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: 2NR5R

Calculation Name: 1O5H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1O5H

Chain ID: A

ChEMBL ID:

UniProt ID: Q9X1P6

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 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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2189575.687846
FMO2-HF: Nuclear repulsion 2108254.032558
FMO2-HF: Total energy -81321.655288
FMO2-MP2: Total energy -81550.030666


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:GLU)


Summations of interaction energy for fragment #1(A:2:GLU)
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.
-33.708-46.89956.639-22.122-21.3250.108
Interaction energy analysis for fragmet #1(A:2:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.879 / q_NPA : -0.952
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].
3A4GLU-1-0.826-0.9151.92521.63724.0607.340-5.310-4.453-0.063
4A5ARG10.7820.8901.890-117.582-129.78033.694-11.034-10.4620.096
5A6LEU0-0.0300.0065.278-1.345-1.169-0.001-0.012-0.1630.000
6A7SER0-0.038-0.0557.424-2.835-2.8350.0000.0000.0000.000
7A8LEU00.0610.01011.1380.1880.1880.0000.0000.0000.000
8A9LYS10.8390.89713.467-16.740-16.7400.0000.0000.0000.000
9A10GLU-1-0.826-0.87210.32026.15626.1560.0000.0000.0000.000
10A11PHE00.0280.0058.695-0.118-0.1180.0000.0000.0000.000
11A12CYS0-0.026-0.01611.239-0.684-0.6840.0000.0000.0000.000
12A13ASP-1-0.831-0.88714.86016.81016.8100.0000.0000.0000.000
13A14MET0-0.030-0.0289.4480.4220.4220.0000.0000.0000.000
14A15VAL0-0.0140.00712.686-0.055-0.0550.0000.0000.0000.000
15A16ALA0-0.076-0.03814.705-0.892-0.8920.0000.0000.0000.000
16A17GLU-1-0.830-0.89514.38720.24920.2490.0000.0000.0000.000
17A18ARG10.9130.97117.674-13.627-13.6270.0000.0000.0000.000
18A19LYS10.7780.85513.323-22.549-22.5490.0000.0000.0000.000
19A20PRO0-0.005-0.00215.535-0.341-0.3410.0000.0000.0000.000
20A21THR0-0.0300.0009.394-0.291-0.2910.0000.0000.0000.000
21A22PRO00.0330.0239.6950.8030.8030.0000.0000.0000.000
22A23GLY00.0950.04211.414-1.471-1.4710.0000.0000.0000.000
23A24GLY0-0.002-0.01614.0500.3890.3890.0000.0000.0000.000
24A25GLY00.0640.02615.110-0.026-0.0260.0000.0000.0000.000
25A26ALA00.0440.0239.9250.2670.2670.0000.0000.0000.000
26A27VAL0-0.036-0.02211.6930.1900.1900.0000.0000.0000.000
27A28GLY00.0180.01713.751-0.348-0.3480.0000.0000.0000.000
28A29SER00.0540.02110.921-0.255-0.2550.0000.0000.0000.000
29A30VAL0-0.024-0.0039.547-0.104-0.1040.0000.0000.0000.000
30A31VAL0-0.046-0.03412.028-0.653-0.6530.0000.0000.0000.000
31A32GLY00.0670.02415.091-0.641-0.6410.0000.0000.0000.000
32A33ALA00.0000.00511.338-0.663-0.6630.0000.0000.0000.000
33A34MET0-0.044-0.03013.309-0.573-0.5730.0000.0000.0000.000
34A35ALA0-0.0020.00815.385-0.745-0.7450.0000.0000.0000.000
35A36CYS0-0.002-0.01015.292-0.634-0.6340.0000.0000.0000.000
36A37ALA0-0.0030.00015.065-0.444-0.4440.0000.0000.0000.000
37A38LEU0-0.0050.00916.984-0.507-0.5070.0000.0000.0000.000
38A39ALA00.0410.02120.341-0.495-0.4950.0000.0000.0000.000
39A40GLH0-0.041-0.05716.372-0.322-0.3220.0000.0000.0000.000
40A41MET0-0.049-0.01820.270-0.259-0.2590.0000.0000.0000.000
41A42VAL0-0.002-0.00422.040-0.416-0.4160.0000.0000.0000.000
42A43ALA00.0510.04023.075-0.425-0.4250.0000.0000.0000.000
43A44ASN00.005-0.02220.556-0.562-0.5620.0000.0000.0000.000
44A45PHE0-0.099-0.03424.565-0.352-0.3520.0000.0000.0000.000
45A46THR0-0.025-0.02527.446-0.489-0.4890.0000.0000.0000.000
46A47ARG10.8050.92024.683-10.762-10.7620.0000.0000.0000.000
47A48LYS10.8790.92826.801-10.001-10.0010.0000.0000.0000.000
48A49LYS10.8910.96931.401-8.407-8.4070.0000.0000.0000.000
49A50LYS10.9290.96433.723-6.940-6.9400.0000.0000.0000.000
50A51GLY0-0.068-0.04337.408-0.003-0.0030.0000.0000.0000.000
51A52TYR00.0280.01533.256-0.039-0.0390.0000.0000.0000.000
52A53GLU-1-0.805-0.91433.7767.7427.7420.0000.0000.0000.000
53A54ASP-1-0.966-0.97734.9567.6837.6830.0000.0000.0000.000
54A55VAL00.0130.00532.2920.0350.0350.0000.0000.0000.000
55A56GLU-1-0.811-0.90529.6149.5899.5890.0000.0000.0000.000
56A57PRO0-0.009-0.00528.9450.3150.3150.0000.0000.0000.000
57A58GLU-1-0.732-0.84628.04110.22610.2260.0000.0000.0000.000
58A59MET0-0.0070.00926.5300.4480.4480.0000.0000.0000.000
59A60GLU-1-0.879-0.94524.38510.62210.6220.0000.0000.0000.000
60A61ARG10.7160.82023.051-10.382-10.3820.0000.0000.0000.000
61A62ILE00.0080.01122.2120.4650.4650.0000.0000.0000.000
62A63VAL0-0.039-0.02619.5960.5780.5780.0000.0000.0000.000
63A64GLU-1-0.910-0.94818.15514.64614.6460.0000.0000.0000.000
64A65ALA00.0100.00717.4270.7320.7320.0000.0000.0000.000
65A66MET0-0.061-0.03917.0150.6500.6500.0000.0000.0000.000
66A67GLU-1-0.782-0.83813.29317.58517.5850.0000.0000.0000.000
67A68GLU-1-0.840-0.91212.59218.68918.6890.0000.0000.0000.000
68A69ALA0-0.017-0.01412.9000.9660.9660.0000.0000.0000.000
69A70ARG10.8240.90210.465-16.651-16.6510.0000.0000.0000.000
70A71LEU0-0.0120.0097.8361.6441.6440.0000.0000.0000.000
71A72LYS10.8740.9338.307-14.592-14.5920.0000.0000.0000.000
72A73LEU0-0.0050.0109.5831.1401.1400.0000.0000.0000.000
73A74PHE00.006-0.0285.4830.6800.6800.0000.0000.0000.000
74A75ASP-1-0.852-0.8985.27133.55533.5550.0000.0000.0000.000
75A76LEU0-0.012-0.0216.3232.1642.1640.0000.0000.0000.000
76A77ALA00.0320.0276.964-0.401-0.4010.0000.0000.0000.000
77A78LYS10.8280.9011.756-99.367-103.11215.607-5.764-6.0980.075
78A79LYS10.8440.9055.689-28.234-28.2340.0000.0000.0000.000
79A80ASP-1-0.857-0.9159.00319.85819.8580.0000.0000.0000.000
80A81MET0-0.025-0.0106.7240.3380.3380.0000.0000.0000.000
81A82GLU-1-0.925-0.9745.22548.03448.187-0.001-0.002-0.1490.000
82A83ALA0-0.019-0.0099.479-2.183-2.1830.0000.0000.0000.000
83A84PHE00.0180.00712.804-2.115-2.1150.0000.0000.0000.000
84A85GLU-1-0.874-0.93810.25823.07223.0720.0000.0000.0000.000
85A86LYS10.7970.88313.195-19.521-19.5210.0000.0000.0000.000
86A87VAL00.0340.01814.927-1.215-1.2150.0000.0000.0000.000
87A88MET00.0070.01116.676-0.885-0.8850.0000.0000.0000.000
88A89LYS10.7340.84012.664-23.966-23.9660.0000.0000.0000.000
89A90ALA00.0250.01318.220-0.034-0.0340.0000.0000.0000.000
90A91TYR0-0.0240.00820.981-0.772-0.7720.0000.0000.0000.000
91A92LYS10.9170.96221.540-14.576-14.5760.0000.0000.0000.000
92A93SER0-0.108-0.06422.623-0.308-0.3080.0000.0000.0000.000
93A94SER0-0.052-0.06424.978-0.383-0.3830.0000.0000.0000.000
94A95GLU-1-0.795-0.92225.68611.39111.3910.0000.0000.0000.000
95A96GLY0-0.033-0.00426.9390.0080.0080.0000.0000.0000.000
96A97GLU-1-0.795-0.86621.81413.52013.5200.0000.0000.0000.000
97A98LEU00.0310.03421.7100.6460.6460.0000.0000.0000.000
98A99GLN00.0120.01422.2910.5130.5130.0000.0000.0000.000
99A100ASN0-0.046-0.03319.6630.4640.4640.0000.0000.0000.000
100A101ALA00.0110.00718.0320.5130.5130.0000.0000.0000.000
101A102LEU00.0370.00418.5880.6710.6710.0000.0000.0000.000
102A103LYS10.8100.90520.641-11.701-11.7010.0000.0000.0000.000
103A104GLU-1-0.815-0.87415.78818.18218.1820.0000.0000.0000.000
104A105ALA00.0310.00015.9090.5690.5690.0000.0000.0000.000
105A106ALA0-0.012-0.00816.9380.1700.1700.0000.0000.0000.000
106A107SER0-0.054-0.04117.169-0.560-0.5600.0000.0000.0000.000
107A108VAL00.0100.02211.9800.0350.0350.0000.0000.0000.000
108A109PRO00.0270.02014.889-0.093-0.0930.0000.0000.0000.000
109A110MET00.0110.00216.701-0.525-0.5250.0000.0000.0000.000
110A111ASP-1-0.858-0.93114.87316.18616.1860.0000.0000.0000.000
111A112VAL0-0.044-0.01413.061-0.343-0.3430.0000.0000.0000.000
112A113ILE0-0.011-0.01415.632-0.601-0.6010.0000.0000.0000.000
113A114ARG10.7530.85418.566-14.388-14.3880.0000.0000.0000.000
114A115VAL00.0200.01414.385-0.438-0.4380.0000.0000.0000.000
115A116MET0-0.025-0.00316.386-0.579-0.5790.0000.0000.0000.000
116A117LYS10.9010.94719.895-12.647-12.6470.0000.0000.0000.000
117A118ASP-1-0.928-0.96919.68312.65512.6550.0000.0000.0000.000
118A119LEU0-0.037-0.02718.833-0.361-0.3610.0000.0000.0000.000
119A120ALA00.0330.01021.498-0.427-0.4270.0000.0000.0000.000
120A121HIS0-0.006-0.01924.827-0.705-0.7050.0000.0000.0000.000
121A122GLU-1-0.769-0.85622.41310.73910.7390.0000.0000.0000.000
122A123LEU0-0.0200.00222.997-0.303-0.3030.0000.0000.0000.000
123A124GLU-1-0.749-0.84026.2338.5818.5810.0000.0000.0000.000
124A125LYS10.7980.90026.976-10.414-10.4140.0000.0000.0000.000
125A126LEU0-0.031-0.02524.148-0.245-0.2450.0000.0000.0000.000
126A127ALA0-0.021-0.00928.735-0.225-0.2250.0000.0000.0000.000
127A128GLU-1-0.943-0.97831.2957.7917.7910.0000.0000.0000.000
128A129PHE0-0.091-0.05431.964-0.254-0.2540.0000.0000.0000.000
129A130GLY00.0380.01929.9680.0220.0220.0000.0000.0000.000
130A131ASN0-0.053-0.05530.081-0.532-0.5320.0000.0000.0000.000
131A132LYS10.9990.98831.547-7.863-7.8630.0000.0000.0000.000
132A133ASN0-0.109-0.04433.018-0.048-0.0480.0000.0000.0000.000
133A134LEU00.0340.01426.6970.0620.0620.0000.0000.0000.000
134A135ALA00.0430.03528.7060.2840.2840.0000.0000.0000.000
135A136SER00.0410.01229.1760.0820.0820.0000.0000.0000.000
136A137ASP-1-0.896-0.95324.73110.57410.5740.0000.0000.0000.000
137A138THR00.0250.00825.0590.3880.3880.0000.0000.0000.000
138A139LEU00.000-0.00126.2880.1950.1950.0000.0000.0000.000
139A140ASN0-0.027-0.00824.6550.0070.0070.0000.0000.0000.000
140A141ALA00.0030.00222.1120.3210.3210.0000.0000.0000.000
141A142ALA00.0070.00123.1000.3220.3220.0000.0000.0000.000
142A143ASP-1-0.801-0.89925.4839.9009.9000.0000.0000.0000.000
143A144LEU0-0.058-0.02219.7670.2010.2010.0000.0000.0000.000
144A145CYS0-0.025-0.01120.9120.2640.2640.0000.0000.0000.000
145A146HIS0-0.018-0.02421.9740.4380.4380.0000.0000.0000.000
146A147ALA00.0240.01222.4730.0550.0550.0000.0000.0000.000
147A148VAL0-0.0050.00516.9440.2360.2360.0000.0000.0000.000
148A149PHE00.0170.01119.8870.2670.2670.0000.0000.0000.000
149A150GLN0-0.020-0.01721.9260.0850.0850.0000.0000.0000.000
150A151VAL0-0.073-0.03618.054-0.010-0.0100.0000.0000.0000.000
151A152GLU-1-0.735-0.90515.48717.06017.0600.0000.0000.0000.000
152A153LYS10.8170.90619.550-10.263-10.2630.0000.0000.0000.000
153A154VAL0-0.029-0.01522.709-0.211-0.2110.0000.0000.0000.000
154A155ASN0-0.044-0.01017.723-0.291-0.2910.0000.0000.0000.000
155A156VAL00.0360.01920.3860.1390.1390.0000.0000.0000.000
156A157LEU0-0.026-0.01921.743-0.258-0.2580.0000.0000.0000.000
157A158ILE0-0.088-0.04520.058-0.352-0.3520.0000.0000.0000.000
158A159ASN0-0.015-0.01718.6180.0490.0490.0000.0000.0000.000
159A160LEU00.0360.01422.665-0.322-0.3220.0000.0000.0000.000
160A161LYS10.7770.89325.570-11.711-11.7110.0000.0000.0000.000
161A162GLU-1-0.865-0.91524.65811.08411.0840.0000.0000.0000.000
162A163ILE0-0.053-0.00323.163-0.065-0.0650.0000.0000.0000.000
163A164SER00.0180.00327.388-0.372-0.3720.0000.0000.0000.000
164A165ASP-1-0.802-0.89028.51810.11410.1140.0000.0000.0000.000
165A166GLU-1-0.921-0.97430.1258.8588.8580.0000.0000.0000.000
166A167THR0-0.0090.00231.5130.1030.1030.0000.0000.0000.000
167A168PHE00.010-0.00222.1690.0210.0210.0000.0000.0000.000
168A169ARG10.8840.94427.574-9.653-9.6530.0000.0000.0000.000
169A170LYS10.8550.92029.026-9.001-9.0010.0000.0000.0000.000
170A171ASN0-0.008-0.02228.397-0.303-0.3030.0000.0000.0000.000
171A172MET00.0290.02721.6260.0260.0260.0000.0000.0000.000
172A173LEU0-0.031-0.02826.1290.1480.1480.0000.0000.0000.000
173A174GLU-1-0.831-0.90028.6508.8718.8710.0000.0000.0000.000
174A175GLU-1-0.824-0.87923.40712.35612.3560.0000.0000.0000.000
175A176LEU0-0.028-0.01324.0380.0800.0800.0000.0000.0000.000
176A177GLU-1-0.930-0.96126.2098.8628.8620.0000.0000.0000.000
177A178GLU-1-0.950-0.97428.5689.3809.3800.0000.0000.0000.000
178A179GLN0-0.027-0.01523.3770.3470.3470.0000.0000.0000.000
179A180GLU-1-0.756-0.84926.25910.04510.0450.0000.0000.0000.000
180A181ALA0-0.0130.00727.770-0.138-0.1380.0000.0000.0000.000
181A182GLN0-0.035-0.02627.4400.0910.0910.0000.0000.0000.000
182A183ILE00.0250.01323.058-0.122-0.1220.0000.0000.0000.000
183A184GLU-1-0.814-0.91027.1189.4729.4720.0000.0000.0000.000
184A185GLY0-0.043-0.01130.125-0.224-0.2240.0000.0000.0000.000
185A186CYS0-0.035-0.02728.308-0.176-0.1760.0000.0000.0000.000
186A187TYR0-0.008-0.00428.003-0.212-0.2120.0000.0000.0000.000
187A188GLN0-0.031-0.02229.730-0.241-0.2410.0000.0000.0000.000
188A189ARG10.7210.83432.091-8.985-8.9850.0000.0000.0000.000
189A190VAL00.0330.02928.818-0.179-0.1790.0000.0000.0000.000
190A191LYS10.8610.92230.740-9.450-9.4500.0000.0000.0000.000
191A192LYS10.9120.95833.424-7.589-7.5890.0000.0000.0000.000
192A193MET0-0.061-0.02734.538-0.151-0.1510.0000.0000.0000.000
193A194LEU0-0.020-0.00930.746-0.073-0.0730.0000.0000.0000.000
194A195GLU-1-0.923-0.95534.9107.4367.4360.0000.0000.0000.000
195A196GLY00.0440.01236.593-0.051-0.0510.0000.0000.0000.000
196A197ILE0-0.0320.00132.483-0.132-0.1320.0000.0000.0000.000
197A198VAL0-0.055-0.01635.5430.0070.0070.0000.0000.0000.000
198A199TRP0-0.047-0.01937.350-0.080-0.0800.0000.0000.0000.000
199A200SER0-0.112-0.05940.297-0.174-0.1740.0000.0000.0000.000
200A201SER0-0.0010.00639.9570.0600.0600.0000.0000.0000.000