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: RYYM8

Calculation Name: 4I2O-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4I2O

Chain ID: A

ChEMBL ID:

UniProt ID: O69245

Base Structure: X-ray

Registration Date: 2023-09-27

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 OptH
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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2133006.808171
FMO2-HF: Nuclear repulsion 2055894.408488
FMO2-HF: Total energy -77112.399683
FMO2-MP2: Total energy -77337.187261


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:38:LEU)


Summations of interaction energy for fragment #1(A:38:LEU)
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.
-1.7480.5540.014-0.676-1.6420.001
Interaction energy analysis for fragmet #1(A:38:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / q_NPA : -0.018
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].
3A40ALA0-0.012-0.0043.8411.0122.338-0.008-0.467-0.8510.001
4A41THR0-0.057-0.0255.951-0.270-0.2700.0000.0000.0000.000
5A42GLU-1-0.900-0.9579.686-0.125-0.1250.0000.0000.0000.000
6A43PHE0-0.024-0.00912.6310.0450.0450.0000.0000.0000.000
7A44SER0-0.014-0.02015.520-0.036-0.0360.0000.0000.0000.000
8A45TYR00.0160.02216.1730.0310.0310.0000.0000.0000.000
9A46ARG10.9740.98921.186-0.104-0.1040.0000.0000.0000.000
10A47LYS10.8940.93424.742-0.041-0.0410.0000.0000.0000.000
11A48ASP-1-0.924-0.96226.3900.0660.0660.0000.0000.0000.000
12A49GLU-1-0.903-0.93222.7590.1480.1480.0000.0000.0000.000
13A50GLU-1-0.925-0.97022.7310.1850.1850.0000.0000.0000.000
14A51ILE0-0.099-0.05016.7600.0060.0060.0000.0000.0000.000
15A52TYR0-0.023-0.01316.1110.0520.0520.0000.0000.0000.000
16A53GLY00.0830.04420.259-0.027-0.0270.0000.0000.0000.000
17A54GLU-1-0.943-1.01022.3630.1680.1680.0000.0000.0000.000
18A55ASP-1-0.970-0.97223.7580.1780.1780.0000.0000.0000.000
19A56GLU-1-0.898-0.93619.5380.3330.3330.0000.0000.0000.000
20A57PRO0-0.003-0.02018.6770.0200.0200.0000.0000.0000.000
21A58ALA0-0.008-0.00815.4320.0160.0160.0000.0000.0000.000
22A59GLU-1-0.938-0.96512.7770.7250.7250.0000.0000.0000.000
23A60TYR0-0.028-0.0219.9420.3530.3530.0000.0000.0000.000
24A61VAL0-0.034-0.0128.367-0.144-0.1440.0000.0000.0000.000
25A62TYR00.0580.0219.2140.2010.2010.0000.0000.0000.000
26A63GLN0-0.038-0.0229.771-0.146-0.1460.0000.0000.0000.000
27A64VAL00.0110.01811.601-0.006-0.0060.0000.0000.0000.000
28A65VAL0-0.037-0.00712.939-0.056-0.0560.0000.0000.0000.000
29A66THR0-0.026-0.04615.380-0.014-0.0140.0000.0000.0000.000
30A67GLY00.0590.02419.1020.0210.0210.0000.0000.0000.000
31A68ALA0-0.041-0.03420.986-0.012-0.0120.0000.0000.0000.000
32A69VAL00.0130.03018.1380.0060.0060.0000.0000.0000.000
33A70ARG10.7600.87221.283-0.097-0.0970.0000.0000.0000.000
34A71SER00.046-0.00220.1780.0230.0230.0000.0000.0000.000
35A72TYR0-0.044-0.04222.942-0.020-0.0200.0000.0000.0000.000
36A73LYS10.9350.98925.983-0.131-0.1310.0000.0000.0000.000
37A74LEU00.0160.00428.494-0.011-0.0110.0000.0000.0000.000
38A75LEU0-0.010-0.00231.7480.0020.0020.0000.0000.0000.000
39A76SER00.0550.00735.0920.0000.0000.0000.0000.0000.000
40A77ASP-1-0.914-0.92937.1590.0620.0620.0000.0000.0000.000
41A78GLY00.0200.00436.082-0.004-0.0040.0000.0000.0000.000
42A79ARG10.8090.90035.820-0.061-0.0610.0000.0000.0000.000
43A80ARG10.8510.90829.655-0.069-0.0690.0000.0000.0000.000
44A81GLN0-0.051-0.00529.712-0.009-0.0090.0000.0000.0000.000
45A82ILE0-0.043-0.03726.1330.0100.0100.0000.0000.0000.000
46A83GLY0-0.007-0.01325.466-0.009-0.0090.0000.0000.0000.000
47A84ALA00.0080.00321.870-0.007-0.0070.0000.0000.0000.000
48A85PHE00.0140.00623.1770.0070.0070.0000.0000.0000.000
49A86HIS00.0030.04417.5680.0080.0080.0000.0000.0000.000
50A87LEU00.006-0.01219.1920.0040.0040.0000.0000.0000.000
51A88PRO00.008-0.00617.2860.0030.0030.0000.0000.0000.000
52A89GLY00.0020.00914.088-0.017-0.0170.0000.0000.0000.000
53A90ASP-1-0.802-0.88113.657-0.025-0.0250.0000.0000.0000.000
54A91VAL0-0.043-0.04110.0290.0090.0090.0000.0000.0000.000
55A92PHE0-0.005-0.00212.674-0.015-0.0150.0000.0000.0000.000
56A93GLY00.0690.02412.9410.0820.0820.0000.0000.0000.000
57A94LEU0-0.039-0.01810.3140.1000.1000.0000.0000.0000.000
58A95GLU-1-0.786-0.89613.2730.2130.2130.0000.0000.0000.000
59A96SER0-0.046-0.01614.3780.0820.0820.0000.0000.0000.000
60A97GLY00.0150.00016.2240.0110.0110.0000.0000.0000.000
61A98PRO0-0.004-0.00417.0630.0450.0450.0000.0000.0000.000
62A99SER00.0140.00018.8140.0240.0240.0000.0000.0000.000
63A100HIS10.8830.97415.236-0.435-0.4350.0000.0000.0000.000
64A101ARG10.9540.98919.927-0.257-0.2570.0000.0000.0000.000
65A102LEU0-0.055-0.03121.700-0.030-0.0300.0000.0000.0000.000
66A103ALA00.0810.05221.6950.0270.0270.0000.0000.0000.000
67A104ALA00.0050.00019.535-0.014-0.0140.0000.0000.0000.000
68A105GLU-1-0.815-0.91321.5480.1200.1200.0000.0000.0000.000
69A106ALA0-0.0060.00621.691-0.009-0.0090.0000.0000.0000.000
70A107ILE0-0.069-0.03722.861-0.008-0.0080.0000.0000.0000.000
71A108ILE0-0.090-0.05224.064-0.009-0.0090.0000.0000.0000.000
72A109ASP-1-0.816-0.89823.7370.0510.0510.0000.0000.0000.000
73A110THR0-0.052-0.04918.006-0.017-0.0170.0000.0000.0000.000
74A111SER00.0290.05716.6450.0170.0170.0000.0000.0000.000
75A112VAL00.0270.01013.132-0.019-0.0190.0000.0000.0000.000
76A113ARG10.9150.9597.7990.5340.5340.0000.0000.0000.000
77A114LEU00.0110.0118.6960.0370.0370.0000.0000.0000.000
78A115VAL00.007-0.0013.404-0.0360.2370.014-0.092-0.1950.000
79A116LYS10.9910.9946.082-2.047-2.0470.0000.0000.0000.000
80A117ARG10.8750.9356.9160.0430.0430.0000.0000.0000.000
81A118SER00.004-0.0128.7040.1370.1370.0000.0000.0000.000
82A119SER0-0.024-0.0193.573-0.757-0.4500.009-0.077-0.2400.000
83A120LEU00.0030.0043.914-0.465-0.1980.000-0.023-0.2440.000
84A121GLU-1-0.860-0.9235.7860.0010.0010.0000.0000.0000.000
85A122LYS10.9490.9815.704-0.816-0.8160.0000.0000.0000.000
86A123ALA0-0.012-0.0104.189-0.425-0.296-0.001-0.017-0.1120.000
87A124ALA00.002-0.0016.354-0.211-0.2110.0000.0000.0000.000
88A125GLY00.0160.0199.148-0.067-0.0670.0000.0000.0000.000
89A126ILE0-0.102-0.0426.143-0.029-0.0290.0000.0000.0000.000
90A127ASP-1-0.843-0.9388.958-0.417-0.4170.0000.0000.0000.000
91A128VAL00.0510.02110.8240.0270.0270.0000.0000.0000.000
92A129GLN00.005-0.01711.6690.0430.0430.0000.0000.0000.000
93A130VAL0-0.0120.0126.315-0.011-0.0110.0000.0000.0000.000
94A131ALA00.0380.0189.1860.0880.0880.0000.0000.0000.000
95A132ARG10.9010.96311.7010.0510.0510.0000.0000.0000.000
96A133LYS10.9630.9839.9100.2190.2190.0000.0000.0000.000
97A134LEU00.0430.0058.0180.0200.0200.0000.0000.0000.000
98A135TRP00.0100.01711.7670.0040.0040.0000.0000.0000.000
99A136ALA0-0.046-0.03615.005-0.003-0.0030.0000.0000.0000.000
100A137MET0-0.062-0.02210.013-0.041-0.0410.0000.0000.0000.000
101A138THR00.0870.04814.9300.0040.0040.0000.0000.0000.000
102A139ALA0-0.020-0.01417.204-0.011-0.0110.0000.0000.0000.000
103A140GLY0-0.068-0.03118.459-0.012-0.0120.0000.0000.0000.000
104A141GLU-1-0.915-0.96116.3430.1890.1890.0000.0000.0000.000
105A142LEU0-0.0070.00220.330-0.002-0.0020.0000.0000.0000.000
106A143ARG10.9650.99020.672-0.007-0.0070.0000.0000.0000.000
107A144HIS0-0.065-0.03522.9710.0010.0010.0000.0000.0000.000
108A145ALA00.0540.02824.582-0.003-0.0030.0000.0000.0000.000
109A146GLU-1-0.930-0.98826.3560.0440.0440.0000.0000.0000.000
110A147ASP-1-0.922-0.95428.3160.0130.0130.0000.0000.0000.000
111A148HIS0-0.059-0.04828.140-0.006-0.0060.0000.0000.0000.000
112A149MET0-0.027-0.01429.3720.0010.0010.0000.0000.0000.000
113A150LEU0-0.0070.01632.388-0.002-0.0020.0000.0000.0000.000
114A151LEU0-0.042-0.01832.327-0.003-0.0030.0000.0000.0000.000
115A152LEU0-0.020-0.01831.437-0.002-0.0020.0000.0000.0000.000
116A153GLY0-0.027-0.00335.5140.0000.0000.0000.0000.0000.000
117A154ARG10.8630.90637.896-0.031-0.0310.0000.0000.0000.000
118A155LYS10.9441.02034.404-0.015-0.0150.0000.0000.0000.000
119A156THR00.013-0.00639.6390.0020.0020.0000.0000.0000.000
120A157ALA00.0400.00240.2580.0000.0000.0000.0000.0000.000
121A158MET0-0.010-0.00339.8590.0000.0000.0000.0000.0000.000
122A159GLU-1-0.784-0.87039.1750.0120.0120.0000.0000.0000.000
123A160ARG10.7840.90235.934-0.033-0.0330.0000.0000.0000.000
124A161VAL00.006-0.00835.1450.0000.0000.0000.0000.0000.000
125A162ALA00.0140.00635.719-0.002-0.0020.0000.0000.0000.000
126A163THR00.018-0.00431.753-0.003-0.0030.0000.0000.0000.000
127A164PHE00.0210.00829.339-0.003-0.0030.0000.0000.0000.000
128A165LEU0-0.041-0.03331.026-0.003-0.0030.0000.0000.0000.000
129A166LEU00.0330.01832.077-0.005-0.0050.0000.0000.0000.000
130A167GLU-1-0.838-0.87225.6920.0130.0130.0000.0000.0000.000
131A168MET0-0.017-0.02825.757-0.005-0.0050.0000.0000.0000.000
132A169ASP-1-0.775-0.86927.900-0.040-0.0400.0000.0000.0000.000
133A170ARG10.9280.97723.8370.0190.0190.0000.0000.0000.000
134A171ARG10.7270.84220.532-0.020-0.0200.0000.0000.0000.000
135A172LEU00.0070.00423.472-0.005-0.0050.0000.0000.0000.000
136A173ALA0-0.057-0.00825.717-0.001-0.0010.0000.0000.0000.000
137A174VAL00.0280.01226.775-0.009-0.0090.0000.0000.0000.000
138A175ALA0-0.035-0.02029.2490.0050.0050.0000.0000.0000.000
139A176GLY0-0.006-0.00531.9730.0040.0040.0000.0000.0000.000
140A177MET0-0.017-0.00932.6520.0050.0050.0000.0000.0000.000
141A178MET0-0.0020.02130.220-0.004-0.0040.0000.0000.0000.000
142A179ALA00.0300.02229.1540.0040.0040.0000.0000.0000.000
143A180LEU0-0.024-0.02428.6010.0010.0010.0000.0000.0000.000
144A181PRO00.0560.01725.2810.0010.0010.0000.0000.0000.000
145A182MET00.0010.02627.0740.0020.0020.0000.0000.0000.000
146A183SER0-0.054-0.02629.811-0.006-0.0060.0000.0000.0000.000
147A184ARG10.9520.95133.122-0.011-0.0110.0000.0000.0000.000
148A185ARG10.9950.99434.561-0.047-0.0470.0000.0000.0000.000
149A186ASP-1-0.763-0.86429.1480.0620.0620.0000.0000.0000.000
150A187ILE0-0.022-0.01831.3620.0010.0010.0000.0000.0000.000
151A188GLY0-0.025-0.01632.7180.0000.0000.0000.0000.0000.000
152A189ASP-1-0.756-0.87732.0650.0590.0590.0000.0000.0000.000
153A190TYR0-0.099-0.04526.4920.0050.0050.0000.0000.0000.000
154A191LEU00.0020.00030.792-0.001-0.0010.0000.0000.0000.000
155A192GLY00.0790.04633.855-0.003-0.0030.0000.0000.0000.000
156A193LEU0-0.105-0.04635.995-0.004-0.0040.0000.0000.0000.000
157A194THR00.0750.04137.7040.0020.0020.0000.0000.0000.000
158A195LEU00.0610.01138.111-0.002-0.0020.0000.0000.0000.000
159A196GLU-1-0.912-0.96339.2840.0260.0260.0000.0000.0000.000
160A197THR0-0.011-0.00841.564-0.004-0.0040.0000.0000.0000.000
161A198VAL00.0410.02836.522-0.003-0.0030.0000.0000.0000.000
162A199SER0-0.060-0.03139.723-0.004-0.0040.0000.0000.0000.000
163A200ARG10.9780.98241.720-0.020-0.0200.0000.0000.0000.000
164A201ALA00.0530.04040.929-0.002-0.0020.0000.0000.0000.000
165A202LEU00.025-0.00437.219-0.003-0.0030.0000.0000.0000.000
166A203SER0-0.035-0.02041.338-0.003-0.0030.0000.0000.0000.000
167A204GLN0-0.0100.00744.826-0.001-0.0010.0000.0000.0000.000
168A205LEU00.007-0.00639.825-0.002-0.0020.0000.0000.0000.000
169A206HIS0-0.049-0.02043.408-0.003-0.0030.0000.0000.0000.000
170A207THR0-0.0140.00444.581-0.002-0.0020.0000.0000.0000.000
171A208GLN0-0.017-0.01346.5050.0000.0000.0000.0000.0000.000
172A209GLY00.0360.01946.340-0.001-0.0010.0000.0000.0000.000
173A210ILE0-0.067-0.03340.752-0.002-0.0020.0000.0000.0000.000
174A211LEU00.0050.01238.554-0.002-0.0020.0000.0000.0000.000
175A212GLY0-0.022-0.01239.9590.0010.0010.0000.0000.0000.000
176A213PHE00.011-0.00238.5820.0000.0000.0000.0000.0000.000
177A214SER0-0.013-0.00538.209-0.002-0.0020.0000.0000.0000.000
178A215GLY00.0780.04138.6410.0000.0000.0000.0000.0000.000
179A216ALA0-0.014-0.01638.191-0.001-0.0010.0000.0000.0000.000
180A217ARG10.9580.96931.752-0.019-0.0190.0000.0000.0000.000
181A218GLN00.0490.04832.265-0.004-0.0040.0000.0000.0000.000
182A219ILE00.0140.00634.3360.0010.0010.0000.0000.0000.000
183A220VAL00.0100.02034.823-0.003-0.0030.0000.0000.0000.000
184A221LEU00.0120.00534.2480.0030.0030.0000.0000.0000.000
185A222ARG10.9470.96337.6440.0160.0160.0000.0000.0000.000
186A223ASN00.0020.00240.624-0.002-0.0020.0000.0000.0000.000
187A224ARG10.8770.89833.3670.0350.0350.0000.0000.0000.000
188A225GLN00.0360.03638.2430.0000.0000.0000.0000.0000.000
189A226ARG10.8690.91740.5940.0120.0120.0000.0000.0000.000
190A227LEU00.0030.00236.3350.0020.0020.0000.0000.0000.000
191A228HIS00.0440.00934.940-0.001-0.0010.0000.0000.0000.000
192A229ASN0-0.044-0.02638.6460.0010.0010.0000.0000.0000.000
193A230LEU0-0.059-0.01241.1360.0010.0010.0000.0000.0000.000
194A231ASP-1-0.939-0.95536.2910.0000.0000.0000.0000.0000.000
195A232ALA00.0050.00338.3220.0000.0000.0000.0000.0000.000
196A233ALA0-0.008-0.00838.275-0.001-0.0010.0000.0000.0000.000
197A234ALA0-0.010-0.00536.4290.0020.0020.0000.0000.0000.000
198A235ALA00.0010.00238.543-0.002-0.0020.0000.0000.0000.000