FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: J35L9

Calculation Name: 3P0S-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3P0S

Chain ID: A

ChEMBL ID:

UniProt ID: Q8V0M6

Base Structure: X-ray

Registration Date: 2023-06-20

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 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 412
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -6964641.169575
FMO2-HF: Nuclear repulsion 6801435.305665
FMO2-HF: Total energy -163205.86391
FMO2-MP2: Total energy -163683.77623


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:43:ALA)


Summations of interaction energy for fragment #1(A:43: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.
-4.135-0.9250.034-1.461-1.7830.001
Interaction energy analysis for fragmet #1(A:43:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / q_NPA : 0.010
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].
3A45ASP-1-0.827-0.9053.226-5.932-2.9250.036-1.439-1.6040.001
4A46GLY0-0.007-0.0044.7580.9581.089-0.001-0.009-0.1210.000
5A47ARG10.8670.9345.2661.2821.2820.0000.0000.0000.000
6A48GLN0-0.0070.0054.418-0.288-0.216-0.001-0.013-0.0580.000
7A49ASP-1-0.916-0.9556.6320.0510.0510.0000.0000.0000.000
8A50ILE0-0.029-0.01510.021-0.061-0.0610.0000.0000.0000.000
9A51PHE0-0.024-0.02412.5470.0340.0340.0000.0000.0000.000
10A52SER00.0140.00914.1150.0160.0160.0000.0000.0000.000
11A53GLY00.0000.00916.1430.0020.0020.0000.0000.0000.000
12A54ALA00.002-0.01519.7250.0280.0280.0000.0000.0000.000
13A55PRO0-0.049-0.01322.167-0.013-0.0130.0000.0000.0000.000
14A56GLN0-0.0010.00925.6950.0020.0020.0000.0000.0000.000
15A57PRO00.040-0.00527.6700.0060.0060.0000.0000.0000.000
16A58ASN00.0110.01329.619-0.013-0.0130.0000.0000.0000.000
17A59GLN0-0.020-0.01233.0380.0020.0020.0000.0000.0000.000
18A60HIS00.021-0.00733.1850.0050.0050.0000.0000.0000.000
19A61HIS00.0110.01537.048-0.001-0.0010.0000.0000.0000.000
20A62THR00.0030.01040.2150.0010.0010.0000.0000.0000.000
21A63LEU0-0.011-0.00342.553-0.003-0.0030.0000.0000.0000.000
22A64VAL00.013-0.00546.2760.0020.0020.0000.0000.0000.000
23A65TYR00.0020.01048.874-0.003-0.0030.0000.0000.0000.000
24A66GLY00.020-0.02052.5830.0020.0020.0000.0000.0000.000
25A67LYS10.8500.95155.862-0.029-0.0290.0000.0000.0000.000
26A68SER0-0.018-0.01859.6430.0010.0010.0000.0000.0000.000
27A69TYR0-0.047-0.03161.046-0.001-0.0010.0000.0000.0000.000
28A70HIS00.0090.00066.1500.0010.0010.0000.0000.0000.000
29A71PHE0-0.0120.00066.389-0.001-0.0010.0000.0000.0000.000
30A72THR0-0.025-0.01471.5780.0000.0000.0000.0000.0000.000
31A73ILE00.0250.02272.4640.0000.0000.0000.0000.0000.000
32A74THR0-0.009-0.02475.9720.0000.0000.0000.0000.0000.000
33A75ASN00.0410.01678.7920.0000.0000.0000.0000.0000.000
34A76GLY00.0580.01581.1630.0000.0000.0000.0000.0000.000
35A77LEU0-0.0020.00181.5670.0010.0010.0000.0000.0000.000
36A78PRO0-0.018-0.01381.0230.0000.0000.0000.0000.0000.000
37A79GLU-1-0.800-0.87581.4670.0190.0190.0000.0000.0000.000
38A80PHE00.0210.00381.3760.0010.0010.0000.0000.0000.000
39A81ARG10.8420.91578.085-0.021-0.0210.0000.0000.0000.000
40A82HIS00.0600.03281.4900.0010.0010.0000.0000.0000.000
41A83LEU0-0.074-0.04576.256-0.001-0.0010.0000.0000.0000.000
42A84ALA00.0540.03979.3880.0000.0000.0000.0000.0000.000
43A85THR0-0.018-0.01975.2590.0000.0000.0000.0000.0000.000
44A86THR0-0.006-0.01374.5930.0000.0000.0000.0000.0000.000
45A87ASN00.004-0.01372.8690.0000.0000.0000.0000.0000.000
46A88SER00.0050.00376.3240.0000.0000.0000.0000.0000.000
47A89GLY00.0150.04276.0080.0000.0000.0000.0000.0000.000
48A90TYR00.0330.00676.829-0.001-0.0010.0000.0000.0000.000
49A91TYR0-0.011-0.00772.4430.0000.0000.0000.0000.0000.000
50A92ALA00.0470.04477.698-0.001-0.0010.0000.0000.0000.000
51A93GLN0-0.0030.01374.9850.0000.0000.0000.0000.0000.000
52A94GLN00.0490.02677.2070.0000.0000.0000.0000.0000.000
53A95ARG10.8390.91476.680-0.020-0.0200.0000.0000.0000.000
54A96PHE00.0610.01675.377-0.001-0.0010.0000.0000.0000.000
55A97LYS10.8320.92776.482-0.019-0.0190.0000.0000.0000.000
56A98HIS0-0.0170.00977.457-0.001-0.0010.0000.0000.0000.000
57A99ILE0-0.024-0.00571.9700.0000.0000.0000.0000.0000.000
58A100HIS00.0420.01871.8990.0000.0000.0000.0000.0000.000
59A101GLY00.0230.01968.1160.0010.0010.0000.0000.0000.000
60A102ILE0-0.0010.00763.320-0.001-0.0010.0000.0000.0000.000
61A103PRO00.0550.03563.8660.0010.0010.0000.0000.0000.000
62A104TRP0-0.057-0.04156.7310.0000.0000.0000.0000.0000.000
63A105GLU-1-0.794-0.91158.1670.0340.0340.0000.0000.0000.000
64A106ARG10.9020.96357.913-0.028-0.0280.0000.0000.0000.000
65A107LEU00.0600.02453.2030.0000.0000.0000.0000.0000.000
66A108LEU00.005-0.01256.7970.0000.0000.0000.0000.0000.000
67A109MET0-0.0130.02459.424-0.001-0.0010.0000.0000.0000.000
68A110TYR0-0.071-0.04155.2270.0000.0000.0000.0000.0000.000
69A111VAL0-0.048-0.02453.3170.0000.0000.0000.0000.0000.000
70A112SER00.0390.02856.480-0.001-0.0010.0000.0000.0000.000
71A113GLU-1-0.772-0.91757.5010.0220.0220.0000.0000.0000.000
72A114GLY00.0160.00657.7710.0000.0000.0000.0000.0000.000
73A115GLU-1-0.895-0.95253.6540.0270.0270.0000.0000.0000.000
74A116LEU00.0090.01252.9020.0010.0010.0000.0000.0000.000
75A117LEU00.000-0.01353.3090.0010.0010.0000.0000.0000.000
76A118ARG10.9240.96949.617-0.025-0.0250.0000.0000.0000.000
77A119MET00.0360.04248.5990.0010.0010.0000.0000.0000.000
78A120PHE00.033-0.00148.5700.0030.0030.0000.0000.0000.000
79A121ARG10.8500.91448.933-0.021-0.0210.0000.0000.0000.000
80A122ASP-1-0.868-0.92045.2860.0270.0270.0000.0000.0000.000
81A123TYR0-0.0360.00541.9480.0010.0010.0000.0000.0000.000
82A124THR00.015-0.00240.026-0.002-0.0020.0000.0000.0000.000
83A125SER00.019-0.01241.7540.0010.0010.0000.0000.0000.000
84A126LEU0-0.0530.00743.1560.0010.0010.0000.0000.0000.000
85A127LYS10.8820.96443.097-0.065-0.0650.0000.0000.0000.000
86A128VAL0-0.0200.00145.7440.0000.0000.0000.0000.0000.000
87A129GLU-1-0.868-0.95442.0460.0700.0700.0000.0000.0000.000
88A130GLU-1-0.948-1.01146.3270.0560.0560.0000.0000.0000.000
89A131VAL0-0.0080.02549.452-0.002-0.0020.0000.0000.0000.000
90A132VAL0-0.031-0.02852.7980.0010.0010.0000.0000.0000.000
91A133CYS00.0040.00655.440-0.002-0.0020.0000.0000.0000.000
92A134GLU-1-0.855-0.90758.1280.0350.0350.0000.0000.0000.000
93A135VAL00.0490.02061.404-0.001-0.0010.0000.0000.0000.000
94A136TYR0-0.059-0.04461.3560.0000.0000.0000.0000.0000.000
95A137SER00.0320.03167.450-0.001-0.0010.0000.0000.0000.000
96A138LEU00.0390.00570.9330.0000.0000.0000.0000.0000.000
97A139GLY00.0230.01873.669-0.001-0.0010.0000.0000.0000.000
98A140VAL0-0.022-0.01076.6040.0000.0000.0000.0000.0000.000
99A141ARG10.8910.94777.230-0.019-0.0190.0000.0000.0000.000
100A142LEU00.035-0.00682.2460.0000.0000.0000.0000.0000.000
101A143PRO00.009-0.00185.6190.0000.0000.0000.0000.0000.000
102A144PHE0-0.0050.00688.7960.0000.0000.0000.0000.0000.000
103A145VAL00.0500.01991.6340.0000.0000.0000.0000.0000.000
104A146THR0-0.041-0.00991.6110.0000.0000.0000.0000.0000.000
105A147SER00.0130.00793.5330.0000.0000.0000.0000.0000.000
106A148ALA00.027-0.00293.9040.0000.0000.0000.0000.0000.000
107A149THR00.0220.02194.8220.0000.0000.0000.0000.0000.000
108A150THR00.0180.00693.2830.0000.0000.0000.0000.0000.000
109A151SER0-0.053-0.01390.0120.0000.0000.0000.0000.0000.000
110A152SER00.0530.01288.4130.0000.0000.0000.0000.0000.000
111A153VAL0-0.0280.00482.9380.0000.0000.0000.0000.0000.000
112A154ALA00.006-0.01084.6760.0000.0000.0000.0000.0000.000
113A155ASN00.0210.02786.4560.0000.0000.0000.0000.0000.000
114A156ALA00.018-0.01381.0760.0000.0000.0000.0000.0000.000
115A157ASN0-0.028-0.00581.9510.0010.0010.0000.0000.0000.000
116A158ALA00.0240.00883.5970.0000.0000.0000.0000.0000.000
117A159GLN0-0.042-0.02281.1250.0010.0010.0000.0000.0000.000
118A160TYR00.0250.00680.0570.0010.0010.0000.0000.0000.000
119A161PRO00.0300.02478.2210.0010.0010.0000.0000.0000.000
120A162ILE00.0000.00672.8510.0000.0000.0000.0000.0000.000
121A163GLY00.0320.00371.9360.0000.0000.0000.0000.0000.000
122A164CYS0-0.069-0.02465.4730.0000.0000.0000.0000.0000.000
123A165PHE00.0400.00468.9650.0000.0000.0000.0000.0000.000
124A166HIS00.000-0.00665.2790.0010.0010.0000.0000.0000.000
125A167PHE00.0730.03966.7370.0010.0010.0000.0000.0000.000
126A168ASP-1-0.892-0.97163.9470.0360.0360.0000.0000.0000.000
127A169GLU-1-0.873-0.94061.2210.0430.0430.0000.0000.0000.000
128A170ALA0-0.042-0.02364.8550.0010.0010.0000.0000.0000.000
129A171TYR00.0090.00867.8120.0000.0000.0000.0000.0000.000
130A172GLU-1-0.869-0.92268.0670.0310.0310.0000.0000.0000.000
131A173THR00.0300.00367.259-0.001-0.0010.0000.0000.0000.000
132A174ASN0-0.105-0.05267.7400.0000.0000.0000.0000.0000.000
133A175TYR00.0230.00665.150-0.001-0.0010.0000.0000.0000.000
134A176GLY00.0600.03970.0300.0000.0000.0000.0000.0000.000
135A177ILE00.016-0.01768.8590.0000.0000.0000.0000.0000.000
136A178ASN00.024-0.00569.9240.0000.0000.0000.0000.0000.000
137A179ASN0-0.033-0.00872.0670.0000.0000.0000.0000.0000.000
138A180VAL00.0330.01665.5700.0000.0000.0000.0000.0000.000
139A181ALA0-0.039-0.01967.7320.0000.0000.0000.0000.0000.000
140A182ASP-1-0.820-0.91168.7810.0190.0190.0000.0000.0000.000
141A183ILE0-0.003-0.00766.8540.0000.0000.0000.0000.0000.000
142A184ILE00.008-0.01063.1440.0000.0000.0000.0000.0000.000
143A185ASN0-0.024-0.00866.1620.0000.0000.0000.0000.0000.000
144A186LYS10.8680.96168.546-0.020-0.0200.0000.0000.0000.000
145A187ALA0-0.0100.00564.5030.0000.0000.0000.0000.0000.000
146A188LEU0-0.054-0.02461.7840.0000.0000.0000.0000.0000.000
147A189GLY0-0.015-0.00665.249-0.001-0.0010.0000.0000.0000.000
148A190THR0-0.032-0.01467.4480.0000.0000.0000.0000.0000.000
149A191GLU-1-0.845-0.92266.6310.0140.0140.0000.0000.0000.000
150A192TRP00.0150.00069.422-0.001-0.0010.0000.0000.0000.000
151A193LYS10.8450.93166.945-0.015-0.0150.0000.0000.0000.000
152A194ASN00.0180.00470.5960.0000.0000.0000.0000.0000.000
153A195ALA0-0.025-0.01466.434-0.001-0.0010.0000.0000.0000.000
154A196THR0-0.0170.00168.294-0.001-0.0010.0000.0000.0000.000
155A197ARG10.9590.96370.102-0.005-0.0050.0000.0000.0000.000
156A198PRO00.0360.02873.1760.0000.0000.0000.0000.0000.000
157A199THR00.0330.00776.5850.0000.0000.0000.0000.0000.000
158A200ALA00.0160.01578.4780.0000.0000.0000.0000.0000.000
159A201ALA0-0.054-0.01376.4520.0000.0000.0000.0000.0000.000
160A202VAL00.0050.00078.3480.0000.0000.0000.0000.0000.000
161A203THR0-0.045-0.01680.1440.0010.0010.0000.0000.0000.000
162A204THR00.0460.00880.2690.0000.0000.0000.0000.0000.000
163A205ALA0-0.009-0.00382.2140.0000.0000.0000.0000.0000.000
164A206TRP00.000-0.00277.2930.0000.0000.0000.0000.0000.000
165A207SER00.000-0.01480.7640.0000.0000.0000.0000.0000.000
166A208GLU-1-0.903-0.93979.8630.0120.0120.0000.0000.0000.000
167A209GLN0-0.016-0.00979.7630.0010.0010.0000.0000.0000.000
168A210PHE0-0.026-0.01474.0960.0000.0000.0000.0000.0000.000
169A211PRO0-0.018-0.00174.8420.0000.0000.0000.0000.0000.000
170A212ASN0-0.015-0.03970.3610.0010.0010.0000.0000.0000.000
171A213ILE00.0030.03271.5520.0000.0000.0000.0000.0000.000
172A214SER00.0390.00666.4190.0010.0010.0000.0000.0000.000
173A215ALA00.0210.00568.1820.0000.0000.0000.0000.0000.000
174A216SER0-0.023-0.02164.8210.0010.0010.0000.0000.0000.000
175A217SER0-0.085-0.04066.7730.0000.0000.0000.0000.0000.000
176A218THR00.003-0.00769.599-0.001-0.0010.0000.0000.0000.000
177A219SER0-0.0290.00472.0630.0000.0000.0000.0000.0000.000
178A220ARG10.9630.97971.608-0.018-0.0180.0000.0000.0000.000
179A221ASP-1-0.943-0.96073.4200.0190.0190.0000.0000.0000.000
180A222ILE0-0.007-0.00470.1190.0000.0000.0000.0000.0000.000
181A223ASN00.0260.00473.8690.0000.0000.0000.0000.0000.000
182A224ASN0-0.054-0.05368.710-0.001-0.0010.0000.0000.0000.000
183A225PRO00.0000.01072.0970.0010.0010.0000.0000.0000.000
184A226VAL00.0230.02370.0970.0000.0000.0000.0000.0000.000
185A227ILE0-0.047-0.03372.098-0.001-0.0010.0000.0000.0000.000
186A228VAL00.006-0.00172.0460.0010.0010.0000.0000.0000.000
187A229ASP-1-0.855-0.93671.8430.0250.0250.0000.0000.0000.000
188A230TYR00.006-0.00573.3900.0010.0010.0000.0000.0000.000
189A231SER00.001-0.01572.054-0.001-0.0010.0000.0000.0000.000
190A232LEU0-0.056-0.02974.9160.0000.0000.0000.0000.0000.000
191A233PRO0-0.0160.00273.997-0.001-0.0010.0000.0000.0000.000
192A234TYR0-0.022-0.00973.0660.0000.0000.0000.0000.0000.000
193A235PHE0-0.021-0.01878.8920.0000.0000.0000.0000.0000.000
194A236GLU-1-0.934-0.95781.9750.0220.0220.0000.0000.0000.000
195A237ASN0-0.033-0.00678.3960.0010.0010.0000.0000.0000.000
196A238ASN00.0280.02076.081-0.001-0.0010.0000.0000.0000.000
197A239VAL00.018-0.00477.3300.0010.0010.0000.0000.0000.000
198A240PRO0-0.045-0.00575.2360.0000.0000.0000.0000.0000.000
199A241LYS10.9710.97878.031-0.026-0.0260.0000.0000.0000.000
200A242ASP-1-0.933-0.96877.9360.0240.0240.0000.0000.0000.000
201A243VAL0-0.008-0.00273.0220.0000.0000.0000.0000.0000.000
202A244GLY00.0410.02375.726-0.001-0.0010.0000.0000.0000.000
203A245ILE0-0.021-0.02574.2860.0010.0010.0000.0000.0000.000
204A246TYR0-0.044-0.03874.1130.0000.0000.0000.0000.0000.000
205A247ASP-1-0.915-0.93372.9610.0290.0290.0000.0000.0000.000
206A248TYR0-0.070-0.04368.3470.0020.0020.0000.0000.0000.000
207A249VAL00.0020.00170.2910.0000.0000.0000.0000.0000.000
208A250ASP-1-0.895-0.92367.4260.0340.0340.0000.0000.0000.000
209A251ILE0-0.035-0.03970.7230.0000.0000.0000.0000.0000.000
210A252LYS10.8970.95567.765-0.030-0.0300.0000.0000.0000.000
211A253ASN00.0750.01973.929-0.001-0.0010.0000.0000.0000.000
212A254GLY00.0380.01176.1390.0000.0000.0000.0000.0000.000
213A255THR0-0.081-0.03177.0570.0000.0000.0000.0000.0000.000
214A256THR00.007-0.00376.4310.0000.0000.0000.0000.0000.000
215A257ALA0-0.0290.00172.0780.0010.0010.0000.0000.0000.000
216A258TYR0-0.008-0.00372.7410.0000.0000.0000.0000.0000.000
217A259GLY00.0380.01568.8950.0000.0000.0000.0000.0000.000
218A260LYS10.8540.94259.585-0.035-0.0350.0000.0000.0000.000
219A261CYS0-0.050-0.01465.8800.0000.0000.0000.0000.0000.000
220A262TRP00.0440.01463.8930.0010.0010.0000.0000.0000.000
221A263GLU-1-0.865-0.95556.4690.0400.0400.0000.0000.0000.000
222A264LYS10.8940.98358.553-0.037-0.0370.0000.0000.0000.000
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