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: R9818

Calculation Name: 5N9J-Y-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5N9J

Chain ID: Y

ChEMBL ID:

UniProt ID: P87310

Base Structure: X-ray

Registration Date: 2023-06-21

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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2075263.993693
FMO2-HF: Nuclear repulsion 2000960.445373
FMO2-HF: Total energy -74303.548321
FMO2-MP2: Total energy -74523.305793


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(Y:2:PRO)


Summations of interaction energy for fragment #1(Y:2:PRO)
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.
-17.523-1.98710.793-11.59-14.741-0.057
Interaction energy analysis for fragmet #1(Y:2:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.078 / q_NPA : 0.050
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].
3Y4HIS00.021-0.0032.728-1.8122.6130.277-2.024-2.6790.007
4Y5GLY0-0.034-0.0175.1940.0020.054-0.001-0.005-0.0460.000
5Y6VAL0-0.014-0.0038.8970.0520.0520.0000.0000.0000.000
6Y7ILE00.0260.00711.7570.0290.0290.0000.0000.0000.000
7Y8TYR0-0.014-0.01514.8410.0120.0120.0000.0000.0000.000
8Y9TYR00.0680.02518.0330.0110.0110.0000.0000.0000.000
9Y10SER00.025-0.00521.5770.0060.0060.0000.0000.0000.000
10Y11SER0-0.0010.01225.1150.0060.0060.0000.0000.0000.000
11Y12PRO00.0170.00526.957-0.002-0.0020.0000.0000.0000.000
12Y13SER00.0350.00628.2170.0010.0010.0000.0000.0000.000
13Y14MET0-0.001-0.01021.2490.0050.0050.0000.0000.0000.000
14Y15ALA00.034-0.02524.567-0.002-0.0020.0000.0000.0000.000
15Y16THR0-0.035-0.02926.4060.0000.0000.0000.0000.0000.000
16Y17PHE00.0130.01920.0430.0040.0040.0000.0000.0000.000
17Y18LEU00.0060.02220.1610.0020.0020.0000.0000.0000.000
18Y19SER0-0.0020.00722.4530.0020.0020.0000.0000.0000.000
19Y20PRO00.0230.01324.2750.0030.0030.0000.0000.0000.000
20Y21ALA00.0060.00820.4620.0020.0020.0000.0000.0000.000
21Y22GLN00.0600.07019.6480.0090.0090.0000.0000.0000.000
22Y23ASP-1-0.854-0.91920.705-0.037-0.0370.0000.0000.0000.000
23Y24ASN0-0.015-0.02022.5050.0110.0110.0000.0000.0000.000
24Y25LEU00.0260.07615.3640.0030.0030.0000.0000.0000.000
25Y26VAL0-0.003-0.01919.5500.0060.0060.0000.0000.0000.000
26Y27ARG10.9280.96820.6560.0330.0330.0000.0000.0000.000
27Y28THR0-0.116-0.11522.6080.0030.0030.0000.0000.0000.000
28Y29TYR0-0.019-0.01717.576-0.001-0.0010.0000.0000.0000.000
29Y30PHE0-0.045-0.00817.8580.0040.0040.0000.0000.0000.000
30Y31ALA0-0.0100.01116.0620.0070.0070.0000.0000.0000.000
31Y32GLN00.0460.02314.5600.0070.0070.0000.0000.0000.000
32Y33HIS0-0.016-0.00515.365-0.013-0.0130.0000.0000.0000.000
33Y34LEU0-0.025-0.01311.6070.0140.0140.0000.0000.0000.000
34Y35LYS10.9460.98110.578-0.065-0.0650.0000.0000.0000.000
35Y36LYS11.0260.98915.5760.0180.0180.0000.0000.0000.000
36Y37TRP0-0.034-0.02012.822-0.003-0.0030.0000.0000.0000.000
37Y38VAL00.0380.01416.4890.0000.0000.0000.0000.0000.000
38Y39VAL0-0.0180.00515.955-0.002-0.0020.0000.0000.0000.000
39Y40GLN00.0300.00519.0660.0030.0030.0000.0000.0000.000
40Y41TYR00.0280.02322.048-0.002-0.0020.0000.0000.0000.000
41Y42LYS10.9240.95923.5940.0580.0580.0000.0000.0000.000
42Y43LEU0-0.036-0.01326.869-0.003-0.0030.0000.0000.0000.000
43Y44TYR0-0.0330.00129.1590.0040.0040.0000.0000.0000.000
44Y45ARG10.9640.97532.1500.0520.0520.0000.0000.0000.000
45Y46ASN00.0400.05334.7460.0030.0030.0000.0000.0000.000
46Y47ALA00.0760.02837.731-0.002-0.0020.0000.0000.0000.000
47Y48VAL0-0.039-0.01438.9360.0000.0000.0000.0000.0000.000
48Y49THR0-0.101-0.05937.864-0.002-0.0020.0000.0000.0000.000
49Y50PRO00.0190.04334.367-0.003-0.0030.0000.0000.0000.000
50Y51LYS10.8840.94328.7080.0860.0860.0000.0000.0000.000
51Y52THR00.0470.04028.9240.0020.0020.0000.0000.0000.000
52Y53LEU0-0.037-0.02024.0710.0000.0000.0000.0000.0000.000
53Y54GLU-1-0.850-0.92923.961-0.055-0.0550.0000.0000.0000.000
54Y55PHE0-0.061-0.02115.838-0.008-0.0080.0000.0000.0000.000
55Y56LEU00.0100.02219.889-0.002-0.0020.0000.0000.0000.000
56Y57LYS10.8640.93410.8450.3200.3200.0000.0000.0000.000
57Y58GLN00.0900.05515.7520.0080.0080.0000.0000.0000.000
58Y59ASN0-0.090-0.06211.6740.0320.0320.0000.0000.0000.000
59Y60ILE0-0.026-0.02613.1460.0190.0190.0000.0000.0000.000
60Y61ASN00.0320.01315.420-0.008-0.0080.0000.0000.0000.000
61Y62PRO0-0.018-0.01517.962-0.002-0.0020.0000.0000.0000.000
62Y63SER0-0.0090.02417.0080.0070.0070.0000.0000.0000.000
63Y64MET00.0190.01918.367-0.016-0.0160.0000.0000.0000.000
64Y65LEU0-0.063-0.02615.891-0.004-0.0040.0000.0000.0000.000
65Y66ALA00.0340.00920.350-0.007-0.0070.0000.0000.0000.000
66Y67CYS0-0.010-0.01222.9310.0000.0000.0000.0000.0000.000
67Y68VAL00.017-0.00824.9010.0020.0020.0000.0000.0000.000
68Y69ASP-1-0.848-0.97127.630-0.070-0.0700.0000.0000.0000.000
69Y70GLU-1-0.984-1.03426.196-0.103-0.1030.0000.0000.0000.000
70Y71ALA0-0.0020.03924.885-0.009-0.0090.0000.0000.0000.000
71Y72THR00.0290.01824.520-0.004-0.0040.0000.0000.0000.000
72Y73MET00.005-0.01918.929-0.008-0.0080.0000.0000.0000.000
73Y74ILE0-0.068-0.01622.4740.0040.0040.0000.0000.0000.000
74Y75ASP-1-0.900-0.95318.005-0.073-0.0730.0000.0000.0000.000
75Y76ALA0-0.032-0.01221.4210.0110.0110.0000.0000.0000.000
76Y77GLU-1-0.852-0.94623.244-0.002-0.0020.0000.0000.0000.000
77Y78PRO00.041-0.00223.928-0.004-0.0040.0000.0000.0000.000
78Y79GLU-1-0.883-0.92726.733-0.010-0.0100.0000.0000.0000.000
79Y80LEU0-0.0100.00127.2590.0000.0000.0000.0000.0000.000
80Y81GLU-1-0.776-0.88227.433-0.045-0.0450.0000.0000.0000.000
81Y82ASP-1-0.894-0.94430.044-0.023-0.0230.0000.0000.0000.000
82Y83ILE0-0.062-0.03132.6450.0010.0010.0000.0000.0000.000
83Y84ILE00.0190.00531.0320.0010.0010.0000.0000.0000.000
84Y85VAL0-0.0240.00233.6120.0000.0000.0000.0000.0000.000
85Y86ARG10.9050.94236.0670.0140.0140.0000.0000.0000.000
86Y87THR0-0.055-0.02537.2950.0010.0010.0000.0000.0000.000
87Y88LYS10.9070.97138.8950.0210.0210.0000.0000.0000.000
88Y89LEU00.025-0.00437.560-0.001-0.0010.0000.0000.0000.000
89Y90TRP00.020-0.01032.7900.0000.0000.0000.0000.0000.000
90Y91ASN00.0060.01036.8080.0020.0020.0000.0000.0000.000
91Y92PHE00.012-0.00335.681-0.001-0.0010.0000.0000.0000.000
92Y93ARG10.7720.86430.1960.0410.0410.0000.0000.0000.000
93Y94GLN00.0040.00930.5790.0040.0040.0000.0000.0000.000
94Y95SER0-0.071-0.03927.880-0.003-0.0030.0000.0000.0000.000
95Y96PHE0-0.0150.01324.2000.0010.0010.0000.0000.0000.000
96Y97THR0-0.045-0.02322.8050.0010.0010.0000.0000.0000.000
97Y98ILE00.0270.01117.447-0.005-0.0050.0000.0000.0000.000
98Y99GLU-1-0.873-0.94119.873-0.064-0.0640.0000.0000.0000.000
99Y100GLY00.006-0.00718.348-0.004-0.0040.0000.0000.0000.000
100Y101SER0-0.092-0.04016.8300.0150.0150.0000.0000.0000.000
101Y102ILE0-0.0300.00110.893-0.016-0.0160.0000.0000.0000.000
102Y103TYR0-0.067-0.08913.0370.0280.0280.0000.0000.0000.000
103Y104GLU-1-0.945-0.9729.7850.0810.0810.0000.0000.0000.000
104Y105VAL00.000-0.01811.0010.0070.0070.0000.0000.0000.000
105Y106GLY00.0260.01511.139-0.012-0.0120.0000.0000.0000.000
106Y107SER00.0320.0228.5850.0140.0140.0000.0000.0000.000
107Y108PHE00.037-0.0016.471-0.009-0.0090.0000.0000.0000.000
108Y109LYS10.9290.9836.357-0.206-0.2060.0000.0000.0000.000
109Y110VAL00.0110.0057.712-0.087-0.0870.0000.0000.0000.000
110Y111ALA0-0.016-0.00610.4150.0430.0430.0000.0000.0000.000
111Y112ILE00.0080.02012.753-0.023-0.0230.0000.0000.0000.000
112Y113ALA00.021-0.01016.2790.0200.0200.0000.0000.0000.000
113Y114ASN00.0490.01518.401-0.010-0.0100.0000.0000.0000.000
114Y115VAL0-0.0020.01119.919-0.002-0.0020.0000.0000.0000.000
115Y116LEU0-0.089-0.04122.4620.0070.0070.0000.0000.0000.000
116Y117GLN00.0950.03425.739-0.003-0.0030.0000.0000.0000.000
117Y118LYS10.9720.98128.5040.0500.0500.0000.0000.0000.000
118Y119SER0-0.003-0.00529.1140.0050.0050.0000.0000.0000.000
119Y120VAL0-0.0050.01730.1060.0010.0010.0000.0000.0000.000
120Y121TRP0-0.030-0.00424.4650.0050.0050.0000.0000.0000.000
121Y122LYS10.9441.01425.9580.0720.0720.0000.0000.0000.000
122Y123GLY00.0450.04224.260-0.001-0.0010.0000.0000.0000.000
123Y124ILE0-0.0080.00618.802-0.005-0.0050.0000.0000.0000.000
124Y125LEU0-0.030-0.01013.807-0.011-0.0110.0000.0000.0000.000
125Y126PHE0-0.007-0.01613.4800.0190.0190.0000.0000.0000.000
126Y127HIS0-0.021-0.0247.046-0.071-0.0710.0000.0000.0000.000
127Y128VAL00.0090.0127.3330.0660.0660.0000.0000.0000.000
128Y129THR0-0.017-0.0162.862-0.789-0.1690.117-0.166-0.5710.001
129Y130TYR0-0.035-0.0093.505-0.1910.2930.011-0.098-0.3970.000
130Y131ASP-1-0.957-0.9722.732-1.9970.1030.688-1.180-1.607-0.011
131Y132GLY00.0520.0143.320-0.375-0.0590.021-0.051-0.287-0.001
132Y133THR0-0.036-0.0254.340-0.1670.120-0.001-0.027-0.2600.000
133Y134GLU-1-0.832-0.8972.567-2.7820.3731.998-2.750-2.404-0.031
134Y135SER0-0.0040.0134.717-0.162-0.135-0.001-0.009-0.0180.000
135Y136VAL00.033-0.0067.861-0.029-0.0290.0000.0000.0000.000
136Y137ASP-1-0.925-0.9648.973-0.278-0.2780.0000.0000.0000.000
137Y138LEU0-0.002-0.0069.7270.0370.0370.0000.0000.0000.000
138Y139ALA00.0210.0156.3060.0260.0260.0000.0000.0000.000
139Y140ARG10.9460.9838.2620.4120.4120.0000.0000.0000.000
140Y141PRO00.005-0.01210.9780.0260.0260.0000.0000.0000.000
141Y142ILE00.0470.0369.4370.0320.0320.0000.0000.0000.000
142Y143ILE0-0.023-0.0196.4760.0210.0210.0000.0000.0000.000
143Y144GLN0-0.043-0.02310.7030.0440.0440.0000.0000.0000.000
144Y145GLU-1-0.965-0.96314.184-0.085-0.0850.0000.0000.0000.000
145Y146PHE00.0580.01310.9940.0210.0210.0000.0000.0000.000
146Y147PHE0-0.020-0.01913.5290.0160.0160.0000.0000.0000.000
147Y148LEU0-0.014-0.00715.1220.0170.0170.0000.0000.0000.000
148Y149LYS10.9920.99317.1970.0790.0790.0000.0000.0000.000
149Y150CYS0-0.092-0.04216.4760.0130.0130.0000.0000.0000.000
150Y151PHE0-0.045-0.02015.1070.0070.0070.0000.0000.0000.000
151Y152LEU00.0270.01420.3440.0000.0000.0000.0000.0000.000
152Y153GLN0-0.078-0.04022.9240.0000.0000.0000.0000.0000.000
153Y154ASN00.0510.00424.8130.0060.0060.0000.0000.0000.000
154Y155ASN00.0220.04420.197-0.002-0.0020.0000.0000.0000.000
155Y156LYS10.9780.98323.7550.0620.0620.0000.0000.0000.000
156Y157SER0-0.047-0.01926.8490.0030.0030.0000.0000.0000.000
157Y158VAL0-0.049-0.02624.3790.0030.0030.0000.0000.0000.000
158Y159THR00.0340.02123.073-0.002-0.0020.0000.0000.0000.000
159Y160PRO0-0.051-0.02018.9390.0060.0060.0000.0000.0000.000
160Y161VAL0-0.0070.00721.1830.0070.0070.0000.0000.0000.000
161Y162TYR0-0.045-0.03315.5510.0070.0070.0000.0000.0000.000
162Y163GLU-1-0.851-0.92614.520-0.270-0.2700.0000.0000.0000.000
163Y164SER0-0.077-0.02613.959-0.007-0.0070.0000.0000.0000.000
164Y165PHE00.0230.0059.115-0.019-0.0190.0000.0000.0000.000
165Y166PHE0-0.052-0.0127.4050.1990.1990.0000.0000.0000.000
166Y167ASN0-0.057-0.0652.668-1.1550.5170.520-0.770-1.4220.006
167Y168GLN0-0.010-0.0093.3420.1441.4720.002-0.682-0.6480.002
168Y169PRO00.0850.0421.943-7.525-8.9246.774-2.914-2.460-0.025
169Y170ARG10.8990.9593.2321.2502.0640.160-0.261-0.712-0.002
170Y171HIS00.0980.0423.099-2.791-1.1930.229-0.660-1.168-0.003
171Y172SER0-0.040-0.0134.137-0.160-0.103-0.0010.007-0.0620.000
172Y173LEU00.0180.0226.984-0.081-0.0810.0000.0000.0000.000
173Y174ASP-1-0.819-0.9408.384-0.123-0.1230.0000.0000.0000.000
174Y175SER00.012-0.01310.828-0.004-0.0040.0000.0000.0000.000
175Y176LYS11.0181.00414.3540.1450.1450.0000.0000.0000.000
176Y177LEU00.0250.02311.4490.0140.0140.0000.0000.0000.000
177Y178LEU00.0400.00913.5190.0150.0150.0000.0000.0000.000
178Y179LEU00.0090.01415.7010.0250.0250.0000.0000.0000.000
179Y180GLN00.0350.01017.5260.0230.0230.0000.0000.0000.000
180Y181LEU0-0.019-0.01114.9110.0120.0120.0000.0000.0000.000
181Y182PHE00.016-0.00818.5870.0200.0200.0000.0000.0000.000
182Y183LYS10.8120.92221.6240.1250.1250.0000.0000.0000.000
183Y184GLN0-0.018-0.00720.0210.0110.0110.0000.0000.0000.000
184Y185ARG10.8610.94620.8660.1820.1820.0000.0000.0000.000
185Y186ILE0-0.055-0.00824.3120.0140.0140.0000.0000.0000.000