FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: LNMQ9

Calculation Name: 2B1E-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2B1E

Chain ID: A

ChEMBL ID:

UniProt ID: P19658

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 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 545
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -9675144.15857
FMO2-HF: Nuclear repulsion 9455524.938697
FMO2-HF: Total energy -219619.219873
FMO2-MP2: Total energy -220260.674824


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:67:THR)


Summations of interaction energy for fragment #1(A:67: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.
-0.6931.825-0.007-0.837-1.6740.002
Interaction energy analysis for fragmet #1(A:67:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.023 / q_NPA : -0.026
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].
3A69ASN00.025-0.0203.8340.3942.195-0.014-0.723-1.0630.002
4A70SER00.0200.0105.329-0.107-0.015-0.001-0.005-0.0860.000
5A71VAL0-0.021-0.0076.280-0.081-0.0810.0000.0000.0000.000
6A72ALA0-0.0120.0244.050-0.0960.022-0.001-0.018-0.0990.000
7A73SER00.005-0.0216.172-0.070-0.0700.0000.0000.0000.000
8A74VAL00.0870.0347.950-0.058-0.0580.0000.0000.0000.000
9A75LYS10.9580.98110.0640.3060.3060.0000.0000.0000.000
10A76ASP-1-0.884-0.9255.831-0.489-0.4890.0000.0000.0000.000
11A77LEU00.0350.0224.259-0.337-0.209-0.001-0.011-0.1170.000
12A78ALA00.0570.0316.7070.0660.0660.0000.0000.0000.000
13A79ASN0-0.064-0.0227.2350.1790.1790.0000.0000.0000.000
14A80GLU-1-0.836-0.9163.393-2.698-2.3190.010-0.080-0.3090.000
15A81ALA00.0620.0326.8280.0650.0650.0000.0000.0000.000
16A82SER0-0.030-0.0289.759-0.018-0.0180.0000.0000.0000.000
17A83LYS10.7760.8735.8081.4891.4890.0000.0000.0000.000
18A84TYR00.0140.0015.316-0.304-0.3040.0000.0000.0000.000
19A85GLU-1-0.761-0.84911.386-0.022-0.0220.0000.0000.0000.000
20A86ILE0-0.023-0.01114.1640.0000.0000.0000.0000.0000.000
21A87ILE0-0.058-0.03311.5750.0040.0040.0000.0000.0000.000
22A88LEU00.0370.01614.7450.0050.0050.0000.0000.0000.000
23A89GLN0-0.046-0.01617.2380.0120.0120.0000.0000.0000.000
24A90LYS10.8800.95217.2200.1880.1880.0000.0000.0000.000
25A91GLY00.0030.01020.8740.0050.0050.0000.0000.0000.000
26A92ILE00.0280.00721.800-0.010-0.0100.0000.0000.0000.000
27A93ASN0-0.0030.00122.885-0.005-0.0050.0000.0000.0000.000
28A94GLN0-0.032-0.01022.069-0.014-0.0140.0000.0000.0000.000
29A95VAL0-0.032-0.00117.158-0.012-0.0120.0000.0000.0000.000
30A96GLY00.0300.03219.509-0.012-0.0120.0000.0000.0000.000
31A97LEU00.0230.00219.993-0.002-0.0020.0000.0000.0000.000
32A98LYS10.9560.98919.2990.0860.0860.0000.0000.0000.000
33A99GLN00.0300.00515.9980.0170.0170.0000.0000.0000.000
34A100TYR00.0150.00515.3880.0040.0040.0000.0000.0000.000
35A101THR00.0190.01216.5130.0130.0130.0000.0000.0000.000
36A102GLN0-0.020-0.00111.5470.0280.0280.0000.0000.0000.000
37A103VAL0-0.018-0.01211.4820.0220.0220.0000.0000.0000.000
38A104VAL00.002-0.00512.2780.0570.0570.0000.0000.0000.000
39A105HIS00.0580.03013.2310.0400.0400.0000.0000.0000.000
40A106LYS10.7940.9186.717-0.075-0.0750.0000.0000.0000.000
41A107LEU0-0.032-0.0169.5040.1560.1560.0000.0000.0000.000
42A108ASP-1-0.850-0.93211.4010.1700.1700.0000.0000.0000.000
43A109ASP-1-0.822-0.9059.6490.1740.1740.0000.0000.0000.000
44A110MET0-0.089-0.0385.710-0.062-0.0620.0000.0000.0000.000
45A111LEU0-0.028-0.0269.258-0.026-0.0260.0000.0000.0000.000
46A112GLU-1-0.893-0.94412.7090.1530.1530.0000.0000.0000.000
47A113ASP-1-0.869-0.9318.6570.4140.4140.0000.0000.0000.000
48A114ILE0-0.164-0.0879.244-0.005-0.0050.0000.0000.0000.000
49A115GLN00.0250.01111.794-0.037-0.0370.0000.0000.0000.000
50A116SER00.0450.04014.002-0.028-0.0280.0000.0000.0000.000
51A117GLY00.018-0.00216.6360.0090.0090.0000.0000.0000.000
52A118GLN0-0.165-0.08817.831-0.011-0.0110.0000.0000.0000.000
53A119ALA00.0090.01913.0140.0100.0100.0000.0000.0000.000
54A120ASN0-0.033-0.02715.0230.0030.0030.0000.0000.0000.000
55A121ARG10.8440.9278.332-0.394-0.3940.0000.0000.0000.000
56A122GLU-1-0.936-0.95715.6720.1340.1340.0000.0000.0000.000
57A123GLU-1-0.846-0.91018.1520.1170.1170.0000.0000.0000.000
58A124ASN0-0.030-0.01517.549-0.015-0.0150.0000.0000.0000.000
59A125SER00.0490.00119.5240.0060.0060.0000.0000.0000.000
60A126GLU-1-0.947-0.97013.8970.0420.0420.0000.0000.0000.000
61A127PHE00.0390.00713.6630.0040.0040.0000.0000.0000.000
62A128HIS0-0.029-0.03315.9410.0000.0000.0000.0000.0000.000
63A129GLY00.0040.01217.897-0.003-0.0030.0000.0000.0000.000
64A130ILE0-0.010-0.0089.912-0.010-0.0100.0000.0000.0000.000
65A131LEU0-0.0010.02314.3500.0160.0160.0000.0000.0000.000
66A132THR00.0120.00216.028-0.007-0.0070.0000.0000.0000.000
67A133HIS0-0.120-0.06713.6840.0090.0090.0000.0000.0000.000
68A134LEU00.0250.00310.798-0.014-0.0140.0000.0000.0000.000
69A135GLU-1-0.847-0.91814.9390.0910.0910.0000.0000.0000.000
70A136GLN0-0.044-0.03518.208-0.013-0.0130.0000.0000.0000.000
71A137LEU0-0.025-0.00613.969-0.017-0.0170.0000.0000.0000.000
72A138ILE00.0530.04514.461-0.022-0.0220.0000.0000.0000.000
73A139LYS10.9250.96118.064-0.061-0.0610.0000.0000.0000.000
74A140ARG10.8110.88518.811-0.010-0.0100.0000.0000.0000.000
75A141SER0-0.006-0.01818.335-0.014-0.0140.0000.0000.0000.000
76A142GLU-1-0.794-0.87520.3210.0320.0320.0000.0000.0000.000
77A143ALA0-0.039-0.02522.571-0.005-0.0050.0000.0000.0000.000
78A144GLN0-0.035-0.01923.238-0.007-0.0070.0000.0000.0000.000
79A145LEU00.0260.01220.686-0.006-0.0060.0000.0000.0000.000
80A146ARG10.8860.93524.687-0.019-0.0190.0000.0000.0000.000
81A147VAL0-0.017-0.00128.292-0.002-0.0020.0000.0000.0000.000
82A148TYR0-0.032-0.03327.146-0.002-0.0020.0000.0000.0000.000
83A149PHE00.0220.01028.706-0.002-0.0020.0000.0000.0000.000
84A150ILE00.0300.00730.302-0.001-0.0010.0000.0000.0000.000
85A151SER0-0.043-0.01532.2470.0000.0000.0000.0000.0000.000
86A152ILE00.0230.01629.9220.0000.0000.0000.0000.0000.000
87A153LEU00.0230.04334.0030.0000.0000.0000.0000.0000.000
88A154ASN0-0.082-0.04036.3030.0010.0010.0000.0000.0000.000
89A155SER0-0.049-0.02636.8480.0000.0000.0000.0000.0000.000
90A156ILE0-0.0110.01138.8050.0000.0000.0000.0000.0000.000
91A157LYS10.8520.91140.1920.0220.0220.0000.0000.0000.000
92A158PRO00.010-0.02044.7380.0000.0000.0000.0000.0000.000
93A159PHE0-0.023-0.01047.279-0.001-0.0010.0000.0000.0000.000
94A160ASP-1-0.806-0.91750.579-0.010-0.0100.0000.0000.0000.000
95A161PRO00.021-0.00152.219-0.001-0.0010.0000.0000.0000.000
96A162GLN00.0380.01454.0290.0000.0000.0000.0000.0000.000
97A163ILE0-0.031-0.00255.0760.0000.0000.0000.0000.0000.000
98A164ASN0-0.019-0.01050.6470.0000.0000.0000.0000.0000.000
99A165ILE00.0810.05154.7190.0000.0000.0000.0000.0000.000
100A166THR0-0.047-0.02957.3200.0000.0000.0000.0000.0000.000
101A167LYS10.8740.92356.5180.0140.0140.0000.0000.0000.000
102A168LYS10.8470.93856.8870.0110.0110.0000.0000.0000.000
103A169MET0-0.040-0.01552.187-0.001-0.0010.0000.0000.0000.000
104A170PRO00.0440.01348.5000.0010.0010.0000.0000.0000.000
105A171PHE0-0.045-0.01947.6820.0000.0000.0000.0000.0000.000
106A172PRO00.001-0.00144.420-0.001-0.0010.0000.0000.0000.000
107A173TYR0-0.062-0.06339.5100.0020.0020.0000.0000.0000.000
108A174TYR0-0.056-0.03236.3670.0000.0000.0000.0000.0000.000
109A175GLU-1-0.880-0.91934.521-0.039-0.0390.0000.0000.0000.000
110A176ASP-1-0.817-0.92434.427-0.032-0.0320.0000.0000.0000.000
111A177GLN0-0.072-0.05130.867-0.001-0.0010.0000.0000.0000.000
112A178GLN0-0.010-0.01330.4990.0000.0000.0000.0000.0000.000
113A179LEU00.0320.02231.5660.0010.0010.0000.0000.0000.000
114A180GLY00.0300.02429.3190.0010.0010.0000.0000.0000.000
115A181ALA0-0.044-0.03526.9030.0000.0000.0000.0000.0000.000
116A182LEU0-0.021-0.01627.3910.0030.0030.0000.0000.0000.000
117A183SER00.0390.00128.8630.0030.0030.0000.0000.0000.000
118A184TRP0-0.018-0.02318.896-0.002-0.0020.0000.0000.0000.000
119A185ILE0-0.028-0.01523.9840.0030.0030.0000.0000.0000.000
120A186LEU0-0.021-0.00125.6020.0060.0060.0000.0000.0000.000
121A187ASP-1-0.864-0.93324.057-0.011-0.0110.0000.0000.0000.000
122A188TYR0-0.107-0.08117.9100.0030.0030.0000.0000.0000.000
123A189PHE0-0.006-0.02422.3310.0050.0050.0000.0000.0000.000
124A190HIS0-0.096-0.05524.7460.0060.0060.0000.0000.0000.000
125A191GLY0-0.035-0.00821.9320.0030.0030.0000.0000.0000.000
126A192ASN00.0010.00718.7170.0050.0050.0000.0000.0000.000
127A193SER0-0.030-0.01322.1930.0020.0020.0000.0000.0000.000
128A194GLU-1-0.815-0.89625.2390.0230.0230.0000.0000.0000.000
129A195GLY00.0190.00727.344-0.004-0.0040.0000.0000.0000.000
130A196SER00.000-0.00729.350-0.002-0.0020.0000.0000.0000.000
131A197ILE00.0490.03028.848-0.003-0.0030.0000.0000.0000.000
132A198ILE0-0.022-0.00528.557-0.003-0.0030.0000.0000.0000.000
133A199GLN00.0160.01230.878-0.003-0.0030.0000.0000.0000.000
134A200ASP-1-0.868-0.94233.7970.0050.0050.0000.0000.0000.000
135A201ILE0-0.054-0.01731.328-0.002-0.0020.0000.0000.0000.000
136A202LEU00.0030.00633.949-0.002-0.0020.0000.0000.0000.000
137A203VAL00.004-0.00535.677-0.002-0.0020.0000.0000.0000.000
138A204GLY00.0190.01738.488-0.001-0.0010.0000.0000.0000.000
139A205GLU-1-0.833-0.90836.565-0.010-0.0100.0000.0000.0000.000
140A206ARG10.8180.87338.6740.0120.0120.0000.0000.0000.000
141A207SER0-0.006-0.01241.1790.0000.0000.0000.0000.0000.000
142A208LYS10.8000.88640.1620.0080.0080.0000.0000.0000.000
143A209LEU0-0.033-0.00941.5470.0000.0000.0000.0000.0000.000
144A210ILE00.0660.02844.1650.0000.0000.0000.0000.0000.000
145A211LEU00.0020.00947.1600.0000.0000.0000.0000.0000.000
146A212LYS10.9040.95346.0170.0100.0100.0000.0000.0000.000
147A213CYS0-0.0660.00147.916-0.001-0.0010.0000.0000.0000.000
148A214MET00.0090.00250.8660.0000.0000.0000.0000.0000.000
149A215ALA0-0.0090.00252.7970.0000.0000.0000.0000.0000.000
150A216PHE0-0.039-0.01951.6650.0000.0000.0000.0000.0000.000
151A217LEU0-0.047-0.02256.1540.0000.0000.0000.0000.0000.000
152A218GLU-1-0.880-0.93157.124-0.005-0.0050.0000.0000.0000.000
153A219PRO0-0.016-0.00858.9170.0000.0000.0000.0000.0000.000
154A220PHE0-0.050-0.02060.9150.0000.0000.0000.0000.0000.000
155A221ALA0-0.0170.01461.4630.0010.0010.0000.0000.0000.000
156A234LYS10.8580.91373.2060.0050.0050.0000.0000.0000.000
157A235GLY0-0.009-0.00969.5840.0000.0000.0000.0000.0000.000
158A236SER0-0.028-0.01769.2150.0000.0000.0000.0000.0000.000
159A237SER0-0.029-0.00567.4600.0000.0000.0000.0000.0000.000
160A238GLY00.0850.04564.3510.0000.0000.0000.0000.0000.000
161A239MET0-0.038-0.02560.4850.0000.0000.0000.0000.0000.000
162A240ASN0-0.015-0.00661.8320.0000.0000.0000.0000.0000.000
163A241SER00.0840.04659.9820.0000.0000.0000.0000.0000.000
164A242TYR0-0.013-0.00756.2520.0000.0000.0000.0000.0000.000
165A243THR00.0320.02156.8090.0000.0000.0000.0000.0000.000
166A244GLU-1-0.894-0.95056.588-0.010-0.0100.0000.0000.0000.000
167A245ALA0-0.013-0.02054.0730.0000.0000.0000.0000.0000.000
168A246LEU0-0.004-0.00451.7100.0000.0000.0000.0000.0000.000
169A247LEU0-0.017-0.00851.8560.0000.0000.0000.0000.0000.000
170A248GLY00.0200.02151.1790.0000.0000.0000.0000.0000.000
171A249PHE00.004-0.02247.059-0.001-0.0010.0000.0000.0000.000
172A250ILE0-0.021-0.00346.9780.0000.0000.0000.0000.0000.000
173A251ALA0-0.014-0.00747.0050.0000.0000.0000.0000.0000.000
174A252ASN00.012-0.00544.857-0.001-0.0010.0000.0000.0000.000
175A253GLU-1-0.740-0.84342.145-0.012-0.0120.0000.0000.0000.000
176A254LYN0-0.050-0.01341.7900.0010.0010.0000.0000.0000.000
177A255SER0-0.011-0.00641.6870.0000.0000.0000.0000.0000.000
178A256LEU00.0480.03737.112-0.001-0.0010.0000.0000.0000.000
179A257VAL0-0.032-0.02237.306-0.001-0.0010.0000.0000.0000.000
180A258ASP-1-0.882-0.95436.682-0.010-0.0100.0000.0000.0000.000
181A259ASP-1-0.878-0.90636.069-0.021-0.0210.0000.0000.0000.000
182A260LEU0-0.083-0.03832.518-0.002-0.0020.0000.0000.0000.000
183A261TYR0-0.0050.01431.5670.0010.0010.0000.0000.0000.000
184A262SER00.0540.03229.996-0.002-0.0020.0000.0000.0000.000
185A263GLN0-0.007-0.01532.6030.0030.0030.0000.0000.0000.000
186A264TYR0-0.034-0.03935.0650.0010.0010.0000.0000.0000.000
187A265THR00.0050.01631.9520.0010.0010.0000.0000.0000.000
188A266GLU-1-0.865-0.96034.5710.0060.0060.0000.0000.0000.000
189A267SER00.0340.04233.812-0.001-0.0010.0000.0000.0000.000
190A268LYS10.8180.91735.9850.0090.0090.0000.0000.0000.000
191A269PRO0-0.028-0.02138.257-0.001-0.0010.0000.0000.0000.000
192A270HIS00.0520.03938.4800.0000.0000.0000.0000.0000.000
193A271VAL00.0140.00436.0070.0000.0000.0000.0000.0000.000
194A272LEU00.0150.00039.3940.0000.0000.0000.0000.0000.000
195A273SER00.0050.01042.3040.0000.0000.0000.0000.0000.000
196A274GLN00.0160.00839.310-0.001-0.0010.0000.0000.0000.000
197A275ILE0-0.0330.00239.3590.0000.0000.0000.0000.0000.000
198A276LEU00.012-0.00243.7360.0000.0000.0000.0000.0000.000
199A277SER0-0.017-0.01946.9550.0000.0000.0000.0000.0000.000
200A278PRO0-0.005-0.00546.2150.0000.0000.0000.0000.0000.000
201A279LEU00.0260.01347.4240.0000.0000.0000.0000.0000.000
202A280ILE00.0030.00550.9530.0000.0000.0000.0000.0000.000
203A281SER0-0.030-0.00952.5470.0000.0000.0000.0000.0000.000
204A282ALA0-0.013-0.00853.5690.0000.0000.0000.0000.0000.000
205A283TYR00.020-0.00555.1990.0000.0000.0000.0000.0000.000
206A284ALA00.024-0.00156.9730.0000.0000.0000.0000.0000.000
207A285LYS10.9480.97858.3030.0020.0020.0000.0000.0000.000
208A286LEU00.0040.01259.1360.0000.0000.0000.0000.0000.000
209A287PHE00.013-0.01061.1130.0000.0000.0000.0000.0000.000
210A288GLY00.0110.00162.8160.0000.0000.0000.0000.0000.000
211A289ALA0-0.019-0.01264.2910.0000.0000.0000.0000.0000.000
212A290ASN0-0.026-0.02164.9470.0000.0000.0000.0000.0000.000
213A291LEU0-0.0150.00267.1060.0000.0000.0000.0000.0000.000
214A292LYS10.8570.93266.5420.0010.0010.0000.0000.0000.000
215A293ILE0-0.139-0.04170.2020.0000.0000.0000.0000.0000.000
216A294VAL00.0120.00572.0390.0000.0000.0000.0000.0000.000
217A295ARG10.9410.96274.4570.0020.0020.0000.0000.0000.000
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