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: Z6N7N

Calculation Name: 3PHS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3PHS

Chain ID: A

ChEMBL ID:

UniProt ID: Q8E0S8

Base Structure: X-ray

Registration Date: 2023-06-22

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 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 238
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2657814.896719
FMO2-HF: Nuclear repulsion 2567451.57879
FMO2-HF: Total energy -90363.317929
FMO2-MP2: Total energy -90634.543529


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:30:SER)


Summations of interaction energy for fragment #1(A:30: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.
-21.822-17.56910.742-6.488-8.506-0.019
Interaction energy analysis for fragmet #1(A:30:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.066 / q_NPA : -0.030
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].
3A32GLN0-0.063-0.0423.8451.6813.649-0.017-1.045-0.9060.004
4A33LEU00.0410.0306.872-0.129-0.1290.0000.0000.0000.000
5A34THR0-0.062-0.0369.5940.4060.4060.0000.0000.0000.000
6A35ILE0-0.0120.00212.991-0.042-0.0420.0000.0000.0000.000
7A36VAL0-0.020-0.02015.9130.0750.0750.0000.0000.0000.000
8A37HIS00.0430.03919.206-0.020-0.0200.0000.0000.0000.000
9A38LEU0-0.020-0.01522.1640.0210.0210.0000.0000.0000.000
10A39GLU-1-0.923-0.95625.444-0.147-0.1470.0000.0000.0000.000
11A40ALA00.0140.00828.4930.0050.0050.0000.0000.0000.000
12A41ARG10.8740.91430.4090.1740.1740.0000.0000.0000.000
13A42ASP-1-0.798-0.89032.495-0.182-0.1820.0000.0000.0000.000
14A43ILE0-0.050-0.03333.316-0.010-0.0100.0000.0000.0000.000
15A44ASP-1-0.794-0.86730.620-0.197-0.1970.0000.0000.0000.000
16A45ARG10.7980.89222.2820.3530.3530.0000.0000.0000.000
17A46PRO00.0170.02029.8340.0040.0040.0000.0000.0000.000
18A47ASN0-0.001-0.00728.562-0.014-0.0140.0000.0000.0000.000
19A48PRO00.0220.01825.963-0.025-0.0250.0000.0000.0000.000
20A49GLN0-0.002-0.01522.629-0.033-0.0330.0000.0000.0000.000
21A50LEU00.0080.00217.6470.0110.0110.0000.0000.0000.000
22A51GLU-1-0.834-0.92015.414-1.063-1.0630.0000.0000.0000.000
23A52ILE0-0.065-0.01118.736-0.004-0.0040.0000.0000.0000.000
24A53ALA0-0.004-0.00422.2590.0250.0250.0000.0000.0000.000
25A54PRO0-0.078-0.03323.3890.0160.0160.0000.0000.0000.000
26A55LYS10.9170.94126.8020.2350.2350.0000.0000.0000.000
27A56GLU-1-0.912-0.94329.611-0.188-0.1880.0000.0000.0000.000
28A57GLY00.005-0.02427.921-0.013-0.0130.0000.0000.0000.000
29A58THR0-0.0130.00828.2250.0010.0010.0000.0000.0000.000
30A59PRO0-0.0090.00424.492-0.008-0.0080.0000.0000.0000.000
31A60ILE0-0.0040.00224.6820.0190.0190.0000.0000.0000.000
32A61GLU-1-0.971-0.98123.322-0.059-0.0590.0000.0000.0000.000
33A62GLY00.0630.03522.9370.0040.0040.0000.0000.0000.000
34A63VAL0-0.080-0.04121.8390.0110.0110.0000.0000.0000.000
35A64LEU00.0080.01518.494-0.015-0.0150.0000.0000.0000.000
36A65TYR0-0.023-0.05216.406-0.037-0.0370.0000.0000.0000.000
37A66GLN00.0300.02115.7410.0250.0250.0000.0000.0000.000
38A67LEU00.0130.00011.600-0.047-0.0470.0000.0000.0000.000
39A68TYR0-0.057-0.05213.1420.1060.1060.0000.0000.0000.000
40A69GLN00.014-0.0037.4640.0540.0540.0000.0000.0000.000
41A70LEU00.003-0.00211.6680.1210.1210.0000.0000.0000.000
42A71LYS10.8900.96012.936-0.130-0.1300.0000.0000.0000.000
43A72SER0-0.024-0.01115.4420.0140.0140.0000.0000.0000.000
44A73THR00.021-0.00815.255-0.034-0.0340.0000.0000.0000.000
45A74GLU-1-0.948-0.96818.200-0.146-0.1460.0000.0000.0000.000
46A75ASP-1-0.890-0.93421.837-0.161-0.1610.0000.0000.0000.000
47A76GLY00.011-0.00522.356-0.031-0.0310.0000.0000.0000.000
48A77ASP-1-0.961-0.96324.669-0.208-0.2080.0000.0000.0000.000
49A78LEU00.0220.01617.2430.0060.0060.0000.0000.0000.000
50A79LEU0-0.013-0.02120.1730.0090.0090.0000.0000.0000.000
51A80ALA0-0.027-0.01721.7860.0170.0170.0000.0000.0000.000
52A81HIS00.0360.00921.5410.0150.0150.0000.0000.0000.000
53A82TRP00.0160.00417.5050.0220.0220.0000.0000.0000.000
54A83ASN0-0.029-0.01421.9370.0080.0080.0000.0000.0000.000
55A84SER0-0.103-0.04424.4330.0190.0190.0000.0000.0000.000
56A85LEU0-0.0150.01721.6600.0210.0210.0000.0000.0000.000
57A86THR0-0.027-0.02225.480-0.001-0.0010.0000.0000.0000.000
58A87ILE00.019-0.00622.8520.0000.0000.0000.0000.0000.000
59A88THR0-0.024-0.01922.9000.0040.0040.0000.0000.0000.000
60A89GLU-1-0.907-0.95723.634-0.016-0.0160.0000.0000.0000.000
61A90LEU00.0370.03719.4520.0050.0050.0000.0000.0000.000
62A91LYS10.9670.97817.043-0.186-0.1860.0000.0000.0000.000
63A92LYS10.8770.94319.2430.0020.0020.0000.0000.0000.000
64A93GLN00.0370.02920.0050.0050.0050.0000.0000.0000.000
65A94ALA0-0.0090.02014.914-0.017-0.0170.0000.0000.0000.000
66A95GLN0-0.052-0.03411.598-0.007-0.0070.0000.0000.0000.000
67A96GLN00.0270.0088.4690.0930.0930.0000.0000.0000.000
68A97VAL0-0.034-0.02212.462-0.110-0.1100.0000.0000.0000.000
69A98PHE0-0.0100.0087.3250.0470.0470.0000.0000.0000.000
70A99GLU-1-0.955-0.98512.1620.0040.0040.0000.0000.0000.000
71A100ALA00.0180.01713.2420.0500.0500.0000.0000.0000.000
72A101THR00.0160.01415.292-0.040-0.0400.0000.0000.0000.000
73A102THR0-0.080-0.05318.2440.0080.0080.0000.0000.0000.000
74A103ASN00.1280.06217.7690.0070.0070.0000.0000.0000.000
75A104GLN00.044-0.00120.759-0.017-0.0170.0000.0000.0000.000
76A105GLN0-0.062-0.02420.7030.0000.0000.0000.0000.0000.000
77A106GLY00.0440.02321.881-0.035-0.0350.0000.0000.0000.000
78A107LYS10.8820.95316.4590.3830.3830.0000.0000.0000.000
79A108ALA00.0360.03815.5910.0610.0610.0000.0000.0000.000
80A109THR0-0.054-0.03111.671-0.085-0.0850.0000.0000.0000.000
81A110PHE00.004-0.0058.5660.2010.2010.0000.0000.0000.000
82A111ASN00.0180.0036.481-0.659-0.6590.0000.0000.0000.000
83A112GLN0-0.004-0.0072.304-8.002-5.8872.581-1.786-2.9100.019
84A113LEU00.0130.0242.6810.5400.2561.3100.350-1.375-0.010
85A114PRO0-0.0190.0012.180-6.162-5.9566.848-3.993-3.061-0.031
86A115ASP-1-0.812-0.8693.325-4.561-4.3750.021-0.006-0.201-0.001
87A116GLY00.0260.0144.6991.0101.072-0.001-0.008-0.0530.000
88A117ILE00.0030.0208.093-0.249-0.2490.0000.0000.0000.000
89A118TYR0-0.025-0.0495.6540.4940.4940.0000.0000.0000.000
90A119TYR00.016-0.00411.999-0.027-0.0270.0000.0000.0000.000
91A120GLY00.0110.00615.3680.0370.0370.0000.0000.0000.000
92A121LEU0-0.019-0.01516.2780.0120.0120.0000.0000.0000.000
93A122ALA00.0440.02619.2740.0060.0060.0000.0000.0000.000
94A123VAL0-0.036-0.01321.0180.0090.0090.0000.0000.0000.000
95A124LYS10.9230.94423.4690.0750.0750.0000.0000.0000.000
96A125ALA0-0.0010.00226.8080.0010.0010.0000.0000.0000.000
97A126GLY0-0.0030.00026.4600.0020.0020.0000.0000.0000.000
98A127GLU-1-0.823-0.89226.936-0.039-0.0390.0000.0000.0000.000
99A128LYS10.9400.98423.7550.1760.1760.0000.0000.0000.000
100A129ASN00.0350.01725.1230.0100.0100.0000.0000.0000.000
101A130ARG10.8620.91726.2380.0760.0760.0000.0000.0000.000
102A131ASN00.002-0.00128.654-0.011-0.0110.0000.0000.0000.000
103A132VAL00.0050.01922.181-0.011-0.0110.0000.0000.0000.000
104A133SER0-0.063-0.03424.1980.0120.0120.0000.0000.0000.000
105A134ALA0-0.0050.00020.605-0.022-0.0220.0000.0000.0000.000
106A135PHE0-0.035-0.02014.5860.0070.0070.0000.0000.0000.000
107A136LEU00.0290.00715.7340.0180.0180.0000.0000.0000.000
108A137VAL0-0.056-0.03510.9190.0050.0050.0000.0000.0000.000
109A138ASP-1-0.882-0.94511.609-1.133-1.1330.0000.0000.0000.000
110A139LEU0-0.082-0.0435.1300.0650.0650.0000.0000.0000.000
111A140SER00.0760.0306.617-0.528-0.5280.0000.0000.0000.000
112A141GLU-1-0.897-0.9426.830-2.103-2.1030.0000.0000.0000.000
113A142ASP-1-0.856-0.9276.448-4.476-4.4760.0000.0000.0000.000
114A143LYS10.8100.9148.6042.0952.0950.0000.0000.0000.000
115A144VAL0-0.017-0.02011.3350.1110.1110.0000.0000.0000.000
116A145ILE00.0130.01413.9400.0480.0480.0000.0000.0000.000
117A146TYR00.0650.02316.5120.0540.0540.0000.0000.0000.000
118A147PRO00.0360.02818.7900.0150.0150.0000.0000.0000.000
119A148LYS10.9240.96021.1520.3600.3600.0000.0000.0000.000
120A149ILE00.0040.00923.2580.0110.0110.0000.0000.0000.000
121A150ILE0-0.038-0.00426.8350.0010.0010.0000.0000.0000.000
122A151TRP00.047-0.01330.3860.0140.0140.0000.0000.0000.000
123A152SER0-0.035-0.00132.6860.0090.0090.0000.0000.0000.000
124A153THR00.002-0.00436.1840.0010.0010.0000.0000.0000.000
125A154GLY00.0300.01738.970-0.002-0.0020.0000.0000.0000.000
126A155GLU-1-0.905-0.94342.388-0.055-0.0550.0000.0000.0000.000
127A156LEU0-0.0050.00945.143-0.002-0.0020.0000.0000.0000.000
128A157ASP-1-0.845-0.91446.959-0.041-0.0410.0000.0000.0000.000
129A158LEU0-0.0010.00450.435-0.001-0.0010.0000.0000.0000.000
130A159LEU0-0.050-0.02052.1520.0020.0020.0000.0000.0000.000
131A160LYN00.0470.01155.3670.0000.0000.0000.0000.0000.000
132A161VAL0-0.020-0.02257.1860.0010.0010.0000.0000.0000.000
133A162GLY00.0370.01460.5690.0000.0000.0000.0000.0000.000
134A163VAL0-0.075-0.05462.5680.0000.0000.0000.0000.0000.000
135A164ASP-1-0.913-0.97365.377-0.017-0.0170.0000.0000.0000.000
136A165GLY00.0180.01169.0940.0000.0000.0000.0000.0000.000
137A166ASP-1-0.942-0.97068.696-0.025-0.0250.0000.0000.0000.000
138A167THR0-0.019-0.00169.300-0.001-0.0010.0000.0000.0000.000
139A168LYS10.8470.89362.5580.0320.0320.0000.0000.0000.000
140A169LYS10.9450.97965.0950.0190.0190.0000.0000.0000.000
141A170PRO00.0230.00861.4000.0000.0000.0000.0000.0000.000
142A171LEU0-0.029-0.00460.3160.0020.0020.0000.0000.0000.000
143A172ALA0-0.0220.01359.239-0.001-0.0010.0000.0000.0000.000
144A173GLY00.0350.01657.6210.0010.0010.0000.0000.0000.000
145A174VAL0-0.0380.00054.7230.0010.0010.0000.0000.0000.000
146A175VAL00.0410.02350.806-0.002-0.0020.0000.0000.0000.000
147A176PHE00.026-0.00548.717-0.001-0.0010.0000.0000.0000.000
148A177GLU-1-0.876-0.93544.298-0.017-0.0170.0000.0000.0000.000
149A178LEU00.0200.00441.716-0.002-0.0020.0000.0000.0000.000
150A179TYR0-0.030-0.00739.0850.0030.0030.0000.0000.0000.000
151A180GLU-1-0.876-0.94233.186-0.087-0.0870.0000.0000.0000.000
152A181LYS10.9560.96136.8080.0870.0870.0000.0000.0000.000
153A182ASN0-0.060-0.03334.9030.0000.0000.0000.0000.0000.000
154A183GLY00.0260.03435.0010.0010.0010.0000.0000.0000.000
155A184ARG10.8870.91531.9890.0310.0310.0000.0000.0000.000
156A185THR0-0.052-0.03334.1660.0080.0080.0000.0000.0000.000
157A186PRO0-0.0070.00037.295-0.005-0.0050.0000.0000.0000.000
158A187ILE0-0.024-0.00637.5800.0010.0010.0000.0000.0000.000
159A188ARG10.8000.89236.4320.0210.0210.0000.0000.0000.000
160A189VAL00.0350.00740.759-0.005-0.0050.0000.0000.0000.000
161A190LYS10.7790.84742.2110.0230.0230.0000.0000.0000.000
162A191ASN0-0.009-0.00644.565-0.001-0.0010.0000.0000.0000.000
163A192GLY00.0360.02647.025-0.002-0.0020.0000.0000.0000.000
164A193VAL0-0.019-0.00141.204-0.004-0.0040.0000.0000.0000.000
165A194HIS0-0.0190.00336.4570.0000.0000.0000.0000.0000.000
166A195SER0-0.006-0.00438.845-0.001-0.0010.0000.0000.0000.000
167A196GLN00.010-0.01531.6890.0000.0000.0000.0000.0000.000
168A197ASP-1-0.796-0.86536.358-0.019-0.0190.0000.0000.0000.000
169A198ILE0-0.022-0.01337.3510.0000.0000.0000.0000.0000.000
170A199ASP-1-0.817-0.90039.669-0.010-0.0100.0000.0000.0000.000
171A200ALA0-0.0410.00540.627-0.001-0.0010.0000.0000.0000.000
172A201ALA00.0580.02642.3330.0030.0030.0000.0000.0000.000
173A202LYS10.9520.96342.4800.0050.0050.0000.0000.0000.000
174A203HIS0-0.043-0.01344.120-0.001-0.0010.0000.0000.0000.000
175A204LEU0-0.0180.00545.288-0.001-0.0010.0000.0000.0000.000
176A205GLU-1-0.878-0.93649.273-0.015-0.0150.0000.0000.0000.000
177A206THR0-0.049-0.03353.047-0.001-0.0010.0000.0000.0000.000
178A207ASP-1-0.719-0.81855.305-0.027-0.0270.0000.0000.0000.000
179A208SER0-0.024-0.03757.3940.0000.0000.0000.0000.0000.000
180A209SER0-0.115-0.09258.6300.0000.0000.0000.0000.0000.000
181A210GLY00.0180.00258.742-0.001-0.0010.0000.0000.0000.000
182A211HIS10.8090.87554.6130.0360.0360.0000.0000.0000.000
183A212ILE00.0560.05449.1030.0020.0020.0000.0000.0000.000
184A213ARG10.8880.94949.7910.0380.0380.0000.0000.0000.000
185A214ILE0-0.0070.00643.4810.0020.0020.0000.0000.0000.000
186A215SER00.0400.02544.384-0.004-0.0040.0000.0000.0000.000
187A216GLY00.021-0.00640.3590.0020.0020.0000.0000.0000.000
188A217LEU00.0030.00438.8730.0000.0000.0000.0000.0000.000
189A218ILE00.0160.01932.444-0.003-0.0030.0000.0000.0000.000
190A219HIS0-0.0030.01234.425-0.001-0.0010.0000.0000.0000.000
191A220GLY00.0090.00935.630-0.008-0.0080.0000.0000.0000.000
192A221ASP-1-0.868-0.91236.961-0.089-0.0890.0000.0000.0000.000
193A222TYR0-0.042-0.06737.0900.0000.0000.0000.0000.0000.000
194A223VAL0-0.014-0.00940.551-0.001-0.0010.0000.0000.0000.000
195A224LEU0-0.0010.00843.1320.0020.0020.0000.0000.0000.000
196A225LYS10.9740.97845.2960.0220.0220.0000.0000.0000.000
197A226GLU-1-0.767-0.89447.458-0.025-0.0250.0000.0000.0000.000
198A227ILE0-0.114-0.05847.5720.0010.0010.0000.0000.0000.000
199A228GLU-1-0.925-0.97351.565-0.008-0.0080.0000.0000.0000.000
200A229THR0-0.039-0.05855.196-0.002-0.0020.0000.0000.0000.000
201A230GLN0-0.032-0.02958.1040.0020.0020.0000.0000.0000.000
202A231SER00.000-0.00361.5610.0000.0000.0000.0000.0000.000
203A232GLY0-0.003-0.00864.4110.0000.0000.0000.0000.0000.000
204A233TYR0-0.069-0.03361.973-0.001-0.0010.0000.0000.0000.000
205A234GLN0-0.0010.00060.3830.0020.0020.0000.0000.0000.000
206A235ILE00.0300.02353.770-0.001-0.0010.0000.0000.0000.000
207A236GLY0-0.071-0.02657.0540.0010.0010.0000.0000.0000.000
208A237GLN0-0.040-0.04051.9060.0000.0000.0000.0000.0000.000
209A238ALA00.0220.01250.3110.0000.0000.0000.0000.0000.000
210A239GLU-1-0.910-0.95544.718-0.037-0.0370.0000.0000.0000.000
211A240THR0-0.0200.00547.5540.0000.0000.0000.0000.0000.000
212A241ALA0-0.0120.00044.087-0.001-0.0010.0000.0000.0000.000
213A242VAL00.007-0.00343.6600.0010.0010.0000.0000.0000.000
214A243THR00.005-0.01340.596-0.001-0.0010.0000.0000.0000.000
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216A245GLU-1-0.834-0.92040.409-0.096-0.0960.0000.0000.0000.000
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