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: K9GR3

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 OptAll
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 -2070878.891026
FMO2-HF: Nuclear repulsion 1996571.809379
FMO2-HF: Total energy -74307.081646
FMO2-MP2: Total energy -74526.33394


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.
-22.244-5.31811.059-11.125-16.863-0.074
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 : 0.039 / q_NPA : 0.039
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].
3Y4HIS00.009-0.0182.191-1.1712.3781.544-2.184-2.9100.005
4Y5GLY00.0090.0165.334-0.0300.025-0.001-0.004-0.0490.000
5Y6VAL0-0.030-0.0138.7970.0720.0720.0000.0000.0000.000
6Y7ILE00.0270.01711.456-0.005-0.0050.0000.0000.0000.000
7Y8TYR0-0.016-0.01514.8370.0260.0260.0000.0000.0000.000
8Y9TYR00.0550.01718.086-0.008-0.0080.0000.0000.0000.000
9Y10SER00.0150.00221.6460.0070.0070.0000.0000.0000.000
10Y11SER00.0330.01725.0370.0050.0050.0000.0000.0000.000
11Y12PRO00.0340.01426.9350.0010.0010.0000.0000.0000.000
12Y13SER00.0260.00728.4430.0030.0030.0000.0000.0000.000
13Y14MET00.0300.01421.2540.0060.0060.0000.0000.0000.000
14Y15ALA0-0.0060.01024.5310.0030.0030.0000.0000.0000.000
15Y16THR0-0.046-0.03626.2810.0070.0070.0000.0000.0000.000
16Y17PHE00.0100.01020.9120.0040.0040.0000.0000.0000.000
17Y18LEU0-0.0020.01620.0380.0010.0010.0000.0000.0000.000
18Y19SER0-0.019-0.02122.1840.0020.0020.0000.0000.0000.000
19Y20PRO00.0350.01423.9120.0000.0000.0000.0000.0000.000
20Y21ALA00.0020.00920.532-0.002-0.0020.0000.0000.0000.000
21Y22GLN00.0410.02718.6190.0070.0070.0000.0000.0000.000
22Y23ASP-1-0.827-0.90020.667-0.011-0.0110.0000.0000.0000.000
23Y24ASN0-0.037-0.02522.1260.0070.0070.0000.0000.0000.000
24Y25LEU0-0.0110.01515.069-0.001-0.0010.0000.0000.0000.000
25Y26VAL0-0.002-0.00719.3030.0010.0010.0000.0000.0000.000
26Y27ARG10.9090.95720.6760.0240.0240.0000.0000.0000.000
27Y28THR0-0.083-0.06022.300-0.001-0.0010.0000.0000.0000.000
28Y29TYR00.020-0.00317.219-0.007-0.0070.0000.0000.0000.000
29Y30PHE0-0.023-0.00417.562-0.001-0.0010.0000.0000.0000.000
30Y31ALA0-0.0160.00915.9470.0090.0090.0000.0000.0000.000
31Y32GLN00.0200.01413.8770.0140.0140.0000.0000.0000.000
32Y33HIS00.0610.03715.524-0.007-0.0070.0000.0000.0000.000
33Y34LEU0-0.023-0.00611.3530.0170.0170.0000.0000.0000.000
34Y35LYS10.8910.9429.492-0.368-0.3680.0000.0000.0000.000
35Y36LYS10.9220.93715.309-0.047-0.0470.0000.0000.0000.000
36Y37TRP0-0.040-0.02013.4340.0190.0190.0000.0000.0000.000
37Y38VAL00.0420.01216.499-0.017-0.0170.0000.0000.0000.000
38Y39VAL0-0.039-0.01915.9790.0150.0150.0000.0000.0000.000
39Y40GLN0-0.0090.00519.222-0.009-0.0090.0000.0000.0000.000
40Y41TYR00.026-0.00321.6810.0020.0020.0000.0000.0000.000
41Y42LYS10.8200.90323.521-0.029-0.0290.0000.0000.0000.000
42Y43LEU0-0.0120.00026.709-0.001-0.0010.0000.0000.0000.000
43Y44TYR0-0.054-0.06928.8520.0000.0000.0000.0000.0000.000
44Y45ARG10.9480.97931.7700.0140.0140.0000.0000.0000.000
45Y46ASN00.0410.03934.4140.0000.0000.0000.0000.0000.000
46Y47ALA00.0290.01037.097-0.002-0.0020.0000.0000.0000.000
47Y48VAL0-0.0030.01039.186-0.001-0.0010.0000.0000.0000.000
48Y49THR0-0.052-0.03737.905-0.003-0.0030.0000.0000.0000.000
49Y50PRO0-0.0270.01433.827-0.003-0.0030.0000.0000.0000.000
50Y51LYS10.8520.89428.3580.0450.0450.0000.0000.0000.000
51Y52THR00.0100.01028.7190.0030.0030.0000.0000.0000.000
52Y53LEU0-0.005-0.01223.274-0.004-0.0040.0000.0000.0000.000
53Y54GLU-1-0.745-0.82823.7120.0170.0170.0000.0000.0000.000
54Y55PHE0-0.037-0.02615.569-0.007-0.0070.0000.0000.0000.000
55Y56LEU00.0220.02019.6910.0110.0110.0000.0000.0000.000
56Y57LYS10.8380.92611.128-0.016-0.0160.0000.0000.0000.000
57Y58GLN00.0600.00916.5970.0140.0140.0000.0000.0000.000
58Y59ASN0-0.021-0.01110.9760.0220.0220.0000.0000.0000.000
59Y60ILE0-0.034-0.02013.1130.0400.0400.0000.0000.0000.000
60Y61ASN00.0150.00715.348-0.010-0.0100.0000.0000.0000.000
61Y62PRO00.0160.00217.923-0.011-0.0110.0000.0000.0000.000
62Y63SER0-0.0170.00916.3770.0100.0100.0000.0000.0000.000
63Y64MET0-0.0140.02318.014-0.004-0.0040.0000.0000.0000.000
64Y65LEU0-0.039-0.02015.504-0.005-0.0050.0000.0000.0000.000
65Y66ALA00.0390.01420.077-0.011-0.0110.0000.0000.0000.000
66Y67CYS0-0.0320.00122.860-0.004-0.0040.0000.0000.0000.000
67Y68VAL00.0380.02224.8200.0000.0000.0000.0000.0000.000
68Y69ASP-1-0.758-0.86727.300-0.029-0.0290.0000.0000.0000.000
69Y70GLU-1-0.910-0.97625.882-0.054-0.0540.0000.0000.0000.000
70Y71ALA00.0090.00624.357-0.008-0.0080.0000.0000.0000.000
71Y72THR00.005-0.01123.9900.0020.0020.0000.0000.0000.000
72Y73MET0-0.043-0.02918.7160.0020.0020.0000.0000.0000.000
73Y74ILE0-0.009-0.00522.3730.0040.0040.0000.0000.0000.000
74Y75ASP-1-0.859-0.90917.5550.0720.0720.0000.0000.0000.000
75Y76ALA0-0.004-0.00320.7990.0020.0020.0000.0000.0000.000
76Y77GLU-1-0.881-0.93822.4030.0950.0950.0000.0000.0000.000
77Y78PRO00.015-0.02623.869-0.009-0.0090.0000.0000.0000.000
78Y79GLU-1-0.855-0.91826.6830.0430.0430.0000.0000.0000.000
79Y80LEU0-0.027-0.01026.909-0.006-0.0060.0000.0000.0000.000
80Y81GLU-1-0.759-0.85827.3510.0240.0240.0000.0000.0000.000
81Y82ASP-1-0.889-0.94330.0300.0290.0290.0000.0000.0000.000
82Y83ILE0-0.018-0.00532.179-0.004-0.0040.0000.0000.0000.000
83Y84ILE00.0010.00530.098-0.004-0.0040.0000.0000.0000.000
84Y85VAL0-0.0050.00233.377-0.004-0.0040.0000.0000.0000.000
85Y86ARG10.9040.94835.820-0.029-0.0290.0000.0000.0000.000
86Y87THR0-0.061-0.03836.678-0.002-0.0020.0000.0000.0000.000
87Y88LYS10.9090.95538.734-0.014-0.0140.0000.0000.0000.000
88Y89LEU00.0150.01738.332-0.002-0.0020.0000.0000.0000.000
89Y90TRP00.009-0.01132.837-0.001-0.0010.0000.0000.0000.000
90Y91ASN0-0.0090.01036.7740.0010.0010.0000.0000.0000.000
91Y92PHE00.026-0.01135.7390.0010.0010.0000.0000.0000.000
92Y93ARG10.7710.85728.928-0.017-0.0170.0000.0000.0000.000
93Y94GLN0-0.0190.00729.8330.0030.0030.0000.0000.0000.000
94Y95SER0-0.067-0.05927.9170.0030.0030.0000.0000.0000.000
95Y96PHE0-0.0140.00723.714-0.001-0.0010.0000.0000.0000.000
96Y97THR0-0.051-0.04422.9240.0100.0100.0000.0000.0000.000
97Y98ILE00.0120.01117.145-0.012-0.0120.0000.0000.0000.000
98Y99GLU-1-0.851-0.91020.0640.0120.0120.0000.0000.0000.000
99Y100GLY00.0600.01718.305-0.014-0.0140.0000.0000.0000.000
100Y101SER0-0.118-0.05016.8840.0180.0180.0000.0000.0000.000
101Y102ILE00.0060.01210.638-0.017-0.0170.0000.0000.0000.000
102Y103TYR0-0.020-0.03112.5260.0130.0130.0000.0000.0000.000
103Y104GLU-1-0.821-0.90010.0130.2050.2050.0000.0000.0000.000
104Y105VAL0-0.003-0.01410.9850.0060.0060.0000.0000.0000.000
105Y106GLY00.0550.03411.708-0.035-0.0350.0000.0000.0000.000
106Y107SER0-0.006-0.0058.9180.0330.0330.0000.0000.0000.000
107Y108PHE00.0170.0056.477-0.122-0.1220.0000.0000.0000.000
108Y109LYS10.8190.9166.054-0.215-0.2150.0000.0000.0000.000
109Y110VAL00.0060.0007.749-0.069-0.0690.0000.0000.0000.000
110Y111ALA0-0.014-0.00210.2670.0580.0580.0000.0000.0000.000
111Y112ILE0-0.0050.00012.412-0.037-0.0370.0000.0000.0000.000
112Y113ALA00.008-0.01215.9260.0220.0220.0000.0000.0000.000
113Y114ASN00.0210.01618.264-0.020-0.0200.0000.0000.0000.000
114Y115VAL00.0120.00819.2880.0070.0070.0000.0000.0000.000
115Y116LEU0-0.069-0.02121.924-0.002-0.0020.0000.0000.0000.000
116Y117GLN00.1140.05425.4390.0020.0020.0000.0000.0000.000
117Y118LYS10.9530.97328.2490.0010.0010.0000.0000.0000.000
118Y119SER00.0090.00229.1850.0010.0010.0000.0000.0000.000
119Y120VAL0-0.0230.00330.211-0.002-0.0020.0000.0000.0000.000
120Y121TRP0-0.011-0.00925.037-0.003-0.0030.0000.0000.0000.000
121Y122LYS10.9260.95625.4360.0420.0420.0000.0000.0000.000
122Y123GLY00.0440.03823.781-0.004-0.0040.0000.0000.0000.000
123Y124ILE0-0.0050.00918.5470.0010.0010.0000.0000.0000.000
124Y125LEU0-0.023-0.00413.473-0.014-0.0140.0000.0000.0000.000
125Y126PHE00.016-0.00613.7240.0230.0230.0000.0000.0000.000
126Y127HIS0-0.025-0.0256.1090.1050.1050.0000.0000.0000.000
127Y128VAL00.0320.0077.7520.0800.0800.0000.0000.0000.000
128Y129THR0-0.0220.0073.162-0.801-0.1340.091-0.188-0.5700.000
129Y130TYR00.002-0.0163.854-0.1440.2390.001-0.066-0.3180.000
130Y131ASP-1-0.891-0.9462.621-3.510-1.2930.960-1.377-1.799-0.017
131Y132GLY00.0220.0073.853-0.0620.0650.003-0.002-0.1280.000
132Y133THR0-0.024-0.0234.833-0.232-0.085-0.001-0.006-0.1400.000
133Y134GLU-1-0.831-0.9062.405-5.920-2.9613.318-3.104-3.174-0.034
134Y135SER0-0.010-0.0094.691-0.129-0.148-0.001-0.0090.0280.000
135Y136VAL00.0400.0078.0330.0170.0170.0000.0000.0000.000
136Y137ASP-1-0.829-0.8979.181-0.397-0.3970.0000.0000.0000.000
137Y138LEU0-0.021-0.00910.1100.0670.0670.0000.0000.0000.000
138Y139ALA00.0110.0066.8550.0450.0450.0000.0000.0000.000
139Y140ARG10.8290.9138.8050.5750.5750.0000.0000.0000.000
140Y141PRO00.000-0.00311.8120.0530.0530.0000.0000.0000.000
141Y142ILE00.0280.0259.9990.0490.0490.0000.0000.0000.000
142Y143ILE00.004-0.0036.8460.0510.0510.0000.0000.0000.000
143Y144GLN00.007-0.00210.9230.0570.0570.0000.0000.0000.000
144Y145GLU-1-0.833-0.89414.621-0.140-0.1400.0000.0000.0000.000
145Y146PHE00.0300.01411.4660.0330.0330.0000.0000.0000.000
146Y147PHE0-0.009-0.01214.0180.0330.0330.0000.0000.0000.000
147Y148LEU0-0.013-0.00715.4650.0270.0270.0000.0000.0000.000
148Y149LYS10.8350.89516.8820.1720.1720.0000.0000.0000.000
149Y150CYS0-0.068-0.02316.6830.0160.0160.0000.0000.0000.000
150Y151PHE0-0.015-0.00415.5360.0170.0170.0000.0000.0000.000
151Y152LEU00.0120.00920.7960.0070.0070.0000.0000.0000.000
152Y153GLN0-0.080-0.03823.3480.0030.0030.0000.0000.0000.000
153Y154ASN00.0350.01324.5590.0070.0070.0000.0000.0000.000
154Y155ASN0-0.005-0.00320.0610.0010.0010.0000.0000.0000.000
155Y156LYS10.9560.98223.8250.0750.0750.0000.0000.0000.000
156Y157SER0-0.0020.00327.1090.0020.0020.0000.0000.0000.000
157Y158VAL0-0.046-0.02424.2060.0050.0050.0000.0000.0000.000
158Y159THR00.0350.02723.662-0.007-0.0070.0000.0000.0000.000
159Y160PRO0-0.038-0.01719.2170.0100.0100.0000.0000.0000.000
160Y161VAL0-0.003-0.00220.6760.0010.0010.0000.0000.0000.000
161Y162TYR0-0.068-0.03715.5930.0090.0090.0000.0000.0000.000
162Y163GLU-1-0.745-0.85214.049-0.202-0.2020.0000.0000.0000.000
163Y164SER0-0.045-0.01613.662-0.003-0.0030.0000.0000.0000.000
164Y165PHE0-0.001-0.0189.812-0.035-0.0350.0000.0000.0000.000
165Y166PHE0-0.031-0.0137.3250.1110.1110.0000.0000.0000.000
166Y167ASN0-0.044-0.0393.409-0.2080.7230.020-0.455-0.4960.002
167Y168GLN00.0470.0143.6950.7541.4550.000-0.303-0.3980.001
168Y169PRO00.0860.0392.224-7.255-5.6562.892-2.030-2.461-0.021
169Y170ARG10.8440.9343.2171.4872.2020.211-0.020-0.9060.000
170Y171HIS00.0450.0152.757-5.496-2.6562.015-1.433-3.423-0.010
171Y172SER0-0.042-0.0333.648-0.431-0.3760.0070.056-0.1190.000
172Y173LEU00.0130.0256.779-0.044-0.0440.0000.0000.0000.000
173Y174ASP-1-0.730-0.8648.0940.1110.1110.0000.0000.0000.000
174Y175SER0-0.042-0.02410.100-0.016-0.0160.0000.0000.0000.000
175Y176LYS10.9110.94013.684-0.045-0.0450.0000.0000.0000.000
176Y177LEU00.0150.00910.867-0.003-0.0030.0000.0000.0000.000
177Y178LEU0-0.014-0.01213.6470.0010.0010.0000.0000.0000.000
178Y179LEU00.0110.00715.3460.0050.0050.0000.0000.0000.000
179Y180GLN00.0480.01517.2820.0160.0160.0000.0000.0000.000
180Y181LEU0-0.024-0.01614.550-0.002-0.0020.0000.0000.0000.000
181Y182PHE0-0.005-0.00518.4810.0060.0060.0000.0000.0000.000
182Y183LYS10.8300.92621.4250.0590.0590.0000.0000.0000.000
183Y184GLN0-0.061-0.02319.2050.0090.0090.0000.0000.0000.000
184Y185ARG10.7630.86618.5860.1370.1370.0000.0000.0000.000
185Y186ILE0-0.0480.00324.0490.0080.0080.0000.0000.0000.000