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

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FMODB ID: NNQ7Q

Calculation Name: 3SH4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3SH4

Chain ID: A

ChEMBL ID:

UniProt ID: P98160

Base Structure: X-ray

Registration Date: 2023-09-23

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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2020026.284727
FMO2-HF: Nuclear repulsion 1948712.327118
FMO2-HF: Total energy -71313.95761
FMO2-MP2: Total energy -71525.611584


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:1:ASP)


Summations of interaction energy for fragment #1(A:1:ASP)
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.
10.27710.23610.16-5.004-5.115-0.015
Interaction energy analysis for fragmet #1(A:1:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.942 / q_NPA : -0.976
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].
3A3PRO0-0.021-0.0313.883-0.8580.806-0.017-0.834-0.8130.003
4A4GLY00.0080.0107.167-1.749-1.7490.0000.0000.0000.000
5A5GLN00.0190.0121.9161.601-2.0308.949-2.879-2.439-0.031
6A6TYR00.0340.0062.659-12.794-10.8681.228-1.291-1.8630.013
7A7GLY00.023-0.0157.429-2.271-2.2710.0000.0000.0000.000
8A8ALA0-0.0070.01510.5000.5490.5490.0000.0000.0000.000
9A9TYR0-0.007-0.01813.371-0.603-0.6030.0000.0000.0000.000
10A10PHE0-0.0020.01116.5490.1420.1420.0000.0000.0000.000
11A11HIS00.029-0.02220.1170.3860.3860.0000.0000.0000.000
12A12ASP-1-0.852-0.90823.50011.05811.0580.0000.0000.0000.000
13A13ASP-1-0.849-0.92826.06110.31410.3140.0000.0000.0000.000
14A14GLY0-0.0350.00422.327-0.008-0.0080.0000.0000.0000.000
15A15PHE0-0.072-0.04320.572-0.028-0.0280.0000.0000.0000.000
16A16LEU00.0220.01214.1030.2950.2950.0000.0000.0000.000
17A17ALA00.0130.00518.308-0.426-0.4260.0000.0000.0000.000
18A18PHE00.0240.02213.0370.4160.4160.0000.0000.0000.000
19A19PRO00.0400.03117.495-0.796-0.7960.0000.0000.0000.000
20A20GLY00.0730.02919.8370.5420.5420.0000.0000.0000.000
21A21HIS0-0.019-0.00817.7510.2990.2990.0000.0000.0000.000
22A22VAL0-0.019-0.00515.7360.4750.4750.0000.0000.0000.000
23A23PHE00.0180.00317.7320.5250.5250.0000.0000.0000.000
24A24SER0-0.038-0.02820.596-0.974-0.9740.0000.0000.0000.000
25A25ARG10.8590.92422.739-12.147-12.1470.0000.0000.0000.000
26A26SER0-0.050-0.05325.9090.0290.0290.0000.0000.0000.000
27A27LEU00.0170.02828.691-0.269-0.2690.0000.0000.0000.000
28A28PRO00.028-0.00931.1640.2200.2200.0000.0000.0000.000
29A29GLU-1-0.892-0.95932.7378.7558.7550.0000.0000.0000.000
30A30VAL0-0.059-0.00427.0250.0660.0660.0000.0000.0000.000
31A31PRO0-0.0040.01327.0670.0990.0990.0000.0000.0000.000
32A32GLU-1-0.811-0.89424.17212.25712.2570.0000.0000.0000.000
33A33THR0-0.058-0.04020.004-0.274-0.2740.0000.0000.0000.000
34A34ILE0-0.0090.00419.2380.4860.4860.0000.0000.0000.000
35A35GLU-1-0.820-0.87117.17516.08516.0850.0000.0000.0000.000
36A36LEU0-0.0210.00315.7251.0551.0550.0000.0000.0000.000
37A37GLU-1-0.771-0.84413.64020.37520.3750.0000.0000.0000.000
38A38VAL0-0.008-0.01416.2000.6820.6820.0000.0000.0000.000
39A39ARG10.9750.98916.600-16.108-16.1080.0000.0000.0000.000
40A40THR0-0.016-0.03120.3960.0150.0150.0000.0000.0000.000
41A41SER00.0850.04023.407-0.030-0.0300.0000.0000.0000.000
42A42THR0-0.070-0.03325.622-0.476-0.4760.0000.0000.0000.000
43A43ALA00.0280.02128.1530.1220.1220.0000.0000.0000.000
44A44SER00.0180.00330.8470.0710.0710.0000.0000.0000.000
45A45GLY00.0120.01928.047-0.085-0.0850.0000.0000.0000.000
46A46LEU0-0.061-0.02124.7360.0570.0570.0000.0000.0000.000
47A47LEU0-0.003-0.00121.2970.3360.3360.0000.0000.0000.000
48A48LEU0-0.003-0.00719.2820.7060.7060.0000.0000.0000.000
49A49TRP00.0370.01222.343-0.666-0.6660.0000.0000.0000.000
50A50GLN00.0120.03023.5530.4090.4090.0000.0000.0000.000
51A51GLY00.0470.01625.412-0.334-0.3340.0000.0000.0000.000
52A52VAL0-0.008-0.00628.5370.2840.2840.0000.0000.0000.000
53A53GLU-1-0.839-0.89428.57010.59610.5960.0000.0000.0000.000
54A54VAL0-0.003-0.00630.593-0.323-0.3230.0000.0000.0000.000
55A55GLY00.0090.00132.484-0.058-0.0580.0000.0000.0000.000
56A56GLU-1-0.835-0.89933.6358.7328.7320.0000.0000.0000.000
57A57ALA0-0.0170.00835.4570.1470.1470.0000.0000.0000.000
58A58GLY00.0180.01737.700-0.244-0.2440.0000.0000.0000.000
59A59GLN0-0.047-0.07731.4220.1120.1120.0000.0000.0000.000
60A60GLY00.012-0.00335.3050.1160.1160.0000.0000.0000.000
61A61LYS10.9230.94935.987-8.002-8.0020.0000.0000.0000.000
62A62ASP-1-0.763-0.88032.5679.0169.0160.0000.0000.0000.000
63A63PHE0-0.070-0.03829.5300.0480.0480.0000.0000.0000.000
64A64ILE0-0.020-0.00225.467-0.237-0.2370.0000.0000.0000.000
65A65SER0-0.066-0.03225.6010.1390.1390.0000.0000.0000.000
66A66LEU00.0390.01221.570-0.164-0.1640.0000.0000.0000.000
67A67GLY00.0260.00625.2620.1210.1210.0000.0000.0000.000
68A68LEU0-0.0070.01025.2320.1360.1360.0000.0000.0000.000
69A69GLN00.0390.01528.559-0.347-0.3470.0000.0000.0000.000
70A70ASP-1-0.891-0.95132.3968.4938.4930.0000.0000.0000.000
71A71GLY00.023-0.00230.265-0.127-0.1270.0000.0000.0000.000
72A72HIS10.7920.91729.440-8.764-8.7640.0000.0000.0000.000
73A73LEU00.0570.03524.6370.0480.0480.0000.0000.0000.000
74A74VAL0-0.047-0.02227.882-0.439-0.4390.0000.0000.0000.000
75A75PHE00.0190.00926.1880.4430.4430.0000.0000.0000.000
76A76ARG10.8410.90928.581-9.366-9.3660.0000.0000.0000.000
77A77TYR0-0.001-0.00729.6400.3430.3430.0000.0000.0000.000
78A78GLN00.0170.01931.615-0.415-0.4150.0000.0000.0000.000
79A79LEU0-0.0100.00232.4090.2300.2300.0000.0000.0000.000
80A80GLY00.0780.03635.496-0.104-0.1040.0000.0000.0000.000
81A81SER0-0.082-0.04338.779-0.160-0.1600.0000.0000.0000.000
82A82GLY0-0.020-0.02439.229-0.214-0.2140.0000.0000.0000.000
83A83GLU-1-0.793-0.87336.0708.7648.7640.0000.0000.0000.000
84A84ALA00.0060.01433.902-0.223-0.2230.0000.0000.0000.000
85A85ARG10.8560.89633.342-8.317-8.3170.0000.0000.0000.000
86A86LEU0-0.0050.03430.871-0.257-0.2570.0000.0000.0000.000
87A87VAL0-0.017-0.02931.4870.2190.2190.0000.0000.0000.000
88A88SER00.0070.00129.307-0.057-0.0570.0000.0000.0000.000
89A89GLU-1-0.907-0.94431.4488.3438.3430.0000.0000.0000.000
90A90ASP-1-0.819-0.91431.7408.9128.9120.0000.0000.0000.000
91A91PRO0-0.125-0.05230.7740.2410.2410.0000.0000.0000.000
92A92ILE00.0380.00524.0550.1910.1910.0000.0000.0000.000
93A93ASN0-0.080-0.03025.6760.3270.3270.0000.0000.0000.000
94A94ASP-1-0.765-0.87225.94711.37011.3700.0000.0000.0000.000
95A95GLY0-0.036-0.00624.700-0.161-0.1610.0000.0000.0000.000
96A96GLU-1-0.926-0.95722.88012.83412.8340.0000.0000.0000.000
97A97TRP0-0.122-0.09214.8540.7480.7480.0000.0000.0000.000
98A98HIS10.8570.90020.021-12.709-12.7090.0000.0000.0000.000
99A99ARG10.7840.86414.238-18.190-18.1900.0000.0000.0000.000
100A100VAL0-0.024-0.00519.695-0.843-0.8430.0000.0000.0000.000
101A101THR00.015-0.02120.4400.6200.6200.0000.0000.0000.000
102A102ALA0-0.021-0.01122.521-0.717-0.7170.0000.0000.0000.000
103A103LEU00.0040.01123.6040.5100.5100.0000.0000.0000.000
104A104ARG10.8030.87726.321-11.144-11.1440.0000.0000.0000.000
105A105GLU-1-0.838-0.90428.48010.25710.2570.0000.0000.0000.000
106A106GLY00.0490.02431.302-0.358-0.3580.0000.0000.0000.000
107A107ARG10.9040.96233.134-7.855-7.8550.0000.0000.0000.000
108A108ARG10.8010.90433.482-9.499-9.4990.0000.0000.0000.000
109A109GLY00.0740.03230.9130.2840.2840.0000.0000.0000.000
110A110SER0-0.036-0.03429.481-0.275-0.2750.0000.0000.0000.000
111A111ILE0-0.009-0.00527.0080.3420.3420.0000.0000.0000.000
112A112GLN0-0.035-0.01924.755-0.039-0.0390.0000.0000.0000.000
113A113VAL00.0410.00824.4250.4060.4060.0000.0000.0000.000
114A114ASP-1-0.766-0.87122.29513.12613.1260.0000.0000.0000.000
115A115GLY0-0.050-0.01323.5360.1430.1430.0000.0000.0000.000
116A116GLU-1-0.949-0.96024.76310.51910.5190.0000.0000.0000.000
117A117GLU-1-0.913-0.96028.4339.9799.9790.0000.0000.0000.000
118A118LEU0-0.051-0.02427.7560.1400.1400.0000.0000.0000.000
119A119VAL00.0380.03430.840-0.401-0.4010.0000.0000.0000.000
120A120SER0-0.035-0.03731.6760.2200.2200.0000.0000.0000.000
121A121GLY00.0330.00834.025-0.215-0.2150.0000.0000.0000.000
122A122ARG10.9190.94935.214-7.993-7.9930.0000.0000.0000.000
123A123SER00.0570.05436.135-0.070-0.0700.0000.0000.0000.000
124A124PRO00.0020.00137.827-0.100-0.1000.0000.0000.0000.000
125A125GLY0-0.0120.02540.5340.1560.1560.0000.0000.0000.000
126A126PRO00.010-0.01042.428-0.113-0.1130.0000.0000.0000.000
127A127ASN0-0.018-0.02338.317-0.073-0.0730.0000.0000.0000.000
128A128VAL00.0390.01336.3650.0950.0950.0000.0000.0000.000
129A129ALA0-0.020-0.02033.1330.2950.2950.0000.0000.0000.000
130A130VAL0-0.0040.01128.658-0.216-0.2160.0000.0000.0000.000
131A131ASN0-0.064-0.05231.0800.1860.1860.0000.0000.0000.000
132A132ALA0-0.044-0.01128.6790.0270.0270.0000.0000.0000.000
133A133LYS10.8290.91026.871-9.552-9.5520.0000.0000.0000.000
134A134GLY00.0100.01626.1330.2830.2830.0000.0000.0000.000
135A135SER0-0.049-0.04722.5070.1730.1730.0000.0000.0000.000
136A136VAL0-0.032-0.00719.362-0.448-0.4480.0000.0000.0000.000
137A137TYR00.006-0.00519.9640.5790.5790.0000.0000.0000.000
138A138ILE00.002-0.01516.4560.0030.0030.0000.0000.0000.000
139A139GLY00.0200.01319.6560.0470.0470.0000.0000.0000.000
140A140GLY00.0710.02420.981-0.530-0.5300.0000.0000.0000.000
141A141ALA0-0.041-0.03023.6830.3040.3040.0000.0000.0000.000
142A142PRO0-0.011-0.00225.293-0.241-0.2410.0000.0000.0000.000
143A143ASP-1-0.763-0.84828.1318.6458.6450.0000.0000.0000.000
144A144VAL0-0.0050.00527.3570.0720.0720.0000.0000.0000.000
145A145ALA00.0310.04529.984-0.061-0.0610.0000.0000.0000.000
146A146THR0-0.044-0.06233.494-0.197-0.1970.0000.0000.0000.000
147A147LEU0-0.058-0.01326.306-0.053-0.0530.0000.0000.0000.000
148A148THR0-0.029-0.02829.167-0.057-0.0570.0000.0000.0000.000
149A149GLY0-0.026-0.00631.734-0.161-0.1610.0000.0000.0000.000
150A150GLY0-0.034-0.02535.074-0.235-0.2350.0000.0000.0000.000
151A151ARG10.6820.82933.005-9.001-9.0010.0000.0000.0000.000
152A152PHE00.0120.00329.4380.0700.0700.0000.0000.0000.000
153A153SER00.0280.00432.276-0.128-0.1280.0000.0000.0000.000
154A154SER00.0080.01629.734-0.221-0.2210.0000.0000.0000.000
155A155GLY00.0410.01525.4730.1480.1480.0000.0000.0000.000
156A156ILE0-0.057-0.01920.549-0.306-0.3060.0000.0000.0000.000
157A157THR0-0.009-0.00623.2490.1360.1360.0000.0000.0000.000
158A158GLY00.0050.01620.942-0.341-0.3410.0000.0000.0000.000
159A159CYS0-0.188-0.06311.368-1.343-1.3430.0000.0000.0000.000
160A160VAL00.0470.02915.229-0.634-0.6340.0000.0000.0000.000
161A161LYS10.8320.91811.024-20.763-20.7630.0000.0000.0000.000
162A162ASN0-0.051-0.0459.3961.0751.0750.0000.0000.0000.000
163A163LEU00.0180.02011.507-1.010-1.0100.0000.0000.0000.000
164A164VAL0-0.0020.01413.1241.1791.1790.0000.0000.0000.000
165A165LEU00.0130.00114.954-1.394-1.3940.0000.0000.0000.000
166A166HIS00.0350.00517.2960.9180.9180.0000.0000.0000.000
167A167SER00.0370.01519.857-0.847-0.8470.0000.0000.0000.000
168A168ALA0-0.0050.01823.0310.3260.3260.0000.0000.0000.000
169A169ARG10.9180.95023.848-13.264-13.2640.0000.0000.0000.000
170A170PRO00.015-0.01024.8830.4130.4130.0000.0000.0000.000
171A171GLY0-0.0040.00025.114-0.087-0.0870.0000.0000.0000.000
172A172ALA0-0.044-0.00820.9170.3870.3870.0000.0000.0000.000
173A173PRO0-0.0020.00316.404-0.222-0.2220.0000.0000.0000.000
174A174PRO00.006-0.01115.354-0.369-0.3690.0000.0000.0000.000
175A175PRO0-0.0030.02315.2570.9620.9620.0000.0000.0000.000
176A176GLN0-0.014-0.0249.5681.9011.9010.0000.0000.0000.000
177A177PRO0-0.007-0.0058.296-1.590-1.5900.0000.0000.0000.000
178A178LEU0-0.024-0.0039.1722.3512.3510.0000.0000.0000.000
179A179ASP-1-0.802-0.8906.20635.03835.0380.0000.0000.0000.000
180A180LEU0-0.042-0.0328.241-2.579-2.5790.0000.0000.0000.000
181A181GLN0-0.018-0.0028.375-3.154-3.1540.0000.0000.0000.000
182A182HIS0-0.076-0.0526.133-2.673-2.6730.0000.0000.0000.000
183A183ARG10.9120.95710.542-24.425-24.4250.0000.0000.0000.000
184A184ALA00.0100.02313.032-1.013-1.0130.0000.0000.0000.000
185A185GLN0-0.024-0.02015.735-0.142-0.1420.0000.0000.0000.000
186A186ALA0-0.023-0.01419.268-0.710-0.7100.0000.0000.0000.000
187A187GLY00.0370.01019.1970.7280.7280.0000.0000.0000.000
188A188ALA0-0.033-0.00920.269-0.450-0.4500.0000.0000.0000.000
189A189ASN0-0.017-0.01221.1110.4900.4900.0000.0000.0000.000
190A190THR00.0380.01216.8970.3340.3340.0000.0000.0000.000
191A191ARG10.8980.95315.042-14.896-14.8960.0000.0000.0000.000
192A192PRO00.0540.0329.880-0.066-0.0660.0000.0000.0000.000
193A194PRO00.0110.01210.6131.6311.6310.0000.0000.0000.000
194A195SER00.000-0.00311.047-1.753-1.7530.0000.0000.0000.000