FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: QVR1Y

Calculation Name: 1Y6N-R-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Y6N

Chain ID: R

ChEMBL ID:

UniProt ID: Q13651

Base Structure: X-ray

Registration Date: 2023-09-24

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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2165511.880936
FMO2-HF: Nuclear repulsion 2084899.231133
FMO2-HF: Total energy -80612.649803
FMO2-MP2: Total energy -80849.044226


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(R:2:GLY)


Summations of interaction energy for fragment #1(R:2: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.
0.2351.204-0.004-0.357-0.6080.001
Interaction energy analysis for fragmet #1(R:2:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / q_NPA : -0.009
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].
3R4GLU-1-0.927-0.9613.8030.1320.921-0.002-0.309-0.4780.001
4R5LEU0-0.056-0.0164.2860.6230.703-0.001-0.021-0.0580.000
5R6PRO00.0380.0025.473-0.282-0.2820.0000.0000.0000.000
6R7SER00.0570.0288.010-0.081-0.0810.0000.0000.0000.000
7R8PRO0-0.010-0.00311.7840.0740.0740.0000.0000.0000.000
8R9PRO0-0.0490.00813.646-0.057-0.0570.0000.0000.0000.000
9R10SER0-0.005-0.00515.619-0.054-0.0540.0000.0000.0000.000
10R11VAL00.028-0.00419.0720.0120.0120.0000.0000.0000.000
11R12TRP0-0.106-0.06821.276-0.010-0.0100.0000.0000.0000.000
12R13PHE00.0610.01625.2990.0040.0040.0000.0000.0000.000
13R14GLU-1-0.884-0.91928.3090.1480.1480.0000.0000.0000.000
14R15ALA0-0.026-0.00431.047-0.002-0.0020.0000.0000.0000.000
15R16GLU-1-0.880-0.92134.2370.0810.0810.0000.0000.0000.000
16R17PHE0-0.024-0.03837.809-0.001-0.0010.0000.0000.0000.000
17R18PHE0-0.030-0.02038.568-0.001-0.0010.0000.0000.0000.000
18R19HIS00.0150.01034.589-0.001-0.0010.0000.0000.0000.000
19R20HIS0-0.001-0.03132.9980.0030.0030.0000.0000.0000.000
20R21ILE00.0300.02728.5190.0000.0000.0000.0000.0000.000
21R22LEU0-0.065-0.02323.6340.0010.0010.0000.0000.0000.000
22R23HIS00.0680.01524.2330.0150.0150.0000.0000.0000.000
23R24TRP0-0.024-0.01517.923-0.024-0.0240.0000.0000.0000.000
24R25THR0-0.0220.00816.837-0.004-0.0040.0000.0000.0000.000
25R26PRO00.0280.00415.3310.0060.0060.0000.0000.0000.000
26R27ILE00.0020.0129.1480.0060.0060.0000.0000.0000.000
27R28PRO0-0.014-0.0158.496-0.060-0.0600.0000.0000.0000.000
28R29GLN0-0.026-0.0327.1420.2350.2350.0000.0000.0000.000
29R30GLN0-0.0160.0119.3090.1510.1510.0000.0000.0000.000
30R31SER00.0190.02610.128-0.108-0.1080.0000.0000.0000.000
31R32GLU-1-0.879-0.96911.9790.1930.1930.0000.0000.0000.000
32R33SER0-0.101-0.05512.569-0.009-0.0090.0000.0000.0000.000
33R34THR0-0.0270.01311.5380.0030.0030.0000.0000.0000.000
34R35CYS0-0.091-0.05013.998-0.018-0.0180.0000.0000.0000.000
35R36TYR0-0.013-0.02014.3980.0500.0500.0000.0000.0000.000
36R37GLU-1-0.776-0.85917.8440.0210.0210.0000.0000.0000.000
37R38VAL00.0030.00019.8760.0090.0090.0000.0000.0000.000
38R39ALA0-0.004-0.00322.632-0.017-0.0170.0000.0000.0000.000
39R40LEU0-0.006-0.01924.5530.0090.0090.0000.0000.0000.000
40R41LEU0-0.0080.00427.717-0.008-0.0080.0000.0000.0000.000
41R42ARG10.8900.93229.480-0.028-0.0280.0000.0000.0000.000
42R43TYR0-0.017-0.03232.597-0.003-0.0030.0000.0000.0000.000
43R44GLY0-0.015-0.00734.239-0.001-0.0010.0000.0000.0000.000
44R45ILE00.0200.00833.898-0.003-0.0030.0000.0000.0000.000
45R46GLU-1-0.946-0.95831.1750.0130.0130.0000.0000.0000.000
46R47SER0-0.022-0.04929.454-0.006-0.0060.0000.0000.0000.000
47R48TRP0-0.0480.00425.0090.0070.0070.0000.0000.0000.000
48R49ASN00.0060.00927.577-0.012-0.0120.0000.0000.0000.000
49R50SER0-0.007-0.00123.2310.0150.0150.0000.0000.0000.000
50R51ILE0-0.050-0.02825.503-0.005-0.0050.0000.0000.0000.000
51R52SER00.0150.00323.928-0.006-0.0060.0000.0000.0000.000
52R53GLN00.0400.01422.3500.0130.0130.0000.0000.0000.000
53R55SER00.0060.00920.424-0.019-0.0190.0000.0000.0000.000
54R56GLN00.0000.00118.8240.0050.0050.0000.0000.0000.000
55R57THR0-0.017-0.02320.757-0.006-0.0060.0000.0000.0000.000
56R58LEU00.012-0.00818.3700.0290.0290.0000.0000.0000.000
57R59SER00.0160.00921.684-0.006-0.0060.0000.0000.0000.000
58R60TYR00.0130.01324.690-0.004-0.0040.0000.0000.0000.000
59R61ASP-1-0.804-0.88726.8210.0810.0810.0000.0000.0000.000
60R62LEU0-0.002-0.00227.040-0.006-0.0060.0000.0000.0000.000
61R63THR00.0080.02531.006-0.007-0.0070.0000.0000.0000.000
62R64ALA0-0.010-0.00434.387-0.005-0.0050.0000.0000.0000.000
63R65VAL0-0.0040.00130.891-0.005-0.0050.0000.0000.0000.000
64R66THR0-0.054-0.04932.276-0.002-0.0020.0000.0000.0000.000
65R67LEU0-0.015-0.00935.2440.0010.0010.0000.0000.0000.000
66R68ASP-1-0.766-0.85938.3900.0320.0320.0000.0000.0000.000
67R69LEU0-0.071-0.02235.690-0.002-0.0020.0000.0000.0000.000
68R70TYR0-0.044-0.04838.5440.0010.0010.0000.0000.0000.000
69R71HIS0-0.021-0.01141.723-0.002-0.0020.0000.0000.0000.000
70R72SER0-0.072-0.01438.376-0.002-0.0020.0000.0000.0000.000
71R73ASN0-0.014-0.01338.1460.0020.0020.0000.0000.0000.000
72R74GLY00.0360.00435.1900.0020.0020.0000.0000.0000.000
73R75TYR00.027-0.00931.003-0.006-0.0060.0000.0000.0000.000
74R76ARG10.7970.90326.735-0.074-0.0740.0000.0000.0000.000
75R77ALA00.0490.03725.602-0.007-0.0070.0000.0000.0000.000
76R78ARG10.8830.95920.860-0.046-0.0460.0000.0000.0000.000
77R79VAL00.0240.01517.732-0.010-0.0100.0000.0000.0000.000
78R80ARG10.8830.93614.865-0.027-0.0270.0000.0000.0000.000
79R81ALA00.0140.01711.721-0.023-0.0230.0000.0000.0000.000
80R82VAL0-0.007-0.01913.047-0.049-0.0490.0000.0000.0000.000
81R83ASP-1-0.805-0.9069.9850.4780.4780.0000.0000.0000.000
82R84GLY00.0130.01511.377-0.092-0.0920.0000.0000.0000.000
83R85SER0-0.059-0.03712.9250.0030.0030.0000.0000.0000.000
84R86ARG10.9300.9844.241-0.911-0.811-0.001-0.027-0.0720.000
85R87HIS00.031-0.00611.5060.1150.1150.0000.0000.0000.000
86R88SER0-0.0100.02910.174-0.068-0.0680.0000.0000.0000.000
87R89GLN0-0.001-0.01011.198-0.044-0.0440.0000.0000.0000.000
88R90TRP0-0.053-0.03413.5900.0420.0420.0000.0000.0000.000
89R91THR00.004-0.00715.747-0.009-0.0090.0000.0000.0000.000
90R92VAL0-0.030-0.03617.962-0.006-0.0060.0000.0000.0000.000
91R93THR00.0220.02121.7490.0080.0080.0000.0000.0000.000
92R94ASN00.0410.01223.119-0.010-0.0100.0000.0000.0000.000
93R95THR0-0.074-0.05625.406-0.010-0.0100.0000.0000.0000.000
94R96ARG10.8560.92328.612-0.049-0.0490.0000.0000.0000.000
95R97PHE00.0280.03230.421-0.001-0.0010.0000.0000.0000.000
96R98SER00.0560.00732.149-0.006-0.0060.0000.0000.0000.000
97R99VAL00.0490.01535.9370.0040.0040.0000.0000.0000.000
98R100ASP-1-0.897-0.94737.2430.0560.0560.0000.0000.0000.000
99R101GLU-1-0.896-0.91331.5220.0940.0940.0000.0000.0000.000
100R102VAL0-0.0470.00734.7780.0050.0050.0000.0000.0000.000
101R103THR0-0.023-0.01535.910-0.002-0.0020.0000.0000.0000.000
102R104LEU00.0020.01538.360-0.001-0.0010.0000.0000.0000.000
103R105THR00.0390.01040.4420.0010.0010.0000.0000.0000.000
104R106VAL0-0.009-0.00743.439-0.003-0.0030.0000.0000.0000.000
105R107GLY00.013-0.00845.8950.0020.0020.0000.0000.0000.000
106R108SER0-0.094-0.06047.5080.0010.0010.0000.0000.0000.000
107R109VAL00.0220.01049.730-0.001-0.0010.0000.0000.0000.000
108R110ASN00.0380.02752.8530.0000.0000.0000.0000.0000.000
109R111LEU00.0260.01555.577-0.001-0.0010.0000.0000.0000.000
110R112GLU-1-0.827-0.90458.8960.0290.0290.0000.0000.0000.000
111R113ILE00.0330.01862.6390.0000.0000.0000.0000.0000.000
112R114HIS0-0.030-0.03065.599-0.001-0.0010.0000.0000.0000.000
113R115ASN0-0.038-0.02168.475-0.001-0.0010.0000.0000.0000.000
114R116GLY00.0590.03270.2870.0000.0000.0000.0000.0000.000
115R117PHE0-0.066-0.04065.4070.0000.0000.0000.0000.0000.000
116R118ILE00.0270.03560.3560.0000.0000.0000.0000.0000.000
117R119LEU0-0.032-0.02062.2290.0000.0000.0000.0000.0000.000
118R120GLY00.0200.01057.9780.0010.0010.0000.0000.0000.000
119R121LYS10.8260.90357.280-0.032-0.0320.0000.0000.0000.000
120R122ILE0-0.009-0.00651.1590.0010.0010.0000.0000.0000.000
121R123GLN0-0.061-0.01351.589-0.001-0.0010.0000.0000.0000.000
122R124LEU00.0030.02048.5750.0030.0030.0000.0000.0000.000
123R125PRO0-0.031-0.00744.232-0.001-0.0010.0000.0000.0000.000
124R126ARG10.8960.94246.308-0.041-0.0410.0000.0000.0000.000
125R127PRO00.0040.02041.9130.0000.0000.0000.0000.0000.000
126R128LYS10.9910.96639.905-0.058-0.0580.0000.0000.0000.000
127R129MET0-0.030-0.02236.920-0.002-0.0020.0000.0000.0000.000
128R130ALA00.0030.03142.216-0.001-0.0010.0000.0000.0000.000
129R131PRO00.0170.01742.822-0.002-0.0020.0000.0000.0000.000
130R132ALA00.0030.00645.9430.0000.0000.0000.0000.0000.000
131R133GLN0-0.024-0.02248.4890.0010.0010.0000.0000.0000.000
132R134ASP-1-0.810-0.89044.9980.0360.0360.0000.0000.0000.000
133R135THR00.0270.02346.9270.0030.0030.0000.0000.0000.000
134R136TYR00.0500.00844.5640.0000.0000.0000.0000.0000.000
135R137GLU-1-0.793-0.92948.0020.0380.0380.0000.0000.0000.000
136R138SER0-0.100-0.02949.931-0.001-0.0010.0000.0000.0000.000
137R139ILE0-0.0170.01344.2010.0000.0000.0000.0000.0000.000
138R140PHE0-0.037-0.02842.6210.0000.0000.0000.0000.0000.000
139R141SER00.0740.03548.6960.0000.0000.0000.0000.0000.000
140R142HIS0-0.043-0.02551.686-0.001-0.0010.0000.0000.0000.000
141R143PHE0-0.007-0.02251.1090.0010.0010.0000.0000.0000.000
142R144ARG10.8140.91650.061-0.035-0.0350.0000.0000.0000.000
143R145GLU-1-0.947-0.98050.3920.0390.0390.0000.0000.0000.000
144R146TYR0-0.050-0.10949.6750.0030.0030.0000.0000.0000.000
145R147GLU-1-0.975-0.97448.7730.0470.0470.0000.0000.0000.000
146R148ILE0-0.010-0.02850.3240.0010.0010.0000.0000.0000.000
147R149ALA00.0320.02450.218-0.001-0.0010.0000.0000.0000.000
148R150ILE0-0.016-0.01152.1870.0000.0000.0000.0000.0000.000
149R151ARG10.8740.93551.232-0.051-0.0510.0000.0000.0000.000
150R152LYS10.9330.97555.166-0.037-0.0370.0000.0000.0000.000
151R153VAL00.0040.01755.2600.0020.0020.0000.0000.0000.000
152R154PRO00.058-0.00158.405-0.001-0.0010.0000.0000.0000.000
153R155GLY0-0.0140.00357.966-0.001-0.0010.0000.0000.0000.000
154R156GLN00.0020.00254.8750.0030.0030.0000.0000.0000.000
155R157PHE00.0140.00646.785-0.001-0.0010.0000.0000.0000.000
156R158THR0-0.040-0.01451.1620.0010.0010.0000.0000.0000.000
157R159PHE00.033-0.00149.091-0.001-0.0010.0000.0000.0000.000
158R160THR0-0.061-0.01253.594-0.001-0.0010.0000.0000.0000.000
159R161HIS00.0350.00949.6930.0000.0000.0000.0000.0000.000
160R162LYS10.8860.94954.212-0.037-0.0370.0000.0000.0000.000
161R163LYS10.9380.98650.146-0.045-0.0450.0000.0000.0000.000
162R164VAL0-0.056-0.03754.482-0.002-0.0020.0000.0000.0000.000
163R165LYS10.9320.96354.571-0.035-0.0350.0000.0000.0000.000
164R166HIS00.0420.03356.5330.0000.0000.0000.0000.0000.000
165R167GLU-1-0.714-0.77953.3250.0390.0390.0000.0000.0000.000
166R168GLN00.0360.01255.6930.0010.0010.0000.0000.0000.000
167R169PHE0-0.0210.00955.415-0.001-0.0010.0000.0000.0000.000
168R170SER00.0500.01159.8280.0000.0000.0000.0000.0000.000
169R171LEU0-0.066-0.03358.1030.0000.0000.0000.0000.0000.000
170R172LEU00.0560.03362.6740.0000.0000.0000.0000.0000.000
171R173THR00.0420.01764.9740.0010.0010.0000.0000.0000.000
172R174SER0-0.006-0.01066.498-0.001-0.0010.0000.0000.0000.000
173R175GLY0-0.014-0.00567.934-0.001-0.0010.0000.0000.0000.000
174R176GLU-1-0.961-0.98667.1450.0310.0310.0000.0000.0000.000
175R177VAL0-0.072-0.02261.8370.0010.0010.0000.0000.0000.000
176R178GLY00.0480.02263.856-0.001-0.0010.0000.0000.0000.000
177R179GLU-1-0.886-0.97357.3760.0410.0410.0000.0000.0000.000
178R180PHE0-0.045-0.03658.3500.0000.0000.0000.0000.0000.000
179R181CYS00.0230.01552.5000.0000.0000.0000.0000.0000.000
180R182VAL0-0.044-0.03952.8630.0000.0000.0000.0000.0000.000
181R183GLN0-0.037-0.02946.1140.0010.0010.0000.0000.0000.000
182R184VAL00.016-0.01848.480-0.002-0.0020.0000.0000.0000.000
183R185LYS10.9610.99143.096-0.059-0.0590.0000.0000.0000.000
184R186PRO00.0020.01244.976-0.002-0.0020.0000.0000.0000.000
185R187SER00.004-0.01645.3910.0030.0030.0000.0000.0000.000
186R188VAL00.0390.01046.415-0.002-0.0020.0000.0000.0000.000
187R189ALA0-0.0070.00647.4310.0010.0010.0000.0000.0000.000
188R190SER0-0.039-0.01148.6380.0010.0010.0000.0000.0000.000
189R191ARG10.9210.96342.628-0.046-0.0460.0000.0000.0000.000
190R192SER00.0360.01241.015-0.001-0.0010.0000.0000.0000.000
191R193ASN0-0.058-0.03639.7910.0010.0010.0000.0000.0000.000
192R194LYS10.9490.99735.367-0.093-0.0930.0000.0000.0000.000
193R195GLY00.017-0.00540.020-0.002-0.0020.0000.0000.0000.000
194R196MET0-0.066-0.04536.8210.0030.0030.0000.0000.0000.000
195R197TRP0-0.021-0.01141.389-0.004-0.0040.0000.0000.0000.000
196R198SER00.0280.03943.1670.0020.0020.0000.0000.0000.000
197R199LYS10.9800.99144.862-0.055-0.0550.0000.0000.0000.000
198R200GLU-1-0.857-0.92146.2260.0530.0530.0000.0000.0000.000
199R201GLU-1-0.946-0.95649.3360.0450.0450.0000.0000.0000.000
200R203ILE0-0.0250.03055.701-0.001-0.0010.0000.0000.0000.000