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: 394GL

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 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 203
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2332391.938498
FMO2-HF: Nuclear repulsion 2252700.45022
FMO2-HF: Total energy -79691.488279
FMO2-MP2: Total energy -79926.998943


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.
-3.496-1.310.303-1.302-1.1870.008
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 : 0.038 / q_NPA : 0.010
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].
3B36ARG10.8600.8953.8571.9893.129-0.015-0.661-0.4640.002
4B37SER00.0780.0297.2270.2730.2730.0000.0000.0000.000
5B38ALA00.0350.0393.249-1.083-0.1310.319-0.634-0.6370.006
6B39LYS10.8840.9315.261-2.115-2.021-0.001-0.007-0.0860.000
7B40LEU00.0210.0166.708-0.442-0.4420.0000.0000.0000.000
8B41GLY00.0530.0318.821-0.232-0.2320.0000.0000.0000.000
9B42GLN00.0180.0097.581-0.159-0.1590.0000.0000.0000.000
10B43VAL0-0.009-0.0169.641-0.276-0.2760.0000.0000.0000.000
11B44ILE00.0420.01412.304-0.146-0.1460.0000.0000.0000.000
12B45HIS00.0480.04112.243-0.154-0.1540.0000.0000.0000.000
13B46HIS0-0.028-0.01112.4060.0050.0050.0000.0000.0000.000
14B47CYS0-0.044-0.00515.504-0.081-0.0810.0000.0000.0000.000
15B48PHE00.0250.01517.480-0.052-0.0520.0000.0000.0000.000
16B49TYR0-0.061-0.04517.645-0.035-0.0350.0000.0000.0000.000
17B50LYS10.8230.91519.488-0.287-0.2870.0000.0000.0000.000
18B51THR0-0.012-0.01821.421-0.035-0.0350.0000.0000.0000.000
19B52GLY00.0380.01723.318-0.022-0.0220.0000.0000.0000.000
20B53LEU0-0.0220.00622.874-0.018-0.0180.0000.0000.0000.000
21B54ILE0-0.011-0.00924.601-0.018-0.0180.0000.0000.0000.000
22B55ILE00.0020.00627.448-0.014-0.0140.0000.0000.0000.000
23B56LEU00.0240.00427.724-0.013-0.0130.0000.0000.0000.000
24B57GLU-1-0.785-0.88528.8720.1130.1130.0000.0000.0000.000
25B58SER0-0.041-0.02130.928-0.010-0.0100.0000.0000.0000.000
26B59ARG10.7190.83233.327-0.113-0.1130.0000.0000.0000.000
27B60LEU0-0.0140.01631.837-0.008-0.0080.0000.0000.0000.000
28B61ASN0-0.003-0.00232.784-0.010-0.0100.0000.0000.0000.000
29B70GLU-1-0.825-0.92527.6200.1050.1050.0000.0000.0000.000
30B71SER00.0180.00927.6000.0090.0090.0000.0000.0000.000
31B72SER0-0.018-0.00425.0060.0010.0010.0000.0000.0000.000
32B73LYS10.7760.89623.279-0.126-0.1260.0000.0000.0000.000
33B74ASN0-0.022-0.02923.1640.0060.0060.0000.0000.0000.000
34B75ASN00.0290.00218.8440.0220.0220.0000.0000.0000.000
35B76LYS10.8460.90318.979-0.167-0.1670.0000.0000.0000.000
36B77TRP00.0210.01915.7120.0240.0240.0000.0000.0000.000
37B78PHE00.012-0.01415.626-0.024-0.0240.0000.0000.0000.000
38B79ASN00.0200.02819.154-0.003-0.0030.0000.0000.0000.000
39B80LEU00.0130.01321.591-0.024-0.0240.0000.0000.0000.000
40B81GLU-1-0.794-0.86923.1500.1660.1660.0000.0000.0000.000
41B82ILE0-0.0050.00924.351-0.011-0.0110.0000.0000.0000.000
42B83VAL00.0220.01824.9930.0150.0150.0000.0000.0000.000
43B84GLU-1-0.772-0.86521.3160.2540.2540.0000.0000.0000.000
44B85THR00.005-0.01026.088-0.013-0.0130.0000.0000.0000.000
45B86GLU-1-0.804-0.90824.7890.1450.1450.0000.0000.0000.000
46B87LEU0-0.0010.00425.8450.0070.0070.0000.0000.0000.000
47B88TYR0-0.053-0.03922.060-0.005-0.0050.0000.0000.0000.000
48B89ALA00.0260.01621.4610.0110.0110.0000.0000.0000.000
49B90GLU-1-0.781-0.86922.0120.1720.1720.0000.0000.0000.000
50B91GLN00.0250.00424.3480.0030.0030.0000.0000.0000.000
51B92PHE00.012-0.00117.1290.0130.0130.0000.0000.0000.000
52B93LYS10.7940.87819.670-0.144-0.1440.0000.0000.0000.000
53B94ILE00.007-0.00320.9300.0050.0050.0000.0000.0000.000
54B95TRP0-0.030-0.03118.7790.0140.0140.0000.0000.0000.000
55B96LYS10.8690.91914.362-0.438-0.4380.0000.0000.0000.000
56B97ASN0-0.077-0.03318.9530.0130.0130.0000.0000.0000.000
57B98ILE0-0.039-0.00321.186-0.021-0.0210.0000.0000.0000.000
58B99GLU-1-0.776-0.86320.2920.2140.2140.0000.0000.0000.000
59B100LEU0-0.042-0.01616.364-0.002-0.0020.0000.0000.0000.000
60B101SER00.0450.02320.918-0.017-0.0170.0000.0000.0000.000
61B102PRO00.0100.00522.8600.0120.0120.0000.0000.0000.000
62B103SER00.0220.00422.406-0.010-0.0100.0000.0000.0000.000
63B104ARG10.7220.83617.425-0.185-0.1850.0000.0000.0000.000
64B105LYS10.8570.93418.624-0.196-0.1960.0000.0000.0000.000
65B106ILE00.0200.00517.677-0.005-0.0050.0000.0000.0000.000
66B107PRO00.0610.03519.871-0.012-0.0120.0000.0000.0000.000
67B108PRO0-0.0150.00222.3660.0240.0240.0000.0000.0000.000
68B109MET0-0.0220.00522.9670.0050.0050.0000.0000.0000.000
69B110VAL0-0.008-0.00325.063-0.003-0.0030.0000.0000.0000.000
70B111LEU0-0.027-0.02728.4520.0030.0030.0000.0000.0000.000
71B112HIS0-0.0160.00130.401-0.010-0.0100.0000.0000.0000.000
72B113THR0-0.029-0.03034.1350.0020.0020.0000.0000.0000.000
73B114TYR00.0290.01635.792-0.006-0.0060.0000.0000.0000.000
74B115LEU0-0.002-0.00139.2760.0020.0020.0000.0000.0000.000
75B116ASP-1-0.812-0.89541.4470.0740.0740.0000.0000.0000.000
76B117ILE00.0270.00044.449-0.001-0.0010.0000.0000.0000.000
77B118SER00.039-0.00945.717-0.001-0.0010.0000.0000.0000.000
78B119ASP-1-0.781-0.84947.2790.0550.0550.0000.0000.0000.000
79B120LEU00.0020.01750.096-0.002-0.0020.0000.0000.0000.000
80B121SER0-0.077-0.02051.284-0.002-0.0020.0000.0000.0000.000
81B146LYS10.8610.90239.306-0.079-0.0790.0000.0000.0000.000
82B147ILE0-0.011-0.00343.342-0.001-0.0010.0000.0000.0000.000
83B148VAL0-0.0030.01837.5860.0030.0030.0000.0000.0000.000
84B149LEU0-0.044-0.03339.534-0.004-0.0040.0000.0000.0000.000
85B150GLU-1-0.779-0.87135.5370.1050.1050.0000.0000.0000.000
86B151ARG10.8340.92233.583-0.102-0.1020.0000.0000.0000.000
87B152TRP0-0.008-0.03329.9340.0010.0010.0000.0000.0000.000
88B153ILE00.0220.00828.5070.0020.0020.0000.0000.0000.000
89B154VAL00.0030.01122.9770.0000.0000.0000.0000.0000.000
90B155ASN00.0530.01323.5510.0150.0150.0000.0000.0000.000
91B156LEU0-0.0150.01017.0440.0080.0080.0000.0000.0000.000
92B157ASP-1-0.813-0.89921.2300.1590.1590.0000.0000.0000.000
93B158GLY00.011-0.00921.5370.0240.0240.0000.0000.0000.000
94B159GLU-1-0.922-0.93822.5590.1130.1130.0000.0000.0000.000
95B160ALA00.0220.00524.266-0.003-0.0030.0000.0000.0000.000
96B161LEU0-0.028-0.02018.2430.0150.0150.0000.0000.0000.000
97B162SER0-0.033-0.00121.136-0.018-0.0180.0000.0000.0000.000
98B163THR00.0510.02919.470-0.021-0.0210.0000.0000.0000.000
99B164PRO0-0.035-0.02014.6520.0430.0430.0000.0000.0000.000
100B165LEU0-0.013-0.01216.362-0.025-0.0250.0000.0000.0000.000
101B166GLU-1-0.748-0.82713.1320.1080.1080.0000.0000.0000.000
102B167LEU0-0.035-0.0328.8100.0410.0410.0000.0000.0000.000
103B168ALA00.0390.01413.4150.0160.0160.0000.0000.0000.000
104B169VAL0-0.008-0.00116.210-0.008-0.0080.0000.0000.0000.000
105B170LEU00.0140.00714.155-0.003-0.0030.0000.0000.0000.000
106B171TYR00.010-0.01615.0470.0090.0090.0000.0000.0000.000
107B172LYS10.9630.98317.183-0.132-0.1320.0000.0000.0000.000
108B173LYS10.9260.96920.649-0.204-0.2040.0000.0000.0000.000
109B174LEU00.0350.01716.960-0.010-0.0100.0000.0000.0000.000
110B175VAL0-0.0170.00119.781-0.010-0.0100.0000.0000.0000.000
111B176VAL0-0.0060.00222.155-0.013-0.0130.0000.0000.0000.000
112B177LEU00.0160.02222.997-0.012-0.0120.0000.0000.0000.000
113B178PHE00.034-0.01019.590-0.012-0.0120.0000.0000.0000.000
114B179ARG10.8630.93324.983-0.152-0.1520.0000.0000.0000.000
115B180SER0-0.0050.01527.782-0.010-0.0100.0000.0000.0000.000
116B181LEU00.002-0.00426.721-0.010-0.0100.0000.0000.0000.000
117B182TYR00.010-0.01428.188-0.009-0.0090.0000.0000.0000.000
118B183THR0-0.032-0.01229.982-0.011-0.0110.0000.0000.0000.000
119B184TYR00.0240.00132.668-0.008-0.0080.0000.0000.0000.000
120B185THR0-0.003-0.01131.066-0.008-0.0080.0000.0000.0000.000
121B186HIS10.8660.93232.019-0.117-0.1170.0000.0000.0000.000
122B187LEU00.0210.02536.669-0.006-0.0060.0000.0000.0000.000
123B188MET0-0.0350.01136.042-0.004-0.0040.0000.0000.0000.000
124B189PRO00.000-0.00439.520-0.002-0.0020.0000.0000.0000.000
125B190LEU00.0560.02037.915-0.003-0.0030.0000.0000.0000.000
126B191TRP00.0440.04236.6640.0010.0010.0000.0000.0000.000
127B192LYS10.9000.94540.042-0.073-0.0730.0000.0000.0000.000
128B193LEU0-0.0030.00643.025-0.003-0.0030.0000.0000.0000.000
129B194LYS10.9310.95237.995-0.089-0.0890.0000.0000.0000.000
130B195SER0-0.002-0.00542.271-0.002-0.0020.0000.0000.0000.000
131B196LYS10.7980.89244.304-0.055-0.0550.0000.0000.0000.000
132B197ILE00.0230.00743.706-0.002-0.0020.0000.0000.0000.000
133B198HIS00.0240.01140.297-0.005-0.0050.0000.0000.0000.000
134B199LYS10.8940.94445.746-0.050-0.0500.0000.0000.0000.000
135B200LEU0-0.0040.00549.229-0.002-0.0020.0000.0000.0000.000
136B201ARG10.8890.94144.708-0.059-0.0590.0000.0000.0000.000
137B202ALA00.0020.00649.0320.0000.0000.0000.0000.0000.000
138B203HIS0-0.031-0.01352.317-0.001-0.0010.0000.0000.0000.000
139B204GLY00.0030.00852.5050.0010.0010.0000.0000.0000.000
140B205THR00.009-0.00652.924-0.001-0.0010.0000.0000.0000.000
141B206SER0-0.071-0.04449.0990.0010.0010.0000.0000.0000.000
142B207LEU0-0.0100.01345.7480.0010.0010.0000.0000.0000.000
143B208LYS10.8450.89741.374-0.061-0.0610.0000.0000.0000.000
144B209VAL0-0.009-0.01037.895-0.001-0.0010.0000.0000.0000.000
145B210GLY0-0.0120.00536.2410.0010.0010.0000.0000.0000.000
146B211CYS0-0.011-0.00830.3400.0020.0020.0000.0000.0000.000
147B212ALA00.0030.02331.6340.0050.0050.0000.0000.0000.000
148B213LEU0-0.010-0.01624.1550.0000.0000.0000.0000.0000.000
149B214SER00.0180.01028.146-0.008-0.0080.0000.0000.0000.000
150B215THR00.004-0.00126.0730.0210.0210.0000.0000.0000.000
151B216ASP-1-0.884-0.93027.7520.1260.1260.0000.0000.0000.000
152B217ASP-1-0.811-0.92031.4620.1070.1070.0000.0000.0000.000
153B218VAL0-0.023-0.02533.950-0.006-0.0060.0000.0000.0000.000
154B219LEU00.0100.00532.3130.0010.0010.0000.0000.0000.000
155B220SER0-0.0020.00435.696-0.002-0.0020.0000.0000.0000.000
156B221ASN0-0.035-0.00338.541-0.005-0.0050.0000.0000.0000.000
157B222ASP-1-0.915-0.95540.5140.0630.0630.0000.0000.0000.000
158B223PHE0-0.042-0.03637.2560.0020.0020.0000.0000.0000.000
159B224LEU0-0.007-0.00142.9010.0000.0000.0000.0000.0000.000
160B225PRO00.0690.04241.3870.0040.0040.0000.0000.0000.000
161B226ILE00.013-0.01538.733-0.003-0.0030.0000.0000.0000.000
162B227SER0-0.0050.00141.392-0.001-0.0010.0000.0000.0000.000
163B228ALA00.0340.01344.059-0.003-0.0030.0000.0000.0000.000
164B229PRO0-0.056-0.02646.6010.0020.0020.0000.0000.0000.000
165B230ILE00.0630.02848.693-0.001-0.0010.0000.0000.0000.000
166B231SER00.0290.01651.172-0.001-0.0010.0000.0000.0000.000
167B232SER00.0440.01653.7410.0010.0010.0000.0000.0000.000
168B233SER00.0030.00555.4500.0000.0000.0000.0000.0000.000
169B234LEU0-0.059-0.03149.9170.0000.0000.0000.0000.0000.000
170B235GLY00.0150.00352.5370.0010.0010.0000.0000.0000.000
171B236SER0-0.0150.00547.4390.0010.0010.0000.0000.0000.000
172B237SER00.0590.04848.0630.0020.0020.0000.0000.0000.000
173B238ILE00.0210.00340.8400.0020.0020.0000.0000.0000.000
174B239ALA00.004-0.00441.483-0.003-0.0030.0000.0000.0000.000
175B240THR0-0.017-0.03036.3540.0040.0040.0000.0000.0000.000
176B241PHE0-0.0090.01632.901-0.005-0.0050.0000.0000.0000.000
177B242SER00.0220.00731.6860.0040.0040.0000.0000.0000.000
178B243PHE0-0.0170.00228.463-0.005-0.0050.0000.0000.0000.000
179B244SER00.0020.00027.419-0.004-0.0040.0000.0000.0000.000
180B245PRO0-0.0060.01226.1420.0140.0140.0000.0000.0000.000
181B246VAL0-0.045-0.02620.326-0.006-0.0060.0000.0000.0000.000
182B247GLY00.0710.04221.2900.0250.0250.0000.0000.0000.000
183B248THR0-0.054-0.04316.1640.0180.0180.0000.0000.0000.000
184B249PRO0-0.019-0.01714.199-0.021-0.0210.0000.0000.0000.000
185B250ALA00.003-0.00214.5040.0030.0030.0000.0000.0000.000
186B251GLY00.0510.03916.579-0.006-0.0060.0000.0000.0000.000
187B252ASP-1-0.807-0.91520.3620.1790.1790.0000.0000.0000.000
188B253PHE00.0000.00719.7260.0030.0030.0000.0000.0000.000
189B254ARG10.7950.86121.801-0.180-0.1800.0000.0000.0000.000
190B255ILE00.0410.01824.5800.0080.0080.0000.0000.0000.000
191B256SER0-0.045-0.02827.543-0.014-0.0140.0000.0000.0000.000
192B257VAL0-0.0090.00431.1640.0050.0050.0000.0000.0000.000
193B258GLN00.0160.01833.864-0.004-0.0040.0000.0000.0000.000
194B259TYR00.014-0.00437.2550.0000.0000.0000.0000.0000.000
195B260ARG10.8340.91839.615-0.074-0.0740.0000.0000.0000.000
196B261LYS10.8650.92743.297-0.062-0.0620.0000.0000.0000.000
197B262ASN0-0.0190.00345.645-0.001-0.0010.0000.0000.0000.000
198B263CYS00.007-0.00945.7650.0040.0040.0000.0000.0000.000
199B264HIS00.0890.04148.187-0.002-0.0020.0000.0000.0000.000
200B265PHE0-0.017-0.00849.947-0.002-0.0020.0000.0000.0000.000
201B266GLU-1-0.850-0.92650.8400.0450.0450.0000.0000.0000.000
202B267VAL0-0.0130.00953.560-0.001-0.0010.0000.0000.0000.000
203B268HIS0-0.0110.01751.8090.0010.0010.0000.0000.0000.000