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: NN1NQ

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 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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1920452.613752
FMO2-HF: Nuclear repulsion 1848688.627048
FMO2-HF: Total energy -71763.986704
FMO2-MP2: Total energy -71975.597856


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.
0.0991.67-0.025-0.847-0.6980.001
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 : 0.027 / 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].
3A28ARG10.8580.9193.8000.6972.268-0.025-0.847-0.6980.001
4A29TRP00.0660.0325.906-0.098-0.0980.0000.0000.0000.000
5A30SER0-0.0170.0068.3310.0700.0700.0000.0000.0000.000
6A31PRO00.0830.01810.068-0.080-0.0800.0000.0000.0000.000
7A32ARG10.8900.94912.717-0.124-0.1240.0000.0000.0000.000
8A33LEU00.0370.0116.816-0.028-0.0280.0000.0000.0000.000
9A34THR00.0340.02410.995-0.057-0.0570.0000.0000.0000.000
10A35VAL0-0.014-0.00613.017-0.005-0.0050.0000.0000.0000.000
11A36PHE00.014-0.00212.5600.0080.0080.0000.0000.0000.000
12A37ASP-1-0.794-0.87711.318-0.530-0.5300.0000.0000.0000.000
13A38ALA0-0.0100.00514.8080.0140.0140.0000.0000.0000.000
14A39MET0-0.064-0.04117.9840.0170.0170.0000.0000.0000.000
15A40HIS0-0.0010.00417.0110.0100.0100.0000.0000.0000.000
16A41GLN00.0200.01218.4060.0070.0070.0000.0000.0000.000
17A42LEU0-0.091-0.04920.0680.0190.0190.0000.0000.0000.000
18A43LEU0-0.006-0.02322.0070.0140.0140.0000.0000.0000.000
19A44GLU-1-0.895-0.92719.951-0.205-0.2050.0000.0000.0000.000
20A45SER0-0.038-0.02124.3660.0100.0100.0000.0000.0000.000
21A46ARG10.8430.93126.2880.1070.1070.0000.0000.0000.000
22A47ASP-1-0.763-0.86127.848-0.059-0.0590.0000.0000.0000.000
23A48TRP00.0520.01124.861-0.001-0.0010.0000.0000.0000.000
24A49SER0-0.018-0.01728.3790.0040.0040.0000.0000.0000.000
25A50ALA0-0.048-0.01031.3070.0040.0040.0000.0000.0000.000
26A51VAL00.0460.04025.106-0.002-0.0020.0000.0000.0000.000
27A52THR0-0.027-0.00828.5170.0080.0080.0000.0000.0000.000
28A53MET00.0420.02424.776-0.008-0.0080.0000.0000.0000.000
29A54SER0-0.008-0.01525.4560.0000.0000.0000.0000.0000.000
30A55ASP-1-0.787-0.88826.335-0.054-0.0540.0000.0000.0000.000
31A56VAL00.0380.02720.704-0.008-0.0080.0000.0000.0000.000
32A57ALA0-0.028-0.01621.482-0.007-0.0070.0000.0000.0000.000
33A58LYS10.8170.89922.3410.0490.0490.0000.0000.0000.000
34A59ALA00.0010.00521.014-0.004-0.0040.0000.0000.0000.000
35A60ALA00.0100.00617.493-0.021-0.0210.0000.0000.0000.000
36A61GLY0-0.0010.02217.741-0.002-0.0020.0000.0000.0000.000
37A62LEU0-0.0100.00216.5630.0240.0240.0000.0000.0000.000
38A63SER00.0160.01320.610-0.004-0.0040.0000.0000.0000.000
39A64ARG11.0330.98423.4340.0080.0080.0000.0000.0000.000
40A65GLN0-0.0100.00426.009-0.002-0.0020.0000.0000.0000.000
41A66THR00.0530.00519.3860.0110.0110.0000.0000.0000.000
42A67LEU0-0.0020.00720.1400.0080.0080.0000.0000.0000.000
43A68TYR0-0.020-0.01222.3950.0030.0030.0000.0000.0000.000
44A69SER0-0.0230.00322.7020.0060.0060.0000.0000.0000.000
45A70THR0-0.039-0.01217.9680.0070.0070.0000.0000.0000.000
46A71PHE00.007-0.00716.5690.0060.0060.0000.0000.0000.000
47A72GLY00.0450.04222.140-0.005-0.0050.0000.0000.0000.000
48A73ASN00.000-0.01925.933-0.008-0.0080.0000.0000.0000.000
49A74ARG10.9510.94325.5070.0320.0320.0000.0000.0000.000
50A75GLN0-0.0100.00325.891-0.003-0.0030.0000.0000.0000.000
51A76GLY00.0270.01723.811-0.002-0.0020.0000.0000.0000.000
52A77LEU0-0.012-0.02421.0490.0030.0030.0000.0000.0000.000
53A78ALA00.0380.01720.950-0.007-0.0070.0000.0000.0000.000
54A79GLN0-0.0010.00122.3320.0030.0030.0000.0000.0000.000
55A80ALA0-0.016-0.00917.4700.0030.0030.0000.0000.0000.000
56A81TYR0-0.042-0.04017.345-0.006-0.0060.0000.0000.0000.000
57A82ALA00.0190.01718.029-0.012-0.0120.0000.0000.0000.000
58A83LEU0-0.008-0.00816.7880.0000.0000.0000.0000.0000.000
59A84GLN0-0.052-0.02711.222-0.058-0.0580.0000.0000.0000.000
60A85LEU0-0.023-0.00314.996-0.016-0.0160.0000.0000.0000.000
61A86SER0-0.056-0.02917.540-0.004-0.0040.0000.0000.0000.000
62A87GLU-1-0.836-0.91111.0100.0750.0750.0000.0000.0000.000
63A88LYS10.8670.92413.3450.2500.2500.0000.0000.0000.000
64A89PHE00.000-0.01914.367-0.015-0.0150.0000.0000.0000.000
65A90ALA00.0270.01717.010-0.002-0.0020.0000.0000.0000.000
66A91GLY00.003-0.00213.7050.0100.0100.0000.0000.0000.000
67A92GLU-1-0.803-0.86314.660-0.224-0.2240.0000.0000.0000.000
68A93ILE00.0100.00816.7430.0010.0010.0000.0000.0000.000
69A94ARG10.8560.91911.5510.0750.0750.0000.0000.0000.000
70A95ASP-1-0.870-0.93512.808-0.201-0.2010.0000.0000.0000.000
71A96SER0-0.020-0.03615.823-0.007-0.0070.0000.0000.0000.000
72A97ILE0-0.009-0.01219.4150.0050.0050.0000.0000.0000.000
73A98ILE0-0.056-0.02114.8370.0070.0070.0000.0000.0000.000
74A99ARG10.8130.90715.2850.1760.1760.0000.0000.0000.000
75A100HIS0-0.063-0.04119.1760.0060.0060.0000.0000.0000.000
76A101PRO00.0250.01021.8170.0100.0100.0000.0000.0000.000
77A102GLY00.005-0.00824.253-0.001-0.0010.0000.0000.0000.000
78A103GLN0-0.018-0.00426.6090.0060.0060.0000.0000.0000.000
79A104ILE00.0150.00226.669-0.004-0.0040.0000.0000.0000.000
80A105GLU-1-0.862-0.93527.588-0.037-0.0370.0000.0000.0000.000
81A106LEU0-0.0140.00225.695-0.003-0.0030.0000.0000.0000.000
82A107ALA00.0230.01523.239-0.008-0.0080.0000.0000.0000.000
83A108LEU00.0020.00323.599-0.006-0.0060.0000.0000.0000.000
84A109SER00.0210.02225.476-0.006-0.0060.0000.0000.0000.000
85A110GLU-1-0.769-0.83520.885-0.135-0.1350.0000.0000.0000.000
86A111GLY00.0270.00920.874-0.010-0.0100.0000.0000.0000.000
87A112ILE0-0.027-0.01021.781-0.007-0.0070.0000.0000.0000.000
88A113ASN00.0260.01124.261-0.003-0.0030.0000.0000.0000.000
89A114GLY0-0.022-0.00720.513-0.007-0.0070.0000.0000.0000.000
90A115PHE0-0.019-0.02320.315-0.012-0.0120.0000.0000.0000.000
91A116LEU00.0310.02021.290-0.003-0.0030.0000.0000.0000.000
92A117ARG10.9460.97718.8620.1900.1900.0000.0000.0000.000
93A118SER0-0.105-0.09017.593-0.011-0.0110.0000.0000.0000.000
94A119SER00.0270.00620.3520.0010.0010.0000.0000.0000.000
95A120SER0-0.043-0.00222.8380.0050.0050.0000.0000.0000.000
96A121ARG10.8690.92418.7110.2080.2080.0000.0000.0000.000
97A122ASP-1-0.694-0.83819.947-0.143-0.1430.0000.0000.0000.000
98A123PRO0-0.0100.00320.7440.0170.0170.0000.0000.0000.000
99A124LEU0-0.028-0.01322.5570.0140.0140.0000.0000.0000.000
100A125ILE0-0.0050.00022.5580.0120.0120.0000.0000.0000.000
101A126ARG10.9810.98925.5420.1020.1020.0000.0000.0000.000
102A127ALA00.0050.00927.0190.0070.0070.0000.0000.0000.000
103A128LEU0-0.0440.01527.6360.0080.0080.0000.0000.0000.000
104A129VAL00.0400.02130.0180.0060.0060.0000.0000.0000.000
105A130THR0-0.030-0.00132.1570.0020.0020.0000.0000.0000.000
106A131GLY00.0360.01232.294-0.005-0.0050.0000.0000.0000.000
107A132ASH0-0.077-0.08732.2880.0010.0010.0000.0000.0000.000
108A133ILE00.005-0.00936.4680.0010.0010.0000.0000.0000.000
109A134LYS10.8510.91133.5240.0490.0490.0000.0000.0000.000
110A135PRO0-0.0180.01732.3580.0010.0010.0000.0000.0000.000
111A136ASP-1-0.836-0.91732.867-0.017-0.0170.0000.0000.0000.000
112A137LEU0-0.033-0.03329.5910.0020.0020.0000.0000.0000.000
113A138LEU0-0.005-0.00826.7170.0020.0020.0000.0000.0000.000
114A139ARG10.9250.95329.1700.0320.0320.0000.0000.0000.000
115A140LEU00.0310.01230.2520.0020.0020.0000.0000.0000.000
116A141ILE0-0.040-0.01624.3080.0040.0040.0000.0000.0000.000
117A142THR0-0.010-0.01027.0200.0000.0000.0000.0000.0000.000
118A143THR0-0.067-0.02628.302-0.002-0.0020.0000.0000.0000.000
119A144GLU-1-0.920-0.94930.8990.0100.0100.0000.0000.0000.000
120A145ALA0-0.014-0.01525.5240.0050.0050.0000.0000.0000.000
121A146GLY00.0360.02626.533-0.005-0.0050.0000.0000.0000.000
122A147PRO00.0200.00122.4710.0030.0030.0000.0000.0000.000
123A148LEU0-0.0050.01321.3060.0050.0050.0000.0000.0000.000
124A149ILE00.0370.02121.4960.0000.0000.0000.0000.0000.000
125A150GLU-1-0.891-0.91821.9240.0630.0630.0000.0000.0000.000
126A151ARG10.7980.88414.087-0.107-0.1070.0000.0000.0000.000
127A152ALA00.0330.01218.1160.0050.0050.0000.0000.0000.000
128A153THR0-0.009-0.03819.620-0.002-0.0020.0000.0000.0000.000
129A154GLU-1-0.868-0.91517.1450.1300.1300.0000.0000.0000.000
130A155VAL0-0.052-0.02414.1940.0120.0120.0000.0000.0000.000
131A156LEU0-0.004-0.01516.632-0.006-0.0060.0000.0000.0000.000
132A157MET0-0.0140.01319.863-0.003-0.0030.0000.0000.0000.000
133A158PRO00.0520.02816.895-0.010-0.0100.0000.0000.0000.000
134A159ALA0-0.0200.00418.193-0.009-0.0090.0000.0000.0000.000
135A160LEU0-0.0290.00319.298-0.012-0.0120.0000.0000.0000.000
136A161SER0-0.061-0.03522.4180.0010.0010.0000.0000.0000.000
137A162GLU-1-0.933-0.96818.4410.1170.1170.0000.0000.0000.000
138A163SER0-0.050-0.04119.906-0.001-0.0010.0000.0000.0000.000
139A164TRP0-0.019-0.03120.9330.0110.0110.0000.0000.0000.000
140A165MET0-0.0230.00323.752-0.001-0.0010.0000.0000.0000.000
141A166ARG10.8800.95821.867-0.032-0.0320.0000.0000.0000.000
142A167ILE00.0180.02026.0550.0010.0010.0000.0000.0000.000
143A168GLU-1-0.848-0.92926.7760.0500.0500.0000.0000.0000.000
144A169ALA00.0460.02425.903-0.003-0.0030.0000.0000.0000.000
145A170SER0-0.013-0.01526.982-0.002-0.0020.0000.0000.0000.000
146A171GLN00.0260.00030.0300.0000.0000.0000.0000.0000.000
147A172ALA00.0250.02324.715-0.004-0.0040.0000.0000.0000.000
148A173ARG10.9060.93123.575-0.063-0.0630.0000.0000.0000.000
149A174LEU0-0.0190.00126.444-0.003-0.0030.0000.0000.0000.000
150A175ALA00.0410.01927.788-0.003-0.0030.0000.0000.0000.000
151A176ALA00.0060.00723.306-0.005-0.0050.0000.0000.0000.000
152A177SER0-0.030-0.01825.084-0.005-0.0050.0000.0000.0000.000
153A178ILE0-0.014-0.01026.902-0.004-0.0040.0000.0000.0000.000
154A179ILE00.0340.01524.136-0.005-0.0050.0000.0000.0000.000
155A180ALA0-0.007-0.00123.650-0.006-0.0060.0000.0000.0000.000
156A181ARG10.9210.95225.054-0.014-0.0140.0000.0000.0000.000
157A182ILE00.0160.00628.455-0.003-0.0030.0000.0000.0000.000
158A183GLY00.0290.01725.370-0.004-0.0040.0000.0000.0000.000
159A184ILE00.003-0.01924.490-0.005-0.0050.0000.0000.0000.000
160A185SER0-0.020-0.00226.908-0.002-0.0020.0000.0000.0000.000
161A186PHE00.012-0.00128.442-0.001-0.0010.0000.0000.0000.000
162A187ILE0-0.045-0.01223.786-0.006-0.0060.0000.0000.0000.000
163A188SER0-0.077-0.03928.1700.0000.0000.0000.0000.0000.000
164A189LEU0-0.014-0.00431.097-0.001-0.0010.0000.0000.0000.000
165A190PRO0-0.023-0.00730.9540.0000.0000.0000.0000.0000.000
166A191PRO0-0.049-0.02030.5870.0040.0040.0000.0000.0000.000
167A192GLU-1-0.941-0.97133.583-0.039-0.0390.0000.0000.0000.000
168A193ASP-1-0.887-0.92435.398-0.045-0.0450.0000.0000.0000.000
169A194PRO0-0.042-0.02531.711-0.001-0.0010.0000.0000.0000.000
170A195ASP-1-0.876-0.95730.490-0.078-0.0780.0000.0000.0000.000
171A196GLN0-0.111-0.06832.0740.0020.0020.0000.0000.0000.000
172A197LEU00.0400.04230.1470.0040.0040.0000.0000.0000.000
173A198ALA00.0140.00528.4030.0030.0030.0000.0000.0000.000
174A199SER00.007-0.00930.1490.0020.0020.0000.0000.0000.000
175A200GLY00.0550.03632.2580.0030.0030.0000.0000.0000.000
176A201LEU0-0.018-0.01928.8100.0040.0040.0000.0000.0000.000
177A202THR0-0.034-0.03829.5970.0020.0020.0000.0000.0000.000
178A203GLU-1-0.943-0.95531.020-0.028-0.0280.0000.0000.0000.000
179A204VAL0-0.041-0.01134.0270.0040.0040.0000.0000.0000.000
180A205ILE0-0.039-0.03028.7790.0040.0040.0000.0000.0000.000
181A206ALA00.0270.01631.1100.0030.0030.0000.0000.0000.000
182A207PRO00.0490.03032.0550.0030.0030.0000.0000.0000.000
183A208TYR0-0.061-0.03130.5420.0040.0040.0000.0000.0000.000
184A209LEU00.009-0.00927.1030.0040.0040.0000.0000.0000.000
185A210GLN0-0.015-0.02230.9890.0050.0050.0000.0000.0000.000
186A211LYS10.9060.97333.412-0.001-0.0010.0000.0000.0000.000
187A212VAL0-0.026-0.02431.0920.0030.0030.0000.0000.0000.000
188A213VAL0-0.0020.02028.3240.0030.0030.0000.0000.0000.000
189A214GLN0-0.103-0.04030.270-0.002-0.0020.0000.0000.0000.000