Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: QY52Y

Calculation Name: 3NCY-W-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NCY

Chain ID: W

ChEMBL ID:

UniProt ID: P60066

Base Structure: X-ray

Registration Date: 2023-06-26

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 209
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2121458.386733
FMO2-HF: Nuclear repulsion 2038533.677581
FMO2-HF: Total energy -82924.709151
FMO2-MP2: Total energy -83161.845592


3D Structure
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(W:1:GLU)


Summations of interaction energy for fragment #1(W:1:GLU)
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.
-35.972-32.7551.248-1.765-2.70.007
Interaction energy analysis for fragmet #1(W:1:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.951 / q_NPA : -0.986
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].
3W3VAL00.019-0.0043.805-3.630-1.935-0.022-0.707-0.9660.004
4W4MET00.0170.0165.849-2.902-2.9020.0000.0000.0000.000
5W5THR0-0.010-0.0019.160-1.807-1.8070.0000.0000.0000.000
6W6GLN00.0380.01711.4970.0590.0590.0000.0000.0000.000
7W7SER0-0.0070.02114.717-0.300-0.3000.0000.0000.0000.000
8W8PRO00.0510.01018.207-0.165-0.1650.0000.0000.0000.000
9W9ALA00.0550.02718.8810.2140.2140.0000.0000.0000.000
10W10ILE00.0070.00019.835-0.009-0.0090.0000.0000.0000.000
11W11MET0-0.027-0.00223.337-0.018-0.0180.0000.0000.0000.000
12W12SER00.0320.00926.143-0.140-0.1400.0000.0000.0000.000
13W13ALA0-0.032-0.00529.620-0.046-0.0460.0000.0000.0000.000
14W14SER0-0.034-0.03632.034-0.072-0.0720.0000.0000.0000.000
15W15PRO00.024-0.00335.0550.1250.1250.0000.0000.0000.000
16W16GLY00.0200.02135.881-0.205-0.2050.0000.0000.0000.000
17W17GLU-1-0.862-0.90732.9108.8078.8070.0000.0000.0000.000
18W18LYS10.9920.99830.326-8.982-8.9820.0000.0000.0000.000
19W19VAL00.0000.00626.1920.1370.1370.0000.0000.0000.000
20W20THR0-0.056-0.05424.430-0.027-0.0270.0000.0000.0000.000
21W21MET0-0.0130.03320.5410.2090.2090.0000.0000.0000.000
22W22THR0-0.023-0.02318.9440.1380.1380.0000.0000.0000.000
23W23CYS0-0.061-0.03013.5410.4580.4580.0000.0000.0000.000
24W24SER0-0.0160.02213.278-0.121-0.1210.0000.0000.0000.000
25W25ALA00.0610.01510.0800.6230.6230.0000.0000.0000.000
26W26SER0-0.051-0.0136.5040.4080.4080.0000.0000.0000.000
27W27SER00.006-0.0017.637-0.632-0.6320.0000.0000.0000.000
28W28SER00.014-0.0069.847-0.459-0.4590.0000.0000.0000.000
29W29VAL0-0.0030.0019.1791.0391.0390.0000.0000.0000.000
30W30ASN0-0.024-0.00811.931-1.013-1.0130.0000.0000.0000.000
31W36TYR0-0.010-0.00614.4600.0120.0120.0000.0000.0000.000
32W37MET0-0.0100.01211.7031.3441.3440.0000.0000.0000.000
33W38HIS0-0.018-0.01713.890-1.754-1.7540.0000.0000.0000.000
34W39TRP00.0500.01015.7700.7670.7670.0000.0000.0000.000
35W40TYR0-0.048-0.03915.122-1.278-1.2780.0000.0000.0000.000
36W41GLN0-0.006-0.00919.6380.1050.1050.0000.0000.0000.000
37W42GLN0-0.044-0.03019.6700.0890.0890.0000.0000.0000.000
38W43LYS10.8850.93122.398-9.937-9.9370.0000.0000.0000.000
39W44SER00.0570.03325.663-0.175-0.1750.0000.0000.0000.000
40W45GLY00.0160.01622.786-0.238-0.2380.0000.0000.0000.000
41W46THR0-0.059-0.03723.1630.3230.3230.0000.0000.0000.000
42W47SER00.0180.00822.4040.3960.3960.0000.0000.0000.000
43W48PRO00.0170.00118.411-0.472-0.4720.0000.0000.0000.000
44W49LYS10.9681.00521.357-10.918-10.9180.0000.0000.0000.000
45W50ARG10.9470.96421.338-10.629-10.6290.0000.0000.0000.000
46W51TRP0-0.015-0.02621.589-0.549-0.5490.0000.0000.0000.000
47W52ILE00.0010.00220.581-0.410-0.4100.0000.0000.0000.000
48W53TYR00.0110.02819.2470.7530.7530.0000.0000.0000.000
49W54ASP-1-0.800-0.91218.68912.80812.8080.0000.0000.0000.000
50W55THR0-0.0150.01518.307-0.279-0.2790.0000.0000.0000.000
51W56SER0-0.060-0.04719.829-0.086-0.0860.0000.0000.0000.000
52W57LYS10.8500.93022.900-12.303-12.3030.0000.0000.0000.000
53W58LEU00.0420.02424.1160.3950.3950.0000.0000.0000.000
54W59ALA0-0.034-0.01524.833-0.099-0.0990.0000.0000.0000.000
55W60SER0-0.001-0.01026.710-0.099-0.0990.0000.0000.0000.000
56W61GLY00.0010.00429.973-0.215-0.2150.0000.0000.0000.000
57W62VAL0-0.041-0.00126.292-0.148-0.1480.0000.0000.0000.000
58W63PRO00.0500.03429.689-0.149-0.1490.0000.0000.0000.000
59W64ALA00.035-0.00630.9800.2270.2270.0000.0000.0000.000
60W65ARG10.7890.88231.685-8.821-8.8210.0000.0000.0000.000
61W66PHE00.0130.00925.6860.1740.1740.0000.0000.0000.000
62W67SER00.0050.00526.654-0.149-0.1490.0000.0000.0000.000
63W68GLY00.0140.01522.8320.2660.2660.0000.0000.0000.000
64W69SER0-0.027-0.01821.984-0.355-0.3550.0000.0000.0000.000
65W70GLY00.0590.01919.8570.5070.5070.0000.0000.0000.000
66W71SER0-0.028-0.02718.089-0.326-0.3260.0000.0000.0000.000
67W72GLY00.0510.03315.435-0.006-0.0060.0000.0000.0000.000
68W73THR00.0180.00612.4560.6910.6910.0000.0000.0000.000
69W74SER00.0010.01614.3980.3920.3920.0000.0000.0000.000
70W75TYR0-0.031-0.01814.396-1.184-1.1840.0000.0000.0000.000
71W76SER0-0.007-0.01817.9850.2430.2430.0000.0000.0000.000
72W77LEU0-0.0410.00320.327-0.349-0.3490.0000.0000.0000.000
73W78THR0-0.048-0.03422.306-0.171-0.1710.0000.0000.0000.000
74W79ILE00.0290.00225.969-0.027-0.0270.0000.0000.0000.000
75W80SER0-0.045-0.02029.247-0.065-0.0650.0000.0000.0000.000
76W81SER00.0320.02232.752-0.070-0.0700.0000.0000.0000.000
77W82MET0-0.033-0.00830.5680.2210.2210.0000.0000.0000.000
78W83GLU-1-0.881-0.95032.3267.8187.8180.0000.0000.0000.000
79W84ALA00.0110.00532.5440.2540.2540.0000.0000.0000.000
80W85GLU-1-0.903-0.96432.3078.7978.7970.0000.0000.0000.000
81W86ASP-1-0.730-0.82928.7589.8239.8230.0000.0000.0000.000
82W87ALA00.0120.04027.4850.4810.4810.0000.0000.0000.000
83W88ALA0-0.031-0.02524.789-0.048-0.0480.0000.0000.0000.000
84W89THR00.0110.01519.1200.0560.0560.0000.0000.0000.000
85W90TYR0-0.039-0.03519.9810.0490.0490.0000.0000.0000.000
86W91TYR0-0.017-0.01614.3770.4550.4550.0000.0000.0000.000
87W93GLN00.0460.02910.919-0.036-0.0360.0000.0000.0000.000
88W94GLN00.0700.0205.988-2.626-2.6260.0000.0000.0000.000
89W95TRP0-0.021-0.0289.0631.3821.3820.0000.0000.0000.000
90W96SER0-0.0260.0009.678-0.522-0.5220.0000.0000.0000.000
91W97TYR0-0.0020.0055.352-0.348-0.3480.0000.0000.0000.000
92W98ASN0-0.0250.0195.072-3.397-3.3970.0000.0000.0000.000
93W99PRO00.023-0.0082.6401.5292.8441.270-1.021-1.5640.003
94W100PRO00.0210.0204.9982.4062.451-0.001-0.002-0.0420.000
95W101THR0-0.044-0.0253.946-0.1490.0130.001-0.035-0.1280.000
96W102PHE00.028-0.0127.421-2.938-2.9380.0000.0000.0000.000
97W103GLY00.0350.0118.9331.8881.8880.0000.0000.0000.000
98W104GLY0-0.048-0.02811.360-0.142-0.1420.0000.0000.0000.000
99W105GLY0-0.0020.00713.234-0.703-0.7030.0000.0000.0000.000
100W106THR0-0.041-0.02316.2890.0910.0910.0000.0000.0000.000
101W107LYS10.8190.89219.512-11.654-11.6540.0000.0000.0000.000
102W108LEU0-0.013-0.00522.530-0.217-0.2170.0000.0000.0000.000
103W109GLU-1-0.822-0.89025.67510.50210.5020.0000.0000.0000.000
104W110ILE00.0580.02329.046-0.053-0.0530.0000.0000.0000.000
105W111LYS10.8590.94432.551-8.872-8.8720.0000.0000.0000.000
106W112ARG10.8290.90334.974-7.698-7.6980.0000.0000.0000.000
107W113ALA00.0060.00338.4910.0500.0500.0000.0000.0000.000
108W114ASP-1-0.808-0.90439.5327.7607.7600.0000.0000.0000.000
109W115ALA0-0.0190.00041.460-0.187-0.1870.0000.0000.0000.000
110W116ALA00.0370.01142.4290.1610.1610.0000.0000.0000.000
111W117PRO0-0.016-0.01242.392-0.032-0.0320.0000.0000.0000.000
112W118THR0-0.0250.00744.416-0.217-0.2170.0000.0000.0000.000
113W119VAL0-0.021-0.01345.5120.0370.0370.0000.0000.0000.000
114W120SER00.0090.01846.872-0.241-0.2410.0000.0000.0000.000
115W121ILE0-0.014-0.00947.4000.1610.1610.0000.0000.0000.000
116W122PHE0-0.005-0.01047.320-0.119-0.1190.0000.0000.0000.000
117W123PRO00.0090.01450.0010.0840.0840.0000.0000.0000.000
118W124PRO0-0.015-0.00650.4150.0820.0820.0000.0000.0000.000
119W125SER00.0260.01950.494-0.100-0.1000.0000.0000.0000.000
120W126SER00.0710.01152.609-0.003-0.0030.0000.0000.0000.000
121W127GLU-1-0.881-0.93551.8265.9635.9630.0000.0000.0000.000
122W128GLN0-0.0260.00847.8230.2050.2050.0000.0000.0000.000
123W129LEU00.0320.01951.4940.0120.0120.0000.0000.0000.000
124W130THR0-0.086-0.04354.363-0.072-0.0720.0000.0000.0000.000
125W131SER0-0.047-0.03750.9200.0080.0080.0000.0000.0000.000
126W132GLY0-0.0190.00951.3570.0740.0740.0000.0000.0000.000
127W133GLY0-0.0020.00249.0650.1110.1110.0000.0000.0000.000
128W134ALA0-0.010-0.00948.980-0.131-0.1310.0000.0000.0000.000
129W135SER00.027-0.00245.4730.1820.1820.0000.0000.0000.000
130W136VAL0-0.038-0.00247.200-0.086-0.0860.0000.0000.0000.000
131W137VAL00.0250.01643.6490.1920.1920.0000.0000.0000.000
132W138CYS0-0.101-0.04744.117-0.090-0.0900.0000.0000.0000.000
133W139PHE0-0.014-0.01242.0320.1880.1880.0000.0000.0000.000
134W140LEU00.0100.00941.108-0.164-0.1640.0000.0000.0000.000
135W141ASN00.0420.00040.8950.3330.3330.0000.0000.0000.000
136W142ASN0-0.006-0.01540.685-0.170-0.1700.0000.0000.0000.000
137W143PHE0-0.0410.00536.687-0.147-0.1470.0000.0000.0000.000
138W144TYR00.0190.01433.5590.2300.2300.0000.0000.0000.000
139W145PRO00.0330.00334.741-0.192-0.1920.0000.0000.0000.000
140W146LYS10.8940.91628.069-10.539-10.5390.0000.0000.0000.000
141W147ASP-1-0.918-0.95532.7999.3779.3770.0000.0000.0000.000
142W148ILE0-0.005-0.00134.987-0.310-0.3100.0000.0000.0000.000
143W149ASN0-0.004-0.01236.9900.1610.1610.0000.0000.0000.000
144W150VAL00.0110.01739.284-0.175-0.1750.0000.0000.0000.000
145W151LYS10.8540.93041.161-7.563-7.5630.0000.0000.0000.000
146W152TRP00.0440.00837.9260.0010.0010.0000.0000.0000.000
147W153LYS10.8320.92243.524-7.274-7.2740.0000.0000.0000.000
148W154LYS10.9530.93846.742-6.341-6.3410.0000.0000.0000.000
149W155ILE0-0.047-0.01250.246-0.045-0.0450.0000.0000.0000.000
150W156ASP-1-0.719-0.87752.8225.6125.6120.0000.0000.0000.000
151W157GLY0-0.032-0.00954.636-0.064-0.0640.0000.0000.0000.000
152W158SER00.0080.00452.1140.0850.0850.0000.0000.0000.000
153W159GLU-1-0.912-0.94947.1486.6756.6750.0000.0000.0000.000
154W160ARG10.8690.96444.319-6.971-6.9710.0000.0000.0000.000
155W161GLN00.0390.01140.535-0.024-0.0240.0000.0000.0000.000
156W162ASN0-0.001-0.02039.8800.0400.0400.0000.0000.0000.000
157W163GLY00.0810.03840.469-0.187-0.1870.0000.0000.0000.000
158W164VAL0-0.046-0.02039.300-0.089-0.0890.0000.0000.0000.000
159W165LEU0-0.0030.00536.7360.2680.2680.0000.0000.0000.000
160W166ASN00.0280.00835.378-0.360-0.3600.0000.0000.0000.000
161W167SER0-0.0110.00233.3970.2640.2640.0000.0000.0000.000
162W168TRP0-0.018-0.01831.660-0.285-0.2850.0000.0000.0000.000
163W169THR00.0020.00332.2030.2070.2070.0000.0000.0000.000
164W170ASP-1-0.924-0.95828.11510.70510.7050.0000.0000.0000.000
165W171GLN0-0.008-0.03331.0410.2270.2270.0000.0000.0000.000
166W172ASP-1-0.825-0.89533.2187.9627.9620.0000.0000.0000.000
167W173SER0-0.026-0.02534.413-0.028-0.0280.0000.0000.0000.000
168W174LYS10.9040.94535.869-7.266-7.2660.0000.0000.0000.000
169W175ASP-1-0.781-0.84838.8737.4027.4020.0000.0000.0000.000
170W176SER0-0.0020.01735.495-0.026-0.0260.0000.0000.0000.000
171W177THR0-0.089-0.05536.3180.1190.1190.0000.0000.0000.000
172W178TYR0-0.012-0.01131.2500.1860.1860.0000.0000.0000.000
173W179SER00.022-0.00136.189-0.333-0.3330.0000.0000.0000.000
174W180MET0-0.029-0.00636.2510.2230.2230.0000.0000.0000.000
175W181SER00.0070.01937.493-0.331-0.3310.0000.0000.0000.000
176W182SER00.0510.01338.4460.1170.1170.0000.0000.0000.000
177W183THR0-0.020-0.01640.173-0.318-0.3180.0000.0000.0000.000
178W184LEU0-0.040-0.02241.9450.1450.1450.0000.0000.0000.000
179W185THR00.0050.00443.220-0.109-0.1090.0000.0000.0000.000
180W186LEU0-0.053-0.03045.1380.0740.0740.0000.0000.0000.000
181W187THR00.021-0.00947.5610.0630.0630.0000.0000.0000.000
182W188LYS10.8440.91450.346-5.623-5.6230.0000.0000.0000.000
183W189ASP-1-0.880-0.94453.5525.7345.7340.0000.0000.0000.000
184W190GLU-1-0.829-0.91650.4716.1316.1310.0000.0000.0000.000
185W191TYR0-0.044-0.02652.606-0.048-0.0480.0000.0000.0000.000
186W192GLU-1-0.880-0.94354.2765.4095.4090.0000.0000.0000.000
187W193ARG10.8910.96556.233-5.663-5.6630.0000.0000.0000.000
188W194HIS0-0.043-0.01454.337-0.011-0.0110.0000.0000.0000.000
189W195ASN0-0.058-0.05657.5820.0320.0320.0000.0000.0000.000
190W196SER0-0.0090.01756.833-0.022-0.0220.0000.0000.0000.000
191W197TYR00.0440.05250.8360.1730.1730.0000.0000.0000.000
192W198THR00.002-0.00851.296-0.063-0.0630.0000.0000.0000.000
193W200GLU-1-0.845-0.91546.9836.3746.3740.0000.0000.0000.000
194W201ALA00.0710.02043.8780.1630.1630.0000.0000.0000.000
195W202THR0-0.031-0.01541.965-0.108-0.1080.0000.0000.0000.000
196W203HIS00.0400.03738.598-0.011-0.0110.0000.0000.0000.000
197W204LYS10.9110.95138.280-7.943-7.9430.0000.0000.0000.000
198W205THR0-0.023-0.03042.199-0.079-0.0790.0000.0000.0000.000
199W206SER0-0.049-0.02844.356-0.209-0.2090.0000.0000.0000.000
200W207THR0-0.008-0.00546.1750.0930.0930.0000.0000.0000.000
201W208SER0-0.0170.00447.719-0.022-0.0220.0000.0000.0000.000
202W209PRO00.020-0.00547.2900.0250.0250.0000.0000.0000.000
203W210ILE0-0.0050.01947.273-0.155-0.1550.0000.0000.0000.000
204W211VAL0-0.004-0.00548.3780.1290.1290.0000.0000.0000.000
205W212LYS10.8690.93450.140-6.248-6.2480.0000.0000.0000.000
206W213SER0-0.007-0.02851.5070.0550.0550.0000.0000.0000.000
207W214PHE0-0.026-0.01752.147-0.049-0.0490.0000.0000.0000.000
208W215ASN00.0380.01756.0790.0920.0920.0000.0000.0000.000
209W216ARG10.9000.97557.049-5.554-5.5540.0000.0000.0000.000