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

tag_button

FMODB ID: G5391

Calculation Name: 1S7H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1S7H

Chain ID: A

ChEMBL ID:

UniProt ID: O34911

Base Structure: X-ray

Registration Date: 2023-09-24

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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1964465.001431
FMO2-HF: Nuclear repulsion 1891766.576724
FMO2-HF: Total energy -72698.424707
FMO2-MP2: Total energy -72907.078539


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:8:SER)


Summations of interaction energy for fragment #1(A:8:SER)
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.
-4.185-1.85310.438-6.506-6.263-0.031
Interaction energy analysis for fragmet #1(A:8:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / q_NPA : -0.011
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].
3A10ILE0-0.035-0.0102.834-0.5421.7620.243-1.013-1.5340.004
4A11ALA00.0260.0245.280-0.631-0.606-0.001-0.003-0.0210.000
5A12GLY00.019-0.0149.075-0.003-0.0030.0000.0000.0000.000
6A13PHE00.003-0.01511.497-0.004-0.0040.0000.0000.0000.000
7A14ARG10.9260.97315.2380.0090.0090.0000.0000.0000.000
8A15PHE0-0.002-0.00517.5810.0010.0010.0000.0000.0000.000
9A16SER00.0290.00321.039-0.008-0.0080.0000.0000.0000.000
10A17LEU0-0.005-0.00624.5030.0060.0060.0000.0000.0000.000
11A18TYR0-0.001-0.02327.229-0.006-0.0060.0000.0000.0000.000
12A19PRO0-0.026-0.00230.7090.0010.0010.0000.0000.0000.000
13A20MET0-0.056-0.03133.516-0.004-0.0040.0000.0000.0000.000
14A21THR00.007-0.00936.467-0.001-0.0010.0000.0000.0000.000
15A22ASP-1-0.885-0.94737.7830.0210.0210.0000.0000.0000.000
16A23ASP-1-0.936-0.96438.1450.0280.0280.0000.0000.0000.000
17A24PHE00.033-0.00232.8130.0030.0030.0000.0000.0000.000
18A25ILE00.004-0.00332.2440.0030.0030.0000.0000.0000.000
19A26SER0-0.033-0.02132.0610.0020.0020.0000.0000.0000.000
20A27VAL00.0160.02131.7830.0050.0050.0000.0000.0000.000
21A28ILE00.0020.00127.2090.0060.0060.0000.0000.0000.000
22A29LYS10.9330.97227.791-0.029-0.0290.0000.0000.0000.000
23A30SER0-0.028-0.02828.4340.0070.0070.0000.0000.0000.000
24A31ALA00.0690.04627.2040.0050.0050.0000.0000.0000.000
25A32LEU00.0220.00522.0560.0100.0100.0000.0000.0000.000
26A33LYS10.8630.94024.272-0.050-0.0500.0000.0000.0000.000
27A34LYS10.9180.95126.468-0.063-0.0630.0000.0000.0000.000
28A35THR0-0.0230.01021.3100.0070.0070.0000.0000.0000.000
29A36ASP-1-0.840-0.89920.8450.1640.1640.0000.0000.0000.000
30A37THR0-0.008-0.02818.1640.0220.0220.0000.0000.0000.000
31A38SER0-0.057-0.04317.1420.0170.0170.0000.0000.0000.000
32A39LYS10.8570.93914.363-0.264-0.2640.0000.0000.0000.000
33A40VAL00.012-0.00212.1900.1070.1070.0000.0000.0000.000
34A41TRP00.0080.03811.040-0.081-0.0810.0000.0000.0000.000
35A42THR0-0.006-0.02012.8750.0040.0040.0000.0000.0000.000
36A43LYS10.9470.98015.8120.0330.0330.0000.0000.0000.000
37A44THR00.0110.00117.6900.0110.0110.0000.0000.0000.000
38A45ASP-1-0.914-0.92921.057-0.024-0.0240.0000.0000.0000.000
39A46HIS00.003-0.01223.3990.0090.0090.0000.0000.0000.000
40A47ILE0-0.014-0.00224.3420.0040.0040.0000.0000.0000.000
41A48SER0-0.021-0.00821.2370.0050.0050.0000.0000.0000.000
42A49THR00.0020.00018.725-0.011-0.0110.0000.0000.0000.000
43A50VAL0-0.078-0.02813.5620.0030.0030.0000.0000.0000.000
44A51LEU0-0.008-0.00614.202-0.003-0.0030.0000.0000.0000.000
45A52ARG10.7960.8926.2450.5090.5090.0000.0000.0000.000
46A53GLY00.0750.0398.387-0.051-0.0510.0000.0000.0000.000
47A54SER0-0.013-0.0038.1080.1500.1500.0000.0000.0000.000
48A55ILE00.0680.0199.090-0.190-0.1900.0000.0000.0000.000
49A56ASP-1-0.874-0.92911.2570.4800.4800.0000.0000.0000.000
50A57HIS00.0130.00112.2930.0020.0020.0000.0000.0000.000
51A58VAL0-0.0140.01111.284-0.082-0.0820.0000.0000.0000.000
52A59PHE00.0490.01414.266-0.068-0.0680.0000.0000.0000.000
53A60ASP-1-0.903-0.93816.7550.2050.2050.0000.0000.0000.000
54A61ALA00.0330.01117.160-0.037-0.0370.0000.0000.0000.000
55A62ALA0-0.0100.00118.330-0.033-0.0330.0000.0000.0000.000
56A63LYS10.9530.98720.058-0.194-0.1940.0000.0000.0000.000
57A64ALA0-0.0150.00022.247-0.019-0.0190.0000.0000.0000.000
58A65ILE0-0.008-0.00720.469-0.018-0.0180.0000.0000.0000.000
59A66TYR0-0.021-0.03624.293-0.013-0.0130.0000.0000.0000.000
60A67LEU00.0360.00926.277-0.011-0.0110.0000.0000.0000.000
61A68HIS0-0.019-0.01426.006-0.016-0.0160.0000.0000.0000.000
62A69ALA0-0.025-0.01128.332-0.008-0.0080.0000.0000.0000.000
63A70ALA00.0180.01030.083-0.007-0.0070.0000.0000.0000.000
64A71ASN0-0.059-0.03332.020-0.008-0.0080.0000.0000.0000.000
65A72SER0-0.076-0.02133.798-0.005-0.0050.0000.0000.0000.000
66A73GLU-1-0.939-0.98835.4650.0410.0410.0000.0000.0000.000
67A74GLN0-0.0300.00135.651-0.005-0.0050.0000.0000.0000.000
68A75HIS00.0040.03535.4940.0010.0010.0000.0000.0000.000
69A76ILE0-0.0250.00129.882-0.003-0.0030.0000.0000.0000.000
70A77VAL00.0310.02228.9240.0020.0020.0000.0000.0000.000
71A78MET0-0.0570.00222.8090.0010.0010.0000.0000.0000.000
72A79ASN0-0.0030.00225.1930.0030.0030.0000.0000.0000.000
73A80GLY00.0350.00621.085-0.003-0.0030.0000.0000.0000.000
74A81THR0-0.047-0.01617.285-0.002-0.0020.0000.0000.0000.000
75A82PHE00.0070.02115.196-0.001-0.0010.0000.0000.0000.000
76A83SER0-0.036-0.02712.625-0.023-0.0230.0000.0000.0000.000
77A84ILE00.0470.0197.4960.0430.0430.0000.0000.0000.000
78A85GLY00.0460.0217.8780.0290.0290.0000.0000.0000.000
79A86CYS0-0.0340.0018.8600.0570.0570.0000.0000.0000.000
80A87PRO00.0420.0089.223-0.171-0.1710.0000.0000.0000.000
81A88GLY0-0.017-0.0099.3090.0100.0100.0000.0000.0000.000
82A89ASP-1-0.906-0.9386.395-0.963-0.9630.0000.0000.0000.000
83A90THR00.0130.0136.592-0.507-0.5070.0000.0000.0000.000
84A91GLN0-0.019-0.0202.148-2.757-3.11510.186-5.377-4.451-0.036
85A92GLY0-0.012-0.0054.4220.4150.489-0.001-0.003-0.0690.000
86A93ASP-1-0.917-0.9577.029-0.192-0.1920.0000.0000.0000.000
87A94THR00.022-0.0125.1760.0220.0220.0000.0000.0000.000
88A95TYR0-0.0130.0178.386-0.145-0.1450.0000.0000.0000.000
89A96LEU0-0.030-0.0253.8930.0590.3460.011-0.110-0.1880.001
90A97SER00.007-0.0218.501-0.221-0.2210.0000.0000.0000.000
91A98LYS10.9540.9768.850-0.591-0.5910.0000.0000.0000.000
92A99GLY0-0.002-0.00410.708-0.065-0.0650.0000.0000.0000.000
93A100ASP-1-0.824-0.88013.9300.2840.2840.0000.0000.0000.000
94A101LYS10.9290.96815.284-0.130-0.1300.0000.0000.0000.000
95A102ARG10.7900.86215.456-0.331-0.3310.0000.0000.0000.000
96A103VAL0-0.011-0.01018.506-0.024-0.0240.0000.0000.0000.000
97A104ASN0-0.014-0.00720.350-0.046-0.0460.0000.0000.0000.000
98A105GLU-1-0.943-0.96021.9070.1710.1710.0000.0000.0000.000
99A106ASP-1-0.911-0.97823.8370.1220.1220.0000.0000.0000.000
100A107ALA0-0.054-0.01726.467-0.011-0.0110.0000.0000.0000.000
101A108VAL00.016-0.00325.121-0.009-0.0090.0000.0000.0000.000
102A109ARG10.9540.99928.038-0.107-0.1070.0000.0000.0000.000
103A110GLY0-0.055-0.03128.901-0.004-0.0040.0000.0000.0000.000
104A111LEU0-0.044-0.00229.508-0.006-0.0060.0000.0000.0000.000
105A112LYS10.9150.95731.260-0.080-0.0800.0000.0000.0000.000
106A113ALA0-0.001-0.01931.061-0.003-0.0030.0000.0000.0000.000
107A114GLU-1-0.878-0.92131.6450.0780.0780.0000.0000.0000.000
108A115ALA0-0.034-0.02328.7040.0000.0000.0000.0000.0000.000
109A116PRO00.0470.06730.0690.0050.0050.0000.0000.0000.000
110A117CYS0-0.069-0.05125.8680.0010.0010.0000.0000.0000.000
111A118GLN0-0.0130.01328.802-0.003-0.0030.0000.0000.0000.000
112A119PHE00.008-0.01923.5710.0030.0030.0000.0000.0000.000
113A120ALA00.0280.02124.139-0.005-0.0050.0000.0000.0000.000
114A121LEU0-0.0060.00218.4000.0060.0060.0000.0000.0000.000
115A122TYR0-0.032-0.03219.700-0.013-0.0130.0000.0000.0000.000
116A123PRO00.0420.01517.7080.0000.0000.0000.0000.0000.000
117A124MET0-0.019-0.01716.362-0.016-0.0160.0000.0000.0000.000
118A125ASN0-0.092-0.05117.2490.0110.0110.0000.0000.0000.000
119A126GLU-1-0.761-0.87318.4740.1400.1400.0000.0000.0000.000
120A127PRO0-0.051-0.03720.336-0.007-0.0070.0000.0000.0000.000
121A128ASP-1-0.901-0.96122.5810.0860.0860.0000.0000.0000.000
122A129TYR00.0110.01022.2820.0030.0030.0000.0000.0000.000
123A130MET0-0.037-0.02323.2110.0030.0030.0000.0000.0000.000
124A131GLY00.0440.03025.832-0.001-0.0010.0000.0000.0000.000
125A132LEU00.0240.01218.7880.0020.0020.0000.0000.0000.000
126A133ILE0-0.046-0.01422.9260.0060.0060.0000.0000.0000.000
127A134MET0-0.040-0.01724.816-0.002-0.0020.0000.0000.0000.000
128A135GLU-1-0.778-0.91022.5040.1390.1390.0000.0000.0000.000
129A136ALA0-0.045-0.02722.8730.0040.0040.0000.0000.0000.000
130A137VAL0-0.048-0.02224.180-0.001-0.0010.0000.0000.0000.000
131A138ASP-1-0.903-0.95727.3580.0810.0810.0000.0000.0000.000
132A139ILE0-0.027-0.00521.5090.0000.0000.0000.0000.0000.000
133A140ALA00.019-0.00225.780-0.001-0.0010.0000.0000.0000.000
134A141LYS10.8800.95227.594-0.077-0.0770.0000.0000.0000.000
135A142ALA0-0.0280.00227.918-0.004-0.0040.0000.0000.0000.000
136A143GLN0-0.038-0.02623.9260.0110.0110.0000.0000.0000.000
137A144GLY0-0.051-0.01528.828-0.002-0.0020.0000.0000.0000.000
138A145THR00.000-0.01427.483-0.005-0.0050.0000.0000.0000.000
139A146PHE0-0.029-0.01530.267-0.003-0.0030.0000.0000.0000.000
140A147VAL0-0.0060.02131.534-0.004-0.0040.0000.0000.0000.000
141A148GLN0-0.066-0.04933.417-0.007-0.0070.0000.0000.0000.000
142A149GLY00.0030.01532.7180.0050.0050.0000.0000.0000.000
143A150VAL0-0.017-0.00532.874-0.005-0.0050.0000.0000.0000.000
144A151HIS0-0.005-0.01933.2340.0030.0030.0000.0000.0000.000
145A152TYR0-0.058-0.04230.068-0.001-0.0010.0000.0000.0000.000
146A153ALA0-0.0070.01128.6580.0020.0020.0000.0000.0000.000
147A154SER00.0090.01427.538-0.003-0.0030.0000.0000.0000.000
148A155GLU-1-0.900-0.96029.0600.0600.0600.0000.0000.0000.000
149A156LEU0-0.045-0.03725.7030.0040.0040.0000.0000.0000.000
150A157ASP-1-0.859-0.95130.4230.0630.0630.0000.0000.0000.000
151A158GLY00.0650.05331.6180.0050.0050.0000.0000.0000.000
152A159ASP-1-0.745-0.89530.5880.0960.0960.0000.0000.0000.000
153A160ALA00.029-0.00327.3280.0070.0070.0000.0000.0000.000
154A161HIS0-0.085-0.03925.9680.0250.0250.0000.0000.0000.000
155A162ASP-1-0.890-0.94225.4130.1210.1210.0000.0000.0000.000
156A163VAL00.0080.01725.9090.0100.0100.0000.0000.0000.000
157A164PHE0-0.020-0.04821.3080.0100.0100.0000.0000.0000.000
158A165SER0-0.0330.00621.2090.0250.0250.0000.0000.0000.000
159A166THR00.0350.03221.5160.0090.0090.0000.0000.0000.000
160A167LEU0-0.007-0.01020.8000.0080.0080.0000.0000.0000.000
161A168GLU-1-0.737-0.85715.7150.3700.3700.0000.0000.0000.000
162A169ALA0-0.0070.00917.0380.0310.0310.0000.0000.0000.000
163A170VAL00.0000.00018.6710.0070.0070.0000.0000.0000.000
164A171PHE0-0.018-0.02611.9810.0140.0140.0000.0000.0000.000
165A172ARG10.8020.88111.469-0.451-0.4510.0000.0000.0000.000
166A173MET0-0.0380.02914.6920.0140.0140.0000.0000.0000.000
167A174ALA00.0400.00016.6440.0020.0020.0000.0000.0000.000
168A175GLU-1-0.962-0.99010.1790.6040.6040.0000.0000.0000.000
169A176GLN0-0.049-0.01811.3060.0120.0120.0000.0000.0000.000
170A177GLN0-0.036-0.01013.3940.0040.0040.0000.0000.0000.000
171A178THR0-0.003-0.00614.569-0.016-0.0160.0000.0000.0000.000
172A179ASN0-0.022-0.0199.7320.1360.1360.0000.0000.0000.000
173A180HIS0-0.0080.01010.8700.0130.0130.0000.0000.0000.000
174A181ILE00.0370.03612.840-0.018-0.0180.0000.0000.0000.000
175A182THR0-0.041-0.02814.192-0.003-0.0030.0000.0000.0000.000
176A183MET00.0150.00616.7670.0100.0100.0000.0000.0000.000
177A184THR0-0.0230.00119.3380.0070.0070.0000.0000.0000.000
178A185VAL00.0250.00321.4310.0070.0070.0000.0000.0000.000
179A186ASN00.002-0.01023.875-0.006-0.0060.0000.0000.0000.000
180A187LEU00.0510.02624.6160.0000.0000.0000.0000.0000.000
181A188SER0-0.004-0.00528.580-0.004-0.0040.0000.0000.0000.000
182A189ALA00.0710.03331.3160.0020.0020.0000.0000.0000.000
183A190ASN0-0.033-0.03533.223-0.004-0.0040.0000.0000.0000.000
184A191SER0-0.024-0.01636.499-0.003-0.0030.0000.0000.0000.000
185A192PRO0-0.014-0.00637.9970.0000.0000.0000.0000.0000.000
186A193SER0-0.0080.00040.2440.0000.0000.0000.0000.0000.000