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: KGZ33

Calculation Name: 1KA9-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1KA9

Chain ID: H

ChEMBL ID:

UniProt ID: Q7SIC0

Base Structure: X-ray

Registration Date: 2023-09-23

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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2150824.296398
FMO2-HF: Nuclear repulsion 2077217.36487
FMO2-HF: Total energy -73606.931527
FMO2-MP2: Total energy -73824.160558


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(H:3:MET)


Summations of interaction energy for fragment #1(H:3:MET)
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.
-13.6-6.41112.388-6.014-13.565-0.011
Interaction energy analysis for fragmet #1(H:3:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.002 / q_NPA : -0.006
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].
3H5ALA0-0.0050.0003.796-0.9310.766-0.021-0.682-0.9940.003
4H6LEU0-0.033-0.0095.687-0.065-0.0650.0000.0000.0000.000
5H7LEU0-0.072-0.0479.4590.1000.1000.0000.0000.0000.000
6H8ILE00.012-0.01511.625-0.049-0.0490.0000.0000.0000.000
7H9ASP-1-0.940-0.97614.6470.0630.0630.0000.0000.0000.000
8H10TYR0-0.012-0.05917.573-0.022-0.0220.0000.0000.0000.000
9H11GLY00.0490.03220.823-0.005-0.0050.0000.0000.0000.000
10H12SER0-0.080-0.03021.4050.0090.0090.0000.0000.0000.000
11H13GLY00.0640.02218.3830.0030.0030.0000.0000.0000.000
12H14ASN0-0.052-0.03417.3080.0200.0200.0000.0000.0000.000
13H15LEU00.0670.03315.4720.0170.0170.0000.0000.0000.000
14H16ARG11.0021.02215.414-0.065-0.0650.0000.0000.0000.000
15H17SER00.0350.00115.928-0.001-0.0010.0000.0000.0000.000
16H18ALA00.0660.03213.2240.0180.0180.0000.0000.0000.000
17H19ALA00.0250.02111.5500.0620.0620.0000.0000.0000.000
18H20LYS10.8780.93211.218-0.076-0.0760.0000.0000.0000.000
19H21ALA00.0020.00212.514-0.008-0.0080.0000.0000.0000.000
20H22LEU0-0.003-0.0056.8660.0640.0640.0000.0000.0000.000
21H23GLU-1-0.882-0.9477.7730.0500.0500.0000.0000.0000.000
22H24ALA0-0.062-0.0259.110-0.053-0.0530.0000.0000.0000.000
23H25ALA0-0.038-0.0158.202-0.032-0.0320.0000.0000.0000.000
24H26GLY0-0.026-0.0185.8980.1540.1540.0000.0000.0000.000
25H27PHE0-0.043-0.0142.137-2.484-2.6485.301-1.533-3.6040.005
26H28SER00.0270.0293.8940.2320.674-0.001-0.115-0.3260.000
27H29VAL00.001-0.0155.560-0.230-0.2300.0000.0000.0000.000
28H30ALA0-0.021-0.0048.2550.0210.0210.0000.0000.0000.000
29H31VAL0-0.0060.02511.0090.0220.0220.0000.0000.0000.000
30H32ALA00.005-0.02913.815-0.029-0.0290.0000.0000.0000.000
31H33GLN00.0480.03316.2430.0100.0100.0000.0000.0000.000
32H34ASP-1-0.873-0.93918.424-0.095-0.0950.0000.0000.0000.000
33H35PRO0-0.025-0.00816.889-0.025-0.0250.0000.0000.0000.000
34H36LYS10.8810.94515.9510.1900.1900.0000.0000.0000.000
35H37ALA00.0130.02015.958-0.006-0.0060.0000.0000.0000.000
36H38HIS0-0.034-0.04310.889-0.053-0.0530.0000.0000.0000.000
37H39GLU-1-0.877-0.95011.859-0.283-0.2830.0000.0000.0000.000
38H40GLU-1-0.914-0.9648.617-0.584-0.5840.0000.0000.0000.000
39H41ALA0-0.090-0.0276.845-0.185-0.1850.0000.0000.0000.000
40H42ASP-1-0.826-0.9072.266-5.837-5.3614.635-2.252-2.859-0.016
41H43LEU0-0.066-0.0392.909-1.0530.3710.300-0.381-1.344-0.001
42H44LEU0-0.0070.0104.2230.1900.2480.000-0.021-0.0370.000
43H45VAL0-0.010-0.0177.9900.2260.2260.0000.0000.0000.000
44H46LEU00.0330.03010.197-0.100-0.1000.0000.0000.0000.000
45H47PRO0-0.0050.01813.6960.0520.0520.0000.0000.0000.000
46H48GLY00.1080.05516.246-0.034-0.0340.0000.0000.0000.000
47H49GLN0-0.060-0.05219.9460.0260.0260.0000.0000.0000.000
48H50GLY00.0180.00723.333-0.010-0.0100.0000.0000.0000.000
49H51HIS00.0180.01725.9100.0030.0030.0000.0000.0000.000
50H52PHE00.0790.04823.422-0.001-0.0010.0000.0000.0000.000
51H53GLY00.0370.01025.759-0.006-0.0060.0000.0000.0000.000
52H54GLN0-0.078-0.05226.008-0.009-0.0090.0000.0000.0000.000
53H55VAL00.0210.01121.131-0.005-0.0050.0000.0000.0000.000
54H56MET00.0300.01120.672-0.002-0.0020.0000.0000.0000.000
55H57ARG10.9660.98524.023-0.024-0.0240.0000.0000.0000.000
56H58ALA0-0.0020.00224.635-0.008-0.0080.0000.0000.0000.000
57H59PHE0-0.018-0.01416.449-0.002-0.0020.0000.0000.0000.000
58H60GLN0-0.046-0.02421.037-0.015-0.0150.0000.0000.0000.000
59H61GLU-1-0.978-0.97823.644-0.012-0.0120.0000.0000.0000.000
60H62SER00.0140.00620.083-0.009-0.0090.0000.0000.0000.000
61H63GLY00.0420.01820.854-0.012-0.0120.0000.0000.0000.000
62H64PHE00.011-0.01514.174-0.018-0.0180.0000.0000.0000.000
63H65VAL00.0180.03616.619-0.019-0.0190.0000.0000.0000.000
64H66GLU-1-0.878-0.95017.526-0.104-0.1040.0000.0000.0000.000
65H67ARG10.8090.91911.6710.3310.3310.0000.0000.0000.000
66H68VAL00.0400.01912.575-0.059-0.0590.0000.0000.0000.000
67H69ARG10.9310.97013.2690.0460.0460.0000.0000.0000.000
68H70ARG10.9600.97413.9780.2300.2300.0000.0000.0000.000
69H71HIS0-0.075-0.0325.7880.1810.1810.0000.0000.0000.000
70H72LEU0-0.023-0.02210.186-0.065-0.0650.0000.0000.0000.000
71H73GLU-1-0.951-0.95912.067-0.174-0.1740.0000.0000.0000.000
72H74ARG10.8910.94811.1710.5040.5040.0000.0000.0000.000
73H75GLY00.0320.02410.446-0.077-0.0770.0000.0000.0000.000
74H76LEU0-0.037-0.0126.007-0.123-0.1230.0000.0000.0000.000
75H77PRO0-0.021-0.0082.254-0.0680.2281.099-0.232-1.163-0.001
76H78PHE00.0570.0304.834-0.074-0.028-0.001-0.004-0.0410.000
77H79LEU00.003-0.0087.7200.2180.2180.0000.0000.0000.000
78H80GLY00.0140.0139.565-0.121-0.1210.0000.0000.0000.000
79H81ILE0-0.006-0.02212.1390.0200.0200.0000.0000.0000.000
80H82CYS0-0.0140.00115.576-0.055-0.0550.0000.0000.0000.000
81H83VAL00.0110.02319.357-0.008-0.0080.0000.0000.0000.000
82H84GLY00.0170.01016.446-0.021-0.0210.0000.0000.0000.000
83H85MET0-0.064-0.02116.442-0.011-0.0110.0000.0000.0000.000
84H86GLN0-0.004-0.02117.632-0.030-0.0300.0000.0000.0000.000
85H87VAL00.0280.01717.947-0.017-0.0170.0000.0000.0000.000
86H88LEU0-0.039-0.00814.462-0.021-0.0210.0000.0000.0000.000
87H89TYR0-0.025-0.01318.761-0.003-0.0030.0000.0000.0000.000
88H90GLU-1-0.852-0.93022.2880.0100.0100.0000.0000.0000.000
89H91GLY00.0600.03925.196-0.008-0.0080.0000.0000.0000.000
90H92SER00.0040.00126.6050.0090.0090.0000.0000.0000.000
91H93GLU-1-0.763-0.86928.5790.0440.0440.0000.0000.0000.000
92H94GLU-1-0.937-0.97128.0280.0660.0660.0000.0000.0000.000
93H95ALA0-0.066-0.03829.234-0.003-0.0030.0000.0000.0000.000
94H96PRO00.006-0.00730.868-0.002-0.0020.0000.0000.0000.000
95H97GLY00.0440.03633.020-0.001-0.0010.0000.0000.0000.000
96H98VAL0-0.081-0.03126.908-0.004-0.0040.0000.0000.0000.000
97H99ARG10.9630.98925.5420.0160.0160.0000.0000.0000.000
98H100GLY00.0160.00323.3940.0000.0000.0000.0000.0000.000
99H101LEU0-0.065-0.05316.751-0.012-0.0120.0000.0000.0000.000
100H102GLY0-0.020-0.00820.785-0.014-0.0140.0000.0000.0000.000
101H103LEU0-0.043-0.01515.579-0.011-0.0110.0000.0000.0000.000
102H104VAL0-0.037-0.01918.6500.0020.0020.0000.0000.0000.000
103H105PRO00.0010.01521.087-0.003-0.0030.0000.0000.0000.000
104H106GLY00.020-0.00124.9080.0110.0110.0000.0000.0000.000
105H107GLU-1-0.935-0.97326.2490.0350.0350.0000.0000.0000.000
106H108VAL0-0.014-0.01624.3910.0050.0050.0000.0000.0000.000
107H109ARG10.9200.96927.254-0.055-0.0550.0000.0000.0000.000
108H110ARG10.9320.97729.819-0.049-0.0490.0000.0000.0000.000
109H111PHE00.0090.00328.248-0.003-0.0030.0000.0000.0000.000
110H112ARG10.7960.86633.360-0.053-0.0530.0000.0000.0000.000
111H113ALA00.0620.02436.451-0.003-0.0030.0000.0000.0000.000
112H114GLY00.0510.04636.1240.0040.0040.0000.0000.0000.000
113H115ARG10.9540.97435.876-0.061-0.0610.0000.0000.0000.000
114H116VAL00.0170.07333.0810.0050.0050.0000.0000.0000.000
115H117PRO0-0.046-0.05529.740-0.005-0.0050.0000.0000.0000.000
116H118GLN00.0210.04126.592-0.001-0.0010.0000.0000.0000.000
117H119MET0-0.048-0.04428.4870.0110.0110.0000.0000.0000.000
118H120GLY00.0090.01127.558-0.008-0.0080.0000.0000.0000.000
119H121TRP0-0.065-0.03422.3630.0180.0180.0000.0000.0000.000
120H122ASN00.0280.00925.639-0.013-0.0130.0000.0000.0000.000
121H123ALA0-0.0060.00924.8590.0180.0180.0000.0000.0000.000
122H124LEU0-0.041-0.01520.770-0.004-0.0040.0000.0000.0000.000
123H125GLU-1-0.930-0.94923.8190.1450.1450.0000.0000.0000.000
124H126PHE0-0.005-0.01717.4380.0250.0250.0000.0000.0000.000
125H127GLY00.1080.06119.814-0.021-0.0210.0000.0000.0000.000
126H128GLY0-0.005-0.02317.3980.0350.0350.0000.0000.0000.000
127H129ALA0-0.008-0.01713.219-0.013-0.0130.0000.0000.0000.000
128H130PHE00.005-0.00310.5820.0140.0140.0000.0000.0000.000
129H131ALA00.0280.03315.996-0.015-0.0150.0000.0000.0000.000
130H132PRO0-0.026-0.02216.876-0.016-0.0160.0000.0000.0000.000
131H133LEU0-0.067-0.02515.014-0.008-0.0080.0000.0000.0000.000
132H134THR00.0480.03519.3660.0000.0000.0000.0000.0000.000
133H135GLY00.0010.00822.695-0.010-0.0100.0000.0000.0000.000
134H136ARG10.8740.94218.975-0.220-0.2200.0000.0000.0000.000
135H137HIS00.0340.00823.3600.0100.0100.0000.0000.0000.000
136H138PHE0-0.037-0.03417.3350.0230.0230.0000.0000.0000.000
137H139TYR00.0030.00321.614-0.025-0.0250.0000.0000.0000.000
138H140PHE00.013-0.00122.0650.0250.0250.0000.0000.0000.000
139H141ALA00.0410.00424.421-0.013-0.0130.0000.0000.0000.000
140H142ASN0-0.024-0.00324.6780.0010.0010.0000.0000.0000.000
141H143SER00.0550.02026.779-0.006-0.0060.0000.0000.0000.000
142H144TYR00.0140.01127.276-0.007-0.0070.0000.0000.0000.000
143H145TYR00.0000.00225.6850.0120.0120.0000.0000.0000.000
144H146GLY00.0820.04723.911-0.012-0.0120.0000.0000.0000.000
145H147PRO0-0.0010.00224.9800.0060.0060.0000.0000.0000.000
146H148LEU00.0130.00125.1660.0070.0070.0000.0000.0000.000
147H149THR00.0280.01922.103-0.010-0.0100.0000.0000.0000.000
148H150PRO0-0.010-0.01422.6750.0100.0100.0000.0000.0000.000
149H151TYR00.0740.02918.007-0.005-0.0050.0000.0000.0000.000
150H152SER0-0.015-0.01918.6530.0320.0320.0000.0000.0000.000
151H153LEU0-0.0230.00615.594-0.013-0.0130.0000.0000.0000.000
152H154GLY00.0240.01319.2660.0020.0020.0000.0000.0000.000
153H155LYS10.8980.92420.098-0.144-0.1440.0000.0000.0000.000
154H156GLY00.0680.02623.7260.0080.0080.0000.0000.0000.000
155H157GLU-1-0.909-0.95226.3590.0810.0810.0000.0000.0000.000
156H158TYR0-0.020-0.05729.5990.0060.0060.0000.0000.0000.000
157H159GLU-1-0.928-0.96131.3570.0640.0640.0000.0000.0000.000
158H160GLY00.0240.02234.322-0.005-0.0050.0000.0000.0000.000
159H161THR0-0.074-0.03030.939-0.005-0.0050.0000.0000.0000.000
160H162PRO0-0.009-0.01129.8320.0090.0090.0000.0000.0000.000
161H163PHE0-0.052-0.02323.901-0.002-0.0020.0000.0000.0000.000
162H164THR0-0.0050.01520.6200.0060.0060.0000.0000.0000.000
163H165ALA0-0.021-0.00721.0240.0040.0040.0000.0000.0000.000
164H166LEU0-0.047-0.02013.7160.0350.0350.0000.0000.0000.000
165H167LEU00.0060.01416.106-0.026-0.0260.0000.0000.0000.000
166H168ALA0-0.037-0.04113.8760.0790.0790.0000.0000.0000.000
167H169LYS10.8830.95313.314-0.056-0.0560.0000.0000.0000.000
168H170GLU-1-0.865-0.94512.2310.0080.0080.0000.0000.0000.000
169H171ASN00.0000.0066.0320.1830.1830.0000.0000.0000.000
170H172LEU00.0210.0337.8440.0050.0050.0000.0000.0000.000
171H173LEU0-0.038-0.0228.2320.0210.0210.0000.0000.0000.000
172H174ALA00.0160.00011.3420.0140.0140.0000.0000.0000.000
173H175PRO0-0.0290.00913.065-0.053-0.0530.0000.0000.0000.000
174H176GLN00.0500.00316.092-0.032-0.0320.0000.0000.0000.000
175H177PHE0-0.0120.00015.831-0.022-0.0220.0000.0000.0000.000
176H178HIS00.0520.01417.6310.0330.0330.0000.0000.0000.000
177H179PRO00.0090.01313.305-0.031-0.0310.0000.0000.0000.000
178H180GLU-1-0.871-0.95314.7680.2890.2890.0000.0000.0000.000
179H181LYS10.8270.93416.167-0.221-0.2210.0000.0000.0000.000
180H182SER00.0310.01118.238-0.027-0.0270.0000.0000.0000.000
181H183GLY00.0150.01019.878-0.001-0.0010.0000.0000.0000.000
182H184LYS10.9750.96517.837-0.135-0.1350.0000.0000.0000.000
183H185ALA00.0230.03017.0670.0260.0260.0000.0000.0000.000
184H186GLY00.0520.01716.2490.0390.0390.0000.0000.0000.000
185H187LEU0-0.012-0.00512.6450.0780.0780.0000.0000.0000.000
186H188ALA0-0.023-0.00712.2770.0680.0680.0000.0000.0000.000
187H189PHE00.0460.01411.8920.0780.0780.0000.0000.0000.000
188H190LEU00.0170.0039.1040.1430.1430.0000.0000.0000.000
189H191ALA00.0020.0098.0390.3760.3760.0000.0000.0000.000
190H192LEU0-0.034-0.0287.8770.1210.1210.0000.0000.0000.000
191H193ALA00.0100.0037.6960.0030.0030.0000.0000.0000.000
192H194ARG10.9270.9732.980-0.7290.5840.158-0.279-1.1920.000
193H195ARG10.8850.9533.829-0.587-0.0350.010-0.178-0.385-0.001
194H196TYR0-0.053-0.0216.407-0.312-0.3120.0000.0000.0000.000
195H197PHE00.0420.0213.364-2.457-1.4080.908-0.337-1.6200.000