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: 1NY3Z

Calculation Name: 1OU0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1OU0

Chain ID: A

ChEMBL ID:

UniProt ID: Q9HKE7

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 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 190
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2036771.053372
FMO2-HF: Nuclear repulsion 1963417.312812
FMO2-HF: Total energy -73353.74056
FMO2-MP2: Total energy -73563.343518


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:17:SER)


Summations of interaction energy for fragment #1(A:17: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.
-5.179-0.4990.235-1.849-3.0640.003
Interaction energy analysis for fragmet #1(A:17:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.020 / q_NPA : 0.002
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].
3A19ALA00.0200.0152.949-4.106-1.2750.116-1.314-1.6330.004
4A20ALA00.0120.0082.947-1.0090.0030.116-0.318-0.810-0.001
5A21ILE0-0.0100.0043.9630.0760.6370.003-0.182-0.3820.000
6A22ASP-1-0.866-0.9336.1860.3940.3940.0000.0000.0000.000
7A23SER0-0.051-0.0227.631-0.083-0.0830.0000.0000.0000.000
8A24MET0-0.032-0.0188.303-0.030-0.0300.0000.0000.0000.000
9A25ILE0-0.055-0.02210.3720.0250.0250.0000.0000.0000.000
10A26ASP-1-0.809-0.89012.8220.1090.1090.0000.0000.0000.000
11A27PRO0-0.006-0.02415.3410.0240.0240.0000.0000.0000.000
12A28ASP-1-0.884-0.93616.9940.1170.1170.0000.0000.0000.000
13A29ILE0-0.088-0.02316.4690.0040.0040.0000.0000.0000.000
14A30SER00.0300.01517.3870.0400.0400.0000.0000.0000.000
15A31GLY00.0110.00619.600-0.013-0.0130.0000.0000.0000.000
16A32PRO0-0.018-0.03718.6720.0290.0290.0000.0000.0000.000
17A33MET00.0370.02617.7930.0260.0260.0000.0000.0000.000
18A34ARG10.8330.92112.388-0.291-0.2910.0000.0000.0000.000
19A35HIS0-0.056-0.03012.8870.0930.0930.0000.0000.0000.000
20A36ILE0-0.034-0.01413.1160.0420.0420.0000.0000.0000.000
21A37VAL00.0530.02212.7600.0150.0150.0000.0000.0000.000
22A38VAL00.0550.0288.8150.0350.0350.0000.0000.0000.000
23A39LYS10.8600.9418.852-0.114-0.1140.0000.0000.0000.000
24A40ALA00.0130.02110.452-0.032-0.0320.0000.0000.0000.000
25A41ILE00.0210.0047.515-0.036-0.0360.0000.0000.0000.000
26A42HIS0-0.024-0.0214.1900.5310.650-0.001-0.009-0.1080.000
27A43ALA0-0.068-0.0297.054-0.263-0.2630.0000.0000.0000.000
28A44ALA0-0.045-0.0259.870-0.101-0.1010.0000.0000.0000.000
29A45GLY0-0.0260.0076.972-0.087-0.0870.0000.0000.0000.000
30A46ASP-1-0.812-0.9218.0430.0660.0660.0000.0000.0000.000
31A47PHE00.014-0.0063.753-0.1560.0010.001-0.026-0.1310.000
32A48ALA00.0240.0229.842-0.041-0.0410.0000.0000.0000.000
33A49ILE0-0.010-0.01112.438-0.025-0.0250.0000.0000.0000.000
34A50ALA00.0120.01511.4890.0010.0010.0000.0000.0000.000
35A51PRO0-0.0040.00513.588-0.007-0.0070.0000.0000.0000.000
36A52LEU0-0.019-0.00816.733-0.018-0.0180.0000.0000.0000.000
37A53ILE0-0.054-0.01014.007-0.009-0.0090.0000.0000.0000.000
38A54ARG10.8950.95318.232-0.089-0.0890.0000.0000.0000.000
39A55TYR00.008-0.01419.1010.0040.0040.0000.0000.0000.000
40A56SER00.0230.00323.5270.0000.0000.0000.0000.0000.000
41A57ASP-1-0.871-0.94026.0440.0920.0920.0000.0000.0000.000
42A58GLY0-0.030-0.00727.7170.0050.0050.0000.0000.0000.000
43A59PHE00.0380.01121.3410.0020.0020.0000.0000.0000.000
44A60PHE00.018-0.00821.7120.0010.0010.0000.0000.0000.000
45A61LYS10.9500.96624.789-0.081-0.0810.0000.0000.0000.000
46A62SER00.0410.02728.316-0.003-0.0030.0000.0000.0000.000
47A63MET00.0120.00722.834-0.007-0.0070.0000.0000.0000.000
48A64LEU0-0.049-0.03324.639-0.003-0.0030.0000.0000.0000.000
49A65ALA0-0.0030.01126.942-0.003-0.0030.0000.0000.0000.000
50A66LYS10.8500.92629.166-0.056-0.0560.0000.0000.0000.000
51A67LEU0-0.031-0.01923.893-0.002-0.0020.0000.0000.0000.000
52A68LYS10.8870.93627.848-0.102-0.1020.0000.0000.0000.000
53A69GLU-1-0.958-0.98329.7100.0620.0620.0000.0000.0000.000
54A70GLY0-0.0220.02631.126-0.004-0.0040.0000.0000.0000.000
55A71CYS0-0.078-0.03829.847-0.003-0.0030.0000.0000.0000.000
56A72THR0-0.045-0.02031.422-0.002-0.0020.0000.0000.0000.000
57A73ILE00.018-0.01724.8820.0020.0020.0000.0000.0000.000
58A74ILE00.0100.00628.498-0.004-0.0040.0000.0000.0000.000
59A75CYS0-0.043-0.00725.7020.0050.0050.0000.0000.0000.000
60A76ASP-1-0.714-0.85825.5900.0220.0220.0000.0000.0000.000
61A77SER0-0.045-0.03024.282-0.008-0.0080.0000.0000.0000.000
62A78GLU-1-0.757-0.91525.7040.0070.0070.0000.0000.0000.000
63A79MET0-0.033-0.01119.9700.0010.0010.0000.0000.0000.000
64A80VAL0-0.0120.00820.8710.0010.0010.0000.0000.0000.000
65A81ARG10.9110.95721.784-0.005-0.0050.0000.0000.0000.000
66A82ALA0-0.043-0.02422.2310.0030.0030.0000.0000.0000.000
67A83GLY00.0030.01318.667-0.005-0.0050.0000.0000.0000.000
68A84ILE0-0.036-0.01718.1530.0140.0140.0000.0000.0000.000
69A85TYR00.0280.00313.7400.0100.0100.0000.0000.0000.000
70A86SER0-0.006-0.00818.9650.0010.0010.0000.0000.0000.000
71A87ARG10.9991.00920.305-0.094-0.0940.0000.0000.0000.000
72A88PRO0-0.051-0.03321.619-0.006-0.0060.0000.0000.0000.000
73A89VAL00.0270.01721.703-0.002-0.0020.0000.0000.0000.000
74A90LEU00.0170.00423.653-0.006-0.0060.0000.0000.0000.000
75A91GLU-1-0.914-0.96826.2790.0600.0600.0000.0000.0000.000
76A92ARG10.8780.94727.359-0.086-0.0860.0000.0000.0000.000
77A93ASN0-0.046-0.00427.126-0.004-0.0040.0000.0000.0000.000
78A94ARG10.9320.98228.907-0.043-0.0430.0000.0000.0000.000
79A95VAL00.0230.02525.1110.0020.0020.0000.0000.0000.000
80A96VAL0-0.013-0.00728.258-0.005-0.0050.0000.0000.0000.000
81A97CYS0-0.0100.00628.5880.0010.0010.0000.0000.0000.000
82A98TYR00.004-0.00730.627-0.003-0.0030.0000.0000.0000.000
83A99LEU0-0.0230.00729.896-0.001-0.0010.0000.0000.0000.000
84A100ASN0-0.051-0.04931.276-0.002-0.0020.0000.0000.0000.000
85A101ASP-1-0.787-0.84835.0600.0080.0080.0000.0000.0000.000
86A102VAL00.017-0.01437.766-0.001-0.0010.0000.0000.0000.000
87A103ARG10.8340.88139.587-0.013-0.0130.0000.0000.0000.000
88A104SER0-0.023-0.02736.7040.0010.0010.0000.0000.0000.000
89A105LYS10.9150.94039.4080.0040.0040.0000.0000.0000.000
90A106GLU-1-0.901-0.94240.7470.0030.0030.0000.0000.0000.000
91A107MET00.0170.02041.5180.0000.0000.0000.0000.0000.000
92A108ALA0-0.025-0.02139.1650.0010.0010.0000.0000.0000.000
93A109ASP-1-0.909-0.95641.160-0.001-0.0010.0000.0000.0000.000
94A110VAL0-0.058-0.02144.1270.0000.0000.0000.0000.0000.000
95A111ASN0-0.092-0.06843.1800.0010.0010.0000.0000.0000.000
96A112GLY00.0180.04043.3360.0000.0000.0000.0000.0000.000
97A113ILE0-0.047-0.00938.7170.0010.0010.0000.0000.0000.000
98A114THR0-0.011-0.03134.041-0.001-0.0010.0000.0000.0000.000
99A115ARG11.0161.01134.7080.0030.0030.0000.0000.0000.000
100A116SER00.021-0.00230.6110.0000.0000.0000.0000.0000.000
101A117ALA0-0.0050.00732.7950.0030.0030.0000.0000.0000.000
102A118ALA00.0200.01234.8450.0020.0020.0000.0000.0000.000
103A119GLY00.0330.01634.2840.0010.0010.0000.0000.0000.000
104A120ILE0-0.036-0.01329.9590.0020.0020.0000.0000.0000.000
105A121ARG10.8660.91933.972-0.014-0.0140.0000.0000.0000.000
106A122ILE00.0130.00437.6410.0010.0010.0000.0000.0000.000
107A123ALA00.0150.01133.9300.0010.0010.0000.0000.0000.000
108A124MET0-0.052-0.03134.4070.0020.0020.0000.0000.0000.000
109A125GLN0-0.050-0.01036.6850.0000.0000.0000.0000.0000.000
110A126ASP-1-0.797-0.88238.4020.0170.0170.0000.0000.0000.000
111A127HIS0-0.060-0.02135.499-0.001-0.0010.0000.0000.0000.000
112A128ARG10.8690.92636.475-0.035-0.0350.0000.0000.0000.000
113A129ASN00.0370.01834.6030.0040.0040.0000.0000.0000.000
114A130SER0-0.009-0.00631.9560.0020.0020.0000.0000.0000.000
115A131VAL00.0920.04126.1160.0030.0030.0000.0000.0000.000
116A132ILE00.0170.01528.286-0.004-0.0040.0000.0000.0000.000
117A133VAL0-0.002-0.00822.3130.0070.0070.0000.0000.0000.000
118A134ILE0-0.032-0.02224.523-0.008-0.0080.0000.0000.0000.000
119A135GLY00.006-0.01721.5940.0080.0080.0000.0000.0000.000
120A136ASN0-0.058-0.04621.862-0.007-0.0070.0000.0000.0000.000
121A137ALA00.0360.02324.487-0.001-0.0010.0000.0000.0000.000
122A138PRO00.0410.01627.3750.0040.0040.0000.0000.0000.000
123A139THR00.0360.02429.2200.0020.0020.0000.0000.0000.000
124A140ALA00.0030.01229.2030.0000.0000.0000.0000.0000.000
125A141LEU00.0120.01326.7700.0020.0020.0000.0000.0000.000
126A142LEU0-0.010-0.01529.9240.0010.0010.0000.0000.0000.000
127A143GLU-1-0.704-0.80833.2900.0200.0200.0000.0000.0000.000
128A144ALA00.010-0.00331.3630.0000.0000.0000.0000.0000.000
129A145MET0-0.0250.00331.7060.0020.0020.0000.0000.0000.000
130A146ARG10.8600.91834.230-0.021-0.0210.0000.0000.0000.000
131A147MET0-0.021-0.01336.566-0.001-0.0010.0000.0000.0000.000
132A148ILE0-0.0160.00532.8270.0000.0000.0000.0000.0000.000
133A149GLU-1-0.916-0.97336.4580.0330.0330.0000.0000.0000.000
134A150GLU-1-0.995-0.99239.2270.0200.0200.0000.0000.0000.000
135A151ASN0-0.114-0.06840.627-0.002-0.0020.0000.0000.0000.000
136A152GLY00.0030.01140.6110.0000.0000.0000.0000.0000.000
137A153TRP0-0.060-0.03737.5020.0010.0010.0000.0000.0000.000
138A154TYR00.0620.01635.5290.0020.0020.0000.0000.0000.000
139A155ASP-1-0.792-0.86834.6170.0480.0480.0000.0000.0000.000
140A156ILE0-0.081-0.04131.5730.0040.0040.0000.0000.0000.000
141A157PRO0-0.0280.01627.3690.0000.0000.0000.0000.0000.000
142A158ILE00.018-0.02026.585-0.003-0.0030.0000.0000.0000.000
143A159VAL0-0.030-0.00720.8530.0070.0070.0000.0000.0000.000
144A160GLY00.0610.01723.683-0.008-0.0080.0000.0000.0000.000
145A161ILE0-0.0550.00818.3060.0040.0040.0000.0000.0000.000
146A162PRO0-0.0120.01021.490-0.005-0.0050.0000.0000.0000.000
147A163VAL00.0240.01920.4540.0050.0050.0000.0000.0000.000
148A164GLY00.001-0.00422.900-0.004-0.0040.0000.0000.0000.000
149A165PHE00.012-0.01224.3160.0010.0010.0000.0000.0000.000
150A166ILE00.0270.02627.2880.0050.0050.0000.0000.0000.000
151A167ASN00.019-0.01329.0160.0050.0050.0000.0000.0000.000
152A168ALA00.0470.02225.3370.0020.0020.0000.0000.0000.000
153A169SER0-0.0050.00426.3930.0060.0060.0000.0000.0000.000
154A170LYS10.9950.99927.349-0.010-0.0100.0000.0000.0000.000
155A171ALA0-0.0100.00029.0900.0020.0020.0000.0000.0000.000
156A172LYS10.8060.89921.831-0.053-0.0530.0000.0000.0000.000
157A173GLU-1-0.957-0.95827.3340.0330.0330.0000.0000.0000.000
158A174GLY00.0230.00029.2570.0010.0010.0000.0000.0000.000
159A175LEU00.020-0.02426.3290.0010.0010.0000.0000.0000.000
160A176VAL0-0.056-0.01325.8740.0020.0020.0000.0000.0000.000
161A177SER0-0.040-0.00828.6450.0010.0010.0000.0000.0000.000
162A178SER0-0.046-0.01431.467-0.002-0.0020.0000.0000.0000.000
163A179HIS00.0070.00232.9650.0040.0040.0000.0000.0000.000
164A180ILE0-0.014-0.00730.5980.0000.0000.0000.0000.0000.000
165A181GLU-1-0.837-0.88228.7560.0790.0790.0000.0000.0000.000
166A182TYR00.009-0.01524.5430.0010.0010.0000.0000.0000.000
167A183ILE00.0160.00618.2890.0090.0090.0000.0000.0000.000
168A184SER0-0.048-0.04621.643-0.011-0.0110.0000.0000.0000.000
169A185VAL0-0.002-0.00217.0490.0170.0170.0000.0000.0000.000
170A186GLU-1-0.862-0.93520.0110.0480.0480.0000.0000.0000.000
171A187GLY00.0320.02020.9630.0030.0030.0000.0000.0000.000
172A188HIS00.0280.00122.2260.0040.0040.0000.0000.0000.000
173A189ARG10.8410.90513.643-0.069-0.0690.0000.0000.0000.000
174A190GLY00.0540.00318.3520.0080.0080.0000.0000.0000.000
175A191GLY00.0280.00217.714-0.007-0.0070.0000.0000.0000.000
176A192SER00.025-0.01318.3550.0170.0170.0000.0000.0000.000
177A193PRO00.0160.02213.6030.0120.0120.0000.0000.0000.000
178A194ILE00.0430.03013.5100.0210.0210.0000.0000.0000.000
179A195ALA00.0470.03115.1970.0190.0190.0000.0000.0000.000
180A196ALA00.0220.00417.0430.0080.0080.0000.0000.0000.000
181A197SER0-0.110-0.05612.9300.0240.0240.0000.0000.0000.000
182A198ILE00.0650.02714.9970.0250.0250.0000.0000.0000.000
183A199VAL00.0450.02817.1680.0050.0050.0000.0000.0000.000
184A200ASN00.015-0.01215.9450.0020.0020.0000.0000.0000.000
185A201GLY0-0.061-0.02816.0020.0100.0100.0000.0000.0000.000
186A202PHE00.0440.00616.7080.0150.0150.0000.0000.0000.000
187A203GLY0-0.036-0.00419.803-0.006-0.0060.0000.0000.0000.000
188A204ARG10.8980.96113.270-0.370-0.3700.0000.0000.0000.000
189A205PHE0-0.014-0.01018.4560.0030.0030.0000.0000.0000.000
190A206LEU0-0.0260.01122.987-0.016-0.0160.0000.0000.0000.000