FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: 6GN1Z

Calculation Name: 5O01-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5O01

Chain ID: A

ChEMBL ID:

UniProt ID: A8Y5U5

Base Structure: X-ray

Registration Date: 2023-09-26

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 254
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3093334.325903
FMO2-HF: Nuclear repulsion 2991733.012564
FMO2-HF: Total energy -101601.313338
FMO2-MP2: Total energy -101898.035213


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:ASP)


Summations of interaction energy for fragment #1(A:2:ASP)
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.
-58.829-55.8360.052-1.561-1.4840.009
Interaction energy analysis for fragmet #1(A:2:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.914 / q_NPA : -0.959
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].
3A4ALA00.020-0.0013.899-6.663-4.7010.015-1.180-0.7960.007
4A5LEU00.0110.0086.722-2.980-2.9800.0000.0000.0000.000
5A6GLU-1-0.832-0.9313.72334.90335.6860.035-0.329-0.4890.002
6A7ARG10.9070.9623.929-42.227-41.9790.002-0.052-0.1990.000
7A8GLN0-0.028-0.0276.472-3.467-3.4670.0000.0000.0000.000
8A9ILE00.0640.0468.775-2.902-2.9020.0000.0000.0000.000
9A10ALA00.0030.0217.975-2.723-2.7230.0000.0000.0000.000
10A11SER0-0.039-0.0339.960-2.192-2.1920.0000.0000.0000.000
11A12ALA00.0180.01912.113-1.552-1.5520.0000.0000.0000.000
12A13SER0-0.031-0.03512.648-1.498-1.4980.0000.0000.0000.000
13A14ARG10.9340.98310.209-22.620-22.6200.0000.0000.0000.000
14A15SER00.0660.02415.818-1.116-1.1160.0000.0000.0000.000
15A16VAL0-0.017-0.00517.811-0.951-0.9510.0000.0000.0000.000
16A17GLU-1-0.885-0.93116.74915.05815.0580.0000.0000.0000.000
17A18GLU-1-0.960-0.98118.34114.25514.2550.0000.0000.0000.000
18A19ALA00.0160.00521.808-0.684-0.6840.0000.0000.0000.000
19A20ARG10.8630.91419.533-14.294-14.2940.0000.0000.0000.000
20A21ARG10.7930.88219.935-14.258-14.2580.0000.0000.0000.000
21A22LEU0-0.006-0.00725.870-0.524-0.5240.0000.0000.0000.000
22A23ALA00.0090.01427.727-0.401-0.4010.0000.0000.0000.000
23A24TYR0-0.051-0.03125.864-0.159-0.1590.0000.0000.0000.000
24A25HIS0-0.057-0.02530.112-0.242-0.2420.0000.0000.0000.000
25A26ASP-1-0.830-0.91631.8078.5298.5290.0000.0000.0000.000
26A27PRO00.003-0.01432.7880.1350.1350.0000.0000.0000.000
27A28ILE00.0090.01233.8280.0380.0380.0000.0000.0000.000
28A29ARG10.8410.93530.043-9.581-9.5810.0000.0000.0000.000
29A30VAL00.0230.00329.8890.4000.4000.0000.0000.0000.000
30A31GLY00.0210.00429.2620.3300.3300.0000.0000.0000.000
31A32ALA00.0620.02626.9760.2770.2770.0000.0000.0000.000
32A33LEU0-0.023-0.01023.7820.5380.5380.0000.0000.0000.000
33A34VAL00.0150.00824.3380.5740.5740.0000.0000.0000.000
34A35GLU-1-0.918-0.95224.70211.58211.5820.0000.0000.0000.000
35A36GLN00.0160.03620.4781.2241.2240.0000.0000.0000.000
36A37ILE0-0.010-0.01520.0230.8840.8840.0000.0000.0000.000
37A38SER0-0.046-0.02620.5610.5880.5880.0000.0000.0000.000
38A39VAL00.0260.02516.7730.5630.5630.0000.0000.0000.000
39A40LEU0-0.023-0.01714.2901.1021.1020.0000.0000.0000.000
40A41ALA0-0.024-0.02016.4760.8510.8510.0000.0000.0000.000
41A42ASP-1-0.836-0.92318.58815.10815.1080.0000.0000.0000.000
42A43LEU0-0.087-0.03512.5240.8530.8530.0000.0000.0000.000
43A44ARG10.8420.89511.117-22.029-22.0290.0000.0000.0000.000
44A45GLN00.011-0.00815.710-0.333-0.3330.0000.0000.0000.000
45A46LYS10.8820.96613.217-21.606-21.6060.0000.0000.0000.000
46A47GLU-1-0.881-0.92811.14325.27325.2730.0000.0000.0000.000
47A48GLY00.0170.01713.8060.0970.0970.0000.0000.0000.000
48A49ASP-1-0.832-0.89615.51316.47016.4700.0000.0000.0000.000
49A50PHE00.0620.00217.317-0.266-0.2660.0000.0000.0000.000
50A51ARG10.9830.99020.872-12.889-12.8890.0000.0000.0000.000
51A52LYS10.8630.93314.287-20.247-20.2470.0000.0000.0000.000
52A53ALA00.0430.02819.637-0.306-0.3060.0000.0000.0000.000
53A54GLU-1-0.818-0.89320.74510.80110.8010.0000.0000.0000.000
54A55SER0-0.082-0.05722.132-0.665-0.6650.0000.0000.0000.000
55A56LEU00.0220.02218.217-0.364-0.3640.0000.0000.0000.000
56A57TYR00.0680.02122.902-0.497-0.4970.0000.0000.0000.000
57A58ARG10.8740.92625.917-11.095-11.0950.0000.0000.0000.000
58A59GLU-1-0.850-0.89823.55412.30412.3040.0000.0000.0000.000
59A60ALA0-0.007-0.01226.407-0.379-0.3790.0000.0000.0000.000
60A61LEU0-0.023-0.00128.118-0.368-0.3680.0000.0000.0000.000
61A62PHE0-0.008-0.01229.506-0.265-0.2650.0000.0000.0000.000
62A63ARG10.8110.86628.455-10.350-10.3500.0000.0000.0000.000
63A64ALA00.003-0.00132.096-0.277-0.2770.0000.0000.0000.000
64A65GLN0-0.009-0.02034.161-0.190-0.1900.0000.0000.0000.000
65A66GLU-1-0.811-0.84933.6649.0539.0530.0000.0000.0000.000
66A67LEU0-0.0440.00535.459-0.174-0.1740.0000.0000.0000.000
67A68ARG10.9620.96738.314-7.614-7.6140.0000.0000.0000.000
68A69LYS10.9300.97541.331-7.185-7.1850.0000.0000.0000.000
69A70GLN0-0.021-0.02339.3650.2110.2110.0000.0000.0000.000
70A71ASP-1-0.816-0.91337.3098.1598.1590.0000.0000.0000.000
71A72PRO00.0400.00638.0710.2260.2260.0000.0000.0000.000
72A73ASP-1-0.787-0.86437.2778.6098.6090.0000.0000.0000.000
73A74LEU00.0080.00731.7970.2890.2890.0000.0000.0000.000
74A75LEU0-0.015-0.00733.6720.3220.3220.0000.0000.0000.000
75A76THR0-0.023-0.00934.6880.1490.1490.0000.0000.0000.000
76A77GLY00.0410.01832.9720.1390.1390.0000.0000.0000.000
77A78ILE0-0.0070.01229.3950.3530.3530.0000.0000.0000.000
78A79TYR0-0.010-0.01130.3710.2730.2730.0000.0000.0000.000
79A80SER0-0.039-0.02731.9380.1300.1300.0000.0000.0000.000
80A81LEU00.0190.00725.9440.2120.2120.0000.0000.0000.000
81A82LEU0-0.033-0.01227.3720.3970.3970.0000.0000.0000.000
82A83ALA0-0.0100.00328.8160.1740.1740.0000.0000.0000.000
83A84HIS0-0.006-0.00326.0180.4750.4750.0000.0000.0000.000
84A85LEU00.0010.01722.8100.2960.2960.0000.0000.0000.000
85A86TYR0-0.085-0.09225.8930.2120.2120.0000.0000.0000.000
86A87ASP-1-0.866-0.94128.43110.84510.8450.0000.0000.0000.000
87A88ARG10.8870.95322.633-13.194-13.1940.0000.0000.0000.000
88A89TRP0-0.063-0.02324.4010.2450.2450.0000.0000.0000.000
89A90GLY00.0290.01625.4050.0690.0690.0000.0000.0000.000
90A91ARG10.8210.92527.463-11.362-11.3620.0000.0000.0000.000
91A92MET00.0400.01430.788-0.044-0.0440.0000.0000.0000.000
92A93ASP-1-0.882-0.95433.5618.4468.4460.0000.0000.0000.000
93A94LYS10.7850.89731.492-9.396-9.3960.0000.0000.0000.000
94A95ALA00.0100.00131.631-0.045-0.0450.0000.0000.0000.000
95A96ALA00.0090.00633.171-0.089-0.0890.0000.0000.0000.000
96A97GLU-1-0.765-0.86636.2988.6868.6860.0000.0000.0000.000
97A98PHE0-0.035-0.03532.444-0.085-0.0850.0000.0000.0000.000
98A99TYR00.0630.02131.6650.0250.0250.0000.0000.0000.000
99A100GLU-1-0.805-0.89536.4737.4207.4200.0000.0000.0000.000
100A101LEU0-0.043-0.01336.673-0.196-0.1960.0000.0000.0000.000
101A102ALA0-0.004-0.00435.919-0.120-0.1200.0000.0000.0000.000
102A103LEU0-0.014-0.01237.983-0.134-0.1340.0000.0000.0000.000
103A104LYS10.8070.91141.215-7.107-7.1070.0000.0000.0000.000
104A105ILE00.0050.00238.272-0.147-0.1470.0000.0000.0000.000
105A106SER0-0.014-0.02340.331-0.131-0.1310.0000.0000.0000.000
106A107ALA00.0050.01542.829-0.121-0.1210.0000.0000.0000.000
107A108GLU-1-0.860-0.91745.6386.7056.7050.0000.0000.0000.000
108A109ASN0-0.083-0.04444.233-0.141-0.1410.0000.0000.0000.000
109A110GLY0-0.009-0.02146.150-0.080-0.0800.0000.0000.0000.000
110A111LEU0-0.037-0.01240.984-0.054-0.0540.0000.0000.0000.000
111A112GLU-1-0.801-0.90943.6367.0467.0460.0000.0000.0000.000
112A113GLU-1-0.862-0.89045.1616.6036.6030.0000.0000.0000.000
113A114SER0-0.015-0.01940.9230.1080.1080.0000.0000.0000.000
114A115ASP-1-0.788-0.87937.0168.4958.4950.0000.0000.0000.000
115A116LYS10.8340.89633.942-8.700-8.7000.0000.0000.0000.000
116A117VAL00.0070.01337.2230.1570.1570.0000.0000.0000.000
117A118ALA00.0720.05440.076-0.002-0.0020.0000.0000.0000.000
118A119THR0-0.025-0.02933.8660.0900.0900.0000.0000.0000.000
119A120ILE0-0.030-0.01635.4250.1500.1500.0000.0000.0000.000
120A121LYS10.8270.92437.080-7.055-7.0550.0000.0000.0000.000
121A122ASN00.0780.04035.938-0.218-0.2180.0000.0000.0000.000
122A123ASN0-0.047-0.03032.136-0.128-0.1280.0000.0000.0000.000
123A124LEU0-0.019-0.00535.8550.1000.1000.0000.0000.0000.000
124A125ALA00.0140.01338.054-0.057-0.0570.0000.0000.0000.000
125A126MET0-0.028-0.00534.9120.0010.0010.0000.0000.0000.000
126A127ILE00.0020.00433.0120.0330.0330.0000.0000.0000.000
127A128PHE00.012-0.00836.949-0.090-0.0900.0000.0000.0000.000
128A129LYS10.9490.99138.707-8.420-8.4200.0000.0000.0000.000
129A130GLN0-0.055-0.03133.269-0.087-0.0870.0000.0000.0000.000
130A131LEU0-0.061-0.03238.317-0.079-0.0790.0000.0000.0000.000
131A132ARG10.8300.92140.444-7.674-7.6740.0000.0000.0000.000
132A133LYS10.9400.97142.887-7.605-7.6050.0000.0000.0000.000
133A134PHE00.0500.02745.1060.1090.1090.0000.0000.0000.000
134A135GLU-1-0.829-0.92046.5966.6416.6410.0000.0000.0000.000
135A136ARG10.7990.88644.123-7.200-7.2000.0000.0000.0000.000
136A137ALA0-0.016-0.00342.8300.0690.0690.0000.0000.0000.000
137A138GLU-1-0.828-0.90044.1426.5136.5130.0000.0000.0000.000
138A139GLY00.0190.01846.903-0.013-0.0130.0000.0000.0000.000
139A140TYR00.0370.00742.6660.0200.0200.0000.0000.0000.000
140A141TYR00.0250.00138.4630.0970.0970.0000.0000.0000.000
141A142CYS0-0.047-0.01743.995-0.001-0.0010.0000.0000.0000.000
142A143GLU-1-0.837-0.91145.7076.8626.8620.0000.0000.0000.000
143A144ALA0-0.043-0.01941.4150.0150.0150.0000.0000.0000.000
144A145LEU0-0.024-0.01743.4400.0520.0520.0000.0000.0000.000
145A146GLU-1-0.844-0.90345.3806.2986.2980.0000.0000.0000.000
146A147THR0-0.047-0.02443.650-0.056-0.0560.0000.0000.0000.000
147A148PHE00.010-0.02438.1150.0700.0700.0000.0000.0000.000
148A149GLN0-0.114-0.06543.956-0.046-0.0460.0000.0000.0000.000
149A150ARG10.7380.84047.318-6.497-6.4970.0000.0000.0000.000
150A151LEU0-0.078-0.01442.343-0.028-0.0280.0000.0000.0000.000
151A152ASP-1-0.812-0.86140.9007.9497.9490.0000.0000.0000.000
152A153GLY00.013-0.00544.346-0.156-0.1560.0000.0000.0000.000
153A154GLU-1-0.727-0.86745.8956.7626.7620.0000.0000.0000.000
154A155GLN0-0.073-0.02646.0090.1440.1440.0000.0000.0000.000
155A156SER00.0720.03441.4670.1250.1250.0000.0000.0000.000
156A157ALA00.0900.03137.171-0.031-0.0310.0000.0000.0000.000
157A158ARG10.7360.81136.551-8.252-8.2520.0000.0000.0000.000
158A159VAL00.0390.03639.3240.0170.0170.0000.0000.0000.000
159A160ALA00.0010.00640.838-0.054-0.0540.0000.0000.0000.000
160A161SER0-0.015-0.01836.311-0.044-0.0440.0000.0000.0000.000
161A162VAL0-0.0040.01939.2300.0580.0580.0000.0000.0000.000
162A163TYR0-0.031-0.03141.445-0.141-0.1410.0000.0000.0000.000
163A164ASN00.0310.00638.102-0.138-0.1380.0000.0000.0000.000
164A165ASN0-0.068-0.05036.9070.0550.0550.0000.0000.0000.000
165A166LEU00.0560.02540.538-0.029-0.0290.0000.0000.0000.000
166A167GLY00.0400.02543.978-0.129-0.1290.0000.0000.0000.000
167A168VAL0-0.054-0.03439.109-0.090-0.0900.0000.0000.0000.000
168A169LEU0-0.022-0.00542.3770.0230.0230.0000.0000.0000.000
169A170TYR0-0.041-0.05443.796-0.064-0.0640.0000.0000.0000.000
170A171TYR0-0.026-0.01443.524-0.044-0.0440.0000.0000.0000.000
171A172SER0-0.108-0.05842.669-0.011-0.0110.0000.0000.0000.000
172A173HIS0-0.039-0.01744.191-0.019-0.0190.0000.0000.0000.000
173A174MET0-0.013-0.01047.975-0.105-0.1050.0000.0000.0000.000
174A175ASP-1-0.802-0.86649.9096.0056.0050.0000.0000.0000.000
175A176VAL00.023-0.01550.5990.1090.1090.0000.0000.0000.000
176A177ASP-1-0.873-0.93051.5335.9305.9300.0000.0000.0000.000
177A178ARG10.8760.91751.257-6.029-6.0290.0000.0000.0000.000
178A179ALA0-0.017-0.00647.3060.1090.1090.0000.0000.0000.000
179A180GLN0-0.053-0.02748.0340.1170.1170.0000.0000.0000.000
180A181VAL0-0.0010.00149.9080.0520.0520.0000.0000.0000.000
181A182MET0-0.037-0.00446.4050.0660.0660.0000.0000.0000.000
182A183HIS00.0380.00641.7020.1190.1190.0000.0000.0000.000
183A184GLU-1-0.843-0.87345.9966.4096.4090.0000.0000.0000.000
184A185ARG10.9100.95848.208-6.298-6.2980.0000.0000.0000.000
185A186ALA00.0150.01142.7750.0480.0480.0000.0000.0000.000
186A187LEU0-0.042-0.02643.9860.1190.1190.0000.0000.0000.000
187A188ALA0-0.013-0.01445.3390.0500.0500.0000.0000.0000.000
188A189ILE0-0.041-0.00943.1330.0000.0000.0000.0000.0000.000
189A190ARG10.8320.89337.048-8.457-8.4570.0000.0000.0000.000
190A191GLN0-0.058-0.03041.7340.0680.0680.0000.0000.0000.000
191A192ASN0-0.083-0.03544.184-0.018-0.0180.0000.0000.0000.000
192A193LEU0-0.030-0.01240.133-0.050-0.0500.0000.0000.0000.000
193A194HIS0-0.0240.00239.8030.2520.2520.0000.0000.0000.000
194A195GLU-1-0.845-0.91536.8658.2638.2630.0000.0000.0000.000
195A196GLY00.004-0.01233.2120.0870.0870.0000.0000.0000.000
196A197GLN0-0.072-0.03833.1290.2280.2280.0000.0000.0000.000
197A198MET0-0.041-0.02934.857-0.109-0.1090.0000.0000.0000.000
198A199ASP-1-0.820-0.88431.21410.27210.2720.0000.0000.0000.000
199A200PRO00.0380.00032.898-0.215-0.2150.0000.0000.0000.000
200A201ALA0-0.037-0.02631.690-0.240-0.2400.0000.0000.0000.000
201A202ASP-1-0.762-0.86733.6909.0799.0790.0000.0000.0000.000
202A203LEU00.0020.01535.668-0.273-0.2730.0000.0000.0000.000
203A204SER0-0.091-0.06235.524-0.170-0.1700.0000.0000.0000.000
204A205GLN00.0390.01235.007-0.261-0.2610.0000.0000.0000.000
205A206THR00.0380.02837.769-0.166-0.1660.0000.0000.0000.000
206A207PHE0-0.005-0.00241.165-0.238-0.2380.0000.0000.0000.000
207A208ILE0-0.006-0.00936.752-0.152-0.1520.0000.0000.0000.000
208A209ASN0-0.043-0.02638.694-0.124-0.1240.0000.0000.0000.000
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