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: V5LM1

Calculation Name: 1L3C-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1L3C

Chain ID: A

ChEMBL ID:

UniProt ID: O26249

Base Structure: X-ray

Registration Date: 2023-09-20

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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1891604.716593
FMO2-HF: Nuclear repulsion 1819378.91091
FMO2-HF: Total energy -72225.805683
FMO2-MP2: Total energy -72428.868449


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-21.899-11.36121.228-9.558-22.209-0.09
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.068 / q_NPA : -0.035
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].
3A3PRO00.0820.0382.785-1.7770.7880.430-1.316-1.679-0.011
4A4ASP-1-0.740-0.8945.0560.7640.919-0.001-0.009-0.1440.000
5A5ASP-1-0.967-1.0017.333-0.882-0.8820.0000.0000.0000.000
6A6GLU-1-0.927-0.9447.897-1.476-1.4760.0000.0000.0000.000
7A7PHE0-0.070-0.0324.9520.1300.1300.0000.0000.0000.000
8A8ILE0-0.046-0.03410.2270.0720.0720.0000.0000.0000.000
9A9LYS10.9510.96211.6460.3140.3140.0000.0000.0000.000
10A10ASN00.0400.01115.2700.0040.0040.0000.0000.0000.000
11A11PRO0-0.011-0.00418.4610.0140.0140.0000.0000.0000.000
12A12SER00.0010.00521.0280.0120.0120.0000.0000.0000.000
13A13VAL0-0.062-0.00815.8050.0140.0140.0000.0000.0000.000
14A14PRO00.0280.02316.137-0.005-0.0050.0000.0000.0000.000
15A15GLY00.0010.02412.2670.0180.0180.0000.0000.0000.000
16A16PRO00.009-0.0187.738-0.076-0.0760.0000.0000.0000.000
17A17THR00.0020.0007.221-0.072-0.0720.0000.0000.0000.000
18A18ALA00.0100.0107.0540.2480.2480.0000.0000.0000.000
19A19MET00.0040.0022.268-1.702-0.8874.050-1.212-3.6530.001
20A20GLU-1-0.793-0.8993.6432.8914.1390.503-0.541-1.211-0.007
21A21VAL0-0.0070.0026.283-0.306-0.254-0.001-0.008-0.0430.000
22A22ARG10.8050.9012.215-0.967-1.9897.035-1.780-4.2330.000
23A23CYS0-0.032-0.0222.298-6.439-4.3943.282-1.913-3.414-0.016
24A24LEU00.0270.0193.1510.175-1.0880.0521.504-0.293-0.001
25A25ILE00.0160.0065.217-0.247-0.2470.0000.0000.0000.000
26A26MET0-0.043-0.0182.618-0.5350.1010.526-0.187-0.9750.000
27A27CYS0-0.078-0.0324.7780.1180.165-0.001-0.002-0.0440.000
28A28LEU00.0070.0037.4220.0310.0310.0000.0000.0000.000
29A29ALA00.0000.0068.0720.0100.0100.0000.0000.0000.000
30A30GLU-1-0.931-0.9449.2750.0280.0280.0000.0000.0000.000
31A31PRO0-0.043-0.0297.2720.0160.0160.0000.0000.0000.000
32A32GLY00.0710.04810.5660.0380.0380.0000.0000.0000.000
33A33LYS10.9590.95213.446-0.158-0.1580.0000.0000.0000.000
34A34ASN0-0.095-0.04814.761-0.003-0.0030.0000.0000.0000.000
35A35ASP-1-0.798-0.89214.029-0.042-0.0420.0000.0000.0000.000
36A36VAL0-0.078-0.04915.300-0.015-0.0150.0000.0000.0000.000
37A37ALA00.0260.01012.3660.0060.0060.0000.0000.0000.000
38A38VAL00.0050.00114.398-0.004-0.0040.0000.0000.0000.000
39A39ASP-1-0.839-0.92011.4170.0340.0340.0000.0000.0000.000
40A40VAL00.006-0.00613.571-0.005-0.0050.0000.0000.0000.000
41A41GLY0-0.0100.00415.4900.0290.0290.0000.0000.0000.000
42A42CYS0-0.003-0.00213.1070.0340.0340.0000.0000.0000.000
43A43GLY00.0410.02912.8850.0190.0190.0000.0000.0000.000
44A44THR0-0.060-0.05410.961-0.036-0.0360.0000.0000.0000.000
45A45GLY00.0520.02310.900-0.080-0.0800.0000.0000.0000.000
46A46GLY0-0.062-0.0386.979-0.114-0.1140.0000.0000.0000.000
47A47VAL00.0590.0126.059-0.043-0.0430.0000.0000.0000.000
48A48THR00.004-0.0067.055-0.290-0.2900.0000.0000.0000.000
49A49LEU0-0.045-0.0216.078-0.050-0.0500.0000.0000.0000.000
50A50GLU-1-0.856-0.9492.449-13.271-8.7835.005-3.850-5.644-0.057
51A51LEU00.013-0.0014.6150.2070.280-0.001-0.006-0.0660.000
52A52ALA00.0340.0267.5930.1380.1380.0000.0000.0000.000
53A53GLY0-0.0120.0058.1540.1140.1140.0000.0000.0000.000
54A54ARG10.8530.9132.6500.6671.3660.349-0.238-0.8100.001
55A55VAL0-0.0120.0229.5480.0470.0470.0000.0000.0000.000
56A56ARG10.9130.96812.3630.0370.0370.0000.0000.0000.000
57A57ARG10.8630.93115.5860.0690.0690.0000.0000.0000.000
58A58VAL00.0450.04111.136-0.003-0.0030.0000.0000.0000.000
59A59TYR0-0.004-0.00614.3260.0070.0070.0000.0000.0000.000
60A60ALA00.0280.00914.1970.0040.0040.0000.0000.0000.000
61A61ILE00.0220.01215.8000.0000.0000.0000.0000.0000.000
62A62ASP-1-0.819-0.94117.6120.0370.0370.0000.0000.0000.000
63A63ARG10.9190.97719.906-0.024-0.0240.0000.0000.0000.000
64A64ASN0-0.008-0.00221.084-0.012-0.0120.0000.0000.0000.000
65A65PRO00.0910.04421.437-0.005-0.0050.0000.0000.0000.000
66A66GLU-1-0.900-0.95421.282-0.064-0.0640.0000.0000.0000.000
67A67ALA0-0.0230.01217.406-0.017-0.0170.0000.0000.0000.000
68A68ILE00.0310.02816.939-0.021-0.0210.0000.0000.0000.000
69A69SER00.0170.01217.902-0.025-0.0250.0000.0000.0000.000
70A70THR0-0.040-0.05314.248-0.023-0.0230.0000.0000.0000.000
71A71THR0-0.028-0.01512.524-0.043-0.0430.0000.0000.0000.000
72A72GLU-1-0.908-0.95613.717-0.172-0.1720.0000.0000.0000.000
73A73MET0-0.038-0.01115.814-0.028-0.0280.0000.0000.0000.000
74A74ASN00.016-0.00110.456-0.101-0.1010.0000.0000.0000.000
75A75LEU00.0270.02310.951-0.095-0.0950.0000.0000.0000.000
76A76GLN00.0330.01712.5710.0040.0040.0000.0000.0000.000
77A77ARG10.8270.91712.6540.2600.2600.0000.0000.0000.000
78A78HIS10.8520.9258.5330.8310.8310.0000.0000.0000.000
79A79GLY0-0.0220.00410.7960.0510.0510.0000.0000.0000.000
80A80LEU0-0.0140.0008.1040.0240.0240.0000.0000.0000.000
81A81GLY00.0540.00412.765-0.003-0.0030.0000.0000.0000.000
82A82ASP-1-0.915-0.93715.031-0.075-0.0750.0000.0000.0000.000
83A83ASN0-0.106-0.05912.6530.0020.0020.0000.0000.0000.000
84A84VAL0-0.019-0.01312.887-0.008-0.0080.0000.0000.0000.000
85A85THR0-0.066-0.02715.8290.0130.0130.0000.0000.0000.000
86A86LEU00.0170.01115.8730.0010.0010.0000.0000.0000.000
87A87MET0-0.055-0.03719.0280.0090.0090.0000.0000.0000.000
88A88GLU-1-0.876-0.94321.193-0.029-0.0290.0000.0000.0000.000
89A89GLY0-0.028-0.01223.3960.0010.0010.0000.0000.0000.000
90A90ASP-1-0.898-0.96223.8630.0120.0120.0000.0000.0000.000
91A91ALA00.0280.00221.456-0.002-0.0020.0000.0000.0000.000
92A92PRO00.0450.02723.148-0.004-0.0040.0000.0000.0000.000
93A93GLU-1-0.901-0.94825.733-0.005-0.0050.0000.0000.0000.000
94A94ALA0-0.035-0.02323.036-0.003-0.0030.0000.0000.0000.000
95A95LEU00.0250.00819.722-0.004-0.0040.0000.0000.0000.000
96A96CYS0-0.026-0.00923.452-0.001-0.0010.0000.0000.0000.000
97A97LYS10.8720.94125.8850.0150.0150.0000.0000.0000.000
98A98ILE0-0.047-0.00719.941-0.004-0.0040.0000.0000.0000.000
99A99PRO0-0.066-0.03021.7260.0050.0050.0000.0000.0000.000
100A100ASP-1-0.837-0.91422.553-0.004-0.0040.0000.0000.0000.000
101A101ILE0-0.089-0.06517.464-0.007-0.0070.0000.0000.0000.000
102A102ASP-1-0.845-0.90616.084-0.018-0.0180.0000.0000.0000.000
103A103ILE0-0.0100.00010.712-0.001-0.0010.0000.0000.0000.000
104A104ALA00.0340.01414.171-0.009-0.0090.0000.0000.0000.000
105A105VAL0-0.025-0.0069.1290.0170.0170.0000.0000.0000.000
106A106VAL00.002-0.00112.402-0.009-0.0090.0000.0000.0000.000
107A107GLY00.0470.01413.8330.0400.0400.0000.0000.0000.000
108A108GLY0-0.024-0.02114.335-0.006-0.0060.0000.0000.0000.000
109A109SER0-0.007-0.01217.626-0.021-0.0210.0000.0000.0000.000
110A110GLY00.0040.00219.994-0.011-0.0110.0000.0000.0000.000
111A111GLY0-0.039-0.01322.717-0.008-0.0080.0000.0000.0000.000
112A112GLU-1-0.818-0.91424.7970.0220.0220.0000.0000.0000.000
113A113LEU00.002-0.00319.5820.0000.0000.0000.0000.0000.000
114A114GLN00.0530.01523.061-0.005-0.0050.0000.0000.0000.000
115A115GLU-1-0.939-0.97425.7070.0160.0160.0000.0000.0000.000
116A116ILE00.0080.00420.009-0.003-0.0030.0000.0000.0000.000
117A117LEU0-0.011-0.01919.191-0.003-0.0030.0000.0000.0000.000
118A118ARG10.9330.97722.488-0.029-0.0290.0000.0000.0000.000
119A119ILE00.0380.03224.126-0.002-0.0020.0000.0000.0000.000
120A120ILE0-0.026-0.02618.070-0.003-0.0030.0000.0000.0000.000
121A121LYS10.8540.92721.936-0.029-0.0290.0000.0000.0000.000
122A122ASP-1-0.956-0.97123.7400.0140.0140.0000.0000.0000.000
123A123LYS10.8060.91922.3490.0040.0040.0000.0000.0000.000
124A124LEU0-0.058-0.00217.951-0.005-0.0050.0000.0000.0000.000
125A125LYS10.9190.96720.6350.0190.0190.0000.0000.0000.000
126A126PRO00.009-0.01821.4330.0020.0020.0000.0000.0000.000
127A127GLY0-0.0130.00120.621-0.002-0.0020.0000.0000.0000.000
128A128GLY00.0150.01117.582-0.004-0.0040.0000.0000.0000.000
129A129ARG10.8210.90613.0270.0390.0390.0000.0000.0000.000
130A130ILE00.0450.02415.013-0.012-0.0120.0000.0000.0000.000
131A131ILE0-0.029-0.0229.4310.0170.0170.0000.0000.0000.000
132A132VAL00.0170.01113.184-0.002-0.0020.0000.0000.0000.000
133A133THR0-0.031-0.00611.3830.0740.0740.0000.0000.0000.000
134A134ALA0-0.004-0.01013.543-0.032-0.0320.0000.0000.0000.000
135A135ILE0-0.012-0.01114.4120.0300.0300.0000.0000.0000.000
136A136LEU00.0010.00217.974-0.012-0.0120.0000.0000.0000.000
137A137LEU00.011-0.00521.2970.0100.0100.0000.0000.0000.000
138A138GLU-1-0.853-0.94723.5530.0760.0760.0000.0000.0000.000
139A139THR0-0.0010.00218.957-0.002-0.0020.0000.0000.0000.000
140A140LYS10.8570.93218.531-0.170-0.1700.0000.0000.0000.000
141A141PHE0-0.021-0.00521.011-0.001-0.0010.0000.0000.0000.000
142A142GLU-1-0.813-0.91923.9920.0510.0510.0000.0000.0000.000
143A143ALA0-0.027-0.01519.560-0.005-0.0050.0000.0000.0000.000
144A144MET0-0.049-0.03720.913-0.004-0.0040.0000.0000.0000.000
145A145GLU-1-0.957-0.95322.7950.0450.0450.0000.0000.0000.000
146A146CYS00.0280.02223.791-0.006-0.0060.0000.0000.0000.000
147A147LEU0-0.004-0.00618.872-0.005-0.0050.0000.0000.0000.000
148A148ARG10.9520.97523.351-0.066-0.0660.0000.0000.0000.000
149A149ASP-1-0.903-0.94426.0270.0390.0390.0000.0000.0000.000
150A150LEU0-0.122-0.05324.079-0.005-0.0050.0000.0000.0000.000
151A151GLY0-0.021-0.01626.921-0.003-0.0030.0000.0000.0000.000
152A152PHE0-0.0220.00021.898-0.002-0.0020.0000.0000.0000.000
153A153ASP-1-0.902-0.93922.9630.0510.0510.0000.0000.0000.000
154A154VAL0-0.057-0.04619.9590.0030.0030.0000.0000.0000.000
155A155ASN0-0.043-0.00817.398-0.002-0.0020.0000.0000.0000.000
156A156ILE00.0330.00116.9410.0060.0060.0000.0000.0000.000
157A157THR0-0.043-0.00913.552-0.011-0.0110.0000.0000.0000.000
158A158GLU-1-0.850-0.92714.7640.2220.2220.0000.0000.0000.000
159A159LEU0-0.023-0.01110.0930.0050.0050.0000.0000.0000.000
160A160ASN00.008-0.00914.259-0.015-0.0150.0000.0000.0000.000
161A161ILE00.0070.01210.034-0.013-0.0130.0000.0000.0000.000
162A162ALA00.0210.00313.890-0.034-0.0340.0000.0000.0000.000
163A163ARG10.7350.8578.507-0.282-0.2820.0000.0000.0000.000
164A164GLY00.0430.01314.2380.0080.0080.0000.0000.0000.000
165A165ARG10.9210.96015.8580.0480.0480.0000.0000.0000.000
166A166ALA00.013-0.00418.2970.0210.0210.0000.0000.0000.000
167A167LEU0-0.062-0.03620.430-0.002-0.0020.0000.0000.0000.000
168A168ASP-1-0.886-0.94923.922-0.081-0.0810.0000.0000.0000.000
169A169ARG10.9370.96827.0350.0460.0460.0000.0000.0000.000
170A170GLY00.0460.02825.2810.0070.0070.0000.0000.0000.000
171A171THR0-0.0030.00519.134-0.012-0.0120.0000.0000.0000.000
172A172MET0-0.028-0.00321.5350.0150.0150.0000.0000.0000.000
173A173MET00.0230.01216.144-0.025-0.0250.0000.0000.0000.000
174A174VAL0-0.038-0.01517.1210.0110.0110.0000.0000.0000.000
175A175SER00.0270.00816.5350.0170.0170.0000.0000.0000.000
176A176ARG10.9110.97012.132-0.135-0.1350.0000.0000.0000.000
177A177ASN00.007-0.00115.278-0.018-0.0180.0000.0000.0000.000
178A178PRO00.0230.01114.9910.0530.0530.0000.0000.0000.000
179A179VAL0-0.0220.00311.781-0.002-0.0020.0000.0000.0000.000
180A180ALA00.0000.00714.2910.0130.0130.0000.0000.0000.000
181A181LEU0-0.019-0.0119.0240.0230.0230.0000.0000.0000.000
182A182ILE00.0140.00413.456-0.021-0.0210.0000.0000.0000.000
183A183TYR0-0.001-0.00813.534-0.007-0.0070.0000.0000.0000.000
184A184THR00.0400.02215.6600.0000.0000.0000.0000.0000.000
185A185GLY0-0.031-0.00816.845-0.001-0.0010.0000.0000.0000.000
186A186VAL0-0.0130.00215.343-0.004-0.0040.0000.0000.0000.000