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: K2283

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 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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2141043.845129
FMO2-HF: Nuclear repulsion 2063930.079284
FMO2-HF: Total energy -77113.765845
FMO2-MP2: Total energy -77338.310631


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.
-0.9471.2610.001-0.776-1.4330.002
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 : -0.019 / q_NPA : -0.019
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].
3A40ALA0-0.022-0.0103.8721.6863.014-0.010-0.593-0.7250.001
4A41THR00.0010.0106.174-0.313-0.3130.0000.0000.0000.000
5A42GLU-1-0.933-0.9779.909-0.098-0.0980.0000.0000.0000.000
6A43PHE0-0.0070.00112.7370.0460.0460.0000.0000.0000.000
7A44SER0-0.057-0.04815.573-0.052-0.0520.0000.0000.0000.000
8A45TYR00.0150.02816.4040.0280.0280.0000.0000.0000.000
9A46ARG10.9160.93521.418-0.121-0.1210.0000.0000.0000.000
10A47LYS10.8420.88224.932-0.042-0.0420.0000.0000.0000.000
11A48ASP-1-0.861-0.89326.8620.0610.0610.0000.0000.0000.000
12A49GLU-1-0.841-0.88023.3980.1320.1320.0000.0000.0000.000
13A50GLU-1-0.916-0.96722.6100.1730.1730.0000.0000.0000.000
14A51ILE0-0.068-0.04216.8690.0070.0070.0000.0000.0000.000
15A52TYR0-0.033-0.01016.1530.0520.0520.0000.0000.0000.000
16A53GLY00.0910.05319.945-0.029-0.0290.0000.0000.0000.000
17A54GLU-1-0.850-0.94222.2370.1430.1430.0000.0000.0000.000
18A55ASP-1-0.892-0.93223.0350.1890.1890.0000.0000.0000.000
19A56GLU-1-0.823-0.88918.5280.3450.3450.0000.0000.0000.000
20A57PRO0-0.010-0.02118.8190.0160.0160.0000.0000.0000.000
21A58ALA00.0100.01315.1070.0220.0220.0000.0000.0000.000
22A59GLU-1-0.887-0.94712.7170.8330.8330.0000.0000.0000.000
23A60TYR0-0.021-0.01710.2580.3140.3140.0000.0000.0000.000
24A61VAL0-0.013-0.0048.566-0.151-0.1510.0000.0000.0000.000
25A62TYR00.0200.0079.2760.2070.2070.0000.0000.0000.000
26A63GLN0-0.007-0.0109.916-0.137-0.1370.0000.0000.0000.000
27A64VAL00.0140.01711.9230.0030.0030.0000.0000.0000.000
28A65VAL0-0.031-0.00413.491-0.048-0.0480.0000.0000.0000.000
29A66THR00.0090.01116.042-0.013-0.0130.0000.0000.0000.000
30A67GLY00.0640.04119.6960.0200.0200.0000.0000.0000.000
31A68ALA0-0.045-0.04021.221-0.013-0.0130.0000.0000.0000.000
32A69VAL00.0140.02518.2940.0080.0080.0000.0000.0000.000
33A70ARG10.7250.82721.436-0.088-0.0880.0000.0000.0000.000
34A71SER00.0590.01319.8890.0200.0200.0000.0000.0000.000
35A72TYR0-0.105-0.09322.655-0.016-0.0160.0000.0000.0000.000
36A73LYS10.8630.92525.471-0.120-0.1200.0000.0000.0000.000
37A74LEU0-0.004-0.00928.221-0.011-0.0110.0000.0000.0000.000
38A75LEU0-0.0080.00431.6140.0010.0010.0000.0000.0000.000
39A76SER00.0300.00235.0990.0000.0000.0000.0000.0000.000
40A77ASP-1-0.854-0.89837.3400.0580.0580.0000.0000.0000.000
41A78GLY00.0140.01236.071-0.003-0.0030.0000.0000.0000.000
42A79ARG10.7780.86735.785-0.055-0.0550.0000.0000.0000.000
43A80ARG10.8220.89029.210-0.067-0.0670.0000.0000.0000.000
44A81GLN0-0.064-0.02729.800-0.009-0.0090.0000.0000.0000.000
45A82ILE0-0.045-0.02825.9080.0090.0090.0000.0000.0000.000
46A83GLY00.0090.00625.422-0.008-0.0080.0000.0000.0000.000
47A84ALA00.0250.00521.839-0.009-0.0090.0000.0000.0000.000
48A85PHE00.0080.00823.3060.0090.0090.0000.0000.0000.000
49A86HIS00.0180.02717.8560.0060.0060.0000.0000.0000.000
50A87LEU0-0.006-0.01719.2400.0070.0070.0000.0000.0000.000
51A88PRO0-0.009-0.00917.708-0.002-0.0020.0000.0000.0000.000
52A89GLY00.0380.02914.702-0.017-0.0170.0000.0000.0000.000
53A90ASP-1-0.807-0.87513.778-0.044-0.0440.0000.0000.0000.000
54A91VAL0-0.037-0.03310.0970.0110.0110.0000.0000.0000.000
55A92PHE00.000-0.00712.679-0.013-0.0130.0000.0000.0000.000
56A93GLY00.0850.02913.0220.0680.0680.0000.0000.0000.000
57A94LEU0-0.051-0.02010.5010.0840.0840.0000.0000.0000.000
58A95GLU-1-0.760-0.87713.2890.2060.2060.0000.0000.0000.000
59A96SER0-0.025-0.01014.0530.0450.0450.0000.0000.0000.000
60A97GLY0-0.0050.01016.370-0.008-0.0080.0000.0000.0000.000
61A98PRO0-0.004-0.01216.9320.0440.0440.0000.0000.0000.000
62A99SER0-0.024-0.02018.6980.0290.0290.0000.0000.0000.000
63A100HIS10.8250.92215.063-0.409-0.4090.0000.0000.0000.000
64A101ARG10.9120.94819.564-0.230-0.2300.0000.0000.0000.000
65A102LEU0-0.055-0.01821.551-0.026-0.0260.0000.0000.0000.000
66A103ALA00.0620.04521.4920.0240.0240.0000.0000.0000.000
67A104ALA0-0.004-0.01419.631-0.013-0.0130.0000.0000.0000.000
68A105GLU-1-0.757-0.82921.7220.1070.1070.0000.0000.0000.000
69A106ALA00.0320.02121.635-0.009-0.0090.0000.0000.0000.000
70A107ILE0-0.077-0.03822.979-0.007-0.0070.0000.0000.0000.000
71A108ILE0-0.069-0.04324.741-0.008-0.0080.0000.0000.0000.000
72A109ASP-1-0.824-0.89624.2750.0540.0540.0000.0000.0000.000
73A110THR0-0.057-0.05018.715-0.017-0.0170.0000.0000.0000.000
74A111SER0-0.007-0.00517.3810.0120.0120.0000.0000.0000.000
75A112VAL00.013-0.01113.443-0.013-0.0130.0000.0000.0000.000
76A113ARG10.8980.9568.1040.5380.5380.0000.0000.0000.000
77A114LEU00.0080.0089.022-0.013-0.0130.0000.0000.0000.000
78A115VAL00.001-0.0043.6440.1180.2670.003-0.038-0.1140.000
79A116LYS10.9110.9626.603-1.666-1.6660.0000.0000.0000.000
80A117ARG10.8100.8766.763-0.024-0.0240.0000.0000.0000.000
81A118SER00.0310.0088.6220.0200.0200.0000.0000.0000.000
82A119SER0-0.008-0.0083.589-0.847-0.5180.010-0.097-0.2420.001
83A120LEU0-0.0010.0044.007-0.755-0.511-0.001-0.020-0.2230.000
84A121GLU-1-0.824-0.8825.6230.0540.0540.0000.0000.0000.000
85A122LYS10.9300.9615.854-0.875-0.8750.0000.0000.0000.000
86A123ALA0-0.012-0.0063.892-0.391-0.233-0.001-0.028-0.1290.000
87A124ALA00.0240.0076.049-0.150-0.1500.0000.0000.0000.000
88A125GLY0-0.0110.0019.171-0.054-0.0540.0000.0000.0000.000
89A126ILE0-0.094-0.0456.4490.0080.0080.0000.0000.0000.000
90A127ASP-1-0.799-0.9069.003-0.371-0.3710.0000.0000.0000.000
91A128VAL00.0440.02410.7230.0240.0240.0000.0000.0000.000
92A129GLN0-0.014-0.01111.7700.0370.0370.0000.0000.0000.000
93A130VAL0-0.018-0.0086.159-0.005-0.0050.0000.0000.0000.000
94A131ALA00.0320.0219.1640.0720.0720.0000.0000.0000.000
95A132ARG10.8810.94711.6180.0660.0660.0000.0000.0000.000
96A133LYS10.9300.96610.1370.2500.2500.0000.0000.0000.000
97A134LEU00.0440.0077.8470.0180.0180.0000.0000.0000.000
98A135TRP00.0330.01511.7100.0120.0120.0000.0000.0000.000
99A136ALA0-0.053-0.03915.0880.0030.0030.0000.0000.0000.000
100A137MET0-0.050-0.0109.789-0.044-0.0440.0000.0000.0000.000
101A138THR00.0650.02915.0690.0070.0070.0000.0000.0000.000
102A139ALA0-0.033-0.01217.231-0.002-0.0020.0000.0000.0000.000
103A140GLY0-0.068-0.03118.529-0.010-0.0100.0000.0000.0000.000
104A141GLU-1-0.878-0.94016.5180.1530.1530.0000.0000.0000.000
105A142LEU0-0.022-0.00220.1610.0000.0000.0000.0000.0000.000
106A143ARG10.9901.00021.5290.0100.0100.0000.0000.0000.000
107A144HIS0-0.039-0.00922.8520.0020.0020.0000.0000.0000.000
108A145ALA00.0480.01224.356-0.001-0.0010.0000.0000.0000.000
109A146GLU-1-0.935-0.97926.1830.0320.0320.0000.0000.0000.000
110A147ASP-1-0.924-0.96627.8390.0030.0030.0000.0000.0000.000
111A148HIS0-0.048-0.03528.030-0.006-0.0060.0000.0000.0000.000
112A149MET0-0.006-0.00128.9430.0020.0020.0000.0000.0000.000
113A150LEU0-0.0100.01032.108-0.001-0.0010.0000.0000.0000.000
114A151LEU0-0.053-0.02731.928-0.002-0.0020.0000.0000.0000.000
115A152LEU0-0.017-0.01631.210-0.001-0.0010.0000.0000.0000.000
116A153GLY0-0.0030.01535.1690.0000.0000.0000.0000.0000.000
117A154ARG10.8420.89637.646-0.025-0.0250.0000.0000.0000.000
118A155LYS10.8800.97434.741-0.006-0.0060.0000.0000.0000.000
119A156THR0-0.019-0.04039.4040.0030.0030.0000.0000.0000.000
120A157ALA00.021-0.00940.1580.0000.0000.0000.0000.0000.000
121A158MET0-0.0110.00739.8590.0000.0000.0000.0000.0000.000
122A159GLU-1-0.741-0.83239.0140.0070.0070.0000.0000.0000.000
123A160ARG10.7610.89835.840-0.028-0.0280.0000.0000.0000.000
124A161VAL00.0190.00334.9890.0000.0000.0000.0000.0000.000
125A162ALA00.012-0.00135.733-0.002-0.0020.0000.0000.0000.000
126A163THR00.006-0.00931.662-0.003-0.0030.0000.0000.0000.000
127A164PHE00.0240.00229.508-0.003-0.0030.0000.0000.0000.000
128A165LEU0-0.030-0.01530.960-0.003-0.0030.0000.0000.0000.000
129A166LEU00.0330.00632.012-0.005-0.0050.0000.0000.0000.000
130A167GLU-1-0.880-0.90825.5990.0020.0020.0000.0000.0000.000
131A168MET00.0060.00125.606-0.004-0.0040.0000.0000.0000.000
132A169ASP-1-0.778-0.87427.709-0.040-0.0400.0000.0000.0000.000
133A170ARG10.9220.96324.6160.0240.0240.0000.0000.0000.000
134A171ARG10.7270.83320.455-0.008-0.0080.0000.0000.0000.000
135A172LEU0-0.024-0.00323.608-0.004-0.0040.0000.0000.0000.000
136A173ALA0-0.032-0.00426.0230.0020.0020.0000.0000.0000.000
137A174VAL00.0110.00827.259-0.009-0.0090.0000.0000.0000.000
138A175ALA0-0.023-0.02029.7810.0050.0050.0000.0000.0000.000
139A176GLY00.0210.02232.2730.0030.0030.0000.0000.0000.000
140A177MET0-0.027-0.02233.2040.0050.0050.0000.0000.0000.000
141A178MET0-0.0080.02230.607-0.003-0.0030.0000.0000.0000.000
142A179ALA00.0420.02429.1560.0040.0040.0000.0000.0000.000
143A180LEU0-0.017-0.01328.8430.0020.0020.0000.0000.0000.000
144A181PRO00.0600.02425.5020.0020.0020.0000.0000.0000.000
145A182MET0-0.0160.00727.1160.0030.0030.0000.0000.0000.000
146A183SER0-0.065-0.06529.890-0.006-0.0060.0000.0000.0000.000
147A184ARG10.8780.91133.282-0.010-0.0100.0000.0000.0000.000
148A185ARG10.9220.96333.881-0.045-0.0450.0000.0000.0000.000
149A186ASP-1-0.735-0.82229.5910.0530.0530.0000.0000.0000.000
150A187ILE00.0100.00231.2030.0010.0010.0000.0000.0000.000
151A188GLY0-0.021-0.00932.835-0.001-0.0010.0000.0000.0000.000
152A189ASP-1-0.718-0.86431.9480.0530.0530.0000.0000.0000.000
153A190TYR0-0.067-0.02626.7220.0050.0050.0000.0000.0000.000
154A191LEU00.0180.00130.8340.0000.0000.0000.0000.0000.000
155A192GLY00.0740.05233.833-0.002-0.0020.0000.0000.0000.000
156A193LEU0-0.091-0.04436.017-0.004-0.0040.0000.0000.0000.000
157A194THR00.0200.00237.8670.0020.0020.0000.0000.0000.000
158A195LEU00.0590.02338.092-0.002-0.0020.0000.0000.0000.000
159A196GLU-1-0.826-0.91239.3130.0230.0230.0000.0000.0000.000
160A197THR0-0.060-0.03641.516-0.003-0.0030.0000.0000.0000.000
161A198VAL00.0500.02636.492-0.003-0.0030.0000.0000.0000.000
162A199SER00.013-0.00339.697-0.003-0.0030.0000.0000.0000.000
163A200ARG10.9260.98441.506-0.017-0.0170.0000.0000.0000.000
164A201ALA00.0610.03741.073-0.002-0.0020.0000.0000.0000.000
165A202LEU00.0310.00737.222-0.002-0.0020.0000.0000.0000.000
166A203SER0-0.024-0.02341.395-0.002-0.0020.0000.0000.0000.000
167A204GLN0-0.030-0.00444.9420.0000.0000.0000.0000.0000.000
168A205LEU00.017-0.00439.927-0.002-0.0020.0000.0000.0000.000
169A206HIS0-0.0040.00242.804-0.003-0.0030.0000.0000.0000.000
170A207THR0-0.027-0.02244.647-0.001-0.0010.0000.0000.0000.000
171A208GLN0-0.0100.01145.8680.0000.0000.0000.0000.0000.000
172A209GLY00.0620.03246.189-0.001-0.0010.0000.0000.0000.000
173A210ILE0-0.072-0.02640.971-0.002-0.0020.0000.0000.0000.000
174A211LEU0-0.0130.00338.644-0.002-0.0020.0000.0000.0000.000
175A212GLY0-0.021-0.02140.3150.0010.0010.0000.0000.0000.000
176A213PHE00.0000.00938.546-0.001-0.0010.0000.0000.0000.000
177A214SER0-0.028-0.01638.371-0.003-0.0030.0000.0000.0000.000
178A215GLY00.0870.04838.979-0.001-0.0010.0000.0000.0000.000
179A216ALA0-0.020-0.02038.605-0.001-0.0010.0000.0000.0000.000
180A217ARG10.9190.96231.548-0.016-0.0160.0000.0000.0000.000
181A218GLN00.0550.05132.485-0.003-0.0030.0000.0000.0000.000
182A219ILE0-0.006-0.01734.7240.0020.0020.0000.0000.0000.000
183A220VAL00.0380.03435.154-0.003-0.0030.0000.0000.0000.000
184A221LEU00.0190.00434.5700.0030.0030.0000.0000.0000.000
185A222ARG10.9200.95637.9080.0150.0150.0000.0000.0000.000
186A223ASN0-0.014-0.01341.122-0.002-0.0020.0000.0000.0000.000
187A224ARG10.8440.87833.8080.0350.0350.0000.0000.0000.000
188A225GLN00.0350.02838.395-0.001-0.0010.0000.0000.0000.000
189A226ARG10.8420.89940.6020.0140.0140.0000.0000.0000.000
190A227LEU0-0.0030.00536.7240.0020.0020.0000.0000.0000.000
191A228HIS00.016-0.01234.494-0.001-0.0010.0000.0000.0000.000
192A229ASN0-0.039-0.01139.0490.0010.0010.0000.0000.0000.000
193A230LEU0-0.060-0.02341.4740.0010.0010.0000.0000.0000.000
194A231ASP-1-0.831-0.91436.836-0.002-0.0020.0000.0000.0000.000
195A232ALA0-0.0120.00239.265-0.001-0.0010.0000.0000.0000.000
196A233ALA00.0200.01038.2140.0000.0000.0000.0000.0000.000
197A234ALA00.0050.00636.3460.0020.0020.0000.0000.0000.000
198A235ALA0-0.0080.00138.496-0.002-0.0020.0000.0000.0000.000