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: 53LVZ

Calculation Name: 2H8R-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2H8R

Chain ID: A

ChEMBL ID:

UniProt ID: P35680

Base Structure: X-ray

Registration Date: 2023-06-21

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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1844936.606083
FMO2-HF: Nuclear repulsion 1771870.832041
FMO2-HF: Total energy -73065.774042
FMO2-MP2: Total energy -73278.571493


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:90:SER)


Summations of interaction energy for fragment #1(A:90:SER)
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.
-17.188-11.312.421-3.227-5.0720.019
Interaction energy analysis for fragmet #1(A:90:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / q_NPA : 0.007
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].
3A92LEU00.0890.0772.633-1.7021.2080.785-1.553-2.1420.007
4A93LYS10.9220.9402.547-11.714-9.5161.631-1.294-2.5360.011
5A94GLU-1-0.892-0.9383.622-1.397-0.6270.005-0.380-0.3940.001
6A95LEU0-0.040-0.0365.637-0.305-0.3050.0000.0000.0000.000
7A96GLN0-0.032-0.0186.836-0.054-0.0540.0000.0000.0000.000
8A97ALA0-0.040-0.0197.955-0.282-0.2820.0000.0000.0000.000
9A98LEU0-0.044-0.0149.590-0.252-0.2520.0000.0000.0000.000
10A99ASN0-0.024-0.01211.623-0.206-0.2060.0000.0000.0000.000
11A100THR0-0.0050.01313.3720.0530.0530.0000.0000.0000.000
12A101GLU-1-0.801-0.89815.6380.4030.4030.0000.0000.0000.000
13A102GLU-1-0.824-0.92617.9680.4790.4790.0000.0000.0000.000
14A103ALA0-0.007-0.02515.074-0.042-0.0420.0000.0000.0000.000
15A104ALA0-0.0190.00517.052-0.024-0.0240.0000.0000.0000.000
16A105GLU-1-0.787-0.87818.7870.2880.2880.0000.0000.0000.000
17A106GLN0-0.100-0.06617.888-0.056-0.0560.0000.0000.0000.000
18A107ARG10.8740.92115.357-0.528-0.5280.0000.0000.0000.000
19A108ALA00.0540.02820.685-0.028-0.0280.0000.0000.0000.000
20A109GLU-1-0.834-0.88124.1190.1810.1810.0000.0000.0000.000
21A110VAL0-0.102-0.06021.908-0.018-0.0180.0000.0000.0000.000
22A111ASP-1-0.872-0.96524.0340.1710.1710.0000.0000.0000.000
23A112ARG10.8400.92725.686-0.189-0.1890.0000.0000.0000.000
24A113MET0-0.062-0.06327.503-0.007-0.0070.0000.0000.0000.000
25A114LEU0-0.164-0.06125.461-0.012-0.0120.0000.0000.0000.000
26A115SER0-0.034-0.00729.591-0.010-0.0100.0000.0000.0000.000
27A116GLU-1-0.818-0.91332.2660.1220.1220.0000.0000.0000.000
28A117ASP-1-0.846-0.91733.9260.0920.0920.0000.0000.0000.000
29A118PRO00.0570.02333.5400.0060.0060.0000.0000.0000.000
30A119TRP0-0.005-0.00234.2980.0070.0070.0000.0000.0000.000
31A120ARG10.9450.95136.561-0.107-0.1070.0000.0000.0000.000
32A121ALA00.0580.04531.0220.0050.0050.0000.0000.0000.000
33A122ALA0-0.009-0.00532.7590.0050.0050.0000.0000.0000.000
34A123LYS10.7970.92433.747-0.095-0.0950.0000.0000.0000.000
35A124MET00.0570.02532.292-0.002-0.0020.0000.0000.0000.000
36A125ILE00.0560.04528.5310.0040.0040.0000.0000.0000.000
37A126LYS10.8660.93331.566-0.097-0.0970.0000.0000.0000.000
38A127GLY0-0.0110.00234.028-0.002-0.0020.0000.0000.0000.000
39A128TYR00.0980.03527.011-0.004-0.0040.0000.0000.0000.000
40A129MET0-0.124-0.03529.0680.0030.0030.0000.0000.0000.000
41A130GLN00.021-0.02531.539-0.007-0.0070.0000.0000.0000.000
42A131GLN0-0.0280.01033.6710.0010.0010.0000.0000.0000.000
43A132HIS00.0750.02230.064-0.006-0.0060.0000.0000.0000.000
44A133ASN0-0.049-0.01431.6640.0000.0000.0000.0000.0000.000
45A134ILE00.0720.04426.6470.0030.0030.0000.0000.0000.000
46A135PRO0-0.018-0.02028.367-0.009-0.0090.0000.0000.0000.000
47A136GLN00.0120.00628.5950.0070.0070.0000.0000.0000.000
48A137ARG10.8980.90924.526-0.157-0.1570.0000.0000.0000.000
49A138GLU-1-0.847-0.90723.1580.2560.2560.0000.0000.0000.000
50A139VAL00.0570.01923.2690.0110.0110.0000.0000.0000.000
51A140VAL0-0.0100.04323.2840.0070.0070.0000.0000.0000.000
52A141ASP-1-0.891-0.92320.7320.1670.1670.0000.0000.0000.000
53A142VAL00.0820.03517.7040.0110.0110.0000.0000.0000.000
54A143THR0-0.149-0.10218.4010.0120.0120.0000.0000.0000.000
55A144GLY00.0510.04019.9350.0000.0000.0000.0000.0000.000
56A145LEU0-0.062-0.03321.397-0.025-0.0250.0000.0000.0000.000
57A146ASN00.0310.02324.954-0.003-0.0030.0000.0000.0000.000
58A147GLN00.0720.01027.909-0.003-0.0030.0000.0000.0000.000
59A148SER00.0450.01129.6510.0000.0000.0000.0000.0000.000
60A149HIS0-0.088-0.05329.9950.0000.0000.0000.0000.0000.000
61A150LEU00.0850.06227.436-0.001-0.0010.0000.0000.0000.000
62A151SER0-0.097-0.03230.887-0.001-0.0010.0000.0000.0000.000
63A152GLN00.1190.03334.143-0.002-0.0020.0000.0000.0000.000
64A153HIS0-0.0080.01130.7760.0080.0080.0000.0000.0000.000
65A154LEU0-0.035-0.01731.1950.0020.0020.0000.0000.0000.000
66A155ASN0-0.037-0.03334.3530.0010.0010.0000.0000.0000.000
67A156LYS10.9160.93337.934-0.063-0.0630.0000.0000.0000.000
68A157GLY00.0350.03336.890-0.002-0.0020.0000.0000.0000.000
69A158THR0-0.048-0.01536.144-0.002-0.0020.0000.0000.0000.000
70A159PRO00.0870.05034.8910.0080.0080.0000.0000.0000.000
71A160MET0-0.0300.00028.690-0.001-0.0010.0000.0000.0000.000
72A161LYS10.9870.98329.006-0.049-0.0490.0000.0000.0000.000
73A162THR00.0930.01726.6190.0050.0050.0000.0000.0000.000
74A163GLN00.1380.07521.0780.0220.0220.0000.0000.0000.000
75A164LYS10.9370.98023.559-0.080-0.0800.0000.0000.0000.000
76A165ARG10.9970.99424.972-0.107-0.1070.0000.0000.0000.000
77A166ALA00.0820.06223.1530.0140.0140.0000.0000.0000.000
78A167ALA0-0.089-0.05020.9830.0300.0300.0000.0000.0000.000
79A168LEU0-0.061-0.01022.1330.0070.0070.0000.0000.0000.000
80A169TYR00.012-0.01624.0730.0100.0100.0000.0000.0000.000
81A170THR00.0790.02318.7750.0150.0150.0000.0000.0000.000
82A171TRP0-0.0190.01520.3880.0120.0120.0000.0000.0000.000
83A172TYR0-0.027-0.02621.3760.0100.0100.0000.0000.0000.000
84A173VAL00.000-0.02921.4360.0110.0110.0000.0000.0000.000
85A174ARG10.9330.96314.573-0.564-0.5640.0000.0000.0000.000
86A175LYS10.7710.87020.196-0.297-0.2970.0000.0000.0000.000
87A176GLN00.0310.05422.370-0.028-0.0280.0000.0000.0000.000
88A177ARG10.9240.94420.555-0.363-0.3630.0000.0000.0000.000
89A178GLU-1-0.832-0.89519.2220.3450.3450.0000.0000.0000.000
90A179ILE0-0.054-0.04821.292-0.020-0.0200.0000.0000.0000.000
91A180LEU0-0.0130.00124.545-0.018-0.0180.0000.0000.0000.000
92A181ARG10.9150.94817.957-0.476-0.4760.0000.0000.0000.000
93A182GLN0-0.165-0.03623.5990.0000.0000.0000.0000.0000.000
94A183PHE00.055-0.02725.067-0.020-0.0200.0000.0000.0000.000
95A184ASN0-0.097-0.00527.695-0.008-0.0080.0000.0000.0000.000
96A185GLN00.0540.00025.671-0.022-0.0220.0000.0000.0000.000
97A186THR0-0.054-0.02025.054-0.007-0.0070.0000.0000.0000.000
98A187VAL00.0370.02827.791-0.009-0.0090.0000.0000.0000.000
99A231MET00.0800.03118.3750.0020.0020.0000.0000.0000.000
100A232ARG10.9140.94819.803-0.135-0.1350.0000.0000.0000.000
101A233ARG10.9591.02423.126-0.112-0.1120.0000.0000.0000.000
102A234ASN0-0.016-0.04425.621-0.022-0.0220.0000.0000.0000.000
103A235ARG10.9710.95827.761-0.096-0.0960.0000.0000.0000.000
104A236PHE0-0.0480.01331.3360.0030.0030.0000.0000.0000.000
105A237LYS10.8610.93334.149-0.111-0.1110.0000.0000.0000.000
106A238TRP00.0930.06236.1640.0060.0060.0000.0000.0000.000
107A239GLY00.0640.02839.1400.0010.0010.0000.0000.0000.000
108A240PRO0-0.008-0.02239.653-0.005-0.0050.0000.0000.0000.000
109A241ALA00.0740.02741.598-0.004-0.0040.0000.0000.0000.000
110A242SER0-0.011-0.03140.450-0.004-0.0040.0000.0000.0000.000
111A243GLN00.012-0.01643.334-0.005-0.0050.0000.0000.0000.000
112A244GLN0-0.0670.00845.132-0.005-0.0050.0000.0000.0000.000
113A245ILE00.0160.01245.904-0.004-0.0040.0000.0000.0000.000
114A246LEU00.003-0.02244.651-0.002-0.0020.0000.0000.0000.000
115A247TYR00.0250.00747.645-0.004-0.0040.0000.0000.0000.000
116A248GLN00.0390.01551.124-0.001-0.0010.0000.0000.0000.000
117A249ALA0-0.037-0.01351.345-0.002-0.0020.0000.0000.0000.000
118A250TYR0-0.046-0.02552.092-0.002-0.0020.0000.0000.0000.000
119A251ASP-1-0.986-0.97454.0300.0450.0450.0000.0000.0000.000
120A252ARG10.8660.93353.623-0.054-0.0540.0000.0000.0000.000
121A253GLN0-0.038-0.04256.063-0.002-0.0020.0000.0000.0000.000
122A254LYS11.0161.00955.301-0.034-0.0340.0000.0000.0000.000
123A255ASN0-0.018-0.02854.4100.0010.0010.0000.0000.0000.000
124A256PRO00.0610.05951.437-0.001-0.0010.0000.0000.0000.000
125A257SER0-0.0280.00052.4860.0010.0010.0000.0000.0000.000
126A258LYS10.9380.96446.340-0.058-0.0580.0000.0000.0000.000
127A259GLU-1-0.880-0.92249.6560.0520.0520.0000.0000.0000.000
128A260GLU-1-0.762-0.88650.5130.0540.0540.0000.0000.0000.000
129A261ARG10.8890.92547.463-0.050-0.0500.0000.0000.0000.000
130A262GLU-1-0.873-0.96445.7810.0650.0650.0000.0000.0000.000
131A263ALA00.0540.06246.3270.0040.0040.0000.0000.0000.000
132A264LEU0-0.018-0.02146.8500.0040.0040.0000.0000.0000.000
133A265VAL0-0.127-0.04041.2950.0040.0040.0000.0000.0000.000
134A266GLU-1-0.820-0.92742.1740.0970.0970.0000.0000.0000.000
135A267GLU-1-0.993-0.99743.8210.0720.0720.0000.0000.0000.000
136A268CYS00.0100.00741.9270.0030.0030.0000.0000.0000.000
137A269ASN00.0520.02038.2860.0090.0090.0000.0000.0000.000
138A270ARG10.9741.01439.177-0.077-0.0770.0000.0000.0000.000
139A271ALA0-0.0120.00740.7500.0050.0050.0000.0000.0000.000
140A272GLU-1-0.812-0.90136.9030.1180.1180.0000.0000.0000.000
141A273CYS0-0.029-0.01536.7430.0110.0110.0000.0000.0000.000
142A274LEU00.0440.03337.7270.0040.0040.0000.0000.0000.000
143A275GLN0-0.095-0.04136.743-0.002-0.0020.0000.0000.0000.000
144A276ARG10.7520.89231.919-0.148-0.1480.0000.0000.0000.000
145A277GLY0-0.034-0.02234.2860.0100.0100.0000.0000.0000.000
146A278VAL0-0.086-0.03932.7520.0080.0080.0000.0000.0000.000
147A279SER00.0830.03435.845-0.012-0.0120.0000.0000.0000.000
148A280PRO0-0.018-0.00637.1100.0030.0030.0000.0000.0000.000
149A281SER0-0.073-0.02337.044-0.004-0.0040.0000.0000.0000.000
150A282LYN00.0750.01628.0650.0050.0050.0000.0000.0000.000
151A283ALA00.0900.04733.6850.0090.0090.0000.0000.0000.000
152A284HIS0-0.029-0.02930.023-0.006-0.0060.0000.0000.0000.000
153A285GLY00.0310.01929.4230.0080.0080.0000.0000.0000.000
154A286LEU0-0.024-0.00229.3530.0120.0120.0000.0000.0000.000
155A287GLY0-0.0080.01528.9500.0040.0040.0000.0000.0000.000
156A288SER00.023-0.01828.526-0.011-0.0110.0000.0000.0000.000
157A289ASN0-0.130-0.05330.457-0.019-0.0190.0000.0000.0000.000
158A290LEU00.0140.01132.728-0.007-0.0070.0000.0000.0000.000
159A291VAL0-0.0130.00334.664-0.005-0.0050.0000.0000.0000.000
160A292THR00.0760.01437.2630.0010.0010.0000.0000.0000.000
161A293GLU-1-0.761-0.87240.1190.0770.0770.0000.0000.0000.000
162A294VAL00.0730.02940.170-0.003-0.0030.0000.0000.0000.000
163A295ARG10.8080.90633.478-0.112-0.1120.0000.0000.0000.000
164A296VAL00.1050.02041.250-0.002-0.0020.0000.0000.0000.000
165A297TYR0-0.095-0.01744.342-0.004-0.0040.0000.0000.0000.000
166A298ASN0-0.121-0.07242.650-0.006-0.0060.0000.0000.0000.000
167A299TRP0-0.034-0.03143.909-0.001-0.0010.0000.0000.0000.000
168A300PHE00.0210.04545.795-0.002-0.0020.0000.0000.0000.000
169A301ALA00.1130.02148.084-0.002-0.0020.0000.0000.0000.000
170A302ASN0-0.046-0.00844.436-0.005-0.0050.0000.0000.0000.000
171A303ARG10.8190.88547.819-0.051-0.0510.0000.0000.0000.000
172A304ARG10.7860.92750.615-0.046-0.0460.0000.0000.0000.000
173A305LYS10.8940.90047.006-0.045-0.0450.0000.0000.0000.000
174A306GLU-1-0.854-0.89548.2670.0500.0500.0000.0000.0000.000
175A307GLU-1-0.909-0.94852.4260.0380.0380.0000.0000.0000.000
176A308ALA0-0.063-0.02355.665-0.002-0.0020.0000.0000.0000.000