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: YZ332

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 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 370
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -6704095.399334
FMO2-HF: Nuclear repulsion 6552634.504882
FMO2-HF: Total energy -151460.894452
FMO2-MP2: Total energy -151901.075419


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.
-186.324-191.92436.639-16.837-14.2020.116
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 : -0.868 / q_NPA : -0.925
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].
3A0SER0-0.089-0.0901.577-34.864-44.57531.789-13.582-8.4960.086
4A1MET0-0.034-0.0182.567-14.977-14.4894.670-1.695-3.4630.015
5A2GLU-1-0.926-0.9474.39627.37127.684-0.001-0.035-0.2770.000
6A3GLN00.0190.0136.772-5.087-5.0870.0000.0000.0000.000
7A4VAL00.0140.0127.537-3.001-3.0010.0000.0000.0000.000
8A5SER00.006-0.0088.564-1.669-1.6690.0000.0000.0000.000
9A6ALA00.0140.01110.463-2.361-2.3610.0000.0000.0000.000
10A7SER0-0.042-0.01912.037-1.789-1.7890.0000.0000.0000.000
11A8ILE00.0270.01611.960-1.611-1.6110.0000.0000.0000.000
12A9GLY00.0170.02814.733-1.414-1.4140.0000.0000.0000.000
13A10ASN0-0.012-0.02515.765-1.942-1.9420.0000.0000.0000.000
14A11PHE00.0180.00917.389-0.973-0.9730.0000.0000.0000.000
15A12THR0-0.084-0.07918.250-0.860-0.8600.0000.0000.0000.000
16A13VAL00.0190.01320.619-0.730-0.7300.0000.0000.0000.000
17A14ASP-1-0.814-0.88522.48612.74512.7450.0000.0000.0000.000
18A15LEU0-0.053-0.03522.727-0.630-0.6300.0000.0000.0000.000
19A16PHE0-0.025-0.03124.680-0.565-0.5650.0000.0000.0000.000
20A17ASN00.003-0.00926.664-0.772-0.7720.0000.0000.0000.000
21A18LYS10.8350.91327.966-10.181-10.1810.0000.0000.0000.000
22A19LEU0-0.022-0.00527.699-0.407-0.4070.0000.0000.0000.000
23A20ASN0-0.005-0.02430.569-0.710-0.7100.0000.0000.0000.000
24A21GLU-1-0.897-0.93932.4949.1859.1850.0000.0000.0000.000
25A22THR0-0.056-0.00334.022-0.305-0.3050.0000.0000.0000.000
26A23ASN0-0.042-0.03234.227-0.220-0.2200.0000.0000.0000.000
27A24ARG10.9690.98834.579-8.629-8.6290.0000.0000.0000.000
28A25ASP-1-0.850-0.92137.4987.8547.8540.0000.0000.0000.000
29A26LYS10.8490.91736.646-8.045-8.0450.0000.0000.0000.000
30A27ASN00.0310.01132.8630.1010.1010.0000.0000.0000.000
31A28ILE00.0040.02828.3300.0410.0410.0000.0000.0000.000
32A29PHE0-0.0130.00025.3090.2700.2700.0000.0000.0000.000
33A30PHE00.0330.02022.083-0.119-0.1190.0000.0000.0000.000
34A31SER00.006-0.00119.7610.4700.4700.0000.0000.0000.000
35A32PRO00.0120.00818.1520.1660.1660.0000.0000.0000.000
36A33TRP00.0760.04110.8190.7320.7320.0000.0000.0000.000
37A34SER0-0.0490.01016.1810.4840.4840.0000.0000.0000.000
38A35ILE00.0390.01218.7240.1910.1910.0000.0000.0000.000
39A36SER00.0420.02115.4730.2400.2400.0000.0000.0000.000
40A37SER0-0.013-0.05114.0680.1800.1800.0000.0000.0000.000
41A38ALA0-0.050-0.01815.3930.2770.2770.0000.0000.0000.000
42A39LEU00.0240.00818.848-0.444-0.4440.0000.0000.0000.000
43A40ALA00.0520.04813.890-0.326-0.3260.0000.0000.0000.000
44A41LEU00.0160.00916.0240.0840.0840.0000.0000.0000.000
45A42THR0-0.026-0.01117.785-0.585-0.5850.0000.0000.0000.000
46A43TYR0-0.007-0.00913.473-0.878-0.8780.0000.0000.0000.000
47A44LEU0-0.011-0.00113.714-0.159-0.1590.0000.0000.0000.000
48A45ALA0-0.058-0.02316.755-0.288-0.2880.0000.0000.0000.000
49A46ALA0-0.0290.00919.922-0.942-0.9420.0000.0000.0000.000
50A47LYS10.9260.96020.143-14.317-14.3170.0000.0000.0000.000
51A48GLY00.0420.00422.860-0.379-0.3790.0000.0000.0000.000
52A49SER00.0300.00523.1400.5100.5100.0000.0000.0000.000
53A50THR00.0030.01924.131-0.110-0.1100.0000.0000.0000.000
54A51ALA00.010-0.01319.5990.2320.2320.0000.0000.0000.000
55A52ARG10.7900.86119.920-12.213-12.2130.0000.0000.0000.000
56A53GLU-1-0.715-0.82921.27711.85711.8570.0000.0000.0000.000
57A54MET0-0.067-0.02319.936-0.029-0.0290.0000.0000.0000.000
58A55ALA00.013-0.00616.8330.3210.3210.0000.0000.0000.000
59A56GLU-1-0.746-0.82017.80313.93313.9330.0000.0000.0000.000
60A57VAL00.0030.00720.4790.0630.0630.0000.0000.0000.000
61A58LEU0-0.092-0.05916.874-0.038-0.0380.0000.0000.0000.000
62A59HIS0-0.006-0.00116.2841.6671.6670.0000.0000.0000.000
63A60PHE0-0.098-0.05113.5441.2921.2920.0000.0000.0000.000
64A61THR0-0.021-0.01913.4211.4471.4470.0000.0000.0000.000
65A62GLU-1-0.912-0.94315.97316.12016.1200.0000.0000.0000.000
66A63ALA0-0.020-0.01118.787-0.708-0.7080.0000.0000.0000.000
67A91ALA00.0410.00311.5960.1070.1070.0000.0000.0000.000
68A92GLU-1-0.936-0.9718.33430.17930.1790.0000.0000.0000.000
69A93ASN00.013-0.0014.3842.2632.318-0.001-0.007-0.0470.000
70A94ILE00.0830.0465.9275.9365.9360.0000.0000.0000.000
71A95HIS00.0270.0308.4211.3901.3900.0000.0000.0000.000
72A96SER0-0.006-0.0052.782-11.028-9.0780.137-1.092-0.9950.012
73A97GLY00.0450.0184.1915.5235.689-0.001-0.021-0.1440.000
74A98PHE00.001-0.0025.214-3.079-3.052-0.0010.000-0.0260.000
75A99LYS10.7810.8916.613-46.990-46.9900.0000.0000.0000.000
76A100GLU-1-0.772-0.8503.37944.80445.9160.047-0.405-0.7540.003
77A101LEU0-0.0070.0116.264-2.348-2.3480.0000.0000.0000.000
78A102LEU0-0.029-0.0048.178-3.465-3.4650.0000.0000.0000.000
79A103THR0-0.060-0.0508.377-3.156-3.1560.0000.0000.0000.000
80A104ALA0-0.056-0.0238.144-2.340-2.3400.0000.0000.0000.000
81A105PHE00.002-0.01510.119-2.192-2.1920.0000.0000.0000.000
82A106ASN0-0.058-0.02913.178-2.892-2.8920.0000.0000.0000.000
83A107LYS10.9280.97910.096-26.621-26.6210.0000.0000.0000.000
84A108PRO00.0130.00714.966-0.764-0.7640.0000.0000.0000.000
85A109ARG10.9170.94217.761-15.725-15.7250.0000.0000.0000.000
86A110ASN0-0.0230.01114.3360.1240.1240.0000.0000.0000.000
87A111ASN0-0.011-0.00118.223-0.484-0.4840.0000.0000.0000.000
88A112TYR00.034-0.00114.3850.2690.2690.0000.0000.0000.000
89A113SER0-0.068-0.03519.9940.2900.2900.0000.0000.0000.000
90A114LEU00.0350.02116.176-0.411-0.4110.0000.0000.0000.000
91A115ARG10.8720.94319.858-12.330-12.3300.0000.0000.0000.000
92A116SER00.0670.02919.030-0.371-0.3710.0000.0000.0000.000
93A117ALA0-0.046-0.02621.0040.0080.0080.0000.0000.0000.000
94A118ASN00.0050.00017.646-1.253-1.2530.0000.0000.0000.000
95A119ARG10.9010.95221.278-12.761-12.7610.0000.0000.0000.000
96A120ILE00.0180.02121.870-0.436-0.4360.0000.0000.0000.000
97A121TYR0-0.013-0.02324.5400.1290.1290.0000.0000.0000.000
98A122VAL00.0370.01227.297-0.173-0.1730.0000.0000.0000.000
99A123GLU-1-0.685-0.83029.4198.7958.7950.0000.0000.0000.000
100A124LYS10.9650.98032.394-8.449-8.4490.0000.0000.0000.000
101A125THR0-0.090-0.08134.2170.0350.0350.0000.0000.0000.000
102A126TYR0-0.0040.00430.378-0.123-0.1230.0000.0000.0000.000
103A127ALA0-0.0030.00030.9360.1470.1470.0000.0000.0000.000
104A128LEU00.012-0.01525.6070.1490.1490.0000.0000.0000.000
105A129LEU00.0160.01223.565-0.229-0.2290.0000.0000.0000.000
106A130PRO00.0460.00823.2500.6060.6060.0000.0000.0000.000
107A131THR00.0500.01618.5230.2980.2980.0000.0000.0000.000
108A132TYR0-0.004-0.01518.5780.7410.7410.0000.0000.0000.000
109A133LEU00.004-0.00418.7570.7860.7860.0000.0000.0000.000
110A134GLN0-0.037-0.01517.9150.6060.6060.0000.0000.0000.000
111A135LEU0-0.017-0.00913.4631.2931.2930.0000.0000.0000.000
112A136SER00.016-0.01814.0191.7191.7190.0000.0000.0000.000
113A137LYS10.8230.89615.644-14.374-14.3740.0000.0000.0000.000
114A138LYS10.9000.9609.450-29.637-29.6370.0000.0000.0000.000
115A139TYR00.019-0.0077.268-0.047-0.0470.0000.0000.0000.000
116A140TYR00.052-0.01311.1551.4861.4860.0000.0000.0000.000
117A141LYS10.8530.94511.777-26.898-26.8980.0000.0000.0000.000
118A142ALA00.0250.02516.509-1.139-1.1390.0000.0000.0000.000
119A143GLU-1-0.827-0.88518.56315.19215.1920.0000.0000.0000.000
120A144PRO0-0.0180.00021.304-0.460-0.4600.0000.0000.0000.000
121A145GLN00.0160.01924.1260.1290.1290.0000.0000.0000.000
122A146LYS10.8340.91227.567-10.456-10.4560.0000.0000.0000.000
123A147VAL00.0330.03030.797-0.181-0.1810.0000.0000.0000.000
124A148ASN0-0.020-0.02833.7410.0460.0460.0000.0000.0000.000
125A149PHE00.0340.01031.535-0.151-0.1510.0000.0000.0000.000
126A150LYS10.8870.93437.188-8.740-8.7400.0000.0000.0000.000
127A151THR0-0.006-0.00340.021-0.117-0.1170.0000.0000.0000.000
128A152ALA00.0120.01740.414-0.189-0.1890.0000.0000.0000.000
129A153PRO00.0570.04738.5590.2070.2070.0000.0000.0000.000
130A154GLU-1-0.747-0.86338.3268.2158.2150.0000.0000.0000.000
131A155GLN0-0.019-0.00139.0540.0210.0210.0000.0000.0000.000
132A156SER00.0360.01534.9540.2290.2290.0000.0000.0000.000
133A157ARG10.7850.87034.722-8.096-8.0960.0000.0000.0000.000
134A158LYS10.8880.93235.170-7.571-7.5710.0000.0000.0000.000
135A159GLU-1-0.928-0.94632.9429.9139.9130.0000.0000.0000.000
136A160ILE00.002-0.00129.8120.2870.2870.0000.0000.0000.000
137A161ASN0-0.021-0.02530.9860.5350.5350.0000.0000.0000.000
138A162THR0-0.036-0.02932.802-0.048-0.0480.0000.0000.0000.000
139A163TRP0-0.0210.00423.0960.0200.0200.0000.0000.0000.000
140A164VAL00.031-0.00327.2900.3130.3130.0000.0000.0000.000
141A165GLU-1-0.795-0.85228.4349.4269.4260.0000.0000.0000.000
142A166LYS10.9290.95830.176-9.593-9.5930.0000.0000.0000.000
143A167GLN0-0.0240.00422.841-0.086-0.0860.0000.0000.0000.000
144A168THR0-0.039-0.04425.2860.3200.3200.0000.0000.0000.000
145A169GLU-1-0.815-0.89827.03011.25411.2540.0000.0000.0000.000
146A170SER0-0.030-0.03029.448-0.260-0.2600.0000.0000.0000.000
147A171LYS10.8600.95029.584-10.399-10.3990.0000.0000.0000.000
148A172ILE0-0.0100.01127.269-0.110-0.1100.0000.0000.0000.000
149A173LYS10.8510.92831.331-8.902-8.9020.0000.0000.0000.000
150A174ASN0-0.079-0.06534.1440.0560.0560.0000.0000.0000.000
151A175LEU00.0710.07128.215-0.106-0.1060.0000.0000.0000.000
152A176LEU00.0090.01631.069-0.074-0.0740.0000.0000.0000.000
153A177SER00.0460.00334.194-0.312-0.3120.0000.0000.0000.000
154A178SER00.039-0.01237.8160.1190.1190.0000.0000.0000.000
155A179ASP-1-0.847-0.90440.2097.8477.8470.0000.0000.0000.000
156A180ASP-1-0.781-0.85634.7439.2879.2870.0000.0000.0000.000
157A181VAL0-0.043-0.02135.0410.2430.2430.0000.0000.0000.000
158A182LYS10.8630.91537.506-8.255-8.2550.0000.0000.0000.000
159A183ALA00.0410.02338.7380.1920.1920.0000.0000.0000.000
160A184THR0-0.029-0.01538.0300.0570.0570.0000.0000.0000.000
161A185THR0-0.067-0.03434.3720.1950.1950.0000.0000.0000.000
162A186ARG10.9390.98032.372-9.125-9.1250.0000.0000.0000.000
163A187LEU00.023-0.00225.4950.2120.2120.0000.0000.0000.000
164A188ILE0-0.025-0.00929.026-0.173-0.1730.0000.0000.0000.000
165A189LEU00.0290.03221.7890.2080.2080.0000.0000.0000.000
166A190VAL0-0.021-0.00925.467-0.273-0.2730.0000.0000.0000.000
167A191ASN00.028-0.00421.7240.8320.8320.0000.0000.0000.000
168A192ALA00.0430.03823.598-0.359-0.3590.0000.0000.0000.000
169A193ILE0-0.023-0.02019.2630.6490.6490.0000.0000.0000.000
170A194TYR0-0.0040.00623.385-0.595-0.5950.0000.0000.0000.000
171A195PHE0-0.0100.00320.5370.5890.5890.0000.0000.0000.000
172A196LYS10.8640.92223.478-11.572-11.5720.0000.0000.0000.000
173A197ALA00.0170.00822.7020.7290.7290.0000.0000.0000.000
174A198GLU-1-0.840-0.90924.5969.7679.7670.0000.0000.0000.000
175A199TRP0-0.033-0.03825.4620.6030.6030.0000.0000.0000.000
176A200GLU-1-0.876-0.92624.01212.25012.2500.0000.0000.0000.000
177A201VAL00.0190.01827.076-0.262-0.2620.0000.0000.0000.000
178A202LYS10.8140.89330.645-9.735-9.7350.0000.0000.0000.000
179A203PHE0-0.012-0.00431.891-0.247-0.2470.0000.0000.0000.000
180A204GLN0-0.037-0.02835.6060.1870.1870.0000.0000.0000.000
181A205ALA00.0240.00738.996-0.097-0.0970.0000.0000.0000.000
182A206GLU-1-0.836-0.92540.7037.3427.3420.0000.0000.0000.000
183A207LYS10.8810.94141.190-7.491-7.4910.0000.0000.0000.000
184A208THR0-0.056-0.03339.5580.0480.0480.0000.0000.0000.000
185A209SER0-0.017-0.00141.956-0.212-0.2120.0000.0000.0000.000
186A210ILE0-0.010-0.00743.7140.1460.1460.0000.0000.0000.000
187A211GLN0-0.008-0.01243.476-0.139-0.1390.0000.0000.0000.000
188A212PRO0-0.038-0.00744.3060.1100.1100.0000.0000.0000.000
189A213PHE00.002-0.00136.7300.0550.0550.0000.0000.0000.000
190A214ARG10.7760.83742.181-7.425-7.4250.0000.0000.0000.000
191A215LEU00.0100.00841.2800.1500.1500.0000.0000.0000.000
192A216SER00.0060.01041.7290.0530.0530.0000.0000.0000.000
193A217LYS10.9240.95444.412-6.890-6.8900.0000.0000.0000.000
194A218ASN0-0.045-0.02046.6260.0070.0070.0000.0000.0000.000
195A219LYS10.9960.99646.997-6.514-6.5140.0000.0000.0000.000
196A220SER0-0.022-0.00745.3580.1360.1360.0000.0000.0000.000
197A221LYS10.9000.94942.959-7.310-7.3100.0000.0000.0000.000
198A222PRO00.0290.02544.1940.1190.1190.0000.0000.0000.000
199A223VAL00.0130.01038.9800.0740.0740.0000.0000.0000.000
200A224LYS10.8520.90540.303-7.824-7.8240.0000.0000.0000.000
201A225MET0-0.035-0.00139.2690.3050.3050.0000.0000.0000.000
202A226MET00.0090.03333.368-0.177-0.1770.0000.0000.0000.000
203A227TYR0-0.054-0.05638.216-0.041-0.0410.0000.0000.0000.000
204A228MET0-0.030-0.00232.758-0.025-0.0250.0000.0000.0000.000
205A229ARG10.8360.92337.577-7.295-7.2950.0000.0000.0000.000
206A230ASP-1-0.796-0.89633.2918.9918.9910.0000.0000.0000.000
207A231THR0-0.060-0.03830.573-0.149-0.1490.0000.0000.0000.000
208A232PHE00.001-0.00227.8960.2320.2320.0000.0000.0000.000
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