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: YNNY2

Calculation Name: 3LCY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LCY

Chain ID: A

ChEMBL ID:

UniProt ID: Q8WZ42

Base Structure: X-ray

Registration Date: 2023-09-27

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 196
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1963010.309444
FMO2-HF: Nuclear repulsion 1884527.034072
FMO2-HF: Total energy -78483.275372
FMO2-MP2: Total energy -78709.295952


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(A:2:ALA)


Summations of interaction energy for fragment #1(A:2:ALA)
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.
-8.057-3.3680.649-2.573-2.764-0.003
Interaction energy analysis for fragmet #1(A:2:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : 0.007
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].
3A4SER0-0.029-0.0242.587-2.4860.5710.323-1.603-1.7770.008
4A5GLY00.0610.0312.831-3.123-1.4910.326-0.970-0.987-0.011
5A6GLU-1-0.923-0.9355.512-0.033-0.0330.0000.0000.0000.000
6A7ALA00.0490.0379.0060.0250.0250.0000.0000.0000.000
7A8PRO0-0.024-0.02011.7050.1090.1090.0000.0000.0000.000
8A9GLY00.0530.02714.2720.0150.0150.0000.0000.0000.000
9A10ILE0-0.021-0.01516.7260.0370.0370.0000.0000.0000.000
10A11ARG10.8940.95215.9520.1640.1640.0000.0000.0000.000
11A12LYS10.8080.89121.4430.1110.1110.0000.0000.0000.000
12A13GLU-1-0.743-0.85024.328-0.140-0.1400.0000.0000.0000.000
13A14MET0-0.059-0.00725.9910.0130.0130.0000.0000.0000.000
14A15LYS10.8400.89528.2250.1030.1030.0000.0000.0000.000
15A16ASP-1-0.796-0.88531.857-0.089-0.0890.0000.0000.0000.000
16A17VAL0-0.050-0.01533.4940.0050.0050.0000.0000.0000.000
17A18THR0-0.052-0.01236.4100.0000.0000.0000.0000.0000.000
18A19THR0-0.002-0.01539.1690.0030.0030.0000.0000.0000.000
19A20LYS10.8500.92541.2100.0230.0230.0000.0000.0000.000
20A21LEU00.0070.00043.4610.0000.0000.0000.0000.0000.000
21A22GLY00.0090.00143.4930.0030.0030.0000.0000.0000.000
22A23GLU-1-0.871-0.90442.154-0.021-0.0210.0000.0000.0000.000
23A24ALA0-0.025-0.01536.928-0.004-0.0040.0000.0000.0000.000
24A25ALA00.0120.01435.9940.0010.0010.0000.0000.0000.000
25A26GLN0-0.006-0.00431.927-0.003-0.0030.0000.0000.0000.000
26A27LEU00.0230.02130.350-0.001-0.0010.0000.0000.0000.000
27A28SER00.0300.01227.044-0.007-0.0070.0000.0000.0000.000
28A29CYS0-0.0090.00423.802-0.009-0.0090.0000.0000.0000.000
29A30GLN0-0.006-0.00121.1770.0060.0060.0000.0000.0000.000
30A31ILE00.0080.01516.660-0.006-0.0060.0000.0000.0000.000
31A32VAL00.007-0.00214.6490.0300.0300.0000.0000.0000.000
32A33GLY00.0640.04211.657-0.036-0.0360.0000.0000.0000.000
33A34ARG10.7620.9046.8030.3430.3430.0000.0000.0000.000
34A35PRO00.1600.0395.380-0.336-0.3360.0000.0000.0000.000
35A36LEU0-0.058-0.0057.784-0.027-0.0270.0000.0000.0000.000
36A37PRO0-0.035-0.03211.518-0.034-0.0340.0000.0000.0000.000
37A38ASP-1-0.911-0.93413.579-0.199-0.1990.0000.0000.0000.000
38A39ILE0-0.098-0.06615.846-0.018-0.0180.0000.0000.0000.000
39A40LYS10.8610.92619.4070.2230.2230.0000.0000.0000.000
40A41TRP00.0620.00822.255-0.008-0.0080.0000.0000.0000.000
41A42TYR00.0390.01722.3490.0120.0120.0000.0000.0000.000
42A43ARG10.8180.89128.0900.0910.0910.0000.0000.0000.000
43A44PHE00.004-0.00731.8640.0010.0010.0000.0000.0000.000
44A45GLY00.0210.01330.1430.0020.0020.0000.0000.0000.000
45A46LYS10.9390.97830.0450.0930.0930.0000.0000.0000.000
46A47GLU-1-0.777-0.86423.858-0.171-0.1710.0000.0000.0000.000
47A48LEU0-0.053-0.03127.8680.0120.0120.0000.0000.0000.000
48A49ILE00.0290.01427.297-0.004-0.0040.0000.0000.0000.000
49A50GLN00.0290.01226.6840.0080.0080.0000.0000.0000.000
50A51SER0-0.003-0.00129.3960.0060.0060.0000.0000.0000.000
51A52ARG10.9570.97133.0010.0190.0190.0000.0000.0000.000
52A53LYS10.8110.90335.7460.0560.0560.0000.0000.0000.000
53A54TYR00.0510.02131.213-0.002-0.0020.0000.0000.0000.000
54A55LYS10.9290.95830.6610.0290.0290.0000.0000.0000.000
55A56MET0-0.050-0.01925.395-0.009-0.0090.0000.0000.0000.000
56A57SER00.0040.01325.3010.0110.0110.0000.0000.0000.000
57A58SER00.0490.01219.035-0.022-0.0220.0000.0000.0000.000
58A59ASP-1-0.767-0.85220.510-0.018-0.0180.0000.0000.0000.000
59A60GLY00.0090.00716.5360.0230.0230.0000.0000.0000.000
60A61ARG10.8740.92516.2550.0020.0020.0000.0000.0000.000
61A62THR0-0.053-0.04618.650-0.031-0.0310.0000.0000.0000.000
62A63HIS10.8250.90217.8170.1640.1640.0000.0000.0000.000
63A64THR0-0.032-0.03023.119-0.002-0.0020.0000.0000.0000.000
64A65LEU00.0280.03626.7520.0040.0040.0000.0000.0000.000
65A66THR0-0.038-0.04128.8580.0060.0060.0000.0000.0000.000
66A67VAL00.0090.00832.3150.0000.0000.0000.0000.0000.000
67A68MET0-0.064-0.01835.0640.0040.0040.0000.0000.0000.000
68A69THR0-0.026-0.03338.324-0.001-0.0010.0000.0000.0000.000
69A70GLU-1-0.858-0.90640.599-0.039-0.0390.0000.0000.0000.000
70A71GLU-1-0.945-0.96642.155-0.050-0.0500.0000.0000.0000.000
71A72GLN00.038-0.00443.082-0.001-0.0010.0000.0000.0000.000
72A73GLU-1-0.816-0.91741.849-0.054-0.0540.0000.0000.0000.000
73A74ASP-1-0.795-0.90138.621-0.062-0.0620.0000.0000.0000.000
74A75GLU-1-0.823-0.85938.035-0.061-0.0610.0000.0000.0000.000
75A76GLY0-0.0170.00437.705-0.003-0.0030.0000.0000.0000.000
76A77VAL0-0.026-0.03031.8570.0010.0010.0000.0000.0000.000
77A78TYR0-0.032-0.02030.3690.0010.0010.0000.0000.0000.000
78A79THR00.0200.01925.4840.0050.0050.0000.0000.0000.000
79A80CYS0-0.063-0.00922.8920.0000.0000.0000.0000.0000.000
80A81ILE00.0320.00519.402-0.003-0.0030.0000.0000.0000.000
81A82ALA0-0.028-0.00916.6600.0130.0130.0000.0000.0000.000
82A83THR00.041-0.01414.086-0.017-0.0170.0000.0000.0000.000
83A84ASN0-0.018-0.0299.597-0.046-0.0460.0000.0000.0000.000
84A85GLU-1-0.897-0.9545.697-2.406-2.4060.0000.0000.0000.000
85A86VAL0-0.061-0.0106.864-0.006-0.0060.0000.0000.0000.000
86A87GLY00.0180.0059.4330.1430.1430.0000.0000.0000.000
87A88GLU-1-0.901-0.93713.098-0.426-0.4260.0000.0000.0000.000
88A89VAL0-0.074-0.02116.0570.0280.0280.0000.0000.0000.000
89A90GLU-1-0.876-0.94718.904-0.209-0.2090.0000.0000.0000.000
90A91THR00.003-0.01122.4430.0150.0150.0000.0000.0000.000
91A92SER00.004-0.02025.1620.0020.0020.0000.0000.0000.000
92A93SER0-0.060-0.03028.7270.0010.0010.0000.0000.0000.000
93A94LYS10.9450.96031.8720.0900.0900.0000.0000.0000.000
94A95LEU0-0.022-0.00335.2660.0030.0030.0000.0000.0000.000
95A96LEU00.002-0.01737.1660.0010.0010.0000.0000.0000.000
96A97LEU00.0460.03540.7740.0030.0030.0000.0000.0000.000
97A98GLN0-0.047-0.03443.2620.0030.0030.0000.0000.0000.000
98A99ALA00.024-0.00746.3890.0010.0010.0000.0000.0000.000
99A100THR00.0200.01249.520-0.001-0.0010.0000.0000.0000.000
100A101PRO0-0.065-0.02453.2430.0000.0000.0000.0000.0000.000
101A102GLN0-0.0040.00152.8280.0030.0030.0000.0000.0000.000
102A103PHE00.0070.00855.260-0.002-0.0020.0000.0000.0000.000
103A104HIS00.011-0.01551.314-0.001-0.0010.0000.0000.0000.000
104A105PRO00.0090.02453.8770.0010.0010.0000.0000.0000.000
105A106GLY00.0280.01154.293-0.001-0.0010.0000.0000.0000.000
106A107TYR0-0.031-0.01951.4070.0000.0000.0000.0000.0000.000
107A108PRO0-0.017-0.00257.8700.0000.0000.0000.0000.0000.000
108A109LEU00.0180.01661.0620.0000.0000.0000.0000.0000.000
109A110LYS10.9250.95663.6080.0230.0230.0000.0000.0000.000
110A111GLU-1-0.890-0.94267.131-0.018-0.0180.0000.0000.0000.000
111A112LYS10.8250.89870.2430.0190.0190.0000.0000.0000.000
112A113TYR0-0.015-0.00864.1050.0000.0000.0000.0000.0000.000
113A114TYR00.017-0.00770.6590.0010.0010.0000.0000.0000.000
114A115GLY00.0340.02271.611-0.001-0.0010.0000.0000.0000.000
115A116ALA0-0.0050.00372.9720.0010.0010.0000.0000.0000.000
116A117VAL00.0320.01475.020-0.001-0.0010.0000.0000.0000.000
117A118GLY0-0.0160.00476.6220.0000.0000.0000.0000.0000.000
118A119SER0-0.080-0.04071.912-0.001-0.0010.0000.0000.0000.000
119A120THR0-0.008-0.02566.8050.0000.0000.0000.0000.0000.000
120A121LEU0-0.015-0.00368.2510.0000.0000.0000.0000.0000.000
121A122ARG10.9120.92660.8810.0370.0370.0000.0000.0000.000
122A123LEU0-0.031-0.00363.9360.0010.0010.0000.0000.0000.000
123A124HIS00.0400.02455.1400.0000.0000.0000.0000.0000.000
124A125VAL0-0.0080.00158.7380.0010.0010.0000.0000.0000.000
125A126MET00.0480.04951.634-0.001-0.0010.0000.0000.0000.000
126A127TYR0-0.113-0.08152.1310.0020.0020.0000.0000.0000.000
127A128ILE00.0290.01549.596-0.002-0.0020.0000.0000.0000.000
128A129GLY0-0.006-0.01650.5060.0020.0020.0000.0000.0000.000
129A130ARG10.7610.88445.3690.0480.0480.0000.0000.0000.000
130A131PRO00.0850.01247.3150.0020.0020.0000.0000.0000.000
131A132VAL00.0080.00448.0500.0020.0020.0000.0000.0000.000
132A133PRO0-0.041-0.00450.4590.0000.0000.0000.0000.0000.000
133A134ALA0-0.0060.00154.063-0.001-0.0010.0000.0000.0000.000
134A135MET0-0.0030.00853.8560.0020.0020.0000.0000.0000.000
135A136THR0-0.074-0.04258.8930.0000.0000.0000.0000.0000.000
136A137TRP00.0580.02561.2230.0020.0020.0000.0000.0000.000
137A138PHE0-0.007-0.00365.4100.0000.0000.0000.0000.0000.000
138A139HIS10.8410.93769.0930.0230.0230.0000.0000.0000.000
139A140GLY00.0270.01472.1940.0000.0000.0000.0000.0000.000
140A141GLN00.0230.00973.2710.0000.0000.0000.0000.0000.000
141A142LYS10.8820.95071.4190.0260.0260.0000.0000.0000.000
142A143LEU00.0100.00965.6250.0000.0000.0000.0000.0000.000
143A144LEU0-0.047-0.03366.9420.0000.0000.0000.0000.0000.000
144A145GLN00.0250.00765.8010.0000.0000.0000.0000.0000.000
145A146ASN00.0310.01861.5260.0000.0000.0000.0000.0000.000
146A147SER0-0.011-0.01765.6720.0010.0010.0000.0000.0000.000
147A148GLU-1-0.801-0.88767.697-0.033-0.0330.0000.0000.0000.000
148A149ASN0-0.011-0.02269.426-0.001-0.0010.0000.0000.0000.000
149A150ILE0-0.0210.00366.7390.0000.0000.0000.0000.0000.000
150A151THR00.0250.01061.685-0.001-0.0010.0000.0000.0000.000
151A152ILE0-0.009-0.01960.3490.0010.0010.0000.0000.0000.000
152A153GLU-1-0.881-0.90255.052-0.048-0.0480.0000.0000.0000.000
153A154ASN0-0.0060.00055.5760.0020.0020.0000.0000.0000.000
154A155THR00.0740.03750.176-0.002-0.0020.0000.0000.0000.000
155A156GLU-1-0.878-0.92746.190-0.054-0.0540.0000.0000.0000.000
156A157HIS00.0380.02445.4550.0030.0030.0000.0000.0000.000
157A158TYR0-0.040-0.06050.8070.0020.0020.0000.0000.0000.000
158A159THR0-0.002-0.00654.5550.0000.0000.0000.0000.0000.000
159A160HIS0-0.016-0.01057.6610.0020.0020.0000.0000.0000.000
160A161LEU0-0.0130.01459.6130.0000.0000.0000.0000.0000.000
161A162VAL0-0.032-0.01963.0240.0010.0010.0000.0000.0000.000
162A163MET0-0.035-0.00765.1460.0000.0000.0000.0000.0000.000
163A164LYS10.8800.93568.2470.0330.0330.0000.0000.0000.000
164A165ASN00.000-0.00470.6630.0010.0010.0000.0000.0000.000
165A166VAL00.0120.02072.1940.0010.0010.0000.0000.0000.000
166A167GLN00.0450.01574.9810.0010.0010.0000.0000.0000.000
167A168ARG10.9300.95578.1450.0180.0180.0000.0000.0000.000
168A169LYS10.9610.97780.0350.0190.0190.0000.0000.0000.000
169A170THR00.001-0.00977.0740.0000.0000.0000.0000.0000.000
170A171HIS00.0510.03072.5000.0000.0000.0000.0000.0000.000
171A172ALA00.0320.05074.7320.0000.0000.0000.0000.0000.000
172A173GLY00.0110.00376.2830.0000.0000.0000.0000.0000.000
173A174LYS10.8760.93273.4280.0180.0180.0000.0000.0000.000
174A175TYR0-0.054-0.06368.7240.0000.0000.0000.0000.0000.000
175A176LYS10.8210.91866.4820.0230.0230.0000.0000.0000.000
176A177VAL00.0170.02161.397-0.001-0.0010.0000.0000.0000.000
177A178GLN00.013-0.01662.4250.0020.0020.0000.0000.0000.000
178A179LEU00.0290.02256.637-0.001-0.0010.0000.0000.0000.000
179A180SER00.010-0.02057.7810.0010.0010.0000.0000.0000.000
180A181ASN0-0.002-0.00451.6440.0000.0000.0000.0000.0000.000
181A182VAL00.0150.00350.7710.0010.0010.0000.0000.0000.000
182A183PHE0-0.023-0.00447.9180.0020.0020.0000.0000.0000.000
183A184GLY00.0370.02753.9360.0020.0020.0000.0000.0000.000
184A185THR00.0010.00257.263-0.002-0.0020.0000.0000.0000.000
185A186VAL0-0.0090.01258.4630.0010.0010.0000.0000.0000.000
186A187ASP-1-0.869-0.93861.115-0.023-0.0230.0000.0000.0000.000
187A188ALA00.0560.03863.6980.0010.0010.0000.0000.0000.000
188A189ILE0-0.014-0.02265.463-0.001-0.0010.0000.0000.0000.000
189A190LEU0-0.0020.00665.0930.0000.0000.0000.0000.0000.000
190A191ASP-1-0.810-0.89869.386-0.019-0.0190.0000.0000.0000.000
191A192VAL00.0110.01170.7790.0000.0000.0000.0000.0000.000
192A193GLU-1-0.831-0.90573.407-0.018-0.0180.0000.0000.0000.000
193A194ILE0-0.041-0.02874.636-0.001-0.0010.0000.0000.0000.000
194A195GLN0-0.003-0.00277.2220.0010.0010.0000.0000.0000.000
195A196ASP-1-0.859-0.93378.622-0.020-0.0200.0000.0000.0000.000
196A197LYS10.9040.96476.8830.0210.0210.0000.0000.0000.000