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: 1757Z

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 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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1613668.314216
FMO2-HF: Nuclear repulsion 1541448.022366
FMO2-HF: Total energy -72220.29185
FMO2-MP2: Total energy -72431.143934


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.
-22.799-16.8257.785-5.836-7.922-0.063
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 : -0.019 / q_NPA : -0.001
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].
3B3ILE00.0300.0193.848-0.9350.696-0.009-0.650-0.9720.003
4B4PHE0-0.025-0.0115.977-0.104-0.1040.0000.0000.0000.000
5B5GLY00.0240.0119.0820.1830.1830.0000.0000.0000.000
6B6TYR0-0.076-0.05512.345-0.053-0.0530.0000.0000.0000.000
7B7ALA00.0120.00315.6230.0380.0380.0000.0000.0000.000
8B8ARG10.9140.96019.2780.0280.0280.0000.0000.0000.000
9B9VAL0-0.031-0.00222.6540.0130.0130.0000.0000.0000.000
10B10SER00.0270.01526.453-0.009-0.0090.0000.0000.0000.000
11B11THR00.0450.00829.784-0.002-0.0020.0000.0000.0000.000
12B12SER00.0050.00530.8430.0040.0040.0000.0000.0000.000
13B13GLN00.0710.02925.942-0.007-0.0070.0000.0000.0000.000
14B14GLN00.0290.01327.5450.0060.0060.0000.0000.0000.000
15B15SER0-0.037-0.03227.4370.0070.0070.0000.0000.0000.000
16B16LEU00.0170.02222.1500.0050.0050.0000.0000.0000.000
17B17ASP-1-0.794-0.88923.0380.0670.0670.0000.0000.0000.000
18B18ILE0-0.005-0.00623.3690.0170.0170.0000.0000.0000.000
19B19GLN0-0.050-0.04520.1460.0110.0110.0000.0000.0000.000
20B20ILE00.0210.00419.0020.0260.0260.0000.0000.0000.000
21B21ARG10.8440.90518.619-0.138-0.1380.0000.0000.0000.000
22B22ALA00.0000.00018.9640.0230.0230.0000.0000.0000.000
23B23LEU00.0030.00713.8670.0420.0420.0000.0000.0000.000
24B24LYS10.9120.96414.245-0.087-0.0870.0000.0000.0000.000
25B25ASP-1-0.839-0.90615.4160.2480.2480.0000.0000.0000.000
26B26ALA0-0.032-0.00113.2490.0210.0210.0000.0000.0000.000
27B27GLY00.0070.00711.2320.1340.1340.0000.0000.0000.000
28B28VAL0-0.052-0.02010.4900.0310.0310.0000.0000.0000.000
29B29LYS10.9730.9718.867-0.461-0.4610.0000.0000.0000.000
30B30ALA00.023-0.01113.000-0.035-0.0350.0000.0000.0000.000
31B31ASN0-0.0150.00213.600-0.007-0.0070.0000.0000.0000.000
32B32ARG10.8480.9326.502-0.078-0.0780.0000.0000.0000.000
33B33ILE0-0.0040.00712.064-0.024-0.0240.0000.0000.0000.000
34B34PHE00.0060.01511.857-0.011-0.0110.0000.0000.0000.000
35B35THR0-0.030-0.03716.5630.0190.0190.0000.0000.0000.000
36B36ASP-1-0.745-0.82620.158-0.098-0.0980.0000.0000.0000.000
37B37LYS10.8860.92523.0720.0090.0090.0000.0000.0000.000
38B38ALA00.0250.02626.832-0.006-0.0060.0000.0000.0000.000
39B39SER0-0.006-0.04529.8890.0050.0050.0000.0000.0000.000
40B40GLY0-0.008-0.01332.8460.0000.0000.0000.0000.0000.000
41B41SER0-0.044-0.03034.0760.0000.0000.0000.0000.0000.000
42B42SER0-0.086-0.03829.645-0.002-0.0020.0000.0000.0000.000
43B43THR0-0.012-0.01929.386-0.005-0.0050.0000.0000.0000.000
44B44ASP-1-0.826-0.84726.484-0.057-0.0570.0000.0000.0000.000
45B45ARG10.8410.89021.8640.1250.1250.0000.0000.0000.000
46B46GLU-1-0.852-0.92020.775-0.087-0.0870.0000.0000.0000.000
47B47GLY0-0.017-0.00618.722-0.013-0.0130.0000.0000.0000.000
48B48LEU0-0.015-0.02516.126-0.025-0.0250.0000.0000.0000.000
49B49ASP-1-0.835-0.91616.188-0.228-0.2280.0000.0000.0000.000
50B50LEU0-0.033-0.02816.075-0.030-0.0300.0000.0000.0000.000
51B51LEU0-0.057-0.01910.430-0.022-0.0220.0000.0000.0000.000
52B52ARG10.7670.83211.7330.1510.1510.0000.0000.0000.000
53B53MET0-0.031-0.00712.823-0.073-0.0730.0000.0000.0000.000
54B54LYS10.8570.92910.3540.2390.2390.0000.0000.0000.000
55B55VAL0-0.059-0.0057.041-0.042-0.0420.0000.0000.0000.000
56B56GLU-1-0.799-0.8765.211-0.204-0.2040.0000.0000.0000.000
57B57GLU-1-0.923-0.9575.310-2.129-2.1290.0000.0000.0000.000
58B58GLY0-0.0030.0033.586-1.177-0.7790.011-0.103-0.3060.000
59B59ASP-1-0.781-0.8892.029-16.070-13.0557.267-4.868-5.414-0.065
60B60VAL0-0.017-0.0183.4220.1891.0340.517-0.209-1.153-0.001
61B61ILE0-0.0180.0015.7880.1830.1830.0000.0000.0000.000
62B62LEU0-0.007-0.0078.7070.0620.0620.0000.0000.0000.000
63B63VAL00.0170.00111.482-0.091-0.0910.0000.0000.0000.000
64B64LYS10.8800.96115.251-0.091-0.0910.0000.0000.0000.000
65B65LYS10.8740.92718.121-0.061-0.0610.0000.0000.0000.000
66B66LEU00.0490.01418.027-0.017-0.0170.0000.0000.0000.000
67B67ASP-1-0.833-0.91220.067-0.006-0.0060.0000.0000.0000.000
68B68ARG10.7730.88520.072-0.023-0.0230.0000.0000.0000.000
69B69LEU00.0180.02016.310-0.005-0.0050.0000.0000.0000.000
70B70GLY00.0120.00619.634-0.018-0.0180.0000.0000.0000.000
71B71ARG10.8340.90422.6550.1200.1200.0000.0000.0000.000
72B72ASP-1-0.842-0.92825.779-0.083-0.0830.0000.0000.0000.000
73B73THR00.0420.00824.912-0.006-0.0060.0000.0000.0000.000
74B74ALA00.0290.02323.938-0.013-0.0130.0000.0000.0000.000
75B75ASP-1-0.794-0.85823.660-0.146-0.1460.0000.0000.0000.000
76B76MET00.0200.01119.805-0.013-0.0130.0000.0000.0000.000
77B77ILE0-0.033-0.02219.324-0.024-0.0240.0000.0000.0000.000
78B78GLN0-0.069-0.03419.495-0.019-0.0190.0000.0000.0000.000
79B79LEU00.0140.00117.489-0.034-0.0340.0000.0000.0000.000
80B80ILE0-0.012-0.00614.602-0.048-0.0480.0000.0000.0000.000
81B81LYS10.9000.93814.6520.2010.2010.0000.0000.0000.000
82B82GLU-1-0.818-0.86116.210-0.345-0.3450.0000.0000.0000.000
83B83PHE0-0.0060.00611.456-0.016-0.0160.0000.0000.0000.000
84B84ASP-1-0.845-0.93111.592-0.719-0.7190.0000.0000.0000.000
85B85ALA0-0.059-0.03112.480-0.085-0.0850.0000.0000.0000.000
86B86GLN0-0.092-0.04910.6800.0060.0060.0000.0000.0000.000
87B87GLY00.0760.0359.060-0.216-0.2160.0000.0000.0000.000
88B88VAL0-0.075-0.0237.039-0.545-0.5450.0000.0000.0000.000
89B89ALA00.0100.0125.7500.3400.3400.0000.0000.0000.000
90B90VAL0-0.015-0.0127.5770.1650.1650.0000.0000.0000.000
91B91ARG10.8210.8734.794-1.481-1.396-0.001-0.006-0.0770.000
92B92PHE0-0.004-0.01211.4000.0070.0070.0000.0000.0000.000
93B93ILE00.001-0.00714.0320.0080.0080.0000.0000.0000.000
94B94ASP-1-0.839-0.94216.0510.1390.1390.0000.0000.0000.000
95B95ASP-1-0.855-0.92618.4990.0420.0420.0000.0000.0000.000
96B96GLY00.0050.01716.565-0.018-0.0180.0000.0000.0000.000
97B97ILE0-0.0210.00514.962-0.007-0.0070.0000.0000.0000.000
98B98SER0-0.019-0.0289.9350.1180.1180.0000.0000.0000.000
99B99THR0-0.028-0.02310.567-0.064-0.0640.0000.0000.0000.000
100B100ASP-1-0.741-0.8375.720-0.148-0.1480.0000.0000.0000.000
101B101GLY0-0.007-0.0027.4750.2010.2010.0000.0000.0000.000
102B102ASP-1-0.921-0.9649.016-0.176-0.1760.0000.0000.0000.000
103B103MET0-0.0020.00112.813-0.031-0.0310.0000.0000.0000.000
104B104GLY00.0380.02411.3290.0010.0010.0000.0000.0000.000
105B105GLN00.0740.03012.300-0.009-0.0090.0000.0000.0000.000
106B106MET00.0080.01814.8730.0190.0190.0000.0000.0000.000
107B107VAL00.0070.00514.9240.0140.0140.0000.0000.0000.000
108B108VAL00.0510.03213.9900.0310.0310.0000.0000.0000.000
109B109THR0-0.040-0.00816.9770.0130.0130.0000.0000.0000.000
110B110ILE0-0.001-0.00720.0300.0140.0140.0000.0000.0000.000
111B111LEU00.0270.00817.9960.0130.0130.0000.0000.0000.000
112B112SER0-0.030-0.03520.233-0.003-0.0030.0000.0000.0000.000
113B113ALA0-0.030-0.00722.6420.0090.0090.0000.0000.0000.000
114B114VAL00.0050.00324.6930.0090.0090.0000.0000.0000.000
115B115ALA00.0500.02824.3980.0070.0070.0000.0000.0000.000
116B116GLN0-0.056-0.02326.3210.0140.0140.0000.0000.0000.000
117B117ALA0-0.011-0.00828.4420.0070.0070.0000.0000.0000.000
118B118GLU-1-0.909-0.96027.754-0.087-0.0870.0000.0000.0000.000
119B119ARG10.9780.98126.1520.1340.1340.0000.0000.0000.000
120B120ARG10.8720.92632.0390.0970.0970.0000.0000.0000.000
121B121ARG11.0171.00831.7090.0680.0680.0000.0000.0000.000
122B122ILE0-0.035-0.00234.2690.0040.0040.0000.0000.0000.000
123B123LEU0-0.052-0.02235.1250.0030.0030.0000.0000.0000.000
124B124GLU-1-0.875-0.93638.178-0.057-0.0570.0000.0000.0000.000
125B125ARG11.0351.01840.2330.0500.0500.0000.0000.0000.000
126B126THR0-0.016-0.00141.0500.0020.0020.0000.0000.0000.000
127B127ASN0-0.056-0.05338.158-0.003-0.0030.0000.0000.0000.000
128B128GLU-1-0.872-0.93041.644-0.049-0.0490.0000.0000.0000.000
129B129GLY00.0590.03244.3990.0010.0010.0000.0000.0000.000
130B130ARG10.8630.94237.9170.0810.0810.0000.0000.0000.000
131B131GLN00.009-0.00541.6900.0000.0000.0000.0000.0000.000
132B132GLU-1-0.812-0.89045.524-0.041-0.0410.0000.0000.0000.000
133B133ALA0-0.021-0.01847.7110.0020.0020.0000.0000.0000.000
134B134LYS10.8880.93742.5840.0660.0660.0000.0000.0000.000
135B135LEU0-0.0160.00048.1690.0000.0000.0000.0000.0000.000
136B136LYS10.8540.92350.6550.0440.0440.0000.0000.0000.000
137B137GLY00.0240.02451.6380.0010.0010.0000.0000.0000.000
138B138ILE0-0.061-0.02849.322-0.001-0.0010.0000.0000.0000.000
139B139LYS10.9490.96648.9290.0460.0460.0000.0000.0000.000
140B140PHE00.0060.00443.820-0.002-0.0020.0000.0000.0000.000
141B141GLY00.0200.01342.9990.0000.0000.0000.0000.0000.000
142B142ARG10.9300.96942.6520.0800.0800.0000.0000.0000.000
143B143ARG10.9980.99344.9790.0590.0590.0000.0000.0000.000
144B144ARG10.8960.93448.4320.0550.0550.0000.0000.0000.000
145B145THR00.004-0.00149.0630.0010.0010.0000.0000.0000.000
146B146VAL00.0220.01449.6070.0000.0000.0000.0000.0000.000
147B147ASP-1-0.794-0.88952.607-0.046-0.0460.0000.0000.0000.000
148B148ARG10.7540.83248.9220.0590.0590.0000.0000.0000.000
149B149ASN00.0260.01055.4860.0010.0010.0000.0000.0000.000
150B150VAL00.0210.02457.8530.0010.0010.0000.0000.0000.000
151B151VAL0-0.008-0.00453.1300.0000.0000.0000.0000.0000.000
152B152LEU00.002-0.00255.8750.0000.0000.0000.0000.0000.000
153B153THR00.003-0.00458.1720.0010.0010.0000.0000.0000.000
154B154LEU0-0.045-0.02857.5160.0010.0010.0000.0000.0000.000
155B155HIS00.0610.03655.8290.0000.0000.0000.0000.0000.000
156B156GLN0-0.040-0.01558.4800.0000.0000.0000.0000.0000.000
157B157LYS10.9120.96261.7240.0400.0400.0000.0000.0000.000
158B158GLY00.0080.01460.3120.0010.0010.0000.0000.0000.000
159B159THR0-0.091-0.05057.7680.0000.0000.0000.0000.0000.000
160B160GLY00.0580.02955.664-0.001-0.0010.0000.0000.0000.000
161B161ALA0-0.007-0.01750.509-0.001-0.0010.0000.0000.0000.000
162B162THR0-0.014-0.03149.116-0.002-0.0020.0000.0000.0000.000
163B163GLU-1-0.844-0.90151.300-0.045-0.0450.0000.0000.0000.000
164B164ILE00.007-0.00953.3130.0000.0000.0000.0000.0000.000
165B165ALA0-0.031-0.01748.8890.0000.0000.0000.0000.0000.000
166B166HIS0-0.005-0.00650.913-0.001-0.0010.0000.0000.0000.000
167B167GLN0-0.0070.00652.2760.0000.0000.0000.0000.0000.000
168B168LEU0-0.042-0.02853.0740.0010.0010.0000.0000.0000.000
169B169SER0-0.0220.00850.209-0.001-0.0010.0000.0000.0000.000
170B170ILE0-0.053-0.01747.803-0.003-0.0030.0000.0000.0000.000
171B171ALA00.0360.01443.6940.0000.0000.0000.0000.0000.000
172B172ARG10.9940.97444.2170.0730.0730.0000.0000.0000.000
173B173SER00.0060.00641.9400.0030.0030.0000.0000.0000.000
174B174THR00.012-0.00244.632-0.001-0.0010.0000.0000.0000.000
175B175VAL00.0060.01646.5610.0020.0020.0000.0000.0000.000
176B176TYR00.0470.00945.9170.0010.0010.0000.0000.0000.000
177B177LYS10.9760.99742.4050.0810.0810.0000.0000.0000.000
178B178ILE0-0.027-0.00847.1430.0010.0010.0000.0000.0000.000
179B179LEU0-0.021-0.00450.5840.0020.0020.0000.0000.0000.000
180B180GLU-1-0.860-0.90745.387-0.069-0.0690.0000.0000.0000.000
181B181ASP-1-0.822-0.91047.098-0.067-0.0670.0000.0000.0000.000
182B182GLU-1-0.798-0.87549.733-0.052-0.0520.0000.0000.0000.000
183B183ARG10.7760.88848.4710.0610.0610.0000.0000.0000.000
184B184ALA0-0.018-0.00949.6920.0010.0010.0000.0000.0000.000
185B185SER0-0.051-0.01751.7350.0020.0020.0000.0000.0000.000