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

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FMODB ID: K9N93

Calculation Name: 1KAC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1KAC

Chain ID: A

ChEMBL ID:

UniProt ID: P78310

Base Structure: X-ray

Registration Date: 2023-09-20

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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1898055.214839
FMO2-HF: Nuclear repulsion 1827605.578872
FMO2-HF: Total energy -70449.635967
FMO2-MP2: Total energy -70653.73176


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(A:403:THR)


Summations of interaction energy for fragment #1(A:403:THR)
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.
-21.248-16.35310.442-7.358-7.979-0.032
Interaction energy analysis for fragmet #1(A:403:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : -0.004
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].
3A405TYR0-0.008-0.0062.311-6.050-0.8201.781-2.953-4.0580.018
4A406ASP-1-0.778-0.8651.863-18.980-20.1108.457-4.138-3.189-0.050
5A407PRO0-0.025-0.0212.7301.0441.8390.204-0.267-0.7320.000
6A408LEU0-0.004-0.0045.6650.8140.8140.0000.0000.0000.000
7A409THR0-0.018-0.0377.9960.4420.4420.0000.0000.0000.000
8A410LEU0-0.052-0.0049.042-0.020-0.0200.0000.0000.0000.000
9A411TRP0-0.016-0.02111.349-0.037-0.0370.0000.0000.0000.000
10A412THR00.0440.03613.9990.0400.0400.0000.0000.0000.000
11A413THR0-0.073-0.02913.8240.0500.0500.0000.0000.0000.000
12A414PRO0-0.028-0.02314.9870.0270.0270.0000.0000.0000.000
13A415ASP-1-0.921-0.96817.741-0.378-0.3780.0000.0000.0000.000
14A416PRO0-0.0020.03419.4880.0280.0280.0000.0000.0000.000
15A417PRO00.0290.00320.9760.0090.0090.0000.0000.0000.000
16A418PRO0-0.010-0.01924.173-0.004-0.0040.0000.0000.0000.000
17A419ASN00.0150.01221.1030.0210.0210.0000.0000.0000.000
18A420CYS00.0000.00624.6990.0080.0080.0000.0000.0000.000
19A421SER00.008-0.01027.285-0.006-0.0060.0000.0000.0000.000
20A422LEU0-0.065-0.02728.7690.0070.0070.0000.0000.0000.000
21A423ILE0-0.037-0.01732.2910.0070.0070.0000.0000.0000.000
22A424GLN0-0.027-0.02734.8280.0070.0070.0000.0000.0000.000
23A425GLU-1-0.853-0.91432.232-0.037-0.0370.0000.0000.0000.000
24A426LEU0-0.049-0.02827.185-0.006-0.0060.0000.0000.0000.000
25A427ASP-1-0.751-0.87130.277-0.088-0.0880.0000.0000.0000.000
26A428ALA00.020-0.00229.241-0.006-0.0060.0000.0000.0000.000
27A429LYS10.8780.94724.6260.2240.2240.0000.0000.0000.000
28A430LEU00.0200.00722.386-0.003-0.0030.0000.0000.0000.000
29A431THR00.0010.00619.5190.0010.0010.0000.0000.0000.000
30A432LEU00.003-0.01418.2000.0110.0110.0000.0000.0000.000
31A433CYS0-0.017-0.01014.626-0.075-0.0750.0000.0000.0000.000
32A434LEU0-0.0100.00014.6290.0490.0490.0000.0000.0000.000
33A435THR00.0110.00212.554-0.083-0.0830.0000.0000.0000.000
34A436LYS10.8310.90211.5360.3530.3530.0000.0000.0000.000
35A437ASN0-0.013-0.00212.357-0.123-0.1230.0000.0000.0000.000
36A438GLY00.0520.02814.1620.0660.0660.0000.0000.0000.000
37A439SER0-0.002-0.00616.0450.0060.0060.0000.0000.0000.000
38A440ILE00.0060.01618.2020.0340.0340.0000.0000.0000.000
39A441VAL0-0.0030.02415.591-0.052-0.0520.0000.0000.0000.000
40A442ASN0-0.034-0.01616.3070.0980.0980.0000.0000.0000.000
41A443GLY00.0270.00117.402-0.058-0.0580.0000.0000.0000.000
42A444ILE0-0.026-0.02419.3330.0270.0270.0000.0000.0000.000
43A445VAL0-0.006-0.00520.394-0.019-0.0190.0000.0000.0000.000
44A446SER0-0.0170.00422.9270.0050.0050.0000.0000.0000.000
45A447LEU00.0170.01324.822-0.001-0.0010.0000.0000.0000.000
46A448VAL00.0020.00427.5260.0050.0050.0000.0000.0000.000
47A449GLY00.0180.00829.8020.0030.0030.0000.0000.0000.000
48A450VAL0-0.050-0.03929.774-0.005-0.0050.0000.0000.0000.000
49A451LYS10.8630.93032.8650.0710.0710.0000.0000.0000.000
50A452GLY00.0390.01935.5180.0010.0010.0000.0000.0000.000
51A453ASN00.0470.00138.484-0.003-0.0030.0000.0000.0000.000
52A454LEU00.0060.03132.640-0.003-0.0030.0000.0000.0000.000
53A455LEU0-0.0160.01635.401-0.009-0.0090.0000.0000.0000.000
54A456ASN0-0.075-0.03437.691-0.003-0.0030.0000.0000.0000.000
55A457ILE00.0160.01537.7390.0050.0050.0000.0000.0000.000
56A458GLN00.013-0.00640.8020.0010.0010.0000.0000.0000.000
57A459SER00.0300.00143.691-0.002-0.0020.0000.0000.0000.000
58A460THR00.0140.00345.935-0.002-0.0020.0000.0000.0000.000
59A461THR0-0.0370.00239.1070.0020.0020.0000.0000.0000.000
60A462THR00.0230.00641.489-0.003-0.0030.0000.0000.0000.000
61A463THR0-0.018-0.02535.728-0.006-0.0060.0000.0000.0000.000
62A464VAL00.0220.03532.3970.0060.0060.0000.0000.0000.000
63A465GLY00.021-0.01431.278-0.008-0.0080.0000.0000.0000.000
64A466VAL0-0.0170.00726.3550.0060.0060.0000.0000.0000.000
65A467HIS0-0.002-0.02426.932-0.004-0.0040.0000.0000.0000.000
66A468LEU0-0.0090.01020.413-0.001-0.0010.0000.0000.0000.000
67A469VAL00.0330.00823.727-0.004-0.0040.0000.0000.0000.000
68A470PHE0-0.003-0.01317.5860.0030.0030.0000.0000.0000.000
69A471ASP-1-0.737-0.87120.0430.1860.1860.0000.0000.0000.000
70A472GLU-1-0.856-0.94821.3730.1430.1430.0000.0000.0000.000
71A473GLN0-0.086-0.04717.3950.0560.0560.0000.0000.0000.000
72A474GLY0-0.017-0.01816.6660.0160.0160.0000.0000.0000.000
73A475ARG10.8470.92115.215-0.316-0.3160.0000.0000.0000.000
74A476LEU0-0.019-0.00517.266-0.011-0.0110.0000.0000.0000.000
75A477ILE00.0210.01519.3050.0320.0320.0000.0000.0000.000
76A478THR00.0040.01020.954-0.014-0.0140.0000.0000.0000.000
77A479SER00.0390.01223.7190.0090.0090.0000.0000.0000.000
78A480THR0-0.0070.03827.441-0.007-0.0070.0000.0000.0000.000
79A481PRO0-0.008-0.02728.9880.0100.0100.0000.0000.0000.000
80A482THR0-0.052-0.04922.975-0.020-0.0200.0000.0000.0000.000
81A483ALA0-0.001-0.00225.5420.0040.0040.0000.0000.0000.000
82A484LEU0-0.032-0.01319.458-0.002-0.0020.0000.0000.0000.000
83A485VAL00.0050.00423.5540.0190.0190.0000.0000.0000.000
84A486PRO00.008-0.01622.592-0.005-0.0050.0000.0000.0000.000
85A487GLN00.0120.00721.2890.0210.0210.0000.0000.0000.000
86A488ALA0-0.047-0.01120.375-0.016-0.0160.0000.0000.0000.000
87A489SER00.0000.00015.2530.0440.0440.0000.0000.0000.000
88A490TRP00.025-0.00514.889-0.069-0.0690.0000.0000.0000.000
89A491GLY00.0290.01711.3940.1270.1270.0000.0000.0000.000
90A492TYR00.009-0.0135.9280.0060.0060.0000.0000.0000.000
91A493ARG10.9200.9857.5981.5861.5860.0000.0000.0000.000
92A494GLN00.0710.0336.122-0.478-0.4780.0000.0000.0000.000
93A495GLY00.0170.0227.5960.3990.3990.0000.0000.0000.000
94A496GLN00.0330.00010.440-0.131-0.1310.0000.0000.0000.000
95A497SER00.0530.01411.7870.1540.1540.0000.0000.0000.000
96A498VAL00.0050.00510.232-0.218-0.2180.0000.0000.0000.000
97A499SER0-0.041-0.0186.5970.3410.3410.0000.0000.0000.000
98A500THR00.0200.0018.602-0.045-0.0450.0000.0000.0000.000
99A501ASN0-0.060-0.0166.689-0.224-0.2240.0000.0000.0000.000
100A502THR00.0270.0219.316-0.257-0.2570.0000.0000.0000.000
101A503VAL0-0.010-0.02110.0700.2050.2050.0000.0000.0000.000
102A504THR00.001-0.0039.687-0.082-0.0820.0000.0000.0000.000
103A505ASN00.0300.0338.6990.0570.0570.0000.0000.0000.000
104A506GLY00.1100.04812.033-0.136-0.1360.0000.0000.0000.000
105A507LEU00.0330.02914.342-0.084-0.0840.0000.0000.0000.000
106A508GLY0-0.049-0.02913.871-0.029-0.0290.0000.0000.0000.000
107A509PHE00.002-0.0109.988-0.049-0.0490.0000.0000.0000.000
108A510MET0-0.0420.03615.867-0.009-0.0090.0000.0000.0000.000
109A511PRO00.0310.02119.385-0.007-0.0070.0000.0000.0000.000
110A512ASN00.008-0.00422.4840.0330.0330.0000.0000.0000.000
111A513VAL00.0200.00223.878-0.005-0.0050.0000.0000.0000.000
112A514SER0-0.0210.00326.6720.0070.0070.0000.0000.0000.000
113A515ALA0-0.090-0.04626.769-0.002-0.0020.0000.0000.0000.000
114A516TYR00.005-0.00124.477-0.011-0.0110.0000.0000.0000.000
115A517PRO00.0430.02528.9510.0050.0050.0000.0000.0000.000
116A518ARG10.9240.96025.813-0.038-0.0380.0000.0000.0000.000
117A519PRO0-0.0150.00231.472-0.004-0.0040.0000.0000.0000.000
118A520ASN00.028-0.00633.4670.0030.0030.0000.0000.0000.000
119A521ALA00.0440.06032.841-0.007-0.0070.0000.0000.0000.000
120A522SER0-0.004-0.01033.807-0.008-0.0080.0000.0000.0000.000
121A523GLU-1-0.937-0.96135.058-0.042-0.0420.0000.0000.0000.000
122A524ALA0-0.001-0.00234.700-0.006-0.0060.0000.0000.0000.000
123A525LYS10.9270.97230.5950.0460.0460.0000.0000.0000.000
124A526SER0-0.064-0.03130.210-0.007-0.0070.0000.0000.0000.000
125A527GLN0-0.008-0.01030.288-0.007-0.0070.0000.0000.0000.000
126A528MET00.0060.04326.115-0.009-0.0090.0000.0000.0000.000
127A529VAL0-0.041-0.03630.285-0.003-0.0030.0000.0000.0000.000
128A530SER0-0.0040.01030.934-0.006-0.0060.0000.0000.0000.000
129A531LEU00.0060.00133.2590.0060.0060.0000.0000.0000.000
130A532THR0-0.002-0.01531.096-0.011-0.0110.0000.0000.0000.000
131A533TYR00.0430.02533.7320.0090.0090.0000.0000.0000.000
132A534LEU00.0590.04534.205-0.010-0.0100.0000.0000.0000.000
133A535GLN0-0.025-0.03234.535-0.002-0.0020.0000.0000.0000.000
134A536GLY0-0.038-0.00733.556-0.009-0.0090.0000.0000.0000.000
135A537ASP-1-0.816-0.87534.206-0.127-0.1270.0000.0000.0000.000
136A538THR00.036-0.00237.5910.0030.0030.0000.0000.0000.000
137A539SER0-0.106-0.07139.3220.0070.0070.0000.0000.0000.000
138A540LYS10.8100.90439.4110.1230.1230.0000.0000.0000.000
139A541PRO0-0.0030.00938.481-0.007-0.0070.0000.0000.0000.000
140A542ILE0-0.0130.00833.8890.0070.0070.0000.0000.0000.000
141A543THR0-0.014-0.00535.571-0.005-0.0050.0000.0000.0000.000
142A544MET00.0030.01027.157-0.001-0.0010.0000.0000.0000.000
143A545LYS10.8570.92631.9220.0810.0810.0000.0000.0000.000
144A546VAL00.0090.00525.3640.0010.0010.0000.0000.0000.000
145A547ALA0-0.025-0.01128.7610.0050.0050.0000.0000.0000.000
146A548PHE0-0.013-0.02324.906-0.005-0.0050.0000.0000.0000.000
147A549ASN0-0.011-0.04225.1240.0110.0110.0000.0000.0000.000
148A550GLY00.0630.01927.8260.0090.0090.0000.0000.0000.000
149A551ILE0-0.033-0.00528.2640.0060.0060.0000.0000.0000.000
150A552THR0-0.097-0.03226.8800.0060.0060.0000.0000.0000.000
151A553SER00.0370.02127.8880.0020.0020.0000.0000.0000.000
152A554LEU00.039-0.00128.974-0.007-0.0070.0000.0000.0000.000
153A555ASN0-0.075-0.01926.165-0.005-0.0050.0000.0000.0000.000
154A556GLY00.0380.03324.5200.0110.0110.0000.0000.0000.000
155A557TYR0-0.025-0.01921.988-0.015-0.0150.0000.0000.0000.000
156A558SER00.0220.00223.9640.0020.0020.0000.0000.0000.000
157A559LEU00.0070.03120.387-0.008-0.0080.0000.0000.0000.000
158A560THR0-0.0090.00724.7630.0110.0110.0000.0000.0000.000
159A561PHE00.0220.01622.639-0.009-0.0090.0000.0000.0000.000
160A562MET00.0020.01728.6830.0080.0080.0000.0000.0000.000
161A563TRP00.0480.01526.789-0.003-0.0030.0000.0000.0000.000
162A564SER0-0.005-0.02433.7790.0090.0090.0000.0000.0000.000
163A565GLY00.003-0.00237.481-0.006-0.0060.0000.0000.0000.000
164A566LEU0-0.015-0.01036.305-0.001-0.0010.0000.0000.0000.000
165A567SER00.0240.00540.5210.0020.0020.0000.0000.0000.000
166A568ASN0-0.054-0.00944.0490.0040.0040.0000.0000.0000.000
167A569TYR0-0.028-0.02440.370-0.002-0.0020.0000.0000.0000.000
168A570ILE00.0150.00742.6930.0010.0010.0000.0000.0000.000
169A571ASN00.002-0.00443.883-0.002-0.0020.0000.0000.0000.000
170A572GLN00.0070.01539.790-0.008-0.0080.0000.0000.0000.000
171A573PRO00.0400.03535.8100.0040.0040.0000.0000.0000.000
172A574PHE0-0.016-0.03331.028-0.003-0.0030.0000.0000.0000.000
173A575SER00.0340.00431.747-0.009-0.0090.0000.0000.0000.000
174A576THR00.0010.01728.3150.0070.0070.0000.0000.0000.000
175A577PRO00.0470.02729.320-0.011-0.0110.0000.0000.0000.000
176A578SER0-0.004-0.00423.8430.0080.0080.0000.0000.0000.000
177A579CYS0-0.052-0.03025.5430.0100.0100.0000.0000.0000.000
178A580SER00.0280.02123.594-0.016-0.0160.0000.0000.0000.000
179A581PHE0-0.036-0.02921.1460.0310.0310.0000.0000.0000.000
180A582SER00.0240.00221.716-0.031-0.0310.0000.0000.0000.000
181A583TYR0-0.038-0.03518.5910.0180.0180.0000.0000.0000.000
182A584ILE00.0450.01521.015-0.023-0.0230.0000.0000.0000.000
183A585THR00.005-0.00916.8190.0040.0040.0000.0000.0000.000
184A586GLN00.0170.00519.852-0.003-0.0030.0000.0000.0000.000
185A587GLU-1-0.948-0.96316.6530.1380.1380.0000.0000.0000.000