0000.000
18A57PRO00.0440.03436.467-0.233-0.2330.0000.0000.0000.000
19A58LEU00.0550.02233.1240.0250.0250.0000.0000.0000.000
20A59LYS10.8240.91032.4849.0399.0390.0000.0000.0000.000
21A60ASN0-0.018-0.02727.895-0.160-0.1600.0000.0000.0000.000
22A61ILE00.0160.00828.690-0.354-0.3540.0000.0000.0000.000
23A62LYS10.8990.97630.9408.3898.3890.0000.0000.0000.000
24A63ARG10.8780.93132.4818.7658.7650.0000.0000.0000.000
25A64LEU00.0340.02030.6660.2410.2410.0000.0000.0000.000
26A65ALA00.030-0.00232.326-0.256-0.2560.0000.0000.0000.000
27A66GLY0-0.0020.00833.765-0.114-0.1140.0000.0000.0000.000
28A67VAL0-0.0130.00127.931-0.001-0.0010.0000.0000.0000.000
29A68PRO0-0.020-0.00628.7210.0990.0990.0000.0000.0000.000
30A69LEU0-0.0010.02027.979-0.353-0.3530.0000.0000.0000.000
31A70ILE00.0340.00023.914-0.284-0.2840.0000.0000.0000.000
32A71GLY00.0020.00523.509-0.564-0.5640.0000.0000.0000.000
33A72TRP0-0.067-0.03823.807-0.430-0.4300.0000.0000.0000.000
34A73VAL00.0320.01519.955-0.358-0.3580.0000.0000.0000.000
35A74LEU0-0.004-0.00719.060-0.739-0.7390.0000.0000.0000.000
36A75ARG10.9170.97118.79411.08711.0870.0000.0000.0000.000
37A76ALA00.0020.00419.020-0.530-0.5300.0000.0000.0000.000
38A77ALA00.013-0.00915.332-0.764-0.7640.0000.0000.0000.000
39A78LEU0-0.024-0.01114.281-1.482-1.4820.0000.0000.0000.000
40A79ASP-1-0.792-0.88114.759-15.863-15.8630.0000.0000.0000.000
41A80ALA0-0.042-0.02013.6030.0460.0460.0000.0000.0000.000
42A81GLY0-0.029-0.00811.973-0.625-0.6250.0000.0000.0000.000
43A82VAL0-0.031-0.0118.300-1.832-1.8320.0000.0000.0000.000
44A83PHE0-0.030-0.0097.294-2.913-2.9130.0000.0000.0000.000
46A85SER0-0.0080.0077.2602.2262.2260.0000.0000.0000.000
47A86VAL00.0270.01010.876-0.096-0.0960.0000.0000.0000.000
48A87TRP00.0040.00012.9041.8801.8800.0000.0000.0000.000
49A88VAL0-0.0060.00316.9670.3500.3500.0000.0000.0000.000
50A89SER00.0320.02020.5020.1540.1540.0000.0000.0000.000
51A90THR0-0.028-0.02822.1220.5200.5200.0000.0000.0000.000
52A91ASP-1-0.730-0.86125.857-10.429-10.4290.0000.0000.0000.000
53A92HIS0-0.015-0.00829.0460.1100.1100.0000.0000.0000.000
54A93ASP-1-0.771-0.87529.264-10.107-10.1070.0000.0000.0000.000
55A94GLU-1-0.929-0.96730.058-9.061-9.0610.0000.0000.0000.000
56A95ILE0-0.037-0.01726.157-0.181-0.1810.0000.0000.0000.000
57A96GLU-1-0.814-0.88625.088-12.284-12.2840.0000.0000.0000.000
58A97ASN0-0.025-0.01325.538-0.564-0.5640.0000.0000.0000.000
59A98VAL00.017-0.00226.862-0.215-0.2150.0000.0000.0000.000
60A99ALA00.006-0.00422.345-0.260-0.2600.0000.0000.0000.000
61A100LYS10.9090.95722.28311.87311.8730.0000.0000.0000.000
62A101GLN0-0.061-0.02923.152-0.026-0.0260.0000.0000.0000.000
63A102PHE0-0.059-0.02422.5530.2230.2230.0000.0000.0000.000
64A103GLY00.0170.01519.727-0.505-0.5050.0000.0000.0000.000
65A104ALA0-0.026-0.00517.677-0.994-0.9940.0000.0000.0000.000
66A105GLN0-0.020-0.01113.805-0.383-0.3830.0000.0000.0000.000
67A106VAL0-0.019-0.02118.1520.2470.2470.0000.0000.0000.000
68A107HIS0-0.045-0.02019.527-0.708-0.7080.0000.0000.0000.000
69A108ARG10.7320.82421.39311.31611.3160.0000.0000.0000.000
70A109ARG10.8240.90424.23911.88411.8840.0000.0000.0000.000
71A110SER0-0.003-0.02526.0350.6100.6100.0000.0000.0000.000
72A111SER00.0540.01028.985-0.053-0.0530.0000.0000.0000.000
73A112GLU-1-0.970-0.97930.770-9.604-9.6040.0000.0000.0000.000
74A113THR00.0050.00925.8870.1590.1590.0000.0000.0000.000
75A114SER0-0.008-0.00727.931-0.377-0.3770.0000.0000.0000.000
76A115LYS10.9570.99030.2519.3609.3600.0000.0000.0000.000
77A116ASP-1-0.818-0.90732.294-8.963-8.9630.0000.0000.0000.000
78A117SER0-0.068-0.04434.061-0.014-0.0140.0000.0000.0000.000
79A118SER0-0.022-0.00429.1600.0800.0800.0000.0000.0000.000
80A119THR0-0.020-0.02427.214-0.197-0.1970.0000.0000.0000.000
81A120SER00.041-0.00623.012-0.065-0.0650.0000.0000.0000.000
82A121LEU00.0020.02321.660-0.587-0.5870.0000.0000.0000.000
83A122ASP-1-0.792-0.87622.785-11.648-11.6480.0000.0000.0000.000
84A123ALA0-0.007-0.01223.670-0.275-0.2750.0000.0000.0000.000
85A124ILE0-0.033-0.01517.427-0.508-0.5080.0000.0000.0000.000
86A125VAL00.0380.02418.946-0.882-0.8820.0000.0000.0000.000
87A126GLU-1-0.764-0.84720.858-12.905-12.9050.0000.0000.0000.000
88A127PHE0-0.009-0.00814.307-0.066-0.0660.0000.0000.0000.000
89A128LEU00.001-0.01813.922-0.748-0.7480.0000.0000.0000.000
90A129ASN0-0.054-0.01217.230-0.587-0.5870.0000.0000.0000.000
91A130TYR0-0.040-0.01819.2460.2010.2010.0000.0000.0000.000
92A131HIS10.8040.89614.09218.93218.9320.0000.0000.0000.000
93A132ASN00.0450.01014.087-0.899-0.8990.0000.0000.0000.000
94A133GLU-1-0.874-0.91410.080-26.195-26.1950.0000.0000.0000.000
95A134VAL0-0.0180.0068.801-3.556-3.5560.0000.0000.0000.000
96A135ASP-1-0.818-0.8886.458-42.380-42.3800.0000.0000.0000.000
97A136ILE0-0.050-0.0386.4472.6882.6880.0000.0000.0000.000
98A137VAL00.0310.0249.808-0.711-0.7110.0000.0000.0000.000
99A138GLY00.0350.01512.4800.5860.5860.0000.0000.0000.000
100A139ASN0-0.022-0.01213.7190.4780.4780.0000.0000.0000.000
101A140ILE0-0.009-0.01215.5200.4140.4140.0000.0000.0000.000
102A141GLN00.0040.00119.3940.1640.1640.0000.0000.0000.000
103A142ALA00.012-0.00323.2110.1340.1340.0000.0000.0000.000
104A143THR0-0.046-0.04625.2470.0950.0950.0000.0000.0000.000
105A144SER00.0350.02624.5760.4220.4220.0000.0000.0000.000
106A145PRO00.0010.00624.858-0.446-0.4460.0000.0000.0000.000
107A146CYS0-0.055-0.02726.2150.0590.0590.0000.0000.0000.000
108A147LEU00.0540.03119.4640.0320.0320.0000.0000.0000.000
109A148HIS10.8490.91321.53012.20912.2090.0000.0000.0000.000
110A149PRO00.0600.04617.294-0.238-0.2380.0000.0000.0000.000
111A150THR0-0.003-0.01016.321-0.663-0.6630.0000.0000.0000.000
112A151ASP-1-0.857-0.90517.246-14.249-14.2490.0000.0000.0000.000
113A152LEU0-0.022-0.00814.037-0.547-0.5470.0000.0000.0000.000
114A153GLN0-0.032-0.01912.300-0.553-0.5530.0000.0000.0000.000
115A154LYS10.9931.00312.39613.43013.4300.0000.0000.0000.000
116A155VAL00.0160.01013.515-0.349-0.3490.0000.0000.0000.000
117A156ALA00.0020.0008.589-0.766-0.7660.0000.0000.0000.000
118A157GLU-1-0.964-0.9789.559-21.865-21.8650.0000.0000.0000.000
119A158MET0-0.017-0.00311.208-0.306-0.3060.0000.0000.0000.000
120A159ILE0-0.044-0.0298.8380.0080.0080.0000.0000.0000.000
121A160ARG10.8850.9586.65328.42628.4260.0000.0000.0000.000
122A161GLU-1-0.967-0.9949.013-20.167-20.1670.0000.0000.0000.000
123A162GLU-1-0.841-0.89612.170-16.042-16.0420.0000.0000.0000.000
124A163GLY0-0.0010.02211.5500.8950.8950.0000.0000.0000.000
125A164TYR0-0.097-0.07712.6180.7040.7040.0000.0000.0000.000
126A165ASP-1-0.815-0.90912.783-22.017-22.0170.0000.0000.0000.000
127A166SER00.012-0.00114.478-0.119-0.1190.0000.0000.0000.000
128A167VAL00.0020.00614.8530.4840.4840.0000.0000.0000.000
129A168PHE00.0100.01517.114-0.304-0.3040.0000.0000.0000.000
130A169SER00.0030.00019.8500.1090.1090.0000.0000.0000.000
131A170VAL0-0.019-0.00922.0820.4590.4590.0000.0000.0000.000
132A171VAL00.002-0.00725.550-0.045-0.0450.0000.0000.0000.000
133A172ARG10.8530.91528.70210.11110.1110.0000.0000.0000.000
134A173ARG10.9120.96131.6059.5639.5630.0000.0000.0000.000
135A174HIS00.0190.01835.099-0.138-0.1380.0000.0000.0000.000
136A175GLN0-0.048-0.03036.9940.2820.2820.0000.0000.0000.000
137A176PHE0-0.016-0.01440.276-0.043-0.0430.0000.0000.0000.000
138A177ARG10.8940.93237.5688.1188.1180.0000.0000.0000.000
139A178TRP00.000-0.01342.8210.1560.1560.0000.0000.0000.000
140A179SER00.0140.02145.069-0.105-0.1050.0000.0000.0000.000
141A180GLU-1-0.900-0.93045.692-6.709-6.7090.0000.0000.0000.000
142A181ILE0-0.030-0.00647.9420.0430.0430.0000.0000.0000.000
143A182GLN00.0610.02149.1060.0240.0240.0000.0000.0000.000
144A183LYS10.9200.94551.8426.1006.1000.0000.0000.0000.000
145A184GLY00.0300.03154.4080.1020.1020.0000.0000.0000.000
146A185VAL00.0320.00757.309-0.013-0.0130.0000.0000.0000.000
147A186ARG10.9330.96959.2795.0675.0670.0000.0000.0000.000
148A187GLU0-0.032-0.01352.513-0.003-0.0030.0000.0000.0000.000
149A188VAL00.0080.00754.6740.0280.0280.0000.0000.0000.000
150A189THR0-0.029-0.02049.575-0.082-0.0820.0000.0000.0000.000
151A190GLU-1-0.910-0.96849.596-6.086-6.0860.0000.0000.0000.000
152A191PRO0-0.047-0.02047.710-0.127-0.1270.0000.0000.0000.000
153A192LEU00.018-0.01342.818-0.039-0.0390.0000.0000.0000.000
154A193ASN0-0.053-0.01639.508-0.172-0.1720.0000.0000.0000.000
155A194LEU00.0020.00343.122-0.062-0.0620.0000.0000.0000.000
156A195ASN00.0670.02945.9700.1550.1550.0000.0000.0000.000
157A196PRO00.007-0.00549.6170.0150.0150.0000.0000.0000.000
158A197ALA00.0190.02051.9360.0670.0670.0000.0000.0000.000
159A198LYS10.8470.91951.0315.8485.8480.0000.0000.0000.000
160A199ARG11.0121.01048.4656.2296.2290.0000.0000.0000.000
161A200PRO00.0060.02644.4360.0930.0930.0000.0000.0000.000
162A201ARG10.8320.86745.9976.4736.4730.0000.0000.0000.000
163A202ARG10.8840.93640.3747.4327.4320.0000.0000.0000.000
164A203GLN00.0770.02240.772-0.158-0.1580.0000.0000.0000.000
165A204ASP-1-0.822-0.85942.155-6.729-6.7290.0000.0000.0000.000
166A205TRP0-0.028-0.02438.9650.0200.0200.0000.0000.0000.000
167A206ASP-1-0.874-0.92534.996-8.808-8.8080.0000.0000.0000.000
168A207GLY0-0.077-0.03436.2270.1120.1120.0000.0000.0000.000
169A208GLU-1-0.765-0.86333.850-8.441-8.4410.0000.0000.0000.000
170A209LEU0-0.010-0.00327.3400.0050.0050.0000.0000.0000.000
171A210TYR0-0.048-0.03930.3720.1000.1000.0000.0000.0000.000
172A211GLU-1-0.794-0.87425.710-11.929-11.9290.0000.0000.0000.000
173A212ASN0-0.035-0.03924.5580.1030.1030.0000.0000.0000.000
174A213GLY00.0350.03425.1820.1470.1470.0000.0000.0000.000
175A214SER0-0.013-0.01222.720-0.480-0.4800.0000.0000.0000.000
176A215PHE00.014-0.02517.630-0.441-0.4410.0000.0000.0000.000
177A216TYR0-0.043-0.04118.5020.2090.2090.0000.0000.0000.000
178A217PHE00.0070.00211.306-0.449-0.4490.0000.0000.0000.000
179A218ALA00.0190.00614.0030.7690.7690.0000.0000.0000.000
180A219LYS10.8400.9249.97223.69423.6940.0000.0000.0000.000
181A220ARG10.8060.88812.23624.36724.3670.0000.0000.0000.000
182A221HIS00.000-0.00713.4381.9511.9510.0000.0000.0000.000
183A222LEU0-0.0020.01116.4001.1531.1530.0000.0000.0000.000
184A223ILE00.0090.01415.1651.0351.0350.0000.0000.0000.000
185A224GLU-1-0.871-0.93517.181-18.093-18.0930.0000.0000.0000.000
186A225MET0-0.088-0.02719.3590.9520.9520.0000.0000.0000.000
187A226GLY00.0080.00422.0830.6600.6600.0000.0000.0000.000
188A227TYR0-0.071-0.04521.4570.6660.6660.0000.0000.0000.000
189A228LEU00.002-0.00819.493-0.724-0.7240.0000.0000.0000.000
190A229GLN0-0.073-0.04319.214-0.542-0.5420.0000.0000.0000.000
191A230GLY00.0540.00320.0980.6580.6580.0000.0000.0000.000
192A231GLY00.0120.00818.640-0.758-0.7580.0000.0000.0000.000
193A232LYS10.8450.91116.41017.98617.9860.0000.0000.0000.000
194A233MET00.0010.01117.566-0.777-0.7770.0000.0000.0000.000
195A234ALA00.0180.01818.2720.3440.3440.0000.0000.0000.000
196A235TYR0-0.014-0.00820.092-0.033-0.0330.0000.0000.0000.000
197A236TYR0-0.012-0.04818.911-0.307-0.3070.0000.0000.0000.000
198A237GLU-1-0.821-0.88621.087-10.296-10.2960.0000.0000.0000.000
199A238MET0-0.0250.02022.482-0.185-0.1850.0000.0000.0000.000
200A239ARG10.8630.92024.80110.73410.7340.0000.0000.0000.000
201A240ALA00.0390.03027.763-0.092-0.0920.0000.0000.0000.000
202A241GLU-1-0.854-0.92229.809-9.687-9.6870.0000.0000.0000.000
203A242HIS0-0.061-0.04125.707-0.190-0.1900.0000.0000.0000.000
204A243SER0-0.010-0.00626.495-0.523-0.5230.0000.0000.0000.000
205A244VAL0-0.063-0.02828.5180.2160.2160.0000.0000.0000.000
206A245ASP-1-0.775-0.85929.184-10.376-10.3760.0000.0000.0000.000
207A246ILE0-0.006-0.01730.5860.3340.3340.0000.0000.0000.000
208A247ASP-1-0.864-0.93432.825-8.899-8.8990.0000.0000.0000.000
209A248VAL0-0.065-0.02833.5620.2370.2370.0000.0000.0000.000
210A249ASP-1-0.730-0.83935.142-8.410-8.4100.0000.0000.0000.000
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