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: VKKR1

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 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 196
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1963150.541293
FMO2-HF: Nuclear repulsion 1884666.687655
FMO2-HF: Total energy -78483.853637
FMO2-MP2: Total energy -78710.140299


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.
-6.044-1.6890.521-2.454-2.422-0.004
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 : 0.044 / q_NPA : 0.023
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].
3A4SER0-0.039-0.0262.697-1.0092.1000.128-1.668-1.5690.005
4A5GLY00.0500.0282.778-2.824-1.5780.393-0.786-0.853-0.009
5A6GLU-1-0.906-0.9065.476-0.049-0.0490.0000.0000.0000.000
6A7ALA00.0650.0449.2180.0310.0310.0000.0000.0000.000
7A8PRO0-0.041-0.01911.8650.1090.1090.0000.0000.0000.000
8A9GLY00.0750.04114.4870.0250.0250.0000.0000.0000.000
9A10ILE0-0.039-0.02716.5690.0420.0420.0000.0000.0000.000
10A11ARG10.8950.94415.7030.1490.1490.0000.0000.0000.000
11A12LYS10.7970.88921.4820.0970.0970.0000.0000.0000.000
12A13GLU-1-0.766-0.86124.629-0.123-0.1230.0000.0000.0000.000
13A14MET0-0.0260.01125.9310.0130.0130.0000.0000.0000.000
14A15LYS10.8570.90728.3040.0910.0910.0000.0000.0000.000
15A16ASP-1-0.757-0.86632.030-0.078-0.0780.0000.0000.0000.000
16A17VAL0-0.034-0.00633.4330.0040.0040.0000.0000.0000.000
17A18THR0-0.044-0.02536.4860.0000.0000.0000.0000.0000.000
18A19THR0-0.003-0.01739.6910.0030.0030.0000.0000.0000.000
19A20LYS10.8670.93141.6690.0170.0170.0000.0000.0000.000
20A21LEU0-0.004-0.01043.7910.0000.0000.0000.0000.0000.000
21A22GLY00.0050.00243.8810.0020.0020.0000.0000.0000.000
22A23GLU-1-0.867-0.89742.184-0.014-0.0140.0000.0000.0000.000
23A24ALA0-0.008-0.00536.973-0.003-0.0030.0000.0000.0000.000
24A25ALA00.0140.02136.3580.0000.0000.0000.0000.0000.000
25A26GLN0-0.018-0.02031.854-0.001-0.0010.0000.0000.0000.000
26A27LEU00.0040.01530.5640.0000.0000.0000.0000.0000.000
27A28SER0-0.005-0.01627.411-0.005-0.0050.0000.0000.0000.000
28A29CYS0-0.030-0.00523.711-0.008-0.0080.0000.0000.0000.000
29A30GLN00.0460.01821.2550.0150.0150.0000.0000.0000.000
30A31ILE00.0240.01617.089-0.006-0.0060.0000.0000.0000.000
31A32VAL0-0.0070.00814.7270.0280.0280.0000.0000.0000.000
32A33GLY00.0560.03111.498-0.038-0.0380.0000.0000.0000.000
33A34ARG10.7650.8706.5300.3280.3280.0000.0000.0000.000
34A35PRO00.1180.0455.236-0.361-0.3610.0000.0000.0000.000
35A36LEU0-0.032-0.0157.798-0.063-0.0630.0000.0000.0000.000
36A37PRO0-0.060-0.02511.637-0.042-0.0420.0000.0000.0000.000
37A38ASP-1-0.861-0.90413.861-0.167-0.1670.0000.0000.0000.000
38A39ILE0-0.101-0.07015.815-0.022-0.0220.0000.0000.0000.000
39A40LYS10.8420.91319.4240.2000.2000.0000.0000.0000.000
40A41TRP00.0430.00522.348-0.009-0.0090.0000.0000.0000.000
41A42TYR00.0320.00722.5890.0090.0090.0000.0000.0000.000
42A43ARG10.8060.87728.3440.0810.0810.0000.0000.0000.000
43A44PHE0-0.008-0.01332.154-0.002-0.0020.0000.0000.0000.000
44A45GLY00.0250.01830.9320.0020.0020.0000.0000.0000.000
45A46LYS10.9300.97230.1300.0850.0850.0000.0000.0000.000
46A47GLU-1-0.766-0.86023.947-0.154-0.1540.0000.0000.0000.000
47A48LEU0-0.055-0.02528.0560.0110.0110.0000.0000.0000.000
48A49ILE00.0320.01427.226-0.004-0.0040.0000.0000.0000.000
49A50GLN00.0400.01126.6620.0060.0060.0000.0000.0000.000
50A51SER0-0.013-0.00529.2860.0060.0060.0000.0000.0000.000
51A52ARG10.9530.96333.0070.0120.0120.0000.0000.0000.000
52A53LYS10.8050.91435.9470.0470.0470.0000.0000.0000.000
53A54TYR00.0270.00831.607-0.002-0.0020.0000.0000.0000.000
54A55LYS10.9270.95530.6140.0200.0200.0000.0000.0000.000
55A56MET0-0.049-0.01825.485-0.008-0.0080.0000.0000.0000.000
56A57SER00.0090.02325.6650.0090.0090.0000.0000.0000.000
57A58SER00.0520.00119.438-0.027-0.0270.0000.0000.0000.000
58A59ASP-1-0.794-0.84420.5260.0030.0030.0000.0000.0000.000
59A60GLY00.0380.03016.8710.0290.0290.0000.0000.0000.000
60A61ARG10.8510.91116.300-0.024-0.0240.0000.0000.0000.000
61A62THR0-0.054-0.06618.449-0.033-0.0330.0000.0000.0000.000
62A63HIS10.8320.89117.7490.1350.1350.0000.0000.0000.000
63A64THR00.0030.00723.152-0.009-0.0090.0000.0000.0000.000
64A65LEU00.0260.04726.8610.0070.0070.0000.0000.0000.000
65A66THR0-0.041-0.04328.9810.0060.0060.0000.0000.0000.000
66A67VAL00.0180.02032.3420.0010.0010.0000.0000.0000.000
67A68MET0-0.041-0.01735.1650.0050.0050.0000.0000.0000.000
68A69THR0-0.013-0.01738.410-0.002-0.0020.0000.0000.0000.000
69A70GLU-1-0.889-0.93540.846-0.031-0.0310.0000.0000.0000.000
70A71GLU-1-0.927-0.95641.633-0.044-0.0440.0000.0000.0000.000
71A72GLN00.031-0.00243.3730.0000.0000.0000.0000.0000.000
72A73GLU-1-0.841-0.92842.118-0.049-0.0490.0000.0000.0000.000
73A74ASP-1-0.725-0.85538.711-0.052-0.0520.0000.0000.0000.000
74A75GLU-1-0.848-0.88838.163-0.054-0.0540.0000.0000.0000.000
75A76GLY00.0100.01438.235-0.004-0.0040.0000.0000.0000.000
76A77VAL0-0.019-0.02732.4010.0010.0010.0000.0000.0000.000
77A78TYR0-0.046-0.02730.5810.0020.0020.0000.0000.0000.000
78A79THR0-0.006-0.01025.7390.0050.0050.0000.0000.0000.000
79A80CYS0-0.084-0.03722.9030.0050.0050.0000.0000.0000.000
80A81ILE00.0450.02119.530-0.003-0.0030.0000.0000.0000.000
81A82ALA0-0.023-0.01317.2390.0220.0220.0000.0000.0000.000
82A83THR00.031-0.02714.329-0.017-0.0170.0000.0000.0000.000
83A84ASN0-0.033-0.0449.627-0.064-0.0640.0000.0000.0000.000
84A85GLU-1-0.895-0.9585.762-2.009-2.0090.0000.0000.0000.000
85A86VAL0-0.059-0.0146.837-0.079-0.0790.0000.0000.0000.000
86A87GLY00.0040.0009.4980.1360.1360.0000.0000.0000.000
87A88GLU-1-0.902-0.93013.232-0.385-0.3850.0000.0000.0000.000
88A89VAL0-0.063-0.01816.1270.0150.0150.0000.0000.0000.000
89A90GLU-1-0.812-0.89419.287-0.179-0.1790.0000.0000.0000.000
90A91THR0-0.040-0.01922.7820.0120.0120.0000.0000.0000.000
91A92SER00.0650.00325.3280.0000.0000.0000.0000.0000.000
92A93SER0-0.106-0.04828.8540.0030.0030.0000.0000.0000.000
93A94LYS10.8420.90932.2140.0810.0810.0000.0000.0000.000
94A95LEU00.0000.01135.6250.0030.0030.0000.0000.0000.000
95A96LEU00.002-0.00937.3790.0000.0000.0000.0000.0000.000
96A97LEU00.0310.03140.9600.0030.0030.0000.0000.0000.000
97A98GLN0-0.040-0.02343.3370.0020.0020.0000.0000.0000.000
98A99ALA00.023-0.00346.5020.0010.0010.0000.0000.0000.000
99A100THR00.0280.01849.666-0.001-0.0010.0000.0000.0000.000
100A101PRO0-0.050-0.02253.4800.0000.0000.0000.0000.0000.000
101A102GLN00.0050.01453.0780.0030.0030.0000.0000.0000.000
102A103PHE00.013-0.00255.569-0.002-0.0020.0000.0000.0000.000
103A104HIS0-0.003-0.00751.1700.0000.0000.0000.0000.0000.000
104A105PRO00.0140.01753.6600.0000.0000.0000.0000.0000.000
105A106GLY00.0290.01254.289-0.001-0.0010.0000.0000.0000.000
106A107TYR0-0.019-0.01251.6990.0000.0000.0000.0000.0000.000
107A108PRO0-0.028-0.01358.0870.0000.0000.0000.0000.0000.000
108A109LEU00.0170.01761.0150.0000.0000.0000.0000.0000.000
109A110LYS10.9200.95763.7880.0210.0210.0000.0000.0000.000
110A111GLU-1-0.869-0.93267.407-0.016-0.0160.0000.0000.0000.000
111A112LYS10.8000.89270.5440.0160.0160.0000.0000.0000.000
112A113TYR00.0060.00664.1830.0000.0000.0000.0000.0000.000
113A114TYR00.019-0.00370.7870.0010.0010.0000.0000.0000.000
114A115GLY00.0350.02371.421-0.001-0.0010.0000.0000.0000.000
115A116ALA0-0.0020.01473.2650.0010.0010.0000.0000.0000.000
116A117VAL00.0330.02075.495-0.001-0.0010.0000.0000.0000.000
117A118GLY0-0.0070.00676.9290.0000.0000.0000.0000.0000.000
118A119SER0-0.077-0.04772.129-0.001-0.0010.0000.0000.0000.000
119A120THR00.000-0.01367.2850.0000.0000.0000.0000.0000.000
120A121LEU0-0.0130.00868.5960.0000.0000.0000.0000.0000.000
121A122ARG10.8950.90860.8000.0340.0340.0000.0000.0000.000
122A123LEU0-0.016-0.00564.1180.0010.0010.0000.0000.0000.000
123A124HIS00.0230.02255.2210.0000.0000.0000.0000.0000.000
124A125VAL0-0.029-0.01859.1130.0010.0010.0000.0000.0000.000
125A126MET00.0460.04851.506-0.001-0.0010.0000.0000.0000.000
126A127TYR0-0.117-0.08151.9960.0020.0020.0000.0000.0000.000
127A128ILE00.0330.02349.571-0.002-0.0020.0000.0000.0000.000
128A129GLY00.007-0.00950.4020.0020.0020.0000.0000.0000.000
129A130ARG10.7300.84445.5930.0420.0420.0000.0000.0000.000
130A131PRO00.0850.02147.3680.0020.0020.0000.0000.0000.000
131A132VAL00.0060.00947.8750.0020.0020.0000.0000.0000.000
132A133PRO0-0.058-0.00550.3790.0000.0000.0000.0000.0000.000
133A134ALA00.0200.01554.080-0.001-0.0010.0000.0000.0000.000
134A135MET0-0.0110.00853.8010.0020.0020.0000.0000.0000.000
135A136THR0-0.065-0.03958.8830.0000.0000.0000.0000.0000.000
136A137TRP00.0560.01861.4620.0010.0010.0000.0000.0000.000
137A138PHE00.000-0.00165.5680.0000.0000.0000.0000.0000.000
138A139HIS10.8170.90969.3270.0210.0210.0000.0000.0000.000
139A140GLY00.0210.01572.5410.0000.0000.0000.0000.0000.000
140A141GLN00.0210.00373.2720.0000.0000.0000.0000.0000.000
141A142LYS10.8500.92971.4770.0230.0230.0000.0000.0000.000
142A143LEU00.0360.02666.1160.0000.0000.0000.0000.0000.000
143A144LEU0-0.036-0.02167.2600.0000.0000.0000.0000.0000.000
144A145GLN00.0260.00266.0520.0000.0000.0000.0000.0000.000
145A146ASN00.0400.02261.3510.0010.0010.0000.0000.0000.000
146A147SER0-0.025-0.01365.6150.0010.0010.0000.0000.0000.000
147A148GLU-1-0.779-0.87967.876-0.030-0.0300.0000.0000.0000.000
148A149ASN00.002-0.01569.8680.0000.0000.0000.0000.0000.000
149A150ILE0-0.0160.00367.2690.0010.0010.0000.0000.0000.000
150A151THR00.002-0.00462.175-0.001-0.0010.0000.0000.0000.000
151A152ILE0-0.002-0.01660.5210.0010.0010.0000.0000.0000.000
152A153GLU-1-0.872-0.89055.359-0.043-0.0430.0000.0000.0000.000
153A154ASN0-0.011-0.01355.9620.0020.0020.0000.0000.0000.000
154A155THR00.0560.03550.387-0.001-0.0010.0000.0000.0000.000
155A156GLU-1-0.847-0.91946.316-0.049-0.0490.0000.0000.0000.000
156A157HIS00.0640.04145.6930.0040.0040.0000.0000.0000.000
157A158TYR0-0.047-0.06650.9780.0020.0020.0000.0000.0000.000
158A159THR00.0200.00754.7240.0000.0000.0000.0000.0000.000
159A160HIS00.000-0.00257.8520.0020.0020.0000.0000.0000.000
160A161LEU00.0010.02559.993-0.001-0.0010.0000.0000.0000.000
161A162VAL0-0.020-0.01363.1230.0000.0000.0000.0000.0000.000
162A163MET0-0.037-0.00865.3910.0000.0000.0000.0000.0000.000
163A164LYS10.8480.91768.8220.0300.0300.0000.0000.0000.000
164A165ASN00.0150.00970.8550.0010.0010.0000.0000.0000.000
165A166VAL0-0.0120.00272.2350.0010.0010.0000.0000.0000.000
166A167GLN00.0410.00475.0390.0010.0010.0000.0000.0000.000
167A168ARG10.9030.93878.6410.0160.0160.0000.0000.0000.000
168A169LYS10.9590.97380.1490.0180.0180.0000.0000.0000.000
169A170THR00.0050.00177.1180.0000.0000.0000.0000.0000.000
170A171HIS00.0520.04272.7690.0000.0000.0000.0000.0000.000
171A172ALA00.0160.03674.8090.0000.0000.0000.0000.0000.000
172A173GLY00.0210.01076.6900.0000.0000.0000.0000.0000.000
173A174LYS10.8810.92573.7970.0160.0160.0000.0000.0000.000
174A175TYR0-0.048-0.04969.156-0.001-0.0010.0000.0000.0000.000
175A176LYS10.7990.90666.5910.0200.0200.0000.0000.0000.000
176A177VAL00.0220.02661.578-0.001-0.0010.0000.0000.0000.000
177A178GLN00.0450.00162.7440.0020.0020.0000.0000.0000.000
178A179LEU00.0340.02456.500-0.001-0.0010.0000.0000.0000.000
179A180SER0-0.041-0.02957.7320.0020.0020.0000.0000.0000.000
180A181ASN00.0010.00151.6720.0000.0000.0000.0000.0000.000
181A182VAL00.0220.00150.5750.0010.0010.0000.0000.0000.000
182A183PHE0-0.0180.00548.0570.0010.0010.0000.0000.0000.000
183A184GLY00.0130.00954.0250.0020.0020.0000.0000.0000.000
184A185THR0-0.050-0.03757.470-0.001-0.0010.0000.0000.0000.000
185A186VAL00.0190.01658.7550.0010.0010.0000.0000.0000.000
186A187ASP-1-0.860-0.93161.393-0.020-0.0200.0000.0000.0000.000
187A188ALA00.0580.03863.8960.0010.0010.0000.0000.0000.000
188A189ILE0-0.022-0.01465.628-0.001-0.0010.0000.0000.0000.000
189A190LEU00.0120.01765.4550.0000.0000.0000.0000.0000.000
190A191ASP-1-0.818-0.91769.799-0.017-0.0170.0000.0000.0000.000
191A192VAL00.0190.01770.9150.0000.0000.0000.0000.0000.000
192A193GLU-1-0.825-0.90073.494-0.016-0.0160.0000.0000.0000.000
193A194ILE0-0.033-0.02074.3910.0000.0000.0000.0000.0000.000
194A195GLN00.009-0.00577.2810.0010.0010.0000.0000.0000.000
195A196ASP-1-0.871-0.94578.878-0.018-0.0180.0000.0000.0000.000
196A197LYS10.9070.96876.9350.0190.0190.0000.0000.0000.000