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: 166VZ

Calculation Name: 5D19-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5D19

Chain ID: A

ChEMBL ID:

UniProt ID: O07229

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 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 202
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2138900.817649
FMO2-HF: Nuclear repulsion 2059775.062641
FMO2-HF: Total energy -79125.755008
FMO2-MP2: Total energy -79357.217801


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:12:GLY)


Summations of interaction energy for fragment #1(A:12:GLY)
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.
-4.481-0.7240.145-1.599-2.3030.005
Interaction energy analysis for fragmet #1(A:12:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : -0.005
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].
3A14ARG10.9440.9833.268-5.508-3.2790.061-1.057-1.2330.006
4A15SER00.0220.0052.860-1.797-0.8860.044-0.342-0.613-0.001
5A16ARG10.8340.9164.3912.2962.539-0.001-0.083-0.1590.000
6A17GLU-1-0.804-0.8936.1640.1640.1640.0000.0000.0000.000
7A18SER0-0.038-0.0247.5790.1850.1850.0000.0000.0000.000
8A19ILE00.0230.0057.7240.1360.1360.0000.0000.0000.000
9A20LEU0-0.0150.01010.4440.1340.1340.0000.0000.0000.000
10A21ASP-1-0.796-0.87512.225-0.094-0.0940.0000.0000.0000.000
11A22ALA0-0.062-0.02913.3960.0550.0550.0000.0000.0000.000
12A23THR0-0.024-0.04814.2650.0390.0390.0000.0000.0000.000
13A24GLU-1-0.871-0.93216.456-0.139-0.1390.0000.0000.0000.000
14A25ARG10.9380.96818.0260.1640.1640.0000.0000.0000.000
15A26LEU0-0.051-0.02718.1900.0220.0220.0000.0000.0000.000
16A27MET00.0120.02620.6980.0120.0120.0000.0000.0000.000
17A28ALA00.0260.04322.7620.0140.0140.0000.0000.0000.000
18A29THR0-0.061-0.02324.0470.0140.0140.0000.0000.0000.000
19A30LYS10.8730.92122.8790.1710.1710.0000.0000.0000.000
20A31GLY00.0290.01825.735-0.003-0.0030.0000.0000.0000.000
21A32TYR00.005-0.02023.269-0.014-0.0140.0000.0000.0000.000
22A33ALA0-0.008-0.01124.630-0.013-0.0130.0000.0000.0000.000
23A34ALA0-0.040-0.01526.598-0.004-0.0040.0000.0000.0000.000
24A35THR00.0110.01720.739-0.005-0.0050.0000.0000.0000.000
25A36SER0-0.003-0.02721.914-0.008-0.0080.0000.0000.0000.000
26A37ILE00.049-0.00914.870-0.011-0.0110.0000.0000.0000.000
27A38SER0-0.004-0.00117.706-0.028-0.0280.0000.0000.0000.000
28A39ASP-1-0.803-0.86519.595-0.190-0.1900.0000.0000.0000.000
29A40ILE00.012-0.00514.4310.0000.0000.0000.0000.0000.000
30A41ARG10.9530.98814.9890.2390.2390.0000.0000.0000.000
31A42ASP-1-0.936-0.96115.797-0.211-0.2110.0000.0000.0000.000
32A43ALA0-0.069-0.01916.6830.0170.0170.0000.0000.0000.000
33A44CYS0-0.068-0.03311.243-0.010-0.0100.0000.0000.0000.000
34A45GLY00.0250.02411.950-0.025-0.0250.0000.0000.0000.000
35A46LEU0-0.015-0.0166.993-0.041-0.0410.0000.0000.0000.000
36A47ALA00.002-0.00211.6500.0600.0600.0000.0000.0000.000
37A48PRO00.0900.04412.250-0.090-0.0900.0000.0000.0000.000
38A49SER00.011-0.01313.097-0.041-0.0410.0000.0000.0000.000
39A50SER0-0.060-0.0368.244-0.047-0.0470.0000.0000.0000.000
40A51ILE00.0420.0198.126-0.231-0.2310.0000.0000.0000.000
41A52TYR0-0.026-0.02910.210-0.045-0.0450.0000.0000.0000.000
42A53TRP0-0.020-0.0057.7610.0180.0180.0000.0000.0000.000
43A54HIS0-0.057-0.0093.230-0.2230.1510.041-0.117-0.2980.000
44A55PHE0-0.003-0.0197.6120.0320.0320.0000.0000.0000.000
45A56GLY00.0460.03811.2750.0740.0740.0000.0000.0000.000
46A57SER0-0.035-0.03214.0080.0560.0560.0000.0000.0000.000
47A58LYS10.8640.94715.4060.1670.1670.0000.0000.0000.000
48A59GLU-1-0.817-0.93117.384-0.251-0.2510.0000.0000.0000.000
49A60GLY00.0320.01815.3330.0090.0090.0000.0000.0000.000
50A61VAL0-0.048-0.01812.462-0.036-0.0360.0000.0000.0000.000
51A62LEU00.010-0.00614.3600.0010.0010.0000.0000.0000.000
52A63ALA00.0110.01216.7170.0250.0250.0000.0000.0000.000
53A64ALA00.0190.00712.2050.0230.0230.0000.0000.0000.000
54A65MET0-0.0230.00814.3400.0300.0300.0000.0000.0000.000
55A66MET00.0260.03115.6340.0500.0500.0000.0000.0000.000
56A67GLU-1-0.762-0.85916.267-0.201-0.2010.0000.0000.0000.000
57A68ARG10.7190.82312.1560.3040.3040.0000.0000.0000.000
58A69GLY0-0.007-0.02015.9680.0420.0420.0000.0000.0000.000
59A70ALA0-0.004-0.00119.1720.0250.0250.0000.0000.0000.000
60A71GLN0-0.047-0.03115.7530.0260.0260.0000.0000.0000.000
61A72ARG10.9220.96115.2000.1280.1280.0000.0000.0000.000
62A73PHE00.0200.02220.4780.0140.0140.0000.0000.0000.000
63A74PHE00.015-0.02223.1870.0100.0100.0000.0000.0000.000
64A75ALA0-0.0200.00421.3940.0080.0080.0000.0000.0000.000
65A76ALA0-0.0150.00623.5070.0110.0110.0000.0000.0000.000
66A77ILE0-0.0180.00826.0450.0030.0030.0000.0000.0000.000
67A78PRO00.0450.05828.031-0.001-0.0010.0000.0000.0000.000
68A79THR0-0.029-0.07228.479-0.006-0.0060.0000.0000.0000.000
69A80TRP00.031-0.00131.0930.0040.0040.0000.0000.0000.000
70A81ASP-1-0.909-0.97233.4250.0100.0100.0000.0000.0000.000
71A82GLU-1-0.861-0.89127.8630.0220.0220.0000.0000.0000.000
72A83ALA0-0.060-0.00632.6220.0020.0020.0000.0000.0000.000
73A84HIS00.0290.00833.4690.0010.0010.0000.0000.0000.000
74A85GLY00.0120.00137.445-0.003-0.0030.0000.0000.0000.000
75A86PRO0-0.031-0.00940.9120.0010.0010.0000.0000.0000.000
76A87VAL00.0470.00341.906-0.001-0.0010.0000.0000.0000.000
77A88GLU-1-0.877-0.93743.2180.0050.0050.0000.0000.0000.000
78A89GLN00.0260.00343.3510.0000.0000.0000.0000.0000.000
79A90ARG10.8430.94536.746-0.014-0.0140.0000.0000.0000.000
80A91SER00.0560.01238.2200.0000.0000.0000.0000.0000.000
81A92GLU-1-0.865-0.90338.827-0.005-0.0050.0000.0000.0000.000
82A93ARG10.8170.89137.177-0.005-0.0050.0000.0000.0000.000
83A94GLN00.0210.02332.692-0.001-0.0010.0000.0000.0000.000
84A95LEU0-0.031-0.01134.372-0.003-0.0030.0000.0000.0000.000
85A96THR0-0.004-0.01836.265-0.003-0.0030.0000.0000.0000.000
86A97GLU-1-0.869-0.92331.2960.0010.0010.0000.0000.0000.000
87A98LEU0-0.031-0.00731.213-0.004-0.0040.0000.0000.0000.000
88A99VAL00.0170.00132.709-0.004-0.0040.0000.0000.0000.000
89A100SER0-0.0020.02232.799-0.004-0.0040.0000.0000.0000.000
90A101LEU0-0.010-0.00426.932-0.002-0.0020.0000.0000.0000.000
91A102GLN0-0.006-0.02530.194-0.009-0.0090.0000.0000.0000.000
92A103SER0-0.070-0.04732.247-0.002-0.0020.0000.0000.0000.000
93A104GLN0-0.086-0.03628.355-0.002-0.0020.0000.0000.0000.000
94A105HIS0-0.049-0.00230.384-0.001-0.0010.0000.0000.0000.000
95A106PRO00.0100.01825.276-0.006-0.0060.0000.0000.0000.000
96A107ASP-1-0.766-0.86023.531-0.126-0.1260.0000.0000.0000.000
97A108PHE0-0.012-0.00921.329-0.012-0.0120.0000.0000.0000.000
98A109LEU00.0170.02123.088-0.010-0.0100.0000.0000.0000.000
99A110ARG10.8620.89625.5420.1140.1140.0000.0000.0000.000
100A111LEU0-0.021-0.00919.943-0.003-0.0030.0000.0000.0000.000
101A112PHE0-0.012-0.01823.822-0.007-0.0070.0000.0000.0000.000
102A113TYR0-0.022-0.05324.874-0.002-0.0020.0000.0000.0000.000
103A114LEU0-0.038-0.01225.7700.0030.0030.0000.0000.0000.000
104A115LEU0-0.018-0.01320.497-0.003-0.0030.0000.0000.0000.000
105A116SER0-0.073-0.02924.8720.0040.0040.0000.0000.0000.000
106A117MET0-0.046-0.01627.2830.0070.0070.0000.0000.0000.000
107A118GLU-1-0.883-0.91625.336-0.133-0.1330.0000.0000.0000.000
108A119ARG10.8940.95627.4950.1000.1000.0000.0000.0000.000
109A120SER0-0.016-0.02523.0710.0010.0010.0000.0000.0000.000
110A121GLN0-0.002-0.00222.5860.0000.0000.0000.0000.0000.000
111A122ASP-1-0.816-0.91317.776-0.290-0.2900.0000.0000.0000.000
112A123PRO00.0340.00821.1170.0030.0030.0000.0000.0000.000
113A124ALA00.0110.00816.8780.0120.0120.0000.0000.0000.000
114A125VAL00.0240.01018.816-0.005-0.0050.0000.0000.0000.000
115A126ALA00.0270.01520.1380.0110.0110.0000.0000.0000.000
116A127ALA0-0.032-0.01719.9540.0150.0150.0000.0000.0000.000
117A128VAL0-0.0150.00116.7600.0150.0150.0000.0000.0000.000
118A129VAL00.0320.02219.8070.0170.0170.0000.0000.0000.000
119A130ARG10.9290.97123.0780.1110.1110.0000.0000.0000.000
120A131ARG10.8220.87816.5190.2210.2210.0000.0000.0000.000
121A132VAL00.0390.02420.6330.0150.0150.0000.0000.0000.000
122A133ARG10.8260.89023.1570.0860.0860.0000.0000.0000.000
123A134ASN0-0.007-0.03325.7890.0090.0090.0000.0000.0000.000
124A135THR0-0.022-0.00323.5250.0110.0110.0000.0000.0000.000
125A136ALA00.0350.02025.9890.0090.0090.0000.0000.0000.000
126A137ILE00.000-0.00228.5140.0070.0070.0000.0000.0000.000
127A138ALA0-0.0080.00028.4850.0060.0060.0000.0000.0000.000
128A139ARG10.8150.88726.3250.0250.0250.0000.0000.0000.000
129A140PHE00.0490.02230.6300.0040.0040.0000.0000.0000.000
130A141ARG10.8770.93333.5500.0310.0310.0000.0000.0000.000
131A142ASP-1-0.869-0.93633.002-0.005-0.0050.0000.0000.0000.000
132A143SER0-0.002-0.00234.9250.0020.0020.0000.0000.0000.000
133A144ILE0-0.034-0.02136.9080.0020.0020.0000.0000.0000.000
134A145THR0-0.019-0.02137.8820.0010.0010.0000.0000.0000.000
135A146HIS10.8030.90236.2970.0050.0050.0000.0000.0000.000
136A147LEU0-0.0170.00040.9440.0010.0010.0000.0000.0000.000
137A148LEU0-0.034-0.00243.3370.0000.0000.0000.0000.0000.000
138A149PRO00.0200.01445.6470.0010.0010.0000.0000.0000.000
139A150SER0-0.005-0.01547.8470.0000.0000.0000.0000.0000.000
140A151ASP-1-0.956-0.96948.914-0.004-0.0040.0000.0000.0000.000
141A152ILE0-0.0070.00347.179-0.001-0.0010.0000.0000.0000.000
142A153PRO0-0.0160.00247.3170.0000.0000.0000.0000.0000.000
143A154PRO00.045-0.01742.569-0.001-0.0010.0000.0000.0000.000
144A155GLY0-0.0260.00044.161-0.002-0.0020.0000.0000.0000.000
145A156LYS10.9050.95046.3120.0100.0100.0000.0000.0000.000
146A157ALA00.0280.02643.515-0.001-0.0010.0000.0000.0000.000
147A158ASP-1-0.839-0.90539.635-0.021-0.0210.0000.0000.0000.000
148A159LEU0-0.016-0.01641.844-0.002-0.0020.0000.0000.0000.000
149A160VAL00.0810.04644.097-0.002-0.0020.0000.0000.0000.000
150A161VAL00.012-0.00238.913-0.002-0.0020.0000.0000.0000.000
151A162ALA0-0.056-0.02738.774-0.002-0.0020.0000.0000.0000.000
152A163GLU-1-0.918-0.94639.474-0.030-0.0300.0000.0000.0000.000
153A164LEU00.0280.00841.757-0.002-0.0020.0000.0000.0000.000
154A165THR0-0.036-0.03935.274-0.001-0.0010.0000.0000.0000.000
155A166ALA0-0.028-0.01236.913-0.003-0.0030.0000.0000.0000.000
156A167PHE00.0060.01237.975-0.003-0.0030.0000.0000.0000.000
157A168ALA00.010-0.00437.616-0.001-0.0010.0000.0000.0000.000
158A169VAL0-0.043-0.02432.827-0.002-0.0020.0000.0000.0000.000
159A170ALA00.0030.00935.090-0.003-0.0030.0000.0000.0000.000
160A171LEU00.007-0.00237.417-0.002-0.0020.0000.0000.0000.000
161A172SER00.0170.01233.0770.0010.0010.0000.0000.0000.000
162A173ASP-1-0.801-0.85032.077-0.070-0.0700.0000.0000.0000.000
163A174GLY00.0040.00134.291-0.003-0.0030.0000.0000.0000.000
164A175VAL0-0.014-0.01035.7700.0010.0010.0000.0000.0000.000
165A176TYR0-0.007-0.01728.421-0.002-0.0020.0000.0000.0000.000
166A177PHE0-0.016-0.02532.475-0.002-0.0020.0000.0000.0000.000
167A178ALA00.0200.02635.9460.0000.0000.0000.0000.0000.000
168A179GLY00.0250.01236.5710.0020.0020.0000.0000.0000.000
169A180HIS0-0.032-0.01231.695-0.001-0.0010.0000.0000.0000.000
170A181LEU0-0.071-0.04135.771-0.001-0.0010.0000.0000.0000.000
171A182GLU-1-0.951-0.97339.045-0.040-0.0400.0000.0000.0000.000
172A183PRO00.0060.01137.7050.0020.0020.0000.0000.0000.000
173A184ASP-1-0.954-0.96739.594-0.029-0.0290.0000.0000.0000.000
174A185THR0-0.047-0.03342.9720.0020.0020.0000.0000.0000.000
175A186THR0-0.043-0.01239.4730.0020.0020.0000.0000.0000.000
176A187ASP-1-0.836-0.90541.327-0.017-0.0170.0000.0000.0000.000
177A188VAL00.0710.01935.7100.0000.0000.0000.0000.0000.000
178A189GLU-1-0.797-0.88339.098-0.010-0.0100.0000.0000.0000.000
179A190ARG10.8260.89340.6190.0180.0180.0000.0000.0000.000
180A191MET0-0.0040.00040.6750.0010.0010.0000.0000.0000.000
181A192TYR00.0500.00834.354-0.001-0.0010.0000.0000.0000.000
182A193ARG10.8150.89240.5150.0130.0130.0000.0000.0000.000
183A194ARG10.8760.92343.7580.0170.0170.0000.0000.0000.000
184A195LEU00.0230.03038.7440.0000.0000.0000.0000.0000.000
185A196ARG10.8540.92942.4390.0100.0100.0000.0000.0000.000
186A197GLN00.0570.02943.6570.0000.0000.0000.0000.0000.000
187A198ALA0-0.0180.00345.4640.0010.0010.0000.0000.0000.000
188A199LEU00.002-0.00740.6780.0000.0000.0000.0000.0000.000
189A200GLU-1-0.884-0.95645.323-0.010-0.0100.0000.0000.0000.000
190A201ALA0-0.036-0.01347.7690.0010.0010.0000.0000.0000.000
191A202LEU0-0.009-0.01746.2980.0000.0000.0000.0000.0000.000
192A203ILE00.0100.01744.5550.0000.0000.0000.0000.0000.000
193A204PRO00.0180.00848.5300.0000.0000.0000.0000.0000.000
194A205VAL0-0.011-0.00451.7160.0000.0000.0000.0000.0000.000
195A206LEU00.0590.02046.5990.0000.0000.0000.0000.0000.000
196A207LEU0-0.045-0.01348.4990.0000.0000.0000.0000.0000.000
197A208GLU-1-0.918-0.96751.618-0.010-0.0100.0000.0000.0000.000
198A209GLU-1-0.958-0.96552.593-0.018-0.0180.0000.0000.0000.000
199A210THR0-0.038-0.02849.5810.0000.0000.0000.0000.0000.000
200A211HIS0-0.099-0.03153.0590.0010.0010.0000.0000.0000.000
201A212HIS0-0.0040.01556.3030.0010.0010.0000.0000.0000.000
202A213HIS0-0.070-0.04052.5840.0000.0000.0000.0000.0000.000