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: 3JKVL

Calculation Name: 4XCM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4XCM

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SLM7

Base Structure: X-ray

Registration Date: 2023-09-22

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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1621414.611675
FMO2-HF: Nuclear repulsion 1555048.118484
FMO2-HF: Total energy -66366.49319
FMO2-MP2: Total energy -66563.435796


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:17:ALA)


Summations of interaction energy for fragment #1(A:17:ALA)
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.
-0.9952.6260.254-1.706-2.168-0.001
Interaction energy analysis for fragmet #1(A:17:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / 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].
3A19TYR0-0.063-0.0683.7950.7502.712-0.033-1.110-0.8190.001
4A20THR0-0.019-0.0026.654-0.346-0.3460.0000.0000.0000.000
5A21VAL0-0.042-0.01310.3690.0560.0560.0000.0000.0000.000
6A22ALA00.0420.01512.9380.0210.0210.0000.0000.0000.000
7A23PRO0-0.010-0.01715.440-0.044-0.0440.0000.0000.0000.000
8A24GLY00.0280.00919.0210.0110.0110.0000.0000.0000.000
9A25ASP-1-0.827-0.84913.4880.1190.1190.0000.0000.0000.000
10A26THR00.011-0.00715.544-0.029-0.0290.0000.0000.0000.000
11A27LEU00.0820.02312.974-0.005-0.0050.0000.0000.0000.000
12A28TYR0-0.0010.00113.843-0.036-0.0360.0000.0000.0000.000
13A29SER00.0120.00314.821-0.028-0.0280.0000.0000.0000.000
14A30ILE00.0350.0258.9630.0190.0190.0000.0000.0000.000
15A31ALA00.0050.0009.953-0.051-0.0510.0000.0000.0000.000
16A32ARG10.9190.96811.3870.0100.0100.0000.0000.0000.000
17A33ARG10.9020.9689.221-0.352-0.3520.0000.0000.0000.000
18A34TYR0-0.055-0.0455.7510.2600.2600.0000.0000.0000.000
19A35GLY0-0.0080.0188.479-0.155-0.1550.0000.0000.0000.000
20A36THR00.0240.0258.8730.0000.0000.0000.0000.0000.000
21A37THR00.008-0.01311.3800.0960.0960.0000.0000.0000.000
22A38VAL00.027-0.00812.957-0.062-0.0620.0000.0000.0000.000
23A39GLU-1-0.914-0.94614.761-0.318-0.3180.0000.0000.0000.000
24A40GLU-1-0.806-0.88510.323-0.866-0.8660.0000.0000.0000.000
25A41LEU00.0130.0148.261-0.099-0.0990.0000.0000.0000.000
26A42MET0-0.0240.00011.276-0.029-0.0290.0000.0000.0000.000
27A43ARG10.8610.90311.3910.6320.6320.0000.0000.0000.000
28A44LEU0-0.072-0.0336.3220.0380.0380.0000.0000.0000.000
29A45ASN0-0.074-0.0448.537-0.126-0.1260.0000.0000.0000.000
30A46GLY0-0.0040.01611.4450.0740.0740.0000.0000.0000.000
31A47LEU0-0.045-0.01813.8860.0530.0530.0000.0000.0000.000
32A48GLU-1-0.906-0.94916.499-0.197-0.1970.0000.0000.0000.000
33A49SER0-0.051-0.03219.3440.0320.0320.0000.0000.0000.000
34A50PHE00.011-0.01918.667-0.024-0.0240.0000.0000.0000.000
35A51LEU0-0.046-0.01419.1750.0130.0130.0000.0000.0000.000
36A52LEU00.0430.01213.842-0.029-0.0290.0000.0000.0000.000
37A53GLN0-0.0230.00417.7900.0160.0160.0000.0000.0000.000
38A54PRO00.021-0.00616.653-0.007-0.0070.0000.0000.0000.000
39A55GLY0-0.0100.00114.645-0.006-0.0060.0000.0000.0000.000
40A56GLN00.0020.01113.0870.0350.0350.0000.0000.0000.000
41A57VAL0-0.010-0.0117.9140.0430.0430.0000.0000.0000.000
42A58LEU0-0.033-0.0138.545-0.073-0.0730.0000.0000.0000.000
43A59LYS10.9720.9655.0590.7440.7440.0000.0000.0000.000
44A60LEU0-0.009-0.0042.629-0.3130.8880.283-0.487-0.996-0.001
45A61PRO0-0.0140.0083.857-0.934-0.4760.004-0.109-0.353-0.001
46A117PRO00.009-0.0118.9500.0590.0590.0000.0000.0000.000
47A118PRO0-0.065-0.02712.153-0.060-0.0600.0000.0000.0000.000
48A119PRO00.0370.01513.0140.0020.0020.0000.0000.0000.000
49A120PRO00.0210.00816.2810.0140.0140.0000.0000.0000.000
50A121GLU-1-0.907-0.95218.8100.0080.0080.0000.0000.0000.000
51A122PRO0-0.073-0.03320.8820.0020.0020.0000.0000.0000.000
52A123GLU-1-0.821-0.89224.1850.0300.0300.0000.0000.0000.000
53A124ALA0-0.040-0.04026.230-0.009-0.0090.0000.0000.0000.000
54A125LEU0-0.0080.00228.0360.0060.0060.0000.0000.0000.000
55A126ASP-1-0.825-0.91929.1460.0260.0260.0000.0000.0000.000
56A127PRO0-0.030-0.02628.958-0.003-0.0030.0000.0000.0000.000
57A128GLU-1-0.949-0.96131.9400.0230.0230.0000.0000.0000.000
58A129SER0-0.046-0.02233.3640.0020.0020.0000.0000.0000.000
59A130PRO00.012-0.00435.185-0.004-0.0040.0000.0000.0000.000
60A131LEU00.0490.02836.565-0.002-0.0020.0000.0000.0000.000
61A132LEU00.0350.02032.502-0.003-0.0030.0000.0000.0000.000
62A133ARG10.9920.98436.566-0.016-0.0160.0000.0000.0000.000
63A134ALA00.0140.02038.666-0.002-0.0020.0000.0000.0000.000
64A135VAL0-0.008-0.01138.181-0.002-0.0020.0000.0000.0000.000
65A136LEU0-0.040-0.04134.987-0.003-0.0030.0000.0000.0000.000
66A137ARG10.8430.94039.427-0.006-0.0060.0000.0000.0000.000
67A138TYR0-0.024-0.02242.948-0.002-0.0020.0000.0000.0000.000
68A139LEU0-0.0040.01837.133-0.002-0.0020.0000.0000.0000.000
69A140GLY0-0.0050.00441.452-0.001-0.0010.0000.0000.0000.000
70A141VAL0-0.019-0.02643.269-0.001-0.0010.0000.0000.0000.000
71A142PRO0-0.074-0.03846.5930.0000.0000.0000.0000.0000.000
72A143TYR00.009-0.00248.1670.0010.0010.0000.0000.0000.000
73A144LYS10.9370.96050.0630.0120.0120.0000.0000.0000.000
74A145TYR00.009-0.00853.5780.0010.0010.0000.0000.0000.000
75A146GLY00.008-0.00655.2690.0010.0010.0000.0000.0000.000
76A147ALA0-0.033-0.01158.357-0.001-0.0010.0000.0000.0000.000
77A148ASN0-0.004-0.00859.650-0.001-0.0010.0000.0000.0000.000
78A149SER0-0.052-0.02655.5230.0000.0000.0000.0000.0000.000
79A150PRO00.0510.02855.870-0.001-0.0010.0000.0000.0000.000
80A151LEU00.1010.03848.2180.0010.0010.0000.0000.0000.000
81A152ALA0-0.014-0.01051.1220.0000.0000.0000.0000.0000.000
82A153LEU0-0.052-0.02052.4790.0010.0010.0000.0000.0000.000
83A154ASP-1-0.746-0.85150.948-0.009-0.0090.0000.0000.0000.000
84A155CYS0-0.074-0.00747.0060.0000.0000.0000.0000.0000.000
85A156SER00.009-0.00547.4540.0000.0000.0000.0000.0000.000
86A157ALA0-0.013-0.00149.5400.0010.0010.0000.0000.0000.000
87A158PHE0-0.007-0.00342.3010.0010.0010.0000.0000.0000.000
88A159VAL00.0090.00143.9320.0010.0010.0000.0000.0000.000
89A160ALA00.009-0.00446.1400.0020.0020.0000.0000.0000.000
90A161GLN0-0.0160.00248.1790.0010.0010.0000.0000.0000.000
91A162VAL00.0120.00641.9280.0010.0010.0000.0000.0000.000
92A163TYR0-0.034-0.04540.8270.0020.0020.0000.0000.0000.000
93A164ALA00.0260.02645.6080.0020.0020.0000.0000.0000.000
94A165GLU-1-0.873-0.92545.1880.0040.0040.0000.0000.0000.000
95A166LEU0-0.076-0.05140.7270.0010.0010.0000.0000.0000.000
96A167GLY0-0.0220.00945.0890.0020.0020.0000.0000.0000.000
97A168VAL0-0.039-0.01644.7010.0010.0010.0000.0000.0000.000
98A169ALA0-0.0040.00247.909-0.001-0.0010.0000.0000.0000.000
99A170LEU00.024-0.01046.2450.0000.0000.0000.0000.0000.000
100A171PRO0-0.0200.00350.692-0.001-0.0010.0000.0000.0000.000
101A172ARG11.0031.00652.0400.0000.0000.0000.0000.0000.000
102A173THR0-0.016-0.01052.723-0.001-0.0010.0000.0000.0000.000
103A174THR00.0800.02548.7750.0010.0010.0000.0000.0000.000
104A175LYS10.9750.99750.5880.0060.0060.0000.0000.0000.000
105A176GLU-1-0.851-0.92252.5510.0000.0000.0000.0000.0000.000
106A177GLN0-0.027-0.02648.1480.0000.0000.0000.0000.0000.000
107A178TYR0-0.043-0.03245.7960.0010.0010.0000.0000.0000.000
108A179GLN0-0.053-0.04349.0520.0000.0000.0000.0000.0000.000
109A180ALA0-0.0220.00351.2640.0010.0010.0000.0000.0000.000
110A181PHE0-0.0180.00646.1700.0010.0010.0000.0000.0000.000
111A182PRO00.0070.01044.682-0.001-0.0010.0000.0000.0000.000
112A183PRO00.001-0.03143.8430.0000.0000.0000.0000.0000.000
113A184VAL0-0.046-0.00337.4580.0020.0020.0000.0000.0000.000
114A185GLU-1-0.956-0.97336.605-0.007-0.0070.0000.0000.0000.000
115A186ALA00.0180.00432.893-0.003-0.0030.0000.0000.0000.000
116A187PRO0-0.062-0.01734.4580.0030.0030.0000.0000.0000.000
117A188ARG10.8580.89832.350-0.029-0.0290.0000.0000.0000.000
118A189PRO0-0.041-0.03430.741-0.002-0.0020.0000.0000.0000.000
119A190GLY00.0450.03033.8280.0040.0040.0000.0000.0000.000
120A191ASP-1-0.824-0.89237.1560.0090.0090.0000.0000.0000.000
121A192LEU0-0.015-0.00639.092-0.002-0.0020.0000.0000.0000.000
122A193VAL0-0.045-0.01637.6320.0000.0000.0000.0000.0000.000
123A194PHE00.0380.00541.029-0.001-0.0010.0000.0000.0000.000
124A195PHE0-0.008-0.02039.597-0.002-0.0020.0000.0000.0000.000
125A196SER0-0.040-0.03245.0670.0010.0010.0000.0000.0000.000
126A197PHE0-0.051-0.04744.075-0.002-0.0020.0000.0000.0000.000
127A198GLY00.0050.00948.486-0.001-0.0010.0000.0000.0000.000
128A199GLY0-0.047-0.02050.1410.0000.0000.0000.0000.0000.000
129A200LYS10.8890.94251.1580.0150.0150.0000.0000.0000.000
130A201GLU-1-0.882-0.94252.908-0.008-0.0080.0000.0000.0000.000
131A202VAL0-0.014-0.00147.931-0.001-0.0010.0000.0000.0000.000
132A203ASP-1-0.813-0.89249.456-0.013-0.0130.0000.0000.0000.000
133A204HIS00.0140.01244.315-0.001-0.0010.0000.0000.0000.000
134A205VAL00.0130.00244.6140.0000.0000.0000.0000.0000.000
135A206GLY0-0.007-0.00341.508-0.001-0.0010.0000.0000.0000.000
136A207ILE00.0120.00838.2340.0020.0020.0000.0000.0000.000
137A208TYR0-0.0120.01930.727-0.005-0.0050.0000.0000.0000.000
138A209LEU00.002-0.01433.1700.0030.0030.0000.0000.0000.000
139A210GLY00.0380.02430.2090.0040.0040.0000.0000.0000.000
140A211ARG10.9500.95623.6940.0070.0070.0000.0000.0000.000
141A212GLY00.0650.02927.999-0.006-0.0060.0000.0000.0000.000
142A213VAL0-0.0220.01030.574-0.004-0.0040.0000.0000.0000.000
143A214PHE00.007-0.00732.8880.0050.0050.0000.0000.0000.000
144A215ALA00.0210.01936.392-0.003-0.0030.0000.0000.0000.000
145A216HIS10.8130.89138.9860.0220.0220.0000.0000.0000.000
146A217ALA00.0700.04642.513-0.001-0.0010.0000.0000.0000.000
147A218SER0-0.038-0.02243.388-0.001-0.0010.0000.0000.0000.000
148A219SER00.063-0.00245.3710.0010.0010.0000.0000.0000.000
149A220TYR00.0050.01342.9510.0010.0010.0000.0000.0000.000
150A221GLY00.0060.00147.6490.0000.0000.0000.0000.0000.000
151A222SER0-0.024-0.01748.4130.0010.0010.0000.0000.0000.000
152A223ARG10.8840.96044.8350.0210.0210.0000.0000.0000.000
153A224VAL0-0.0140.02341.206-0.001-0.0010.0000.0000.0000.000
154A225VAL00.0170.01239.341-0.001-0.0010.0000.0000.0000.000
155A226ILE00.024-0.00433.7750.0020.0020.0000.0000.0000.000
156A227GLU-1-0.853-0.89335.243-0.034-0.0340.0000.0000.0000.000
157A228SER00.0410.01531.1610.0040.0040.0000.0000.0000.000
158A229LEU00.002-0.03033.5900.0000.0000.0000.0000.0000.000
159A230GLU-1-0.985-0.99029.141-0.042-0.0420.0000.0000.0000.000
160A231ALA00.0000.01833.223-0.005-0.0050.0000.0000.0000.000
161A232PRO00.021-0.00835.2430.0040.0040.0000.0000.0000.000
162A233PHE0-0.001-0.00837.6660.0020.0020.0000.0000.0000.000
163A234TYR00.011-0.03537.7730.0030.0030.0000.0000.0000.000
164A235ARG10.9710.99331.4500.0390.0390.0000.0000.0000.000
165A236LYS10.8960.96138.4180.0380.0380.0000.0000.0000.000
166A237VAL0-0.0330.00041.9480.0020.0020.0000.0000.0000.000
167A238TYR00.0460.03138.7170.0030.0030.0000.0000.0000.000
168A239ARG10.9080.94842.0250.0160.0160.0000.0000.0000.000
169A240GLY00.0400.04341.3290.0020.0020.0000.0000.0000.000
170A241ALA00.0120.00739.150-0.001-0.0010.0000.0000.0000.000
171A242ARG10.8380.93241.1740.0020.0020.0000.0000.0000.000
172A243ARG10.9801.00536.482-0.016-0.0160.0000.0000.0000.000
173A244VAL00.0180.00642.1680.0000.0000.0000.0000.0000.000
174A245MET00.0050.00540.5560.0000.0000.0000.0000.0000.000
175A246ALA0-0.0130.00638.4080.0010.0010.0000.0000.0000.000