Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 3JLZL

Calculation Name: 5KBC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5KBC

Chain ID: A

ChEMBL ID:

UniProt ID: G4NNC6

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 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 196
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2237693.090225
FMO2-HF: Nuclear repulsion 2159492.941897
FMO2-HF: Total energy -78200.148328
FMO2-MP2: Total energy -78427.410442


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:6:PRO)


Summations of interaction energy for fragment #1(A:6:PRO)
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.
0.1121.781-0.01-0.893-0.7670.004
Interaction energy analysis for fragmet #1(A:6:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.032 / 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].
3A8LYS10.9620.9653.8870.4832.152-0.010-0.893-0.7670.004
4A9THR0-0.015-0.0036.5740.2750.2750.0000.0000.0000.000
5A10HIS00.0220.0168.498-0.147-0.1470.0000.0000.0000.000
6A11ILE00.0310.01610.738-0.025-0.0250.0000.0000.0000.000
7A12PRO0-0.013-0.02514.5210.0500.0500.0000.0000.0000.000
8A13THR0-0.031-0.01817.863-0.034-0.0340.0000.0000.0000.000
9A14THR00.0480.02518.7570.0060.0060.0000.0000.0000.000
10A15ALA00.0170.00820.7400.0050.0050.0000.0000.0000.000
11A16LYS10.9861.01522.0290.0410.0410.0000.0000.0000.000
12A17TYR0-0.036-0.03416.179-0.002-0.0020.0000.0000.0000.000
13A18PHE0-0.029-0.00120.7920.0190.0190.0000.0000.0000.000
14A19PRO00.0090.01422.846-0.006-0.0060.0000.0000.0000.000
15A20THR00.0220.00924.733-0.011-0.0110.0000.0000.0000.000
16A21ILE0-0.018-0.00326.5490.0080.0080.0000.0000.0000.000
17A22GLY00.1050.04029.305-0.007-0.0070.0000.0000.0000.000
18A23ASP-1-0.853-0.90029.1360.0080.0080.0000.0000.0000.000
19A24PRO0-0.052-0.02425.284-0.003-0.0030.0000.0000.0000.000
20A25TYR0-0.088-0.07227.296-0.010-0.0100.0000.0000.0000.000
21A26ALA00.0230.03129.614-0.002-0.0020.0000.0000.0000.000
22A27PRO0-0.044-0.01731.914-0.005-0.0050.0000.0000.0000.000
23A28ILE0-0.0070.00034.051-0.003-0.0030.0000.0000.0000.000
24A29ASN0-0.013-0.01028.6860.0040.0040.0000.0000.0000.000
25A30ILE00.0260.01431.809-0.003-0.0030.0000.0000.0000.000
26A31THR0-0.036-0.01728.2440.0010.0010.0000.0000.0000.000
27A32VAL00.0360.02330.917-0.003-0.0030.0000.0000.0000.000
28A33PHE0-0.018-0.01227.3370.0040.0040.0000.0000.0000.000
29A34GLU-1-0.747-0.90631.1680.0330.0330.0000.0000.0000.000
30A35GLU-1-0.690-0.81831.1690.0590.0590.0000.0000.0000.000
31A36PRO0-0.031-0.02030.899-0.001-0.0010.0000.0000.0000.000
32A37SER0-0.027-0.04133.7270.0010.0010.0000.0000.0000.000
33A38CYS0-0.055-0.00536.562-0.005-0.0050.0000.0000.0000.000
34A39SER00.001-0.00338.2980.0010.0010.0000.0000.0000.000
35A40ALA00.0600.03741.3470.0010.0010.0000.0000.0000.000
36A42GLU-1-0.978-0.96739.3420.0390.0390.0000.0000.0000.000
37A43GLU-1-0.904-0.93541.5600.0240.0240.0000.0000.0000.000
38A44PHE00.009-0.00336.3410.0000.0000.0000.0000.0000.000
39A45SER0-0.005-0.03237.7890.0000.0000.0000.0000.0000.000
40A46SER0-0.085-0.05739.3660.0020.0020.0000.0000.0000.000
41A47GLU-1-0.922-0.95242.7680.0240.0240.0000.0000.0000.000
42A48VAL0-0.029-0.01040.975-0.001-0.0010.0000.0000.0000.000
43A49PHE00.009-0.00232.867-0.001-0.0010.0000.0000.0000.000
44A50PRO00.001-0.00838.676-0.001-0.0010.0000.0000.0000.000
45A51LEU0-0.0080.00840.525-0.001-0.0010.0000.0000.0000.000
46A52ILE00.000-0.00136.825-0.002-0.0020.0000.0000.0000.000
47A53LYS10.8250.88134.808-0.036-0.0360.0000.0000.0000.000
48A54LYS10.9450.98737.909-0.021-0.0210.0000.0000.0000.000
49A55HIS0-0.003-0.00641.108-0.001-0.0010.0000.0000.0000.000
50A56PHE00.0060.01338.285-0.003-0.0030.0000.0000.0000.000
51A57VAL0-0.0170.01033.276-0.002-0.0020.0000.0000.0000.000
52A58ASP-1-0.844-0.91235.6770.0290.0290.0000.0000.0000.000
53A59THR0-0.065-0.04137.7130.0000.0000.0000.0000.0000.000
54A60GLY00.0240.02135.267-0.002-0.0020.0000.0000.0000.000
55A61GLU-1-0.873-0.91735.852-0.008-0.0080.0000.0000.0000.000
56A62ALA0-0.037-0.03434.291-0.005-0.0050.0000.0000.0000.000
57A63SER0-0.011-0.00829.0770.0030.0030.0000.0000.0000.000
58A64LEU0-0.003-0.00330.659-0.003-0.0030.0000.0000.0000.000
59A65THR0-0.055-0.03126.1480.0040.0040.0000.0000.0000.000
60A66LEU00.0210.02028.114-0.003-0.0030.0000.0000.0000.000
61A67VAL0-0.0070.00725.1540.0110.0110.0000.0000.0000.000
62A68PRO0-0.0410.00524.963-0.002-0.0020.0000.0000.0000.000
63A69VAL00.0170.00126.2620.0020.0020.0000.0000.0000.000
64A70CYS0-0.102-0.05628.2110.0070.0070.0000.0000.0000.000
65A71PHE00.0370.02229.7400.0000.0000.0000.0000.0000.000
66A72ILE00.0030.01732.557-0.002-0.0020.0000.0000.0000.000
67A73ARG10.9210.94734.417-0.046-0.0460.0000.0000.0000.000
68A74GLY00.0770.02534.202-0.003-0.0030.0000.0000.0000.000
69A75SER0-0.018-0.02832.2230.0050.0050.0000.0000.0000.000
70A76MET00.0190.03326.1260.0110.0110.0000.0000.0000.000
71A77PRO00.004-0.00628.2520.0100.0100.0000.0000.0000.000
72A78ALA00.0860.03429.0640.0090.0090.0000.0000.0000.000
73A79ALA00.0390.02426.9960.0040.0040.0000.0000.0000.000
74A80GLN0-0.045-0.03823.0130.0260.0260.0000.0000.0000.000
75A81ALA00.0110.00224.8300.0140.0140.0000.0000.0000.000
76A82LEU00.0350.03126.7740.0090.0090.0000.0000.0000.000
77A83LEU0-0.0080.00021.2000.0040.0040.0000.0000.0000.000
78A84CYS0-0.119-0.07221.9930.0370.0370.0000.0000.0000.000
79A85VAL0-0.0140.00823.4620.0130.0130.0000.0000.0000.000
80A86TYR00.0150.00420.2680.0070.0070.0000.0000.0000.000
81A87HIS0-0.019-0.01517.6660.0150.0150.0000.0000.0000.000
82A88HIS0-0.056-0.03220.2980.0460.0460.0000.0000.0000.000
83A89ASP-1-0.831-0.91821.4390.2350.2350.0000.0000.0000.000
84A90PRO0-0.033-0.03816.5970.0020.0020.0000.0000.0000.000
85A91LYS10.8860.96216.445-0.186-0.1860.0000.0000.0000.000
86A92ARG10.9490.95817.547-0.131-0.1310.0000.0000.0000.000
87A93PRO00.0460.03418.027-0.001-0.0010.0000.0000.0000.000
88A94ASP-1-0.770-0.89621.1670.1240.1240.0000.0000.0000.000
89A95PRO0-0.032-0.01523.9470.0010.0010.0000.0000.0000.000
90A96GLU-1-0.875-0.93526.5100.0580.0580.0000.0000.0000.000
91A97ALA00.0090.02727.883-0.004-0.0040.0000.0000.0000.000
92A98TYR0-0.099-0.08426.3110.0030.0030.0000.0000.0000.000
93A99MET00.0050.00528.445-0.004-0.0040.0000.0000.0000.000
94A100GLU-1-0.758-0.85531.3160.0650.0650.0000.0000.0000.000
95A101TYR0-0.040-0.04729.4490.0010.0010.0000.0000.0000.000
96A102PHE0-0.002-0.01629.7980.0000.0000.0000.0000.0000.000
97A103HIS00.1050.07332.709-0.003-0.0030.0000.0000.0000.000
98A104ARG10.7050.82635.531-0.079-0.0790.0000.0000.0000.000
99A105ILE0-0.067-0.03631.638-0.001-0.0010.0000.0000.0000.000
100A106LEU0-0.0210.00034.969-0.002-0.0020.0000.0000.0000.000
101A107THR00.019-0.00737.625-0.002-0.0020.0000.0000.0000.000
102A108TYR0-0.046-0.00139.004-0.001-0.0010.0000.0000.0000.000
103A109LYS11.0121.00440.905-0.038-0.0380.0000.0000.0000.000
104A110LYS10.8370.90537.576-0.051-0.0510.0000.0000.0000.000
105A111THR00.013-0.00142.4590.0000.0000.0000.0000.0000.000
106A112LYS10.8560.94039.871-0.070-0.0700.0000.0000.0000.000
107A113GLY00.0550.03542.1130.0010.0010.0000.0000.0000.000
108A114SER0-0.015-0.03337.3380.0020.0020.0000.0000.0000.000
109A115HIS0-0.0030.01337.2380.0070.0070.0000.0000.0000.000
110A116TRP00.007-0.01235.4030.0030.0030.0000.0000.0000.000
111A117ALA00.0310.03233.7380.0020.0020.0000.0000.0000.000
112A118THR0-0.047-0.05734.1240.0050.0050.0000.0000.0000.000
113A119PRO00.024-0.00331.8580.0000.0000.0000.0000.0000.000
114A120GLU-1-0.808-0.89433.5270.0960.0960.0000.0000.0000.000
115A121VAL0-0.0250.00636.631-0.001-0.0010.0000.0000.0000.000
116A122LEU00.0190.01231.104-0.001-0.0010.0000.0000.0000.000
117A123ALA00.0020.00833.2520.0020.0020.0000.0000.0000.000
118A124LYS10.7990.89234.140-0.079-0.0790.0000.0000.0000.000
119A125LEU0-0.0010.00235.607-0.004-0.0040.0000.0000.0000.000
120A126ALA00.0160.00831.780-0.001-0.0010.0000.0000.0000.000
121A127GLU-1-0.857-0.91133.6820.0890.0890.0000.0000.0000.000
122A128LYS10.9370.96836.258-0.080-0.0800.0000.0000.0000.000
123A129ILE00.0240.03932.032-0.006-0.0060.0000.0000.0000.000
124A130PRO0-0.0050.01033.3890.0050.0050.0000.0000.0000.000
125A131THR0-0.028-0.01629.0610.0060.0060.0000.0000.0000.000
126A132HIS0-0.063-0.03027.805-0.003-0.0030.0000.0000.0000.000
127A133SER00.007-0.02123.152-0.016-0.0160.0000.0000.0000.000
128A134GLY00.0400.05025.035-0.002-0.0020.0000.0000.0000.000
129A135ARG10.8320.90723.941-0.209-0.2090.0000.0000.0000.000
130A136GLU-1-0.883-0.93327.5240.1040.1040.0000.0000.0000.000
131A137ILE0-0.0130.00127.9790.0180.0180.0000.0000.0000.000
132A138ASN00.0050.00328.780-0.010-0.0100.0000.0000.0000.000
133A139PRO00.0800.02729.5680.0100.0100.0000.0000.0000.000
134A140LYS10.9700.98530.664-0.134-0.1340.0000.0000.0000.000
135A141GLY00.0120.01626.5540.0070.0070.0000.0000.0000.000
136A142LEU00.0350.03125.8760.0140.0140.0000.0000.0000.000
137A143ILE00.0320.00827.4120.0020.0020.0000.0000.0000.000
138A144GLN0-0.035-0.01123.7950.0160.0160.0000.0000.0000.000
139A146ILE00.0210.01123.9360.0030.0030.0000.0000.0000.000
140A147ASN0-0.044-0.03726.295-0.009-0.0090.0000.0000.0000.000
141A148SER0-0.057-0.02021.1510.0120.0120.0000.0000.0000.000
142A149GLN0-0.050-0.02021.8660.0080.0080.0000.0000.0000.000
143A150ARG10.9750.99217.436-0.385-0.3850.0000.0000.0000.000
144A151PHE00.0350.00217.8290.0160.0160.0000.0000.0000.000
145A152THR00.0060.00520.254-0.024-0.0240.0000.0000.0000.000
146A153GLU-1-0.824-0.88617.7360.0890.0890.0000.0000.0000.000
147A154GLN0-0.019-0.00616.984-0.010-0.0100.0000.0000.0000.000
148A155LEU00.0520.01319.258-0.021-0.0210.0000.0000.0000.000
149A156LYS10.8430.91322.006-0.111-0.1110.0000.0000.0000.000
150A157LYS10.8690.93114.828-0.085-0.0850.0000.0000.0000.000
151A158ASN0-0.0040.00021.211-0.014-0.0140.0000.0000.0000.000
152A159ASN00.009-0.00523.633-0.008-0.0080.0000.0000.0000.000
153A160ILE0-0.017-0.00522.686-0.007-0.0070.0000.0000.0000.000
154A161TYR00.000-0.00223.078-0.003-0.0030.0000.0000.0000.000
155A162GLY00.0540.01925.135-0.005-0.0050.0000.0000.0000.000
156A163SER00.007-0.00628.463-0.004-0.0040.0000.0000.0000.000
157A164GLN0-0.025-0.01726.4210.0020.0020.0000.0000.0000.000
158A165ILE0-0.050-0.02726.808-0.005-0.0050.0000.0000.0000.000
159A166MET0-0.0210.00630.1830.0010.0010.0000.0000.0000.000
160A167GLY00.0030.01632.4290.0010.0010.0000.0000.0000.000
161A168GLY0-0.047-0.02532.9950.0000.0000.0000.0000.0000.000
162A169GLN0-0.084-0.04434.2810.0030.0030.0000.0000.0000.000
163A170LEU0-0.057-0.04730.8730.0020.0020.0000.0000.0000.000
164A171ALA00.0100.02734.9230.0040.0040.0000.0000.0000.000
165A172THR0-0.087-0.03033.7090.0020.0020.0000.0000.0000.000
166A173PRO00.0630.01636.3410.0010.0010.0000.0000.0000.000
167A174THR0-0.002-0.02534.816-0.003-0.0030.0000.0000.0000.000
168A175ALA0-0.036-0.01634.4550.0030.0030.0000.0000.0000.000
169A176VAL0-0.010-0.00132.208-0.003-0.0030.0000.0000.0000.000
170A177VAL00.0200.01433.5610.0010.0010.0000.0000.0000.000
171A178GLY00.0400.00433.518-0.003-0.0030.0000.0000.0000.000
172A179ASP-1-0.997-1.01132.691-0.046-0.0460.0000.0000.0000.000
173A180TYR0-0.030-0.00734.7120.0000.0000.0000.0000.0000.000
174A181LEU0-0.023-0.00234.9500.0030.0030.0000.0000.0000.000
175A182ILE0-0.018-0.00737.190-0.001-0.0010.0000.0000.0000.000
176A183GLU-1-0.852-0.92738.4410.0040.0040.0000.0000.0000.000
177A184ASP-1-0.892-0.95340.0480.0160.0160.0000.0000.0000.000
178A185PRO0-0.0600.00138.5150.0000.0000.0000.0000.0000.000
179A186THR00.016-0.04541.8520.0030.0030.0000.0000.0000.000
180A187PHE00.007-0.02042.744-0.001-0.0010.0000.0000.0000.000
181A188ASP-1-0.835-0.90344.636-0.002-0.0020.0000.0000.0000.000
182A189GLU-1-0.822-0.88643.9380.0000.0000.0000.0000.0000.000
183A190ILE00.0040.00239.011-0.003-0.0030.0000.0000.0000.000
184A191GLU-1-0.890-0.94242.0120.0010.0010.0000.0000.0000.000
185A192ARG10.8650.94144.3050.0020.0020.0000.0000.0000.000
186A193VAL0-0.0050.00539.818-0.003-0.0030.0000.0000.0000.000
187A194ILE0-0.0130.00337.726-0.003-0.0030.0000.0000.0000.000
188A195THR0-0.035-0.04641.266-0.003-0.0030.0000.0000.0000.000
189A196GLN0-0.025-0.00544.160-0.001-0.0010.0000.0000.0000.000
190A197LEU0-0.013-0.01337.421-0.003-0.0030.0000.0000.0000.000
191A198ARG10.8340.89341.2150.0040.0040.0000.0000.0000.000
192A199HIS0-0.036-0.01342.1300.0000.0000.0000.0000.0000.000
193A200LEU0-0.052-0.03140.636-0.001-0.0010.0000.0000.0000.000
194A201GLN00.000-0.00538.103-0.004-0.0040.0000.0000.0000.000
195A202ALA0-0.0370.01341.230-0.001-0.0010.0000.0000.0000.000
196A203ILE0-0.067-0.03742.2520.0000.0000.0000.0000.0000.000