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: 3JKQL

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 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 219
LigandCharge SEP=-2
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2841993.882805
FMO2-HF: Nuclear repulsion 2752950.093878
FMO2-HF: Total energy -89043.788927
FMO2-MP2: Total energy -89300.671302


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.
0.9642.291-0.009-0.654-0.6640.003
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 : 0.049 / q_NPA : 0.022
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].
3A40LYS10.9130.9613.9271.7003.027-0.009-0.654-0.6640.003
4A41ILE00.0300.0206.3990.3510.3510.0000.0000.0000.000
5A42ASN0-0.065-0.0329.015-0.077-0.0770.0000.0000.0000.000
6A43LEU00.0300.01912.0970.1050.1050.0000.0000.0000.000
7A44LYS10.8810.93015.4170.3710.3710.0000.0000.0000.000
8A45LYS10.9070.91718.5960.2470.2470.0000.0000.0000.000
9A46ASP-1-0.900-0.93121.919-0.244-0.2440.0000.0000.0000.000
10A47CYS0-0.079-0.01719.1370.0000.0000.0000.0000.0000.000
11A48VAL00.0160.01521.2190.0170.0170.0000.0000.0000.000
12A49ILE0-0.025-0.01617.259-0.036-0.0360.0000.0000.0000.000
13A50LEU0-0.0110.00120.3000.0360.0360.0000.0000.0000.000
14A51PHE00.0100.00717.848-0.023-0.0230.0000.0000.0000.000
15A52GLN00.0580.02021.6470.0360.0360.0000.0000.0000.000
16A53GLY0-0.008-0.02022.396-0.013-0.0130.0000.0000.0000.000
17A54ASP-1-0.753-0.88524.876-0.126-0.1260.0000.0000.0000.000
18A55SEP-2-1.674-1.81327.750-0.176-0.1760.0000.0000.0000.000
19A56ILE0-0.055-0.01723.7170.0010.0010.0000.0000.0000.000
20A57THR0-0.043-0.00923.254-0.009-0.0090.0000.0000.0000.000
21A58ASP-1-0.790-0.85525.168-0.120-0.1200.0000.0000.0000.000
22A59CYS0-0.037-0.02128.2310.0020.0020.0000.0000.0000.000
23A60GLY00.0320.01530.057-0.001-0.0010.0000.0000.0000.000
24A61ARG10.8550.95428.9630.1480.1480.0000.0000.0000.000
25A62ASP-1-0.833-0.91232.154-0.097-0.0970.0000.0000.0000.000
26A63ARG10.8170.88533.4970.0970.0970.0000.0000.0000.000
27A64ASN0-0.059-0.03334.841-0.002-0.0020.0000.0000.0000.000
28A65SER0-0.0270.00432.8620.0000.0000.0000.0000.0000.000
29A66ASN00.0580.00933.659-0.009-0.0090.0000.0000.0000.000
30A67ARG10.8710.94532.7540.1160.1160.0000.0000.0000.000
31A68CYS00.0160.02027.1730.0000.0000.0000.0000.0000.000
32A69ASN0-0.024-0.03725.6130.0010.0010.0000.0000.0000.000
33A70THR0-0.031-0.01527.8300.0060.0060.0000.0000.0000.000
34A71MET00.0490.02129.705-0.010-0.0100.0000.0000.0000.000
35A72GLU-1-0.779-0.88531.367-0.123-0.1230.0000.0000.0000.000
36A73GLN0-0.0340.00528.113-0.005-0.0050.0000.0000.0000.000
37A74PHE00.006-0.01224.859-0.008-0.0080.0000.0000.0000.000
38A75GLY00.0730.05027.697-0.002-0.0020.0000.0000.0000.000
39A76SER0-0.047-0.03329.2380.0000.0000.0000.0000.0000.000
40A77GLY00.0720.02526.1940.0070.0070.0000.0000.0000.000
41A78TYR00.041-0.01119.036-0.009-0.0090.0000.0000.0000.000
42A79VAL00.0270.04421.397-0.019-0.0190.0000.0000.0000.000
43A80LEU00.0110.02222.324-0.018-0.0180.0000.0000.0000.000
44A81PHE0-0.028-0.01822.028-0.006-0.0060.0000.0000.0000.000
45A82THR00.015-0.01016.670-0.012-0.0120.0000.0000.0000.000
46A83ALA00.0070.00818.951-0.030-0.0300.0000.0000.0000.000
47A84THR0-0.016-0.02021.355-0.012-0.0120.0000.0000.0000.000
48A85GLN00.0020.00717.253-0.021-0.0210.0000.0000.0000.000
49A86LEU0-0.028-0.00915.178-0.027-0.0270.0000.0000.0000.000
50A87LEU0-0.062-0.04318.543-0.006-0.0060.0000.0000.0000.000
51A88GLU-1-0.824-0.90219.840-0.239-0.2390.0000.0000.0000.000
52A89GLY0-0.0070.00317.5770.0020.0020.0000.0000.0000.000
53A90LYS10.8360.92412.3040.6020.6020.0000.0000.0000.000
54A91ALA00.0770.04318.1680.0000.0000.0000.0000.0000.000
55A92ALA0-0.036-0.02120.3840.0110.0110.0000.0000.0000.000
56A93LEU0-0.052-0.02416.4800.0040.0040.0000.0000.0000.000
57A94GLN0-0.019-0.01021.0670.0080.0080.0000.0000.0000.000
58A95PRO00.0310.03019.9700.0050.0050.0000.0000.0000.000
59A96LYS10.9390.97822.2260.2670.2670.0000.0000.0000.000
60A97ILE0-0.011-0.00620.433-0.017-0.0170.0000.0000.0000.000
61A98TYR00.014-0.01023.7070.0250.0250.0000.0000.0000.000
62A99ASN0-0.042-0.03824.032-0.025-0.0250.0000.0000.0000.000
63A100ARG10.8540.91825.9190.1720.1720.0000.0000.0000.000
64A101GLY00.0380.04526.8570.0090.0090.0000.0000.0000.000
65A102ILE0-0.085-0.03027.6050.0080.0080.0000.0000.0000.000
66A103SER00.042-0.01030.4760.0010.0010.0000.0000.0000.000
67A104GLY00.0050.02031.9840.0020.0020.0000.0000.0000.000
68A105ASN0-0.021-0.02229.515-0.003-0.0030.0000.0000.0000.000
69A106LYS10.9080.96829.2910.0790.0790.0000.0000.0000.000
70A107VAL00.021-0.01325.522-0.007-0.0070.0000.0000.0000.000
71A108TYR00.0290.01928.086-0.006-0.0060.0000.0000.0000.000
72A109GLN0-0.036-0.01731.4360.0010.0010.0000.0000.0000.000
73A110LEU0-0.049-0.00625.052-0.006-0.0060.0000.0000.0000.000
74A111ARG10.8360.87729.0480.1290.1290.0000.0000.0000.000
75A112GLU-1-0.873-0.93930.120-0.093-0.0930.0000.0000.0000.000
76A113ARG10.7720.86928.4260.1470.1470.0000.0000.0000.000
77A114TRP00.0320.00223.080-0.005-0.0050.0000.0000.0000.000
78A115GLU-1-0.759-0.84228.964-0.153-0.1530.0000.0000.0000.000
79A116ILE00.0080.00231.312-0.006-0.0060.0000.0000.0000.000
80A117ASP-1-0.843-0.91429.320-0.150-0.1500.0000.0000.0000.000
81A118CYS0-0.049-0.04824.355-0.021-0.0210.0000.0000.0000.000
82A119LEU00.0000.00226.146-0.011-0.0110.0000.0000.0000.000
83A120ALA0-0.0180.00427.989-0.008-0.0080.0000.0000.0000.000
84A121PHE0-0.049-0.02826.1830.0020.0020.0000.0000.0000.000
85A122GLN0-0.054-0.01325.476-0.013-0.0130.0000.0000.0000.000
86A123PRO0-0.0010.01021.021-0.015-0.0150.0000.0000.0000.000
87A124ASP-1-0.747-0.84918.541-0.409-0.4090.0000.0000.0000.000
88A125VAL0-0.051-0.03414.767-0.073-0.0730.0000.0000.0000.000
89A126LEU00.0080.01317.2110.0540.0540.0000.0000.0000.000
90A127SER00.0230.01316.951-0.056-0.0560.0000.0000.0000.000
91A128ILE00.001-0.00417.7900.0410.0410.0000.0000.0000.000
92A129LEU0-0.0100.00618.599-0.013-0.0130.0000.0000.0000.000
93A130ILE00.0060.00220.8710.0120.0120.0000.0000.0000.000
94A131GLY00.0660.02422.801-0.004-0.0040.0000.0000.0000.000
95A132VAL00.0360.03125.2360.0120.0120.0000.0000.0000.000
96A133ASN0-0.004-0.02427.0990.0060.0060.0000.0000.0000.000
97A134ASP-1-0.829-0.91927.775-0.097-0.0970.0000.0000.0000.000
98A135TYR0-0.0080.00129.1770.0060.0060.0000.0000.0000.000
99A136TRP00.0530.02330.8460.0040.0040.0000.0000.0000.000
100A137HIS00.0170.01932.8000.0060.0060.0000.0000.0000.000
101A138THR0-0.104-0.05033.8970.0040.0040.0000.0000.0000.000
102A139LEU0-0.048-0.02034.5310.0040.0040.0000.0000.0000.000
103A140THR0-0.018-0.01236.7360.0020.0020.0000.0000.0000.000
104A141HIS0-0.042-0.03136.7420.0020.0020.0000.0000.0000.000
105A142GLY00.0050.02539.8530.0000.0000.0000.0000.0000.000
106A143TYR00.0310.00431.9470.0010.0010.0000.0000.0000.000
107A144LYS10.8730.90937.4820.0380.0380.0000.0000.0000.000
108A145GLY00.0060.02533.8880.0020.0020.0000.0000.0000.000
109A146THR00.0350.01432.7730.0000.0000.0000.0000.0000.000
110A147VAL00.0600.01926.623-0.006-0.0060.0000.0000.0000.000
111A148GLU-1-0.925-0.95827.888-0.038-0.0380.0000.0000.0000.000
112A149THR0-0.0160.00029.180-0.005-0.0050.0000.0000.0000.000
113A150TYR0-0.007-0.00122.459-0.007-0.0070.0000.0000.0000.000
114A151GLU-1-0.730-0.83723.087-0.070-0.0700.0000.0000.0000.000
115A152ASN0-0.056-0.04324.865-0.013-0.0130.0000.0000.0000.000
116A153ASP-1-0.858-0.93327.068-0.101-0.1010.0000.0000.0000.000
117A154LEU0-0.032-0.01820.789-0.013-0.0130.0000.0000.0000.000
118A155ARG10.7750.85321.8510.0720.0720.0000.0000.0000.000
119A156ALA0-0.0040.00023.451-0.015-0.0150.0000.0000.0000.000
120A157LEU0-0.020-0.00924.434-0.006-0.0060.0000.0000.0000.000
121A158LEU0-0.0140.01018.462-0.021-0.0210.0000.0000.0000.000
122A159LYS10.8450.90321.4200.1170.1170.0000.0000.0000.000
123A160TYR0-0.045-0.05123.240-0.007-0.0070.0000.0000.0000.000
124A161THR0-0.004-0.02221.180-0.003-0.0030.0000.0000.0000.000
125A162LYS10.8580.93316.5970.4530.4530.0000.0000.0000.000
126A163GLU-1-0.855-0.90421.235-0.154-0.1540.0000.0000.0000.000
127A164LYS10.8980.95324.6900.1570.1570.0000.0000.0000.000
128A165LEU0-0.016-0.00722.6220.0060.0060.0000.0000.0000.000
129A166PRO00.0460.02820.845-0.035-0.0350.0000.0000.0000.000
130A167ASN0-0.049-0.03018.287-0.039-0.0390.0000.0000.0000.000
131A168THR0-0.024-0.01317.583-0.045-0.0450.0000.0000.0000.000
132A169GLN0-0.038-0.01412.350-0.184-0.1840.0000.0000.0000.000
133A170ILE00.0330.01014.5440.0410.0410.0000.0000.0000.000
134A171VAL00.0030.00312.099-0.106-0.1060.0000.0000.0000.000
135A172LEU0-0.0060.00513.6520.0700.0700.0000.0000.0000.000
136A173CYS0-0.054-0.02914.167-0.026-0.0260.0000.0000.0000.000
137A174GLU-1-0.787-0.88615.953-0.037-0.0370.0000.0000.0000.000
138A175PRO0-0.013-0.00317.6040.0040.0040.0000.0000.0000.000
139A176PHE0-0.014-0.02720.6280.0100.0100.0000.0000.0000.000
140A177THR00.0070.01122.6850.0020.0020.0000.0000.0000.000
141A178LEU0-0.044-0.00324.7270.0080.0080.0000.0000.0000.000
142A179ARG10.9200.93427.208-0.008-0.0080.0000.0000.0000.000
143A180ASP-1-0.889-0.92529.917-0.010-0.0100.0000.0000.0000.000
144A181GLY00.0110.00431.618-0.002-0.0020.0000.0000.0000.000
145A182ALA0-0.064-0.05432.3940.0030.0030.0000.0000.0000.000
146A183ALA0-0.028-0.01633.4380.0020.0020.0000.0000.0000.000
147A184ILE0-0.052-0.00230.115-0.001-0.0010.0000.0000.0000.000
148A185GLU-1-0.781-0.86933.633-0.010-0.0100.0000.0000.0000.000
149A186ASP-1-0.779-0.91232.303-0.001-0.0010.0000.0000.0000.000
150A187SER0-0.026-0.01033.8580.0000.0000.0000.0000.0000.000
151A188LYS10.8170.89136.1260.0160.0160.0000.0000.0000.000
152A189TRP00.0260.02628.456-0.006-0.0060.0000.0000.0000.000
153A190TYR0-0.043-0.01726.9040.0010.0010.0000.0000.0000.000
154A191PRO00.016-0.00529.0190.0020.0020.0000.0000.0000.000
155A192MET00.0040.00128.2790.0000.0000.0000.0000.0000.000
156A193PHE00.0500.02224.627-0.005-0.0050.0000.0000.0000.000
157A194ASP-1-0.851-0.93024.134-0.007-0.0070.0000.0000.0000.000
158A195GLU-1-0.862-0.91823.2910.0080.0080.0000.0000.0000.000
159A196PHE00.017-0.00124.105-0.007-0.0070.0000.0000.0000.000
160A197ARG10.7850.88318.8810.0000.0000.0000.0000.0000.000
161A198LYS10.8260.90119.081-0.027-0.0270.0000.0000.0000.000
162A199SER0-0.007-0.00819.5200.0000.0000.0000.0000.0000.000
163A200ALA0-0.0010.00118.481-0.015-0.0150.0000.0000.0000.000
164A201ARG10.9480.98511.696-0.017-0.0170.0000.0000.0000.000
165A202LYS10.9040.95715.1000.0210.0210.0000.0000.0000.000
166A203LEU0-0.016-0.00616.861-0.011-0.0110.0000.0000.0000.000
167A204SER0-0.058-0.04112.952-0.034-0.0340.0000.0000.0000.000
168A205GLU-1-0.903-0.95711.987-0.077-0.0770.0000.0000.0000.000
169A206GLU-1-0.834-0.88913.292-0.124-0.1240.0000.0000.0000.000
170A207PHE0-0.048-0.02815.7060.0010.0010.0000.0000.0000.000
171A208ASN0-0.075-0.0288.7510.0370.0370.0000.0000.0000.000
172A209THR0-0.059-0.03010.967-0.123-0.1230.0000.0000.0000.000
173A210ILE0-0.0030.0016.898-0.021-0.0210.0000.0000.0000.000
174A211PHE00.0360.0079.2950.1520.1520.0000.0000.0000.000
175A212VAL00.0090.00510.205-0.019-0.0190.0000.0000.0000.000
176A213PRO0-0.023-0.00310.9520.0390.0390.0000.0000.0000.000
177A214PHE00.058-0.00214.0210.0270.0270.0000.0000.0000.000
178A215GLN0-0.011-0.00817.0500.0050.0050.0000.0000.0000.000
179A216SER00.0130.00715.1090.0150.0150.0000.0000.0000.000
180A217GLY00.0290.00916.7490.0180.0180.0000.0000.0000.000
181A218PHE00.013-0.00917.4880.0100.0100.0000.0000.0000.000
182A219ASP-1-0.867-0.92420.1730.0200.0200.0000.0000.0000.000
183A220ALA0-0.049-0.02418.9060.0140.0140.0000.0000.0000.000
184A221ALA00.0370.01920.9280.0050.0050.0000.0000.0000.000
185A222VAL0-0.008-0.01122.6880.0020.0020.0000.0000.0000.000
186A223LYS10.8240.91422.365-0.046-0.0460.0000.0000.0000.000
187A224LEU0-0.058-0.01922.1840.0040.0040.0000.0000.0000.000
188A225ALA00.0130.01026.593-0.002-0.0020.0000.0000.0000.000
189A226PRO00.0590.03228.239-0.001-0.0010.0000.0000.0000.000
190A227ALA00.0620.01928.244-0.006-0.0060.0000.0000.0000.000
191A228ARG10.8800.93229.2130.0130.0130.0000.0000.0000.000
192A229TYR0-0.069-0.01427.217-0.004-0.0040.0000.0000.0000.000
193A230TRP0-0.029-0.02723.548-0.012-0.0120.0000.0000.0000.000
194A231SER0-0.007-0.03827.221-0.010-0.0100.0000.0000.0000.000
195A232ASN0-0.0160.01129.1080.0080.0080.0000.0000.0000.000
196A233ASP-1-0.744-0.84831.222-0.058-0.0580.0000.0000.0000.000
197A234GLY00.0490.03329.0490.0040.0040.0000.0000.0000.000
198A235VAL0-0.024-0.00727.856-0.001-0.0010.0000.0000.0000.000
199A236HIS10.7680.83226.8170.0680.0680.0000.0000.0000.000
200A237PRO00.0070.03824.1050.0080.0080.0000.0000.0000.000
201A238ASP-1-0.801-0.89526.824-0.071-0.0710.0000.0000.0000.000
202A239LEU0-0.006-0.02826.815-0.007-0.0070.0000.0000.0000.000
203A240PRO0-0.0010.00325.759-0.011-0.0110.0000.0000.0000.000
204A241GLY00.0590.02723.424-0.003-0.0030.0000.0000.0000.000
205A242ARG10.7790.88022.0740.0880.0880.0000.0000.0000.000
206A243GLN00.0470.01921.265-0.035-0.0350.0000.0000.0000.000
207A244LEU0-0.0080.00718.415-0.018-0.0180.0000.0000.0000.000
208A245MET0-0.024-0.00217.435-0.008-0.0080.0000.0000.0000.000
209A246ALA00.0180.01216.466-0.037-0.0370.0000.0000.0000.000
210A247ASN00.0240.00915.618-0.063-0.0630.0000.0000.0000.000
211A248MET00.0180.03012.832-0.030-0.0300.0000.0000.0000.000
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