Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 14L3Z

Calculation Name: 4LUB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4LUB

Chain ID: A

ChEMBL ID:

UniProt ID: Q8DUV6

Base Structure: X-ray

Registration Date: 2023-06-19

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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2112265.939002
FMO2-HF: Nuclear repulsion 2039026.184897
FMO2-HF: Total energy -73239.754104
FMO2-MP2: Total energy -73459.080806


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:THR)


Summations of interaction energy for fragment #1(A:5:THR)
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.
0.7553.183-0.013-0.797-1.6190.002
Interaction energy analysis for fragmet #1(A:5:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / 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].
3A7LYS10.9200.9623.7920.8172.456-0.017-0.648-0.9740.002
4A8ILE0-0.011-0.0105.9440.3260.3260.0000.0000.0000.000
5A9ALA00.0330.0329.1900.1010.1010.0000.0000.0000.000
6A10TYR0-0.035-0.02312.2090.0550.0550.0000.0000.0000.000
7A11LEU00.0230.01915.013-0.007-0.0070.0000.0000.0000.000
8A12GLY00.0010.02518.1010.0250.0250.0000.0000.0000.000
9A13PRO00.000-0.01218.862-0.004-0.0040.0000.0000.0000.000
10A14SER00.020-0.02615.5270.0040.0040.0000.0000.0000.000
11A15GLY0-0.013-0.00317.384-0.005-0.0050.0000.0000.0000.000
12A16SER0-0.041-0.00318.975-0.001-0.0010.0000.0000.0000.000
13A17PHE00.039-0.01119.4480.0160.0160.0000.0000.0000.000
14A18THR00.0750.02617.1550.0120.0120.0000.0000.0000.000
15A19HIS00.0510.05612.273-0.019-0.0190.0000.0000.0000.000
16A20ASN00.016-0.00814.9110.0460.0460.0000.0000.0000.000
17A21VAL0-0.0170.00916.8060.0220.0220.0000.0000.0000.000
18A22ALA00.004-0.00212.1950.0220.0220.0000.0000.0000.000
19A23LEU0-0.046-0.02811.4440.0720.0720.0000.0000.0000.000
20A24HIS0-0.028-0.00812.6760.0700.0700.0000.0000.0000.000
21A25ALA0-0.0240.00313.8240.0240.0240.0000.0000.0000.000
22A26PHE00.014-0.0208.7020.0060.0060.0000.0000.0000.000
23A27PRO00.0450.0328.7790.1060.1060.0000.0000.0000.000
24A28ALA0-0.071-0.0374.991-0.057-0.0570.0000.0000.0000.000
25A29ALA0-0.033-0.0073.9381.2531.6810.003-0.087-0.3450.000
26A30ASP-1-0.871-0.9243.866-0.731-0.3480.002-0.061-0.3240.000
27A31LEU00.0040.0045.243-0.449-0.471-0.001-0.0010.0240.000
28A32LEU0-0.012-0.0167.9510.0720.0720.0000.0000.0000.000
29A33PRO00.0000.01111.232-0.028-0.0280.0000.0000.0000.000
30A34PHE00.006-0.01212.640-0.019-0.0190.0000.0000.0000.000
31A35GLU-1-0.910-0.94617.535-0.023-0.0230.0000.0000.0000.000
32A36ASN00.021-0.00521.1450.0020.0020.0000.0000.0000.000
33A37ILE00.0440.01021.093-0.017-0.0170.0000.0000.0000.000
34A38THR0-0.029-0.04521.206-0.021-0.0210.0000.0000.0000.000
35A39GLU-1-0.930-0.98319.541-0.151-0.1510.0000.0000.0000.000
36A40VAL0-0.072-0.01716.228-0.036-0.0360.0000.0000.0000.000
37A41ILE0-0.007-0.00516.540-0.047-0.0470.0000.0000.0000.000
38A42LYS10.9500.97618.0350.1020.1020.0000.0000.0000.000
39A43ALA00.0060.04113.755-0.036-0.0360.0000.0000.0000.000
40A44TYR0-0.016-0.00713.288-0.085-0.0850.0000.0000.0000.000
41A45GLU-1-0.839-0.89614.880-0.220-0.2200.0000.0000.0000.000
42A46SER0-0.100-0.07416.247-0.013-0.0130.0000.0000.0000.000
43A47LYS10.8990.94313.0470.4200.4200.0000.0000.0000.000
44A48GLN0-0.033-0.00711.054-0.110-0.1100.0000.0000.0000.000
45A49VAL0-0.052-0.0248.674-0.273-0.2730.0000.0000.0000.000
46A50CYS0-0.062-0.0377.692-0.163-0.1630.0000.0000.0000.000
47A51PHE00.0440.0159.5680.1740.1740.0000.0000.0000.000
48A52ALA00.0050.01212.074-0.057-0.0570.0000.0000.0000.000
49A53ILE0-0.037-0.00612.7820.0410.0410.0000.0000.0000.000
50A54VAL00.0220.00316.2270.0010.0010.0000.0000.0000.000
51A55PRO0-0.045-0.01119.8210.0090.0090.0000.0000.0000.000
52A56VAL00.0260.01522.906-0.010-0.0100.0000.0000.0000.000
53A57GLU-1-0.791-0.88325.640-0.006-0.0060.0000.0000.0000.000
54A58ASN00.0270.00827.5550.0100.0100.0000.0000.0000.000
55A59SER0-0.009-0.00429.811-0.002-0.0020.0000.0000.0000.000
56A60ILE0-0.057-0.03032.2840.0000.0000.0000.0000.0000.000
57A61GLU-1-0.913-0.95832.1460.0010.0010.0000.0000.0000.000
58A62GLY00.0160.03033.036-0.003-0.0030.0000.0000.0000.000
59A63SER0-0.017-0.03930.4990.0010.0010.0000.0000.0000.000
60A64VAL0-0.024-0.00726.5390.0000.0000.0000.0000.0000.000
61A65HIS00.025-0.00329.033-0.008-0.0080.0000.0000.0000.000
62A66GLU-1-0.797-0.86925.713-0.062-0.0620.0000.0000.0000.000
63A67THR00.034-0.00323.512-0.010-0.0100.0000.0000.0000.000
64A68PHE00.0350.01426.103-0.010-0.0100.0000.0000.0000.000
65A69ASP-1-0.797-0.85928.738-0.047-0.0470.0000.0000.0000.000
66A70TYR0-0.008-0.02222.8640.0040.0040.0000.0000.0000.000
67A71LEU00.0430.01922.519-0.009-0.0090.0000.0000.0000.000
68A72PHE0-0.0040.01326.366-0.005-0.0050.0000.0000.0000.000
69A73HIS0-0.046-0.02829.991-0.005-0.0050.0000.0000.0000.000
70A74GLN0-0.093-0.03526.858-0.004-0.0040.0000.0000.0000.000
71A75ALA00.0450.04723.113-0.008-0.0080.0000.0000.0000.000
72A76LYS10.8720.92723.9450.1280.1280.0000.0000.0000.000
73A77ILE00.0100.00919.397-0.014-0.0140.0000.0000.0000.000
74A78GLU-1-0.768-0.86321.282-0.080-0.0800.0000.0000.0000.000
75A79ALA0-0.022-0.01520.127-0.018-0.0180.0000.0000.0000.000
76A80VAL0-0.0090.00415.9270.0100.0100.0000.0000.0000.000
77A81ALA0-0.004-0.01917.2540.0230.0230.0000.0000.0000.000
78A82GLU-1-0.745-0.81619.248-0.015-0.0150.0000.0000.0000.000
79A83ILE00.0000.00416.3900.0150.0150.0000.0000.0000.000
80A84ILE0-0.025-0.01121.101-0.010-0.0100.0000.0000.0000.000
81A85LEU0-0.035-0.02420.0780.0100.0100.0000.0000.0000.000
82A173GLU-1-0.912-0.95825.397-0.010-0.0100.0000.0000.0000.000
83A174ASN0-0.028-0.03124.666-0.002-0.0020.0000.0000.0000.000
84A175TYR0-0.045-0.04025.2590.0060.0060.0000.0000.0000.000
85A176THR0-0.0040.00925.9020.0060.0060.0000.0000.0000.000
86A177ARG10.7190.84124.7100.0130.0130.0000.0000.0000.000
87A178PHE00.0280.00219.677-0.005-0.0050.0000.0000.0000.000
88A179TRP0-0.011-0.01520.4970.0010.0010.0000.0000.0000.000
89A180VAL00.000-0.00814.228-0.006-0.0060.0000.0000.0000.000
90A181LEU0-0.022-0.01416.6900.0010.0010.0000.0000.0000.000
91A182GLY00.048-0.00215.022-0.043-0.0430.0000.0000.0000.000
92A183ASP-1-0.985-0.97414.961-0.255-0.2550.0000.0000.0000.000
93A184GLU-1-0.916-0.96214.513-0.167-0.1670.0000.0000.0000.000
94A185THR0-0.018-0.02614.525-0.014-0.0140.0000.0000.0000.000
95A186PRO0-0.0320.01110.8490.0230.0230.0000.0000.0000.000
96A187THR0-0.018-0.02410.4470.0080.0080.0000.0000.0000.000
97A188ILE0-0.0020.00411.3540.1000.1000.0000.0000.0000.000
98A189HIS0-0.060-0.0199.999-0.091-0.0910.0000.0000.0000.000
99A190LEU0-0.020-0.01914.924-0.016-0.0160.0000.0000.0000.000
100A191LYS10.8560.92518.431-0.064-0.0640.0000.0000.0000.000
101A192GLU-1-0.840-0.90820.6310.0410.0410.0000.0000.0000.000
102A193GLU-1-0.880-0.92322.3930.0490.0490.0000.0000.0000.000
103A194ASP-1-0.812-0.90825.1240.0030.0030.0000.0000.0000.000
104A195GLN0-0.0070.01022.701-0.006-0.0060.0000.0000.0000.000
105A196LYS10.9040.96526.1490.0010.0010.0000.0000.0000.000
106A197ILE00.0010.00026.664-0.006-0.0060.0000.0000.0000.000
107A198SER0-0.031-0.01627.7170.0030.0030.0000.0000.0000.000
108A199LEU0-0.004-0.01429.210-0.008-0.0080.0000.0000.0000.000
109A200ALA0-0.0120.00231.7800.0040.0040.0000.0000.0000.000
110A201LEU0-0.010-0.01233.319-0.003-0.0030.0000.0000.0000.000
111A202THR00.0200.00536.9510.0000.0000.0000.0000.0000.000
112A203LEU0-0.026-0.01839.5200.0000.0000.0000.0000.0000.000
113A204PRO00.0240.00243.180-0.001-0.0010.0000.0000.0000.000
114A205ASP-1-0.925-0.96146.224-0.028-0.0280.0000.0000.0000.000
115A206ASN0-0.070-0.03442.6570.0000.0000.0000.0000.0000.000
116A207LEU00.0490.03144.7900.0010.0010.0000.0000.0000.000
117A208PRO00.020-0.01244.7160.0000.0000.0000.0000.0000.000
118A209GLY0-0.027-0.00345.8270.0010.0010.0000.0000.0000.000
119A210ALA0-0.003-0.00546.5630.0010.0010.0000.0000.0000.000
120A211LEU00.0340.02141.000-0.001-0.0010.0000.0000.0000.000
121A212TYR00.0410.00644.2240.0000.0000.0000.0000.0000.000
122A213LYS10.9491.00246.2610.0240.0240.0000.0000.0000.000
123A214ALA00.0530.03840.7690.0000.0000.0000.0000.0000.000
124A215LEU00.021-0.00240.8160.0000.0000.0000.0000.0000.000
125A216SER0-0.032-0.03742.7710.0020.0020.0000.0000.0000.000
126A217THR0-0.046-0.01741.1990.0000.0000.0000.0000.0000.000
127A218PHE00.0110.00436.4410.0000.0000.0000.0000.0000.000
128A219ALA00.0230.01841.0170.0010.0010.0000.0000.0000.000
129A220TRP0-0.113-0.06643.6460.0020.0020.0000.0000.0000.000
130A221ARG10.7600.86140.4750.0250.0250.0000.0000.0000.000
131A222GLY0-0.007-0.00341.7490.0000.0000.0000.0000.0000.000
132A223ILE0-0.061-0.02136.0780.0010.0010.0000.0000.0000.000
133A224ASP-1-0.860-0.92137.377-0.006-0.0060.0000.0000.0000.000
134A225LEU0-0.051-0.03936.001-0.001-0.0010.0000.0000.0000.000
135A226THR0-0.034-0.02332.8110.0030.0030.0000.0000.0000.000
136A227LYS10.8150.90430.4650.0190.0190.0000.0000.0000.000
137A228ILE0-0.024-0.01535.151-0.003-0.0030.0000.0000.0000.000
138A229GLU-1-0.828-0.87433.728-0.015-0.0150.0000.0000.0000.000
139A230SER0-0.075-0.02636.492-0.003-0.0030.0000.0000.0000.000
140A231ARG10.8430.89433.3390.0350.0350.0000.0000.0000.000
141A232PRO00.005-0.00836.844-0.001-0.0010.0000.0000.0000.000
142A233LEU0-0.021-0.00637.241-0.003-0.0030.0000.0000.0000.000
143A234LYS10.8200.90134.1600.0410.0410.0000.0000.0000.000
144A235THR00.009-0.00739.194-0.001-0.0010.0000.0000.0000.000
145A236ILE0-0.013-0.00742.2250.0020.0020.0000.0000.0000.000
146A237LEU0-0.013-0.02044.5060.0000.0000.0000.0000.0000.000
147A238GLY00.0010.00045.3430.0010.0010.0000.0000.0000.000
148A239GLU-1-0.810-0.86543.096-0.034-0.0340.0000.0000.0000.000
149A240TYR0-0.057-0.03740.0860.0000.0000.0000.0000.0000.000
150A241PHE0-0.0060.01032.545-0.001-0.0010.0000.0000.0000.000
151A242PHE00.027-0.02137.3360.0030.0030.0000.0000.0000.000
152A243ILE0-0.0270.00531.088-0.004-0.0040.0000.0000.0000.000
153A244ILE0-0.008-0.00233.9360.0050.0050.0000.0000.0000.000
154A245ASP-1-0.768-0.85730.389-0.026-0.0260.0000.0000.0000.000
155A246PHE0-0.028-0.03231.7300.0030.0030.0000.0000.0000.000
156A247GLU-1-0.848-0.91931.233-0.002-0.0020.0000.0000.0000.000
157A248ASN0-0.100-0.07527.530-0.005-0.0050.0000.0000.0000.000
158A249HIS0-0.020-0.01030.158-0.002-0.0020.0000.0000.0000.000
159A250ASN0-0.014-0.01232.396-0.003-0.0030.0000.0000.0000.000
160A251GLU-1-0.780-0.88728.011-0.043-0.0430.0000.0000.0000.000
161A252LYS10.8200.92132.4850.0350.0350.0000.0000.0000.000
162A253LEU0-0.031-0.02135.538-0.001-0.0010.0000.0000.0000.000
163A254VAL00.0660.03032.327-0.001-0.0010.0000.0000.0000.000
164A255SER0-0.028-0.00434.486-0.003-0.0030.0000.0000.0000.000
165A256PHE0-0.024-0.01535.803-0.001-0.0010.0000.0000.0000.000
166A257ALA00.0330.03037.6800.0000.0000.0000.0000.0000.000
167A258LEU00.0000.01032.9700.0000.0000.0000.0000.0000.000
168A259GLU-1-0.842-0.92637.704-0.040-0.0400.0000.0000.0000.000
169A260GLU-1-0.747-0.84940.362-0.024-0.0240.0000.0000.0000.000
170A261LEU0-0.0140.00137.6780.0010.0010.0000.0000.0000.000
171A262THR0-0.004-0.01939.542-0.001-0.0010.0000.0000.0000.000
172A263SER0-0.107-0.04941.7840.0010.0010.0000.0000.0000.000
173A264ILE0-0.059-0.02744.7020.0020.0020.0000.0000.0000.000
174A265GLY0-0.023-0.00744.5430.0010.0010.0000.0000.0000.000
175A266ILE0-0.085-0.04139.9090.0000.0000.0000.0000.0000.000
176A267HIS00.0080.00938.191-0.004-0.0040.0000.0000.0000.000
177A268TYR00.009-0.00833.0170.0010.0010.0000.0000.0000.000
178A269LYS10.7740.87328.1400.0910.0910.0000.0000.0000.000
179A270ILE00.009-0.00426.8980.0060.0060.0000.0000.0000.000
180A271LEU0-0.021-0.01026.708-0.010-0.0100.0000.0000.0000.000
181A272GLY00.0500.01624.144-0.009-0.0090.0000.0000.0000.000
182A273LYS10.8280.91523.6960.0960.0960.0000.0000.0000.000
183A274TYR0-0.051-0.02321.653-0.007-0.0070.0000.0000.0000.000
184A275ALA00.0750.05520.5890.0030.0030.0000.0000.0000.000
185A276VAL0-0.041-0.03221.6620.0010.0010.0000.0000.0000.000
186A277TYR0-0.007-0.03718.5610.0110.0110.0000.0000.0000.000
187A278ARG10.8210.89821.621-0.055-0.0550.0000.0000.0000.000
188A279LEU0-0.002-0.00219.1980.0100.0100.0000.0000.0000.000