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: JQ439

Calculation Name: 4Q9A-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name: phosphoserine

ligand 3-letter code: SEP

PDB ID: 4Q9A

Chain ID: A

ChEMBL ID:
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UniProt ID: A7ABD4

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 219
LigandCharge SEP=-2
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2838691.718864
FMO2-HF: Nuclear repulsion 2749649.067702
FMO2-HF: Total energy -89042.651163
FMO2-MP2: Total energy -89299.508655


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:38:ALA)


Summations of interaction energy for fragment #1(A:38: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.
0.9242.242-0.008-0.65-0.660.003
Interaction energy analysis for fragmet #1(A:38:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.052 / q_NPA : 0.024
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].
3A40LYS10.9360.9823.9271.8163.134-0.008-0.650-0.6600.003
4A41ILE00.0420.0196.3380.3710.3710.0000.0000.0000.000
5A42ASN0-0.107-0.0579.431-0.124-0.1240.0000.0000.0000.000
6A43LEU00.0450.02312.0670.1040.1040.0000.0000.0000.000
7A44LYS10.9490.98515.3850.3930.3930.0000.0000.0000.000
8A45LYS10.9190.93918.6130.2490.2490.0000.0000.0000.000
9A46ASP-1-0.913-0.95421.893-0.250-0.2500.0000.0000.0000.000
10A47CYS0-0.087-0.01319.102-0.005-0.0050.0000.0000.0000.000
11A48VAL00.0270.01221.1810.0160.0160.0000.0000.0000.000
12A49ILE0-0.025-0.01517.503-0.037-0.0370.0000.0000.0000.000
13A50LEU0-0.0180.00020.2320.0380.0380.0000.0000.0000.000
14A51PHE00.0000.00117.826-0.024-0.0240.0000.0000.0000.000
15A52GLN00.0430.00621.5750.0400.0400.0000.0000.0000.000
16A53GLY00.024-0.00122.323-0.014-0.0140.0000.0000.0000.000
17A54ASP-1-0.754-0.88824.804-0.134-0.1340.0000.0000.0000.000
18A55SEP-2-1.676-1.80427.682-0.177-0.1770.0000.0000.0000.000
19A56ILE0-0.030-0.00423.6120.0010.0010.0000.0000.0000.000
20A57THR0-0.031-0.00523.024-0.014-0.0140.0000.0000.0000.000
21A58ASP-1-0.803-0.88125.103-0.127-0.1270.0000.0000.0000.000
22A59CYS0-0.070-0.03328.1330.0010.0010.0000.0000.0000.000
23A60GLY00.0540.01929.9980.0000.0000.0000.0000.0000.000
24A61ARG10.8570.96328.8170.1540.1540.0000.0000.0000.000
25A62ASP-1-0.862-0.93932.092-0.101-0.1010.0000.0000.0000.000
26A63ARG10.8380.89533.5830.1010.1010.0000.0000.0000.000
27A64ASN0-0.022-0.00434.772-0.003-0.0030.0000.0000.0000.000
28A65SER0-0.0230.01032.7110.0000.0000.0000.0000.0000.000
29A66ASN00.0570.00933.591-0.007-0.0070.0000.0000.0000.000
30A67ARG10.9150.96532.6800.1230.1230.0000.0000.0000.000
31A68CYS00.0100.02327.0960.0000.0000.0000.0000.0000.000
32A69ASN0-0.016-0.03625.5630.0020.0020.0000.0000.0000.000
33A70THR00.0100.01827.7760.0050.0050.0000.0000.0000.000
34A71MET00.0460.01529.650-0.011-0.0110.0000.0000.0000.000
35A72GLU-1-0.864-0.93231.320-0.121-0.1210.0000.0000.0000.000
36A73GLN0-0.034-0.00627.943-0.007-0.0070.0000.0000.0000.000
37A74PHE00.002-0.01124.962-0.008-0.0080.0000.0000.0000.000
38A75GLY00.0780.05527.638-0.003-0.0030.0000.0000.0000.000
39A76SER0-0.033-0.02529.186-0.001-0.0010.0000.0000.0000.000
40A77GLY00.0580.01726.1430.0070.0070.0000.0000.0000.000
41A78TYR00.0630.00219.226-0.009-0.0090.0000.0000.0000.000
42A79VAL00.0280.06721.347-0.020-0.0200.0000.0000.0000.000
43A80LEU00.0050.02322.271-0.018-0.0180.0000.0000.0000.000
44A81PHE0-0.020-0.02122.035-0.006-0.0060.0000.0000.0000.000
45A82THR00.011-0.03716.651-0.009-0.0090.0000.0000.0000.000
46A83ALA00.0080.00918.906-0.031-0.0310.0000.0000.0000.000
47A84THR0-0.018-0.02021.306-0.013-0.0130.0000.0000.0000.000
48A85GLN00.0050.01517.167-0.022-0.0220.0000.0000.0000.000
49A86LEU0-0.030-0.01515.188-0.026-0.0260.0000.0000.0000.000
50A87LEU0-0.063-0.04218.499-0.006-0.0060.0000.0000.0000.000
51A88GLU-1-0.938-0.96320.490-0.225-0.2250.0000.0000.0000.000
52A89GLY00.0140.00117.5430.0010.0010.0000.0000.0000.000
53A90LYS10.8540.93411.9970.6500.6500.0000.0000.0000.000
54A91ALA00.0850.04718.1370.0000.0000.0000.0000.0000.000
55A92ALA0-0.038-0.02220.3570.0120.0120.0000.0000.0000.000
56A93LEU0-0.058-0.02716.4740.0040.0040.0000.0000.0000.000
57A94GLN0-0.015-0.00821.0400.0070.0070.0000.0000.0000.000
58A95PRO00.0290.03219.8070.0050.0050.0000.0000.0000.000
59A96LYS10.9630.97922.1860.2570.2570.0000.0000.0000.000
60A97ILE0-0.016-0.00320.732-0.017-0.0170.0000.0000.0000.000
61A98TYR00.003-0.01723.6460.0280.0280.0000.0000.0000.000
62A99ASN0-0.044-0.04123.964-0.025-0.0250.0000.0000.0000.000
63A100ARG10.8640.93625.8470.1800.1800.0000.0000.0000.000
64A101GLY00.0060.03026.8140.0090.0090.0000.0000.0000.000
65A102ILE0-0.063-0.03227.5340.0080.0080.0000.0000.0000.000
66A103SER00.008-0.01430.4050.0000.0000.0000.0000.0000.000
67A104GLY00.0100.01831.8730.0020.0020.0000.0000.0000.000
68A105ASN0-0.019-0.01629.283-0.004-0.0040.0000.0000.0000.000
69A106LYS10.9210.97729.2010.0820.0820.0000.0000.0000.000
70A107VAL00.0320.00025.519-0.008-0.0080.0000.0000.0000.000
71A108TYR00.0080.00028.011-0.006-0.0060.0000.0000.0000.000
72A109GLN00.0100.00731.360-0.003-0.0030.0000.0000.0000.000
73A110LEU0-0.0320.00424.910-0.006-0.0060.0000.0000.0000.000
74A111ARG10.9070.94128.8090.1310.1310.0000.0000.0000.000
75A112GLU-1-0.930-0.97430.041-0.097-0.0970.0000.0000.0000.000
76A113ARG10.7730.88928.3060.1540.1540.0000.0000.0000.000
77A114TRP00.020-0.00123.064-0.007-0.0070.0000.0000.0000.000
78A115GLU-1-0.811-0.88428.885-0.156-0.1560.0000.0000.0000.000
79A116ILE0-0.002-0.00231.233-0.006-0.0060.0000.0000.0000.000
80A117ASP-1-0.848-0.92429.365-0.153-0.1530.0000.0000.0000.000
81A118CYS0-0.036-0.05224.487-0.022-0.0220.0000.0000.0000.000
82A119LEU0-0.003-0.00226.114-0.012-0.0120.0000.0000.0000.000
83A120ALA0-0.0260.00027.911-0.008-0.0080.0000.0000.0000.000
84A121PHE0-0.061-0.02826.0290.0020.0020.0000.0000.0000.000
85A122GLN0-0.048-0.01825.475-0.016-0.0160.0000.0000.0000.000
86A123PRO0-0.0020.00920.950-0.015-0.0150.0000.0000.0000.000
87A124ASP-1-0.809-0.89318.732-0.412-0.4120.0000.0000.0000.000
88A125VAL0-0.053-0.03214.809-0.076-0.0760.0000.0000.0000.000
89A126LEU00.0100.01417.1280.0560.0560.0000.0000.0000.000
90A127SER00.0150.00416.788-0.054-0.0540.0000.0000.0000.000
91A128ILE00.002-0.00617.7130.0420.0420.0000.0000.0000.000
92A129LEU0-0.0180.00318.526-0.015-0.0150.0000.0000.0000.000
93A130ILE00.0140.00520.8010.0120.0120.0000.0000.0000.000
94A131GLY00.0630.02522.733-0.004-0.0040.0000.0000.0000.000
95A132VAL00.0410.03025.1700.0130.0130.0000.0000.0000.000
96A133ASN0-0.027-0.05627.0390.0030.0030.0000.0000.0000.000
97A134ASP-1-0.835-0.92827.826-0.100-0.1000.0000.0000.0000.000
98A135TYR0-0.0040.00029.1360.0070.0070.0000.0000.0000.000
99A136TRP00.0520.02930.7860.0050.0050.0000.0000.0000.000
100A137HIS00.0060.01032.7420.0050.0050.0000.0000.0000.000
101A138THR0-0.106-0.05233.8400.0040.0040.0000.0000.0000.000
102A139LEU0-0.046-0.01834.3720.0040.0040.0000.0000.0000.000
103A140THR0-0.027-0.01836.4870.0020.0020.0000.0000.0000.000
104A141HIS0-0.016-0.01036.8050.0020.0020.0000.0000.0000.000
105A142GLY0-0.0020.02039.7910.0000.0000.0000.0000.0000.000
106A143TYR00.022-0.00132.2700.0010.0010.0000.0000.0000.000
107A144LYS10.8740.90937.4180.0400.0400.0000.0000.0000.000
108A145GLY00.0060.02533.8200.0020.0020.0000.0000.0000.000
109A146THR00.0390.01632.7110.0000.0000.0000.0000.0000.000
110A147VAL00.0570.01526.490-0.007-0.0070.0000.0000.0000.000
111A148GLU-1-0.935-0.96427.871-0.041-0.0410.0000.0000.0000.000
112A149THR0-0.032-0.00929.163-0.005-0.0050.0000.0000.0000.000
113A150TYR00.0000.00022.404-0.007-0.0070.0000.0000.0000.000
114A151GLU-1-0.779-0.87923.104-0.072-0.0720.0000.0000.0000.000
115A152ASN0-0.032-0.02624.849-0.012-0.0120.0000.0000.0000.000
116A153ASP-1-0.877-0.94627.051-0.103-0.1030.0000.0000.0000.000
117A154LEU0-0.020-0.01021.020-0.014-0.0140.0000.0000.0000.000
118A155ARG10.8210.89622.2420.0720.0720.0000.0000.0000.000
119A156ALA0-0.016-0.00623.435-0.015-0.0150.0000.0000.0000.000
120A157LEU0-0.016-0.00924.313-0.006-0.0060.0000.0000.0000.000
121A158LEU0-0.0140.01318.422-0.021-0.0210.0000.0000.0000.000
122A159LYS10.8980.95321.4050.1160.1160.0000.0000.0000.000
123A160TYR0-0.053-0.06223.226-0.006-0.0060.0000.0000.0000.000
124A161THR0-0.005-0.02821.091-0.002-0.0020.0000.0000.0000.000
125A162LYS10.9070.96816.0230.4740.4740.0000.0000.0000.000
126A163GLU-1-0.905-0.95321.221-0.161-0.1610.0000.0000.0000.000
127A164LYS10.8990.95324.6780.1610.1610.0000.0000.0000.000
128A165LEU0-0.018-0.00322.5230.0070.0070.0000.0000.0000.000
129A166PRO00.0310.02320.846-0.036-0.0360.0000.0000.0000.000
130A167ASN0-0.061-0.04218.267-0.050-0.0500.0000.0000.0000.000
131A168THR0-0.027-0.01717.583-0.046-0.0460.0000.0000.0000.000
132A169GLN0-0.048-0.02511.916-0.206-0.2060.0000.0000.0000.000
133A170ILE00.0300.01014.5170.0420.0420.0000.0000.0000.000
134A171VAL00.0050.00412.080-0.111-0.1110.0000.0000.0000.000
135A172LEU0-0.0080.00413.5680.0730.0730.0000.0000.0000.000
136A173CYS0-0.053-0.02914.097-0.030-0.0300.0000.0000.0000.000
137A174GLU-1-0.854-0.93215.901-0.045-0.0450.0000.0000.0000.000
138A175PRO00.0030.00617.5450.0040.0040.0000.0000.0000.000
139A176PHE0-0.038-0.03320.4680.0110.0110.0000.0000.0000.000
140A177THR0-0.0060.01622.6370.0020.0020.0000.0000.0000.000
141A178LEU0-0.0210.00124.6750.0080.0080.0000.0000.0000.000
142A179ARG10.9450.95827.204-0.007-0.0070.0000.0000.0000.000
143A180ASP-1-0.888-0.92529.886-0.009-0.0090.0000.0000.0000.000
144A181GLY0-0.016-0.00331.616-0.002-0.0020.0000.0000.0000.000
145A182ALA0-0.068-0.05232.3590.0030.0030.0000.0000.0000.000
146A183ALA0-0.029-0.01933.3030.0020.0020.0000.0000.0000.000
147A184ILE0-0.067-0.00429.958-0.001-0.0010.0000.0000.0000.000
148A185GLU-1-0.880-0.94133.592-0.013-0.0130.0000.0000.0000.000
149A186ASP-1-0.842-0.95132.548-0.004-0.0040.0000.0000.0000.000
150A187SER0-0.021-0.01433.8220.0000.0000.0000.0000.0000.000
151A188LYS10.9410.97436.0830.0180.0180.0000.0000.0000.000
152A189TRP00.0330.03028.476-0.006-0.0060.0000.0000.0000.000
153A190TYR0-0.031-0.01727.1790.0010.0010.0000.0000.0000.000
154A191PRO00.019-0.00429.0140.0020.0020.0000.0000.0000.000
155A192MET0-0.008-0.00328.2380.0000.0000.0000.0000.0000.000
156A193PHE00.0570.02524.253-0.005-0.0050.0000.0000.0000.000
157A194ASP-1-0.900-0.97024.095-0.007-0.0070.0000.0000.0000.000
158A195GLU-1-0.916-0.96323.2460.0030.0030.0000.0000.0000.000
159A196PHE00.0150.00224.052-0.006-0.0060.0000.0000.0000.000
160A197ARG10.8770.95419.4450.0050.0050.0000.0000.0000.000
161A198LYS10.9010.96019.028-0.034-0.0340.0000.0000.0000.000
162A199SER00.0170.01419.504-0.002-0.0020.0000.0000.0000.000
163A200ALA00.0000.00318.329-0.015-0.0150.0000.0000.0000.000
164A201ARG10.9410.97911.769-0.011-0.0110.0000.0000.0000.000
165A202LYS10.9190.97815.0840.0170.0170.0000.0000.0000.000
166A203LEU0-0.017-0.01016.848-0.011-0.0110.0000.0000.0000.000
167A204SER0-0.053-0.03212.978-0.039-0.0390.0000.0000.0000.000
168A205GLU-1-0.901-0.95212.197-0.071-0.0710.0000.0000.0000.000
169A206GLU-1-0.875-0.93513.279-0.130-0.1300.0000.0000.0000.000
170A207PHE0-0.056-0.03415.6930.0000.0000.0000.0000.0000.000
171A208ASN0-0.068-0.0279.107-0.039-0.0390.0000.0000.0000.000
172A209THR0-0.055-0.02410.953-0.119-0.1190.0000.0000.0000.000
173A210ILE0-0.010-0.0026.768-0.025-0.0250.0000.0000.0000.000
174A211PHE00.0360.0039.2240.1580.1580.0000.0000.0000.000
175A212VAL00.0060.00510.146-0.024-0.0240.0000.0000.0000.000
176A213PRO0-0.026-0.00510.8500.0480.0480.0000.0000.0000.000
177A214PHE00.054-0.00113.9770.0280.0280.0000.0000.0000.000
178A215GLN0-0.012-0.00317.0070.0080.0080.0000.0000.0000.000
179A216SER00.0380.01515.0590.0060.0060.0000.0000.0000.000
180A217GLY00.0210.00716.7450.0180.0180.0000.0000.0000.000
181A218PHE0-0.001-0.01617.4680.0100.0100.0000.0000.0000.000
182A219ASP-1-0.895-0.94920.1080.0150.0150.0000.0000.0000.000
183A220ALA0-0.062-0.03218.8840.0140.0140.0000.0000.0000.000
184A221ALA00.0270.00920.9220.0050.0050.0000.0000.0000.000
185A222VAL0-0.005-0.00922.6780.0030.0030.0000.0000.0000.000
186A223LYS10.8830.95023.119-0.055-0.0550.0000.0000.0000.000
187A224LEU0-0.057-0.01722.2790.0050.0050.0000.0000.0000.000
188A225ALA00.0080.00626.594-0.002-0.0020.0000.0000.0000.000
189A226PRO00.0560.02728.227-0.001-0.0010.0000.0000.0000.000
190A227ALA00.0680.02328.223-0.006-0.0060.0000.0000.0000.000
191A228ARG10.8950.93829.1860.0180.0180.0000.0000.0000.000
192A229TYR0-0.066-0.01027.398-0.003-0.0030.0000.0000.0000.000
193A230TRP0-0.018-0.01823.414-0.013-0.0130.0000.0000.0000.000
194A231SER00.018-0.00727.187-0.010-0.0100.0000.0000.0000.000
195A232ASN00.0120.02529.0720.0070.0070.0000.0000.0000.000
196A233ASP-1-0.717-0.83131.049-0.063-0.0630.0000.0000.0000.000
197A234GLY00.0430.02429.0140.0050.0050.0000.0000.0000.000
198A235VAL0-0.030-0.01227.810-0.002-0.0020.0000.0000.0000.000
199A236HIS10.7290.81726.7660.0710.0710.0000.0000.0000.000
200A237PRO00.0020.01824.0460.0080.0080.0000.0000.0000.000
201A238ASP-1-0.821-0.91226.780-0.074-0.0740.0000.0000.0000.000
202A239LEU0-0.013-0.02926.779-0.008-0.0080.0000.0000.0000.000
203A240PRO0-0.0030.00325.740-0.011-0.0110.0000.0000.0000.000
204A241GLY00.0620.03023.388-0.003-0.0030.0000.0000.0000.000
205A242ARG10.8020.89222.0380.0960.0960.0000.0000.0000.000
206A243GLN00.0320.01421.047-0.039-0.0390.0000.0000.0000.000
207A244LEU00.0040.01418.616-0.019-0.0190.0000.0000.0000.000
208A245MET0-0.030-0.00617.405-0.009-0.0090.0000.0000.0000.000
209A246ALA00.0170.01316.431-0.040-0.0400.0000.0000.0000.000
210A247ASN00.0240.00115.602-0.065-0.0650.0000.0000.0000.000
211A248MET00.0160.03112.802-0.033-0.0330.0000.0000.0000.000
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