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: G6411

Calculation Name: 5HC1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5HC1

Chain ID: A

ChEMBL ID:

UniProt ID: P19811

Base Structure: X-ray

Registration Date: 2023-06-26

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

DOI:


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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2487168.247602
FMO2-HF: Nuclear repulsion 2401948.717408
FMO2-HF: Total energy -85219.530194
FMO2-MP2: Total energy -85464.758343


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:0:GLY)


Summations of interaction energy for fragment #1(A:0:GLY)
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.
-0.041.261-0.02-0.692-0.589-0.001
Interaction energy analysis for fragmet #1(A:0:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / q_NPA : -0.006
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].
3A2ASN00.0120.0183.8221.1522.453-0.020-0.692-0.589-0.001
4A3LYS10.8820.9496.968-0.359-0.3590.0000.0000.0000.000
5A4ILE00.0060.02110.0760.0240.0240.0000.0000.0000.000
6A5SER00.0500.02212.815-0.056-0.0560.0000.0000.0000.000
7A6CYS00.0000.02816.0060.0090.0090.0000.0000.0000.000
8A7LEU00.0480.01719.7440.0210.0210.0000.0000.0000.000
9A8PRO00.0550.02720.601-0.016-0.0160.0000.0000.0000.000
10A9ARG10.8960.94422.387-0.044-0.0440.0000.0000.0000.000
11A10VAL0-0.043-0.01023.106-0.008-0.0080.0000.0000.0000.000
12A11ALA00.0340.00621.092-0.009-0.0090.0000.0000.0000.000
13A12GLN0-0.007-0.00523.209-0.007-0.0070.0000.0000.0000.000
14A13ASN0-0.113-0.06525.6500.0010.0010.0000.0000.0000.000
15A14LEU0-0.061-0.02325.140-0.003-0.0030.0000.0000.0000.000
16A15GLY0-0.0350.00127.017-0.005-0.0050.0000.0000.0000.000
17A16TYR0-0.041-0.01821.448-0.006-0.0060.0000.0000.0000.000
18A17HIS00.030-0.01023.0920.0120.0120.0000.0000.0000.000
19A18TYR0-0.004-0.00419.6510.0120.0120.0000.0000.0000.000
20A19SER00.008-0.00814.654-0.010-0.0100.0000.0000.0000.000
21A20PRO0-0.009-0.00412.2020.0350.0350.0000.0000.0000.000
22A21ASP-1-0.820-0.9099.436-0.066-0.0660.0000.0000.0000.000
23A22LEU0-0.045-0.02211.0910.1250.1250.0000.0000.0000.000
24A23PRO00.003-0.00112.924-0.009-0.0090.0000.0000.0000.000
25A24GLY0-0.023-0.00915.382-0.013-0.0130.0000.0000.0000.000
26A25PHE0-0.027-0.00616.809-0.029-0.0290.0000.0000.0000.000
27A26CYS0-0.036-0.01119.2280.0210.0210.0000.0000.0000.000
28A27PRO00.0570.03417.122-0.012-0.0120.0000.0000.0000.000
29A28ILE00.008-0.01616.550-0.016-0.0160.0000.0000.0000.000
30A29PRO00.0000.00115.7100.0100.0100.0000.0000.0000.000
31A30LYS10.9610.97511.562-0.147-0.1470.0000.0000.0000.000
32A31GLU-1-0.875-0.94113.9270.0310.0310.0000.0000.0000.000
33A32LEU00.001-0.01216.766-0.012-0.0120.0000.0000.0000.000
34A33ALA0-0.0280.00015.293-0.002-0.0020.0000.0000.0000.000
35A34GLU-1-0.938-0.97317.140-0.108-0.1080.0000.0000.0000.000
36A35HIS0-0.072-0.03219.0920.0010.0010.0000.0000.0000.000
37A36TRP0-0.026-0.01421.1320.0110.0110.0000.0000.0000.000
38A37PRO00.0060.01120.772-0.011-0.0110.0000.0000.0000.000
39A38VAL0-0.0400.00116.2330.0170.0170.0000.0000.0000.000
40A39VAL00.0180.01416.956-0.019-0.0190.0000.0000.0000.000
41A40SER00.0000.00511.681-0.002-0.0020.0000.0000.0000.000
42A41ASN0-0.051-0.0399.5170.0400.0400.0000.0000.0000.000
43A42ASP-1-0.917-0.9408.654-0.930-0.9300.0000.0000.0000.000
44A43ARG10.8210.91011.5400.3310.3310.0000.0000.0000.000
45A44TYR00.0590.01011.6240.0010.0010.0000.0000.0000.000
46A45PRO0-0.005-0.00817.113-0.001-0.0010.0000.0000.0000.000
47A46ASN00.0340.01720.6570.0070.0070.0000.0000.0000.000
48A47CYS0-0.034-0.00416.0930.0040.0040.0000.0000.0000.000
49A48LEU00.0080.04219.198-0.004-0.0040.0000.0000.0000.000
50A49GLN00.0260.00712.8440.0580.0580.0000.0000.0000.000
51A50ILE0-0.034-0.02314.7480.0230.0230.0000.0000.0000.000
52A51THR00.003-0.00712.968-0.084-0.0840.0000.0000.0000.000
53A52LEU00.0540.01510.7770.0620.0620.0000.0000.0000.000
54A53GLN0-0.006-0.01014.3790.0410.0410.0000.0000.0000.000
55A54GLN0-0.024-0.00116.417-0.010-0.0100.0000.0000.0000.000
56A55VAL0-0.0150.00515.469-0.031-0.0310.0000.0000.0000.000
57A56CYS0-0.059-0.03218.0670.0050.0050.0000.0000.0000.000
58A57GLU-1-0.888-0.95221.741-0.120-0.1200.0000.0000.0000.000
59A58LEU0-0.023-0.01924.6470.0100.0100.0000.0000.0000.000
60A59SER0-0.036-0.01920.0680.0020.0020.0000.0000.0000.000
61A60LYS10.9090.95722.5520.0670.0670.0000.0000.0000.000
62A61PRO00.0030.01322.393-0.003-0.0030.0000.0000.0000.000
63A62CYS0-0.020-0.01422.4190.0140.0140.0000.0000.0000.000
64A63SER0-0.014-0.00422.6300.0020.0020.0000.0000.0000.000
65A64ALA0-0.010-0.01223.5710.0040.0040.0000.0000.0000.000
66A65GLY00.0680.06622.8410.0010.0010.0000.0000.0000.000
67A66TYR0-0.048-0.02916.571-0.016-0.0160.0000.0000.0000.000
68A67MET00.0070.00417.2780.0010.0010.0000.0000.0000.000
69A68VAL0-0.0080.01111.441-0.015-0.0150.0000.0000.0000.000
70A69GLY00.001-0.01613.0740.0670.0670.0000.0000.0000.000
71A70GLN00.017-0.01913.531-0.084-0.0840.0000.0000.0000.000
72A71SER0-0.0370.00616.451-0.026-0.0260.0000.0000.0000.000
73A72VAL00.005-0.01117.7870.0010.0010.0000.0000.0000.000
74A73PHE0-0.032-0.01716.3100.0070.0070.0000.0000.0000.000
75A74VAL0-0.008-0.00321.102-0.012-0.0120.0000.0000.0000.000
76A75GLN0-0.009-0.00723.1470.0020.0020.0000.0000.0000.000
77A76THR00.0180.00922.7820.0050.0050.0000.0000.0000.000
78A77PRO0-0.0090.00824.831-0.009-0.0090.0000.0000.0000.000
79A78GLY00.0070.00627.6350.0000.0000.0000.0000.0000.000
80A79VAL0-0.027-0.01021.439-0.010-0.0100.0000.0000.0000.000
81A80THR0-0.043-0.01220.2620.0130.0130.0000.0000.0000.000
82A81SER0-0.056-0.06719.686-0.004-0.0040.0000.0000.0000.000
83A82TYR00.009-0.01217.2350.0030.0030.0000.0000.0000.000
84A83TRP00.0260.01717.5770.0100.0100.0000.0000.0000.000
85A84LEU0-0.037-0.01417.949-0.010-0.0100.0000.0000.0000.000
86A85THR00.0030.00618.3810.0020.0020.0000.0000.0000.000
87A86GLU-1-0.838-0.91519.855-0.082-0.0820.0000.0000.0000.000
88A87TRP0-0.036-0.04117.6070.0010.0010.0000.0000.0000.000
89A88VAL00.004-0.01022.2020.0120.0120.0000.0000.0000.000
90A89ASP-1-0.861-0.93225.162-0.076-0.0760.0000.0000.0000.000
91A90GLY0-0.039-0.01722.135-0.002-0.0020.0000.0000.0000.000
92A91LYS10.9170.96322.4910.0760.0760.0000.0000.0000.000
93A92ALA00.0260.02322.4280.0040.0040.0000.0000.0000.000
94A93ARG10.8890.93724.2360.0770.0770.0000.0000.0000.000
95A94ALA00.0090.00626.012-0.004-0.0040.0000.0000.0000.000
96A95LEU00.0090.00923.2880.0070.0070.0000.0000.0000.000
97A96PRO0-0.024-0.00227.8370.0010.0010.0000.0000.0000.000
98A97ASP-1-0.824-0.93529.376-0.049-0.0490.0000.0000.0000.000
99A98SER0-0.084-0.08529.0720.0060.0060.0000.0000.0000.000
100A99LEU0-0.0070.01930.292-0.003-0.0030.0000.0000.0000.000
101A100PHE00.0190.01226.001-0.001-0.0010.0000.0000.0000.000
102A101SER0-0.005-0.01528.1250.0020.0020.0000.0000.0000.000
103A102SER0-0.006-0.00626.753-0.001-0.0010.0000.0000.0000.000
104A103GLY00.0560.02425.4390.0030.0030.0000.0000.0000.000
105A104ARG10.7770.90926.456-0.015-0.0150.0000.0000.0000.000
106A105PHE0-0.009-0.00729.2730.0050.0050.0000.0000.0000.000
107A106GLU-1-0.868-0.94425.0800.0610.0610.0000.0000.0000.000
108A107THR0-0.038-0.01824.6760.0110.0110.0000.0000.0000.000
109A108ASN0-0.074-0.02827.461-0.007-0.0070.0000.0000.0000.000
110A109SER00.0370.03030.121-0.004-0.0040.0000.0000.0000.000
111A110ARG10.8960.92931.905-0.050-0.0500.0000.0000.0000.000
112A111ALA00.0170.02232.532-0.003-0.0030.0000.0000.0000.000
113A112PHE00.020-0.00133.524-0.001-0.0010.0000.0000.0000.000
114A113LEU0-0.043-0.02428.8910.0020.0020.0000.0000.0000.000
115A114ASP-1-0.832-0.89131.173-0.002-0.0020.0000.0000.0000.000
116A115GLU-1-0.845-0.93333.4680.0060.0060.0000.0000.0000.000
117A116ALA00.011-0.01535.5970.0000.0000.0000.0000.0000.000
118A117GLU-1-0.755-0.88234.0810.0120.0120.0000.0000.0000.000
119A118GLU-1-0.906-0.94637.0190.0140.0140.0000.0000.0000.000
120A119LYS10.8990.94939.626-0.001-0.0010.0000.0000.0000.000
121A120PHE0-0.0090.00939.2880.0000.0000.0000.0000.0000.000
122A121ALA00.0470.01540.787-0.001-0.0010.0000.0000.0000.000
123A122ALA0-0.015-0.00642.4230.0000.0000.0000.0000.0000.000
124A123ALA0-0.049-0.02944.101-0.001-0.0010.0000.0000.0000.000
125A124HIS10.8170.91343.1460.0030.0030.0000.0000.0000.000
126A125PRO00.0740.03645.4670.0010.0010.0000.0000.0000.000
127A126HIS0-0.060-0.05747.6350.0020.0020.0000.0000.0000.000
128A127ALA00.0060.02042.9280.0000.0000.0000.0000.0000.000
129A128CYS0-0.025-0.00142.8850.0010.0010.0000.0000.0000.000
130A129LEU0-0.032-0.01044.2120.0020.0020.0000.0000.0000.000
131A130GLY0-0.026-0.01247.145-0.001-0.0010.0000.0000.0000.000
132A131GLU-1-0.826-0.92445.6040.0160.0160.0000.0000.0000.000
133A132ILE0-0.022-0.01348.3410.0000.0000.0000.0000.0000.000
134A133ASN0-0.050-0.02250.4610.0000.0000.0000.0000.0000.000
135A134LYS10.9560.99849.210-0.008-0.0080.0000.0000.0000.000
136A135SER00.007-0.00146.768-0.001-0.0010.0000.0000.0000.000
137A136THR0-0.011-0.03548.5920.0010.0010.0000.0000.0000.000
138A137VAL0-0.0570.01943.247-0.001-0.0010.0000.0000.0000.000
139A138GLY0-0.002-0.00946.3100.0010.0010.0000.0000.0000.000
140A139GLY00.0550.01242.4700.0010.0010.0000.0000.0000.000
141A140SER0-0.076-0.02242.441-0.002-0.0020.0000.0000.0000.000
142A141ALA00.0430.01441.5070.0010.0010.0000.0000.0000.000
143A142PHE00.0190.02336.6610.0000.0000.0000.0000.0000.000
144A143ILE0-0.036-0.02432.8060.0010.0010.0000.0000.0000.000
145A144PHE00.0020.00036.0730.0020.0020.0000.0000.0000.000
146A145SER0-0.039-0.00437.9660.0000.0000.0000.0000.0000.000
147A146GLN00.0320.00341.6620.0010.0010.0000.0000.0000.000
148A147TYR0-0.016-0.02644.0790.0010.0010.0000.0000.0000.000
149A148LEU0-0.0200.01639.1200.0000.0000.0000.0000.0000.000
150A149PRO0-0.0070.00142.2470.0000.0000.0000.0000.0000.000
151A150PRO00.0280.00840.1830.0010.0010.0000.0000.0000.000
152A151LEU0-0.029-0.01137.3280.0030.0030.0000.0000.0000.000
153A152LEU00.015-0.00836.255-0.004-0.0040.0000.0000.0000.000
154A153PRO00.0190.03135.5840.0030.0030.0000.0000.0000.000
155A154ALA00.0750.00633.100-0.004-0.0040.0000.0000.0000.000
156A155ASP-1-0.900-0.95335.2490.0450.0450.0000.0000.0000.000
157A156ALA0-0.0020.01037.891-0.003-0.0030.0000.0000.0000.000
158A157VAL0-0.043-0.01937.866-0.004-0.0040.0000.0000.0000.000
159A158ALA0-0.002-0.01437.2330.0020.0020.0000.0000.0000.000
160A159LEU0-0.0230.00730.367-0.003-0.0030.0000.0000.0000.000
161A160VAL00.0290.01034.367-0.002-0.0020.0000.0000.0000.000
162A161GLY00.0230.02331.3870.0000.0000.0000.0000.0000.000
163A162ALA0-0.017-0.01630.7230.0000.0000.0000.0000.0000.000
164A163SER0-0.047-0.02832.197-0.005-0.0050.0000.0000.0000.000
165A164LEU0-0.0240.00534.6140.0030.0030.0000.0000.0000.000
166A165ALA0-0.0080.00534.1760.0000.0000.0000.0000.0000.000
167A166GLY00.0420.01735.969-0.001-0.0010.0000.0000.0000.000
168A167LYS10.9120.93138.171-0.033-0.0330.0000.0000.0000.000
169A168ALA00.0410.03941.656-0.002-0.0020.0000.0000.0000.000
170A169ALA00.0050.00442.929-0.001-0.0010.0000.0000.0000.000
171A170LYS10.9260.95245.071-0.017-0.0170.0000.0000.0000.000
172A171ALA00.0260.02441.6690.0020.0020.0000.0000.0000.000
173A172ALA0-0.018-0.00243.298-0.002-0.0020.0000.0000.0000.000
174A173CYS00.0260.01141.927-0.001-0.0010.0000.0000.0000.000
175A174SER0-0.036-0.02039.4420.0000.0000.0000.0000.0000.000
176A175VAL00.0270.03535.296-0.002-0.0020.0000.0000.0000.000
177A176VAL00.015-0.00136.0410.0000.0000.0000.0000.0000.000
178A177ASP-1-0.773-0.91330.1490.0350.0350.0000.0000.0000.000
179A178VAL00.0290.00731.3290.0000.0000.0000.0000.0000.000
180A179TYR0-0.039-0.03130.683-0.001-0.0010.0000.0000.0000.000
181A180ALA00.0270.01532.664-0.004-0.0040.0000.0000.0000.000
182A181PRO00.009-0.00734.807-0.002-0.0020.0000.0000.0000.000
183A182SER0-0.054-0.02732.650-0.004-0.0040.0000.0000.0000.000
184A183PHE00.013-0.01034.682-0.002-0.0020.0000.0000.0000.000
185A184GLU-1-0.840-0.91437.935-0.013-0.0130.0000.0000.0000.000
186A185PRO0-0.004-0.00436.2240.0000.0000.0000.0000.0000.000
187A186TYR0-0.034-0.01435.735-0.001-0.0010.0000.0000.0000.000
188A187LEU0-0.037-0.03341.7110.0020.0020.0000.0000.0000.000
189A188HIS0-0.055-0.02243.7340.0020.0020.0000.0000.0000.000
190A189PRO0-0.079-0.02446.503-0.001-0.0010.0000.0000.0000.000
191A190GLU-1-0.845-0.93448.249-0.017-0.0170.0000.0000.0000.000
192A191THR0-0.061-0.02551.2580.0010.0010.0000.0000.0000.000
193A192LEU0-0.037-0.02052.2560.0000.0000.0000.0000.0000.000
194A193SER00.0050.00851.3630.0000.0000.0000.0000.0000.000
195A194ARG11.0000.99246.4490.0150.0150.0000.0000.0000.000
196A195VAL00.0250.00745.3790.0010.0010.0000.0000.0000.000
197A196TYR00.0040.01141.328-0.002-0.0020.0000.0000.0000.000
198A197LYS10.9080.94340.6880.0180.0180.0000.0000.0000.000
199A198ILE00.0460.02536.695-0.003-0.0030.0000.0000.0000.000
200A199MET0-0.0040.00932.1940.0010.0010.0000.0000.0000.000
201A200ILE00.0350.04131.686-0.002-0.0020.0000.0000.0000.000
202A201ASP-1-0.761-0.88427.7710.0120.0120.0000.0000.0000.000
203A202PHE00.007-0.01424.7160.0000.0000.0000.0000.0000.000
204A203LYS10.9440.99030.027-0.012-0.0120.0000.0000.0000.000
205A204PRO0-0.017-0.01732.8700.0000.0000.0000.0000.0000.000
206A205CYS0-0.064-0.03636.1360.0040.0040.0000.0000.0000.000
207A206ARG10.9360.97838.9660.0030.0030.0000.0000.0000.000
208A207LEU00.0430.03239.7810.0020.0020.0000.0000.0000.000
209A208MET0-0.049-0.00942.507-0.002-0.0020.0000.0000.0000.000
210A209VAL00.013-0.01044.2390.0010.0010.0000.0000.0000.000
211A210TRP0-0.0040.00647.155-0.001-0.0010.0000.0000.0000.000
212A211ARG10.9970.99849.4950.0110.0110.0000.0000.0000.000
213A212ASN0-0.028-0.02249.3890.0000.0000.0000.0000.0000.000
214A213ALA0-0.0120.01550.1990.0010.0010.0000.0000.0000.000
215A214THR0-0.026-0.02347.6750.0010.0010.0000.0000.0000.000
216A215PHE0-0.009-0.00840.233-0.002-0.0020.0000.0000.0000.000
217A216TYR00.0390.01342.8960.0010.0010.0000.0000.0000.000
218A217VAL00.0470.03137.930-0.002-0.0020.0000.0000.0000.000
219A218GLN0-0.020-0.01841.1710.0000.0000.0000.0000.0000.000