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: QVL9Y

Calculation Name: 3LPM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LPM

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-23

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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2765597.297332
FMO2-HF: Nuclear repulsion 2678212.424935
FMO2-HF: Total energy -87384.872397
FMO2-MP2: Total energy -87642.190256


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:5:LYS)


Summations of interaction energy for fragment #1(A:5:LYS)
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.
-11.794-10.097-0.004-0.803-0.890.002
Interaction energy analysis for fragmet #1(A:5:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.998 / q_NPA : 0.990
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].
3A7LYS10.9090.9543.71431.36733.064-0.004-0.803-0.8900.002
4A8LEU00.0210.0215.6820.5900.5900.0000.0000.0000.000
5A9ILE0-0.067-0.0408.8980.2520.2520.0000.0000.0000.000
6A10GLY0-0.023-0.00211.6740.7970.7970.0000.0000.0000.000
7A11ASP-1-0.742-0.91714.457-14.854-14.8540.0000.0000.0000.000
8A12GLU-1-0.809-0.90812.324-22.274-22.2740.0000.0000.0000.000
9A13ARG10.9520.98913.37014.57414.5740.0000.0000.0000.000
10A14LEU0-0.051-0.0169.048-0.314-0.3140.0000.0000.0000.000
11A15ASP-1-0.830-0.92612.967-15.259-15.2590.0000.0000.0000.000
12A16TYR0-0.039-0.03514.300-1.388-1.3880.0000.0000.0000.000
13A17LEU0-0.0010.01316.6540.8290.8290.0000.0000.0000.000
14A18LEU00.002-0.02218.599-0.333-0.3330.0000.0000.0000.000
15A19ALA00.0140.02720.588-0.057-0.0570.0000.0000.0000.000
16A20GLU-1-0.923-0.98118.862-13.698-13.6980.0000.0000.0000.000
17A21ASN0-0.070-0.02916.950-1.339-1.3390.0000.0000.0000.000
18A22LEU00.0220.03113.757-1.184-1.1840.0000.0000.0000.000
19A23ARG10.8620.93710.69821.50821.5080.0000.0000.0000.000
20A24ILE00.0070.01312.979-0.717-0.7170.0000.0000.0000.000
21A25ILE0-0.0140.0019.0970.5190.5190.0000.0000.0000.000
22A26GLN0-0.018-0.02013.2501.1391.1390.0000.0000.0000.000
23A27SER00.0160.02116.371-0.227-0.2270.0000.0000.0000.000
24A28PRO00.0040.00918.7380.4140.4140.0000.0000.0000.000
25A29SER0-0.028-0.02620.9340.6100.6100.0000.0000.0000.000
26A30VAL0-0.122-0.03319.7280.2600.2600.0000.0000.0000.000
27A31PHE00.013-0.00520.4390.3320.3320.0000.0000.0000.000
28A32SER00.0240.00020.357-0.797-0.7970.0000.0000.0000.000
29A33PHE0-0.023-0.00119.8590.6070.6070.0000.0000.0000.000
30A34SER00.0420.02423.1270.1480.1480.0000.0000.0000.000
31A35ILE00.0690.00426.388-0.239-0.2390.0000.0000.0000.000
32A36ASP-1-0.839-0.91828.612-9.755-9.7550.0000.0000.0000.000
33A37ALA0-0.0050.00524.6740.0730.0730.0000.0000.0000.000
34A38VAL00.0370.01824.182-0.071-0.0710.0000.0000.0000.000
35A39LEU0-0.016-0.01126.4440.1220.1220.0000.0000.0000.000
36A40LEU00.0130.01428.2930.2150.2150.0000.0000.0000.000
37A41ALA00.0030.00425.1070.1240.1240.0000.0000.0000.000
38A42LYS10.9040.95427.06511.18811.1880.0000.0000.0000.000
39A43PHE0-0.011-0.00229.2850.2530.2530.0000.0000.0000.000
40A44SER0-0.010-0.00128.9360.3540.3540.0000.0000.0000.000
41A45TYR0-0.015-0.00630.252-0.182-0.1820.0000.0000.0000.000
42A46LEU00.008-0.01325.806-0.029-0.0290.0000.0000.0000.000
43A47PRO0-0.025-0.00128.5990.3290.3290.0000.0000.0000.000
44A48ILE00.0120.00629.912-0.238-0.2380.0000.0000.0000.000
45A49ARG10.9770.97928.8069.3529.3520.0000.0000.0000.000
46A50LYS10.9170.97026.20911.72811.7280.0000.0000.0000.000
47A51GLY00.0650.02127.2620.0400.0400.0000.0000.0000.000
48A52LYS10.9080.95125.36811.04011.0400.0000.0000.0000.000
49A53ILE00.0220.00724.0090.5820.5820.0000.0000.0000.000
50A54ILE00.0250.01423.944-0.477-0.4770.0000.0000.0000.000
51A55ASP-1-0.775-0.89322.746-12.789-12.7890.0000.0000.0000.000
52A56LEU0-0.009-0.02324.055-0.363-0.3630.0000.0000.0000.000
53A57CYS0-0.058-0.03725.7910.2190.2190.0000.0000.0000.000
54A58SER0-0.018-0.04120.686-0.269-0.2690.0000.0000.0000.000
55A59GLY00.0130.01921.360-0.281-0.2810.0000.0000.0000.000
56A60ASN0-0.024-0.02517.214-0.102-0.1020.0000.0000.0000.000
57A61GLY00.0430.01116.716-1.060-1.0600.0000.0000.0000.000
58A62ILE00.0110.01218.008-0.093-0.0930.0000.0000.0000.000
59A63ILE00.0240.01119.7300.0580.0580.0000.0000.0000.000
60A64PRO0-0.026-0.01518.2250.1220.1220.0000.0000.0000.000
61A65LEU00.0530.02213.654-0.185-0.1850.0000.0000.0000.000
62A66LEU00.0020.02117.5950.1560.1560.0000.0000.0000.000
63A67LEU0-0.083-0.05220.8720.4720.4720.0000.0000.0000.000
64A68SER0-0.040-0.01917.6180.2620.2620.0000.0000.0000.000
65A69THR00.0290.03218.1970.3580.3580.0000.0000.0000.000
66A70ARG10.8430.91520.44012.13212.1320.0000.0000.0000.000
67A71THR0-0.0250.01123.0070.5470.5470.0000.0000.0000.000
68A72LYS10.9830.98121.90212.91912.9190.0000.0000.0000.000
69A73ALA0-0.112-0.06022.332-0.271-0.2710.0000.0000.0000.000
70A74LYS10.9000.96718.49615.71015.7100.0000.0000.0000.000
71A75ILE00.002-0.00119.4870.8880.8880.0000.0000.0000.000
72A76VAL00.0200.02719.326-0.680-0.6800.0000.0000.0000.000
73A77GLY00.0270.00119.4750.6950.6950.0000.0000.0000.000
74A78VAL0-0.037-0.01919.935-0.571-0.5710.0000.0000.0000.000
75A79GLU-1-0.856-0.93920.146-13.086-13.0860.0000.0000.0000.000
76A80ILE0-0.012-0.00521.157-0.449-0.4490.0000.0000.0000.000
77A81GLN0-0.038-0.01522.9060.1030.1030.0000.0000.0000.000
78A82GLU-1-0.866-0.94017.775-17.419-17.4190.0000.0000.0000.000
79A83ARG10.9900.99915.94616.63916.6390.0000.0000.0000.000
80A84LEU0-0.027-0.01617.130-0.892-0.8920.0000.0000.0000.000
81A85ALA00.0700.03717.120-0.943-0.9430.0000.0000.0000.000
82A86ASP-1-0.852-0.89912.614-26.510-26.5100.0000.0000.0000.000
83A87MET0-0.025-0.00512.493-1.666-1.6660.0000.0000.0000.000
84A88ALA00.0040.02212.966-1.268-1.2680.0000.0000.0000.000
85A89LYS10.9120.95411.08819.56619.5660.0000.0000.0000.000
86A90ARG10.7680.8658.07324.13224.1320.0000.0000.0000.000
87A91SER00.006-0.0108.152-2.977-2.9770.0000.0000.0000.000
88A92VAL0-0.019-0.00410.317-0.122-0.1220.0000.0000.0000.000
89A93ALA00.0150.0135.638-0.372-0.3720.0000.0000.0000.000
90A94TYR0-0.080-0.0385.215-2.726-2.7260.0000.0000.0000.000
91A95ASN0-0.045-0.0526.5860.4500.4500.0000.0000.0000.000
92A96GLN0-0.052-0.0087.2643.0183.0180.0000.0000.0000.000
93A97LEU00.0240.0069.1502.4642.4640.0000.0000.0000.000
94A98GLU-1-0.873-0.9466.835-36.425-36.4250.0000.0000.0000.000
95A99ASP-1-0.899-0.92911.541-21.063-21.0630.0000.0000.0000.000
96A100GLN0-0.180-0.11014.2781.4091.4090.0000.0000.0000.000
97A101ILE0-0.022-0.01614.8341.5221.5220.0000.0000.0000.000
98A102GLU-1-0.905-0.94514.616-17.745-17.7450.0000.0000.0000.000
99A103ILE0-0.039-0.01215.0091.0471.0470.0000.0000.0000.000
100A104ILE0-0.009-0.01416.808-0.335-0.3350.0000.0000.0000.000
101A105GLU-1-0.880-0.94117.318-17.318-17.3180.0000.0000.0000.000
102A106TYR0-0.066-0.05421.2570.2540.2540.0000.0000.0000.000
103A107ASP-1-0.853-0.93124.886-10.243-10.2430.0000.0000.0000.000
104A108LEU00.0850.03128.2250.1390.1390.0000.0000.0000.000
105A109LYS10.8750.93429.2869.6909.6900.0000.0000.0000.000
106A110LYS10.9200.95930.62310.54710.5470.0000.0000.0000.000
107A111ILE00.0800.05625.114-0.109-0.1090.0000.0000.0000.000
108A112THR0-0.026-0.02328.490-0.169-0.1690.0000.0000.0000.000
109A113ASP-1-0.915-0.93929.360-9.887-9.8870.0000.0000.0000.000
110A114LEU0-0.070-0.03023.595-0.205-0.2050.0000.0000.0000.000
111A115ILE0-0.027-0.00624.497-0.246-0.2460.0000.0000.0000.000
112A116PRO0-0.024-0.01427.8140.4360.4360.0000.0000.0000.000
113A117LYS10.9750.99331.1638.1158.1150.0000.0000.0000.000
114A118GLU-1-0.957-0.99633.859-8.180-8.1800.0000.0000.0000.000
115A119ARG10.8910.94630.5489.6979.6970.0000.0000.0000.000
116A120ALA0-0.0220.00229.025-0.217-0.2170.0000.0000.0000.000
117A121ASP-1-0.878-0.94829.542-9.962-9.9620.0000.0000.0000.000
118A122ILE0-0.010-0.00328.5580.3390.3390.0000.0000.0000.000
119A123VAL00.0060.01328.407-0.392-0.3920.0000.0000.0000.000
120A124THR0-0.043-0.00825.6810.4960.4960.0000.0000.0000.000
121A125CYS00.0030.01028.083-0.300-0.3000.0000.0000.0000.000
122A126ASN00.0420.01927.0340.7570.7570.0000.0000.0000.000
123A127PRO00.0310.01428.309-0.300-0.3000.0000.0000.0000.000
124A128PRO0-0.0080.01527.6200.2150.2150.0000.0000.0000.000
125A152MET00.0510.01439.621-0.040-0.0400.0000.0000.0000.000
126A153CYS00.025-0.00540.268-0.050-0.0500.0000.0000.0000.000
127A154THR00.0480.02834.501-0.049-0.0490.0000.0000.0000.000
128A155LEU00.0060.01335.948-0.205-0.2050.0000.0000.0000.000
129A156GLU-1-0.792-0.90637.375-7.512-7.5120.0000.0000.0000.000
130A157ASP-1-0.880-0.93835.536-8.630-8.6300.0000.0000.0000.000
131A158THR0-0.017-0.01132.163-0.144-0.1440.0000.0000.0000.000
132A159ILE00.0200.01534.109-0.157-0.1570.0000.0000.0000.000
133A160ARG10.9150.96136.7158.4858.4850.0000.0000.0000.000
134A161VAL0-0.018-0.00331.3470.0090.0090.0000.0000.0000.000
135A162ALA00.0490.02532.344-0.124-0.1240.0000.0000.0000.000
136A163ALA00.0390.01933.365-0.055-0.0550.0000.0000.0000.000
137A164SER0-0.120-0.06034.5180.0480.0480.0000.0000.0000.000
138A165LEU00.0750.02629.083-0.032-0.0320.0000.0000.0000.000
139A166LEU0-0.070-0.00531.970-0.180-0.1800.0000.0000.0000.000
140A167LYS10.8930.96332.4909.9089.9080.0000.0000.0000.000
141A168GLN0-0.001-0.01336.1340.0930.0930.0000.0000.0000.000
142A169GLY0-0.027-0.01838.351-0.088-0.0880.0000.0000.0000.000
143A170GLY0-0.0150.00234.940-0.135-0.1350.0000.0000.0000.000
144A171LYS10.8970.94533.7229.1839.1830.0000.0000.0000.000
145A172ALA00.0260.01632.855-0.345-0.3450.0000.0000.0000.000
146A173ASN0-0.015-0.01230.6680.5570.5570.0000.0000.0000.000
147A174PHE00.0150.00031.592-0.319-0.3190.0000.0000.0000.000
148A175VAL00.0510.03130.5810.2030.2030.0000.0000.0000.000
149A176HIS00.001-0.01333.661-0.161-0.1610.0000.0000.0000.000
150A177ARG10.9460.98533.8928.9838.9830.0000.0000.0000.000
151A178PRO00.0180.01239.3050.0890.0890.0000.0000.0000.000
152A179GLU-1-0.865-0.93141.891-7.513-7.5130.0000.0000.0000.000
153A180ARG10.9050.95040.7447.7257.7250.0000.0000.0000.000
154A181LEU0-0.0060.00941.6350.0150.0150.0000.0000.0000.000
155A182LEU00.035-0.00243.403-0.046-0.0460.0000.0000.0000.000
156A183ASP-1-0.824-0.90045.166-6.792-6.7920.0000.0000.0000.000
157A184ILE0-0.054-0.03538.777-0.091-0.0910.0000.0000.0000.000
158A185ILE0-0.017-0.01042.630-0.083-0.0830.0000.0000.0000.000
159A186ASP-1-0.889-0.93544.546-6.629-6.6290.0000.0000.0000.000
160A187ILE0-0.053-0.03741.082-0.018-0.0180.0000.0000.0000.000
161A188MET0-0.046-0.02038.953-0.073-0.0730.0000.0000.0000.000
162A189ARG10.8830.94641.9706.7026.7020.0000.0000.0000.000
163A190LYS10.8900.97344.5247.1357.1350.0000.0000.0000.000
164A191TYR0-0.094-0.05340.5690.0270.0270.0000.0000.0000.000
165A192ARG10.8010.86841.2517.2317.2310.0000.0000.0000.000
166A193LEU0-0.002-0.00636.845-0.126-0.1260.0000.0000.0000.000
167A194GLU-1-0.825-0.90141.307-6.782-6.7820.0000.0000.0000.000
168A195PRO00.0040.00441.488-0.185-0.1850.0000.0000.0000.000
169A196LYS10.8030.89741.0177.3407.3400.0000.0000.0000.000
170A197ARG10.8200.92835.2188.8598.8590.0000.0000.0000.000
171A198ILE00.0340.02739.603-0.127-0.1270.0000.0000.0000.000
172A199GLN0-0.028-0.02935.792-0.079-0.0790.0000.0000.0000.000
173A200PHE00.0220.02038.780-0.118-0.1180.0000.0000.0000.000
174A201VAL00.0170.00935.239-0.046-0.0460.0000.0000.0000.000
175A202HIS00.008-0.00938.4140.0650.0650.0000.0000.0000.000
176A203PRO0-0.0040.00037.981-0.101-0.1010.0000.0000.0000.000
177A204ARG11.0111.00838.9267.5007.5000.0000.0000.0000.000
178A205SER0-0.008-0.01641.6870.0220.0220.0000.0000.0000.000
179A206ASP-1-0.837-0.89944.419-6.662-6.6620.0000.0000.0000.000
180A207ARG10.8550.92343.2216.9416.9410.0000.0000.0000.000
181A208GLU-1-0.915-0.94644.653-6.872-6.8720.0000.0000.0000.000
182A209ALA0-0.045-0.02941.640-0.158-0.1580.0000.0000.0000.000
183A210ASN00.0520.01837.0380.0820.0820.0000.0000.0000.000
184A211THR0-0.029-0.01934.312-0.069-0.0690.0000.0000.0000.000
185A212VAL0-0.034-0.01837.6560.1740.1740.0000.0000.0000.000
186A213LEU0-0.021-0.00432.799-0.217-0.2170.0000.0000.0000.000
187A214VAL00.0250.00936.0500.3130.3130.0000.0000.0000.000
188A215GLU-1-0.816-0.92635.656-8.896-8.8960.0000.0000.0000.000
189A216GLY00.029-0.00137.0430.3190.3190.0000.0000.0000.000
190A217ILE0-0.045-0.00837.550-0.230-0.2300.0000.0000.0000.000
191A218LYS10.8710.94337.8138.5048.5040.0000.0000.0000.000
192A219ASP-1-0.791-0.88739.738-7.429-7.4290.0000.0000.0000.000
193A220GLY0-0.024-0.00242.7100.1130.1130.0000.0000.0000.000
194A221LYS10.9570.96943.8056.6166.6160.0000.0000.0000.000
195A222PRO00.0720.02946.506-0.121-0.1210.0000.0000.0000.000
196A223GLY0-0.006-0.00547.6750.0840.0840.0000.0000.0000.000
197A224VAL0-0.022-0.00343.951-0.159-0.1590.0000.0000.0000.000
198A225LYS10.9440.97443.3267.1837.1830.0000.0000.0000.000
199A226TYR00.023-0.00243.229-0.136-0.1360.0000.0000.0000.000
200A227VAL0-0.040-0.01838.5310.1050.1050.0000.0000.0000.000
201A228PRO00.0060.01140.4780.0450.0450.0000.0000.0000.000
202A229PRO00.0400.03739.929-0.221-0.2210.0000.0000.0000.000
203A230VAL0-0.006-0.00934.837-0.014-0.0140.0000.0000.0000.000
204A231ILE00.0180.00838.1840.0800.0800.0000.0000.0000.000
205A232VAL0-0.007-0.00233.562-0.144-0.1440.0000.0000.0000.000
206A233TYR0-0.054-0.01033.142-0.251-0.2510.0000.0000.0000.000
207A234ASP-1-0.808-0.91737.426-7.696-7.6960.0000.0000.0000.000
208A235GLU-1-0.991-1.01340.342-6.943-6.9430.0000.0000.0000.000
209A236LEU0-0.017-0.00440.4920.0990.0990.0000.0000.0000.000
210A237GLY0-0.089-0.03638.5500.0040.0040.0000.0000.0000.000
211A238GLU-1-0.902-0.95032.177-9.657-9.6570.0000.0000.0000.000
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