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: LNQ39

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 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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1622177.465659
FMO2-HF: Nuclear repulsion 1555810.179961
FMO2-HF: Total energy -66367.285698
FMO2-MP2: Total energy -66564.260585


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.
-1.0012.6330.28-1.708-2.205-0.001
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 : 0.002 / 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].
3A19TYR0-0.053-0.0503.7950.6752.661-0.033-1.114-0.8390.001
4A20THR0-0.015-0.0016.650-0.358-0.3580.0000.0000.0000.000
5A21VAL0-0.025-0.00310.3650.0540.0540.0000.0000.0000.000
6A22ALA00.0490.03212.9350.0190.0190.0000.0000.0000.000
7A23PRO00.003-0.01615.435-0.043-0.0430.0000.0000.0000.000
8A24GLY00.0200.01019.0170.0110.0110.0000.0000.0000.000
9A25ASP-1-0.796-0.87613.3150.1040.1040.0000.0000.0000.000
10A26THR0-0.013-0.01115.565-0.029-0.0290.0000.0000.0000.000
11A27LEU00.0750.02313.256-0.005-0.0050.0000.0000.0000.000
12A28TYR0-0.003-0.00213.843-0.034-0.0340.0000.0000.0000.000
13A29SER0-0.0040.00114.691-0.028-0.0280.0000.0000.0000.000
14A30ILE00.0160.0168.9010.0150.0150.0000.0000.0000.000
15A31ALA00.0020.0049.952-0.051-0.0510.0000.0000.0000.000
16A32ARG10.8610.91811.3880.0030.0030.0000.0000.0000.000
17A33ARG10.8630.9419.270-0.322-0.3220.0000.0000.0000.000
18A34TYR0-0.060-0.0406.3760.2300.2300.0000.0000.0000.000
19A35GLY0-0.0090.0188.479-0.156-0.1560.0000.0000.0000.000
20A36THR00.0180.0048.812-0.005-0.0050.0000.0000.0000.000
21A37THR00.0240.00311.3820.0780.0780.0000.0000.0000.000
22A38VAL00.023-0.00612.960-0.062-0.0620.0000.0000.0000.000
23A39GLU-1-0.921-0.95014.763-0.314-0.3140.0000.0000.0000.000
24A40GLU-1-0.798-0.87110.617-0.800-0.8000.0000.0000.0000.000
25A41LEU0-0.0070.0038.560-0.098-0.0980.0000.0000.0000.000
26A42MET0-0.020-0.00211.279-0.026-0.0260.0000.0000.0000.000
27A43ARG10.8660.90310.8090.6500.6500.0000.0000.0000.000
28A44LEU0-0.075-0.0346.2950.0390.0390.0000.0000.0000.000
29A45ASN0-0.076-0.0458.485-0.107-0.1070.0000.0000.0000.000
30A46GLY0-0.0090.01311.4510.0730.0730.0000.0000.0000.000
31A47LEU0-0.047-0.01813.8020.0530.0530.0000.0000.0000.000
32A48GLU-1-0.900-0.94616.501-0.190-0.1900.0000.0000.0000.000
33A49SER0-0.051-0.03719.3500.0300.0300.0000.0000.0000.000
34A50PHE00.015-0.01718.669-0.023-0.0230.0000.0000.0000.000
35A51LEU0-0.039-0.00619.1750.0120.0120.0000.0000.0000.000
36A52LEU00.017-0.00113.664-0.030-0.0300.0000.0000.0000.000
37A53GLN0-0.0050.01117.7890.0210.0210.0000.0000.0000.000
38A54PRO00.019-0.01216.650-0.006-0.0060.0000.0000.0000.000
39A55GLY0-0.0090.00414.710-0.007-0.0070.0000.0000.0000.000
40A56GLN00.0050.01213.2960.0330.0330.0000.0000.0000.000
41A57VAL0-0.005-0.0108.0240.0350.0350.0000.0000.0000.000
42A58LEU0-0.033-0.0078.455-0.078-0.0780.0000.0000.0000.000
43A59LYS10.9700.9675.0630.6920.6920.0000.0000.0000.000
44A60LEU0-0.004-0.0012.591-0.2360.9560.309-0.482-1.018-0.001
45A61PRO0-0.0110.0073.846-0.922-0.4660.004-0.112-0.348-0.001
46A117PRO00.004-0.0209.8210.0560.0560.0000.0000.0000.000
47A118PRO0-0.0220.00212.151-0.058-0.0580.0000.0000.0000.000
48A119PRO00.0370.01413.0520.0010.0010.0000.0000.0000.000
49A120PRO00.0170.00616.2800.0140.0140.0000.0000.0000.000
50A121GLU-1-0.787-0.86819.244-0.001-0.0010.0000.0000.0000.000
51A122PRO0-0.072-0.03120.8800.0020.0020.0000.0000.0000.000
52A123GLU-1-0.782-0.85624.1830.0320.0320.0000.0000.0000.000
53A124ALA0-0.033-0.03326.193-0.009-0.0090.0000.0000.0000.000
54A125LEU0-0.0120.00528.0340.0060.0060.0000.0000.0000.000
55A126ASP-1-0.796-0.89929.0460.0290.0290.0000.0000.0000.000
56A127PRO0-0.018-0.01728.979-0.003-0.0030.0000.0000.0000.000
57A128GLU-1-0.848-0.90231.9370.0220.0220.0000.0000.0000.000
58A129SER0-0.042-0.02733.4210.0010.0010.0000.0000.0000.000
59A130PRO00.024-0.00335.182-0.003-0.0030.0000.0000.0000.000
60A131LEU00.0400.02836.590-0.002-0.0020.0000.0000.0000.000
61A132LEU00.0240.00932.543-0.003-0.0030.0000.0000.0000.000
62A133ARG10.8480.90636.494-0.019-0.0190.0000.0000.0000.000
63A134ALA00.0090.01438.664-0.002-0.0020.0000.0000.0000.000
64A135VAL0-0.010-0.01238.128-0.002-0.0020.0000.0000.0000.000
65A136LEU0-0.037-0.03734.991-0.003-0.0030.0000.0000.0000.000
66A137ARG10.8320.92239.425-0.007-0.0070.0000.0000.0000.000
67A138TYR0-0.038-0.04042.946-0.002-0.0020.0000.0000.0000.000
68A139LEU0-0.0010.02137.171-0.002-0.0020.0000.0000.0000.000
69A140GLY00.0070.01041.450-0.001-0.0010.0000.0000.0000.000
70A141VAL0-0.021-0.02343.268-0.001-0.0010.0000.0000.0000.000
71A142PRO0-0.063-0.02946.5920.0000.0000.0000.0000.0000.000
72A143TYR00.000-0.01148.1700.0010.0010.0000.0000.0000.000
73A144LYS10.8680.93850.0620.0120.0120.0000.0000.0000.000
74A145TYR00.0100.00353.5770.0010.0010.0000.0000.0000.000
75A146GLY00.015-0.00855.2680.0010.0010.0000.0000.0000.000
76A147ALA0-0.026-0.00858.356-0.001-0.0010.0000.0000.0000.000
77A148ASN0-0.013-0.01859.620-0.001-0.0010.0000.0000.0000.000
78A149SER0-0.033-0.00655.6250.0000.0000.0000.0000.0000.000
79A150PRO00.0420.02055.880-0.001-0.0010.0000.0000.0000.000
80A151LEU00.0900.03448.3460.0010.0010.0000.0000.0000.000
81A152ALA00.006-0.00251.1210.0000.0000.0000.0000.0000.000
82A153LEU0-0.052-0.01752.4790.0010.0010.0000.0000.0000.000
83A154ASP-1-0.721-0.82550.837-0.009-0.0090.0000.0000.0000.000
84A155CYS0-0.111-0.03246.9730.0010.0010.0000.0000.0000.000
85A156SER00.040-0.00647.4530.0000.0000.0000.0000.0000.000
86A157ALA0-0.0110.00249.5390.0010.0010.0000.0000.0000.000
87A158PHE0-0.006-0.00542.1200.0010.0010.0000.0000.0000.000
88A159VAL00.002-0.00544.0260.0010.0010.0000.0000.0000.000
89A160ALA00.010-0.00146.1380.0020.0020.0000.0000.0000.000
90A161GLN0-0.0020.01847.9990.0010.0010.0000.0000.0000.000
91A162VAL00.010-0.00641.9430.0010.0010.0000.0000.0000.000
92A163TYR0-0.031-0.05240.4120.0020.0020.0000.0000.0000.000
93A164ALA00.0370.03245.6050.0020.0020.0000.0000.0000.000
94A165GLU-1-0.846-0.88445.3720.0050.0050.0000.0000.0000.000
95A166LEU0-0.080-0.04940.6110.0020.0020.0000.0000.0000.000
96A167GLY0-0.0240.00645.0870.0020.0020.0000.0000.0000.000
97A168VAL0-0.052-0.02644.6070.0000.0000.0000.0000.0000.000
98A169ALA00.0030.00647.906-0.001-0.0010.0000.0000.0000.000
99A170LEU00.023-0.00446.3200.0000.0000.0000.0000.0000.000
100A171PRO0-0.0160.00350.690-0.001-0.0010.0000.0000.0000.000
101A172ARG10.9891.00252.039-0.001-0.0010.0000.0000.0000.000
102A173THR0-0.023-0.03252.722-0.001-0.0010.0000.0000.0000.000
103A174THR00.0650.01648.7860.0010.0010.0000.0000.0000.000
104A175LYS10.8800.93450.5870.0060.0060.0000.0000.0000.000
105A176GLU-1-0.807-0.87452.5500.0000.0000.0000.0000.0000.000
106A177GLN0-0.042-0.03548.1470.0000.0000.0000.0000.0000.000
107A178TYR0-0.049-0.03545.6680.0010.0010.0000.0000.0000.000
108A179GLN0-0.048-0.03749.0510.0000.0000.0000.0000.0000.000
109A180ALA0-0.0200.00451.2350.0010.0010.0000.0000.0000.000
110A181PHE0-0.0130.00546.1860.0010.0010.0000.0000.0000.000
111A182PRO00.0140.01544.657-0.001-0.0010.0000.0000.0000.000
112A183PRO0-0.001-0.02843.8300.0000.0000.0000.0000.0000.000
113A184VAL0-0.041-0.00737.4550.0020.0020.0000.0000.0000.000
114A185GLU-1-0.944-0.96436.892-0.006-0.0060.0000.0000.0000.000
115A186ALA0-0.002-0.00632.891-0.003-0.0030.0000.0000.0000.000
116A187PRO0-0.056-0.01734.7250.0030.0030.0000.0000.0000.000
117A188ARG10.8160.86432.064-0.030-0.0300.0000.0000.0000.000
118A189PRO0-0.024-0.02730.700-0.002-0.0020.0000.0000.0000.000
119A190GLY00.0550.03333.8260.0040.0040.0000.0000.0000.000
120A191ASP-1-0.788-0.85937.1470.0100.0100.0000.0000.0000.000
121A192LEU0-0.0010.00439.090-0.002-0.0020.0000.0000.0000.000
122A193VAL0-0.026-0.00937.6760.0000.0000.0000.0000.0000.000
123A194PHE00.0330.00241.029-0.001-0.0010.0000.0000.0000.000
124A195PHE0-0.010-0.02439.630-0.002-0.0020.0000.0000.0000.000
125A196SER0-0.045-0.04445.0670.0010.0010.0000.0000.0000.000
126A197PHE0-0.043-0.04844.147-0.002-0.0020.0000.0000.0000.000
127A198GLY00.0000.00548.486-0.001-0.0010.0000.0000.0000.000
128A199GLY0-0.051-0.02250.1430.0000.0000.0000.0000.0000.000
129A200LYS10.8890.94351.1590.0150.0150.0000.0000.0000.000
130A201GLU-1-0.794-0.88652.854-0.007-0.0070.0000.0000.0000.000
131A202VAL0-0.0160.00547.792-0.001-0.0010.0000.0000.0000.000
132A203ASP-1-0.813-0.88549.414-0.013-0.0130.0000.0000.0000.000
133A204HIS00.0270.01744.505-0.001-0.0010.0000.0000.0000.000
134A205VAL00.0090.00944.6830.0000.0000.0000.0000.0000.000
135A206GLY0-0.003-0.00141.512-0.001-0.0010.0000.0000.0000.000
136A207ILE00.0060.00738.4110.0010.0010.0000.0000.0000.000
137A208TYR0-0.0260.00430.919-0.004-0.0040.0000.0000.0000.000
138A209LEU00.006-0.01033.1640.0030.0030.0000.0000.0000.000
139A210GLY00.0430.02830.2000.0040.0040.0000.0000.0000.000
140A211ARG10.8960.92322.502-0.002-0.0020.0000.0000.0000.000
141A212GLY00.0500.02927.998-0.006-0.0060.0000.0000.0000.000
142A213VAL0-0.0210.00630.523-0.004-0.0040.0000.0000.0000.000
143A214PHE00.007-0.00232.8870.0050.0050.0000.0000.0000.000
144A215ALA00.0290.02436.392-0.003-0.0030.0000.0000.0000.000
145A216HIS10.8030.86638.9850.0220.0220.0000.0000.0000.000
146A217ALA00.0680.04542.512-0.001-0.0010.0000.0000.0000.000
147A218SER0-0.043-0.02843.392-0.001-0.0010.0000.0000.0000.000
148A219SER00.057-0.00845.3710.0010.0010.0000.0000.0000.000
149A220TYR00.0150.01742.7860.0010.0010.0000.0000.0000.000
150A221GLY00.0230.00547.6490.0000.0000.0000.0000.0000.000
151A222SER0-0.032-0.04648.4080.0010.0010.0000.0000.0000.000
152A223ARG10.8640.95145.1070.0200.0200.0000.0000.0000.000
153A224VAL00.0010.02541.252-0.001-0.0010.0000.0000.0000.000
154A225VAL00.0090.01139.381-0.001-0.0010.0000.0000.0000.000
155A226ILE00.021-0.00433.8550.0020.0020.0000.0000.0000.000
156A227GLU-1-0.824-0.86735.269-0.032-0.0320.0000.0000.0000.000
157A228SER00.0410.01531.2190.0020.0020.0000.0000.0000.000
158A229LEU00.010-0.02233.6120.0000.0000.0000.0000.0000.000
159A230GLU-1-0.853-0.89729.920-0.035-0.0350.0000.0000.0000.000
160A231ALA0-0.0070.01333.224-0.005-0.0050.0000.0000.0000.000
161A232PRO00.024-0.00735.1330.0040.0040.0000.0000.0000.000
162A233PHE0-0.001-0.00437.6670.0020.0020.0000.0000.0000.000
163A234TYR00.005-0.02837.7750.0030.0030.0000.0000.0000.000
164A235ARG10.8470.90431.2400.0390.0390.0000.0000.0000.000
165A236LYS10.8970.95938.4180.0370.0370.0000.0000.0000.000
166A237VAL0-0.033-0.00741.9490.0020.0020.0000.0000.0000.000
167A238TYR00.0730.04838.3990.0030.0030.0000.0000.0000.000
168A239ARG10.8800.93742.0260.0160.0160.0000.0000.0000.000
169A240GLY00.0320.03941.3340.0020.0020.0000.0000.0000.000
170A241ALA00.0220.00939.150-0.001-0.0010.0000.0000.0000.000
171A242ARG10.8370.92741.1730.0020.0020.0000.0000.0000.000
172A243ARG10.8870.95937.208-0.014-0.0140.0000.0000.0000.000
173A244VAL00.0150.00042.1570.0000.0000.0000.0000.0000.000
174A245MET0-0.0030.00440.7880.0000.0000.0000.0000.0000.000
175A246ALA0-0.0030.00938.4050.0010.0010.0000.0000.0000.000