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: LNQJ9

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 OptAll
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 -2851808.292005
FMO2-HF: Nuclear repulsion 2762763.997095
FMO2-HF: Total energy -89044.29491
FMO2-MP2: Total energy -89301.12264


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.
0.2281.9260.018-0.876-0.8410.003
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 : 0.041 / q_NPA : 0.018
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].
3A40LYS10.8790.9453.5351.1002.7980.018-0.876-0.8410.003
4A41ILE00.0070.0116.0520.3290.3290.0000.0000.0000.000
5A42ASN0-0.055-0.0258.715-0.115-0.1150.0000.0000.0000.000
6A43LEU00.0250.00711.7820.1060.1060.0000.0000.0000.000
7A44LYS10.8860.94515.2950.3910.3910.0000.0000.0000.000
8A45LYS10.9220.92818.5830.2480.2480.0000.0000.0000.000
9A46ASP-1-0.884-0.92221.571-0.252-0.2520.0000.0000.0000.000
10A47CYS0-0.055-0.00719.0790.0100.0100.0000.0000.0000.000
11A48VAL0-0.0030.01421.1830.0220.0220.0000.0000.0000.000
12A49ILE0-0.021-0.00916.997-0.038-0.0380.0000.0000.0000.000
13A50LEU0-0.0030.00419.9060.0360.0360.0000.0000.0000.000
14A51PHE00.0150.01017.437-0.026-0.0260.0000.0000.0000.000
15A52GLN00.0260.00321.3780.0350.0350.0000.0000.0000.000
16A53GLY00.026-0.00222.143-0.012-0.0120.0000.0000.0000.000
17A54ASP-1-0.770-0.88524.489-0.111-0.1110.0000.0000.0000.000
18A55SEP-2-1.623-1.78827.081-0.161-0.1610.0000.0000.0000.000
19A56ILE0-0.052-0.00923.3660.0020.0020.0000.0000.0000.000
20A57THR0-0.054-0.01222.901-0.013-0.0130.0000.0000.0000.000
21A58ASP-1-0.823-0.87024.853-0.111-0.1110.0000.0000.0000.000
22A59CYS0-0.022-0.00427.7150.0030.0030.0000.0000.0000.000
23A60GLY00.0300.02429.5820.0010.0010.0000.0000.0000.000
24A61ARG10.8410.93828.6320.1420.1420.0000.0000.0000.000
25A62ASP-1-0.853-0.91931.760-0.094-0.0940.0000.0000.0000.000
26A63ARG10.8270.88732.9620.0900.0900.0000.0000.0000.000
27A64ASN0-0.055-0.03734.236-0.004-0.0040.0000.0000.0000.000
28A65SER0-0.0070.01532.579-0.002-0.0020.0000.0000.0000.000
29A66ASN00.0570.01932.748-0.011-0.0110.0000.0000.0000.000
30A67ARG10.8460.91732.1780.1100.1100.0000.0000.0000.000
31A68CYS00.0160.01926.576-0.001-0.0010.0000.0000.0000.000
32A69ASN0-0.030-0.03525.0870.0010.0010.0000.0000.0000.000
33A70THR0-0.025-0.02427.2920.0070.0070.0000.0000.0000.000
34A71MET00.0400.02129.363-0.008-0.0080.0000.0000.0000.000
35A72GLU-1-0.773-0.86531.147-0.117-0.1170.0000.0000.0000.000
36A73GLN0-0.0220.01127.577-0.005-0.0050.0000.0000.0000.000
37A74PHE00.019-0.00924.438-0.007-0.0070.0000.0000.0000.000
38A75GLY00.0680.04327.276-0.002-0.0020.0000.0000.0000.000
39A76SER0-0.057-0.03328.766-0.001-0.0010.0000.0000.0000.000
40A77GLY00.0760.02425.8770.0090.0090.0000.0000.0000.000
41A78TYR00.040-0.01418.712-0.009-0.0090.0000.0000.0000.000
42A79VAL00.0060.03221.168-0.016-0.0160.0000.0000.0000.000
43A80LEU00.0310.03222.094-0.017-0.0170.0000.0000.0000.000
44A81PHE0-0.0090.00621.642-0.005-0.0050.0000.0000.0000.000
45A82THR00.013-0.01716.399-0.011-0.0110.0000.0000.0000.000
46A83ALA00.0110.00918.706-0.029-0.0290.0000.0000.0000.000
47A84THR0-0.038-0.03721.020-0.005-0.0050.0000.0000.0000.000
48A85GLN0-0.009-0.01017.007-0.017-0.0170.0000.0000.0000.000
49A86LEU0-0.037-0.01114.869-0.028-0.0280.0000.0000.0000.000
50A87LEU0-0.050-0.03518.127-0.007-0.0070.0000.0000.0000.000
51A88GLU-1-0.788-0.86819.274-0.203-0.2030.0000.0000.0000.000
52A89GLY00.0160.02416.932-0.003-0.0030.0000.0000.0000.000
53A90LYS10.8020.87712.6340.4670.4670.0000.0000.0000.000
54A91ALA00.0460.04117.896-0.004-0.0040.0000.0000.0000.000
55A92ALA0-0.027-0.01820.4300.0080.0080.0000.0000.0000.000
56A93LEU0-0.046-0.02216.2700.0040.0040.0000.0000.0000.000
57A94GLN0-0.030-0.01820.8990.0070.0070.0000.0000.0000.000
58A95PRO00.0360.02819.6040.0030.0030.0000.0000.0000.000
59A96LYS10.8820.93821.8220.2790.2790.0000.0000.0000.000
60A97ILE00.000-0.00320.054-0.014-0.0140.0000.0000.0000.000
61A98TYR00.003-0.01223.3290.0250.0250.0000.0000.0000.000
62A99ASN0-0.045-0.04223.612-0.025-0.0250.0000.0000.0000.000
63A100ARG10.8260.90625.5350.1680.1680.0000.0000.0000.000
64A101GLY00.0600.04926.3330.0060.0060.0000.0000.0000.000
65A102ILE0-0.088-0.03927.0750.0070.0070.0000.0000.0000.000
66A103SER00.0610.00329.9600.0000.0000.0000.0000.0000.000
67A104GLY00.0010.01031.7720.0000.0000.0000.0000.0000.000
68A105ASN0-0.020-0.01929.230-0.004-0.0040.0000.0000.0000.000
69A106LYS10.8780.95329.0260.0780.0780.0000.0000.0000.000
70A107VAL00.008-0.00824.981-0.008-0.0080.0000.0000.0000.000
71A108TYR00.0280.01727.583-0.008-0.0080.0000.0000.0000.000
72A109GLN0-0.060-0.04230.8630.0020.0020.0000.0000.0000.000
73A110LEU0-0.032-0.00124.525-0.006-0.0060.0000.0000.0000.000
74A111ARG10.7820.84428.5370.1340.1340.0000.0000.0000.000
75A112GLU-1-0.859-0.92329.919-0.092-0.0920.0000.0000.0000.000
76A113ARG10.7790.87327.9990.1420.1420.0000.0000.0000.000
77A114TRP00.0320.00922.694-0.003-0.0030.0000.0000.0000.000
78A115GLU-1-0.742-0.83428.651-0.159-0.1590.0000.0000.0000.000
79A116ILE0-0.0140.00330.930-0.006-0.0060.0000.0000.0000.000
80A117ASP-1-0.817-0.91228.851-0.151-0.1510.0000.0000.0000.000
81A118CYS0-0.063-0.04423.830-0.021-0.0210.0000.0000.0000.000
82A119LEU00.002-0.00425.354-0.012-0.0120.0000.0000.0000.000
83A120ALA00.0100.01627.244-0.009-0.0090.0000.0000.0000.000
84A121PHE0-0.043-0.02425.7670.0000.0000.0000.0000.0000.000
85A122GLN0-0.068-0.02424.990-0.015-0.0150.0000.0000.0000.000
86A123PRO00.0050.01720.375-0.016-0.0160.0000.0000.0000.000
87A124ASP-1-0.742-0.85517.918-0.440-0.4400.0000.0000.0000.000
88A125VAL0-0.040-0.02114.366-0.083-0.0830.0000.0000.0000.000
89A126LEU00.0210.01616.7000.0570.0570.0000.0000.0000.000
90A127SER00.0140.01416.485-0.047-0.0470.0000.0000.0000.000
91A128ILE00.007-0.00517.2630.0380.0380.0000.0000.0000.000
92A129LEU0-0.0140.00618.249-0.007-0.0070.0000.0000.0000.000
93A130ILE00.0250.01520.6540.0100.0100.0000.0000.0000.000
94A131GLY00.0700.02922.475-0.003-0.0030.0000.0000.0000.000
95A132VAL0-0.0030.00724.9330.0120.0120.0000.0000.0000.000
96A133ASN0-0.016-0.03126.5850.0090.0090.0000.0000.0000.000
97A134ASP-1-0.811-0.91727.332-0.092-0.0920.0000.0000.0000.000
98A135TYR0-0.022-0.00928.6220.0050.0050.0000.0000.0000.000
99A136TRP00.0490.02530.3770.0030.0030.0000.0000.0000.000
100A137HIS00.0330.02332.3440.0050.0050.0000.0000.0000.000
101A138THR0-0.094-0.05333.6950.0030.0030.0000.0000.0000.000
102A139LEU0-0.038-0.01234.3840.0030.0030.0000.0000.0000.000
103A140THR0-0.006-0.00836.1980.0020.0020.0000.0000.0000.000
104A141HIS0-0.055-0.03636.1630.0020.0020.0000.0000.0000.000
105A142GLY00.0120.03039.527-0.001-0.0010.0000.0000.0000.000
106A143TYR00.0140.00031.7680.0010.0010.0000.0000.0000.000
107A144LYS10.8730.91037.1320.0370.0370.0000.0000.0000.000
108A145GLY00.0040.02933.1860.0010.0010.0000.0000.0000.000
109A146THR0-0.003-0.03532.2340.0010.0010.0000.0000.0000.000
110A147VAL00.0300.00426.145-0.007-0.0070.0000.0000.0000.000
111A148GLU-1-0.855-0.90027.338-0.042-0.0420.0000.0000.0000.000
112A149THR0-0.0080.00928.986-0.005-0.0050.0000.0000.0000.000
113A150TYR0-0.024-0.00621.927-0.009-0.0090.0000.0000.0000.000
114A151GLU-1-0.713-0.81522.984-0.075-0.0750.0000.0000.0000.000
115A152ASN0-0.029-0.03224.669-0.018-0.0180.0000.0000.0000.000
116A153ASP-1-0.847-0.92727.187-0.103-0.1030.0000.0000.0000.000
117A154LEU0-0.025-0.01120.315-0.014-0.0140.0000.0000.0000.000
118A155ARG10.7620.83822.2660.0780.0780.0000.0000.0000.000
119A156ALA0-0.007-0.00623.588-0.014-0.0140.0000.0000.0000.000
120A157LEU0-0.017-0.00323.850-0.009-0.0090.0000.0000.0000.000
121A158LEU0-0.0140.01418.046-0.021-0.0210.0000.0000.0000.000
122A159LYS10.8330.90021.4120.1330.1330.0000.0000.0000.000
123A160TYR0-0.033-0.04323.210-0.009-0.0090.0000.0000.0000.000
124A161THR0-0.004-0.03020.956-0.001-0.0010.0000.0000.0000.000
125A162LYS10.8310.90816.3880.4920.4920.0000.0000.0000.000
126A163GLU-1-0.823-0.89521.517-0.171-0.1710.0000.0000.0000.000
127A164LYS10.8760.94724.9410.1710.1710.0000.0000.0000.000
128A165LEU0-0.0100.00322.5330.0070.0070.0000.0000.0000.000
129A166PRO00.0400.02920.748-0.037-0.0370.0000.0000.0000.000
130A167ASN0-0.025-0.01918.446-0.044-0.0440.0000.0000.0000.000
131A168THR0-0.028-0.00517.368-0.053-0.0530.0000.0000.0000.000
132A169GLN0-0.022-0.01312.360-0.189-0.1890.0000.0000.0000.000
133A170ILE00.0180.00213.6200.0680.0680.0000.0000.0000.000
134A171VAL00.0090.00111.641-0.112-0.1120.0000.0000.0000.000
135A172LEU00.0000.01513.3520.0670.0670.0000.0000.0000.000
136A173CYS0-0.051-0.03013.957-0.011-0.0110.0000.0000.0000.000
137A174GLU-1-0.769-0.87315.755-0.004-0.0040.0000.0000.0000.000
138A175PRO0-0.051-0.01217.4120.0030.0030.0000.0000.0000.000
139A176PHE00.002-0.02020.3800.0140.0140.0000.0000.0000.000
140A177THR00.0080.00622.359-0.001-0.0010.0000.0000.0000.000
141A178LEU0-0.054-0.02324.5880.0090.0090.0000.0000.0000.000
142A179ARG10.9160.94226.582-0.026-0.0260.0000.0000.0000.000
143A180ASP-1-0.852-0.90130.0150.0050.0050.0000.0000.0000.000
144A181GLY00.0580.02632.049-0.002-0.0020.0000.0000.0000.000
145A182ALA0-0.079-0.03732.6240.0030.0030.0000.0000.0000.000
146A183ALA0-0.009-0.00733.4930.0000.0000.0000.0000.0000.000
147A184ILE0-0.048-0.00529.839-0.002-0.0020.0000.0000.0000.000
148A185GLU-1-0.733-0.82733.324-0.002-0.0020.0000.0000.0000.000
149A186ASP-1-0.788-0.90631.8790.0150.0150.0000.0000.0000.000
150A187SER0-0.033-0.03633.6800.0010.0010.0000.0000.0000.000
151A188LYS10.7830.87635.6120.0060.0060.0000.0000.0000.000
152A189TRP00.0260.02528.086-0.006-0.0060.0000.0000.0000.000
153A190TYR0-0.044-0.02026.7230.0000.0000.0000.0000.0000.000
154A191PRO00.0280.00528.4930.0020.0020.0000.0000.0000.000
155A192MET00.0060.00627.8520.0000.0000.0000.0000.0000.000
156A193PHE00.0510.02724.073-0.005-0.0050.0000.0000.0000.000
157A194ASP-1-0.834-0.93123.7260.0110.0110.0000.0000.0000.000
158A195GLU-1-0.861-0.90423.2790.0210.0210.0000.0000.0000.000
159A196PHE00.0170.00223.680-0.008-0.0080.0000.0000.0000.000
160A197ARG10.7880.87918.500-0.027-0.0270.0000.0000.0000.000
161A198LYS10.8120.89319.081-0.033-0.0330.0000.0000.0000.000
162A199SER00.005-0.02619.393-0.004-0.0040.0000.0000.0000.000
163A200ALA0-0.0020.00018.491-0.018-0.0180.0000.0000.0000.000
164A201ARG10.8810.93911.290-0.051-0.0510.0000.0000.0000.000
165A202LYS10.8880.95315.2060.0210.0210.0000.0000.0000.000
166A203LEU0-0.017-0.00117.165-0.017-0.0170.0000.0000.0000.000
167A204SER0-0.054-0.04512.570-0.034-0.0340.0000.0000.0000.000
168A205GLU-1-0.864-0.92512.202-0.078-0.0780.0000.0000.0000.000
169A206GLU-1-0.839-0.90713.674-0.131-0.1310.0000.0000.0000.000
170A207PHE0-0.044-0.02615.850-0.003-0.0030.0000.0000.0000.000
171A208ASN0-0.083-0.0348.6670.0440.0440.0000.0000.0000.000
172A209THR0-0.051-0.02411.082-0.132-0.1320.0000.0000.0000.000
173A210ILE00.0060.0036.498-0.054-0.0540.0000.0000.0000.000
174A211PHE00.0260.0138.9490.1500.1500.0000.0000.0000.000
175A212VAL00.0130.0039.792-0.014-0.0140.0000.0000.0000.000
176A213PRO00.0000.01411.0110.0250.0250.0000.0000.0000.000
177A214PHE00.061-0.00414.0170.0300.0300.0000.0000.0000.000
178A215GLN0-0.037-0.01716.9530.0020.0020.0000.0000.0000.000
179A216SER00.0070.00115.2980.0150.0150.0000.0000.0000.000
180A217GLY00.0150.01316.9270.0210.0210.0000.0000.0000.000
181A218PHE00.010-0.00917.5410.0110.0110.0000.0000.0000.000
182A219ASP-1-0.844-0.91120.2050.0500.0500.0000.0000.0000.000
183A220ALA0-0.043-0.02319.0870.0130.0130.0000.0000.0000.000
184A221ALA00.0350.01621.0680.0020.0020.0000.0000.0000.000
185A222VAL0-0.002-0.01522.847-0.001-0.0010.0000.0000.0000.000
186A223LYS10.8230.91622.473-0.085-0.0850.0000.0000.0000.000
187A224LEU0-0.057-0.01622.2850.0050.0050.0000.0000.0000.000
188A225ALA00.0090.00926.745-0.004-0.0040.0000.0000.0000.000
189A226PRO00.0570.03628.2260.0010.0010.0000.0000.0000.000
190A227ALA00.0470.01128.211-0.005-0.0050.0000.0000.0000.000
191A228ARG10.8260.90029.145-0.003-0.0030.0000.0000.0000.000
192A229TYR0-0.031-0.00527.106-0.005-0.0050.0000.0000.0000.000
193A230TRP0-0.030-0.03223.445-0.010-0.0100.0000.0000.0000.000
194A231SER0-0.014-0.03826.673-0.011-0.0110.0000.0000.0000.000
195A232ASN0-0.049-0.00528.8160.0060.0060.0000.0000.0000.000
196A233ASP-1-0.738-0.85931.108-0.042-0.0420.0000.0000.0000.000
197A234GLY00.0490.03429.0280.0040.0040.0000.0000.0000.000
198A235VAL0-0.022-0.00827.6410.0000.0000.0000.0000.0000.000
199A236HIS10.7810.83626.6940.0550.0550.0000.0000.0000.000
200A237PRO00.0270.04323.8470.0080.0080.0000.0000.0000.000
201A238ASP-1-0.816-0.90326.422-0.055-0.0550.0000.0000.0000.000
202A239LEU0-0.015-0.02026.293-0.004-0.0040.0000.0000.0000.000
203A240PRO00.0190.01525.352-0.009-0.0090.0000.0000.0000.000
204A241GLY00.0610.02822.8990.0000.0000.0000.0000.0000.000
205A242ARG10.7700.86221.6330.0690.0690.0000.0000.0000.000
206A243GLN00.0620.02720.999-0.035-0.0350.0000.0000.0000.000
207A244LEU0-0.0260.00217.905-0.013-0.0130.0000.0000.0000.000
208A245MET0-0.027-0.00917.143-0.004-0.0040.0000.0000.0000.000
209A246ALA00.0240.01816.176-0.034-0.0340.0000.0000.0000.000
210A247ASN00.0080.00415.459-0.060-0.0600.0000.0000.0000.000
211A248MET00.0250.02212.627-0.030-0.0300.0000.0000.0000.000
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