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: RK5G8

Calculation Name: 5FTT-G-Xray549

Preferred Name:

Target Type:

Ligand Name: 2-acetamido-2-deoxy-beta-d-glucopyranose | calcium ion

Ligand 3-letter code: NAG | CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5FTT

Chain ID: G

ChEMBL ID:

UniProt ID: Q80TS3

Base Structure: X-ray

Registration Date: 2025-10-12

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 363
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -6182723.158175
FMO2-HF: Nuclear repulsion 6033326.970933
FMO2-HF: Total energy -149396.187242
FMO2-MP2: Total energy -149827.48367


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(G:97:VAL)


Summations of interaction energy for fragment #1(G:97:VAL)
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.
-178.116-170.1041.011-4.051-4.97-0.037
Interaction energy analysis for fragmet #1(G:97:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.826 / q_NPA : 0.901
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].
3G99ARG10.8620.9052.83841.76044.7940.271-1.561-1.744-0.013
17G113CYS0-0.150-0.0242.2917.7979.2640.444-0.688-1.222-0.007
91G190GLU-1-0.901-0.9513.020-64.642-63.5150.027-0.335-0.818-0.003
92G192VAL00.0590.0302.989-20.790-18.4060.269-1.467-1.186-0.014
4G100ARG10.8140.8755.54223.60923.6090.0000.0000.0000.000
5G101GLU-1-0.921-0.9629.254-23.914-23.9140.0000.0000.0000.000
6G102LEU0-0.015-0.01712.0070.6510.6510.0000.0000.0000.000
7G103SER0-0.0070.00815.6460.0950.0950.0000.0000.0000.000
8G104CYS0-0.048-0.02019.042-0.080-0.0800.0000.0000.0000.000
9G105GLU-1-0.794-0.90122.592-11.220-11.2200.0000.0000.0000.000
10G106SER0-0.090-0.04925.3360.4410.4410.0000.0000.0000.000
11G107TYR00.0020.01322.2200.0720.0720.0000.0000.0000.000
12G108PRO0-0.045-0.02621.054-0.391-0.3910.0000.0000.0000.000
13G109ILE00.0020.01515.223-0.253-0.2530.0000.0000.0000.000
14G110GLU-1-0.942-0.98115.067-17.160-17.1600.0000.0000.0000.000
15G111LEU00.0080.01610.386-1.391-1.3910.0000.0000.0000.000
16G112ARG10.9930.97910.27922.36022.3600.0000.0000.0000.000
18G114PRO00.0180.0085.7584.1134.1130.0000.0000.0000.000
19G115GLY00.009-0.0068.828-0.715-0.7150.0000.0000.0000.000
20G116THR0-0.019-0.02310.8031.6691.6690.0000.0000.0000.000
21G117ASP-1-0.925-0.9495.782-43.288-43.2880.0000.0000.0000.000
22G118VAL0-0.035-0.0108.2962.1492.1490.0000.0000.0000.000
23G119ILE0-0.025-0.0176.975-6.181-6.1810.0000.0000.0000.000
24G120MET00.0130.0096.8294.2384.2380.0000.0000.0000.000
25G121ILE0-0.022-0.0217.899-3.849-3.8490.0000.0000.0000.000
26G122GLU-1-0.949-0.9619.031-29.136-29.1360.0000.0000.0000.000
27G123SER0-0.019-0.02410.8661.9451.9450.0000.0000.0000.000
28G124ALA00.0250.00213.517-1.137-1.1370.0000.0000.0000.000
29G125ASN0-0.007-0.00116.2061.3451.3450.0000.0000.0000.000
30G126TYR00.0300.02119.559-0.218-0.2180.0000.0000.0000.000
31G127GLY00.029-0.00722.2880.5540.5540.0000.0000.0000.000
32G128ARG10.8160.90523.60311.70611.7060.0000.0000.0000.000
33G129THR0-0.044-0.02620.0950.3370.3370.0000.0000.0000.000
34G130ASP-1-0.839-0.91421.559-12.843-12.8430.0000.0000.0000.000
35G131ASP-1-0.807-0.91223.438-10.892-10.8920.0000.0000.0000.000
36G132LYS10.8980.93824.06810.71810.7180.0000.0000.0000.000
37G133ILE0-0.040-0.00618.120-0.113-0.1130.0000.0000.0000.000
38G135ASP-1-0.888-0.93823.482-10.198-10.1980.0000.0000.0000.000
39G136SER0-0.041-0.04726.799-0.036-0.0360.0000.0000.0000.000
40G137ASP-1-0.884-0.93929.960-8.509-8.5090.0000.0000.0000.000
41G138PRO00.033-0.00432.473-0.188-0.1880.0000.0000.0000.000
42G139ALA0-0.0270.00633.749-0.054-0.0540.0000.0000.0000.000
43G140GLN0-0.035-0.02030.9320.1700.1700.0000.0000.0000.000
44G141MET0-0.063-0.01427.602-0.309-0.3090.0000.0000.0000.000
45G142GLU-1-0.953-0.98529.697-9.296-9.2960.0000.0000.0000.000
46G143ASN0-0.047-0.01731.2440.3430.3430.0000.0000.0000.000
47G144ILE0-0.035-0.01529.6230.0950.0950.0000.0000.0000.000
48G145ARG10.9160.97027.53510.30810.3080.0000.0000.0000.000
49G146CYS0-0.102-0.04426.6980.3090.3090.0000.0000.0000.000
50G147TYR00.001-0.00923.167-0.346-0.3460.0000.0000.0000.000
51G148LEU00.0540.03023.4350.5200.5200.0000.0000.0000.000
52G149PRO00.003-0.00722.360-0.648-0.6480.0000.0000.0000.000
53G150ASP-1-0.840-0.91921.403-13.200-13.2000.0000.0000.0000.000
54G151ALA00.0040.01219.733-0.268-0.2680.0000.0000.0000.000
55G152TYR0-0.0020.00312.9170.1840.1840.0000.0000.0000.000
56G153LYS10.8330.91517.22812.15212.1520.0000.0000.0000.000
57G154ILE00.0100.00719.707-0.248-0.2480.0000.0000.0000.000
58G155MET00.0040.00214.7880.2250.2250.0000.0000.0000.000
59G156SER0-0.018-0.02115.256-1.319-1.3190.0000.0000.0000.000
60G157GLN0-0.0100.00416.286-0.069-0.0690.0000.0000.0000.000
61G158ARG10.9170.97117.78915.28015.2800.0000.0000.0000.000
62G159CYS0-0.065-0.03012.9041.6301.6300.0000.0000.0000.000
63G160ASN00.0960.05612.081-3.209-3.2090.0000.0000.0000.000
64G161ASN0-0.007-0.01312.2080.4650.4650.0000.0000.0000.000
65G162ARG10.9140.96312.56019.18619.1860.0000.0000.0000.000
66G163THR00.0140.02210.868-1.223-1.2230.0000.0000.0000.000
67G164GLN0-0.034-0.03011.276-0.995-0.9950.0000.0000.0000.000
68G166ALA00.0500.03915.406-0.506-0.5060.0000.0000.0000.000
69G167VAL0-0.015-0.01817.4310.7610.7610.0000.0000.0000.000
70G168VAL00.0610.02919.976-0.228-0.2280.0000.0000.0000.000
71G169ALA00.0340.03121.2080.1470.1470.0000.0000.0000.000
72G170GLY00.035-0.00223.2110.4390.4390.0000.0000.0000.000
73G171PRO00.0670.02126.754-0.264-0.2640.0000.0000.0000.000
74G172ASP-1-0.882-0.91827.741-10.381-10.3810.0000.0000.0000.000
75G173VAL0-0.069-0.02822.341-0.139-0.1390.0000.0000.0000.000
76G174PHE00.009-0.00319.537-0.433-0.4330.0000.0000.0000.000
77G175PRO0-0.0030.00625.7320.3660.3660.0000.0000.0000.000
78G176ASP-1-0.805-0.91928.103-10.680-10.6800.0000.0000.0000.000
79G177PRO0-0.038-0.00626.9300.3020.3020.0000.0000.0000.000
80G179PRO00.0740.03531.854-0.050-0.0500.0000.0000.0000.000
81G180GLY0-0.034-0.01734.5060.1210.1210.0000.0000.0000.000
82G181THR0-0.0020.00228.8160.0630.0630.0000.0000.0000.000
83G182TYR00.0020.00726.1930.0090.0090.0000.0000.0000.000
84G183LYS10.7900.89025.09310.82110.8210.0000.0000.0000.000
85G184TYR00.0210.01219.3470.2920.2920.0000.0000.0000.000
86G185LEU0-0.038-0.01117.5900.1930.1930.0000.0000.0000.000
87G186GLU-1-0.823-0.88814.662-19.486-19.4860.0000.0000.0000.000
88G187VAL0-0.003-0.00911.9290.3160.3160.0000.0000.0000.000
89G188GLN00.0240.0169.621-0.729-0.7290.0000.0000.0000.000
90G189TYR00.004-0.0047.0450.3900.3900.0000.0000.0000.000
93G193PRO00.028-0.0045.9104.3244.3240.0000.0000.0000.000
94G194TYR00.0480.0109.3571.7881.7880.0000.0000.0000.000
95G195LYS10.8460.94011.93219.88319.8830.0000.0000.0000.000
96G196VAL00.0540.03114.065-1.034-1.0340.0000.0000.0000.000
97G197GLU-1-0.932-0.96516.528-15.271-15.2710.0000.0000.0000.000
98G198GLN0-0.027-0.02719.6360.6070.6070.0000.0000.0000.000
99G199LYS10.8930.93023.24410.65310.6530.0000.0000.0000.000
100G200VAL00.0140.04022.1020.3680.3680.0000.0000.0000.000
101G201PHE00.003-0.00222.2720.0520.0520.0000.0000.0000.000
102G202LEU0-0.043-0.01623.7990.2370.2370.0000.0000.0000.000
103G203CYS00.0080.02826.3240.3580.3580.0000.0000.0000.000
104G204PRO0-0.012-0.00130.085-0.133-0.1330.0000.0000.0000.000
105G205GLY0-0.012-0.01532.4930.0550.0550.0000.0000.0000.000
106G206LEU00.0170.02034.7580.1020.1020.0000.0000.0000.000
107G207LEU0-0.034-0.01238.0190.0750.0750.0000.0000.0000.000
108G208LYS10.9060.95440.5797.7157.7150.0000.0000.0000.000
109G209GLY0-0.016-0.01143.4980.2200.2200.0000.0000.0000.000
110G210VAL00.0000.01543.965-0.186-0.1860.0000.0000.0000.000
111G211TYR0-0.013-0.00545.3620.1760.1760.0000.0000.0000.000
112G212GLN00.0160.01346.342-0.092-0.0920.0000.0000.0000.000
113G213SER0-0.043-0.00443.708-0.066-0.0660.0000.0000.0000.000
114G214GLU-1-0.809-0.90442.175-7.567-7.5670.0000.0000.0000.000
115G215HIS00.0180.02746.7370.0770.0770.0000.0000.0000.000
116G216LEU0-0.043-0.01044.3960.0040.0040.0000.0000.0000.000
117G217PHE0-0.012-0.01747.8150.0990.0990.0000.0000.0000.000
118G218GLU-1-0.878-0.92252.121-5.594-5.5940.0000.0000.0000.000
119G219SER0-0.014-0.01551.8910.0560.0560.0000.0000.0000.000
120G220ASP-1-0.829-0.91053.865-5.841-5.8410.0000.0000.0000.000
121G221HIS10.7760.87153.2746.0496.0490.0000.0000.0000.000
122G222GLN00.0120.01054.268-0.095-0.0950.0000.0000.0000.000
123G223SER00.025-0.00152.111-0.050-0.0500.0000.0000.0000.000
124G224GLY00.008-0.01449.3330.0510.0510.0000.0000.0000.000
125G225ALA00.0330.03343.8690.0020.0020.0000.0000.0000.000
126G226TRP0-0.051-0.05342.366-0.045-0.0450.0000.0000.0000.000
127G227CYS00.0250.02938.176-0.088-0.0880.0000.0000.0000.000
128G228LYS10.9090.96234.8899.1169.1160.0000.0000.0000.000
129G229ASP-1-0.731-0.86630.715-10.606-10.6060.0000.0000.0000.000
130G230PRO00.0040.01930.168-0.106-0.1060.0000.0000.0000.000
131G231LEU00.0120.02325.071-0.323-0.3230.0000.0000.0000.000
132G232GLN0-0.061-0.03326.335-0.488-0.4880.0000.0000.0000.000
133G233ALA0-0.0090.00226.6840.2970.2970.0000.0000.0000.000
134G234SER0-0.025-0.02128.5380.1840.1840.0000.0000.0000.000
135G235ASP-1-0.885-0.95732.147-9.061-9.0610.0000.0000.0000.000
136G236LYS10.8470.92034.5989.2889.2880.0000.0000.0000.000
137G237ILE0-0.0340.00037.093-0.107-0.1070.0000.0000.0000.000
138G238TYR0-0.031-0.02235.1930.0310.0310.0000.0000.0000.000
139G239TYR00.0690.02540.6430.0580.0580.0000.0000.0000.000
140G240MET0-0.004-0.00243.5230.0580.0580.0000.0000.0000.000
141G241PRO00.0150.02046.4270.0210.0210.0000.0000.0000.000
142G242TRP00.0490.01350.0760.1010.1010.0000.0000.0000.000
143G243THR0-0.029-0.03151.5330.1730.1730.0000.0000.0000.000
144G244PRO00.0340.03753.950-0.082-0.0820.0000.0000.0000.000
145G245TYR0-0.064-0.04355.0560.1150.1150.0000.0000.0000.000
146G246ARG10.8890.93054.6145.5345.5340.0000.0000.0000.000
147G247THR00.0720.06448.369-0.031-0.0310.0000.0000.0000.000
148G248ASP-1-0.829-0.91548.476-6.394-6.3940.0000.0000.0000.000
149G249THR0-0.036-0.02246.695-0.068-0.0680.0000.0000.0000.000
150G250LEU00.0340.04039.7760.0140.0140.0000.0000.0000.000
151G251THR0-0.055-0.02344.2800.0410.0410.0000.0000.0000.000
152G252GLU-1-0.751-0.85437.647-8.718-8.7180.0000.0000.0000.000
153G253TYR00.0040.01041.3970.1900.1900.0000.0000.0000.000
154G254SER0-0.024-0.03439.446-0.188-0.1880.0000.0000.0000.000
155G255SER00.005-0.01638.811-0.186-0.1860.0000.0000.0000.000
156G256LYS10.9130.92740.7437.7917.7910.0000.0000.0000.000
157G257ASP-1-0.879-0.94042.633-7.118-7.1180.0000.0000.0000.000
158G258ASP-1-0.843-0.87143.334-7.110-7.1100.0000.0000.0000.000
159G259PHE0-0.035-0.01643.8350.1380.1380.0000.0000.0000.000
160G260ILE00.0050.00445.8500.1310.1310.0000.0000.0000.000
161G261ALA0-0.070-0.02848.4940.1630.1630.0000.0000.0000.000
162G262GLY00.0290.02749.4830.1090.1090.0000.0000.0000.000
163G263ARG10.8400.90447.1916.7356.7350.0000.0000.0000.000
164G264PRO0-0.015-0.01845.514-0.171-0.1710.0000.0000.0000.000
165G265THR0-0.011-0.00439.8980.0790.0790.0000.0000.0000.000
166G266THR0-0.039-0.02040.3900.0230.0230.0000.0000.0000.000
167G267THR00.0350.02843.705-0.011-0.0110.0000.0000.0000.000
168G268TYR0-0.081-0.05237.921-0.043-0.0430.0000.0000.0000.000
169G269LYS10.8790.91243.3816.5766.5760.0000.0000.0000.000
170G270LEU00.0120.02242.657-0.134-0.1340.0000.0000.0000.000
171G271PRO0-0.022-0.00742.7720.1710.1710.0000.0000.0000.000
172G272HIS0-0.040-0.02944.6180.0040.0040.0000.0000.0000.000
173G273ARG10.9290.99047.1735.9635.9630.0000.0000.0000.000
174G274VAL0-0.004-0.00345.499-0.097-0.0970.0000.0000.0000.000
175G275ASP-1-0.748-0.86347.699-6.143-6.1430.0000.0000.0000.000
176G276GLY00.0210.02547.477-0.146-0.1460.0000.0000.0000.000
177G277THR0-0.052-0.04147.073-0.013-0.0130.0000.0000.0000.000
178G278GLY00.0590.04643.536-0.111-0.1110.0000.0000.0000.000
179G279PHE0-0.094-0.06139.974-0.065-0.0650.0000.0000.0000.000
180G280VAL00.0680.04335.743-0.052-0.0520.0000.0000.0000.000
181G281VAL0-0.047-0.03333.4360.0080.0080.0000.0000.0000.000
182G282TYR00.0550.00926.448-0.046-0.0460.0000.0000.0000.000
183G283ASP-1-0.871-0.93225.745-12.570-12.5700.0000.0000.0000.000
184G284GLY0-0.016-0.00828.675-0.053-0.0530.0000.0000.0000.000
185G285ALA0-0.055-0.02731.3170.2960.2960.0000.0000.0000.000
186G286LEU0-0.0200.00133.0900.0100.0100.0000.0000.0000.000
187G287PHE0-0.006-0.00431.688-0.067-0.0670.0000.0000.0000.000
188G288PHE00.0370.00337.5900.1250.1250.0000.0000.0000.000
189G289ASN00.0450.01241.4030.0360.0360.0000.0000.0000.000
190G290LYS10.8390.92144.1667.1817.1810.0000.0000.0000.000
191G291GLU-1-0.809-0.91646.414-5.986-5.9860.0000.0000.0000.000
192G292ARG10.7940.89050.2175.8675.8670.0000.0000.0000.000
193G293THR0-0.041-0.02847.377-0.024-0.0240.0000.0000.0000.000
194G294ARG10.8780.95145.9486.6576.6570.0000.0000.0000.000
195G295ASN0-0.003-0.02543.191-0.139-0.1390.0000.0000.0000.000
196G296ILE00.0270.03338.2060.1150.1150.0000.0000.0000.000
197G297VAL0-0.053-0.02739.648-0.126-0.1260.0000.0000.0000.000
198G298LYS10.9170.97130.12510.39310.3930.0000.0000.0000.000
199G299PHE0-0.008-0.02236.6470.0950.0950.0000.0000.0000.000
200G300ASP-1-0.765-0.85332.322-10.132-10.1320.0000.0000.0000.000
201G301LEU00.0010.00034.3780.2830.2830.0000.0000.0000.000
202G302ARG10.9020.95729.97110.76410.7640.0000.0000.0000.000
203G303THR0-0.087-0.08732.8340.1930.1930.0000.0000.0000.000
204G304ARG10.8550.93135.4788.1928.1920.0000.0000.0000.000
205G305ILE00.0070.01335.2010.2880.2880.0000.0000.0000.000
206G306LYS10.7910.88437.1847.5187.5180.0000.0000.0000.000
207G307SER00.006-0.00933.116-0.055-0.0550.0000.0000.0000.000
208G308GLY00.0280.00934.808-0.185-0.1850.0000.0000.0000.000
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