Manual

About

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: YV382

Calculation Name: 3DGS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DGS

Chain ID: A

ChEMBL ID:

UniProt ID: P03661

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 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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1954549.514608
FMO2-HF: Nuclear repulsion 1882184.013711
FMO2-HF: Total energy -72365.500897
FMO2-MP2: Total energy -72580.870468


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:10:LYS)


Summations of interaction energy for fragment #1(A:10:LYS)
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.
-261.801-257.80119.256-10.877-12.378-0.116
Interaction energy analysis for fragmet #1(A:10:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.883 / q_NPA : 0.933
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].
3A12HIS00.017-0.0063.494-10.360-7.479-0.003-1.484-1.3950.004
4A13ILE0-0.0090.0044.258-0.740-0.590-0.001-0.010-0.1380.000
5A14GLU-1-0.912-0.9277.857-18.155-18.1550.0000.0000.0000.000
6A15GLY00.0350.00711.5710.3160.3160.0000.0000.0000.000
7A16SER0-0.002-0.03013.1770.0180.0180.0000.0000.0000.000
8A17PHE0-0.0220.0076.955-1.643-1.6430.0000.0000.0000.000
9A18THR00.037-0.00313.1752.2282.2280.0000.0000.0000.000
10A19ASN0-0.073-0.04114.072-0.639-0.6390.0000.0000.0000.000
11A20VAL0-0.0060.00214.008-1.025-1.0250.0000.0000.0000.000
12A21TRP00.0350.01912.4830.8940.8940.0000.0000.0000.000
13A22LYS10.8750.92817.11011.98711.9870.0000.0000.0000.000
14A23ASP-1-0.854-0.91518.167-14.641-14.6410.0000.0000.0000.000
15A24ASP-1-0.916-0.97120.019-12.445-12.4450.0000.0000.0000.000
16A25LYS10.9610.98122.38013.16513.1650.0000.0000.0000.000
17A26THR0-0.103-0.10118.4580.3740.3740.0000.0000.0000.000
18A27LEU0-0.0180.00521.3860.0980.0980.0000.0000.0000.000
19A28ASP-1-0.811-0.85416.276-16.501-16.5010.0000.0000.0000.000
20A29TRP00.012-0.00416.327-0.144-0.1440.0000.0000.0000.000
21A30TYR0-0.016-0.02312.100-1.452-1.4520.0000.0000.0000.000
22A31ALA00.0690.04410.5201.3841.3840.0000.0000.0000.000
23A32ASN0-0.025-0.0158.538-3.725-3.7250.0000.0000.0000.000
24A33TYR0-0.001-0.0274.3565.1395.253-0.001-0.010-0.1030.000
25A34GLU-1-0.826-0.8891.680-127.762-129.95614.416-7.474-4.749-0.097
26A35GLY00.000-0.0034.973-4.742-4.674-0.001-0.002-0.0640.000
27A36ILE0-0.069-0.0302.327-1.554-0.5611.227-0.439-1.780-0.005
28A37LEU00.0210.0155.2722.1062.130-0.001-0.002-0.0210.000
29A38TRP0-0.042-0.0512.328-6.736-5.4051.914-0.974-2.271-0.013
30A39LYS10.9030.9538.23921.44521.4450.0000.0000.0000.000
31A40ALA00.0010.00910.776-1.345-1.3450.0000.0000.0000.000
32A41THR0-0.064-0.04511.7651.6701.6700.0000.0000.0000.000
33A42GLY00.0550.01814.182-0.153-0.1530.0000.0000.0000.000
34A43VAL0-0.031-0.01916.2580.6540.6540.0000.0000.0000.000
35A44VAL00.0260.02416.493-0.728-0.7280.0000.0000.0000.000
36A45VAL0-0.029-0.01518.7241.0981.0980.0000.0000.0000.000
37A46ILE00.0330.02719.591-0.824-0.8240.0000.0000.0000.000
38A47THR00.0400.00021.6220.4680.4680.0000.0000.0000.000
39A48GLY0-0.012-0.01523.6790.0500.0500.0000.0000.0000.000
40A49ASP-1-0.874-0.89424.260-12.839-12.8390.0000.0000.0000.000
41A50GLU-1-0.923-0.97522.289-12.806-12.8060.0000.0000.0000.000
42A51THR0-0.060-0.03920.788-0.808-0.8080.0000.0000.0000.000
43A52GLN0-0.005-0.01517.750-1.797-1.7970.0000.0000.0000.000
44A53VAL0-0.0010.00715.8510.7800.7800.0000.0000.0000.000
45A54TYR0-0.076-0.05315.352-1.158-1.1580.0000.0000.0000.000
46A55ALA00.0100.00113.7061.0701.0700.0000.0000.0000.000
47A56ILE00.0080.00810.488-1.267-1.2670.0000.0000.0000.000
48A57TRP0-0.0250.0078.551-0.033-0.0330.0000.0000.0000.000
49A58VAL00.0050.0006.484-3.447-3.4470.0000.0000.0000.000
50A59PRO0-0.029-0.0032.2170.4081.0111.707-0.474-1.836-0.005
51A60VAL0-0.022-0.0324.7312.8362.866-0.001-0.008-0.0210.000
52A61GLY00.0080.0086.5683.3103.3100.0000.0000.0000.000
53A62LEU0-0.028-0.0016.602-4.229-4.2290.0000.0000.0000.000
54A63ALA0-0.025-0.0038.2241.3531.3530.0000.0000.0000.000
55A64ILE00.005-0.0049.5921.3771.3770.0000.0000.0000.000
56A65PRO00.000-0.00112.8540.2930.2930.0000.0000.0000.000
57A66GLU-1-0.911-0.95914.702-16.930-16.9300.0000.0000.0000.000
58A67ASN0-0.061-0.02415.8710.7340.7340.0000.0000.0000.000
59A68GLU-1-0.870-0.89613.339-21.319-21.3190.0000.0000.0000.000
60A92TYR0-0.041-0.03417.8490.0980.0980.0000.0000.0000.000
61A93GLY0-0.0010.00321.0740.1200.1200.0000.0000.0000.000
62A94ASP-1-0.884-0.95520.666-14.142-14.1420.0000.0000.0000.000
63A95THR0-0.031-0.00321.7830.0680.0680.0000.0000.0000.000
64A96PRO0-0.040-0.04322.672-0.200-0.2000.0000.0000.0000.000
65A97ILE0-0.0110.01621.6720.7040.7040.0000.0000.0000.000
66A98PRO0-0.007-0.01724.194-0.340-0.3400.0000.0000.0000.000
67A99GLY00.0450.02424.182-0.353-0.3530.0000.0000.0000.000
68A100TYR0-0.053-0.02924.4560.5840.5840.0000.0000.0000.000
69A101ILE0-0.018-0.01023.347-0.566-0.5660.0000.0000.0000.000
70A102TYR0-0.032-0.02520.8490.7530.7530.0000.0000.0000.000
71A103ILE0-0.031-0.01623.247-0.095-0.0950.0000.0000.0000.000
72A104ASN00.0540.03520.1380.7460.7460.0000.0000.0000.000
73A105PRO0-0.022-0.02723.6350.3190.3190.0000.0000.0000.000
74A106LEU0-0.006-0.01723.8930.5600.5600.0000.0000.0000.000
75A107ASP-1-0.795-0.83822.708-11.781-11.7810.0000.0000.0000.000
76A108GLY00.011-0.00323.702-0.064-0.0640.0000.0000.0000.000
77A109THR0-0.053-0.04525.1420.4160.4160.0000.0000.0000.000
78A110TYR0-0.083-0.04227.5670.3840.3840.0000.0000.0000.000
79A111PRO0-0.0130.00529.3800.0840.0840.0000.0000.0000.000
80A112PRO00.0340.01830.7950.2450.2450.0000.0000.0000.000
81A113GLY0-0.025-0.00133.646-0.099-0.0990.0000.0000.0000.000
82A114THR0-0.070-0.04433.4730.0500.0500.0000.0000.0000.000
83A115GLU-1-0.913-0.96636.785-7.065-7.0650.0000.0000.0000.000
84A116GLN0-0.022-0.00732.2310.0790.0790.0000.0000.0000.000
85A117ASN0-0.015-0.02433.2760.3300.3300.0000.0000.0000.000
86A118PRO00.0300.02436.415-0.112-0.1120.0000.0000.0000.000
87A119ALA0-0.0270.00736.4430.1070.1070.0000.0000.0000.000
88A120ASN00.035-0.00337.217-0.061-0.0610.0000.0000.0000.000
89A121PRO00.0110.00333.369-0.136-0.1360.0000.0000.0000.000
90A122ASN0-0.073-0.03833.064-0.375-0.3750.0000.0000.0000.000
91A123PRO00.0340.02231.2540.1770.1770.0000.0000.0000.000
92A124SER0-0.060-0.05434.0020.0870.0870.0000.0000.0000.000
93A125LEU0-0.006-0.00633.391-0.265-0.2650.0000.0000.0000.000
94A126GLU-1-0.766-0.82936.750-7.654-7.6540.0000.0000.0000.000
95A127GLU-1-0.783-0.87437.995-7.624-7.6240.0000.0000.0000.000
96A128SER0-0.028-0.01239.1320.0110.0110.0000.0000.0000.000
97A129HIS00.0590.04332.7060.0760.0760.0000.0000.0000.000
98A130PRO0-0.030-0.00637.2020.2080.2080.0000.0000.0000.000
99A131LEU00.0120.00639.769-0.094-0.0940.0000.0000.0000.000
100A132ASN0-0.064-0.04041.8280.0190.0190.0000.0000.0000.000
101A133THR0-0.0200.02036.153-0.076-0.0760.0000.0000.0000.000
102A134PHE00.011-0.00934.9230.1090.1090.0000.0000.0000.000
103A135MET0-0.004-0.00929.959-0.130-0.1300.0000.0000.0000.000
104A136PHE0-0.021-0.02428.9910.2060.2060.0000.0000.0000.000
105A137GLN0-0.009-0.03625.836-0.443-0.4430.0000.0000.0000.000
106A138GLY00.1250.07825.780-0.414-0.4140.0000.0000.0000.000
107A139ASN0-0.059-0.02324.904-0.181-0.1810.0000.0000.0000.000
108A140ARG10.9380.95728.3459.2129.2120.0000.0000.0000.000
109A141PHE00.0100.00529.141-0.033-0.0330.0000.0000.0000.000
110A142ARG10.8320.90234.1758.2338.2330.0000.0000.0000.000
111A143ASN00.0260.00137.212-0.133-0.1330.0000.0000.0000.000
112A144ARG10.9220.96439.6667.5157.5150.0000.0000.0000.000
113A145GLN0-0.035-0.03342.360-0.014-0.0140.0000.0000.0000.000
114A146GLY00.0190.01441.1410.0950.0950.0000.0000.0000.000
115A147ALA0-0.0100.01538.610-0.155-0.1550.0000.0000.0000.000
116A148LEU0-0.003-0.00434.7640.0490.0490.0000.0000.0000.000
117A149THR0-0.025-0.01333.690-0.081-0.0810.0000.0000.0000.000
118A150VAL0-0.010-0.02728.7030.0920.0920.0000.0000.0000.000
119A151TYR0-0.022-0.00929.426-0.036-0.0360.0000.0000.0000.000
120A152THR0-0.013-0.00126.817-0.172-0.1720.0000.0000.0000.000
121A153GLY00.1420.07827.471-0.157-0.1570.0000.0000.0000.000
122A154THR0-0.075-0.04728.3550.3240.3240.0000.0000.0000.000
123A155VAL0-0.010-0.01029.435-0.257-0.2570.0000.0000.0000.000
124A156THR0-0.007-0.00831.6120.2470.2470.0000.0000.0000.000
125A157GLN0-0.0210.00231.571-0.166-0.1660.0000.0000.0000.000
126A158GLY00.0520.01934.8240.2380.2380.0000.0000.0000.000
127A159THR0-0.147-0.09237.497-0.057-0.0570.0000.0000.0000.000
128A160ASP-1-0.871-0.91839.727-7.172-7.1720.0000.0000.0000.000
129A161PRO0-0.057-0.03341.8900.1400.1400.0000.0000.0000.000
130A162VAL00.0360.00136.015-0.126-0.1260.0000.0000.0000.000
131A163LYS10.8060.90338.1957.3997.3990.0000.0000.0000.000
132A164THR00.0150.00733.994-0.161-0.1610.0000.0000.0000.000
133A165TYR0-0.038-0.00435.1970.1960.1960.0000.0000.0000.000
134A166TYR0-0.002-0.01833.283-0.428-0.4280.0000.0000.0000.000
135A167GLN00.0300.02229.1520.0250.0250.0000.0000.0000.000
136A168TYR0-0.040-0.02931.773-0.238-0.2380.0000.0000.0000.000
137A169THR00.000-0.01528.3430.3450.3450.0000.0000.0000.000
138A170PRO0-0.027-0.00131.565-0.012-0.0120.0000.0000.0000.000
139A171VAL0-0.021-0.01530.102-0.286-0.2860.0000.0000.0000.000
140A172SER00.0180.00727.0390.2170.2170.0000.0000.0000.000
141A173SER0-0.017-0.01026.7630.0070.0070.0000.0000.0000.000
142A174LYS10.8450.88528.7019.3469.3460.0000.0000.0000.000
143A175ALA00.0300.01928.1870.2900.2900.0000.0000.0000.000
144A176MET0-0.0040.01629.7560.1560.1560.0000.0000.0000.000
145A177TYR00.0330.00131.3790.3830.3830.0000.0000.0000.000
146A178ASP-1-0.800-0.88033.385-8.721-8.7210.0000.0000.0000.000
147A179ALA0-0.061-0.02933.3520.2550.2550.0000.0000.0000.000
148A180TYR00.0290.00935.3020.2820.2820.0000.0000.0000.000
149A181TRP0-0.0010.00336.3070.2080.2080.0000.0000.0000.000
150A182ASN0-0.114-0.04038.3050.0740.0740.0000.0000.0000.000
151A183GLY00.0280.00240.2530.0970.0970.0000.0000.0000.000
152A184LYS10.8730.94234.5099.1039.1030.0000.0000.0000.000
153A185PHE00.0550.03532.874-0.083-0.0830.0000.0000.0000.000
154A186ARG10.9110.95838.9537.4757.4750.0000.0000.0000.000
155A187ASP-1-0.832-0.91739.470-8.002-8.0020.0000.0000.0000.000
156A188VAL00.0200.00837.4090.0750.0750.0000.0000.0000.000
157A189ALA0-0.0090.00839.218-0.002-0.0020.0000.0000.0000.000
158A190PHE0-0.053-0.02640.9190.0500.0500.0000.0000.0000.000
159A191HIS0-0.0220.00643.0540.2840.2840.0000.0000.0000.000
160A192SER0-0.030-0.01545.4480.0070.0070.0000.0000.0000.000
161A193GLY00.0370.01747.8240.0400.0400.0000.0000.0000.000
162A194PHE0-0.041-0.02446.312-0.093-0.0930.0000.0000.0000.000
163A195ASN0-0.003-0.00843.6800.0770.0770.0000.0000.0000.000
164A196GLU-1-0.883-0.95541.161-7.454-7.4540.0000.0000.0000.000
165A197ASP-1-0.925-0.95138.399-8.375-8.3750.0000.0000.0000.000
166A198PRO0-0.099-0.04334.4820.1100.1100.0000.0000.0000.000
167A199LEU00.0410.02837.398-0.010-0.0100.0000.0000.0000.000
168A200VAL00.0050.00033.203-0.237-0.2370.0000.0000.0000.000
169A201ALA0-0.039-0.01234.2510.2130.2130.0000.0000.0000.000
170A202GLU-1-0.885-0.93735.015-8.687-8.6870.0000.0000.0000.000
171A203TYR0-0.059-0.02132.282-0.250-0.2500.0000.0000.0000.000
172A204GLN00.0690.00429.825-0.435-0.4350.0000.0000.0000.000
173A205GLY00.0490.03528.943-0.473-0.4730.0000.0000.0000.000
174A206GLN0-0.075-0.03428.0380.3210.3210.0000.0000.0000.000
175A207LEU00.0210.01727.786-0.382-0.3820.0000.0000.0000.000
176A208SER0-0.036-0.02423.805-0.021-0.0210.0000.0000.0000.000
177A209TYR0-0.011-0.01824.1230.4610.4610.0000.0000.0000.000
178A210LEU00.0020.02918.541-0.398-0.3980.0000.0000.0000.000
179A211PRO00.0130.01816.7920.6310.6310.0000.0000.0000.000
180A212GLN0-0.028-0.00118.142-0.273-0.2730.0000.0000.0000.000
181A213PRO00.0240.01015.6500.3960.3960.0000.0000.0000.000
182A214PRO0-0.004-0.00714.265-0.790-0.7900.0000.0000.0000.000
183A215VAL0-0.003-0.0168.328-0.190-0.1900.0000.0000.0000.000
184A216ASN0-0.034-0.0039.426-0.357-0.3570.0000.0000.0000.000
185A217ALA0-0.0140.01210.7161.5391.5390.0000.0000.0000.000
186A218PRO0-0.015-0.00713.183-0.669-0.6690.0000.0000.0000.000