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

tag_button

FMODB ID: KGV13

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 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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2768621.118746
FMO2-HF: Nuclear repulsion 2681234.222996
FMO2-HF: Total energy -87386.89575
FMO2-MP2: Total energy -87644.220274


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.
-13.268-11.563-0.003-0.798-0.9040.002
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 : 0.991
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].
3A7LYS10.8710.9233.73531.57033.275-0.003-0.798-0.9040.002
4A8LEU00.0430.0355.6990.6920.6920.0000.0000.0000.000
5A9ILE0-0.042-0.0258.9180.1340.1340.0000.0000.0000.000
6A10GLY0-0.0050.00411.6890.7810.7810.0000.0000.0000.000
7A11ASP-1-0.767-0.88414.475-14.733-14.7330.0000.0000.0000.000
8A12GLU-1-0.783-0.86912.498-22.231-22.2310.0000.0000.0000.000
9A13ARG10.8470.90613.35614.96914.9690.0000.0000.0000.000
10A14LEU0-0.0020.0038.645-0.313-0.3130.0000.0000.0000.000
11A15ASP-1-0.727-0.81112.711-15.239-15.2390.0000.0000.0000.000
12A16TYR0-0.030-0.02714.389-1.669-1.6690.0000.0000.0000.000
13A17LEU0-0.0190.01016.4040.8280.8280.0000.0000.0000.000
14A18LEU00.012-0.01418.368-0.351-0.3510.0000.0000.0000.000
15A19ALA00.0030.02220.341-0.061-0.0610.0000.0000.0000.000
16A20GLU-1-0.896-0.97418.830-14.163-14.1630.0000.0000.0000.000
17A21ASN0-0.073-0.03216.791-1.063-1.0630.0000.0000.0000.000
18A22LEU00.0170.03013.368-1.291-1.2910.0000.0000.0000.000
19A23ARG10.8050.88110.48221.72121.7210.0000.0000.0000.000
20A24ILE00.0060.01812.746-0.741-0.7410.0000.0000.0000.000
21A25ILE0-0.016-0.0038.8150.5580.5580.0000.0000.0000.000
22A26GLN0-0.050-0.03713.0521.0001.0000.0000.0000.0000.000
23A27SER00.001-0.02816.393-0.242-0.2420.0000.0000.0000.000
24A28PRO0-0.0190.00118.7590.3410.3410.0000.0000.0000.000
25A29SER0-0.017-0.00421.0890.5440.5440.0000.0000.0000.000
26A30VAL0-0.056-0.02320.2520.3550.3550.0000.0000.0000.000
27A31PHE00.0420.00720.0590.3390.3390.0000.0000.0000.000
28A32SER00.007-0.00820.173-0.796-0.7960.0000.0000.0000.000
29A33PHE00.0140.01319.2560.5800.5800.0000.0000.0000.000
30A34SER00.0390.02022.8960.1440.1440.0000.0000.0000.000
31A35ILE00.0580.00226.127-0.244-0.2440.0000.0000.0000.000
32A36ASP-1-0.799-0.88628.400-9.738-9.7380.0000.0000.0000.000
33A37ALA00.0300.02224.2610.0710.0710.0000.0000.0000.000
34A38VAL00.0290.01423.842-0.066-0.0660.0000.0000.0000.000
35A39LEU0-0.011-0.00926.0580.1310.1310.0000.0000.0000.000
36A40LEU00.0070.01127.9070.2120.2120.0000.0000.0000.000
37A41ALA00.0070.00524.7820.1280.1280.0000.0000.0000.000
38A42LYS10.8540.92626.71510.86010.8600.0000.0000.0000.000
39A43PHE0-0.022-0.00628.9540.2630.2630.0000.0000.0000.000
40A44SER00.0050.01128.6100.3730.3730.0000.0000.0000.000
41A45TYR0-0.042-0.01529.971-0.189-0.1890.0000.0000.0000.000
42A46LEU00.015-0.00725.649-0.033-0.0330.0000.0000.0000.000
43A47PRO0-0.017-0.00228.2130.3150.3150.0000.0000.0000.000
44A48ILE00.0070.00229.532-0.247-0.2470.0000.0000.0000.000
45A49ARG10.9690.97528.3689.4709.4700.0000.0000.0000.000
46A50LYS10.9260.97225.78311.66811.6680.0000.0000.0000.000
47A51GLY00.0710.03126.8580.0420.0420.0000.0000.0000.000
48A52LYS10.9130.95325.00411.29911.2990.0000.0000.0000.000
49A53ILE00.0210.00623.6220.6080.6080.0000.0000.0000.000
50A54ILE00.0170.01123.588-0.488-0.4880.0000.0000.0000.000
51A55ASP-1-0.799-0.89222.386-13.062-13.0620.0000.0000.0000.000
52A56LEU00.006-0.01723.744-0.360-0.3600.0000.0000.0000.000
53A57CYS0-0.058-0.02525.5030.2120.2120.0000.0000.0000.000
54A58SER0-0.030-0.04020.468-0.314-0.3140.0000.0000.0000.000
55A59GLY00.0410.03220.932-0.283-0.2830.0000.0000.0000.000
56A60ASN0-0.045-0.04016.723-0.005-0.0050.0000.0000.0000.000
57A61GLY00.0330.01016.262-1.112-1.1120.0000.0000.0000.000
58A62ILE00.0010.00717.591-0.124-0.1240.0000.0000.0000.000
59A63ILE00.0330.01119.3090.0260.0260.0000.0000.0000.000
60A64PRO0-0.008-0.00717.8950.0950.0950.0000.0000.0000.000
61A65LEU00.0390.02013.235-0.227-0.2270.0000.0000.0000.000
62A66LEU00.0150.03517.2610.1430.1430.0000.0000.0000.000
63A67LEU0-0.071-0.04820.5450.4640.4640.0000.0000.0000.000
64A68SER0-0.044-0.03217.3760.1880.1880.0000.0000.0000.000
65A69THR00.0200.02517.9650.3470.3470.0000.0000.0000.000
66A70ARG10.8370.91020.24012.30912.3090.0000.0000.0000.000
67A71THR0-0.026-0.00322.8330.5550.5550.0000.0000.0000.000
68A72LYS10.9620.97921.60513.14513.1450.0000.0000.0000.000
69A73ALA0-0.094-0.04221.913-0.279-0.2790.0000.0000.0000.000
70A74LYS10.9010.94917.90716.22516.2250.0000.0000.0000.000
71A75ILE00.009-0.00119.1200.9310.9310.0000.0000.0000.000
72A76VAL00.0080.02018.982-0.710-0.7100.0000.0000.0000.000
73A77GLY00.0350.00719.1730.7110.7110.0000.0000.0000.000
74A78VAL0-0.046-0.02719.676-0.560-0.5600.0000.0000.0000.000
75A79GLU-1-0.842-0.93319.961-13.132-13.1320.0000.0000.0000.000
76A80ILE0-0.016-0.00520.996-0.463-0.4630.0000.0000.0000.000
77A81GLN0-0.045-0.02022.7580.1730.1730.0000.0000.0000.000
78A82GLU-1-0.823-0.93318.411-17.038-17.0380.0000.0000.0000.000
79A83ARG10.8770.95515.33217.24017.2400.0000.0000.0000.000
80A84LEU0-0.023-0.01416.935-0.939-0.9390.0000.0000.0000.000
81A85ALA00.0690.03516.666-0.988-0.9880.0000.0000.0000.000
82A86ASP-1-0.844-0.90112.233-26.557-26.5570.0000.0000.0000.000
83A87MET0-0.0110.00512.249-1.708-1.7080.0000.0000.0000.000
84A88ALA00.0050.02312.505-1.341-1.3410.0000.0000.0000.000
85A89LYS10.8850.92310.94319.35719.3570.0000.0000.0000.000
86A90ARG10.7380.8398.07223.48723.4870.0000.0000.0000.000
87A91SER00.012-0.0097.709-3.296-3.2960.0000.0000.0000.000
88A92VAL0-0.025-0.0129.937-0.231-0.2310.0000.0000.0000.000
89A93ALA00.0140.0185.311-0.437-0.4370.0000.0000.0000.000
90A94TYR0-0.084-0.0405.013-3.295-3.2950.0000.0000.0000.000
91A95ASN0-0.027-0.0426.2340.4210.4210.0000.0000.0000.000
92A96GLN0-0.063-0.0126.3483.0063.0060.0000.0000.0000.000
93A97LEU00.0240.0078.8562.7252.7250.0000.0000.0000.000
94A98GLU-1-0.836-0.9316.488-37.636-37.6360.0000.0000.0000.000
95A99ASP-1-0.907-0.93411.184-21.087-21.0870.0000.0000.0000.000
96A100GLN0-0.186-0.09813.9381.5401.5400.0000.0000.0000.000
97A101ILE0-0.015-0.01214.4801.5631.5630.0000.0000.0000.000
98A102GLU-1-0.907-0.94514.285-17.820-17.8200.0000.0000.0000.000
99A103ILE0-0.037-0.01314.5521.0721.0720.0000.0000.0000.000
100A104ILE0-0.014-0.01616.623-0.308-0.3080.0000.0000.0000.000
101A105GLU-1-0.858-0.91117.251-17.570-17.5700.0000.0000.0000.000
102A106TYR0-0.072-0.08221.1350.3250.3250.0000.0000.0000.000
103A107ASP-1-0.785-0.87824.766-10.236-10.2360.0000.0000.0000.000
104A108LEU00.0760.02527.8740.1480.1480.0000.0000.0000.000
105A109LYS10.8030.88429.0909.9889.9880.0000.0000.0000.000
106A110LYS10.8470.92330.47810.59210.5920.0000.0000.0000.000
107A111ILE00.0860.05924.864-0.112-0.1120.0000.0000.0000.000
108A112THR0-0.016-0.01928.314-0.192-0.1920.0000.0000.0000.000
109A113ASP-1-0.852-0.88829.028-10.032-10.0320.0000.0000.0000.000
110A114LEU0-0.047-0.02023.505-0.169-0.1690.0000.0000.0000.000
111A115ILE0-0.032-0.00424.391-0.246-0.2460.0000.0000.0000.000
112A116PRO0-0.020-0.01327.6130.4370.4370.0000.0000.0000.000
113A117LYS10.9430.96230.9548.2108.2100.0000.0000.0000.000
114A118GLU-1-0.866-0.92833.621-8.178-8.1780.0000.0000.0000.000
115A119ARG10.8920.94830.2539.7029.7020.0000.0000.0000.000
116A120ALA0-0.0110.00928.690-0.219-0.2190.0000.0000.0000.000
117A121ASP-1-0.853-0.92729.182-10.072-10.0720.0000.0000.0000.000
118A122ILE00.0030.00228.2280.3600.3600.0000.0000.0000.000
119A123VAL0-0.0170.01028.035-0.392-0.3920.0000.0000.0000.000
120A124THR0-0.009-0.00725.8040.4910.4910.0000.0000.0000.000
121A125CYS0-0.022-0.00727.729-0.317-0.3170.0000.0000.0000.000
122A126ASN00.0760.02426.8980.5690.5690.0000.0000.0000.000
123A127PRO00.0280.01527.870-0.332-0.3320.0000.0000.0000.000
124A128PRO00.0050.02127.1890.2250.2250.0000.0000.0000.000
125A152MET00.0600.01739.2650.0800.0800.0000.0000.0000.000
126A153CYS00.0380.00539.735-0.113-0.1130.0000.0000.0000.000
127A154THR00.0470.02234.467-0.105-0.1050.0000.0000.0000.000
128A155LEU00.0000.01535.701-0.233-0.2330.0000.0000.0000.000
129A156GLU-1-0.727-0.83437.094-7.535-7.5350.0000.0000.0000.000
130A157ASP-1-0.855-0.91335.334-8.663-8.6630.0000.0000.0000.000
131A158THR0-0.023-0.02331.742-0.147-0.1470.0000.0000.0000.000
132A159ILE00.0050.00633.819-0.169-0.1690.0000.0000.0000.000
133A160ARG10.8990.94336.4158.5858.5850.0000.0000.0000.000
134A161VAL0-0.018-0.00331.097-0.001-0.0010.0000.0000.0000.000
135A162ALA00.0490.02232.040-0.131-0.1310.0000.0000.0000.000
136A163ALA00.0480.02133.060-0.068-0.0680.0000.0000.0000.000
137A164SER0-0.103-0.04734.2530.0460.0460.0000.0000.0000.000
138A165LEU00.0680.01828.839-0.033-0.0330.0000.0000.0000.000
139A166LEU0-0.0510.00531.808-0.186-0.1860.0000.0000.0000.000
140A167LYS10.8290.91731.54310.16510.1650.0000.0000.0000.000
141A168GLN0-0.024-0.03535.8050.0950.0950.0000.0000.0000.000
142A169GLY0-0.016-0.01537.987-0.090-0.0900.0000.0000.0000.000
143A170GLY0-0.0190.00234.558-0.139-0.1390.0000.0000.0000.000
144A171LYS10.8180.90033.3239.3339.3330.0000.0000.0000.000
145A172ALA00.0320.02232.470-0.357-0.3570.0000.0000.0000.000
146A173ASN0-0.026-0.02130.5740.4980.4980.0000.0000.0000.000
147A174PHE00.0220.00331.227-0.336-0.3360.0000.0000.0000.000
148A175VAL00.0250.03130.3680.2170.2170.0000.0000.0000.000
149A176HIS0-0.005-0.02533.244-0.103-0.1030.0000.0000.0000.000
150A177ARG10.8950.94033.5539.0409.0400.0000.0000.0000.000
151A178PRO00.0080.00238.8540.0880.0880.0000.0000.0000.000
152A179GLU-1-0.860-0.93841.536-7.596-7.5960.0000.0000.0000.000
153A180ARG10.8160.89540.6117.6067.6060.0000.0000.0000.000
154A181LEU0-0.0170.00341.1410.0160.0160.0000.0000.0000.000
155A182LEU00.028-0.00442.986-0.037-0.0370.0000.0000.0000.000
156A183ASP-1-0.737-0.84244.254-6.945-6.9450.0000.0000.0000.000
157A184ILE0-0.055-0.03738.643-0.083-0.0830.0000.0000.0000.000
158A185ILE0-0.021-0.00742.231-0.079-0.0790.0000.0000.0000.000
159A186ASP-1-0.886-0.93344.169-6.624-6.6240.0000.0000.0000.000
160A187ILE0-0.054-0.03540.852-0.020-0.0200.0000.0000.0000.000
161A188MET0-0.038-0.01938.912-0.077-0.0770.0000.0000.0000.000
162A189ARG10.8310.89241.6416.7556.7550.0000.0000.0000.000
163A190LYS10.8460.92744.3107.2437.2430.0000.0000.0000.000
164A191TYR0-0.091-0.07140.2490.0130.0130.0000.0000.0000.000
165A192ARG10.8160.88240.9397.3917.3910.0000.0000.0000.000
166A193LEU0-0.007-0.00336.550-0.141-0.1410.0000.0000.0000.000
167A194GLU-1-0.759-0.84640.955-6.835-6.8350.0000.0000.0000.000
168A195PRO0-0.0010.00241.157-0.194-0.1940.0000.0000.0000.000
169A196LYS10.7710.87340.5597.3647.3640.0000.0000.0000.000
170A197ARG10.7650.88034.4469.0439.0430.0000.0000.0000.000
171A198ILE00.0390.02639.254-0.132-0.1320.0000.0000.0000.000
172A199GLN0-0.016-0.02035.588-0.072-0.0720.0000.0000.0000.000
173A200PHE00.0300.02738.383-0.121-0.1210.0000.0000.0000.000
174A201VAL00.0160.00534.799-0.045-0.0450.0000.0000.0000.000
175A202HIS00.003-0.01438.0990.0630.0630.0000.0000.0000.000
176A203PRO00.0190.01037.757-0.117-0.1170.0000.0000.0000.000
177A204ARG10.9550.98338.6877.4967.4960.0000.0000.0000.000
178A205SER00.008-0.01141.4480.0040.0040.0000.0000.0000.000
179A206ASP-1-0.825-0.89544.183-6.770-6.7700.0000.0000.0000.000
180A207ARG10.8280.91443.0717.0227.0220.0000.0000.0000.000
181A208GLU-1-0.906-0.94044.565-6.872-6.8720.0000.0000.0000.000
182A209ALA0-0.040-0.02141.310-0.164-0.1640.0000.0000.0000.000
183A210ASN00.0470.01436.3930.1050.1050.0000.0000.0000.000
184A211THR0-0.021-0.01233.848-0.072-0.0720.0000.0000.0000.000
185A212VAL0-0.038-0.01137.2130.1750.1750.0000.0000.0000.000
186A213LEU0-0.0150.00032.634-0.217-0.2170.0000.0000.0000.000
187A214VAL00.0250.00735.6650.3140.3140.0000.0000.0000.000
188A215GLU-1-0.755-0.86935.225-9.131-9.1310.0000.0000.0000.000
189A216GLY00.0320.00236.7220.3200.3200.0000.0000.0000.000
190A217ILE0-0.044-0.00737.162-0.230-0.2300.0000.0000.0000.000
191A218LYS10.7660.87837.4018.6808.6800.0000.0000.0000.000
192A219ASP-1-0.790-0.87739.380-7.565-7.5650.0000.0000.0000.000
193A220GLY0-0.0150.00142.3250.1170.1170.0000.0000.0000.000
194A221LYS10.9420.96543.4196.7446.7440.0000.0000.0000.000
195A222PRO00.0950.04446.122-0.124-0.1240.0000.0000.0000.000
196A223GLY0-0.016-0.00847.3440.0870.0870.0000.0000.0000.000
197A224VAL00.0150.02043.684-0.163-0.1630.0000.0000.0000.000
198A225LYS10.9370.97043.0257.1907.1900.0000.0000.0000.000
199A226TYR00.0320.00142.892-0.197-0.1970.0000.0000.0000.000
200A227VAL0-0.051-0.02137.9920.1020.1020.0000.0000.0000.000
201A228PRO00.0290.01240.4120.0350.0350.0000.0000.0000.000
202A229PRO00.0320.02739.568-0.229-0.2290.0000.0000.0000.000
203A230VAL0-0.021-0.01034.513-0.014-0.0140.0000.0000.0000.000
204A231ILE00.0390.01637.9650.0740.0740.0000.0000.0000.000
205A232VAL0-0.029-0.01233.217-0.149-0.1490.0000.0000.0000.000
206A233TYR0-0.037-0.02231.875-0.155-0.1550.0000.0000.0000.000
207A234ASP-1-0.788-0.90537.175-7.743-7.7430.0000.0000.0000.000
208A235GLU-1-0.972-1.00840.084-6.939-6.9390.0000.0000.0000.000
209A236LEU0-0.0070.00440.1500.1090.1090.0000.0000.0000.000
210A237GLY0-0.101-0.04138.3580.0070.0070.0000.0000.0000.000
211A238GLU-1-0.828-0.91132.157-9.705-9.7050.0000.0000.0000.000
212A239TYR0-0.028-0.00928.6160.1770.1770.0000.0000.0000.000
213A240THR00.0090.00833.8730.1530.1530.0000.0000.0000.000
214A241PRO00.033-0.00233.959-0.280-0.2800.0000.0000.0000.000
215A242VAL00.0370.00933.529-0.216-0.2160.0000.0000.0000.000
216A243ILE0-0.0060.00230.178-0.263-0.2630.0000.0000.0000.000
217A244LYS10.8640.92629.5498.8318.8310.0000.0000.0000.000
218A245GLU-1-0.859-0.90228.435-10.412-10.4120.0000.0000.0000.000
219A246ILE0-0.055-0.04227.242-0.396-0.3960.0000.0000.0000.000
220A247LEU0-0.0140.00425.028-0.464-0.4640.0000.0000.0000.000
221A248TYR0-0.052-0.04223.914-0.299-0.2990.0000.0000.0000.000
222A249GLY0-0.0150.01625.231-0.056-0.0560.0000.0000.0000.000