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: 6Y3GZ

Calculation Name: 3HIM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3HIM

Chain ID: A

ChEMBL ID:

UniProt ID: Q0SD48

Base Structure: X-ray

Registration Date: 2023-09-20

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. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1888799.602304
FMO2-HF: Nuclear repulsion 1817433.420301
FMO2-HF: Total energy -71366.182003
FMO2-MP2: Total energy -71576.922519


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:14:THR)


Summations of interaction energy for fragment #1(A:14:THR)
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.
-1.3150.562-0.028-0.895-0.9550.004
Interaction energy analysis for fragmet #1(A:14:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.042 / q_NPA : 0.013
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].
3A16LYS11.0240.9963.8270.1221.924-0.027-0.892-0.8840.004
4A17ALA00.0160.0076.5420.3450.3450.0000.0000.0000.000
5A18ALA00.0180.0075.2830.0750.0750.0000.0000.0000.000
6A19ALA00.0140.0044.9340.0180.0180.0000.0000.0000.000
7A20ARG10.9730.9756.6910.3470.3470.0000.0000.0000.000
8A21ILE00.0220.0249.9070.0130.0130.0000.0000.0000.000
9A22ARG10.8510.9234.398-1.643-1.568-0.001-0.003-0.0710.000
10A23ALA00.0130.01310.691-0.051-0.0510.0000.0000.0000.000
11A24ALA00.0460.02012.556-0.021-0.0210.0000.0000.0000.000
12A25ALA0-0.017-0.02214.191-0.010-0.0100.0000.0000.0000.000
13A26ILE0-0.0170.00012.984-0.013-0.0130.0000.0000.0000.000
14A27GLU-1-0.866-0.93616.4080.0340.0340.0000.0000.0000.000
15A28VAL0-0.0070.00018.856-0.009-0.0090.0000.0000.0000.000
16A29PHE0-0.060-0.04016.4030.0090.0090.0000.0000.0000.000
17A30ALA0-0.010-0.00320.384-0.008-0.0080.0000.0000.0000.000
18A31ALA0-0.044-0.01022.219-0.010-0.0100.0000.0000.0000.000
19A32LYS10.8250.90424.067-0.134-0.1340.0000.0000.0000.000
20A33GLY00.0610.04724.457-0.002-0.0020.0000.0000.0000.000
21A34TYR00.0440.01018.8200.0020.0020.0000.0000.0000.000
22A35GLY0-0.023-0.01122.8010.0140.0140.0000.0000.0000.000
23A36ALA00.0140.01625.5770.0020.0020.0000.0000.0000.000
24A37THR0-0.0090.01221.005-0.002-0.0020.0000.0000.0000.000
25A38THR00.0250.00122.4290.0270.0270.0000.0000.0000.000
26A39THR00.043-0.00817.710-0.020-0.0200.0000.0000.0000.000
27A40ARG10.9080.95918.325-0.247-0.2470.0000.0000.0000.000
28A41GLU-1-0.730-0.85821.4970.1310.1310.0000.0000.0000.000
29A42ILE00.0250.02515.513-0.011-0.0110.0000.0000.0000.000
30A43ALA0-0.053-0.02617.299-0.010-0.0100.0000.0000.0000.000
31A44ALA00.0240.01218.296-0.031-0.0310.0000.0000.0000.000
32A45SER0-0.060-0.03218.519-0.020-0.0200.0000.0000.0000.000
33A46LEU0-0.066-0.04413.574-0.024-0.0240.0000.0000.0000.000
34A47ASP-1-0.922-0.95117.819-0.049-0.0490.0000.0000.0000.000
35A48MET0-0.081-0.02612.1380.0050.0050.0000.0000.0000.000
36A49SER00.0500.02118.1330.0210.0210.0000.0000.0000.000
37A50PRO00.014-0.01319.1700.0390.0390.0000.0000.0000.000
38A51GLY0-0.001-0.00419.238-0.005-0.0050.0000.0000.0000.000
39A52ALA00.0190.02115.1120.0520.0520.0000.0000.0000.000
40A53VAL00.009-0.00913.6360.0660.0660.0000.0000.0000.000
41A54TYR00.0360.02813.3940.1670.1670.0000.0000.0000.000
42A55PRO0-0.010-0.01712.0360.0770.0770.0000.0000.0000.000
43A56HIS0-0.035-0.0107.6920.1790.1790.0000.0000.0000.000
44A57TYR00.0170.0037.8480.2140.2140.0000.0000.0000.000
45A58LYS10.9260.97813.158-0.912-0.9120.0000.0000.0000.000
46A59THR00.0320.02216.305-0.069-0.0690.0000.0000.0000.000
47A60LYS10.8860.93016.519-0.192-0.1920.0000.0000.0000.000
48A61GLU-1-0.790-0.86117.1770.5680.5680.0000.0000.0000.000
49A62SER00.0230.00813.9910.0690.0690.0000.0000.0000.000
50A63LEU0-0.026-0.00311.8960.1370.1370.0000.0000.0000.000
51A64LEU00.0210.01213.3520.0220.0220.0000.0000.0000.000
52A65TYR00.011-0.00412.345-0.043-0.0430.0000.0000.0000.000
53A66ALA0-0.007-0.0139.1880.0210.0210.0000.0000.0000.000
54A67ILE00.0080.00310.7410.0010.0010.0000.0000.0000.000
55A68SER0-0.004-0.01312.614-0.069-0.0690.0000.0000.0000.000
56A69LEU0-0.0220.00210.010-0.055-0.0550.0000.0000.0000.000
57A70GLU-1-0.862-0.9207.1450.4560.4560.0000.0000.0000.000
58A71GLY00.0150.00510.514-0.111-0.1110.0000.0000.0000.000
59A72HIS10.7860.87313.693-0.349-0.3490.0000.0000.0000.000
60A73HIS00.0470.02310.549-0.091-0.0910.0000.0000.0000.000
61A74SER0-0.0120.01811.625-0.064-0.0640.0000.0000.0000.000
62A75VAL00.0360.02713.109-0.036-0.0360.0000.0000.0000.000
63A76LEU00.0200.01615.939-0.019-0.0190.0000.0000.0000.000
64A77ALA0-0.001-0.00113.554-0.020-0.0200.0000.0000.0000.000
65A78ALA0-0.022-0.00715.641-0.025-0.0250.0000.0000.0000.000
66A79ILE0-0.014-0.01617.679-0.011-0.0110.0000.0000.0000.000
67A80THR0-0.052-0.03918.3060.0000.0000.0000.0000.0000.000
68A81ALA0-0.032-0.01117.673-0.007-0.0070.0000.0000.0000.000
69A82ALA0-0.0280.00819.727-0.010-0.0100.0000.0000.0000.000
70A83ASP-1-0.716-0.82322.9660.0390.0390.0000.0000.0000.000
71A84PHE0-0.020-0.01224.312-0.005-0.0050.0000.0000.0000.000
72A85PRO0-0.041-0.04125.7650.0010.0010.0000.0000.0000.000
73A86ASP-1-0.881-0.92528.9050.0110.0110.0000.0000.0000.000
74A87ILE0-0.079-0.02830.331-0.003-0.0030.0000.0000.0000.000
75A88ALA00.0440.02332.8340.0050.0050.0000.0000.0000.000
76A89ALA00.0290.01133.3220.0000.0000.0000.0000.0000.000
77A90PRO00.0630.01433.3050.0020.0020.0000.0000.0000.000
78A91ASP-1-0.852-0.92632.8760.0010.0010.0000.0000.0000.000
79A92ARG10.8210.91027.788-0.033-0.0330.0000.0000.0000.000
80A93LEU0-0.0060.01828.8780.0030.0030.0000.0000.0000.000
81A94MET00.0000.00529.9610.0010.0010.0000.0000.0000.000
82A95SER0-0.034-0.02126.045-0.005-0.0050.0000.0000.0000.000
83A96THR0-0.009-0.02624.6460.0010.0010.0000.0000.0000.000
84A97VAL0-0.003-0.00425.1330.0060.0060.0000.0000.0000.000
85A98THR0-0.007-0.02526.3770.0010.0010.0000.0000.0000.000
86A99ALA0-0.020-0.00321.651-0.003-0.0030.0000.0000.0000.000
87A100TYR0-0.070-0.02921.8250.0080.0080.0000.0000.0000.000
88A101VAL0-0.017-0.01022.9690.0080.0080.0000.0000.0000.000
89A102THR0-0.025-0.00821.9790.0000.0000.0000.0000.0000.000
90A103TRP00.0000.00314.7230.0070.0070.0000.0000.0000.000
91A104HIS00.020-0.00119.7370.0060.0060.0000.0000.0000.000
92A105ALA00.0000.00821.8180.0040.0040.0000.0000.0000.000
93A106ASP-1-0.925-0.96719.164-0.042-0.0420.0000.0000.0000.000
94A107ASN0-0.114-0.05015.526-0.016-0.0160.0000.0000.0000.000
95A108ARG10.9640.99718.3030.0190.0190.0000.0000.0000.000
96A109ALA00.0050.00918.6300.0200.0200.0000.0000.0000.000
97A110SER00.0330.00413.9360.0380.0380.0000.0000.0000.000
98A111ALA00.0400.02216.7980.0410.0410.0000.0000.0000.000
99A112ARG10.9270.95319.114-0.061-0.0610.0000.0000.0000.000
100A113VAL0-0.0100.00317.3590.0130.0130.0000.0000.0000.000
101A114GLY0-0.025-0.01617.4990.0250.0250.0000.0000.0000.000
102A115GLN00.0230.00418.2580.0290.0290.0000.0000.0000.000
103A116TYR0-0.010-0.00421.694-0.009-0.0090.0000.0000.0000.000
104A117GLU-1-0.854-0.92721.3150.1920.1920.0000.0000.0000.000
105A118LEU0-0.021-0.00920.6240.0220.0220.0000.0000.0000.000
106A119ARG10.9490.96723.000-0.145-0.1450.0000.0000.0000.000
107A120SER0-0.012-0.00522.515-0.011-0.0110.0000.0000.0000.000
108A121LEU0-0.066-0.01617.9200.0310.0310.0000.0000.0000.000
109A122SER00.0120.00919.842-0.033-0.0330.0000.0000.0000.000
110A123PRO00.0480.01021.7250.0140.0140.0000.0000.0000.000
111A124GLU-1-0.911-0.94418.4780.4760.4760.0000.0000.0000.000
112A125HIS10.8360.88915.374-0.604-0.6040.0000.0000.0000.000
113A126PHE00.003-0.00518.610-0.003-0.0030.0000.0000.0000.000
114A127ALA00.0300.00621.422-0.015-0.0150.0000.0000.0000.000
115A128ILE00.0380.04315.115-0.007-0.0070.0000.0000.0000.000
116A129ILE0-0.024-0.02515.643-0.014-0.0140.0000.0000.0000.000
117A130ALA0-0.053-0.03218.563-0.031-0.0310.0000.0000.0000.000
118A131ASP-1-0.837-0.90919.2980.2530.2530.0000.0000.0000.000
119A132ILE0-0.030-0.00914.534-0.024-0.0240.0000.0000.0000.000
120A133ARG10.9170.96518.596-0.243-0.2430.0000.0000.0000.000
121A134ARG10.8520.93521.513-0.156-0.1560.0000.0000.0000.000
122A135SER00.0070.00119.677-0.021-0.0210.0000.0000.0000.000
123A136THR0-0.040-0.04219.877-0.016-0.0160.0000.0000.0000.000
124A137THR00.007-0.00921.894-0.017-0.0170.0000.0000.0000.000
125A138LYS10.8540.94424.337-0.098-0.0980.0000.0000.0000.000
126A139VAL00.0160.01921.954-0.010-0.0100.0000.0000.0000.000
127A140PHE00.0700.02424.905-0.008-0.0080.0000.0000.0000.000
128A141THR0-0.013-0.00628.268-0.004-0.0040.0000.0000.0000.000
129A142ARG10.8420.91223.430-0.071-0.0710.0000.0000.0000.000
130A143ILE0-0.0120.00127.164-0.005-0.0050.0000.0000.0000.000
131A144ILE00.004-0.01130.995-0.005-0.0050.0000.0000.0000.000
132A145GLU-1-0.896-0.96632.4540.0680.0680.0000.0000.0000.000
133A146ALA0-0.022-0.01433.151-0.003-0.0030.0000.0000.0000.000
134A147GLY00.0640.01235.012-0.003-0.0030.0000.0000.0000.000
135A148ALA0-0.018-0.00737.038-0.002-0.0020.0000.0000.0000.000
136A149THR0-0.131-0.06437.165-0.003-0.0030.0000.0000.0000.000
137A150ALA00.0180.01838.883-0.001-0.0010.0000.0000.0000.000
138A151GLY0-0.021-0.00440.656-0.003-0.0030.0000.0000.0000.000
139A152ASP-1-0.903-0.94938.9850.0160.0160.0000.0000.0000.000
140A153PHE0-0.125-0.04734.6660.0000.0000.0000.0000.0000.000
141A154HIS0-0.008-0.01040.4590.0020.0020.0000.0000.0000.000
142A155PRO0-0.0110.00138.2360.0010.0010.0000.0000.0000.000
143A156PHE00.0000.00440.5370.0000.0000.0000.0000.0000.000
144A157ASP-1-0.858-0.93437.4570.0700.0700.0000.0000.0000.000
145A158ILE00.0290.01033.5940.0020.0020.0000.0000.0000.000
146A159GLU-1-0.832-0.90532.2370.1060.1060.0000.0000.0000.000
147A160ALA0-0.007-0.01132.9480.0040.0040.0000.0000.0000.000
148A161ALA00.0260.01534.4780.0010.0010.0000.0000.0000.000
149A162ALA00.0210.01329.4660.0000.0000.0000.0000.0000.000
150A163LEU0-0.021-0.00329.5060.0050.0050.0000.0000.0000.000
151A164ALA0-0.005-0.00230.2260.0030.0030.0000.0000.0000.000
152A165ILE00.0240.01428.112-0.001-0.0010.0000.0000.0000.000
153A166THR0-0.029-0.03225.2480.0020.0020.0000.0000.0000.000
154A167SER0-0.025-0.01726.4160.0050.0050.0000.0000.0000.000
155A168LEU00.0400.02028.6360.0000.0000.0000.0000.0000.000
156A169GLY00.011-0.00525.871-0.004-0.0040.0000.0000.0000.000
157A170ILE0-0.049-0.02722.9670.0020.0020.0000.0000.0000.000
158A171ASP-1-0.753-0.86524.9580.0750.0750.0000.0000.0000.000
159A172VAL00.0140.01725.537-0.005-0.0050.0000.0000.0000.000
160A173SER0-0.033-0.02222.580-0.009-0.0090.0000.0000.0000.000
161A174ARG10.7280.84324.646-0.067-0.0670.0000.0000.0000.000
162A175TRP0-0.055-0.02727.500-0.008-0.0080.0000.0000.0000.000
163A176PHE00.0070.03526.332-0.007-0.0070.0000.0000.0000.000
164A177PRO0-0.077-0.03927.4680.0020.0020.0000.0000.0000.000
165A178SER00.032-0.00330.2430.0020.0020.0000.0000.0000.000
166A179HIS0-0.003-0.01133.795-0.004-0.0040.0000.0000.0000.000
167A180THR0-0.039-0.01136.546-0.002-0.0020.0000.0000.0000.000
168A181TYR00.0250.00632.601-0.003-0.0030.0000.0000.0000.000
169A182SER00.0460.01031.0110.0030.0030.0000.0000.0000.000
170A183ASP-1-0.828-0.91329.930-0.031-0.0310.0000.0000.0000.000
171A184PRO00.018-0.00525.5040.0060.0060.0000.0000.0000.000
172A185ARG10.9790.98627.4160.0450.0450.0000.0000.0000.000
173A186ILE0-0.0160.00929.7000.0040.0040.0000.0000.0000.000
174A187ILE00.0060.00729.1450.0030.0030.0000.0000.0000.000
175A188ALA00.0130.00828.0410.0050.0050.0000.0000.0000.000
176A189ALA00.0090.00830.0220.0040.0040.0000.0000.0000.000
177A190ARG10.8090.88733.310-0.002-0.0020.0000.0000.0000.000
178A191TYR00.011-0.01529.7700.0050.0050.0000.0000.0000.000
179A192VAL00.0060.01330.9060.0040.0040.0000.0000.0000.000
180A193GLU-1-0.808-0.88833.2570.0100.0100.0000.0000.0000.000
181A194LEU0-0.033-0.01835.4660.0020.0020.0000.0000.0000.000
182A195ALA00.0000.00032.8070.0030.0030.0000.0000.0000.000
183A196LEU00.0370.00734.8720.0020.0020.0000.0000.0000.000
184A197ARG10.8950.94037.158-0.018-0.0180.0000.0000.0000.000
185A198MET0-0.084-0.02833.8650.0030.0030.0000.0000.0000.000
186A199VAL0-0.035-0.01335.3560.0020.0020.0000.0000.0000.000
187A200GLY00.0280.02238.6630.0000.0000.0000.0000.0000.000
188A201CYS0-0.034-0.01239.327-0.002-0.0020.0000.0000.0000.000
189A202ALA0-0.0160.00141.4720.0000.0000.0000.0000.0000.000
190A203ASP-1-0.915-0.95442.1870.0070.0070.0000.0000.0000.000