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: 5NN2Z

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 OptH
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 -1962434.867458
FMO2-HF: Nuclear repulsion 1883953.392056
FMO2-HF: Total energy -78481.475402
FMO2-MP2: Total energy -78707.46167


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.
-8.885-4.1771.208-2.892-3.025-0.008
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 : 0.016 / 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].
3A4SER0-0.034-0.0272.346-2.2570.6400.747-1.748-1.8960.006
4A5GLY00.0560.0282.747-3.622-1.8110.461-1.144-1.129-0.014
5A6GLU-1-1.001-1.0045.445-0.191-0.1910.0000.0000.0000.000
6A7ALA00.0370.0318.9510.0280.0280.0000.0000.0000.000
7A8PRO0-0.038-0.02211.7510.1060.1060.0000.0000.0000.000
8A9GLY00.0590.02814.2960.0200.0200.0000.0000.0000.000
9A10ILE0-0.018-0.01216.6990.0390.0390.0000.0000.0000.000
10A11ARG10.9010.95016.6870.1970.1970.0000.0000.0000.000
11A12LYS10.8780.95121.4570.1310.1310.0000.0000.0000.000
12A13GLU-1-0.833-0.91724.320-0.168-0.1680.0000.0000.0000.000
13A14MET0-0.080-0.03425.9950.0150.0150.0000.0000.0000.000
14A15LYS10.9170.95828.2320.1170.1170.0000.0000.0000.000
15A16ASP-1-0.816-0.90431.861-0.100-0.1000.0000.0000.0000.000
16A17VAL0-0.052-0.01933.5250.0050.0050.0000.0000.0000.000
17A18THR0-0.051-0.00636.4100.0010.0010.0000.0000.0000.000
18A19THR0-0.006-0.02639.1530.0030.0030.0000.0000.0000.000
19A20LYS10.9660.99641.2050.0270.0270.0000.0000.0000.000
20A21LEU0-0.002-0.00343.4580.0000.0000.0000.0000.0000.000
21A22GLY0-0.001-0.00843.5060.0030.0030.0000.0000.0000.000
22A23GLU-1-0.961-0.96742.092-0.025-0.0250.0000.0000.0000.000
23A24ALA0-0.019-0.01136.879-0.004-0.0040.0000.0000.0000.000
24A25ALA00.0210.01735.8080.0000.0000.0000.0000.0000.000
25A26GLN0-0.028-0.00531.956-0.002-0.0020.0000.0000.0000.000
26A27LEU00.0210.02230.147-0.002-0.0020.0000.0000.0000.000
27A28SER00.011-0.00126.733-0.006-0.0060.0000.0000.0000.000
28A29CYS0-0.046-0.02723.566-0.010-0.0100.0000.0000.0000.000
29A30GLN0-0.029-0.01121.2910.0010.0010.0000.0000.0000.000
30A31ILE00.0300.01916.518-0.007-0.0070.0000.0000.0000.000
31A32VAL0-0.019-0.01514.6500.0330.0330.0000.0000.0000.000
32A33GLY00.0700.04311.663-0.034-0.0340.0000.0000.0000.000
33A34ARG10.8480.9726.8830.4340.4340.0000.0000.0000.000
34A35PRO00.1670.0405.275-0.369-0.3690.0000.0000.0000.000
35A36LEU0-0.056-0.0147.763-0.015-0.0150.0000.0000.0000.000
36A37PRO0-0.015-0.01511.490-0.034-0.0340.0000.0000.0000.000
37A38ASP-1-0.922-0.94813.588-0.231-0.2310.0000.0000.0000.000
38A39ILE0-0.078-0.05215.868-0.020-0.0200.0000.0000.0000.000
39A40LYS10.9140.97219.3740.2430.2430.0000.0000.0000.000
40A41TRP00.0610.01622.294-0.010-0.0100.0000.0000.0000.000
41A42TYR00.0380.02022.2970.0130.0130.0000.0000.0000.000
42A43ARG10.8180.88728.1420.0980.0980.0000.0000.0000.000
43A44PHE00.000-0.00731.9170.0020.0020.0000.0000.0000.000
44A45GLY00.0210.01330.2200.0030.0030.0000.0000.0000.000
45A46LYS10.9350.97430.1250.0960.0960.0000.0000.0000.000
46A47GLU-1-0.834-0.92224.053-0.169-0.1690.0000.0000.0000.000
47A48LEU0-0.068-0.03627.9270.0130.0130.0000.0000.0000.000
48A49ILE00.0420.02227.247-0.004-0.0040.0000.0000.0000.000
49A50GLN00.008-0.00326.3530.0110.0110.0000.0000.0000.000
50A51SER00.0130.00429.4110.0070.0070.0000.0000.0000.000
51A52ARG10.9530.97233.0110.0210.0210.0000.0000.0000.000
52A53LYS10.8420.91435.7460.0610.0610.0000.0000.0000.000
53A54TYR00.0660.02831.161-0.002-0.0020.0000.0000.0000.000
54A55LYS10.9090.93830.6650.0330.0330.0000.0000.0000.000
55A56MET0-0.038-0.01625.587-0.010-0.0100.0000.0000.0000.000
56A57SER0-0.0070.01325.2510.0090.0090.0000.0000.0000.000
57A58SER00.0500.01219.188-0.021-0.0210.0000.0000.0000.000
58A59ASP-1-0.786-0.85420.456-0.038-0.0380.0000.0000.0000.000
59A60GLY00.0080.00616.4840.0210.0210.0000.0000.0000.000
60A61ARG10.8880.93016.2160.0320.0320.0000.0000.0000.000
61A62THR0-0.022-0.02318.605-0.031-0.0310.0000.0000.0000.000
62A63HIS10.8260.89518.0680.1910.1910.0000.0000.0000.000
63A64THR00.013-0.00423.102-0.009-0.0090.0000.0000.0000.000
64A65LEU00.0200.03226.7370.0050.0050.0000.0000.0000.000
65A66THR0-0.037-0.03528.8570.0060.0060.0000.0000.0000.000
66A67VAL00.0070.00232.3090.0000.0000.0000.0000.0000.000
67A68MET0-0.064-0.01235.0680.0030.0030.0000.0000.0000.000
68A69THR0-0.028-0.03538.3250.0000.0000.0000.0000.0000.000
69A70GLU-1-0.847-0.89540.608-0.043-0.0430.0000.0000.0000.000
70A71GLU-1-0.927-0.96142.664-0.053-0.0530.0000.0000.0000.000
71A72GLN00.033-0.00943.107-0.001-0.0010.0000.0000.0000.000
72A73GLU-1-0.858-0.92441.885-0.059-0.0590.0000.0000.0000.000
73A74ASP-1-0.805-0.89438.786-0.066-0.0660.0000.0000.0000.000
74A75GLU-1-0.822-0.85738.063-0.068-0.0680.0000.0000.0000.000
75A76GLY0-0.0110.00537.742-0.003-0.0030.0000.0000.0000.000
76A77VAL0-0.024-0.03031.9570.0010.0010.0000.0000.0000.000
77A78TYR0-0.042-0.02630.3740.0020.0020.0000.0000.0000.000
78A79THR00.009-0.01425.5580.0030.0030.0000.0000.0000.000
79A80CYS0-0.070-0.02422.6630.0000.0000.0000.0000.0000.000
80A81ILE00.0350.00719.441-0.004-0.0040.0000.0000.0000.000
81A82ALA0-0.036-0.01316.6120.0140.0140.0000.0000.0000.000
82A83THR00.0440.01214.137-0.016-0.0160.0000.0000.0000.000
83A84ASN0-0.020-0.0119.6210.0010.0010.0000.0000.0000.000
84A85GLU-1-0.900-0.9665.356-2.964-2.9640.0000.0000.0000.000
85A86VAL0-0.067-0.0077.158-0.002-0.0020.0000.0000.0000.000
86A87GLY00.0190.0039.5300.1480.1480.0000.0000.0000.000
87A88GLU-1-0.922-0.96913.187-0.440-0.4400.0000.0000.0000.000
88A89VAL0-0.059-0.00916.1290.0270.0270.0000.0000.0000.000
89A90GLU-1-0.884-0.95718.959-0.228-0.2280.0000.0000.0000.000
90A91THR00.004-0.00522.4950.0150.0150.0000.0000.0000.000
91A92SER00.0160.01625.1980.0070.0070.0000.0000.0000.000
92A93SER0-0.0320.00328.7630.0000.0000.0000.0000.0000.000
93A94LYS10.9590.96631.8980.1010.1010.0000.0000.0000.000
94A95LEU0-0.0180.00235.2920.0030.0030.0000.0000.0000.000
95A96LEU0-0.011-0.02337.1840.0010.0010.0000.0000.0000.000
96A97LEU00.0450.03140.7890.0030.0030.0000.0000.0000.000
97A98GLN0-0.044-0.03243.2740.0040.0040.0000.0000.0000.000
98A99ALA00.026-0.00646.3940.0020.0020.0000.0000.0000.000
99A100THR00.0180.00549.527-0.001-0.0010.0000.0000.0000.000
100A101PRO0-0.074-0.02153.2490.0000.0000.0000.0000.0000.000
101A102GLN00.0080.00252.9040.0030.0030.0000.0000.0000.000
102A103PHE0-0.0090.00255.283-0.002-0.0020.0000.0000.0000.000
103A104HIS00.024-0.00551.444-0.001-0.0010.0000.0000.0000.000
104A105PRO00.0180.02753.8500.0010.0010.0000.0000.0000.000
105A106GLY00.0200.00554.320-0.001-0.0010.0000.0000.0000.000
106A107TYR0-0.042-0.02551.3900.0000.0000.0000.0000.0000.000
107A108PRO0-0.022-0.00557.9070.0000.0000.0000.0000.0000.000
108A109LEU00.0250.02161.0950.0000.0000.0000.0000.0000.000
109A110LYS10.9120.94763.6430.0240.0240.0000.0000.0000.000
110A111GLU-1-0.907-0.94867.168-0.020-0.0200.0000.0000.0000.000
111A112LYS10.9030.95470.2770.0200.0200.0000.0000.0000.000
112A113TYR0-0.004-0.00364.3510.0000.0000.0000.0000.0000.000
113A114TYR00.017-0.00470.7070.0010.0010.0000.0000.0000.000
114A115GLY00.0260.02171.669-0.001-0.0010.0000.0000.0000.000
115A116ALA00.0060.00673.0320.0010.0010.0000.0000.0000.000
116A117VAL0-0.0140.04075.086-0.001-0.0010.0000.0000.0000.000
117A118GLY0-0.0190.00776.6930.0000.0000.0000.0000.0000.000
118A119SER0-0.065-0.03571.897-0.001-0.0010.0000.0000.0000.000
119A120THR0-0.010-0.02766.8170.0000.0000.0000.0000.0000.000
120A121LEU0-0.022-0.00368.0710.0000.0000.0000.0000.0000.000
121A122ARG10.9260.95260.8880.0390.0390.0000.0000.0000.000
122A123LEU0-0.027-0.00263.9880.0010.0010.0000.0000.0000.000
123A124HIS00.0370.03255.2000.0000.0000.0000.0000.0000.000
124A125VAL00.0000.00658.7490.0010.0010.0000.0000.0000.000
125A126MET00.0450.03951.797-0.002-0.0020.0000.0000.0000.000
126A127TYR0-0.105-0.05552.0820.0020.0020.0000.0000.0000.000
127A128ILE00.0350.02049.751-0.002-0.0020.0000.0000.0000.000
128A129GLY0-0.017-0.02250.5270.0020.0020.0000.0000.0000.000
129A130ARG10.7490.87645.3920.0530.0530.0000.0000.0000.000
130A131PRO00.0730.00647.4470.0020.0020.0000.0000.0000.000
131A132VAL0-0.004-0.00648.0430.0020.0020.0000.0000.0000.000
132A133PRO0-0.0340.00050.4880.0000.0000.0000.0000.0000.000
133A134ALA0-0.0030.00254.089-0.001-0.0010.0000.0000.0000.000
134A135MET00.0040.00454.1460.0020.0020.0000.0000.0000.000
135A136THR0-0.069-0.03858.9270.0000.0000.0000.0000.0000.000
136A137TRP00.0460.02061.2620.0020.0020.0000.0000.0000.000
137A138PHE0-0.016-0.00865.4500.0000.0000.0000.0000.0000.000
138A139HIS10.8660.94969.1310.0250.0250.0000.0000.0000.000
139A140GLY00.0100.00872.2350.0000.0000.0000.0000.0000.000
140A141GLN00.0250.01273.3040.0000.0000.0000.0000.0000.000
141A142LYS10.9260.95973.2420.0260.0260.0000.0000.0000.000
142A143LEU00.0100.01065.6560.0000.0000.0000.0000.0000.000
143A144LEU0-0.060-0.03667.0050.0000.0000.0000.0000.0000.000
144A145GLN00.0220.00665.8450.0000.0000.0000.0000.0000.000
145A146ASN00.009-0.00161.9590.0000.0000.0000.0000.0000.000
146A147SER0-0.008-0.01665.7310.0010.0010.0000.0000.0000.000
147A148GLU-1-0.855-0.92167.763-0.035-0.0350.0000.0000.0000.000
148A149ASN0-0.058-0.04069.497-0.001-0.0010.0000.0000.0000.000
149A150ILE0-0.0140.00366.7570.0000.0000.0000.0000.0000.000
150A151THR00.0220.01561.675-0.001-0.0010.0000.0000.0000.000
151A152ILE0-0.026-0.02560.3900.0010.0010.0000.0000.0000.000
152A153GLU-1-0.892-0.92854.761-0.052-0.0520.0000.0000.0000.000
153A154ASN0-0.014-0.01055.5330.0020.0020.0000.0000.0000.000
154A155THR00.0780.03450.036-0.002-0.0020.0000.0000.0000.000
155A156GLU-1-0.880-0.93546.277-0.060-0.0600.0000.0000.0000.000
156A157HIS00.0340.02645.5900.0030.0030.0000.0000.0000.000
157A158TYR0-0.012-0.03450.8510.0020.0020.0000.0000.0000.000
158A159THR0-0.0110.00654.600-0.001-0.0010.0000.0000.0000.000
159A160HIS0-0.021-0.03957.7070.0020.0020.0000.0000.0000.000
160A161LEU0-0.0090.01559.6670.0000.0000.0000.0000.0000.000
161A162VAL0-0.030-0.01962.7770.0010.0010.0000.0000.0000.000
162A163MET0-0.036-0.00965.2070.0000.0000.0000.0000.0000.000
163A164LYS10.9990.99667.5090.0360.0360.0000.0000.0000.000
164A165ASN0-0.029-0.01370.7310.0010.0010.0000.0000.0000.000
165A166VAL0-0.0030.02072.3450.0010.0010.0000.0000.0000.000
166A167GLN00.0730.02175.0440.0010.0010.0000.0000.0000.000
167A168ARG11.0321.00478.2030.0190.0190.0000.0000.0000.000
168A169LYS10.9540.97280.0910.0210.0210.0000.0000.0000.000
169A170THR0-0.019-0.02276.9190.0000.0000.0000.0000.0000.000
170A171HIS00.0270.01272.5970.0000.0000.0000.0000.0000.000
171A172ALA00.0460.05174.7830.0000.0000.0000.0000.0000.000
172A173GLY00.0060.00376.3430.0000.0000.0000.0000.0000.000
173A174LYS10.9610.98473.4730.0190.0190.0000.0000.0000.000
174A175TYR0-0.063-0.05468.745-0.001-0.0010.0000.0000.0000.000
175A176LYS10.9620.99866.4930.0250.0250.0000.0000.0000.000
176A177VAL00.0150.02461.432-0.001-0.0010.0000.0000.0000.000
177A178GLN0-0.008-0.02662.4090.0020.0020.0000.0000.0000.000
178A179LEU00.0310.01656.541-0.002-0.0020.0000.0000.0000.000
179A180SER0-0.002-0.01757.7980.0020.0020.0000.0000.0000.000
180A181ASN00.0190.01751.8810.0000.0000.0000.0000.0000.000
181A182VAL00.015-0.00450.7780.0010.0010.0000.0000.0000.000
182A183PHE0-0.035-0.01348.0340.0020.0020.0000.0000.0000.000
183A184GLY00.0380.02653.9370.0020.0020.0000.0000.0000.000
184A185THR0-0.025-0.01057.273-0.002-0.0020.0000.0000.0000.000
185A186VAL00.0260.02358.5750.0010.0010.0000.0000.0000.000
186A187ASP-1-0.954-0.98361.131-0.026-0.0260.0000.0000.0000.000
187A188ALA00.0590.03163.7490.0010.0010.0000.0000.0000.000
188A189ILE0-0.028-0.02965.489-0.001-0.0010.0000.0000.0000.000
189A190LEU0-0.026-0.00665.0910.0000.0000.0000.0000.0000.000
190A191ASP-1-0.887-0.95269.423-0.021-0.0210.0000.0000.0000.000
191A192VAL00.0080.00770.8790.0000.0000.0000.0000.0000.000
192A193GLU-1-0.917-0.96073.453-0.020-0.0200.0000.0000.0000.000
193A194ILE0-0.050-0.02175.065-0.001-0.0010.0000.0000.0000.000
194A195GLN0-0.017-0.01676.5570.0000.0000.0000.0000.0000.000
195A196ASP-1-0.821-0.95978.685-0.021-0.0210.0000.0000.0000.000
196A197LYS10.9120.95977.5590.0210.0210.0000.0000.0000.000