FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: JLRK9

Calculation Name: 4YK8-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YK8

Chain ID: B

ChEMBL ID:

UniProt ID: O36019

Base Structure: X-ray

Registration Date: 2023-06-26

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 203
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2333698.2846
FMO2-HF: Nuclear repulsion 2254008.362763
FMO2-HF: Total energy -79689.921837
FMO2-MP2: Total energy -79925.647824


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:34:GLY)


Summations of interaction energy for fragment #1(B:34: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.
-1.4260.0949999999999990.111-0.838-0.7940.004
Interaction energy analysis for fragmet #1(B:34:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / 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].
3B36ARG10.9300.9523.8090.6611.785-0.015-0.625-0.4840.003
4B37SER00.0490.0226.8720.1250.1250.0000.0000.0000.000
5B38ALA00.0070.0243.044-0.3510.0460.126-0.213-0.3100.001
6B39LYS10.8860.9274.818-0.664-0.6640.0000.0000.0000.000
7B40LEU00.0020.0015.718-0.083-0.0830.0000.0000.0000.000
8B41GLY00.0620.0358.454-0.114-0.1140.0000.0000.0000.000
9B42GLN00.0260.0216.850-0.064-0.0640.0000.0000.0000.000
10B43VAL00.0060.0038.961-0.149-0.1490.0000.0000.0000.000
11B44ILE00.0520.01811.549-0.073-0.0730.0000.0000.0000.000
12B45HIS00.0600.05511.597-0.075-0.0750.0000.0000.0000.000
13B46HIS0-0.015-0.01011.6540.0090.0090.0000.0000.0000.000
14B47CYS0-0.071-0.01214.775-0.059-0.0590.0000.0000.0000.000
15B48PHE00.015-0.02116.831-0.033-0.0330.0000.0000.0000.000
16B49TYR0-0.060-0.04416.914-0.022-0.0220.0000.0000.0000.000
17B50LYS10.8260.92518.560-0.154-0.1540.0000.0000.0000.000
18B51THR0-0.006-0.00520.314-0.025-0.0250.0000.0000.0000.000
19B52GLY00.0470.01722.765-0.015-0.0150.0000.0000.0000.000
20B53LEU0-0.0190.01221.959-0.012-0.0120.0000.0000.0000.000
21B54ILE00.0080.00723.825-0.014-0.0140.0000.0000.0000.000
22B55ILE0-0.003-0.00426.549-0.009-0.0090.0000.0000.0000.000
23B56LEU00.008-0.01227.092-0.009-0.0090.0000.0000.0000.000
24B57GLU-1-0.859-0.92227.7360.0670.0670.0000.0000.0000.000
25B58SER0-0.066-0.03929.765-0.008-0.0080.0000.0000.0000.000
26B59ARG10.7260.83332.367-0.076-0.0760.0000.0000.0000.000
27B60LEU0-0.050-0.00631.779-0.004-0.0040.0000.0000.0000.000
28B61ASN00.0300.02732.323-0.005-0.0050.0000.0000.0000.000
29B70GLU-1-0.849-0.93627.3890.0620.0620.0000.0000.0000.000
30B71SER00.0420.02027.8080.0050.0050.0000.0000.0000.000
31B72SER0-0.014-0.00925.186-0.001-0.0010.0000.0000.0000.000
32B73LYS10.8110.92622.766-0.080-0.0800.0000.0000.0000.000
33B74ASN0-0.016-0.02822.6240.0020.0020.0000.0000.0000.000
34B75ASN00.010-0.00317.8660.0000.0000.0000.0000.0000.000
35B76LYS10.8880.93118.554-0.062-0.0620.0000.0000.0000.000
36B77TRP00.0060.00814.7980.0030.0030.0000.0000.0000.000
37B78PHE0-0.006-0.02214.739-0.012-0.0120.0000.0000.0000.000
38B79ASN00.0210.02018.419-0.004-0.0040.0000.0000.0000.000
39B80LEU00.0190.02020.903-0.012-0.0120.0000.0000.0000.000
40B81GLU-1-0.807-0.89022.8630.0580.0580.0000.0000.0000.000
41B82ILE0-0.0020.00623.902-0.004-0.0040.0000.0000.0000.000
42B83VAL00.0200.01024.3370.0110.0110.0000.0000.0000.000
43B84GLU-1-0.800-0.87420.6020.1650.1650.0000.0000.0000.000
44B85THR00.006-0.01025.335-0.010-0.0100.0000.0000.0000.000
45B86GLU-1-0.841-0.92825.1930.1060.1060.0000.0000.0000.000
46B87LEU00.0280.02026.0150.0090.0090.0000.0000.0000.000
47B88TYR0-0.043-0.04021.4660.0030.0030.0000.0000.0000.000
48B89ALA00.0220.01821.6250.0140.0140.0000.0000.0000.000
49B90GLU-1-0.807-0.87422.1010.1750.1750.0000.0000.0000.000
50B91GLN00.036-0.00424.3810.0120.0120.0000.0000.0000.000
51B92PHE0-0.023-0.01017.0890.0170.0170.0000.0000.0000.000
52B93LYS10.7950.87219.793-0.154-0.1540.0000.0000.0000.000
53B94ILE0-0.0020.00321.1550.0100.0100.0000.0000.0000.000
54B95TRP0-0.021-0.02418.7480.0180.0180.0000.0000.0000.000
55B96LYS10.8310.90014.865-0.415-0.4150.0000.0000.0000.000
56B97ASN0-0.044-0.01319.5310.0390.0390.0000.0000.0000.000
57B98ILE0-0.039-0.00621.579-0.002-0.0020.0000.0000.0000.000
58B99GLU-1-0.764-0.84720.7440.3290.3290.0000.0000.0000.000
59B100LEU0-0.053-0.02816.859-0.009-0.0090.0000.0000.0000.000
60B101SER00.0400.02121.589-0.014-0.0140.0000.0000.0000.000
61B102PRO00.0390.01423.6410.0190.0190.0000.0000.0000.000
62B103SER0-0.006-0.01223.098-0.010-0.0100.0000.0000.0000.000
63B104ARG10.7130.82918.195-0.306-0.3060.0000.0000.0000.000
64B105LYS10.9120.97219.184-0.195-0.1950.0000.0000.0000.000
65B106ILE00.014-0.00617.7550.0010.0010.0000.0000.0000.000
66B107PRO00.0410.02620.285-0.016-0.0160.0000.0000.0000.000
67B108PRO0-0.0030.01622.4360.0140.0140.0000.0000.0000.000
68B109MET0-0.017-0.01922.7860.0070.0070.0000.0000.0000.000
69B110VAL0-0.014-0.00424.886-0.009-0.0090.0000.0000.0000.000
70B111LEU0-0.027-0.02327.9590.0010.0010.0000.0000.0000.000
71B112HIS00.0010.01229.929-0.012-0.0120.0000.0000.0000.000
72B113THR0-0.014-0.01633.6530.0020.0020.0000.0000.0000.000
73B114TYR00.0370.02835.643-0.005-0.0050.0000.0000.0000.000
74B115LEU0-0.011-0.03239.120-0.001-0.0010.0000.0000.0000.000
75B116ASP-1-0.827-0.89241.4350.0640.0640.0000.0000.0000.000
76B117ILE00.020-0.00244.415-0.002-0.0020.0000.0000.0000.000
77B118SER00.0540.00246.0390.0000.0000.0000.0000.0000.000
78B119ASP-1-0.823-0.86047.2040.0440.0440.0000.0000.0000.000
79B120LEU00.0540.03050.026-0.001-0.0010.0000.0000.0000.000
80B121SER0-0.087-0.03050.887-0.001-0.0010.0000.0000.0000.000
81B146LYS10.8680.89839.159-0.070-0.0700.0000.0000.0000.000
82B147ILE00.002-0.01242.8920.0010.0010.0000.0000.0000.000
83B148VAL0-0.0090.00736.9260.0010.0010.0000.0000.0000.000
84B149LEU0-0.054-0.04339.231-0.003-0.0030.0000.0000.0000.000
85B150GLU-1-0.782-0.88935.0830.0730.0730.0000.0000.0000.000
86B151ARG10.8360.92433.405-0.091-0.0910.0000.0000.0000.000
87B152TRP0-0.010-0.04029.257-0.002-0.0020.0000.0000.0000.000
88B153ILE00.0270.01927.8160.0050.0050.0000.0000.0000.000
89B154VAL0-0.0150.00722.167-0.002-0.0020.0000.0000.0000.000
90B155ASN00.0520.00123.2710.0200.0200.0000.0000.0000.000
91B156LEU0-0.0270.01016.854-0.003-0.0030.0000.0000.0000.000
92B157ASP-1-0.859-0.91121.1500.1560.1560.0000.0000.0000.000
93B158GLY00.0140.00121.1870.0120.0120.0000.0000.0000.000
94B159GLU-1-0.917-0.94822.1080.1200.1200.0000.0000.0000.000
95B160ALA00.0360.01923.9620.0020.0020.0000.0000.0000.000
96B161LEU0-0.074-0.01618.6000.0040.0040.0000.0000.0000.000
97B162SER0-0.024-0.00120.738-0.019-0.0190.0000.0000.0000.000
98B163THR00.0690.01318.582-0.016-0.0160.0000.0000.0000.000
99B164PRO0-0.0070.00313.7820.0220.0220.0000.0000.0000.000
100B165LEU0-0.020-0.00815.525-0.037-0.0370.0000.0000.0000.000
101B166GLU-1-0.796-0.89612.883-0.181-0.1810.0000.0000.0000.000
102B167LEU0-0.018-0.0328.5540.0460.0460.0000.0000.0000.000
103B168ALA00.0270.01213.1270.0300.0300.0000.0000.0000.000
104B169VAL00.0060.00516.2720.0180.0180.0000.0000.0000.000
105B170LEU00.0330.02013.5960.0090.0090.0000.0000.0000.000
106B171TYR00.0250.00014.5450.0230.0230.0000.0000.0000.000
107B172LYS10.9640.98816.8710.0090.0090.0000.0000.0000.000
108B173LYS10.9560.97120.166-0.069-0.0690.0000.0000.0000.000
109B174LEU00.0200.00316.0400.0030.0030.0000.0000.0000.000
110B175VAL0-0.042-0.01419.1530.0010.0010.0000.0000.0000.000
111B176VAL0-0.010-0.00621.409-0.003-0.0030.0000.0000.0000.000
112B177LEU00.0170.03122.184-0.003-0.0030.0000.0000.0000.000
113B178PHE00.0450.00518.731-0.005-0.0050.0000.0000.0000.000
114B179ARG10.8860.95724.208-0.053-0.0530.0000.0000.0000.000
115B180SER0-0.0190.00527.038-0.003-0.0030.0000.0000.0000.000
116B181LEU0-0.009-0.02525.872-0.003-0.0030.0000.0000.0000.000
117B182TYR00.0250.02127.567-0.003-0.0030.0000.0000.0000.000
118B183THR0-0.036-0.03829.273-0.005-0.0050.0000.0000.0000.000
119B184TYR00.0370.01531.676-0.003-0.0030.0000.0000.0000.000
120B185THR00.0270.01330.727-0.004-0.0040.0000.0000.0000.000
121B186HIS10.8750.93431.629-0.063-0.0630.0000.0000.0000.000
122B187LEU00.0110.02836.251-0.004-0.0040.0000.0000.0000.000
123B188MET0-0.0210.00735.039-0.002-0.0020.0000.0000.0000.000
124B189PRO00.0440.01338.949-0.001-0.0010.0000.0000.0000.000
125B190LEU00.0370.01437.424-0.002-0.0020.0000.0000.0000.000
126B191TRP00.0480.03836.1480.0010.0010.0000.0000.0000.000
127B192LYS10.9300.95439.200-0.044-0.0440.0000.0000.0000.000
128B193LEU0-0.034-0.02042.310-0.002-0.0020.0000.0000.0000.000
129B194LYS10.9540.97137.618-0.061-0.0610.0000.0000.0000.000
130B195SER00.006-0.00541.765-0.002-0.0020.0000.0000.0000.000
131B196LYS10.8050.92843.651-0.040-0.0400.0000.0000.0000.000
132B197ILE00.002-0.00142.694-0.001-0.0010.0000.0000.0000.000
133B198HIS00.0320.02839.862-0.002-0.0020.0000.0000.0000.000
134B199LYS10.9170.95845.310-0.031-0.0310.0000.0000.0000.000
135B200LEU0-0.056-0.01648.659-0.001-0.0010.0000.0000.0000.000
136B201ARG10.9240.94744.300-0.037-0.0370.0000.0000.0000.000
137B202ALA0-0.014-0.00648.6880.0000.0000.0000.0000.0000.000
138B203HIS0-0.022-0.00252.1880.0000.0000.0000.0000.0000.000
139B204GLY00.0820.03552.0770.0010.0010.0000.0000.0000.000
140B205THR0-0.0150.00853.1040.0000.0000.0000.0000.0000.000
141B206SER0-0.072-0.05948.2630.0000.0000.0000.0000.0000.000
142B207LEU0-0.0220.01444.9950.0000.0000.0000.0000.0000.000
143B208LYS10.8490.89941.178-0.049-0.0490.0000.0000.0000.000
144B209VAL0-0.0060.02237.2140.0000.0000.0000.0000.0000.000
145B210GLY0-0.0070.00635.6820.0000.0000.0000.0000.0000.000
146B211CYS0-0.031-0.00929.6480.0010.0010.0000.0000.0000.000
147B212ALA00.0190.02231.1210.0050.0050.0000.0000.0000.000
148B213LEU00.000-0.01024.2250.0010.0010.0000.0000.0000.000
149B214SER00.0380.01128.076-0.004-0.0040.0000.0000.0000.000
150B215THR00.0170.00126.0730.0130.0130.0000.0000.0000.000
151B216ASP-1-0.923-0.93527.6950.1380.1380.0000.0000.0000.000
152B217ASP-1-0.835-0.92831.3000.1010.1010.0000.0000.0000.000
153B218VAL0-0.048-0.04533.682-0.007-0.0070.0000.0000.0000.000
154B219LEU00.0230.01332.5410.0020.0020.0000.0000.0000.000
155B220SER0-0.0090.01435.733-0.001-0.0010.0000.0000.0000.000
156B221ASN0-0.035-0.01538.923-0.005-0.0050.0000.0000.0000.000
157B222ASP-1-0.935-0.96640.7180.0640.0640.0000.0000.0000.000
158B223PHE0-0.029-0.03537.1710.0000.0000.0000.0000.0000.000
159B224LEU0-0.026-0.01642.7960.0000.0000.0000.0000.0000.000
160B225PRO00.0630.05540.8970.0030.0030.0000.0000.0000.000
161B226ILE00.0330.00738.198-0.003-0.0030.0000.0000.0000.000
162B227SER0-0.008-0.00240.834-0.002-0.0020.0000.0000.0000.000
163B228ALA00.0390.02043.610-0.003-0.0030.0000.0000.0000.000
164B229PRO0-0.063-0.02445.7250.0020.0020.0000.0000.0000.000
165B230ILE00.0590.02148.020-0.002-0.0020.0000.0000.0000.000
166B231SER0-0.0050.00350.616-0.001-0.0010.0000.0000.0000.000
167B232SER00.005-0.00553.3790.0010.0010.0000.0000.0000.000
168B233SER00.0100.01254.7310.0000.0000.0000.0000.0000.000
169B234LEU0-0.048-0.01448.960-0.001-0.0010.0000.0000.0000.000
170B235GLY00.0760.02952.694-0.001-0.0010.0000.0000.0000.000
171B236SER0-0.052-0.02147.1840.0010.0010.0000.0000.0000.000
172B237SER00.0530.03547.2490.0000.0000.0000.0000.0000.000
173B238ILE00.0430.02540.0120.0000.0000.0000.0000.0000.000
174B239ALA00.003-0.01040.470-0.003-0.0030.0000.0000.0000.000
175B240THR0-0.038-0.03335.7860.0040.0040.0000.0000.0000.000
176B241PHE00.0020.02532.025-0.004-0.0040.0000.0000.0000.000
177B242SER00.0310.00730.8260.0050.0050.0000.0000.0000.000
178B243PHE0-0.030-0.00627.461-0.005-0.0050.0000.0000.0000.000
179B244SER00.0310.01127.0270.0010.0010.0000.0000.0000.000
180B245PRO0-0.0280.00425.1030.0050.0050.0000.0000.0000.000
181B246VAL0-0.068-0.03519.522-0.012-0.0120.0000.0000.0000.000
182B247GLY00.0610.03620.9280.0160.0160.0000.0000.0000.000
183B248THR0-0.016-0.01915.4790.0020.0020.0000.0000.0000.000
184B249PRO0-0.066-0.02413.864-0.007-0.0070.0000.0000.0000.000
185B250ALA00.020-0.01914.4930.0230.0230.0000.0000.0000.000
186B251GLY00.0710.03616.5920.0160.0160.0000.0000.0000.000
187B252ASP-1-0.863-0.93720.0600.1160.1160.0000.0000.0000.000
188B253PHE00.0120.00818.9450.0050.0050.0000.0000.0000.000
189B254ARG10.8490.89021.134-0.147-0.1470.0000.0000.0000.000
190B255ILE00.0250.01423.6490.0090.0090.0000.0000.0000.000
191B256SER00.000-0.00326.735-0.012-0.0120.0000.0000.0000.000
192B257VAL0-0.0250.00030.4570.0050.0050.0000.0000.0000.000
193B258GLN00.0110.00033.122-0.001-0.0010.0000.0000.0000.000
194B259TYR00.0340.01936.6660.0000.0000.0000.0000.0000.000
195B260ARG10.8460.92038.837-0.061-0.0610.0000.0000.0000.000
196B261LYS10.8590.92842.543-0.047-0.0470.0000.0000.0000.000
197B262ASN0-0.027-0.00744.512-0.001-0.0010.0000.0000.0000.000
198B263CYS00.021-0.01044.6170.0030.0030.0000.0000.0000.000
199B264HIS00.0920.04447.185-0.002-0.0020.0000.0000.0000.000
200B265PHE0-0.025-0.00448.976-0.002-0.0020.0000.0000.0000.000
201B266GLU-1-0.883-0.97050.2590.0320.0320.0000.0000.0000.000
202B267VAL0-0.0190.00852.880-0.001-0.0010.0000.0000.0000.000
203B268HIS0-0.0030.01351.7130.0010.0010.0000.0000.0000.000