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

tag_button

FMODB ID: N976Q

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 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 203
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2334143.57462
FMO2-HF: Nuclear repulsion 2254455.316603
FMO2-HF: Total energy -79688.258017
FMO2-MP2: Total energy -79924.133396


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.
-1.3140.3170.11-0.845-0.8960.004
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 : 0.030 / q_NPA : 0.007
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].
3B36ARG11.0110.9883.8090.6981.796-0.015-0.616-0.4670.003
4B37SER00.0500.0196.8730.1500.1500.0000.0000.0000.000
5B38ALA0-0.0010.0263.053-0.3570.0530.126-0.221-0.3160.001
6B39LYS10.9140.9564.800-0.711-0.588-0.001-0.008-0.1130.000
7B40LEU00.0260.0125.718-0.090-0.0900.0000.0000.0000.000
8B41GLY00.0670.0378.459-0.115-0.1150.0000.0000.0000.000
9B42GLN00.0130.0116.6490.0360.0360.0000.0000.0000.000
10B43VAL0-0.008-0.0028.961-0.152-0.1520.0000.0000.0000.000
11B44ILE00.0690.01711.549-0.074-0.0740.0000.0000.0000.000
12B45HIS00.0270.01911.598-0.085-0.0850.0000.0000.0000.000
13B46HIS0-0.023-0.02511.6500.0030.0030.0000.0000.0000.000
14B47CYS0-0.093-0.01314.774-0.058-0.0580.0000.0000.0000.000
15B48PHE00.024-0.02416.830-0.034-0.0340.0000.0000.0000.000
16B49TYR0-0.087-0.06016.938-0.024-0.0240.0000.0000.0000.000
17B50LYS10.8430.96718.564-0.162-0.1620.0000.0000.0000.000
18B51THR0-0.013-0.00420.313-0.026-0.0260.0000.0000.0000.000
19B52GLY00.0720.00922.756-0.016-0.0160.0000.0000.0000.000
20B53LEU0-0.0100.01321.903-0.012-0.0120.0000.0000.0000.000
21B54ILE00.0160.02023.862-0.014-0.0140.0000.0000.0000.000
22B55ILE0-0.027-0.01326.549-0.010-0.0100.0000.0000.0000.000
23B56LEU00.009-0.02727.124-0.009-0.0090.0000.0000.0000.000
24B57GLU-1-0.949-0.98327.8120.0690.0690.0000.0000.0000.000
25B58SER0-0.0170.00529.765-0.010-0.0100.0000.0000.0000.000
26B59ARG10.7220.82532.367-0.079-0.0790.0000.0000.0000.000
27B60LEU0-0.053-0.00931.970-0.004-0.0040.0000.0000.0000.000
28B61ASN00.0370.03332.379-0.005-0.0050.0000.0000.0000.000
29B70GLU-1-0.848-0.93427.4570.0640.0640.0000.0000.0000.000
30B71SER00.0390.01627.8080.0050.0050.0000.0000.0000.000
31B72SER0-0.032-0.01725.4850.0040.0040.0000.0000.0000.000
32B73LYS10.8300.93622.781-0.082-0.0820.0000.0000.0000.000
33B74ASN00.0430.00922.6260.0030.0030.0000.0000.0000.000
34B75ASN00.0260.00917.752-0.002-0.0020.0000.0000.0000.000
35B76LYS10.9700.98618.398-0.079-0.0790.0000.0000.0000.000
36B77TRP0-0.0020.00514.162-0.005-0.0050.0000.0000.0000.000
37B78PHE0-0.022-0.03914.865-0.013-0.0130.0000.0000.0000.000
38B79ASN00.005-0.00318.419-0.006-0.0060.0000.0000.0000.000
39B80LEU00.0000.00520.903-0.012-0.0120.0000.0000.0000.000
40B81GLU-1-0.944-0.97822.8630.0560.0560.0000.0000.0000.000
41B82ILE00.0090.00723.794-0.004-0.0040.0000.0000.0000.000
42B83VAL00.0200.00224.3370.0110.0110.0000.0000.0000.000
43B84GLU-1-0.813-0.88520.6580.1670.1670.0000.0000.0000.000
44B85THR00.013-0.01025.335-0.010-0.0100.0000.0000.0000.000
45B86GLU-1-0.843-0.93025.1940.1080.1080.0000.0000.0000.000
46B87LEU00.0270.02326.0140.0090.0090.0000.0000.0000.000
47B88TYR0-0.063-0.06821.5010.0040.0040.0000.0000.0000.000
48B89ALA00.0340.02321.6750.0150.0150.0000.0000.0000.000
49B90GLU-1-0.809-0.87222.1000.1780.1780.0000.0000.0000.000
50B91GLN00.041-0.00924.3800.0150.0150.0000.0000.0000.000
51B92PHE0-0.0260.00117.1970.0160.0160.0000.0000.0000.000
52B93LYS10.7830.86619.844-0.155-0.1550.0000.0000.0000.000
53B94ILE0-0.0060.00121.1540.0110.0110.0000.0000.0000.000
54B95TRP0-0.030-0.02018.8640.0190.0190.0000.0000.0000.000
55B96LYS10.8820.93315.264-0.399-0.3990.0000.0000.0000.000
56B97ASN0-0.053-0.02119.5610.0400.0400.0000.0000.0000.000
57B98ILE0-0.0270.00621.607-0.003-0.0030.0000.0000.0000.000
58B99GLU-1-0.769-0.84420.7140.3360.3360.0000.0000.0000.000
59B100LEU0-0.055-0.02517.031-0.010-0.0100.0000.0000.0000.000
60B101SER00.0440.02121.588-0.012-0.0120.0000.0000.0000.000
61B102PRO00.0250.01323.6400.0190.0190.0000.0000.0000.000
62B103SER00.003-0.01323.138-0.007-0.0070.0000.0000.0000.000
63B104ARG10.7240.82918.173-0.310-0.3100.0000.0000.0000.000
64B105LYS10.8970.96519.183-0.199-0.1990.0000.0000.0000.000
65B106ILE00.000-0.00717.8300.0020.0020.0000.0000.0000.000
66B107PRO00.0280.02920.284-0.018-0.0180.0000.0000.0000.000
67B108PRO00.0250.01822.4350.0150.0150.0000.0000.0000.000
68B109MET0-0.009-0.00922.8090.0080.0080.0000.0000.0000.000
69B110VAL0-0.014-0.00424.886-0.009-0.0090.0000.0000.0000.000
70B111LEU0-0.004-0.01127.6880.0010.0010.0000.0000.0000.000
71B112HIS00.0390.01929.929-0.012-0.0120.0000.0000.0000.000
72B113THR00.007-0.00333.6520.0020.0020.0000.0000.0000.000
73B114TYR00.0160.02435.643-0.003-0.0030.0000.0000.0000.000
74B115LEU0-0.021-0.03539.1200.0000.0000.0000.0000.0000.000
75B116ASP-1-0.821-0.90241.5700.0650.0650.0000.0000.0000.000
76B117ILE00.007-0.01044.415-0.002-0.0020.0000.0000.0000.000
77B118SER00.0550.00846.0360.0000.0000.0000.0000.0000.000
78B119ASP-1-0.848-0.85847.5060.0440.0440.0000.0000.0000.000
79B120LEU0-0.001-0.00850.026-0.002-0.0020.0000.0000.0000.000
80B121SER0-0.046-0.00250.902-0.001-0.0010.0000.0000.0000.000
81B146LYS10.8780.91939.179-0.072-0.0720.0000.0000.0000.000
82B147ILE00.014-0.01942.8920.0010.0010.0000.0000.0000.000
83B148VAL0-0.0100.01537.1340.0010.0010.0000.0000.0000.000
84B149LEU0-0.076-0.05739.235-0.003-0.0030.0000.0000.0000.000
85B150GLU-1-0.766-0.89335.2860.0720.0720.0000.0000.0000.000
86B151ARG10.9170.97833.186-0.092-0.0920.0000.0000.0000.000
87B152TRP0-0.012-0.03029.233-0.002-0.0020.0000.0000.0000.000
88B153ILE00.0280.01627.7080.0050.0050.0000.0000.0000.000
89B154VAL0-0.0180.00722.127-0.003-0.0030.0000.0000.0000.000
90B155ASN00.044-0.00623.2620.0200.0200.0000.0000.0000.000
91B156LEU00.0100.02017.053-0.004-0.0040.0000.0000.0000.000
92B157ASP-1-0.932-0.95921.1490.1600.1600.0000.0000.0000.000
93B158GLY00.0180.00121.1890.0130.0130.0000.0000.0000.000
94B159GLU-1-0.933-0.94822.1080.1200.1200.0000.0000.0000.000
95B160ALA00.0250.00823.9620.0010.0010.0000.0000.0000.000
96B161LEU0-0.0560.00118.6040.0050.0050.0000.0000.0000.000
97B162SER0-0.0290.00320.640-0.020-0.0200.0000.0000.0000.000
98B163THR00.0570.00218.551-0.017-0.0170.0000.0000.0000.000
99B164PRO0-0.0160.00213.7580.0220.0220.0000.0000.0000.000
100B165LEU0-0.014-0.00315.457-0.038-0.0380.0000.0000.0000.000
101B166GLU-1-0.844-0.91113.130-0.171-0.1710.0000.0000.0000.000
102B167LEU0-0.029-0.0468.6830.0500.0500.0000.0000.0000.000
103B168ALA00.0290.01313.1280.0310.0310.0000.0000.0000.000
104B169VAL0-0.011-0.00316.2730.0180.0180.0000.0000.0000.000
105B170LEU00.0520.02713.7130.0080.0080.0000.0000.0000.000
106B171TYR00.0300.02314.4260.0240.0240.0000.0000.0000.000
107B172LYS10.9620.98716.8710.0080.0080.0000.0000.0000.000
108B173LYS10.9450.96220.164-0.069-0.0690.0000.0000.0000.000
109B174LEU00.0230.00716.0790.0030.0030.0000.0000.0000.000
110B175VAL0-0.035-0.00919.2050.0010.0010.0000.0000.0000.000
111B176VAL0-0.010-0.00521.409-0.003-0.0030.0000.0000.0000.000
112B177LEU00.0110.02321.936-0.004-0.0040.0000.0000.0000.000
113B178PHE00.0390.00118.856-0.005-0.0050.0000.0000.0000.000
114B179ARG10.9090.98124.208-0.053-0.0530.0000.0000.0000.000
115B180SER0-0.0040.00127.038-0.004-0.0040.0000.0000.0000.000
116B181LEU0-0.033-0.03325.792-0.004-0.0040.0000.0000.0000.000
117B182TYR00.0060.00627.6090.0000.0000.0000.0000.0000.000
118B183THR0-0.023-0.02629.273-0.005-0.0050.0000.0000.0000.000
119B184TYR00.0100.00031.687-0.003-0.0030.0000.0000.0000.000
120B185THR00.0320.01330.890-0.003-0.0030.0000.0000.0000.000
121B186HIS10.8640.93132.092-0.064-0.0640.0000.0000.0000.000
122B187LEU00.0150.03236.251-0.004-0.0040.0000.0000.0000.000
123B188MET0-0.020-0.00735.264-0.002-0.0020.0000.0000.0000.000
124B189PRO00.0240.01338.949-0.001-0.0010.0000.0000.0000.000
125B190LEU00.0240.00737.248-0.002-0.0020.0000.0000.0000.000
126B191TRP00.0440.03635.9350.0010.0010.0000.0000.0000.000
127B192LYS10.9730.98439.200-0.044-0.0440.0000.0000.0000.000
128B193LEU0-0.048-0.02142.177-0.002-0.0020.0000.0000.0000.000
129B194LYS10.9630.97637.637-0.063-0.0630.0000.0000.0000.000
130B195SER00.005-0.00641.779-0.002-0.0020.0000.0000.0000.000
131B196LYS10.8000.92443.651-0.041-0.0410.0000.0000.0000.000
132B197ILE0-0.003-0.00742.688-0.001-0.0010.0000.0000.0000.000
133B198HIS00.0320.03239.844-0.002-0.0020.0000.0000.0000.000
134B199LYS10.9200.96345.310-0.031-0.0310.0000.0000.0000.000
135B200LEU0-0.052-0.02148.662-0.001-0.0010.0000.0000.0000.000
136B201ARG10.9280.95044.180-0.038-0.0380.0000.0000.0000.000
137B202ALA0-0.012-0.00548.6870.0000.0000.0000.0000.0000.000
138B203HIS0-0.018-0.00152.1870.0000.0000.0000.0000.0000.000
139B204GLY00.0850.03852.0770.0010.0010.0000.0000.0000.000
140B205THR00.0010.01553.0450.0000.0000.0000.0000.0000.000
141B206SER0-0.033-0.07647.9120.0000.0000.0000.0000.0000.000
142B207LEU0-0.0550.01144.7530.0000.0000.0000.0000.0000.000
143B208LYS10.8810.92741.264-0.050-0.0500.0000.0000.0000.000
144B209VAL0-0.0050.02037.4420.0000.0000.0000.0000.0000.000
145B210GLY0-0.036-0.01735.6770.0000.0000.0000.0000.0000.000
146B211CYS0-0.0370.00429.6720.0010.0010.0000.0000.0000.000
147B212ALA00.0030.01531.1200.0060.0060.0000.0000.0000.000
148B213LEU00.002-0.01224.2200.0010.0010.0000.0000.0000.000
149B214SER00.019-0.00128.108-0.004-0.0040.0000.0000.0000.000
150B215THR00.023-0.00225.8940.0130.0130.0000.0000.0000.000
151B216ASP-1-0.913-0.91827.6940.1400.1400.0000.0000.0000.000
152B217ASP-1-0.890-0.96531.3000.1080.1080.0000.0000.0000.000
153B218VAL0-0.079-0.05233.681-0.007-0.0070.0000.0000.0000.000
154B219LEU00.0240.01232.7790.0020.0020.0000.0000.0000.000
155B220SER0-0.056-0.00635.825-0.003-0.0030.0000.0000.0000.000
156B221ASN00.012-0.00338.917-0.007-0.0070.0000.0000.0000.000
157B222ASP-1-0.916-0.95540.7180.0650.0650.0000.0000.0000.000
158B223PHE0-0.035-0.03937.0920.0000.0000.0000.0000.0000.000
159B224LEU0-0.0540.00542.7950.0000.0000.0000.0000.0000.000
160B225PRO00.0660.04340.8990.0020.0020.0000.0000.0000.000
161B226ILE00.040-0.00238.401-0.003-0.0030.0000.0000.0000.000
162B227SER0-0.019-0.00640.833-0.002-0.0020.0000.0000.0000.000
163B228ALA00.0740.03743.610-0.003-0.0030.0000.0000.0000.000
164B229PRO0-0.065-0.04645.7240.0020.0020.0000.0000.0000.000
165B230ILE00.0490.02148.019-0.002-0.0020.0000.0000.0000.000
166B231SER00.0130.01150.670-0.001-0.0010.0000.0000.0000.000
167B232SER0-0.007-0.01453.3970.0010.0010.0000.0000.0000.000
168B233SER00.0110.01354.7310.0000.0000.0000.0000.0000.000
169B234LEU0-0.045-0.01448.9150.0000.0000.0000.0000.0000.000
170B235GLY00.0760.03052.693-0.001-0.0010.0000.0000.0000.000
171B236SER0-0.056-0.02247.4560.0010.0010.0000.0000.0000.000
172B237SER00.0190.01147.2490.0000.0000.0000.0000.0000.000
173B238ILE00.0570.03139.9410.0000.0000.0000.0000.0000.000
174B239ALA0-0.020-0.01040.531-0.002-0.0020.0000.0000.0000.000
175B240THR0-0.009-0.02435.7570.0050.0050.0000.0000.0000.000
176B241PHE0-0.0080.02231.902-0.004-0.0040.0000.0000.0000.000
177B242SER00.0170.00130.8210.0050.0050.0000.0000.0000.000
178B243PHE0-0.017-0.00327.479-0.005-0.0050.0000.0000.0000.000
179B244SER0-0.011-0.00527.5300.0040.0040.0000.0000.0000.000
180B245PRO0-0.0020.00825.1030.0060.0060.0000.0000.0000.000
181B246VAL0-0.039-0.02719.978-0.012-0.0120.0000.0000.0000.000
182B247GLY00.0200.02320.9280.0160.0160.0000.0000.0000.000
183B248THR0-0.023-0.01415.134-0.001-0.0010.0000.0000.0000.000
184B249PRO0-0.065-0.03113.826-0.007-0.0070.0000.0000.0000.000
185B250ALA00.013-0.02314.4950.0230.0230.0000.0000.0000.000
186B251GLY00.0700.03116.5920.0180.0180.0000.0000.0000.000
187B252ASP-1-0.858-0.94520.0600.1280.1280.0000.0000.0000.000
188B253PHE0-0.016-0.00719.0260.0050.0050.0000.0000.0000.000
189B254ARG10.9800.98021.134-0.139-0.1390.0000.0000.0000.000
190B255ILE00.0350.02423.6180.0090.0090.0000.0000.0000.000
191B256SER0-0.023-0.01826.735-0.012-0.0120.0000.0000.0000.000
192B257VAL0-0.0080.00830.4570.0050.0050.0000.0000.0000.000
193B258GLN00.0200.01333.122-0.002-0.0020.0000.0000.0000.000
194B259TYR00.0570.02636.6660.0000.0000.0000.0000.0000.000
195B260ARG10.8390.93938.837-0.061-0.0610.0000.0000.0000.000
196B261LYS10.9130.95242.542-0.047-0.0470.0000.0000.0000.000
197B262ASN0-0.036-0.00744.5110.0000.0000.0000.0000.0000.000
198B263CYS00.011-0.02144.6110.0030.0030.0000.0000.0000.000
199B264HIS00.1140.05447.185-0.002-0.0020.0000.0000.0000.000
200B265PHE0-0.0370.00048.979-0.002-0.0020.0000.0000.0000.000
201B266GLU-1-0.897-0.98050.2580.0330.0330.0000.0000.0000.000
202B267VAL0-0.0270.01152.879-0.001-0.0010.0000.0000.0000.000
203B268HIS00.0030.00951.7130.0010.0010.0000.0000.0000.000