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: V5MM1

Calculation Name: 2H4R-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2H4R

Chain ID: A

ChEMBL ID:

UniProt ID: O73790

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 OptAll
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 370
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -6707803.667861
FMO2-HF: Nuclear repulsion 6556341.39444
FMO2-HF: Total energy -151462.273421
FMO2-MP2: Total energy -151902.291957


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:-2:GLU)


Summations of interaction energy for fragment #1(A:-2:GLU)
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.
-182.794-191.32734.772-15.962-10.280.097
Interaction energy analysis for fragmet #1(A:-2:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.818 / q_NPA : -0.890
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].
3A0SER0-0.061-0.0571.510-36.710-47.75731.520-13.981-6.4930.085
4A1MET0-0.053-0.0282.213-13.679-12.5763.237-1.660-2.6800.011
5A2GLU-1-0.911-0.9484.46528.47428.815-0.001-0.040-0.3010.000
6A3GLN00.0020.0035.886-6.387-6.3870.0000.0000.0000.000
7A4VAL0-0.0120.0137.757-3.134-3.1340.0000.0000.0000.000
8A5SER00.000-0.0168.436-1.903-1.9030.0000.0000.0000.000
9A6ALA00.0350.01810.254-2.228-2.2280.0000.0000.0000.000
10A7SER0-0.072-0.02712.060-1.782-1.7820.0000.0000.0000.000
11A8ILE0-0.001-0.01611.725-1.611-1.6110.0000.0000.0000.000
12A9GLY00.0180.01914.392-1.355-1.3550.0000.0000.0000.000
13A10ASN00.006-0.01215.984-1.883-1.8830.0000.0000.0000.000
14A11PHE00.0280.01117.816-0.946-0.9460.0000.0000.0000.000
15A12THR0-0.051-0.05218.142-0.805-0.8050.0000.0000.0000.000
16A13VAL00.0110.00620.637-0.713-0.7130.0000.0000.0000.000
17A14ASP-1-0.824-0.89822.66812.53812.5380.0000.0000.0000.000
18A15LEU0-0.040-0.02522.756-0.586-0.5860.0000.0000.0000.000
19A16PHE0-0.022-0.01924.676-0.575-0.5750.0000.0000.0000.000
20A17ASN00.002-0.00326.612-0.726-0.7260.0000.0000.0000.000
21A18LYS10.8260.89828.215-10.093-10.0930.0000.0000.0000.000
22A19LEU0-0.034-0.01227.508-0.398-0.3980.0000.0000.0000.000
23A20ASN0-0.012-0.01230.611-0.699-0.6990.0000.0000.0000.000
24A21GLU-1-0.895-0.94632.4449.0869.0860.0000.0000.0000.000
25A22THR0-0.048-0.00933.765-0.328-0.3280.0000.0000.0000.000
26A23ASN0-0.053-0.03433.899-0.279-0.2790.0000.0000.0000.000
27A24ARG10.9570.98534.610-8.534-8.5340.0000.0000.0000.000
28A25ASP-1-0.828-0.90637.5097.8007.8000.0000.0000.0000.000
29A26LYS10.8470.91136.293-8.060-8.0600.0000.0000.0000.000
30A27ASN00.0290.00932.5000.0950.0950.0000.0000.0000.000
31A28ILE0-0.0060.01228.367-0.035-0.0350.0000.0000.0000.000
32A29PHE0-0.021-0.00424.4710.2950.2950.0000.0000.0000.000
33A30PHE00.0140.01022.006-0.100-0.1000.0000.0000.0000.000
34A31SER0-0.004-0.00719.2320.4860.4860.0000.0000.0000.000
35A32PRO00.0050.01018.0080.1000.1000.0000.0000.0000.000
36A33TRP00.0700.03510.9980.8470.8470.0000.0000.0000.000
37A34SER0-0.0570.00116.1140.3770.3770.0000.0000.0000.000
38A35ILE00.0390.01518.6070.1910.1910.0000.0000.0000.000
39A36SER00.0460.02515.8690.1760.1760.0000.0000.0000.000
40A37SER00.010-0.03514.1660.2380.2380.0000.0000.0000.000
41A38ALA0-0.069-0.04015.7360.1160.1160.0000.0000.0000.000
42A39LEU00.0170.00619.324-0.309-0.3090.0000.0000.0000.000
43A40ALA00.0520.04514.110-0.318-0.3180.0000.0000.0000.000
44A41LEU00.0060.01316.1990.2050.2050.0000.0000.0000.000
45A42THR0-0.016-0.01717.971-0.553-0.5530.0000.0000.0000.000
46A43TYR00.0170.00613.372-0.776-0.7760.0000.0000.0000.000
47A44LEU0-0.029-0.01013.943-0.100-0.1000.0000.0000.0000.000
48A45ALA0-0.056-0.02516.840-0.359-0.3590.0000.0000.0000.000
49A46ALA0-0.0070.01320.192-0.800-0.8000.0000.0000.0000.000
50A47LYS10.8900.94920.263-14.284-14.2840.0000.0000.0000.000
51A48GLY00.0410.01123.220-0.341-0.3410.0000.0000.0000.000
52A49SER00.0060.00423.5160.5150.5150.0000.0000.0000.000
53A50THR00.0170.01724.3410.0570.0570.0000.0000.0000.000
54A51ALA00.002-0.00919.4820.3280.3280.0000.0000.0000.000
55A52ARG10.8070.87919.876-12.019-12.0190.0000.0000.0000.000
56A53GLU-1-0.698-0.81721.06311.80511.8050.0000.0000.0000.000
57A54MET0-0.075-0.03919.748-0.017-0.0170.0000.0000.0000.000
58A55ALA00.013-0.00316.6720.4460.4460.0000.0000.0000.000
59A56GLU-1-0.751-0.83417.70013.67513.6750.0000.0000.0000.000
60A57VAL0-0.013-0.00220.2480.2130.2130.0000.0000.0000.000
61A58LEU0-0.081-0.04117.132-0.203-0.2030.0000.0000.0000.000
62A59HIS0-0.014-0.01216.5451.7281.7280.0000.0000.0000.000
63A60PHE0-0.077-0.03913.3791.3591.3590.0000.0000.0000.000
64A61THR0-0.051-0.04013.4451.2741.2740.0000.0000.0000.000
65A62GLU-1-0.891-0.93716.11916.02416.0240.0000.0000.0000.000
66A63ALA0-0.041-0.00818.999-0.926-0.9260.0000.0000.0000.000
67A91ALA00.0480.01311.1750.0670.0670.0000.0000.0000.000
68A92GLU-1-0.930-0.9738.65828.93428.9340.0000.0000.0000.000
69A93ASN00.0210.0134.6070.1920.295-0.001-0.016-0.0870.000
70A94ILE00.0960.0515.8255.6555.6550.0000.0000.0000.000
71A95HIS00.0140.0268.5730.8500.8500.0000.0000.0000.000
72A96SER00.005-0.0064.074-4.497-4.2920.000-0.048-0.1570.000
73A97GLY00.0320.0185.1963.4773.4770.0000.0000.0000.000
74A98PHE0-0.009-0.0115.990-2.775-2.7750.0000.0000.0000.000
75A99LYS10.7920.8906.489-46.453-46.4530.0000.0000.0000.000
76A100GLU-1-0.767-0.8483.61145.59346.3550.017-0.217-0.5620.001
77A101LEU0-0.0030.0026.364-3.473-3.4730.0000.0000.0000.000
78A102LEU0-0.023-0.0018.001-2.783-2.7830.0000.0000.0000.000
79A103THR0-0.048-0.0398.909-3.051-3.0510.0000.0000.0000.000
80A104ALA0-0.054-0.0287.889-1.946-1.9460.0000.0000.0000.000
81A105PHE00.003-0.0139.964-2.012-2.0120.0000.0000.0000.000
82A106ASN0-0.052-0.02813.001-2.685-2.6850.0000.0000.0000.000
83A107LYS10.9530.9949.707-27.251-27.2510.0000.0000.0000.000
84A108PRO00.010-0.00115.084-0.681-0.6810.0000.0000.0000.000
85A109ARG10.9170.94517.556-15.716-15.7160.0000.0000.0000.000
86A110ASN0-0.0180.01214.0310.3290.3290.0000.0000.0000.000
87A111ASN0-0.023-0.01217.738-0.357-0.3570.0000.0000.0000.000
88A112TYR00.0180.00913.780-0.020-0.0200.0000.0000.0000.000
89A113SER0-0.041-0.02019.5640.1970.1970.0000.0000.0000.000
90A114LEU00.0370.01915.651-0.522-0.5220.0000.0000.0000.000
91A115ARG10.8430.93319.343-12.038-12.0380.0000.0000.0000.000
92A116SER00.046-0.00318.944-0.479-0.4790.0000.0000.0000.000
93A117ALA0-0.025-0.01521.071-0.075-0.0750.0000.0000.0000.000
94A118ASN00.0210.03017.932-1.139-1.1390.0000.0000.0000.000
95A119ARG10.8640.93021.535-12.519-12.5190.0000.0000.0000.000
96A120ILE00.0210.02822.426-0.486-0.4860.0000.0000.0000.000
97A121TYR0-0.003-0.01424.9300.0980.0980.0000.0000.0000.000
98A122VAL00.000-0.00828.087-0.101-0.1010.0000.0000.0000.000
99A123GLU-1-0.698-0.83030.1188.6368.6360.0000.0000.0000.000
100A124LYS10.9580.97833.163-8.356-8.3560.0000.0000.0000.000
101A125THR0-0.062-0.06934.5450.0890.0890.0000.0000.0000.000
102A126TYR0-0.054-0.02830.794-0.035-0.0350.0000.0000.0000.000
103A127ALA00.0210.01931.6280.1330.1330.0000.0000.0000.000
104A128LEU0-0.008-0.00726.3920.1650.1650.0000.0000.0000.000
105A129LEU00.0290.01623.990-0.224-0.2240.0000.0000.0000.000
106A130PRO00.0380.00523.6250.6280.6280.0000.0000.0000.000
107A131THR00.0360.01319.1380.3440.3440.0000.0000.0000.000
108A132TYR0-0.006-0.01718.8710.6440.6440.0000.0000.0000.000
109A133LEU0-0.0120.00019.0910.7580.7580.0000.0000.0000.000
110A134GLN0-0.014-0.00518.2590.8900.8900.0000.0000.0000.000
111A135LEU00.0040.00413.8331.2091.2090.0000.0000.0000.000
112A136SER00.008-0.01414.5031.6951.6950.0000.0000.0000.000
113A137LYS10.8340.90015.970-13.882-13.8820.0000.0000.0000.000
114A138LYS10.9090.96010.088-28.039-28.0390.0000.0000.0000.000
115A139TYR0-0.002-0.0058.1641.5981.5980.0000.0000.0000.000
116A140TYR00.039-0.02811.8241.4061.4060.0000.0000.0000.000
117A141LYS10.8460.93611.732-26.969-26.9690.0000.0000.0000.000
118A142ALA00.0360.03217.032-1.137-1.1370.0000.0000.0000.000
119A143GLU-1-0.816-0.88419.27814.65014.6500.0000.0000.0000.000
120A144PRO0-0.0070.00122.054-0.413-0.4130.0000.0000.0000.000
121A145GLN0-0.0180.00625.0540.0610.0610.0000.0000.0000.000
122A146LYS10.8420.91128.425-10.268-10.2680.0000.0000.0000.000
123A147VAL00.0270.02331.352-0.265-0.2650.0000.0000.0000.000
124A148ASN0-0.004-0.01534.2050.0430.0430.0000.0000.0000.000
125A149PHE00.0260.00331.850-0.175-0.1750.0000.0000.0000.000
126A150LYS10.9130.94937.594-8.663-8.6630.0000.0000.0000.000
127A151THR0-0.004-0.00140.371-0.133-0.1330.0000.0000.0000.000
128A152ALA00.0230.02840.717-0.177-0.1770.0000.0000.0000.000
129A153PRO00.0330.03238.7620.2050.2050.0000.0000.0000.000
130A154GLU-1-0.741-0.85838.8258.0418.0410.0000.0000.0000.000
131A155GLN0-0.0330.00239.331-0.052-0.0520.0000.0000.0000.000
132A156SER00.023-0.00135.3010.2190.2190.0000.0000.0000.000
133A157ARG10.8050.87135.079-7.963-7.9630.0000.0000.0000.000
134A158LYS10.8610.92135.611-7.621-7.6210.0000.0000.0000.000
135A159GLU-1-0.860-0.91632.35410.05210.0520.0000.0000.0000.000
136A160ILE00.0340.01630.1310.2150.2150.0000.0000.0000.000
137A161ASN0-0.013-0.01231.2120.5170.5170.0000.0000.0000.000
138A162THR0-0.042-0.03533.395-0.214-0.2140.0000.0000.0000.000
139A163TRP0-0.0130.00523.2710.0100.0100.0000.0000.0000.000
140A164VAL00.0370.00427.3940.2660.2660.0000.0000.0000.000
141A165GLU-1-0.809-0.87628.2209.3209.3200.0000.0000.0000.000
142A166LYS10.9280.97029.901-9.335-9.3350.0000.0000.0000.000
143A167GLN0-0.028-0.01022.506-0.081-0.0810.0000.0000.0000.000
144A168THR0-0.031-0.03825.3550.2020.2020.0000.0000.0000.000
145A169GLU-1-0.832-0.90226.96311.12411.1240.0000.0000.0000.000
146A170SER0-0.017-0.02529.511-0.254-0.2540.0000.0000.0000.000
147A171LYS10.8310.93829.245-10.322-10.3220.0000.0000.0000.000
148A172ILE0-0.0070.00726.892-0.060-0.0600.0000.0000.0000.000
149A173LYS10.8140.90630.977-8.835-8.8350.0000.0000.0000.000
150A174ASN0-0.061-0.05233.9780.0020.0020.0000.0000.0000.000
151A175LEU00.0680.06528.234-0.115-0.1150.0000.0000.0000.000
152A176LEU00.0020.01731.315-0.027-0.0270.0000.0000.0000.000
153A177SER00.0720.01234.537-0.315-0.3150.0000.0000.0000.000
154A178SER00.012-0.01938.1530.1320.1320.0000.0000.0000.000
155A179ASP-1-0.828-0.89540.0867.7587.7580.0000.0000.0000.000
156A180ASP-1-0.787-0.86034.8219.1489.1480.0000.0000.0000.000
157A181VAL0-0.020-0.01235.0120.2430.2430.0000.0000.0000.000
158A182LYS10.8540.91437.506-8.175-8.1750.0000.0000.0000.000
159A183ALA00.0420.03038.9820.2120.2120.0000.0000.0000.000
160A184THR00.000-0.00138.9630.0260.0260.0000.0000.0000.000
161A185THR0-0.086-0.04234.7140.2130.2130.0000.0000.0000.000
162A186ARG10.8770.92932.911-8.979-8.9790.0000.0000.0000.000
163A187LEU00.0180.00325.8400.1990.1990.0000.0000.0000.000
164A188ILE0-0.0190.00229.505-0.148-0.1480.0000.0000.0000.000
165A189LEU00.0010.00422.2780.2280.2280.0000.0000.0000.000
166A190VAL0-0.013-0.00225.770-0.287-0.2870.0000.0000.0000.000
167A191ASN00.034-0.00221.8980.8420.8420.0000.0000.0000.000
168A192ALA00.0650.04623.697-0.242-0.2420.0000.0000.0000.000
169A193ILE0-0.019-0.01419.0800.5230.5230.0000.0000.0000.000
170A194TYR0-0.051-0.02323.246-0.440-0.4400.0000.0000.0000.000
171A195PHE0-0.018-0.00619.6130.6350.6350.0000.0000.0000.000
172A196LYS10.8570.92022.711-11.489-11.4890.0000.0000.0000.000
173A197ALA00.012-0.00622.2130.6490.6490.0000.0000.0000.000
174A198GLU-1-0.839-0.91424.1709.6659.6650.0000.0000.0000.000
175A199TRP0-0.018-0.02624.8660.6540.6540.0000.0000.0000.000
176A200GLU-1-0.871-0.93623.40312.31312.3130.0000.0000.0000.000
177A201VAL00.0110.01426.347-0.280-0.2800.0000.0000.0000.000
178A202LYS10.8150.90329.864-9.777-9.7770.0000.0000.0000.000
179A203PHE0-0.003-0.00731.330-0.246-0.2460.0000.0000.0000.000
180A204GLN0-0.042-0.03834.9660.1310.1310.0000.0000.0000.000
181A205ALA00.0380.01438.470-0.096-0.0960.0000.0000.0000.000
182A206GLU-1-0.809-0.87940.1097.2907.2900.0000.0000.0000.000
183A207LYS10.8470.90840.704-7.499-7.4990.0000.0000.0000.000
184A208THR0-0.068-0.04938.9420.0310.0310.0000.0000.0000.000
185A209SER0-0.0150.00441.402-0.202-0.2020.0000.0000.0000.000
186A210ILE0-0.012-0.00643.0740.1400.1400.0000.0000.0000.000
187A211GLN0-0.011-0.01442.656-0.103-0.1030.0000.0000.0000.000
188A212PRO0-0.0210.00243.7980.0950.0950.0000.0000.0000.000
189A213PHE00.0080.00636.0320.0250.0250.0000.0000.0000.000
190A214ARG10.7820.81741.634-7.397-7.3970.0000.0000.0000.000
191A215LEU00.0080.00040.5410.1210.1210.0000.0000.0000.000
192A216SER0-0.017-0.01541.0920.0570.0570.0000.0000.0000.000
193A217LYS10.8380.90243.628-6.981-6.9810.0000.0000.0000.000
194A218ASN0-0.017-0.00646.228-0.015-0.0150.0000.0000.0000.000
195A219LYS10.9520.97446.271-6.534-6.5340.0000.0000.0000.000
196A220SER0-0.023-0.00144.6650.1470.1470.0000.0000.0000.000
197A221LYS10.9020.94842.484-7.255-7.2550.0000.0000.0000.000
198A222PRO00.0000.00043.6420.1330.1330.0000.0000.0000.000
199A223VAL00.0100.01138.4180.0760.0760.0000.0000.0000.000
200A224LYS10.8410.89039.740-7.788-7.7880.0000.0000.0000.000
201A225MET0-0.0350.00038.5210.3050.3050.0000.0000.0000.000
202A226MET00.0330.04332.851-0.168-0.1680.0000.0000.0000.000
203A227TYR0-0.056-0.04637.5310.0080.0080.0000.0000.0000.000
204A228MET0-0.028-0.00832.330-0.012-0.0120.0000.0000.0000.000
205A229ARG10.8290.90237.458-7.387-7.3870.0000.0000.0000.000
206A230ASP-1-0.807-0.88833.1648.9268.9260.0000.0000.0000.000
207A231THR0-0.058-0.04030.301-0.111-0.1110.0000.0000.0000.000
208A232PHE00.0080.00027.4930.2520.2520.0000.0000.0000.000
209A233PRO0-0.0060.01124.046-0.251-0.2510.0000.0000.0000.000
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