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: K9Q43

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 OptAll
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 -2122641.106998
FMO2-HF: Nuclear repulsion 2039715.427152
FMO2-HF: Total energy -82925.679845
FMO2-MP2: Total energy -83162.796043


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.
-37.766-35.0361.468-1.704-2.4920.008
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 : -0.909 / q_NPA : -0.967
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].
3W3VAL00.0280.0123.867-4.523-2.990-0.010-0.643-0.8790.003
4W4MET00.0150.0065.734-2.544-2.5440.0000.0000.0000.000
5W5THR0-0.041-0.0299.191-1.738-1.7380.0000.0000.0000.000
6W6GLN00.0160.00411.375-0.013-0.0130.0000.0000.0000.000
7W7SER0-0.0200.00414.512-0.193-0.1930.0000.0000.0000.000
8W8PRO00.0520.03018.036-0.197-0.1970.0000.0000.0000.000
9W9ALA00.0560.03518.2540.1850.1850.0000.0000.0000.000
10W10ILE0-0.011-0.01319.291-0.047-0.0470.0000.0000.0000.000
11W11MET0-0.0220.00522.9170.0180.0180.0000.0000.0000.000
12W12SER00.002-0.00525.969-0.037-0.0370.0000.0000.0000.000
13W13ALA00.0070.00529.417-0.057-0.0570.0000.0000.0000.000
14W14SER0-0.020-0.02031.662-0.049-0.0490.0000.0000.0000.000
15W15PRO00.013-0.00634.8800.1140.1140.0000.0000.0000.000
16W16GLY00.0130.01336.350-0.176-0.1760.0000.0000.0000.000
17W17GLU-1-0.802-0.86033.1518.7078.7070.0000.0000.0000.000
18W18LYS10.9720.99030.793-8.850-8.8500.0000.0000.0000.000
19W19VAL00.0080.00326.2640.1080.1080.0000.0000.0000.000
20W20THR0-0.055-0.04424.253-0.051-0.0510.0000.0000.0000.000
21W21MET0-0.0320.01920.5910.1770.1770.0000.0000.0000.000
22W22THR0-0.023-0.02218.7970.0450.0450.0000.0000.0000.000
23W23CYS0-0.035-0.01713.3560.4840.4840.0000.0000.0000.000
24W24SER00.0180.03312.658-0.414-0.4140.0000.0000.0000.000
25W25ALA00.0440.0029.8210.7070.7070.0000.0000.0000.000
26W26SER0-0.040-0.0116.478-0.116-0.1160.0000.0000.0000.000
27W27SER00.0320.0147.9881.1321.1320.0000.0000.0000.000
28W28SER0-0.005-0.0059.899-0.687-0.6870.0000.0000.0000.000
29W29VAL0-0.009-0.0049.2351.0431.0430.0000.0000.0000.000
30W30ASN0-0.039-0.01411.963-1.092-1.0920.0000.0000.0000.000
31W36TYR00.0060.00714.5770.0310.0310.0000.0000.0000.000
32W37MET00.0030.01812.0281.3251.3250.0000.0000.0000.000
33W38HIS0-0.017-0.00214.106-1.760-1.7600.0000.0000.0000.000
34W39TRP00.0460.00415.9090.8450.8450.0000.0000.0000.000
35W40TYR0-0.036-0.03415.069-1.213-1.2130.0000.0000.0000.000
36W41GLN00.0030.00619.6330.0250.0250.0000.0000.0000.000
37W42GLN0-0.011-0.01219.8800.2960.2960.0000.0000.0000.000
38W43LYS10.8490.91622.533-10.071-10.0710.0000.0000.0000.000
39W44SER00.0640.03125.830-0.016-0.0160.0000.0000.0000.000
40W45GLY00.0120.01122.627-0.200-0.2000.0000.0000.0000.000
41W46THR0-0.058-0.02823.3350.2190.2190.0000.0000.0000.000
42W47SER00.011-0.00722.5530.3930.3930.0000.0000.0000.000
43W48PRO00.0040.00318.404-0.477-0.4770.0000.0000.0000.000
44W49LYS10.9450.98621.316-10.908-10.9080.0000.0000.0000.000
45W50ARG10.9540.96621.029-10.753-10.7530.0000.0000.0000.000
46W51TRP0-0.011-0.02421.552-0.543-0.5430.0000.0000.0000.000
47W52ILE00.0100.00820.690-0.472-0.4720.0000.0000.0000.000
48W53TYR0-0.015-0.00419.4690.6490.6490.0000.0000.0000.000
49W54ASP-1-0.790-0.89918.81112.80512.8050.0000.0000.0000.000
50W55THR0-0.0300.00218.196-0.270-0.2700.0000.0000.0000.000
51W56SER0-0.038-0.02519.940-0.121-0.1210.0000.0000.0000.000
52W57LYS10.8300.92423.202-12.221-12.2210.0000.0000.0000.000
53W58LEU00.0550.02524.1880.4450.4450.0000.0000.0000.000
54W59ALA0-0.0100.00024.464-0.097-0.0970.0000.0000.0000.000
55W60SER00.019-0.01726.401-0.124-0.1240.0000.0000.0000.000
56W61GLY0-0.0130.00529.556-0.284-0.2840.0000.0000.0000.000
57W62VAL0-0.0530.00326.366-0.098-0.0980.0000.0000.0000.000
58W63PRO00.0280.02429.801-0.160-0.1600.0000.0000.0000.000
59W64ALA00.026-0.01331.2150.2270.2270.0000.0000.0000.000
60W65ARG10.7750.86931.621-8.887-8.8870.0000.0000.0000.000
61W66PHE0-0.0030.00725.7980.1300.1300.0000.0000.0000.000
62W67SER0-0.0130.00326.969-0.146-0.1460.0000.0000.0000.000
63W68GLY00.0150.00922.9670.3090.3090.0000.0000.0000.000
64W69SER0-0.009-0.00421.934-0.424-0.4240.0000.0000.0000.000
65W70GLY00.0580.00919.6040.5540.5540.0000.0000.0000.000
66W71SER0-0.025-0.01418.476-0.407-0.4070.0000.0000.0000.000
67W72GLY00.0690.03715.7480.0970.0970.0000.0000.0000.000
68W73THR00.0060.00512.6160.7260.7260.0000.0000.0000.000
69W74SER00.0010.00914.5110.3550.3550.0000.0000.0000.000
70W75TYR0-0.035-0.02814.552-1.149-1.1490.0000.0000.0000.000
71W76SER00.002-0.01317.9600.2790.2790.0000.0000.0000.000
72W77LEU0-0.0420.00420.554-0.250-0.2500.0000.0000.0000.000
73W78THR0-0.044-0.03422.544-0.150-0.1500.0000.0000.0000.000
74W79ILE00.0280.00826.186-0.028-0.0280.0000.0000.0000.000
75W80SER0-0.060-0.04429.252-0.183-0.1830.0000.0000.0000.000
76W81SER0-0.022-0.02432.807-0.112-0.1120.0000.0000.0000.000
77W82MET00.0100.02130.1130.3060.3060.0000.0000.0000.000
78W83GLU-1-0.849-0.90832.5537.7427.7420.0000.0000.0000.000
79W84ALA00.0250.00832.7200.2570.2570.0000.0000.0000.000
80W85GLU-1-0.862-0.94232.1918.7598.7590.0000.0000.0000.000
81W86ASP-1-0.746-0.82928.6279.8159.8150.0000.0000.0000.000
82W87ALA00.0180.03427.3500.4450.4450.0000.0000.0000.000
83W88ALA0-0.021-0.01224.368-0.120-0.1200.0000.0000.0000.000
84W89THR00.0090.01218.829-0.166-0.1660.0000.0000.0000.000
85W90TYR0-0.020-0.02019.877-0.009-0.0090.0000.0000.0000.000
86W91TYR0-0.020-0.01814.4820.3890.3890.0000.0000.0000.000
87W93GLN00.0040.00610.913-0.177-0.1770.0000.0000.0000.000
88W94GLN00.0680.0105.989-3.378-3.3780.0000.0000.0000.000
89W95TRP0-0.032-0.0359.4961.3851.3850.0000.0000.0000.000
90W96SER0-0.0070.0099.898-0.833-0.8330.0000.0000.0000.000
91W97TYR0-0.009-0.0016.026-0.496-0.4960.0000.0000.0000.000
92W98ASN0-0.0050.0055.980-2.779-2.7790.0000.0000.0000.000
93W99PRO00.0260.0042.4350.9321.7641.468-0.932-1.3680.005
94W100PRO00.0100.0255.0712.0322.077-0.001-0.002-0.0410.000
95W101THR0-0.045-0.0283.9050.5800.9000.011-0.127-0.2040.000
96W102PHE00.036-0.0027.107-3.089-3.0890.0000.0000.0000.000
97W103GLY00.0060.0058.7631.7491.7490.0000.0000.0000.000
98W104GLY0-0.028-0.02611.292-0.231-0.2310.0000.0000.0000.000
99W105GLY0-0.0090.00212.915-0.776-0.7760.0000.0000.0000.000
100W106THR0-0.032-0.02816.2250.3010.3010.0000.0000.0000.000
101W107LYS10.7640.86419.427-11.505-11.5050.0000.0000.0000.000
102W108LEU00.0120.00222.452-0.115-0.1150.0000.0000.0000.000
103W109GLU-1-0.778-0.84625.63310.37410.3740.0000.0000.0000.000
104W110ILE00.0330.01329.010-0.058-0.0580.0000.0000.0000.000
105W111LYS10.7860.88832.633-8.804-8.8040.0000.0000.0000.000
106W112ARG10.8350.89234.615-7.671-7.6710.0000.0000.0000.000
107W113ALA00.0100.00638.2350.0500.0500.0000.0000.0000.000
108W114ASP-1-0.792-0.88839.8927.6637.6630.0000.0000.0000.000
109W115ALA0-0.031-0.01141.399-0.173-0.1730.0000.0000.0000.000
110W116ALA00.0420.01942.1690.1570.1570.0000.0000.0000.000
111W117PRO0-0.010-0.00741.848-0.049-0.0490.0000.0000.0000.000
112W118THR00.0150.01944.090-0.210-0.2100.0000.0000.0000.000
113W119VAL0-0.044-0.02844.9980.0440.0440.0000.0000.0000.000
114W120SER0-0.0160.00046.357-0.241-0.2410.0000.0000.0000.000
115W121ILE0-0.013-0.02146.8990.1600.1600.0000.0000.0000.000
116W122PHE00.007-0.00446.738-0.112-0.1120.0000.0000.0000.000
117W123PRO00.0080.01349.4700.0830.0830.0000.0000.0000.000
118W124PRO0-0.0210.00149.5910.0910.0910.0000.0000.0000.000
119W125SER00.0170.01349.816-0.093-0.0930.0000.0000.0000.000
120W126SER00.027-0.01051.915-0.009-0.0090.0000.0000.0000.000
121W127GLU-1-0.828-0.91050.9005.9625.9620.0000.0000.0000.000
122W128GLN00.0030.02447.8190.1270.1270.0000.0000.0000.000
123W129LEU00.0360.01651.158-0.005-0.0050.0000.0000.0000.000
124W130THR0-0.050-0.02754.468-0.075-0.0750.0000.0000.0000.000
125W131SER0-0.084-0.06350.8730.0230.0230.0000.0000.0000.000
126W132GLY00.0200.01551.5370.0470.0470.0000.0000.0000.000
127W133GLY0-0.022-0.00348.4990.0490.0490.0000.0000.0000.000
128W134ALA00.012-0.00848.468-0.146-0.1460.0000.0000.0000.000
129W135SER0-0.033-0.02844.3920.0840.0840.0000.0000.0000.000
130W136VAL0-0.0030.00546.662-0.075-0.0750.0000.0000.0000.000
131W137VAL00.0190.00443.1640.1790.1790.0000.0000.0000.000
132W138CYS0-0.102-0.04943.722-0.052-0.0520.0000.0000.0000.000
133W139PHE0-0.025-0.00341.8860.2110.2110.0000.0000.0000.000
134W140LEU00.0270.00540.554-0.184-0.1840.0000.0000.0000.000
135W141ASN00.0380.00140.5090.3360.3360.0000.0000.0000.000
136W142ASN0-0.028-0.02540.718-0.143-0.1430.0000.0000.0000.000
137W143PHE0-0.0180.01936.382-0.118-0.1180.0000.0000.0000.000
138W144TYR00.0460.00733.4340.2120.2120.0000.0000.0000.000
139W145PRO00.0220.01234.557-0.204-0.2040.0000.0000.0000.000
140W146LYS10.9050.91827.951-10.464-10.4640.0000.0000.0000.000
141W147ASP-1-0.913-0.95132.2359.3089.3080.0000.0000.0000.000
142W148ILE0-0.024-0.00334.721-0.305-0.3050.0000.0000.0000.000
143W149ASN0-0.010-0.01836.4310.1480.1480.0000.0000.0000.000
144W150VAL00.0320.04238.842-0.177-0.1770.0000.0000.0000.000
145W151LYS10.8780.92741.011-7.467-7.4670.0000.0000.0000.000
146W152TRP00.023-0.00637.531-0.072-0.0720.0000.0000.0000.000
147W153LYS10.8490.93543.200-7.174-7.1740.0000.0000.0000.000
148W154LYS10.8700.91846.344-6.416-6.4160.0000.0000.0000.000
149W155ILE0-0.005-0.00149.7640.0060.0060.0000.0000.0000.000
150W156ASP-1-0.755-0.86752.3755.6045.6040.0000.0000.0000.000
151W157GLY0-0.0040.00454.230-0.073-0.0730.0000.0000.0000.000
152W158SER00.0010.00751.6030.0420.0420.0000.0000.0000.000
153W159GLU-1-0.910-0.96346.4746.6466.6460.0000.0000.0000.000
154W160ARG10.8340.91244.255-7.030-7.0300.0000.0000.0000.000
155W161GLN00.0030.00140.1700.0280.0280.0000.0000.0000.000
156W162ASN00.0120.00639.7880.0260.0260.0000.0000.0000.000
157W163GLY00.1220.05640.625-0.202-0.2020.0000.0000.0000.000
158W164VAL0-0.058-0.01739.065-0.054-0.0540.0000.0000.0000.000
159W165LEU0-0.0110.00436.2040.2460.2460.0000.0000.0000.000
160W166ASN00.0160.00734.989-0.395-0.3950.0000.0000.0000.000
161W167SER0-0.020-0.00533.2570.2480.2480.0000.0000.0000.000
162W168TRP00.017-0.00431.256-0.259-0.2590.0000.0000.0000.000
163W169THR0-0.0090.00232.1330.1290.1290.0000.0000.0000.000
164W170ASP-1-0.895-0.93227.54210.73510.7350.0000.0000.0000.000
165W171GLN00.016-0.03330.2140.2880.2880.0000.0000.0000.000
166W172ASP-1-0.801-0.88332.5647.9637.9630.0000.0000.0000.000
167W173SER0-0.042-0.03334.3900.0160.0160.0000.0000.0000.000
168W174LYS10.8950.94035.724-7.258-7.2580.0000.0000.0000.000
169W175ASP-1-0.778-0.84239.2587.3567.3560.0000.0000.0000.000
170W176SER0-0.0220.00435.392-0.052-0.0520.0000.0000.0000.000
171W177THR0-0.089-0.05236.1000.1460.1460.0000.0000.0000.000
172W178TYR0-0.020-0.02830.8140.1410.1410.0000.0000.0000.000
173W179SER00.010-0.00235.886-0.354-0.3540.0000.0000.0000.000
174W180MET0-0.043-0.00236.0340.1950.1950.0000.0000.0000.000
175W181SER00.0010.01537.265-0.326-0.3260.0000.0000.0000.000
176W182SER00.0560.00437.9590.1550.1550.0000.0000.0000.000
177W183THR00.0040.01139.935-0.306-0.3060.0000.0000.0000.000
178W184LEU0-0.014-0.00641.4590.1740.1740.0000.0000.0000.000
179W185THR0-0.0150.00742.673-0.179-0.1790.0000.0000.0000.000
180W186LEU0-0.030-0.01144.6310.1100.1100.0000.0000.0000.000
181W187THR00.015-0.02147.3760.0610.0610.0000.0000.0000.000
182W188LYS10.7840.88750.198-5.604-5.6040.0000.0000.0000.000
183W189ASP-1-0.804-0.89553.1985.6385.6380.0000.0000.0000.000
184W190GLU-1-0.831-0.90450.5006.0516.0510.0000.0000.0000.000
185W191TYR0-0.042-0.02252.204-0.069-0.0690.0000.0000.0000.000
186W192GLU-1-0.817-0.90453.8885.4045.4040.0000.0000.0000.000
187W193ARG10.7980.89955.940-5.723-5.7230.0000.0000.0000.000
188W194HIS0-0.039-0.00953.5340.0060.0060.0000.0000.0000.000
189W195ASN0-0.036-0.04256.8030.0230.0230.0000.0000.0000.000
190W196SER0-0.028-0.00656.652-0.024-0.0240.0000.0000.0000.000
191W197TYR00.0360.02350.3740.1660.1660.0000.0000.0000.000
192W198THR00.0020.00850.620-0.073-0.0730.0000.0000.0000.000
193W200GLU-1-0.804-0.89345.9386.3366.3360.0000.0000.0000.000
194W201ALA00.0520.01043.2320.1710.1710.0000.0000.0000.000
195W202THR0-0.058-0.01141.719-0.097-0.0970.0000.0000.0000.000
196W203HIS00.0690.02738.3350.0150.0150.0000.0000.0000.000
197W204LYS10.8580.92137.823-7.886-7.8860.0000.0000.0000.000
198W205THR0-0.012-0.02241.492-0.084-0.0840.0000.0000.0000.000
199W206SER0-0.070-0.05244.031-0.209-0.2090.0000.0000.0000.000
200W207THR0-0.0040.00045.9120.0830.0830.0000.0000.0000.000
201W208SER00.0130.02447.486-0.001-0.0010.0000.0000.0000.000
202W209PRO00.0000.00346.5480.0480.0480.0000.0000.0000.000
203W210ILE00.0190.02246.532-0.156-0.1560.0000.0000.0000.000
204W211VAL00.002-0.00847.7940.1290.1290.0000.0000.0000.000
205W212LYS10.8500.92049.706-6.233-6.2330.0000.0000.0000.000
206W213SER0-0.011-0.02951.1230.0540.0540.0000.0000.0000.000
207W214PHE0-0.010-0.00551.725-0.050-0.0500.0000.0000.0000.000
208W215ASN00.0580.03655.8190.0690.0690.0000.0000.0000.000
209W216ARG10.8620.94956.798-5.528-5.5280.0000.0000.0000.000