Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: YZ9Z2

Calculation Name: 5CY1-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5CY1

Chain ID: B

ChEMBL ID:

UniProt ID: P0ADI2

Base Structure: X-ray

Registration Date: 2023-06-22

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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1607228.373946
FMO2-HF: Nuclear repulsion 1535009.893415
FMO2-HF: Total energy -72218.480531
FMO2-MP2: Total energy -72429.305473


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(B:1:MET)


Summations of interaction energy for fragment #1(B:1:MET)
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.
-10.619-4.0441.745-3.613-4.706-0.017
Interaction energy analysis for fragmet #1(B:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.033 / q_NPA : 0.026
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].
3B3ILE00.0550.0263.806-2.286-0.092-0.019-1.040-1.1340.006
4B4PHE0-0.026-0.0226.1910.2350.2350.0000.0000.0000.000
5B5GLY00.0380.0319.4730.0310.0310.0000.0000.0000.000
6B6TYR0-0.046-0.01112.732-0.006-0.0060.0000.0000.0000.000
7B7ALA00.0030.00516.0940.0050.0050.0000.0000.0000.000
8B8ARG10.9700.99819.672-0.008-0.0080.0000.0000.0000.000
9B9VAL0-0.039-0.02122.9230.0000.0000.0000.0000.0000.000
10B10SER0-0.008-0.00326.605-0.003-0.0030.0000.0000.0000.000
11B11THR00.0500.00829.9440.0010.0010.0000.0000.0000.000
12B12SER0-0.013-0.00730.5630.0040.0040.0000.0000.0000.000
13B13GLN00.0890.03426.036-0.003-0.0030.0000.0000.0000.000
14B14GLN00.0650.03327.4540.0050.0050.0000.0000.0000.000
15B15SER0-0.044-0.03026.9410.0020.0020.0000.0000.0000.000
16B16LEU00.0220.00322.7830.0010.0010.0000.0000.0000.000
17B17ASP-1-0.814-0.91322.7020.0620.0620.0000.0000.0000.000
18B18ILE0-0.067-0.02822.9390.0040.0040.0000.0000.0000.000
19B19GLN0-0.044-0.02919.8520.0040.0040.0000.0000.0000.000
20B20ILE00.0420.02818.4570.0070.0070.0000.0000.0000.000
21B21ARG10.9270.96018.092-0.058-0.0580.0000.0000.0000.000
22B22ALA00.0320.01718.6160.0040.0040.0000.0000.0000.000
23B23LEU0-0.035-0.01713.7810.0080.0080.0000.0000.0000.000
24B24LYS10.8940.94113.681-0.105-0.1050.0000.0000.0000.000
25B25ASP-1-0.907-0.94115.2430.0980.0980.0000.0000.0000.000
26B26ALA0-0.053-0.01512.2720.0020.0020.0000.0000.0000.000
27B27GLY0-0.0100.00710.9210.0120.0120.0000.0000.0000.000
28B28VAL0-0.0250.0009.573-0.009-0.0090.0000.0000.0000.000
29B29LYS10.9270.9548.844-0.518-0.5180.0000.0000.0000.000
30B30ALA00.0500.00212.791-0.017-0.0170.0000.0000.0000.000
31B31ASN00.0050.00013.299-0.017-0.0170.0000.0000.0000.000
32B32ARG10.8470.9406.663-0.576-0.5760.0000.0000.0000.000
33B33ILE00.0090.01312.517-0.030-0.0300.0000.0000.0000.000
34B34PHE00.0200.02112.4250.0070.0070.0000.0000.0000.000
35B35THR0-0.032-0.03317.244-0.004-0.0040.0000.0000.0000.000
36B36ASP-1-0.776-0.88120.6230.0170.0170.0000.0000.0000.000
37B37LYS10.9200.95223.513-0.032-0.0320.0000.0000.0000.000
38B38ALA00.0250.02627.175-0.002-0.0020.0000.0000.0000.000
39B39SER00.041-0.00430.3100.0020.0020.0000.0000.0000.000
40B40GLY00.0020.00333.100-0.002-0.0020.0000.0000.0000.000
41B41SER0-0.047-0.02834.699-0.002-0.0020.0000.0000.0000.000
42B42SER0-0.080-0.04230.280-0.002-0.0020.0000.0000.0000.000
43B43THR00.0040.00430.147-0.003-0.0030.0000.0000.0000.000
44B44ASP-1-0.878-0.91927.1860.0120.0120.0000.0000.0000.000
45B45ARG10.8870.94323.0290.0240.0240.0000.0000.0000.000
46B46GLU-1-0.863-0.93221.8620.0210.0210.0000.0000.0000.000
47B47GLY00.0120.00619.7140.0020.0020.0000.0000.0000.000
48B48LEU0-0.030-0.02517.027-0.001-0.0010.0000.0000.0000.000
49B49ASP-1-0.855-0.93917.423-0.037-0.0370.0000.0000.0000.000
50B50LEU0-0.028-0.02516.692-0.007-0.0070.0000.0000.0000.000
51B51LEU0-0.073-0.02411.4790.0060.0060.0000.0000.0000.000
52B52ARG10.8560.92312.7540.0290.0290.0000.0000.0000.000
53B53MET0-0.044-0.00813.869-0.030-0.0300.0000.0000.0000.000
54B54LYS10.8620.93210.544-0.166-0.1660.0000.0000.0000.000
55B55VAL0-0.052-0.0088.2990.0110.0110.0000.0000.0000.000
56B56GLU-1-0.916-0.9486.119-0.051-0.0510.0000.0000.0000.000
57B57GLU-1-0.922-0.9616.602-1.053-1.0530.0000.0000.0000.000
58B58GLY0-0.030-0.0094.176-0.841-0.6420.000-0.049-0.1510.000
59B59ASP-1-0.902-0.9563.164-4.065-0.5061.611-2.376-2.794-0.023
60B60VAL00.012-0.0013.597-0.4280.2360.154-0.145-0.6720.000
61B61ILE0-0.053-0.0336.313-0.194-0.235-0.001-0.0030.0450.000
62B62LEU0-0.010-0.0079.1260.0300.0300.0000.0000.0000.000
63B63VAL00.006-0.00111.633-0.028-0.0280.0000.0000.0000.000
64B64LYS10.9320.99215.409-0.038-0.0380.0000.0000.0000.000
65B65LYS10.9660.98218.169-0.028-0.0280.0000.0000.0000.000
66B66LEU00.0720.02918.725-0.001-0.0010.0000.0000.0000.000
67B67ASP-1-0.926-0.95820.8510.0110.0110.0000.0000.0000.000
68B68ARG10.8450.92720.635-0.025-0.0250.0000.0000.0000.000
69B69LEU00.0220.02517.2030.0030.0030.0000.0000.0000.000
70B70GLY00.0180.00420.492-0.003-0.0030.0000.0000.0000.000
71B71ARG10.8350.91323.2430.0260.0260.0000.0000.0000.000
72B72ASP-1-0.838-0.91726.319-0.027-0.0270.0000.0000.0000.000
73B73THR00.038-0.00125.6090.0000.0000.0000.0000.0000.000
74B74ALA00.0280.01624.965-0.006-0.0060.0000.0000.0000.000
75B75ASP-1-0.864-0.93923.702-0.042-0.0420.0000.0000.0000.000
76B76MET0-0.0050.00720.588-0.004-0.0040.0000.0000.0000.000
77B77ILE0-0.005-0.01620.210-0.008-0.0080.0000.0000.0000.000
78B78GLN0-0.028-0.00720.500-0.015-0.0150.0000.0000.0000.000
79B79LEU0-0.013-0.00517.969-0.011-0.0110.0000.0000.0000.000
80B80ILE00.000-0.00215.298-0.016-0.0160.0000.0000.0000.000
81B81LYS10.9040.95615.6280.0830.0830.0000.0000.0000.000
82B82GLU-1-0.920-0.95116.777-0.129-0.1290.0000.0000.0000.000
83B83PHE0-0.033-0.02912.012-0.008-0.0080.0000.0000.0000.000
84B84ASP-1-0.844-0.93012.076-0.365-0.3650.0000.0000.0000.000
85B85ALA0-0.071-0.02812.884-0.054-0.0540.0000.0000.0000.000
86B86GLN0-0.067-0.03311.652-0.033-0.0330.0000.0000.0000.000
87B87GLY00.0630.0339.312-0.110-0.1100.0000.0000.0000.000
88B88VAL0-0.085-0.0287.727-0.132-0.1320.0000.0000.0000.000
89B89ALA00.0470.0326.9960.0550.0550.0000.0000.0000.000
90B90VAL0-0.064-0.0398.8660.1020.1020.0000.0000.0000.000
91B91ARG10.8980.9306.605-0.782-0.7820.0000.0000.0000.000
92B92PHE0-0.011-0.01811.662-0.008-0.0080.0000.0000.0000.000
93B93ILE0-0.005-0.02313.8480.0010.0010.0000.0000.0000.000
94B94ASP-1-0.891-0.96115.9770.0470.0470.0000.0000.0000.000
95B95ASP-1-0.920-0.97119.0540.0180.0180.0000.0000.0000.000
96B96GLY0-0.0050.01816.734-0.008-0.0080.0000.0000.0000.000
97B97ILE0-0.037-0.01615.921-0.013-0.0130.0000.0000.0000.000
98B98SER0-0.018-0.01910.7330.0590.0590.0000.0000.0000.000
99B99THR0-0.005-0.00311.306-0.044-0.0440.0000.0000.0000.000
100B100ASP-1-0.776-0.8886.7960.4900.4900.0000.0000.0000.000
101B101GLY0-0.049-0.0307.9740.0760.0760.0000.0000.0000.000
102B102ASP-1-0.914-0.9509.417-0.210-0.2100.0000.0000.0000.000
103B103MET0-0.036-0.01513.140-0.009-0.0090.0000.0000.0000.000
104B104GLY00.0680.03711.9960.0110.0110.0000.0000.0000.000
105B105GLN00.0830.03412.972-0.001-0.0010.0000.0000.0000.000
106B106MET00.0010.01315.5070.0190.0190.0000.0000.0000.000
107B107VAL00.0140.01015.6450.0140.0140.0000.0000.0000.000
108B108VAL00.0790.05014.6710.0220.0220.0000.0000.0000.000
109B109THR0-0.0400.00917.7580.0090.0090.0000.0000.0000.000
110B110ILE00.0010.00020.5670.0100.0100.0000.0000.0000.000
111B111LEU00.0310.01218.9940.0080.0080.0000.0000.0000.000
112B112SER0-0.062-0.09220.8030.0030.0030.0000.0000.0000.000
113B113ALA0-0.059-0.02423.3300.0050.0050.0000.0000.0000.000
114B114VAL00.0060.00325.5540.0060.0060.0000.0000.0000.000
115B115ALA00.0470.02625.5760.0040.0040.0000.0000.0000.000
116B116GLN0-0.084-0.06127.3660.0060.0060.0000.0000.0000.000
117B117ALA0-0.0060.00329.2060.0030.0030.0000.0000.0000.000
118B118GLU-1-0.920-0.96529.658-0.036-0.0360.0000.0000.0000.000
119B119ARG10.9870.99526.9790.0670.0670.0000.0000.0000.000
120B120ARG10.8940.94532.1400.0590.0590.0000.0000.0000.000
121B121ARG11.0160.99932.4550.0380.0380.0000.0000.0000.000
122B122ILE00.0100.01935.7530.0020.0020.0000.0000.0000.000
123B123LEU0-0.091-0.04235.8750.0010.0010.0000.0000.0000.000
124B124GLU-1-0.884-0.91739.394-0.033-0.0330.0000.0000.0000.000
125B125ARG11.0531.01241.1660.0240.0240.0000.0000.0000.000
126B126THR0-0.026-0.00541.7110.0010.0010.0000.0000.0000.000
127B127ASN0-0.085-0.07638.494-0.002-0.0020.0000.0000.0000.000
128B128GLU-1-0.889-0.92742.079-0.032-0.0320.0000.0000.0000.000
129B129GLY00.0600.03444.8210.0010.0010.0000.0000.0000.000
130B130ARG10.8670.93738.9870.0460.0460.0000.0000.0000.000
131B131GLN0-0.016-0.02041.8150.0000.0000.0000.0000.0000.000
132B132GLU-1-0.873-0.92645.968-0.026-0.0260.0000.0000.0000.000
133B133ALA0-0.041-0.02148.0250.0010.0010.0000.0000.0000.000
134B134LYS10.9210.93942.8100.0440.0440.0000.0000.0000.000
135B135LEU0-0.0200.00748.3260.0000.0000.0000.0000.0000.000
136B136LYS10.9360.97050.9370.0260.0260.0000.0000.0000.000
137B137GLY00.0380.03951.8390.0010.0010.0000.0000.0000.000
138B138ILE0-0.075-0.03149.5690.0000.0000.0000.0000.0000.000
139B139LYS10.9500.97149.3310.0280.0280.0000.0000.0000.000
140B140PHE00.0290.01643.9490.0000.0000.0000.0000.0000.000
141B141GLY00.0010.00042.9070.0000.0000.0000.0000.0000.000
142B142ARG10.9660.98042.4460.0450.0450.0000.0000.0000.000
143B143ARG11.0031.00245.1020.0310.0310.0000.0000.0000.000
144B144ARG10.9480.96248.5270.0350.0350.0000.0000.0000.000
145B145THR00.0470.01749.3060.0010.0010.0000.0000.0000.000
146B146VAL0-0.0230.00549.5670.0010.0010.0000.0000.0000.000
147B147ASP-1-0.820-0.91952.325-0.027-0.0270.0000.0000.0000.000
148B148ARG10.8640.92148.9140.0370.0370.0000.0000.0000.000
149B149ASN00.0670.04255.353-0.001-0.0010.0000.0000.0000.000
150B150VAL00.0270.02657.4650.0000.0000.0000.0000.0000.000
151B151VAL0-0.011-0.00852.5780.0000.0000.0000.0000.0000.000
152B152LEU00.0210.00154.7520.0000.0000.0000.0000.0000.000
153B153THR00.0020.00957.5880.0010.0010.0000.0000.0000.000
154B154LEU0-0.048-0.03657.6110.0010.0010.0000.0000.0000.000
155B155HIS00.0510.02255.4210.0000.0000.0000.0000.0000.000
156B156GLN0-0.0100.01658.036-0.001-0.0010.0000.0000.0000.000
157B157LYS10.8830.93761.1380.0240.0240.0000.0000.0000.000
158B158GLY00.0180.02460.0200.0010.0010.0000.0000.0000.000
159B159THR0-0.072-0.02857.2120.0000.0000.0000.0000.0000.000
160B160GLY00.0620.03255.362-0.001-0.0010.0000.0000.0000.000
161B161ALA00.028-0.00450.1570.0000.0000.0000.0000.0000.000
162B162THR0-0.038-0.04349.1020.0000.0000.0000.0000.0000.000
163B163GLU-1-0.889-0.92651.310-0.027-0.0270.0000.0000.0000.000
164B164ILE00.0180.00553.4870.0010.0010.0000.0000.0000.000
165B165ALA0-0.067-0.03549.1810.0000.0000.0000.0000.0000.000
166B166HIS00.0190.00651.2410.0000.0000.0000.0000.0000.000
167B167GLN0-0.0250.00452.8000.0010.0010.0000.0000.0000.000
168B168LEU0-0.048-0.03653.2640.0010.0010.0000.0000.0000.000
169B169SER0-0.0110.01251.1060.0000.0000.0000.0000.0000.000
170B170ILE0-0.049-0.00948.380-0.001-0.0010.0000.0000.0000.000
171B171ALA00.0460.01643.9050.0000.0000.0000.0000.0000.000
172B172ARG11.0370.99943.3090.0490.0490.0000.0000.0000.000
173B173SER0-0.022-0.01741.4710.0020.0020.0000.0000.0000.000
174B174THR00.0090.00044.327-0.001-0.0010.0000.0000.0000.000
175B175VAL00.0410.02346.1200.0010.0010.0000.0000.0000.000
176B176TYR00.005-0.01045.9850.0010.0010.0000.0000.0000.000
177B177LYS10.9981.00841.0560.0550.0550.0000.0000.0000.000
178B178ILE0-0.035-0.01646.4140.0010.0010.0000.0000.0000.000
179B179LEU0-0.009-0.00849.8160.0010.0010.0000.0000.0000.000
180B180GLU-1-0.995-0.99144.951-0.050-0.0500.0000.0000.0000.000
181B181ASP-1-0.893-0.95647.198-0.044-0.0440.0000.0000.0000.000
182B182GLU-1-0.940-0.98649.797-0.033-0.0330.0000.0000.0000.000
183B183ARG10.8980.96948.7590.0420.0420.0000.0000.0000.000
184B184ALA0-0.040-0.01549.5760.0010.0010.0000.0000.0000.000
185B185SER0-0.0320.00151.6220.0010.0010.0000.0000.0000.000