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: R9YQ8

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 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 238
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2658590.684393
FMO2-HF: Nuclear repulsion 2568226.139248
FMO2-HF: Total energy -90364.545145
FMO2-MP2: Total energy -90635.732997


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.
-23.416-21.14213.999-6.891-9.383-0.015
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 : -0.060 / q_NPA : -0.021
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].
3A32GLN0-0.057-0.0363.8451.7463.768-0.017-1.066-0.9390.004
4A33LEU00.0390.0246.804-0.134-0.1340.0000.0000.0000.000
5A34THR0-0.058-0.0329.5220.4110.4110.0000.0000.0000.000
6A35ILE0-0.0080.00512.920-0.042-0.0420.0000.0000.0000.000
7A36VAL0-0.016-0.01815.8420.0780.0780.0000.0000.0000.000
8A37HIS00.0310.02419.134-0.020-0.0200.0000.0000.0000.000
9A38LEU0-0.031-0.02322.0940.0230.0230.0000.0000.0000.000
10A39GLU-1-0.889-0.94325.373-0.153-0.1530.0000.0000.0000.000
11A40ALA00.0090.00328.4940.0060.0060.0000.0000.0000.000
12A41ARG10.8800.90130.3940.1750.1750.0000.0000.0000.000
13A42ASP-1-0.784-0.87532.504-0.180-0.1800.0000.0000.0000.000
14A43ILE0-0.007-0.01433.321-0.011-0.0110.0000.0000.0000.000
15A44ASP-1-0.780-0.84630.769-0.196-0.1960.0000.0000.0000.000
16A45ARG10.8040.90022.1250.3690.3690.0000.0000.0000.000
17A46PRO00.0170.01729.8380.0040.0040.0000.0000.0000.000
18A47ASN0-0.004-0.00228.675-0.020-0.0200.0000.0000.0000.000
19A48PRO00.0430.03025.981-0.024-0.0240.0000.0000.0000.000
20A49GLN00.015-0.01122.608-0.025-0.0250.0000.0000.0000.000
21A50LEU00.0200.01117.8370.0120.0120.0000.0000.0000.000
22A51GLU-1-0.801-0.88915.450-1.096-1.0960.0000.0000.0000.000
23A52ILE0-0.066-0.01818.735-0.003-0.0030.0000.0000.0000.000
24A53ALA00.0070.00322.2590.0250.0250.0000.0000.0000.000
25A54PRO0-0.074-0.02923.3950.0150.0150.0000.0000.0000.000
26A55LYS10.8690.91726.8090.2250.2250.0000.0000.0000.000
27A56GLU-1-0.912-0.94829.618-0.185-0.1850.0000.0000.0000.000
28A57GLY0-0.006-0.02627.848-0.013-0.0130.0000.0000.0000.000
29A58THR0-0.0150.00628.1540.0020.0020.0000.0000.0000.000
30A59PRO0-0.0080.00524.335-0.008-0.0080.0000.0000.0000.000
31A60ILE0-0.0110.00124.6100.0200.0200.0000.0000.0000.000
32A61GLU-1-0.963-0.97023.363-0.058-0.0580.0000.0000.0000.000
33A62GLY00.0640.02922.8820.0040.0040.0000.0000.0000.000
34A63VAL0-0.083-0.04021.9670.0110.0110.0000.0000.0000.000
35A64LEU00.0130.01818.590-0.016-0.0160.0000.0000.0000.000
36A65TYR0-0.020-0.04116.390-0.038-0.0380.0000.0000.0000.000
37A66GLN0-0.0040.00215.6690.0260.0260.0000.0000.0000.000
38A67LEU00.0100.00111.550-0.051-0.0510.0000.0000.0000.000
39A68TYR0-0.051-0.04713.1600.1040.1040.0000.0000.0000.000
40A69GLN00.004-0.0117.3720.0690.0690.0000.0000.0000.000
41A70LEU00.003-0.00111.6720.1280.1280.0000.0000.0000.000
42A71LYS10.8710.92912.928-0.132-0.1320.0000.0000.0000.000
43A72SER0-0.032-0.01515.4330.0140.0140.0000.0000.0000.000
44A73THR00.017-0.01015.189-0.038-0.0380.0000.0000.0000.000
45A74GLU-1-0.944-0.96518.181-0.167-0.1670.0000.0000.0000.000
46A75ASP-1-0.898-0.94121.815-0.171-0.1710.0000.0000.0000.000
47A76GLY00.008-0.00322.339-0.032-0.0320.0000.0000.0000.000
48A77ASP-1-0.957-0.96524.650-0.224-0.2240.0000.0000.0000.000
49A78LEU00.0170.01417.2450.0070.0070.0000.0000.0000.000
50A79LEU0-0.009-0.01920.1260.0090.0090.0000.0000.0000.000
51A80ALA0-0.022-0.01621.7800.0180.0180.0000.0000.0000.000
52A81HIS00.0370.01721.6140.0170.0170.0000.0000.0000.000
53A82TRP00.0210.00217.6400.0210.0210.0000.0000.0000.000
54A83ASN0-0.026-0.01521.9370.0100.0100.0000.0000.0000.000
55A84SER0-0.089-0.03424.4350.0200.0200.0000.0000.0000.000
56A85LEU0-0.0220.01021.6280.0230.0230.0000.0000.0000.000
57A86THR0-0.019-0.02225.488-0.001-0.0010.0000.0000.0000.000
58A87ILE00.0250.00122.972-0.001-0.0010.0000.0000.0000.000
59A88THR0-0.014-0.01422.9150.0020.0020.0000.0000.0000.000
60A89GLU-1-0.841-0.91823.646-0.015-0.0150.0000.0000.0000.000
61A90LEU00.0360.03819.4240.0040.0040.0000.0000.0000.000
62A91LYS10.9690.97717.029-0.182-0.1820.0000.0000.0000.000
63A92LYS10.7980.90019.2530.0200.0200.0000.0000.0000.000
64A93GLN00.0290.01920.0070.0050.0050.0000.0000.0000.000
65A94ALA0-0.0010.02314.987-0.019-0.0190.0000.0000.0000.000
66A95GLN0-0.0210.00511.773-0.020-0.0200.0000.0000.0000.000
67A96GLN00.0060.0038.5040.0740.0740.0000.0000.0000.000
68A97VAL0-0.027-0.02112.476-0.110-0.1100.0000.0000.0000.000
69A98PHE0-0.0030.0127.3240.0430.0430.0000.0000.0000.000
70A99GLU-1-0.901-0.96412.127-0.017-0.0170.0000.0000.0000.000
71A100ALA00.0000.01013.1670.0540.0540.0000.0000.0000.000
72A101THR00.0090.01215.240-0.040-0.0400.0000.0000.0000.000
73A102THR0-0.077-0.05518.1870.0080.0080.0000.0000.0000.000
74A103ASN00.1100.05818.1830.0050.0050.0000.0000.0000.000
75A104GLN00.0430.00120.700-0.019-0.0190.0000.0000.0000.000
76A105GLN0-0.062-0.02720.624-0.004-0.0040.0000.0000.0000.000
77A106GLY00.0460.02221.814-0.035-0.0350.0000.0000.0000.000
78A107LYS10.8890.95516.4120.3580.3580.0000.0000.0000.000
79A108ALA00.0350.03515.8120.0620.0620.0000.0000.0000.000
80A109THR0-0.038-0.02311.586-0.094-0.0940.0000.0000.0000.000
81A110PHE0-0.007-0.0128.5680.1970.1970.0000.0000.0000.000
82A111ASN00.0070.0006.448-0.639-0.6390.0000.0000.0000.000
83A112GLN0-0.004-0.0172.059-9.797-9.5365.799-2.358-3.7020.024
84A113LEU00.0120.0242.6380.7460.1471.4950.517-1.412-0.011
85A114PRO0-0.025-0.0052.198-6.172-5.8496.700-3.958-3.066-0.031
86A115ASP-1-0.807-0.8673.307-4.625-4.4200.023-0.018-0.211-0.001
87A116GLY00.0210.0114.6721.0511.113-0.001-0.008-0.0530.000
88A117ILE00.0070.0158.075-0.244-0.2440.0000.0000.0000.000
89A118TYR0-0.023-0.0375.6560.5050.5050.0000.0000.0000.000
90A119TYR00.0130.00211.999-0.023-0.0230.0000.0000.0000.000
91A120GLY00.0140.00715.3780.0370.0370.0000.0000.0000.000
92A121LEU0-0.024-0.01816.2900.0150.0150.0000.0000.0000.000
93A122ALA00.0430.02619.2210.0070.0070.0000.0000.0000.000
94A123VAL0-0.032-0.01121.0250.0090.0090.0000.0000.0000.000
95A124LYS10.9200.94423.4170.0800.0800.0000.0000.0000.000
96A125ALA00.000-0.00526.7560.0010.0010.0000.0000.0000.000
97A126GLY00.0050.00626.4200.0020.0020.0000.0000.0000.000
98A127GLU-1-0.829-0.89726.867-0.041-0.0410.0000.0000.0000.000
99A128LYS10.9010.95323.5290.1850.1850.0000.0000.0000.000
100A129ASN00.0520.02225.0990.0130.0130.0000.0000.0000.000
101A130ARG10.7930.87526.2530.0780.0780.0000.0000.0000.000
102A131ASN0-0.022-0.01028.668-0.010-0.0100.0000.0000.0000.000
103A132VAL00.0140.02622.225-0.011-0.0110.0000.0000.0000.000
104A133SER0-0.034-0.01423.9930.0120.0120.0000.0000.0000.000
105A134ALA0-0.006-0.00220.628-0.023-0.0230.0000.0000.0000.000
106A135PHE0-0.023-0.01214.6180.0080.0080.0000.0000.0000.000
107A136LEU00.0300.00815.7400.0170.0170.0000.0000.0000.000
108A137VAL0-0.056-0.03710.7720.0060.0060.0000.0000.0000.000
109A138ASP-1-0.869-0.93511.535-1.240-1.2400.0000.0000.0000.000
110A139LEU0-0.067-0.0335.3030.0600.0600.0000.0000.0000.000
111A140SER00.0660.0196.595-0.510-0.5100.0000.0000.0000.000
112A141GLU-1-0.915-0.9426.839-2.088-2.0880.0000.0000.0000.000
113A142ASP-1-0.861-0.9246.450-4.383-4.3830.0000.0000.0000.000
114A143LYS10.7900.8768.6042.0552.0550.0000.0000.0000.000
115A144VAL0-0.028-0.02011.3370.1200.1200.0000.0000.0000.000
116A145ILE0-0.0010.00013.7990.0470.0470.0000.0000.0000.000
117A146TYR00.0490.01916.5200.0860.0860.0000.0000.0000.000
118A147PRO00.0430.03418.8470.0120.0120.0000.0000.0000.000
119A148LYS10.8740.93621.1620.3700.3700.0000.0000.0000.000
120A149ILE00.0080.01123.1370.0110.0110.0000.0000.0000.000
121A150ILE0-0.047-0.01126.8480.0020.0020.0000.0000.0000.000
122A151TRP00.050-0.00930.4760.0140.0140.0000.0000.0000.000
123A152SER0-0.0250.00432.6200.0080.0080.0000.0000.0000.000
124A153THR00.0150.00536.1730.0010.0010.0000.0000.0000.000
125A154GLY0-0.007-0.00138.903-0.002-0.0020.0000.0000.0000.000
126A155GLU-1-0.917-0.94142.386-0.057-0.0570.0000.0000.0000.000
127A156LEU0-0.0050.00845.096-0.002-0.0020.0000.0000.0000.000
128A157ASP-1-0.826-0.90846.968-0.042-0.0420.0000.0000.0000.000
129A158LEU0-0.0030.00750.482-0.001-0.0010.0000.0000.0000.000
130A159LEU0-0.049-0.02052.1680.0020.0020.0000.0000.0000.000
131A160LYN00.0160.01254.9170.0000.0000.0000.0000.0000.000
132A161VAL0-0.011-0.01857.2020.0010.0010.0000.0000.0000.000
133A162GLY00.0530.01260.5840.0000.0000.0000.0000.0000.000
134A163VAL0-0.097-0.06362.6330.0000.0000.0000.0000.0000.000
135A164ASP-1-0.892-0.96665.390-0.018-0.0180.0000.0000.0000.000
136A165GLY00.0240.01169.1080.0000.0000.0000.0000.0000.000
137A166ASP-1-0.937-0.96668.707-0.026-0.0260.0000.0000.0000.000
138A167THR0-0.025-0.00469.332-0.001-0.0010.0000.0000.0000.000
139A168LYS10.8410.89562.6390.0340.0340.0000.0000.0000.000
140A169LYS10.9510.98265.1150.0200.0200.0000.0000.0000.000
141A170PRO00.0250.00761.2360.0000.0000.0000.0000.0000.000
142A171LEU0-0.0420.00760.1780.0020.0020.0000.0000.0000.000
143A172ALA0-0.0080.01259.182-0.001-0.0010.0000.0000.0000.000
144A173GLY00.0350.01357.5570.0010.0010.0000.0000.0000.000
145A174VAL0-0.041-0.00554.7480.0010.0010.0000.0000.0000.000
146A175VAL00.0370.02150.720-0.002-0.0020.0000.0000.0000.000
147A176PHE00.029-0.00348.639-0.001-0.0010.0000.0000.0000.000
148A177GLU-1-0.808-0.87144.249-0.019-0.0190.0000.0000.0000.000
149A178LEU00.0200.00641.800-0.002-0.0020.0000.0000.0000.000
150A179TYR0-0.029-0.02539.2540.0030.0030.0000.0000.0000.000
151A180GLU-1-0.802-0.89833.125-0.096-0.0960.0000.0000.0000.000
152A181LYS10.8870.92836.9260.0960.0960.0000.0000.0000.000
153A182ASN0-0.055-0.03334.842-0.001-0.0010.0000.0000.0000.000
154A183GLY00.0190.03035.0160.0010.0010.0000.0000.0000.000
155A184ARG10.8640.91331.9660.0350.0350.0000.0000.0000.000
156A185THR0-0.009-0.01934.0450.0080.0080.0000.0000.0000.000
157A186PRO0-0.029-0.00337.249-0.006-0.0060.0000.0000.0000.000
158A187ILE0-0.037-0.01837.4550.0010.0010.0000.0000.0000.000
159A188ARG10.7930.89036.6770.0220.0220.0000.0000.0000.000
160A189VAL00.0320.00840.702-0.005-0.0050.0000.0000.0000.000
161A190LYS10.8060.85942.3950.0230.0230.0000.0000.0000.000
162A191ASN0-0.017-0.01344.506-0.001-0.0010.0000.0000.0000.000
163A192GLY00.0390.02946.963-0.002-0.0020.0000.0000.0000.000
164A193VAL0-0.019-0.00241.118-0.004-0.0040.0000.0000.0000.000
165A194HIS0-0.038-0.00736.2440.0000.0000.0000.0000.0000.000
166A195SER0-0.032-0.02238.782-0.001-0.0010.0000.0000.0000.000
167A196GLN00.022-0.00731.839-0.003-0.0030.0000.0000.0000.000
168A197ASP-1-0.785-0.85836.305-0.022-0.0220.0000.0000.0000.000
169A198ILE0-0.001-0.00137.526-0.001-0.0010.0000.0000.0000.000
170A199ASP-1-0.817-0.89739.621-0.011-0.0110.0000.0000.0000.000
171A200ALA0-0.0320.01140.543-0.001-0.0010.0000.0000.0000.000
172A201ALA00.0480.02342.2820.0030.0030.0000.0000.0000.000
173A202LYS10.8760.91142.4860.0090.0090.0000.0000.0000.000
174A203HIS0-0.055-0.02144.0690.0000.0000.0000.0000.0000.000
175A204LEU0-0.0050.01245.279-0.001-0.0010.0000.0000.0000.000
176A205GLU-1-0.888-0.94349.218-0.017-0.0170.0000.0000.0000.000
177A206THR0-0.046-0.03352.992-0.001-0.0010.0000.0000.0000.000
178A207ASP-1-0.707-0.82755.248-0.029-0.0290.0000.0000.0000.000
179A208SER00.020-0.01857.3360.0000.0000.0000.0000.0000.000
180A209SER0-0.149-0.09658.5590.0000.0000.0000.0000.0000.000
181A210GLY00.0260.00758.683-0.001-0.0010.0000.0000.0000.000
182A211HIS10.7910.86454.6030.0370.0370.0000.0000.0000.000
183A212ILE00.0500.05249.0650.0020.0020.0000.0000.0000.000
184A213ARG10.8640.94949.7410.0380.0380.0000.0000.0000.000
185A214ILE0-0.0030.00343.4450.0020.0020.0000.0000.0000.000
186A215SER00.0340.02444.314-0.005-0.0050.0000.0000.0000.000
187A216GLY00.0320.00040.2920.0020.0020.0000.0000.0000.000
188A217LEU0-0.008-0.00138.8120.0000.0000.0000.0000.0000.000
189A218ILE00.0280.02532.359-0.002-0.0020.0000.0000.0000.000
190A219HIS00.0140.02033.982-0.001-0.0010.0000.0000.0000.000
191A220GLY00.0100.00535.642-0.009-0.0090.0000.0000.0000.000
192A221ASP-1-0.823-0.89136.947-0.089-0.0890.0000.0000.0000.000
193A222TYR0-0.046-0.06337.0730.0000.0000.0000.0000.0000.000
194A223VAL0-0.007-0.00540.564-0.001-0.0010.0000.0000.0000.000
195A224LEU0-0.0090.00643.1460.0020.0020.0000.0000.0000.000
196A225LYS10.8800.91644.4900.0290.0290.0000.0000.0000.000
197A226GLU-1-0.768-0.89247.473-0.026-0.0260.0000.0000.0000.000
198A227ILE0-0.104-0.06047.4200.0010.0010.0000.0000.0000.000
199A228GLU-1-0.921-0.96651.517-0.009-0.0090.0000.0000.0000.000
200A229THR0-0.016-0.02355.147-0.002-0.0020.0000.0000.0000.000
201A230GLN0-0.022-0.01758.0540.0020.0020.0000.0000.0000.000
202A231SER00.0300.01261.5100.0000.0000.0000.0000.0000.000
203A232GLY0-0.041-0.03164.3620.0000.0000.0000.0000.0000.000
204A233TYR0-0.064-0.04062.1070.0000.0000.0000.0000.0000.000
205A234GLN00.0110.00860.5660.0020.0020.0000.0000.0000.000
206A235ILE00.0510.03553.807-0.001-0.0010.0000.0000.0000.000
207A236GLY0-0.064-0.02257.0770.0010.0010.0000.0000.0000.000
208A237GLN0-0.046-0.04051.9890.0000.0000.0000.0000.0000.000
209A238ALA00.0280.01550.3870.0000.0000.0000.0000.0000.000
210A239GLU-1-0.836-0.90544.656-0.038-0.0380.0000.0000.0000.000
211A240THR0-0.0210.00147.563-0.001-0.0010.0000.0000.0000.000
212A241ALA0-0.0060.00544.142-0.001-0.0010.0000.0000.0000.000
213A242VAL00.007-0.00643.6280.0010.0010.0000.0000.0000.000
214A243THR00.009-0.00740.457-0.001-0.0010.0000.0000.0000.000
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