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: R9QJ8

Calculation Name: 1O63-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1O63

Chain ID: A

ChEMBL ID:

UniProt ID: Q9X0D2

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 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 202
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2267459.62175
FMO2-HF: Nuclear repulsion 2187261.335509
FMO2-HF: Total energy -80198.286242
FMO2-MP2: Total energy -80432.756293


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:2:LEU)


Summations of interaction energy for fragment #1(A:2:LEU)
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.
-38.511-24.93526.053-14.678-24.954-0.096
Interaction energy analysis for fragmet #1(A:2:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.035 / q_NPA : -0.023
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].
3A4LEU00.0530.0092.499-1.8570.2341.350-1.122-2.3200.006
4A5ALA0-0.032-0.0115.2940.0310.072-0.001-0.003-0.0370.000
5A6ILE00.030-0.0047.809-0.033-0.0330.0000.0000.0000.000
6A7PRO0-0.018-0.00211.2790.0290.0290.0000.0000.0000.000
7A8LYS10.8280.90715.005-0.067-0.0670.0000.0000.0000.000
8A9GLY00.001-0.00917.2450.0180.0180.0000.0000.0000.000
9A10ARG10.8200.86519.7120.0360.0360.0000.0000.0000.000
10A11LEU00.0610.03716.545-0.004-0.0040.0000.0000.0000.000
11A12GLU-1-0.844-0.92014.837-0.080-0.0800.0000.0000.0000.000
12A13GLU-1-0.839-0.92415.323-0.141-0.1410.0000.0000.0000.000
13A14LYS10.8710.93016.0530.1190.1190.0000.0000.0000.000
14A15VAL00.0050.00610.486-0.031-0.0310.0000.0000.0000.000
15A16MET00.0070.00411.075-0.067-0.0670.0000.0000.0000.000
16A17THR0-0.039-0.02712.594-0.059-0.0590.0000.0000.0000.000
17A18TYR0-0.011-0.00610.650-0.024-0.0240.0000.0000.0000.000
18A19LEU00.0290.0136.144-0.063-0.0630.0000.0000.0000.000
19A20LYS10.9881.0019.1550.1810.1810.0000.0000.0000.000
20A21LYS10.8550.91711.8900.2230.2230.0000.0000.0000.000
21A22THR0-0.042-0.0077.470-0.061-0.0610.0000.0000.0000.000
22A23GLY0-0.001-0.0088.969-0.113-0.1130.0000.0000.0000.000
23A24VAL0-0.063-0.0176.147-0.093-0.0930.0000.0000.0000.000
24A25ILE0-0.008-0.0138.8290.1830.1830.0000.0000.0000.000
25A26PHE0-0.027-0.0377.979-0.112-0.1120.0000.0000.0000.000
26A27GLU-1-0.909-0.94111.765-0.173-0.1730.0000.0000.0000.000
27A28ARG10.7810.84613.008-0.051-0.0510.0000.0000.0000.000
28A29GLU-1-0.837-0.91013.289-0.238-0.2380.0000.0000.0000.000
29A30SER00.004-0.00915.4620.0370.0370.0000.0000.0000.000
30A31SER00.016-0.00216.468-0.012-0.0120.0000.0000.0000.000
31A32ILE00.0110.00515.994-0.011-0.0110.0000.0000.0000.000
32A33LEU0-0.0080.01310.4750.0400.0400.0000.0000.0000.000
33A34ARG10.8400.92010.4350.1050.1050.0000.0000.0000.000
34A35GLU-1-0.786-0.8578.7530.1450.1450.0000.0000.0000.000
35A36GLY00.0740.0297.6630.0590.0590.0000.0000.0000.000
36A37LYS10.8450.9176.9241.2171.2170.0000.0000.0000.000
37A38ASP-1-0.832-0.8944.198-1.969-1.670-0.001-0.076-0.2220.000
38A39ILE0-0.024-0.0062.173-9.685-6.8253.149-2.632-3.377-0.030
39A40VAL00.0010.0013.8200.9181.4280.003-0.142-0.3720.000
40A41CYS0-0.0410.0015.655-0.070-0.0700.0000.0000.0000.000
41A42PHE00.0310.0067.8220.0550.0550.0000.0000.0000.000
42A43MET0-0.0350.00110.674-0.049-0.0490.0000.0000.0000.000
43A44VAL00.0330.02113.0800.0070.0070.0000.0000.0000.000
44A45ARG10.9080.94215.521-0.088-0.0880.0000.0000.0000.000
45A46PRO00.0550.01416.5830.0210.0210.0000.0000.0000.000
46A47PHE00.0670.03117.0550.0120.0120.0000.0000.0000.000
47A48ASP-1-0.887-0.91617.1030.1840.1840.0000.0000.0000.000
48A49VAL0-0.0110.01211.2510.0500.0500.0000.0000.0000.000
49A50PRO00.0500.01912.5770.0620.0620.0000.0000.0000.000
50A51THR0-0.024-0.03514.4650.0260.0260.0000.0000.0000.000
51A52TYR00.009-0.00511.0990.0290.0290.0000.0000.0000.000
52A53LEU0-0.044-0.0077.6690.1000.1000.0000.0000.0000.000
53A54VAL00.0030.00011.0080.0480.0480.0000.0000.0000.000
54A55HIS0-0.081-0.04514.329-0.019-0.0190.0000.0000.0000.000
55A56GLY0-0.0010.00610.7390.0240.0240.0000.0000.0000.000
56A57VAL0-0.030-0.0029.5260.2150.2150.0000.0000.0000.000
57A58ALA0-0.020-0.0146.4240.2050.2050.0000.0000.0000.000
58A59ASP-1-0.733-0.8292.4362.5874.8942.791-2.351-2.747-0.024
59A60ILE00.0190.0042.625-1.377-0.4360.830-0.229-1.5420.002
60A61GLY00.0240.0025.297-0.061-0.073-0.001-0.0010.0140.000
61A62PHE00.0190.0157.528-0.023-0.0230.0000.0000.0000.000
62A63CYS0-0.035-0.01511.8570.0200.0200.0000.0000.0000.000
63A64GLY00.0730.04215.581-0.017-0.0170.0000.0000.0000.000
64A65THR00.032-0.01519.0080.0110.0110.0000.0000.0000.000
65A66ASP-1-0.861-0.94121.1710.0360.0360.0000.0000.0000.000
66A67VAL0-0.051-0.02218.0700.0090.0090.0000.0000.0000.000
67A68LEU0-0.014-0.02116.0080.0130.0130.0000.0000.0000.000
68A69LEU0-0.021-0.00119.9720.0060.0060.0000.0000.0000.000
69A70GLU-1-0.820-0.89023.4610.0610.0610.0000.0000.0000.000
70A71LYS10.8080.89519.210-0.163-0.1630.0000.0000.0000.000
71A72GLU-1-0.726-0.82120.0780.0860.0860.0000.0000.0000.000
72A73THR0-0.068-0.03716.5890.0240.0240.0000.0000.0000.000
73A74SER0-0.006-0.00616.809-0.012-0.0120.0000.0000.0000.000
74A75LEU0-0.043-0.01011.3790.0150.0150.0000.0000.0000.000
75A76ILE00.0250.01710.987-0.039-0.0390.0000.0000.0000.000
76A77GLN00.0430.01711.2650.0060.0060.0000.0000.0000.000
77A78PRO0-0.061-0.0159.051-0.011-0.0110.0000.0000.0000.000
78A79PHE00.0470.0229.075-0.023-0.0230.0000.0000.0000.000
79A80PHE00.0010.00214.1240.0240.0240.0000.0000.0000.000
80A81ILE00.001-0.00412.483-0.023-0.0230.0000.0000.0000.000
81A82PRO00.0370.01516.5740.0170.0170.0000.0000.0000.000
82A83THR00.009-0.00218.3910.0090.0090.0000.0000.0000.000
83A84ASN00.0090.01020.8720.0110.0110.0000.0000.0000.000
84A85ILE0-0.046-0.01119.775-0.005-0.0050.0000.0000.0000.000
85A86SER0-0.017-0.01423.4860.0020.0020.0000.0000.0000.000
86A87ARG10.8270.89426.4410.0170.0170.0000.0000.0000.000
87A88MET00.0080.02927.0850.0020.0020.0000.0000.0000.000
88A89VAL0-0.021-0.01629.748-0.002-0.0020.0000.0000.0000.000
89A90LEU00.0400.02533.6000.0040.0040.0000.0000.0000.000
90A91ALA0-0.007-0.01536.782-0.003-0.0030.0000.0000.0000.000
91A92GLY00.0560.01939.1700.0030.0030.0000.0000.0000.000
92A93PRO0-0.026-0.01242.639-0.002-0.0020.0000.0000.0000.000
93A94LYS10.8740.91245.0370.0060.0060.0000.0000.0000.000
94A95GLY0-0.0110.00046.7180.0000.0000.0000.0000.0000.000
95A96ARG10.8630.94946.717-0.010-0.0100.0000.0000.0000.000
96A97GLY00.0230.02547.2350.0000.0000.0000.0000.0000.000
97A98ILE0-0.018-0.02343.1060.0010.0010.0000.0000.0000.000
98A99PRO00.0120.01245.777-0.001-0.0010.0000.0000.0000.000
99A100GLU-1-0.879-0.93147.7600.0110.0110.0000.0000.0000.000
100A101GLY0-0.0050.00149.1740.0010.0010.0000.0000.0000.000
101A102GLU-1-0.806-0.86245.0150.0280.0280.0000.0000.0000.000
102A103LYS10.7940.89642.803-0.018-0.0180.0000.0000.0000.000
103A104ARG10.7990.88142.693-0.018-0.0180.0000.0000.0000.000
104A105ILE00.0060.00237.268-0.003-0.0030.0000.0000.0000.000
105A106ALA00.0360.02537.6940.0030.0030.0000.0000.0000.000
106A107THR0-0.010-0.03532.380-0.001-0.0010.0000.0000.0000.000
107A108LYS10.7890.87728.120-0.022-0.0220.0000.0000.0000.000
108A109PHE0-0.065-0.02825.1990.0060.0060.0000.0000.0000.000
109A110PRO00.0290.00829.237-0.004-0.0040.0000.0000.0000.000
110A111ASN00.000-0.01626.574-0.006-0.0060.0000.0000.0000.000
111A112VAL0-0.001-0.00427.017-0.004-0.0040.0000.0000.0000.000
112A113THR0-0.004-0.01329.665-0.005-0.0050.0000.0000.0000.000
113A114GLN0-0.050-0.03532.649-0.004-0.0040.0000.0000.0000.000
114A115ARG10.8340.88825.476-0.060-0.0600.0000.0000.0000.000
115A116TYR0-0.051-0.05332.718-0.003-0.0030.0000.0000.0000.000
116A117CYS0-0.011-0.01734.656-0.006-0.0060.0000.0000.0000.000
117A118GLU-1-0.837-0.90233.7390.0420.0420.0000.0000.0000.000
118A119SER0-0.118-0.07134.827-0.003-0.0030.0000.0000.0000.000
119A120LYS10.8560.91736.907-0.013-0.0130.0000.0000.0000.000
120A121GLY0-0.0220.00640.182-0.001-0.0010.0000.0000.0000.000
121A122TRP0-0.042-0.03440.7400.0000.0000.0000.0000.0000.000
122A123HIS00.0520.02941.4440.0030.0030.0000.0000.0000.000
123A125ARG10.8270.89040.826-0.028-0.0280.0000.0000.0000.000
124A126ILE00.0240.01434.895-0.002-0.0020.0000.0000.0000.000
125A127ILE0-0.034-0.01837.7900.0020.0020.0000.0000.0000.000
126A128PRO00.001-0.00232.997-0.002-0.0020.0000.0000.0000.000
127A129LEU00.0060.01633.555-0.001-0.0010.0000.0000.0000.000
128A130LYS10.9200.93428.069-0.062-0.0620.0000.0000.0000.000
129A131GLY0-0.006-0.00930.1780.0000.0000.0000.0000.0000.000
130A132SER0-0.019-0.02732.5350.0020.0020.0000.0000.0000.000
131A133VAL00.0230.02433.4230.0010.0010.0000.0000.0000.000
132A134GLU-1-0.855-0.91635.6780.0120.0120.0000.0000.0000.000
133A135LEU00.0280.01438.397-0.001-0.0010.0000.0000.0000.000
134A136ALA0-0.0010.00339.7580.0000.0000.0000.0000.0000.000
135A137PRO0-0.019-0.01240.8440.0000.0000.0000.0000.0000.000
136A138ILE0-0.028-0.00643.668-0.001-0.0010.0000.0000.0000.000
137A139ALA0-0.027-0.01544.2360.0000.0000.0000.0000.0000.000
138A140GLY00.0100.01746.2060.0010.0010.0000.0000.0000.000
139A141LEU0-0.0150.01040.7140.0010.0010.0000.0000.0000.000
140A142SER0-0.057-0.05741.2400.0020.0020.0000.0000.0000.000
141A143ASP-1-0.831-0.90043.6510.0160.0160.0000.0000.0000.000
142A144LEU0-0.003-0.00840.883-0.002-0.0020.0000.0000.0000.000
143A145ILE0-0.022-0.00336.4060.0020.0020.0000.0000.0000.000
144A146VAL00.0420.02732.022-0.002-0.0020.0000.0000.0000.000
145A147ASP-1-0.778-0.84930.6080.0250.0250.0000.0000.0000.000
146A148ILE00.0240.01025.452-0.003-0.0030.0000.0000.0000.000
147A149THR0-0.036-0.01929.710-0.002-0.0020.0000.0000.0000.000
148A150GLU-1-0.771-0.85826.321-0.035-0.0350.0000.0000.0000.000
149A151THR00.0210.00130.1320.0000.0000.0000.0000.0000.000
150A152GLY00.0340.03033.5220.0000.0000.0000.0000.0000.000
151A153ARG10.8120.90235.7370.0170.0170.0000.0000.0000.000
152A154THR00.0840.03534.8690.0000.0000.0000.0000.0000.000
153A155LEU00.0100.01635.8310.0020.0020.0000.0000.0000.000
154A156LYS10.9670.98338.8580.0090.0090.0000.0000.0000.000
155A157GLU-1-0.884-0.93838.415-0.008-0.0080.0000.0000.0000.000
156A158ASN0-0.023-0.00939.5750.0020.0020.0000.0000.0000.000
157A159ASN0-0.052-0.03242.9170.0000.0000.0000.0000.0000.000
158A160LEU00.0060.01739.5510.0010.0010.0000.0000.0000.000
159A161GLU-1-0.842-0.91241.716-0.006-0.0060.0000.0000.0000.000
160A162ILE0-0.019-0.01435.6570.0020.0020.0000.0000.0000.000
161A163LEU0-0.032-0.02239.140-0.001-0.0010.0000.0000.0000.000
162A164ASP-1-0.753-0.84437.1980.0040.0040.0000.0000.0000.000
163A165GLU-1-0.838-0.90732.648-0.011-0.0110.0000.0000.0000.000
164A166ILE0-0.055-0.01330.4690.0000.0000.0000.0000.0000.000
165A167PHE00.0400.00025.2690.0030.0030.0000.0000.0000.000
166A168VAL0-0.022-0.00125.1690.0000.0000.0000.0000.0000.000
167A169ILE0-0.031-0.01022.2950.0040.0040.0000.0000.0000.000
168A170ARG10.9110.95419.5060.0370.0370.0000.0000.0000.000
169A171THR0-0.007-0.00813.9780.0100.0100.0000.0000.0000.000
170A172HIS00.0200.03115.010-0.014-0.0140.0000.0000.0000.000
171A173VAL00.0400.0228.5570.0200.0200.0000.0000.0000.000
172A174VAL0-0.018-0.01710.0310.0050.0050.0000.0000.0000.000
173A175VAL00.014-0.0035.9030.0480.0480.0000.0000.0000.000
174A176ASN00.0270.0267.302-0.246-0.2460.0000.0000.0000.000
175A177PRO00.0350.0098.5350.0460.0460.0000.0000.0000.000
176A178VAL0-0.046-0.02110.431-0.058-0.0580.0000.0000.0000.000
177A179SER00.030-0.0174.907-0.199-0.1990.0000.0000.0000.000
178A180TYR00.0080.0006.636-0.116-0.1160.0000.0000.0000.000
179A181ARG10.9340.9728.096-0.497-0.4970.0000.0000.0000.000
180A182THR0-0.057-0.0478.215-0.095-0.0950.0000.0000.0000.000
181A183LYS10.8080.9012.137-12.141-10.9823.825-2.065-2.9200.016
182A184ARG10.8510.9355.242-0.350-0.3500.0000.0000.0000.000
183A185GLU-1-0.769-0.8906.807-0.372-0.3720.0000.0000.0000.000
184A186GLU-1-0.795-0.8771.985-11.305-10.4658.982-4.043-5.779-0.058
185A187VAL0-0.025-0.0292.512-2.849-0.9640.969-1.020-1.834-0.003
186A188VAL0-0.025-0.0143.3610.3150.2230.0130.250-0.1710.000
187A189SER00.0380.0346.1490.0280.0280.0000.0000.0000.000
188A190PHE0-0.017-0.0172.351-1.289-0.7064.144-1.192-3.535-0.005
189A191LEU0-0.026-0.0274.1800.1170.2810.000-0.052-0.1120.000
190A192GLU-1-0.893-0.9476.676-0.454-0.4540.0000.0000.0000.000
191A193LYS10.9380.9707.4891.0961.0960.0000.0000.0000.000
192A194LEU0-0.063-0.0366.3010.0820.0820.0000.0000.0000.000
193A195GLN00.0080.0038.8040.0950.0950.0000.0000.0000.000
194A196GLU-1-0.885-0.94111.899-0.409-0.4090.0000.0000.0000.000
195A197VAL0-0.050-0.02311.3730.0430.0430.0000.0000.0000.000
196A198ILE0-0.037-0.02810.7020.0410.0410.0000.0000.0000.000
197A199GLU-1-0.949-0.94514.114-0.145-0.1450.0000.0000.0000.000
198A200HIS00.0690.04416.7770.0150.0150.0000.0000.0000.000
199A201ASP-1-0.850-0.89416.416-0.169-0.1690.0000.0000.0000.000
200A202SER0-0.091-0.06917.7730.0210.0210.0000.0000.0000.000
201A203ASN0-0.080-0.04719.6290.0280.0280.0000.0000.0000.000
202A204GLU-1-1.034-1.01221.315-0.121-0.1210.0000.0000.0000.000