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

tag_button

FMODB ID: YZN82

Calculation Name: 4KGO-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4KGO

Chain ID: B

ChEMBL ID:

UniProt ID: Q9NP55

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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2046103.378691
FMO2-HF: Nuclear repulsion 1969553.476403
FMO2-HF: Total energy -76549.902288
FMO2-MP2: Total energy -76775.675174


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:LEU)


Summations of interaction energy for fragment #1(B:34:LEU)
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.
0.4212.523-0.034-1.073-0.9950.001
Interaction energy analysis for fragmet #1(B:34:LEU)
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 : -0.018
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].
3B36VAL00.0110.0173.8050.4022.504-0.034-1.073-0.9950.001
4B37ASN00.019-0.0046.821-0.380-0.3800.0000.0000.0000.000
5B38PRO0-0.0120.01310.0960.1110.1110.0000.0000.0000.000
6B39ALA00.0460.00113.088-0.094-0.0940.0000.0000.0000.000
7B40LEU00.0310.00213.8680.0990.0990.0000.0000.0000.000
8B41PRO00.6020.68814.539-0.005-0.0050.0000.0000.0000.000
9B42LEU0-0.364-0.38216.095-0.024-0.0240.0000.0000.0000.000
10B43SER0-0.330-0.30519.033-0.055-0.0550.0000.0000.0000.000
11B44PRO00.003-0.00521.450-0.001-0.0010.0000.0000.0000.000
12B45THR00.019-0.00415.8390.0270.0270.0000.0000.0000.000
13B46GLY00.0280.01916.803-0.035-0.0350.0000.0000.0000.000
14B47LEU00.0520.05417.789-0.005-0.0050.0000.0000.0000.000
15B48ALA00.0310.00815.963-0.005-0.0050.0000.0000.0000.000
16B49GLY00.0130.00316.961-0.006-0.0060.0000.0000.0000.000
17B50SER0-0.017-0.04217.729-0.003-0.0030.0000.0000.0000.000
18B51LEU0-0.0110.00620.914-0.017-0.0170.0000.0000.0000.000
19B52THR00.0290.01118.376-0.018-0.0180.0000.0000.0000.000
20B53ASN00.0720.02719.637-0.012-0.0120.0000.0000.0000.000
21B54ALA0-0.0040.00822.590-0.013-0.0130.0000.0000.0000.000
22B55LEU00.013-0.00723.932-0.014-0.0140.0000.0000.0000.000
23B56SER0-0.062-0.02123.095-0.016-0.0160.0000.0000.0000.000
24B57ASN00.008-0.01525.193-0.010-0.0100.0000.0000.0000.000
25B58GLY00.0110.01827.791-0.010-0.0100.0000.0000.0000.000
26B59LEU00.0230.00727.031-0.011-0.0110.0000.0000.0000.000
27B60LEU00.0120.01927.046-0.011-0.0110.0000.0000.0000.000
28B61SER0-0.092-0.03830.900-0.009-0.0090.0000.0000.0000.000
29B62GLY0-0.0030.01533.158-0.005-0.0050.0000.0000.0000.000
30B63GLY0-0.006-0.00334.676-0.005-0.0050.0000.0000.0000.000
31B64LEU00.034-0.02329.679-0.006-0.0060.0000.0000.0000.000
32B65LEU0-0.024-0.02030.274-0.004-0.0040.0000.0000.0000.000
33B66GLY00.0180.02333.617-0.003-0.0030.0000.0000.0000.000
34B67ILE0-0.017-0.01536.096-0.005-0.0050.0000.0000.0000.000
35B68MET0-0.052-0.02732.413-0.005-0.0050.0000.0000.0000.000
36B69GLU-1-0.949-0.97435.8620.0660.0660.0000.0000.0000.000
37B70ASN0-0.035-0.01038.191-0.005-0.0050.0000.0000.0000.000
38B71LEU0-0.0090.00536.379-0.003-0.0030.0000.0000.0000.000
39B72PRO00.0430.02940.825-0.001-0.0010.0000.0000.0000.000
40B73LEU00.030-0.00939.219-0.003-0.0030.0000.0000.0000.000
41B74LEU00.0240.00743.626-0.003-0.0030.0000.0000.0000.000
42B75ASP-1-0.869-0.94346.8100.0250.0250.0000.0000.0000.000
43B76ILE0-0.073-0.02443.849-0.002-0.0020.0000.0000.0000.000
44B77LEU0-0.063-0.00747.309-0.002-0.0020.0000.0000.0000.000
45B78LYS10.8560.93450.012-0.027-0.0270.0000.0000.0000.000
46B92LEU00.0500.01964.4000.0000.0000.0000.0000.0000.000
47B93GLY00.0420.01763.4400.0000.0000.0000.0000.0000.000
48B94LYS10.9350.95061.729-0.005-0.0050.0000.0000.0000.000
49B95VAL0-0.012-0.00560.3470.0000.0000.0000.0000.0000.000
50B96THR0-0.0210.00059.0670.0010.0010.0000.0000.0000.000
51B97SER0-0.052-0.02156.9440.0010.0010.0000.0000.0000.000
52B98VAL00.0380.01851.7590.0000.0000.0000.0000.0000.000
53B99ILE0-0.017-0.00450.6630.0000.0000.0000.0000.0000.000
54B100PRO0-0.0120.00847.589-0.001-0.0010.0000.0000.0000.000
55B101GLY00.0310.00350.4120.0010.0010.0000.0000.0000.000
56B102LEU00.0350.01246.1900.0000.0000.0000.0000.0000.000
57B103ASN00.029-0.00449.2370.0020.0020.0000.0000.0000.000
58B104ASN0-0.027-0.01350.9450.0000.0000.0000.0000.0000.000
59B105VAL0-0.062-0.01146.3570.0010.0010.0000.0000.0000.000
60B106ILE0-0.028-0.01549.3620.0000.0000.0000.0000.0000.000
61B107ASP-1-0.870-0.96747.9260.0320.0320.0000.0000.0000.000
62B108ILE0-0.030-0.00742.1670.0000.0000.0000.0000.0000.000
63B109LYS10.9090.97042.619-0.035-0.0350.0000.0000.0000.000
64B110VAL00.0170.00637.3420.0000.0000.0000.0000.0000.000
65B111THR00.0420.00936.2480.0000.0000.0000.0000.0000.000
66B112ASP-1-1.010-1.00532.2240.0870.0870.0000.0000.0000.000
67B113PRO00.0240.04232.1590.0020.0020.0000.0000.0000.000
68B114GLN0-0.041-0.04326.1380.0000.0000.0000.0000.0000.000
69B115LEU00.001-0.00124.609-0.009-0.0090.0000.0000.0000.000
70B116LEU0-0.071-0.02321.4020.0140.0140.0000.0000.0000.000
71B117GLU-1-0.901-0.95917.6260.3610.3610.0000.0000.0000.000
72B118LEU0-0.0050.01119.522-0.018-0.0180.0000.0000.0000.000
73B119GLY00.0390.03017.2100.0380.0380.0000.0000.0000.000
74B120LEU0-0.014-0.02616.647-0.024-0.0240.0000.0000.0000.000
75B121VAL0-0.0180.00015.914-0.002-0.0020.0000.0000.0000.000
76B122GLN00.0570.03816.7730.0110.0110.0000.0000.0000.000
77B123SER0-0.050-0.02617.914-0.028-0.0280.0000.0000.0000.000
78B124PRO00.0280.00217.6320.0050.0050.0000.0000.0000.000
79B125ASP-1-0.800-0.86218.528-0.026-0.0260.0000.0000.0000.000
80B126GLY00.0550.02120.0600.0060.0060.0000.0000.0000.000
81B127HIS10.7950.86820.7420.0190.0190.0000.0000.0000.000
82B128ARG10.9710.98723.0930.0260.0260.0000.0000.0000.000
83B129LEU00.0310.02320.024-0.002-0.0020.0000.0000.0000.000
84B130TYR00.0240.02421.449-0.006-0.0060.0000.0000.0000.000
85B131VAL00.0120.01221.0680.0120.0120.0000.0000.0000.000
86B132THR0-0.019-0.03120.341-0.014-0.0140.0000.0000.0000.000
87B133ILE00.0030.00922.0530.0230.0230.0000.0000.0000.000
88B134PRO00.0100.02221.136-0.016-0.0160.0000.0000.0000.000
89B135LEU00.016-0.00324.2810.0120.0120.0000.0000.0000.000
90B136GLY0-0.031-0.02727.346-0.003-0.0030.0000.0000.0000.000
91B137ILE00.0370.01329.1670.0010.0010.0000.0000.0000.000
92B138LYS10.9200.98930.633-0.081-0.0810.0000.0000.0000.000
93B139LEU00.0330.00934.672-0.002-0.0020.0000.0000.0000.000
94B140GLN00.0090.00838.106-0.003-0.0030.0000.0000.0000.000
95B141VAL00.0080.01141.254-0.001-0.0010.0000.0000.0000.000
96B142ASN0-0.044-0.02644.0490.0010.0010.0000.0000.0000.000
97B143THR00.0260.01047.614-0.002-0.0020.0000.0000.0000.000
98B144PRO00.0110.00950.1150.0010.0010.0000.0000.0000.000
99B145LEU00.0040.00051.924-0.001-0.0010.0000.0000.0000.000
100B146VAL0-0.0230.03651.8230.0010.0010.0000.0000.0000.000
101B147GLY00.040-0.01851.388-0.001-0.0010.0000.0000.0000.000
102B148ALA00.016-0.00547.515-0.001-0.0010.0000.0000.0000.000
103B149SER0-0.0210.00847.1890.0010.0010.0000.0000.0000.000
104B150LEU0-0.021-0.03543.4560.0010.0010.0000.0000.0000.000
105B151LEU0-0.0060.01841.556-0.001-0.0010.0000.0000.0000.000
106B152ARG10.9190.96437.346-0.042-0.0420.0000.0000.0000.000
107B153LEU00.0150.00536.086-0.002-0.0020.0000.0000.0000.000
108B154ALA0-0.010-0.01931.1780.0050.0050.0000.0000.0000.000
109B155VAL0-0.007-0.00331.828-0.005-0.0050.0000.0000.0000.000
110B156LYS10.9470.97224.112-0.087-0.0870.0000.0000.0000.000
111B157MET00.0040.01528.109-0.011-0.0110.0000.0000.0000.000
112B158ASP-1-0.830-0.90922.9460.0800.0800.0000.0000.0000.000
113B159ILE0-0.016-0.00626.285-0.011-0.0110.0000.0000.0000.000
114B160THR0-0.032-0.02723.6200.0080.0080.0000.0000.0000.000
115B161ALA00.0160.02325.940-0.009-0.0090.0000.0000.0000.000
116B162GLU-1-0.936-0.97026.0830.0220.0220.0000.0000.0000.000
117B163ILE0-0.021-0.01624.3880.0030.0030.0000.0000.0000.000
118B164LEU0-0.0080.00226.710-0.003-0.0030.0000.0000.0000.000
119B165ALA00.0220.00328.5310.0070.0070.0000.0000.0000.000
120B166VAL0-0.0150.01130.372-0.005-0.0050.0000.0000.0000.000
121B167ARG10.9660.98134.104-0.016-0.0160.0000.0000.0000.000
122B168ASP-1-0.745-0.87336.9800.0330.0330.0000.0000.0000.000
123B169LYS10.9200.94240.424-0.024-0.0240.0000.0000.0000.000
124B170GLN0-0.048-0.02542.442-0.001-0.0010.0000.0000.0000.000
125B171GLU-1-0.927-0.95939.7640.0220.0220.0000.0000.0000.000
126B172ARG10.8690.95138.041-0.038-0.0380.0000.0000.0000.000
127B173ILE0-0.002-0.02231.819-0.002-0.0020.0000.0000.0000.000
128B174HIS0-0.073-0.02933.7420.0060.0060.0000.0000.0000.000
129B175LEU00.0230.00526.935-0.002-0.0020.0000.0000.0000.000
130B176VAL0-0.075-0.03930.9500.0020.0020.0000.0000.0000.000
131B177LEU00.0170.00329.774-0.001-0.0010.0000.0000.0000.000
132B178GLY0-0.0140.00230.628-0.004-0.0040.0000.0000.0000.000
133B179ASP-1-0.888-0.94530.4700.0110.0110.0000.0000.0000.000
134B180CYS0-0.127-0.06530.2180.0070.0070.0000.0000.0000.000
135B181THR00.0220.01130.196-0.004-0.0040.0000.0000.0000.000
136B182HIS00.0660.02529.5890.0090.0090.0000.0000.0000.000
137B183SER00.0010.01024.561-0.012-0.0120.0000.0000.0000.000
138B184PRO00.0850.09027.1580.0010.0010.0000.0000.0000.000
139B185GLY0-0.029-0.01227.2160.0010.0010.0000.0000.0000.000
140B186SER0-0.100-0.11125.708-0.001-0.0010.0000.0000.0000.000
141B187LEU0-0.024-0.00326.7180.0070.0070.0000.0000.0000.000
142B188GLN0-0.017-0.01024.8260.0000.0000.0000.0000.0000.000
143B189ILE0-0.0030.00129.7750.0080.0080.0000.0000.0000.000
144B190SER0-0.033-0.01230.151-0.005-0.0050.0000.0000.0000.000
145B191LEU0-0.010-0.01232.5610.0030.0030.0000.0000.0000.000
146B192LEU0-0.039-0.02432.2490.0020.0020.0000.0000.0000.000
147B193ASP-1-0.838-0.89234.6460.0370.0370.0000.0000.0000.000
148B194GLY00.017-0.03537.808-0.002-0.0020.0000.0000.0000.000
149B195LEU0-0.028-0.04539.8800.0000.0000.0000.0000.0000.000
150B196GLY00.1020.06741.560-0.002-0.0020.0000.0000.0000.000
151B197PRO0-0.013-0.00742.672-0.002-0.0020.0000.0000.0000.000
152B198LEU00.0270.01045.7560.0000.0000.0000.0000.0000.000
153B199PRO0-0.026-0.00947.135-0.002-0.0020.0000.0000.0000.000
154B200ILE0-0.0060.03044.0900.0000.0000.0000.0000.0000.000
155B201GLN00.0130.00142.3510.0020.0020.0000.0000.0000.000
156B202GLY00.0300.02944.107-0.002-0.0020.0000.0000.0000.000
157B203LEU00.0000.00545.2350.0000.0000.0000.0000.0000.000
158B204LEU00.003-0.01538.4490.0010.0010.0000.0000.0000.000
159B205ASP-1-0.928-0.96341.258-0.001-0.0010.0000.0000.0000.000
160B206SER0-0.0110.00142.591-0.001-0.0010.0000.0000.0000.000
161B207LEU0-0.029-0.03741.3860.0010.0010.0000.0000.0000.000
162B208THR0-0.020-0.01237.4510.0010.0010.0000.0000.0000.000
163B209GLY00.0480.03738.6200.0000.0000.0000.0000.0000.000
164B210ILE0-0.031-0.02540.6480.0000.0000.0000.0000.0000.000
165B211LEU00.011-0.00337.1730.0010.0010.0000.0000.0000.000
166B212ASN0-0.011-0.01435.1460.0040.0040.0000.0000.0000.000
167B213LYS10.9170.96736.849-0.004-0.0040.0000.0000.0000.000
168B214VAL0-0.0140.00639.5390.0000.0000.0000.0000.0000.000
169B215LEU00.0170.00235.1050.0020.0020.0000.0000.0000.000
170B216PRO00.0040.01633.8670.0050.0050.0000.0000.0000.000
171B217GLU-1-0.841-0.93535.0670.0190.0190.0000.0000.0000.000
172B218LEU0-0.054-0.02237.9370.0020.0020.0000.0000.0000.000
173B219VAL00.007-0.00532.2500.0030.0030.0000.0000.0000.000
174B220GLN00.0400.01033.4430.0040.0040.0000.0000.0000.000
175B221GLY0-0.031-0.01434.5550.0010.0010.0000.0000.0000.000
176B222ASN0-0.025-0.01936.934-0.002-0.0020.0000.0000.0000.000
177B223VAL0-0.016-0.01230.6040.0040.0040.0000.0000.0000.000
178B225PRO00.0300.00433.9690.0020.0020.0000.0000.0000.000
179B226LEU00.0340.03432.9130.0020.0020.0000.0000.0000.000
180B227VAL00.0140.00228.5700.0030.0030.0000.0000.0000.000
181B228ASN0-0.073-0.05631.5050.0010.0010.0000.0000.0000.000
182B229GLU-1-0.889-0.92233.6920.0530.0530.0000.0000.0000.000
183B230VAL0-0.017-0.01029.5280.0020.0020.0000.0000.0000.000
184B231LEU0-0.035-0.01827.4340.0040.0040.0000.0000.0000.000
185B232ARG10.9160.96531.005-0.050-0.0500.0000.0000.0000.000
186B233GLY0-0.023-0.00733.487-0.004-0.0040.0000.0000.0000.000
187B234LEU0-0.040-0.00927.3720.0080.0080.0000.0000.0000.000
188B235ASP-1-0.897-0.94729.1780.1060.1060.0000.0000.0000.000
189B236ILE00.0440.00930.109-0.001-0.0010.0000.0000.0000.000
190B237THR0-0.009-0.01527.948-0.003-0.0030.0000.0000.0000.000
191B238LEU00.0180.01923.7050.0020.0020.0000.0000.0000.000
192B239VAL00.0010.00226.0600.0000.0000.0000.0000.0000.000
193B240HIS0-0.023-0.00927.752-0.007-0.0070.0000.0000.0000.000
194B241ASP-1-0.843-0.93824.1460.1020.1020.0000.0000.0000.000
195B242ILE0-0.026-0.01322.530-0.003-0.0030.0000.0000.0000.000
196B243VAL00.0220.00924.217-0.009-0.0090.0000.0000.0000.000
197B244ASN00.0220.00625.923-0.016-0.0160.0000.0000.0000.000
198B245MET00.0020.02120.478-0.013-0.0130.0000.0000.0000.000
199B246LEU0-0.0100.01222.097-0.012-0.0120.0000.0000.0000.000
200B247ILE0-0.068-0.03824.170-0.012-0.0120.0000.0000.0000.000
201B248HIS10.7990.88224.191-0.040-0.0400.0000.0000.0000.000
202B249GLY0-0.0440.00722.317-0.007-0.0070.0000.0000.0000.000
203B250LEU0-0.001-0.00819.012-0.010-0.0100.0000.0000.0000.000
204B251GLN0-0.021-0.03114.3560.0020.0020.0000.0000.0000.000
205B252PHE00.0170.00115.3500.0140.0140.0000.0000.0000.000
206B253VAL0-0.030-0.00714.1460.0480.0480.0000.0000.0000.000
207B254ILE0-0.006-0.0038.197-0.051-0.0510.0000.0000.0000.000
208B255LYS10.8840.9497.7110.0140.0140.0000.0000.0000.000