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: 8929Y

Calculation Name: 5YDP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5YDP

Chain ID: A

ChEMBL ID:

UniProt ID: G3EIL4

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 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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1919290.66811
FMO2-HF: Nuclear repulsion 1847528.121553
FMO2-HF: Total energy -71762.546557
FMO2-MP2: Total energy -71974.29652


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:26:GLY)


Summations of interaction energy for fragment #1(A:26: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.
0.421.934-0.025-0.81-0.6780.001
Interaction energy analysis for fragmet #1(A:26:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.031 / q_NPA : 0.003
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].
3A28ARG10.8630.9233.8000.9372.451-0.025-0.810-0.6780.001
4A29TRP00.0690.0395.960-0.107-0.1070.0000.0000.0000.000
5A30SER0-0.0170.0058.3420.0770.0770.0000.0000.0000.000
6A31PRO00.0860.01710.068-0.084-0.0840.0000.0000.0000.000
7A32ARG10.9440.97412.466-0.140-0.1400.0000.0000.0000.000
8A33LEU00.0420.0066.896-0.034-0.0340.0000.0000.0000.000
9A34THR00.0070.02110.996-0.059-0.0590.0000.0000.0000.000
10A35VAL0-0.0020.00113.018-0.005-0.0050.0000.0000.0000.000
11A36PHE00.012-0.00512.6210.0120.0120.0000.0000.0000.000
12A37ASP-1-0.788-0.87811.461-0.545-0.5450.0000.0000.0000.000
13A38ALA0-0.0090.00414.8100.0140.0140.0000.0000.0000.000
14A39MET0-0.067-0.03817.9850.0170.0170.0000.0000.0000.000
15A40HIS00.0200.01716.9560.0130.0130.0000.0000.0000.000
16A41GLN00.0340.01818.4170.0050.0050.0000.0000.0000.000
17A42LEU0-0.096-0.05920.0700.0190.0190.0000.0000.0000.000
18A43LEU0-0.022-0.02921.9400.0140.0140.0000.0000.0000.000
19A44GLU-1-0.940-0.94720.206-0.207-0.2070.0000.0000.0000.000
20A45SER0-0.062-0.03124.3670.0110.0110.0000.0000.0000.000
21A46ARG10.8820.94726.3440.1090.1090.0000.0000.0000.000
22A47ASP-1-0.817-0.89527.849-0.066-0.0660.0000.0000.0000.000
23A48TRP00.020-0.01524.3620.0000.0000.0000.0000.0000.000
24A49SER0-0.028-0.02328.3810.0040.0040.0000.0000.0000.000
25A50ALA0-0.0380.00031.2750.0040.0040.0000.0000.0000.000
26A51VAL00.0590.04825.136-0.003-0.0030.0000.0000.0000.000
27A52THR0-0.049-0.00828.5190.0090.0090.0000.0000.0000.000
28A53MET00.0500.02124.725-0.008-0.0080.0000.0000.0000.000
29A54SER0-0.025-0.02325.4640.0000.0000.0000.0000.0000.000
30A55ASP-1-0.836-0.91926.336-0.058-0.0580.0000.0000.0000.000
31A56VAL00.0430.02720.696-0.008-0.0080.0000.0000.0000.000
32A57ALA0-0.029-0.01621.483-0.008-0.0080.0000.0000.0000.000
33A58LYS10.8910.94222.3420.0500.0500.0000.0000.0000.000
34A59ALA00.0070.01320.944-0.005-0.0050.0000.0000.0000.000
35A60ALA00.0110.00417.373-0.022-0.0220.0000.0000.0000.000
36A61GLY0-0.0110.02017.742-0.004-0.0040.0000.0000.0000.000
37A62LEU0-0.0050.00016.5240.0240.0240.0000.0000.0000.000
38A63SER00.0170.04220.611-0.003-0.0030.0000.0000.0000.000
39A64ARG11.0350.98523.4340.0090.0090.0000.0000.0000.000
40A65GLN0-0.0090.00226.000-0.003-0.0030.0000.0000.0000.000
41A66THR00.033-0.03919.5180.0100.0100.0000.0000.0000.000
42A67LEU00.0280.02220.1520.0080.0080.0000.0000.0000.000
43A68TYR0-0.037-0.01822.3950.0040.0040.0000.0000.0000.000
44A69SER0-0.061-0.00722.8160.0070.0070.0000.0000.0000.000
45A70THR00.0360.01418.4590.0080.0080.0000.0000.0000.000
46A71PHE0-0.050-0.03016.5940.0070.0070.0000.0000.0000.000
47A72GLY00.0430.04022.141-0.004-0.0040.0000.0000.0000.000
48A73ASN0-0.001-0.02425.934-0.009-0.0090.0000.0000.0000.000
49A74ARG10.9440.93025.5080.0320.0320.0000.0000.0000.000
50A75GLN0-0.0120.00325.893-0.003-0.0030.0000.0000.0000.000
51A76GLY00.0170.01123.811-0.001-0.0010.0000.0000.0000.000
52A77LEU0-0.012-0.01920.8580.0030.0030.0000.0000.0000.000
53A78ALA00.0390.01520.951-0.007-0.0070.0000.0000.0000.000
54A79GLN00.0090.00821.9810.0040.0040.0000.0000.0000.000
55A80ALA0-0.034-0.01617.3900.0050.0050.0000.0000.0000.000
56A81TYR0-0.037-0.02717.346-0.006-0.0060.0000.0000.0000.000
57A82ALA00.0230.01918.031-0.012-0.0120.0000.0000.0000.000
58A83LEU0-0.004-0.01016.7190.0020.0020.0000.0000.0000.000
59A84GLN0-0.056-0.02011.552-0.036-0.0360.0000.0000.0000.000
60A85LEU0-0.0150.00114.998-0.014-0.0140.0000.0000.0000.000
61A86SER0-0.063-0.02717.539-0.003-0.0030.0000.0000.0000.000
62A87GLU-1-0.868-0.94711.3210.1120.1120.0000.0000.0000.000
63A88LYS10.9330.96912.7700.2820.2820.0000.0000.0000.000
64A89PHE00.013-0.01214.366-0.016-0.0160.0000.0000.0000.000
65A90ALA00.0310.01917.024-0.002-0.0020.0000.0000.0000.000
66A91GLY0-0.027-0.02313.7020.0110.0110.0000.0000.0000.000
67A92GLU-1-0.877-0.92314.658-0.207-0.2070.0000.0000.0000.000
68A93ILE00.0080.00816.7420.0010.0010.0000.0000.0000.000
69A94ARG10.9660.98310.6340.0330.0330.0000.0000.0000.000
70A95ASP-1-0.951-0.97912.953-0.166-0.1660.0000.0000.0000.000
71A96SER0-0.037-0.01915.822-0.008-0.0080.0000.0000.0000.000
72A97ILE0-0.006-0.01219.4140.0050.0050.0000.0000.0000.000
73A98ILE0-0.055-0.03114.7010.0070.0070.0000.0000.0000.000
74A99ARG10.8380.91815.5050.1720.1720.0000.0000.0000.000
75A100HIS0-0.051-0.02819.1750.0060.0060.0000.0000.0000.000
76A101PRO00.0240.00821.8230.0100.0100.0000.0000.0000.000
77A102GLY00.002-0.00624.251-0.002-0.0020.0000.0000.0000.000
78A103GLN0-0.029-0.00926.6090.0060.0060.0000.0000.0000.000
79A104ILE00.0240.00326.667-0.004-0.0040.0000.0000.0000.000
80A105GLU-1-0.900-0.95427.587-0.035-0.0350.0000.0000.0000.000
81A106LEU0-0.023-0.00525.830-0.003-0.0030.0000.0000.0000.000
82A107ALA00.0260.01823.166-0.008-0.0080.0000.0000.0000.000
83A108LEU00.0100.00323.597-0.006-0.0060.0000.0000.0000.000
84A109SER00.0100.02225.474-0.007-0.0070.0000.0000.0000.000
85A110GLU-1-0.806-0.88721.149-0.130-0.1300.0000.0000.0000.000
86A111GLY00.0320.01220.873-0.010-0.0100.0000.0000.0000.000
87A112ILE0-0.025-0.00721.780-0.007-0.0070.0000.0000.0000.000
88A113ASN00.013-0.00324.261-0.003-0.0030.0000.0000.0000.000
89A114GLY0-0.012-0.00120.509-0.007-0.0070.0000.0000.0000.000
90A115PHE0-0.003-0.01520.307-0.012-0.0120.0000.0000.0000.000
91A116LEU00.0160.00821.290-0.003-0.0030.0000.0000.0000.000
92A117ARG10.9490.97318.9810.1880.1880.0000.0000.0000.000
93A118SER0-0.109-0.06617.831-0.014-0.0140.0000.0000.0000.000
94A119SER00.011-0.00420.352-0.003-0.0030.0000.0000.0000.000
95A120SER00.0090.01422.8370.0050.0050.0000.0000.0000.000
96A121ARG10.8420.92218.5910.2160.2160.0000.0000.0000.000
97A122ASP-1-0.707-0.86519.611-0.148-0.1480.0000.0000.0000.000
98A123PRO00.0100.01020.7230.0180.0180.0000.0000.0000.000
99A124LEU0-0.030-0.01122.6080.0140.0140.0000.0000.0000.000
100A125ILE0-0.0190.00122.1800.0130.0130.0000.0000.0000.000
101A126ARG10.9931.00025.5420.1020.1020.0000.0000.0000.000
102A127ALA00.0030.00527.0250.0080.0080.0000.0000.0000.000
103A128LEU0-0.064-0.00427.2770.0080.0080.0000.0000.0000.000
104A129VAL00.0460.02630.0180.0060.0060.0000.0000.0000.000
105A130THR0-0.058-0.02532.2720.0020.0020.0000.0000.0000.000
106A131GLY00.0580.02932.633-0.005-0.0050.0000.0000.0000.000
107A132ASH0-0.083-0.08632.3790.0010.0010.0000.0000.0000.000
108A133ILE00.0240.00636.6370.0020.0020.0000.0000.0000.000
109A134LYS10.9190.95134.1490.0450.0450.0000.0000.0000.000
110A135PRO0-0.0430.00832.0390.0020.0020.0000.0000.0000.000
111A136ASP-1-0.821-0.91932.869-0.017-0.0170.0000.0000.0000.000
112A137LEU0-0.039-0.03629.6030.0020.0020.0000.0000.0000.000
113A138LEU00.0100.00326.7960.0030.0030.0000.0000.0000.000
114A139ARG10.9530.98029.1720.0290.0290.0000.0000.0000.000
115A140LEU00.0330.00930.2900.0020.0020.0000.0000.0000.000
116A141ILE0-0.047-0.01524.3900.0040.0040.0000.0000.0000.000
117A142THR0-0.009-0.01127.0220.0010.0010.0000.0000.0000.000
118A143THR0-0.051-0.02328.303-0.002-0.0020.0000.0000.0000.000
119A144GLU-1-0.925-0.94830.8940.0140.0140.0000.0000.0000.000
120A145ALA0-0.025-0.02125.5570.0050.0050.0000.0000.0000.000
121A146GLY00.0300.02226.541-0.005-0.0050.0000.0000.0000.000
122A147PRO00.0430.02522.5580.0040.0040.0000.0000.0000.000
123A148LEU0-0.027-0.00421.3070.0060.0060.0000.0000.0000.000
124A149ILE00.0290.01421.4970.0000.0000.0000.0000.0000.000
125A150GLU-1-0.958-0.96022.0820.0770.0770.0000.0000.0000.000
126A151ARG10.9380.98614.680-0.108-0.1080.0000.0000.0000.000
127A152ALA00.0260.01218.1170.0060.0060.0000.0000.0000.000
128A153THR0-0.017-0.04819.621-0.003-0.0030.0000.0000.0000.000
129A154GLU-1-0.971-0.98217.0370.1480.1480.0000.0000.0000.000
130A155VAL0-0.041-0.01614.2880.0140.0140.0000.0000.0000.000
131A156LEU00.002-0.01316.633-0.006-0.0060.0000.0000.0000.000
132A157MET0-0.0380.00019.861-0.003-0.0030.0000.0000.0000.000
133A158PRO00.0460.02816.876-0.010-0.0100.0000.0000.0000.000
134A159ALA0-0.0060.01218.187-0.009-0.0090.0000.0000.0000.000
135A160LEU0-0.037-0.00719.296-0.013-0.0130.0000.0000.0000.000
136A161SER0-0.049-0.01622.4300.0010.0010.0000.0000.0000.000
137A162GLU-1-0.968-0.99218.4650.1380.1380.0000.0000.0000.000
138A163SER0-0.049-0.03019.9290.0000.0000.0000.0000.0000.000
139A164TRP0-0.020-0.02620.9300.0090.0090.0000.0000.0000.000
140A165MET0-0.031-0.00223.612-0.002-0.0020.0000.0000.0000.000
141A166ARG10.9180.97222.915-0.044-0.0440.0000.0000.0000.000
142A167ILE00.0390.02326.0550.0000.0000.0000.0000.0000.000
143A168GLU-1-0.891-0.94726.7770.0560.0560.0000.0000.0000.000
144A169ALA00.0390.01025.828-0.002-0.0020.0000.0000.0000.000
145A170SER0-0.006-0.01026.983-0.001-0.0010.0000.0000.0000.000
146A171GLN00.037-0.00130.0310.0000.0000.0000.0000.0000.000
147A172ALA00.0320.03424.701-0.004-0.0040.0000.0000.0000.000
148A173ARG10.9840.97624.103-0.075-0.0750.0000.0000.0000.000
149A174LEU0-0.030-0.00126.445-0.003-0.0030.0000.0000.0000.000
150A175ALA00.0530.02928.021-0.004-0.0040.0000.0000.0000.000
151A176ALA00.0030.00923.307-0.006-0.0060.0000.0000.0000.000
152A177SER0-0.038-0.02925.086-0.006-0.0060.0000.0000.0000.000
153A178ILE0-0.002-0.00626.904-0.005-0.0050.0000.0000.0000.000
154A179ILE00.0410.01824.127-0.005-0.0050.0000.0000.0000.000
155A180ALA0-0.0090.00023.710-0.007-0.0070.0000.0000.0000.000
156A181ARG10.9120.94325.052-0.020-0.0200.0000.0000.0000.000
157A182ILE00.0230.01428.456-0.003-0.0030.0000.0000.0000.000
158A183GLY00.0390.01925.370-0.005-0.0050.0000.0000.0000.000
159A184ILE0-0.018-0.02425.008-0.005-0.0050.0000.0000.0000.000
160A185SER0-0.023-0.00826.907-0.002-0.0020.0000.0000.0000.000
161A186PHE00.002-0.00528.298-0.001-0.0010.0000.0000.0000.000
162A187ILE0-0.055-0.01923.656-0.007-0.0070.0000.0000.0000.000
163A188SER0-0.077-0.03528.1690.0000.0000.0000.0000.0000.000
164A189LEU0-0.009-0.00631.097-0.001-0.0010.0000.0000.0000.000
165A190PRO0-0.039-0.00731.0990.0000.0000.0000.0000.0000.000
166A191PRO0-0.040-0.01830.6030.0040.0040.0000.0000.0000.000
167A192GLU-1-0.926-0.97133.583-0.039-0.0390.0000.0000.0000.000
168A193ASP-1-0.934-0.96035.063-0.044-0.0440.0000.0000.0000.000
169A194PRO0-0.056-0.02531.747-0.001-0.0010.0000.0000.0000.000
170A195ASP-1-0.861-0.94830.192-0.079-0.0790.0000.0000.0000.000
171A196GLN0-0.073-0.04432.0740.0000.0000.0000.0000.0000.000
172A197LEU00.0580.05630.0390.0040.0040.0000.0000.0000.000
173A198ALA00.0170.00328.3930.0030.0030.0000.0000.0000.000
174A199SER00.000-0.01630.1480.0030.0030.0000.0000.0000.000
175A200GLY00.0520.03732.2570.0030.0030.0000.0000.0000.000
176A201LEU0-0.010-0.01629.2780.0040.0040.0000.0000.0000.000
177A202THR0-0.030-0.03329.5320.0020.0020.0000.0000.0000.000
178A203GLU-1-0.929-0.95031.018-0.025-0.0250.0000.0000.0000.000
179A204VAL0-0.055-0.01934.0000.0040.0040.0000.0000.0000.000
180A205ILE0-0.039-0.02828.6390.0050.0050.0000.0000.0000.000
181A206ALA00.0300.01931.1050.0040.0040.0000.0000.0000.000
182A207PRO00.0460.02732.0530.0040.0040.0000.0000.0000.000
183A208TYR0-0.044-0.02330.4880.0050.0050.0000.0000.0000.000
184A209LEU00.012-0.00527.1960.0040.0040.0000.0000.0000.000
185A210GLN00.022-0.00130.9880.0030.0030.0000.0000.0000.000
186A211LYS10.9050.97333.410-0.006-0.0060.0000.0000.0000.000
187A212VAL0-0.051-0.03431.1410.0030.0030.0000.0000.0000.000
188A213VAL0-0.0390.00428.6890.0040.0040.0000.0000.0000.000
189A214GLN0-0.050-0.01430.286-0.003-0.0030.0000.0000.0000.000