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: N218Q

Calculation Name: 3D9H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3D9H

Chain ID: A

ChEMBL ID:

UniProt ID: Q96DX5

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:


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 235
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2565892.254588
FMO2-HF: Nuclear repulsion 2476059.781695
FMO2-HF: Total energy -89832.472893
FMO2-MP2: Total energy -90091.07067


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:19:PHE)


Summations of interaction energy for fragment #1(A:19:PHE)
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.
-7.358-11.94536.201-7.263-24.352-0.023
Interaction energy analysis for fragmet #1(A:19:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.002 / q_NPA : 0.016
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].
3A21GLY00.016-0.0172.346-0.6420.6967.686-4.058-4.9670.015
4A22ILE00.0000.0132.9212.306-2.5093.6775.089-3.950-0.013
5A23ARG10.9400.9682.041-3.736-3.1565.050-1.979-3.653-0.013
6A24LEU0-0.0010.0064.3760.2840.4320.000-0.049-0.0980.000
7A25LEU0-0.037-0.0197.1490.1990.1990.0000.0000.0000.000
8A26SER00.0760.0339.6060.0310.0310.0000.0000.0000.000
9A27ASN00.0230.01213.0100.0130.0130.0000.0000.0000.000
10A28PRO00.0180.00315.8160.0170.0170.0000.0000.0000.000
11A29LEU0-0.030-0.01818.5650.0190.0190.0000.0000.0000.000
12A30MET0-0.109-0.04619.4090.0030.0030.0000.0000.0000.000
13A31GLY00.0390.01218.617-0.024-0.0240.0000.0000.0000.000
14A32ASP-1-0.872-0.92719.201-0.124-0.1240.0000.0000.0000.000
15A33ALA0-0.101-0.05016.529-0.019-0.0190.0000.0000.0000.000
16A34VAL00.0170.01213.3650.0090.0090.0000.0000.0000.000
17A35SER0-0.045-0.03011.538-0.050-0.0500.0000.0000.0000.000
18A36ASP-1-0.899-0.95410.963-0.146-0.1460.0000.0000.0000.000
19A37TRP00.0240.00012.3090.0240.0240.0000.0000.0000.000
20A38SER0-0.030-0.04310.303-0.113-0.1130.0000.0000.0000.000
21A39PRO00.0490.01212.4760.0480.0480.0000.0000.0000.000
22A40MET00.0190.0189.5730.0840.0840.0000.0000.0000.000
23A41HIS0-0.042-0.0207.6930.0060.0060.0000.0000.0000.000
24A42GLU-1-0.824-0.89212.596-0.059-0.0590.0000.0000.0000.000
25A43ALA0-0.012-0.01915.4540.0330.0330.0000.0000.0000.000
26A44ALA0-0.067-0.02712.8000.0270.0270.0000.0000.0000.000
27A45ILE00.0390.00614.9490.0370.0370.0000.0000.0000.000
28A46HIS0-0.0460.00517.0740.0360.0360.0000.0000.0000.000
29A47GLY00.007-0.00718.6450.0030.0030.0000.0000.0000.000
30A48HIS0-0.049-0.02318.737-0.017-0.0170.0000.0000.0000.000
31A49GLN00.1170.01917.695-0.027-0.0270.0000.0000.0000.000
32A50LEU0-0.093-0.05118.554-0.020-0.0200.0000.0000.0000.000
33A51SER00.0600.01318.983-0.013-0.0130.0000.0000.0000.000
34A52LEU00.0420.03312.782-0.031-0.0310.0000.0000.0000.000
35A53ARG10.9190.97615.1960.1180.1180.0000.0000.0000.000
36A54ASN0-0.030-0.01817.363-0.015-0.0150.0000.0000.0000.000
37A55LEU00.0350.03214.189-0.014-0.0140.0000.0000.0000.000
38A56ILE00.0400.01611.885-0.041-0.0410.0000.0000.0000.000
39A57SER0-0.132-0.06414.113-0.014-0.0140.0000.0000.0000.000
40A58GLN0-0.025-0.02716.755-0.010-0.0100.0000.0000.0000.000
41A59GLY0-0.0010.01014.184-0.010-0.0100.0000.0000.0000.000
42A60TRP0-0.046-0.00710.172-0.120-0.1200.0000.0000.0000.000
43A61ALA00.011-0.0066.2020.0600.0600.0000.0000.0000.000
44A62VAL00.0650.0236.886-0.023-0.0230.0000.0000.0000.000
45A63ASN0-0.063-0.0221.9630.3330.2392.099-0.579-1.4250.004
46A64ILE00.0070.0012.983-3.217-1.5270.308-0.864-1.135-0.010
47A65ILE0-0.038-0.0182.320-1.2010.6332.049-0.845-3.0380.008
48A66THR00.0470.0334.674-0.476-0.426-0.001-0.003-0.0460.000
49A67ALA00.022-0.0027.2950.1690.1690.0000.0000.0000.000
50A68ASP-1-0.881-0.9269.2960.4200.4200.0000.0000.0000.000
51A69HIS0-0.097-0.0685.614-0.271-0.2710.0000.0000.0000.000
52A70VAL00.0390.0387.6980.3370.3370.0000.0000.0000.000
53A71SER0-0.0090.0035.620-0.344-0.3440.0000.0000.0000.000
54A72PRO00.0550.0106.8510.0830.0830.0000.0000.0000.000
55A73LEU00.0160.0078.5400.0190.0190.0000.0000.0000.000
56A74HIS00.0030.0127.900-0.125-0.1250.0000.0000.0000.000
57A75GLU-1-0.787-0.90211.4760.1000.1000.0000.0000.0000.000
58A76ALA0-0.021-0.01313.165-0.011-0.0110.0000.0000.0000.000
59A77CYS0-0.110-0.04513.463-0.001-0.0010.0000.0000.0000.000
60A78LEU00.0220.01215.701-0.003-0.0030.0000.0000.0000.000
61A79GLY00.0160.01717.620-0.012-0.0120.0000.0000.0000.000
62A80GLY0-0.019-0.00819.166-0.014-0.0140.0000.0000.0000.000
63A81HIS00.0310.02017.804-0.016-0.0160.0000.0000.0000.000
64A82LEU00.0380.00617.971-0.009-0.0090.0000.0000.0000.000
65A83SER0-0.029-0.03318.7200.0000.0000.0000.0000.0000.000
66A84CYS0-0.0130.02715.398-0.028-0.0280.0000.0000.0000.000
67A85VAL00.0530.02814.026-0.025-0.0250.0000.0000.0000.000
68A86LYS10.9640.98014.165-0.026-0.0260.0000.0000.0000.000
69A87ILE0-0.062-0.01514.398-0.011-0.0110.0000.0000.0000.000
70A88LEU00.0390.0139.699-0.050-0.0500.0000.0000.0000.000
71A89LEU00.0210.01210.630-0.037-0.0370.0000.0000.0000.000
72A90LYS10.9010.96512.3770.1100.1100.0000.0000.0000.000
73A91HIS0-0.102-0.05511.406-0.009-0.0090.0000.0000.0000.000
74A92GLY00.0480.0249.216-0.101-0.1010.0000.0000.0000.000
75A93ALA0-0.039-0.0046.645-0.071-0.0710.0000.0000.0000.000
76A94GLN0-0.018-0.0241.825-2.379-7.69715.333-3.975-6.040-0.014
77A95VAL00.0410.0156.2600.1180.1180.0000.0000.0000.000
78A96ASN00.0130.0028.380-0.085-0.0850.0000.0000.0000.000
79A97GLY00.0040.0126.6320.2430.2430.0000.0000.0000.000
80A98VAL00.0130.0137.153-0.428-0.4280.0000.0000.0000.000
81A99THR0-0.0130.0028.2730.3320.3320.0000.0000.0000.000
82A100ALA00.0440.00610.7330.0690.0690.0000.0000.0000.000
83A101ASP-1-0.928-0.94512.4500.3950.3950.0000.0000.0000.000
84A102TRP0-0.012-0.05212.0550.0020.0020.0000.0000.0000.000
85A103HIS0-0.0220.00313.635-0.043-0.0430.0000.0000.0000.000
86A104THR00.0650.03711.4490.1100.1100.0000.0000.0000.000
87A105PRO0-0.003-0.01610.208-0.127-0.1270.0000.0000.0000.000
88A106LEU00.0380.00812.986-0.084-0.0840.0000.0000.0000.000
89A107PHE00.0030.00715.810-0.057-0.0570.0000.0000.0000.000
90A108ASN00.038-0.00714.107-0.026-0.0260.0000.0000.0000.000
91A109ALA0-0.0040.00517.094-0.046-0.0460.0000.0000.0000.000
92A110CYS0-0.075-0.02618.847-0.036-0.0360.0000.0000.0000.000
93A111VAL0-0.024-0.01019.805-0.027-0.0270.0000.0000.0000.000
94A112SER0-0.020-0.00520.400-0.025-0.0250.0000.0000.0000.000
95A113GLY00.0220.02422.397-0.018-0.0180.0000.0000.0000.000
96A114SER00.000-0.00221.435-0.013-0.0130.0000.0000.0000.000
97A115TRP00.0860.01522.3190.0200.0200.0000.0000.0000.000
98A116ASP-1-0.936-0.95123.3340.0870.0870.0000.0000.0000.000
99A117CYS0-0.061-0.03318.312-0.004-0.0040.0000.0000.0000.000
100A118VAL00.0220.01818.7570.0210.0210.0000.0000.0000.000
101A119ASN00.0670.03719.8270.0290.0290.0000.0000.0000.000
102A120LEU0-0.0360.00217.513-0.002-0.0020.0000.0000.0000.000
103A121LEU00.002-0.01613.5400.0030.0030.0000.0000.0000.000
104A122LEU0-0.0130.00116.2570.0230.0230.0000.0000.0000.000
105A123GLN0-0.033-0.01818.756-0.003-0.0030.0000.0000.0000.000
106A124HIS0-0.123-0.04914.140-0.046-0.0460.0000.0000.0000.000
107A125GLY00.0090.00414.3560.0230.0230.0000.0000.0000.000
108A126ALA0-0.029-0.01213.6530.0630.0630.0000.0000.0000.000
109A127SER0-0.041-0.02213.236-0.045-0.0450.0000.0000.0000.000
110A128VAL00.010-0.00215.6780.0220.0220.0000.0000.0000.000
111A129GLN00.0150.01018.5370.0060.0060.0000.0000.0000.000
112A130PRO0-0.014-0.01413.9260.0240.0240.0000.0000.0000.000
113A131GLU-1-0.905-0.95012.9040.9960.9960.0000.0000.0000.000
114A132SER00.0350.04514.812-0.082-0.0820.0000.0000.0000.000
115A133ASP-1-0.903-0.95816.2900.4050.4050.0000.0000.0000.000
116A134LEU0-0.061-0.05617.096-0.054-0.0540.0000.0000.0000.000
117A135ALA00.0010.01216.390-0.032-0.0320.0000.0000.0000.000
118A136SER0-0.0110.01217.8650.0090.0090.0000.0000.0000.000
119A137PRO00.0390.00218.147-0.041-0.0410.0000.0000.0000.000
120A138ILE00.0340.01120.928-0.030-0.0300.0000.0000.0000.000
121A139HIS10.7890.87723.852-0.308-0.3080.0000.0000.0000.000
122A140GLU-1-0.779-0.86222.0360.2340.2340.0000.0000.0000.000
123A141ALA00.002-0.00424.402-0.022-0.0220.0000.0000.0000.000
124A142ALA0-0.017-0.01425.892-0.020-0.0200.0000.0000.0000.000
125A143ARG10.9540.96725.536-0.241-0.2410.0000.0000.0000.000
126A144ARG10.8260.90424.041-0.205-0.2050.0000.0000.0000.000
127A145GLY00.0080.01729.060-0.012-0.0120.0000.0000.0000.000
128A146HIS0-0.077-0.03525.253-0.023-0.0230.0000.0000.0000.000
129A147VAL00.034-0.00128.3890.0110.0110.0000.0000.0000.000
130A148GLU-1-0.880-0.93428.5510.1170.1170.0000.0000.0000.000
131A149CYS0-0.0050.01724.3650.0070.0070.0000.0000.0000.000
132A150VAL0-0.019-0.01125.4710.0160.0160.0000.0000.0000.000
133A151ASN0-0.020-0.02427.5930.0070.0070.0000.0000.0000.000
134A152SER0-0.034-0.03424.362-0.001-0.0010.0000.0000.0000.000
135A153LEU0-0.008-0.01321.1120.0110.0110.0000.0000.0000.000
136A154ILE0-0.0050.00824.2820.0110.0110.0000.0000.0000.000
137A155ALA0-0.017-0.00226.944-0.001-0.0010.0000.0000.0000.000
138A156TYR0-0.057-0.03021.765-0.007-0.0070.0000.0000.0000.000
139A157GLY00.0180.01022.8900.0230.0230.0000.0000.0000.000
140A158GLY0-0.040-0.01323.8640.0140.0140.0000.0000.0000.000
141A159ASN00.006-0.00124.705-0.032-0.0320.0000.0000.0000.000
142A160ILE00.0370.00727.2020.0130.0130.0000.0000.0000.000
143A161ASP-1-0.824-0.90029.7230.1640.1640.0000.0000.0000.000
144A162HIS0-0.093-0.04622.343-0.025-0.0250.0000.0000.0000.000
145A163LYS10.8860.93527.562-0.184-0.1840.0000.0000.0000.000
146A164ILE00.0070.03022.6010.0070.0070.0000.0000.0000.000
147A165SER00.027-0.00726.136-0.027-0.0270.0000.0000.0000.000
148A166HIS0-0.035-0.02226.7020.0050.0050.0000.0000.0000.000
149A167LEU0-0.0160.00024.599-0.004-0.0040.0000.0000.0000.000
150A168GLY00.0320.00928.509-0.017-0.0170.0000.0000.0000.000
151A169THR00.0020.01528.6210.0200.0200.0000.0000.0000.000
152A170PRO0-0.004-0.01327.465-0.004-0.0040.0000.0000.0000.000
153A171LEU00.0530.03729.764-0.007-0.0070.0000.0000.0000.000
154A172TYR0-0.066-0.06032.507-0.007-0.0070.0000.0000.0000.000
155A173LEU00.0250.01427.185-0.003-0.0030.0000.0000.0000.000
156A174ALA00.0170.03031.670-0.006-0.0060.0000.0000.0000.000
157A175CYS0-0.059-0.02233.410-0.012-0.0120.0000.0000.0000.000
158A176GLU-1-0.939-0.96932.3930.1600.1600.0000.0000.0000.000
159A177ASN0-0.093-0.07131.480-0.003-0.0030.0000.0000.0000.000
160A178GLN0-0.037-0.01534.627-0.009-0.0090.0000.0000.0000.000
161A179GLN00.0340.02832.613-0.011-0.0110.0000.0000.0000.000
162A180ARG10.9170.93336.027-0.076-0.0760.0000.0000.0000.000
163A181ALA0-0.015-0.00736.9100.0000.0000.0000.0000.0000.000
164A182CYS00.0260.01132.4500.0040.0040.0000.0000.0000.000
165A183VAL00.0130.01535.0500.0050.0050.0000.0000.0000.000
166A184LYS10.9240.96937.099-0.080-0.0800.0000.0000.0000.000
167A185LYS10.9470.99234.223-0.109-0.1090.0000.0000.0000.000
168A186LEU0-0.015-0.01631.1130.0030.0030.0000.0000.0000.000
169A187LEU0-0.0090.00435.1910.0020.0020.0000.0000.0000.000
170A188GLU-1-0.922-0.97638.5950.0880.0880.0000.0000.0000.000
171A189SER0-0.113-0.05934.336-0.003-0.0030.0000.0000.0000.000
172A190GLY0-0.022-0.00835.5590.0050.0050.0000.0000.0000.000
173A191ALA0-0.055-0.01634.3770.0040.0040.0000.0000.0000.000
174A192ASP-1-0.846-0.95235.3800.1270.1270.0000.0000.0000.000
175A193VAL0-0.022-0.01036.9780.0060.0060.0000.0000.0000.000
176A194ASN00.0240.00939.395-0.003-0.0030.0000.0000.0000.000
177A195GLN0-0.0120.00734.3590.0090.0090.0000.0000.0000.000
178A196GLY00.0270.01035.1140.0030.0030.0000.0000.0000.000
179A197LYS10.9680.98631.039-0.167-0.1670.0000.0000.0000.000
180A198GLY0-0.044-0.01533.248-0.008-0.0080.0000.0000.0000.000
181A199GLN0-0.005-0.02334.9830.0010.0010.0000.0000.0000.000
182A200ASP-1-0.773-0.82237.1230.1210.1210.0000.0000.0000.000
183A201SER00.038-0.03837.5200.0070.0070.0000.0000.0000.000
184A202PRO00.0480.00836.776-0.002-0.0020.0000.0000.0000.000
185A203LEU00.0320.02138.935-0.003-0.0030.0000.0000.0000.000
186A204HIS00.0010.04241.3810.0000.0000.0000.0000.0000.000
187A205ALA0-0.002-0.00338.404-0.004-0.0040.0000.0000.0000.000
188A206VAL00.001-0.00340.121-0.002-0.0020.0000.0000.0000.000
189A207VAL0-0.014-0.00142.117-0.005-0.0050.0000.0000.0000.000
190A208ARG10.8460.93139.453-0.118-0.1180.0000.0000.0000.000
191A209THR0-0.044-0.02040.348-0.003-0.0030.0000.0000.0000.000
192A210ALA0-0.0060.00043.741-0.003-0.0030.0000.0000.0000.000
193A211SER00.010-0.00743.018-0.003-0.0030.0000.0000.0000.000
194A212GLU-1-0.905-0.96545.2020.0660.0660.0000.0000.0000.000
195A213GLU-1-0.870-0.91344.8780.0710.0710.0000.0000.0000.000
196A214LEU0-0.015-0.01539.6890.0010.0010.0000.0000.0000.000
197A215ALA00.0350.01643.4140.0030.0030.0000.0000.0000.000
198A216CYS00.000-0.00745.7350.0000.0000.0000.0000.0000.000
199A217LEU0-0.0130.01341.1960.0000.0000.0000.0000.0000.000
200A218LEU00.003-0.01439.6620.0020.0020.0000.0000.0000.000
201A219MET0-0.039-0.02643.5930.0000.0000.0000.0000.0000.000
202A220ASP-1-0.934-0.94746.6120.0720.0720.0000.0000.0000.000
203A221PHE0-0.086-0.04642.625-0.001-0.0010.0000.0000.0000.000
204A222GLY0-0.008-0.00443.9690.0040.0040.0000.0000.0000.000
205A223ALA0-0.045-0.02443.6900.0020.0020.0000.0000.0000.000
206A224ASP-1-0.880-0.94944.4810.0890.0890.0000.0000.0000.000
207A225THR0-0.025-0.01946.1640.0010.0010.0000.0000.0000.000
208A226GLN0-0.040-0.03648.759-0.002-0.0020.0000.0000.0000.000
209A227ALA00.0150.03043.9000.0000.0000.0000.0000.0000.000
210A228LYS10.9240.95245.598-0.086-0.0860.0000.0000.0000.000
211A229ASN00.0330.02241.8870.0020.0020.0000.0000.0000.000
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