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: 176KZ

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 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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2049503.37683
FMO2-HF: Nuclear repulsion 1972949.768294
FMO2-HF: Total energy -76553.608536
FMO2-MP2: Total energy -76779.207091


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.
0.372.245-0.022-0.967-0.8860.002
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 : -0.016 / 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].
3B36VAL00.0200.0083.8590.2302.105-0.022-0.967-0.8860.002
4B37ASN00.0230.0076.976-0.357-0.3570.0000.0000.0000.000
5B38PRO0-0.0150.00110.3670.1090.1090.0000.0000.0000.000
6B39ALA00.011-0.00813.235-0.073-0.0730.0000.0000.0000.000
7B40LEU0-0.010-0.00614.1690.0970.0970.0000.0000.0000.000
8B41PRO00.0050.02915.5380.0120.0120.0000.0000.0000.000
9B42LEU0-0.036-0.02015.4380.0400.0400.0000.0000.0000.000
10B43SER0-0.036-0.02118.977-0.011-0.0110.0000.0000.0000.000
11B44PRO00.0120.00821.282-0.007-0.0070.0000.0000.0000.000
12B45THR00.004-0.00216.4220.0320.0320.0000.0000.0000.000
13B46GLY00.0570.03917.067-0.030-0.0300.0000.0000.0000.000
14B47LEU00.0320.01018.1220.0070.0070.0000.0000.0000.000
15B48ALA00.0300.01615.759-0.005-0.0050.0000.0000.0000.000
16B49GLY00.0510.02817.089-0.001-0.0010.0000.0000.0000.000
17B50SER0-0.023-0.02617.919-0.007-0.0070.0000.0000.0000.000
18B51LEU00.0040.00920.933-0.010-0.0100.0000.0000.0000.000
19B52THR00.0350.01318.048-0.010-0.0100.0000.0000.0000.000
20B53ASN00.0270.01319.587-0.007-0.0070.0000.0000.0000.000
21B54ALA00.0160.02022.634-0.009-0.0090.0000.0000.0000.000
22B55LEU00.0190.00323.790-0.010-0.0100.0000.0000.0000.000
23B56SER0-0.0030.00723.398-0.014-0.0140.0000.0000.0000.000
24B57ASN0-0.011-0.02525.467-0.011-0.0110.0000.0000.0000.000
25B58GLY00.0230.03528.092-0.008-0.0080.0000.0000.0000.000
26B59LEU00.004-0.00626.894-0.008-0.0080.0000.0000.0000.000
27B60LEU0-0.029-0.02026.754-0.008-0.0080.0000.0000.0000.000
28B61SER0-0.072-0.05430.837-0.007-0.0070.0000.0000.0000.000
29B62GLY0-0.0060.01933.387-0.005-0.0050.0000.0000.0000.000
30B63GLY0-0.0130.00734.459-0.005-0.0050.0000.0000.0000.000
31B64LEU00.008-0.02230.061-0.004-0.0040.0000.0000.0000.000
32B65LEU00.005-0.00529.911-0.004-0.0040.0000.0000.0000.000
33B66GLY00.0380.02633.843-0.004-0.0040.0000.0000.0000.000
34B67ILE00.0110.00736.258-0.004-0.0040.0000.0000.0000.000
35B68MET0-0.038-0.01732.631-0.005-0.0050.0000.0000.0000.000
36B69GLU-1-0.878-0.95536.1120.0600.0600.0000.0000.0000.000
37B70ASN0-0.068-0.03938.414-0.005-0.0050.0000.0000.0000.000
38B71LEU00.0040.01636.181-0.003-0.0030.0000.0000.0000.000
39B72PRO00.0320.02940.7770.0000.0000.0000.0000.0000.000
40B73LEU00.006-0.01739.044-0.003-0.0030.0000.0000.0000.000
41B74LEU00.0190.00643.490-0.002-0.0020.0000.0000.0000.000
42B75ASP-1-0.814-0.89646.7700.0200.0200.0000.0000.0000.000
43B76ILE0-0.051-0.00743.878-0.002-0.0020.0000.0000.0000.000
44B77LEU0-0.040-0.00447.426-0.002-0.0020.0000.0000.0000.000
45B78LYS10.7590.85749.994-0.023-0.0230.0000.0000.0000.000
46B92LEU00.0570.02064.5190.0000.0000.0000.0000.0000.000
47B93GLY00.0520.03063.0490.0000.0000.0000.0000.0000.000
48B94LYS10.9300.94361.415-0.003-0.0030.0000.0000.0000.000
49B95VAL0-0.0080.00460.4690.0000.0000.0000.0000.0000.000
50B96THR0-0.026-0.01159.3690.0010.0010.0000.0000.0000.000
51B97SER0-0.039-0.01356.7470.0010.0010.0000.0000.0000.000
52B98VAL00.003-0.00251.9070.0000.0000.0000.0000.0000.000
53B99ILE00.004-0.00451.7480.0000.0000.0000.0000.0000.000
54B100PRO00.0130.01747.928-0.001-0.0010.0000.0000.0000.000
55B101GLY00.0200.02050.2670.0010.0010.0000.0000.0000.000
56B102LEU00.019-0.00946.4050.0000.0000.0000.0000.0000.000
57B103ASN00.0200.00049.3130.0020.0020.0000.0000.0000.000
58B104ASN0-0.032-0.01151.2100.0000.0000.0000.0000.0000.000
59B105VAL0-0.011-0.00546.8330.0010.0010.0000.0000.0000.000
60B106ILE0-0.042-0.02449.9800.0000.0000.0000.0000.0000.000
61B107ASP-1-0.846-0.94247.6670.0290.0290.0000.0000.0000.000
62B108ILE0-0.034-0.02942.571-0.001-0.0010.0000.0000.0000.000
63B109LYS10.8760.95943.174-0.031-0.0310.0000.0000.0000.000
64B110VAL0-0.001-0.00137.5090.0000.0000.0000.0000.0000.000
65B111THR0-0.049-0.03137.7170.0000.0000.0000.0000.0000.000
66B112ASP-1-0.845-0.90432.4880.0840.0840.0000.0000.0000.000
67B113PRO0-0.0140.00532.5750.0020.0020.0000.0000.0000.000
68B114GLN00.002-0.01026.5750.0040.0040.0000.0000.0000.000
69B115LEU00.0250.00725.116-0.010-0.0100.0000.0000.0000.000
70B116LEU0-0.100-0.04121.7040.0120.0120.0000.0000.0000.000
71B117GLU-1-0.852-0.93917.9680.2790.2790.0000.0000.0000.000
72B118LEU0-0.031-0.00319.569-0.014-0.0140.0000.0000.0000.000
73B119GLY00.0260.03117.3650.0270.0270.0000.0000.0000.000
74B120LEU0-0.012-0.01716.714-0.014-0.0140.0000.0000.0000.000
75B121VAL0-0.029-0.01415.563-0.009-0.0090.0000.0000.0000.000
76B122GLN00.0310.00316.8260.0180.0180.0000.0000.0000.000
77B123SER0-0.021-0.03117.529-0.026-0.0260.0000.0000.0000.000
78B124PRO00.0350.02017.2590.0020.0020.0000.0000.0000.000
79B125ASP-1-0.776-0.85018.222-0.052-0.0520.0000.0000.0000.000
80B126GLY00.0090.00419.4990.0080.0080.0000.0000.0000.000
81B127HIS10.8100.90020.3200.0410.0410.0000.0000.0000.000
82B128ARG10.8800.95322.8080.0430.0430.0000.0000.0000.000
83B129LEU00.0140.00719.950-0.007-0.0070.0000.0000.0000.000
84B130TYR0-0.041-0.04321.048-0.006-0.0060.0000.0000.0000.000
85B131VAL00.0010.00720.6930.0090.0090.0000.0000.0000.000
86B132THR0-0.008-0.00520.670-0.011-0.0110.0000.0000.0000.000
87B133ILE00.0340.00422.4910.0180.0180.0000.0000.0000.000
88B134PRO00.0010.02921.021-0.012-0.0120.0000.0000.0000.000
89B135LEU00.0350.00224.2750.0120.0120.0000.0000.0000.000
90B136GLY0-0.032-0.02227.198-0.002-0.0020.0000.0000.0000.000
91B137ILE00.0040.01529.3290.0030.0030.0000.0000.0000.000
92B138LYS10.8370.91630.347-0.079-0.0790.0000.0000.0000.000
93B139LEU00.0130.01035.154-0.001-0.0010.0000.0000.0000.000
94B140GLN00.0270.00838.638-0.002-0.0020.0000.0000.0000.000
95B141VAL00.0250.02641.770-0.001-0.0010.0000.0000.0000.000
96B142ASN0-0.024-0.02044.4500.0020.0020.0000.0000.0000.000
97B143THR00.0090.00547.931-0.002-0.0020.0000.0000.0000.000
98B144PRO00.0200.01050.6490.0010.0010.0000.0000.0000.000
99B145LEU0-0.0140.00351.517-0.001-0.0010.0000.0000.0000.000
100B146VAL00.0430.02852.1030.0010.0010.0000.0000.0000.000
101B147GLY0-0.023-0.01552.079-0.001-0.0010.0000.0000.0000.000
102B148ALA00.015-0.00747.8360.0000.0000.0000.0000.0000.000
103B149SER00.0080.01747.7590.0010.0010.0000.0000.0000.000
104B150LEU0-0.046-0.03144.3160.0010.0010.0000.0000.0000.000
105B151LEU0-0.0030.00742.814-0.001-0.0010.0000.0000.0000.000
106B152ARG10.8280.88437.062-0.041-0.0410.0000.0000.0000.000
107B153LEU00.0110.00336.237-0.002-0.0020.0000.0000.0000.000
108B154ALA0-0.0040.00231.1430.0050.0050.0000.0000.0000.000
109B155VAL0-0.010-0.01031.958-0.006-0.0060.0000.0000.0000.000
110B156LYS10.8460.90724.348-0.080-0.0800.0000.0000.0000.000
111B157MET00.0050.01527.867-0.010-0.0100.0000.0000.0000.000
112B158ASP-1-0.823-0.92222.7560.0710.0710.0000.0000.0000.000
113B159ILE0-0.022-0.00626.301-0.010-0.0100.0000.0000.0000.000
114B160THR0-0.020-0.00723.6440.0060.0060.0000.0000.0000.000
115B161ALA00.0290.00525.376-0.004-0.0040.0000.0000.0000.000
116B162GLU-1-0.831-0.89925.397-0.004-0.0040.0000.0000.0000.000
117B163ILE0-0.021-0.01323.7540.0050.0050.0000.0000.0000.000
118B164LEU0-0.0080.00026.437-0.004-0.0040.0000.0000.0000.000
119B165ALA00.0300.01428.1890.0050.0050.0000.0000.0000.000
120B166VAL0-0.0160.00230.015-0.004-0.0040.0000.0000.0000.000
121B167ARG10.8550.89933.722-0.006-0.0060.0000.0000.0000.000
122B168ASP-1-0.751-0.84536.7010.0210.0210.0000.0000.0000.000
123B169LYS10.9400.95440.345-0.014-0.0140.0000.0000.0000.000
124B170GLN0-0.061-0.03342.4280.0000.0000.0000.0000.0000.000
125B171GLU-1-0.813-0.86339.8050.0110.0110.0000.0000.0000.000
126B172ARG10.8300.89637.599-0.026-0.0260.0000.0000.0000.000
127B173ILE0-0.021-0.02731.923-0.002-0.0020.0000.0000.0000.000
128B174HIS0-0.048-0.02633.3550.0060.0060.0000.0000.0000.000
129B175LEU00.0080.00626.625-0.002-0.0020.0000.0000.0000.000
130B176VAL0-0.035-0.02230.5620.0020.0020.0000.0000.0000.000
131B177LEU00.0240.01429.535-0.001-0.0010.0000.0000.0000.000
132B178GLY0-0.0020.00630.145-0.003-0.0030.0000.0000.0000.000
133B179ASP-1-0.896-0.95230.5300.0000.0000.0000.0000.0000.000
134B180CYS0-0.149-0.05829.9600.0040.0040.0000.0000.0000.000
135B181THR00.0140.00129.787-0.002-0.0020.0000.0000.0000.000
136B182HIS00.0230.00429.2470.0070.0070.0000.0000.0000.000
137B183SER00.0060.01524.396-0.011-0.0110.0000.0000.0000.000
138B184PRO00.0440.02027.4890.0010.0010.0000.0000.0000.000
139B185GLY00.003-0.00326.8710.0030.0030.0000.0000.0000.000
140B186SER0-0.040-0.03025.6140.0030.0030.0000.0000.0000.000
141B187LEU0-0.038-0.00426.7740.0080.0080.0000.0000.0000.000
142B188GLN0-0.035-0.00724.660-0.001-0.0010.0000.0000.0000.000
143B189ILE00.0200.00129.9650.0070.0070.0000.0000.0000.000
144B190SER0-0.038-0.02330.381-0.003-0.0030.0000.0000.0000.000
145B191LEU0-0.016-0.01232.7300.0030.0030.0000.0000.0000.000
146B192LEU00.002-0.00332.4500.0010.0010.0000.0000.0000.000
147B193ASP-1-0.781-0.83735.3560.0370.0370.0000.0000.0000.000
148B194GLY00.026-0.00738.451-0.002-0.0020.0000.0000.0000.000
149B195LEU0-0.060-0.03039.429-0.001-0.0010.0000.0000.0000.000
150B196GLY00.0610.02541.248-0.003-0.0030.0000.0000.0000.000
151B197PRO0-0.029-0.01442.702-0.001-0.0010.0000.0000.0000.000
152B198LEU00.0180.02346.020-0.001-0.0010.0000.0000.0000.000
153B199PRO00.0140.00947.794-0.002-0.0020.0000.0000.0000.000
154B200ILE0-0.0090.00043.891-0.001-0.0010.0000.0000.0000.000
155B201GLN00.0430.00442.7620.0020.0020.0000.0000.0000.000
156B202GLY00.0420.03144.061-0.001-0.0010.0000.0000.0000.000
157B203LEU0-0.0070.00045.8690.0000.0000.0000.0000.0000.000
158B204LEU00.0220.00538.3810.0010.0010.0000.0000.0000.000
159B205ASP-1-0.932-0.93741.427-0.002-0.0020.0000.0000.0000.000
160B206SER0-0.020-0.01842.5170.0000.0000.0000.0000.0000.000
161B207LEU0-0.029-0.01241.7720.0010.0010.0000.0000.0000.000
162B208THR0-0.041-0.03937.5650.0000.0000.0000.0000.0000.000
163B209GLY00.0370.02638.7200.0000.0000.0000.0000.0000.000
164B210ILE0-0.037-0.02240.980-0.001-0.0010.0000.0000.0000.000
165B211LEU00.0300.00237.4100.0010.0010.0000.0000.0000.000
166B212ASN00.007-0.01134.5670.0030.0030.0000.0000.0000.000
167B213LYS10.9030.95436.888-0.001-0.0010.0000.0000.0000.000
168B214VAL0-0.0060.01239.1210.0000.0000.0000.0000.0000.000
169B215LEU00.0080.00635.2740.0020.0020.0000.0000.0000.000
170B216PRO00.0160.00833.8190.0030.0030.0000.0000.0000.000
171B217GLU-1-0.828-0.92434.9620.0120.0120.0000.0000.0000.000
172B218LEU0-0.014-0.00837.8480.0020.0020.0000.0000.0000.000
173B219VAL00.0020.00632.1580.0030.0030.0000.0000.0000.000
174B220GLN00.0290.01833.6880.0030.0030.0000.0000.0000.000
175B221GLY0-0.017-0.01434.6870.0020.0020.0000.0000.0000.000
176B222ASN0-0.065-0.04037.0320.0000.0000.0000.0000.0000.000
177B223VAL0-0.005-0.00830.4880.0030.0030.0000.0000.0000.000
178B225PRO00.0280.00533.7400.0010.0010.0000.0000.0000.000
179B226LEU00.0130.01832.9690.0020.0020.0000.0000.0000.000
180B227VAL00.0390.00428.1450.0030.0030.0000.0000.0000.000
181B228ASN0-0.050-0.03231.2850.0000.0000.0000.0000.0000.000
182B229GLU-1-0.809-0.88633.5460.0380.0380.0000.0000.0000.000
183B230VAL0-0.019-0.00129.6060.0030.0030.0000.0000.0000.000
184B231LEU0-0.052-0.03027.0920.0040.0040.0000.0000.0000.000
185B232ARG10.8240.90530.696-0.036-0.0360.0000.0000.0000.000
186B233GLY0-0.0100.00333.127-0.003-0.0030.0000.0000.0000.000
187B234LEU0-0.048-0.01326.9110.0070.0070.0000.0000.0000.000
188B235ASP-1-0.856-0.93528.7960.0800.0800.0000.0000.0000.000
189B236ILE00.0320.00929.886-0.001-0.0010.0000.0000.0000.000
190B237THR0-0.036-0.02727.267-0.007-0.0070.0000.0000.0000.000
191B238LEU0-0.021-0.00124.0460.0000.0000.0000.0000.0000.000
192B239VAL00.0210.00325.853-0.002-0.0020.0000.0000.0000.000
193B240HIS00.0060.00627.823-0.009-0.0090.0000.0000.0000.000
194B241ASP-1-0.843-0.92424.2400.0660.0660.0000.0000.0000.000
195B242ILE0-0.022-0.00622.069-0.005-0.0050.0000.0000.0000.000
196B243VAL00.0150.00724.110-0.010-0.0100.0000.0000.0000.000
197B244ASN0-0.029-0.02026.048-0.014-0.0140.0000.0000.0000.000
198B245MET0-0.0180.01020.161-0.012-0.0120.0000.0000.0000.000
199B246LEU00.0090.01921.799-0.012-0.0120.0000.0000.0000.000
200B247ILE0-0.004-0.00623.927-0.011-0.0110.0000.0000.0000.000
201B248HIS10.8070.88223.951-0.018-0.0180.0000.0000.0000.000
202B249GLY0-0.0110.01022.123-0.006-0.0060.0000.0000.0000.000
203B250LEU0-0.029-0.01318.912-0.012-0.0120.0000.0000.0000.000
204B251GLN0-0.021-0.02814.2510.0160.0160.0000.0000.0000.000
205B252PHE00.008-0.00815.3280.0110.0110.0000.0000.0000.000
206B253VAL0-0.0190.00414.2260.0410.0410.0000.0000.0000.000
207B254ILE00.000-0.0028.177-0.051-0.0510.0000.0000.0000.000
208B255LYS10.8940.9597.3180.0560.0560.0000.0000.0000.000