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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: 6Y7RZ

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 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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2191188.468885
FMO2-HF: Nuclear repulsion 2109865.980753
FMO2-HF: Total energy -81322.488132
FMO2-MP2: Total energy -81550.666009


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.
-38.7-57.4664.621-23.989-21.8720.116
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 : -0.851 / q_NPA : -0.937
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-1-0.853-0.9321.89023.60424.17711.056-6.350-5.280-0.067
4A5ARG10.7910.8821.780-121.141-135.21636.313-11.622-10.6150.109
5A6LEU0-0.0150.0165.299-1.651-1.479-0.001-0.011-0.1600.000
6A7SER0-0.041-0.0607.609-2.504-2.5040.0000.0000.0000.000
7A8LEU00.0490.00011.2380.2110.2110.0000.0000.0000.000
8A9LYS10.8380.90413.148-16.727-16.7270.0000.0000.0000.000
9A10GLU-1-0.818-0.86910.64925.36725.3670.0000.0000.0000.000
10A11PHE00.0250.0148.5920.1960.1960.0000.0000.0000.000
11A12CYS0-0.016-0.01611.370-0.711-0.7110.0000.0000.0000.000
12A13ASP-1-0.845-0.90214.73416.52416.5240.0000.0000.0000.000
13A14MET0-0.045-0.0349.4070.2940.2940.0000.0000.0000.000
14A15VAL0-0.0080.00512.519-0.107-0.1070.0000.0000.0000.000
15A16ALA0-0.035-0.00414.810-1.018-1.0180.0000.0000.0000.000
16A17GLU-1-0.854-0.90014.69519.80819.8080.0000.0000.0000.000
17A18ARG10.9080.96317.924-13.599-13.5990.0000.0000.0000.000
18A19LYS10.7820.85113.859-21.920-21.9200.0000.0000.0000.000
19A20PRO00.0060.00615.850-0.134-0.1340.0000.0000.0000.000
20A21THR0-0.040-0.0269.694-0.299-0.2990.0000.0000.0000.000
21A22PRO00.0230.0099.8051.2251.2250.0000.0000.0000.000
22A23GLY00.0820.04311.173-1.626-1.6260.0000.0000.0000.000
23A24GLY00.004-0.01613.5780.3070.3070.0000.0000.0000.000
24A25GLY00.0820.04114.275-0.418-0.4180.0000.0000.0000.000
25A26ALA0-0.0100.0049.3320.4040.4040.0000.0000.0000.000
26A27VAL0-0.046-0.02510.9380.1720.1720.0000.0000.0000.000
27A28GLY00.0120.01613.449-0.409-0.4090.0000.0000.0000.000
28A29SER00.036-0.00710.642-0.380-0.3800.0000.0000.0000.000
29A30VAL0-0.014-0.0049.125-0.137-0.1370.0000.0000.0000.000
30A31VAL0-0.026-0.01911.637-0.670-0.6700.0000.0000.0000.000
31A32GLY00.0710.02914.876-0.754-0.7540.0000.0000.0000.000
32A33ALA00.0290.02011.001-0.614-0.6140.0000.0000.0000.000
33A34MET0-0.054-0.02812.975-0.538-0.5380.0000.0000.0000.000
34A35ALA00.0050.01215.197-0.710-0.7100.0000.0000.0000.000
35A36CYS0-0.008-0.01314.842-0.600-0.6000.0000.0000.0000.000
36A37ALA0-0.006-0.00514.571-0.432-0.4320.0000.0000.0000.000
37A38LEU0-0.027-0.00816.501-0.535-0.5350.0000.0000.0000.000
38A39ALA00.0510.02020.022-0.515-0.5150.0000.0000.0000.000
39A40GLH0-0.030-0.05715.952-0.370-0.3700.0000.0000.0000.000
40A41MET0-0.0080.00719.990-0.245-0.2450.0000.0000.0000.000
41A42VAL0-0.006-0.00321.811-0.417-0.4170.0000.0000.0000.000
42A43ALA00.0610.04622.642-0.406-0.4060.0000.0000.0000.000
43A44ASN0-0.028-0.03120.222-0.579-0.5790.0000.0000.0000.000
44A45PHE0-0.058-0.02224.160-0.332-0.3320.0000.0000.0000.000
45A46THR0-0.036-0.01527.119-0.488-0.4880.0000.0000.0000.000
46A47ARG10.8170.90824.359-10.794-10.7940.0000.0000.0000.000
47A48LYS10.7880.88226.224-9.921-9.9210.0000.0000.0000.000
48A49LYS10.8480.94031.090-8.493-8.4930.0000.0000.0000.000
49A50LYS10.8480.90833.449-7.204-7.2040.0000.0000.0000.000
50A51GLY0-0.045-0.03537.041-0.010-0.0100.0000.0000.0000.000
51A52TYR00.0540.03132.8510.0180.0180.0000.0000.0000.000
52A53GLU-1-0.788-0.89033.5937.7237.7230.0000.0000.0000.000
53A54ASP-1-0.946-0.96835.0067.7637.7630.0000.0000.0000.000
54A55VAL00.0090.00431.8340.0640.0640.0000.0000.0000.000
55A56GLU-1-0.799-0.89329.3649.7099.7090.0000.0000.0000.000
56A57PRO00.0170.01228.5180.3220.3220.0000.0000.0000.000
57A58GLU-1-0.724-0.83427.57910.42110.4210.0000.0000.0000.000
58A59MET0-0.014-0.00126.1490.4810.4810.0000.0000.0000.000
59A60GLU-1-0.877-0.93324.10010.68710.6870.0000.0000.0000.000
60A61ARG10.7230.81822.617-10.602-10.6020.0000.0000.0000.000
61A62ILE00.0090.00522.0250.4540.4540.0000.0000.0000.000
62A63VAL0-0.053-0.03819.2280.5340.5340.0000.0000.0000.000
63A64GLU-1-0.918-0.95618.11314.70114.7010.0000.0000.0000.000
64A65ALA0-0.025-0.01717.0930.7880.7880.0000.0000.0000.000
65A66MET0-0.037-0.01116.6150.5960.5960.0000.0000.0000.000
66A67GLU-1-0.768-0.81012.80818.08318.0830.0000.0000.0000.000
67A68GLU-1-0.820-0.90412.14718.76818.7680.0000.0000.0000.000
68A69ALA0-0.024-0.00612.7970.9220.9220.0000.0000.0000.000
69A70ARG10.8060.87010.149-17.178-17.1780.0000.0000.0000.000
70A71LEU0-0.026-0.0057.4951.7221.7220.0000.0000.0000.000
71A72LYS10.8610.9257.711-14.711-14.7110.0000.0000.0000.000
72A73LEU00.0020.0109.1421.1041.1040.0000.0000.0000.000
73A74PHE00.017-0.0024.8970.4790.4790.0000.0000.0000.000
74A75ASP-1-0.829-0.8904.85236.09636.0960.0000.0000.0000.000
75A76LEU0-0.009-0.0075.8161.8191.8190.0000.0000.0000.000
76A77ALA00.0250.0096.813-0.147-0.1470.0000.0000.0000.000
77A78LYS10.7970.8811.691-101.993-107.58317.254-6.004-5.6600.074
78A79LYS10.8340.8875.419-30.934-30.9340.0000.0000.0000.000
79A80ASP-1-0.858-0.9148.75219.45219.4520.0000.0000.0000.000
80A81MET0-0.0200.0016.723-0.152-0.1520.0000.0000.0000.000
81A82GLU-1-0.907-0.9545.11550.07950.239-0.001-0.002-0.1570.000
82A83ALA00.0240.0159.514-2.096-2.0960.0000.0000.0000.000
83A84PHE00.0360.02113.005-2.025-2.0250.0000.0000.0000.000
84A85GLU-1-0.868-0.92410.47222.40522.4050.0000.0000.0000.000
85A86LYS10.7640.85613.311-19.682-19.6820.0000.0000.0000.000
86A87VAL00.0360.01014.969-1.272-1.2720.0000.0000.0000.000
87A88MET0-0.057-0.02216.801-0.867-0.8670.0000.0000.0000.000
88A89LYS10.8080.88112.910-23.668-23.6680.0000.0000.0000.000
89A90ALA00.0240.03018.625-0.521-0.5210.0000.0000.0000.000
90A91TYR0-0.028-0.00520.867-0.866-0.8660.0000.0000.0000.000
91A92LYS10.8940.95021.383-14.766-14.7660.0000.0000.0000.000
92A93SER0-0.074-0.05722.907-0.220-0.2200.0000.0000.0000.000
93A94SER0-0.065-0.06225.476-0.431-0.4310.0000.0000.0000.000
94A95GLU-1-0.762-0.89925.60211.51011.5100.0000.0000.0000.000
95A96GLY0-0.0250.00126.4510.1450.1450.0000.0000.0000.000
96A97GLU-1-0.787-0.84421.69713.59113.5910.0000.0000.0000.000
97A98LEU00.0230.02221.4800.7090.7090.0000.0000.0000.000
98A99GLN0-0.010-0.02422.2710.4980.4980.0000.0000.0000.000
99A100ASN0-0.067-0.02919.2050.5420.5420.0000.0000.0000.000
100A101ALA00.0250.00517.9530.4970.4970.0000.0000.0000.000
101A102LEU00.0360.01318.2760.6710.6710.0000.0000.0000.000
102A103LYS10.8270.90720.571-11.768-11.7680.0000.0000.0000.000
103A104GLU-1-0.820-0.86715.60118.63018.6300.0000.0000.0000.000
104A105ALA00.013-0.00515.8200.5320.5320.0000.0000.0000.000
105A106ALA0-0.013-0.01416.9010.0460.0460.0000.0000.0000.000
106A107SER0-0.046-0.03617.291-0.601-0.6010.0000.0000.0000.000
107A108VAL0-0.0070.00711.712-0.065-0.0650.0000.0000.0000.000
108A109PRO00.0340.01914.6520.0430.0430.0000.0000.0000.000
109A110MET00.0280.01916.395-0.627-0.6270.0000.0000.0000.000
110A111ASP-1-0.846-0.91814.54416.15716.1570.0000.0000.0000.000
111A112VAL0-0.024-0.00112.787-0.172-0.1720.0000.0000.0000.000
112A113ILE0-0.008-0.00415.384-0.636-0.6360.0000.0000.0000.000
113A114ARG10.7290.82418.145-14.767-14.7670.0000.0000.0000.000
114A115VAL00.0280.02114.213-0.528-0.5280.0000.0000.0000.000
115A116MET0-0.0250.00915.979-0.523-0.5230.0000.0000.0000.000
116A117LYS10.8680.92819.525-12.935-12.9350.0000.0000.0000.000
117A118ASP-1-0.904-0.94119.10412.90312.9030.0000.0000.0000.000
118A119LEU0-0.009-0.02718.403-0.454-0.4540.0000.0000.0000.000
119A120ALA00.0300.01021.120-0.423-0.4230.0000.0000.0000.000
120A121HIS0-0.013-0.02424.452-0.763-0.7630.0000.0000.0000.000
121A122GLU-1-0.788-0.86521.89010.98310.9830.0000.0000.0000.000
122A123LEU0-0.011-0.01022.515-0.266-0.2660.0000.0000.0000.000
123A124GLU-1-0.748-0.83625.8348.6578.6570.0000.0000.0000.000
124A125LYS10.7990.89626.462-10.585-10.5850.0000.0000.0000.000
125A126LEU0-0.014-0.00623.690-0.228-0.2280.0000.0000.0000.000
126A127ALA0-0.0050.01028.276-0.192-0.1920.0000.0000.0000.000
127A128GLU-1-0.906-0.96631.0697.8907.8900.0000.0000.0000.000
128A129PHE0-0.055-0.02231.481-0.247-0.2470.0000.0000.0000.000
129A130GLY00.0460.02729.4770.0160.0160.0000.0000.0000.000
130A131ASN0-0.017-0.03529.672-0.575-0.5750.0000.0000.0000.000
131A132LYS10.8770.92730.851-8.131-8.1310.0000.0000.0000.000
132A133ASN0-0.088-0.04932.564-0.077-0.0770.0000.0000.0000.000
133A134LEU00.0210.01726.0480.0300.0300.0000.0000.0000.000
134A135ALA00.0490.02528.2630.2750.2750.0000.0000.0000.000
135A136SER00.008-0.02128.530-0.001-0.0010.0000.0000.0000.000
136A137ASP-1-0.860-0.92024.20810.59910.5990.0000.0000.0000.000
137A138THR00.0210.01424.4100.4260.4260.0000.0000.0000.000
138A139LEU00.0130.00426.0710.1640.1640.0000.0000.0000.000
139A140ASN0-0.058-0.02824.0530.0200.0200.0000.0000.0000.000
140A141ALA00.0040.00321.6750.3370.3370.0000.0000.0000.000
141A142ALA00.0230.01422.3820.3420.3420.0000.0000.0000.000
142A143ASP-1-0.778-0.87824.8629.9669.9660.0000.0000.0000.000
143A144LEU0-0.044-0.01419.3600.1800.1800.0000.0000.0000.000
144A145CYS0-0.055-0.02920.2640.3330.3330.0000.0000.0000.000
145A146HIS0-0.024-0.02621.3360.4110.4110.0000.0000.0000.000
146A147ALA00.0130.00422.2880.0750.0750.0000.0000.0000.000
147A148VAL0-0.022-0.01216.6150.1970.1970.0000.0000.0000.000
148A149PHE00.0250.01419.6010.2810.2810.0000.0000.0000.000
149A150GLN0-0.011-0.00521.5970.0360.0360.0000.0000.0000.000
150A151VAL0-0.046-0.01818.056-0.087-0.0870.0000.0000.0000.000
151A152GLU-1-0.746-0.89515.56417.20717.2070.0000.0000.0000.000
152A153LYS10.8080.88919.421-10.302-10.3020.0000.0000.0000.000
153A154VAL0-0.041-0.01922.275-0.273-0.2730.0000.0000.0000.000
154A155ASN0-0.046-0.02917.036-0.368-0.3680.0000.0000.0000.000
155A156VAL00.0350.02519.7880.1920.1920.0000.0000.0000.000
156A157LEU0-0.005-0.00321.434-0.221-0.2210.0000.0000.0000.000
157A158ILE0-0.088-0.04819.820-0.414-0.4140.0000.0000.0000.000
158A159ASN00.011-0.00318.3470.0350.0350.0000.0000.0000.000
159A160LEU00.012-0.00222.470-0.321-0.3210.0000.0000.0000.000
160A161LYS10.7730.88125.332-11.927-11.9270.0000.0000.0000.000
161A162GLU-1-0.863-0.90424.43611.18111.1810.0000.0000.0000.000
162A163ILE0-0.0490.00023.049-0.047-0.0470.0000.0000.0000.000
163A164SER00.0120.00827.118-0.381-0.3810.0000.0000.0000.000
164A165ASP-1-0.810-0.87828.42710.12710.1270.0000.0000.0000.000
165A166GLU-1-0.908-0.97229.8919.1309.1300.0000.0000.0000.000
166A167THR00.008-0.00431.1350.0920.0920.0000.0000.0000.000
167A168PHE0-0.002-0.00621.8790.0130.0130.0000.0000.0000.000
168A169ARG10.8580.92827.397-9.724-9.7240.0000.0000.0000.000
169A170LYS10.8440.90528.847-9.072-9.0720.0000.0000.0000.000
170A171ASN0-0.014-0.01528.160-0.269-0.2690.0000.0000.0000.000
171A172MET00.0110.01621.4920.0640.0640.0000.0000.0000.000
172A173LEU0-0.020-0.02626.0880.1220.1220.0000.0000.0000.000
173A174GLU-1-0.821-0.88028.6368.9918.9910.0000.0000.0000.000
174A175GLU-1-0.810-0.86823.01212.56312.5630.0000.0000.0000.000
175A176LEU0-0.024-0.01523.8680.1470.1470.0000.0000.0000.000
176A177GLU-1-0.922-0.96126.0198.9488.9480.0000.0000.0000.000
177A178GLU-1-0.913-0.95328.1269.4389.4380.0000.0000.0000.000
178A179GLN0-0.035-0.03722.9700.3160.3160.0000.0000.0000.000
179A180GLU-1-0.780-0.85825.85310.14110.1410.0000.0000.0000.000
180A181ALA0-0.010-0.00427.420-0.143-0.1430.0000.0000.0000.000
181A182GLN0-0.044-0.03127.1700.1050.1050.0000.0000.0000.000
182A183ILE0-0.0020.00922.543-0.085-0.0850.0000.0000.0000.000
183A184GLU-1-0.804-0.89926.6519.6259.6250.0000.0000.0000.000
184A185GLY0-0.032-0.01029.720-0.286-0.2860.0000.0000.0000.000
185A186CYS0-0.043-0.02627.809-0.205-0.2050.0000.0000.0000.000
186A187TYR0-0.039-0.02227.535-0.179-0.1790.0000.0000.0000.000
187A188GLN0-0.044-0.04029.231-0.228-0.2280.0000.0000.0000.000
188A189ARG10.7240.84231.562-9.082-9.0820.0000.0000.0000.000
189A190VAL00.0340.02128.331-0.196-0.1960.0000.0000.0000.000
190A191LYS10.8340.90630.317-9.500-9.5000.0000.0000.0000.000
191A192LYS10.9480.97732.983-7.595-7.5950.0000.0000.0000.000
192A193MET0-0.075-0.02134.016-0.186-0.1860.0000.0000.0000.000
193A194LEU0-0.014-0.00930.534-0.069-0.0690.0000.0000.0000.000
194A195GLU-1-0.914-0.95934.6587.5197.5190.0000.0000.0000.000
195A196GLY00.0520.01536.236-0.037-0.0370.0000.0000.0000.000
196A197ILE0-0.0290.00632.116-0.139-0.1390.0000.0000.0000.000
197A198VAL0-0.053-0.01335.4300.0220.0220.0000.0000.0000.000
198A199TRP0-0.056-0.01937.049-0.091-0.0910.0000.0000.0000.000
199A200SER0-0.084-0.05439.767-0.204-0.2040.0000.0000.0000.000
200A201SER0-0.0040.00439.3780.0620.0620.0000.0000.0000.000