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: 4J23N

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 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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2163847.05601
FMO2-HF: Nuclear repulsion 2083232.196198
FMO2-HF: Total energy -80614.859811
FMO2-MP2: Total energy -80851.060401


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.
0.3692.2090.003-0.889-0.9530.003
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 : 0.037 / 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].
3R4GLU-1-0.863-0.9133.821-1.1510.347-0.001-0.769-0.7280.003
4R5LEU0-0.066-0.0143.783-1.051-0.8850.006-0.091-0.0820.000
5R6PRO00.031-0.0024.7200.2000.261-0.001-0.003-0.0560.000
6R7SER00.0350.0207.382-0.096-0.0960.0000.0000.0000.000
7R8PRO00.014-0.00111.2030.1130.1130.0000.0000.0000.000
8R9PRO0-0.0270.01212.915-0.021-0.0210.0000.0000.0000.000
9R10SER0-0.0070.00814.911-0.010-0.0100.0000.0000.0000.000
10R11VAL00.0280.00418.416-0.009-0.0090.0000.0000.0000.000
11R12TRP0-0.102-0.05820.6190.0020.0020.0000.0000.0000.000
12R13PHE00.0420.01024.781-0.010-0.0100.0000.0000.0000.000
13R14GLU-1-0.862-0.91527.9600.0730.0730.0000.0000.0000.000
14R15ALA0-0.0150.00230.449-0.005-0.0050.0000.0000.0000.000
15R16GLU-1-0.787-0.86833.4480.0300.0300.0000.0000.0000.000
16R17PHE00.011-0.01637.006-0.004-0.0040.0000.0000.0000.000
17R18PHE0-0.037-0.02638.052-0.001-0.0010.0000.0000.0000.000
18R19HIS0-0.031-0.00834.2700.0010.0010.0000.0000.0000.000
19R20HIS00.0330.01432.4520.0100.0100.0000.0000.0000.000
20R21ILE00.0160.01727.755-0.009-0.0090.0000.0000.0000.000
21R22LEU0-0.040-0.00422.9420.0050.0050.0000.0000.0000.000
22R23HIS00.010-0.01523.558-0.009-0.0090.0000.0000.0000.000
23R24TRP0-0.040-0.02317.098-0.016-0.0160.0000.0000.0000.000
24R25THR00.0060.00316.7970.0120.0120.0000.0000.0000.000
25R26PRO00.0130.00314.641-0.032-0.0320.0000.0000.0000.000
26R27ILE0-0.015-0.0038.4610.0600.0600.0000.0000.0000.000
27R28PRO0-0.008-0.0137.9380.0030.0030.0000.0000.0000.000
28R29GLN0-0.020-0.0277.064-0.145-0.1450.0000.0000.0000.000
29R30GLN0-0.0110.0248.441-0.103-0.1030.0000.0000.0000.000
30R31SER00.0080.0269.3790.0660.0660.0000.0000.0000.000
31R32GLU-1-0.905-0.96411.033-0.053-0.0530.0000.0000.0000.000
32R33SER0-0.048-0.04311.4120.0230.0230.0000.0000.0000.000
33R34THR0-0.059-0.03210.588-0.081-0.0810.0000.0000.0000.000
34R35CYS0-0.095-0.04312.8600.0350.0350.0000.0000.0000.000
35R36TYR00.001-0.02113.699-0.044-0.0440.0000.0000.0000.000
36R37GLU-1-0.778-0.84316.992-0.292-0.2920.0000.0000.0000.000
37R38VAL0-0.002-0.00418.9270.0140.0140.0000.0000.0000.000
38R39ALA0-0.005-0.00821.760-0.007-0.0070.0000.0000.0000.000
39R40LEU0-0.009-0.01023.7910.0160.0160.0000.0000.0000.000
40R41LEU00.0030.00926.934-0.010-0.0100.0000.0000.0000.000
41R42ARG10.8980.93128.9150.0560.0560.0000.0000.0000.000
42R43TYR0-0.008-0.02631.556-0.002-0.0020.0000.0000.0000.000
43R44GLY0-0.009-0.01633.6060.0050.0050.0000.0000.0000.000
44R45ILE00.0200.01833.8210.0000.0000.0000.0000.0000.000
45R46GLU-1-0.925-0.94430.859-0.076-0.0760.0000.0000.0000.000
46R47SER0-0.045-0.03629.344-0.009-0.0090.0000.0000.0000.000
47R48TRP0-0.042-0.02524.3630.0030.0030.0000.0000.0000.000
48R49ASN0-0.031-0.00726.968-0.011-0.0110.0000.0000.0000.000
49R50SER0-0.020-0.03122.3150.0140.0140.0000.0000.0000.000
50R51ILE0-0.043-0.02324.8370.0080.0080.0000.0000.0000.000
51R52SER00.0300.00923.6250.0030.0030.0000.0000.0000.000
52R53GLN00.0180.00021.3920.0110.0110.0000.0000.0000.000
53R55SER00.0140.00219.6240.0210.0210.0000.0000.0000.000
54R56GLN0-0.015-0.00617.4630.0010.0010.0000.0000.0000.000
55R57THR0-0.040-0.01919.6060.0170.0170.0000.0000.0000.000
56R58LEU00.0300.00417.8640.0000.0000.0000.0000.0000.000
57R59SER00.0620.03020.8700.0120.0120.0000.0000.0000.000
58R60TYR0-0.060-0.02723.980-0.013-0.0130.0000.0000.0000.000
59R61ASP-1-0.785-0.86126.133-0.017-0.0170.0000.0000.0000.000
60R62LEU00.0330.01226.342-0.011-0.0110.0000.0000.0000.000
61R63THR0-0.042-0.02430.481-0.001-0.0010.0000.0000.0000.000
62R64ALA0-0.001-0.01033.935-0.001-0.0010.0000.0000.0000.000
63R65VAL0-0.027-0.00730.250-0.003-0.0030.0000.0000.0000.000
64R66THR0-0.035-0.03631.5100.0010.0010.0000.0000.0000.000
65R67LEU00.0190.01634.6030.0060.0060.0000.0000.0000.000
66R68ASP-1-0.789-0.88738.042-0.038-0.0380.0000.0000.0000.000
67R69LEU0-0.0740.00234.4290.0010.0010.0000.0000.0000.000
68R70TYR0-0.014-0.04537.7640.0050.0050.0000.0000.0000.000
69R71HIS0-0.049-0.01841.1510.0020.0020.0000.0000.0000.000
70R72SER0-0.060-0.05238.178-0.004-0.0040.0000.0000.0000.000
71R73ASN0-0.018-0.01037.2940.0060.0060.0000.0000.0000.000
72R74GLY00.0250.01834.8050.0030.0030.0000.0000.0000.000
73R75TYR00.004-0.01130.220-0.008-0.0080.0000.0000.0000.000
74R76ARG10.8130.90926.3170.0250.0250.0000.0000.0000.000
75R77ALA00.0410.02425.229-0.010-0.0100.0000.0000.0000.000
76R78ARG10.8380.94020.1370.1880.1880.0000.0000.0000.000
77R79VAL00.0270.02317.060-0.009-0.0090.0000.0000.0000.000
78R80ARG10.8080.90314.0650.4620.4620.0000.0000.0000.000
79R81ALA00.0470.03410.8820.0310.0310.0000.0000.0000.000
80R82VAL00.000-0.02212.627-0.112-0.1120.0000.0000.0000.000
81R83ASP-1-0.729-0.8438.360-0.999-0.9990.0000.0000.0000.000
82R84GLY00.0210.01410.778-0.194-0.1940.0000.0000.0000.000
83R85SER0-0.032-0.02012.9080.0130.0130.0000.0000.0000.000
84R86ARG10.8420.9293.5353.3173.432-0.001-0.026-0.0870.000
85R87HIS00.0430.00010.7620.1550.1550.0000.0000.0000.000
86R88SER0-0.0030.0139.687-0.141-0.1410.0000.0000.0000.000
87R89GLN0-0.028-0.03110.2790.1640.1640.0000.0000.0000.000
88R90TRP00.0260.00312.7290.0350.0350.0000.0000.0000.000
89R91THR0-0.011-0.01115.1100.0060.0060.0000.0000.0000.000
90R92VAL0-0.005-0.01817.262-0.013-0.0130.0000.0000.0000.000
91R93THR00.0210.01421.1100.0150.0150.0000.0000.0000.000
92R94ASN00.0070.00222.626-0.010-0.0100.0000.0000.0000.000
93R95THR0-0.040-0.03524.910-0.003-0.0030.0000.0000.0000.000
94R96ARG10.8530.92827.9590.0030.0030.0000.0000.0000.000
95R97PHE00.0620.05129.6360.0020.0020.0000.0000.0000.000
96R98SER00.035-0.00831.444-0.006-0.0060.0000.0000.0000.000
97R99VAL00.0640.03235.2850.0040.0040.0000.0000.0000.000
98R100ASP-1-0.836-0.88737.1070.0080.0080.0000.0000.0000.000
99R101GLU-1-0.852-0.90831.1620.0180.0180.0000.0000.0000.000
100R102VAL0-0.075-0.01034.4480.0030.0030.0000.0000.0000.000
101R103THR0-0.042-0.02735.6850.0040.0040.0000.0000.0000.000
102R104LEU0-0.0030.01237.904-0.003-0.0030.0000.0000.0000.000
103R105THR00.010-0.01939.8700.0030.0030.0000.0000.0000.000
104R106VAL0-0.008-0.01242.878-0.002-0.0020.0000.0000.0000.000
105R107GLY0-0.0010.00245.1770.0010.0010.0000.0000.0000.000
106R108SER0-0.051-0.02546.5200.0000.0000.0000.0000.0000.000
107R109VAL0-0.0040.00549.0390.0000.0000.0000.0000.0000.000
108R110ASN0-0.0100.00052.028-0.002-0.0020.0000.0000.0000.000
109R111LEU00.0050.00355.0660.0000.0000.0000.0000.0000.000
110R112GLU-1-0.769-0.85758.2720.0080.0080.0000.0000.0000.000
111R113ILE00.0340.01662.0460.0010.0010.0000.0000.0000.000
112R114HIS0-0.032-0.03264.522-0.001-0.0010.0000.0000.0000.000
113R115ASN0-0.041-0.02667.7760.0000.0000.0000.0000.0000.000
114R116GLY00.0470.02769.5480.0000.0000.0000.0000.0000.000
115R117PHE0-0.076-0.04465.0880.0010.0010.0000.0000.0000.000
116R118ILE00.0530.04559.492-0.001-0.0010.0000.0000.0000.000
117R119LEU0-0.043-0.02961.6710.0000.0000.0000.0000.0000.000
118R120GLY00.0220.00557.6480.0000.0000.0000.0000.0000.000
119R121LYS10.7910.87356.498-0.009-0.0090.0000.0000.0000.000
120R122ILE00.0170.00350.5300.0010.0010.0000.0000.0000.000
121R123GLN0-0.034-0.00751.056-0.002-0.0020.0000.0000.0000.000
122R124LEU00.0320.01247.9250.0010.0010.0000.0000.0000.000
123R125PRO0-0.0290.00343.942-0.001-0.0010.0000.0000.0000.000
124R126ARG10.8180.87946.072-0.001-0.0010.0000.0000.0000.000
125R127PRO00.0340.03741.193-0.001-0.0010.0000.0000.0000.000
126R128LYS10.9840.97039.3690.0160.0160.0000.0000.0000.000
127R129MET0-0.058-0.03035.949-0.004-0.0040.0000.0000.0000.000
128R130ALA00.0160.02941.353-0.003-0.0030.0000.0000.0000.000
129R131PRO0-0.0010.00442.3190.0000.0000.0000.0000.0000.000
130R132ALA00.0040.00845.4780.0020.0020.0000.0000.0000.000
131R133GLN00.0010.00047.9160.0020.0020.0000.0000.0000.000
132R134ASP-1-0.839-0.91244.383-0.018-0.0180.0000.0000.0000.000
133R135THR00.001-0.02445.8380.0010.0010.0000.0000.0000.000
134R136TYR00.0380.00843.8910.0000.0000.0000.0000.0000.000
135R137GLU-1-0.773-0.88247.2980.0010.0010.0000.0000.0000.000
136R138SER0-0.077-0.02448.9230.0000.0000.0000.0000.0000.000
137R139ILE0-0.017-0.00243.4890.0000.0000.0000.0000.0000.000
138R140PHE0-0.033-0.01342.0260.0010.0010.0000.0000.0000.000
139R141SER00.0470.02448.1830.0010.0010.0000.0000.0000.000
140R142HIS0-0.0070.00051.2780.0010.0010.0000.0000.0000.000
141R143PHE00.000-0.01650.5680.0010.0010.0000.0000.0000.000
142R144ARG10.7940.88749.370-0.004-0.0040.0000.0000.0000.000
143R145GLU-1-0.822-0.89649.7830.0190.0190.0000.0000.0000.000
144R146TYR0-0.022-0.04348.9050.0010.0010.0000.0000.0000.000
145R147GLU-1-0.845-0.90947.9530.0300.0300.0000.0000.0000.000
146R148ILE0-0.023-0.01549.966-0.001-0.0010.0000.0000.0000.000
147R149ALA00.0140.02049.7280.0010.0010.0000.0000.0000.000
148R150ILE0-0.020-0.02351.698-0.001-0.0010.0000.0000.0000.000
149R151ARG10.8450.91851.237-0.035-0.0350.0000.0000.0000.000
150R152LYS10.8240.89954.854-0.028-0.0280.0000.0000.0000.000
151R153VAL00.0030.00955.3890.0020.0020.0000.0000.0000.000
152R154PRO00.040-0.00558.244-0.001-0.0010.0000.0000.0000.000
153R155GLY0-0.0070.00357.609-0.001-0.0010.0000.0000.0000.000
154R156GLN00.0080.01054.1860.0020.0020.0000.0000.0000.000
155R157PHE00.0200.01446.136-0.001-0.0010.0000.0000.0000.000
156R158THR0-0.034-0.02150.4520.0020.0020.0000.0000.0000.000
157R159PHE00.013-0.00448.846-0.002-0.0020.0000.0000.0000.000
158R160THR0-0.030-0.00752.9990.0010.0010.0000.0000.0000.000
159R161HIS00.0330.00349.342-0.001-0.0010.0000.0000.0000.000
160R162LYS10.8940.95753.719-0.020-0.0200.0000.0000.0000.000
161R163LYS10.8690.95149.261-0.025-0.0250.0000.0000.0000.000
162R164VAL0-0.040-0.03053.943-0.001-0.0010.0000.0000.0000.000
163R165LYS10.8100.87853.956-0.017-0.0170.0000.0000.0000.000
164R166HIS00.0670.04455.693-0.002-0.0020.0000.0000.0000.000
165R167GLU-1-0.726-0.79652.6920.0100.0100.0000.0000.0000.000
166R168GLN0-0.009-0.00754.9820.0000.0000.0000.0000.0000.000
167R169PHE0-0.0080.00654.6570.0000.0000.0000.0000.0000.000
168R170SER00.0310.02059.3500.0000.0000.0000.0000.0000.000
169R171LEU0-0.028-0.01957.6690.0010.0010.0000.0000.0000.000
170R172LEU00.0330.02262.323-0.001-0.0010.0000.0000.0000.000
171R173THR00.0150.00064.6120.0010.0010.0000.0000.0000.000
172R174SER00.005-0.00365.928-0.001-0.0010.0000.0000.0000.000
173R175GLY0-0.0040.01267.7780.0000.0000.0000.0000.0000.000
174R176GLU-1-0.850-0.92265.2670.0250.0250.0000.0000.0000.000
175R177VAL0-0.045-0.00961.3130.0010.0010.0000.0000.0000.000
176R178GLY00.0120.01063.749-0.001-0.0010.0000.0000.0000.000
177R179GLU-1-0.819-0.88957.3990.0230.0230.0000.0000.0000.000
178R180PHE0-0.023-0.01858.1610.0010.0010.0000.0000.0000.000
179R181CYS00.0010.01151.9520.0010.0010.0000.0000.0000.000
180R182VAL0-0.030-0.02852.5220.0010.0010.0000.0000.0000.000
181R183GLN0-0.017-0.01244.8960.0010.0010.0000.0000.0000.000
182R184VAL00.009-0.00748.1950.0000.0000.0000.0000.0000.000
183R185LYS10.9320.96943.560-0.034-0.0340.0000.0000.0000.000
184R186PRO0-0.0280.01144.050-0.001-0.0010.0000.0000.0000.000
185R187SER0-0.029-0.03844.9330.0030.0030.0000.0000.0000.000
186R188VAL00.0560.01245.729-0.002-0.0020.0000.0000.0000.000
187R189ALA0-0.0180.00246.8130.0010.0010.0000.0000.0000.000
188R190SER0-0.031-0.00948.3240.0010.0010.0000.0000.0000.000
189R191ARG10.8410.87941.089-0.006-0.0060.0000.0000.0000.000
190R192SER00.0160.01339.4560.0010.0010.0000.0000.0000.000
191R193ASN0-0.064-0.03739.1250.0030.0030.0000.0000.0000.000
192R194LYS10.9310.95734.169-0.041-0.0410.0000.0000.0000.000
193R195GLY00.0280.01639.326-0.004-0.0040.0000.0000.0000.000
194R196MET0-0.043-0.02135.9220.0060.0060.0000.0000.0000.000
195R197TRP0-0.037-0.03240.900-0.004-0.0040.0000.0000.0000.000
196R198SER0-0.005-0.00842.5870.0000.0000.0000.0000.0000.000
197R199LYS10.8740.92244.407-0.018-0.0180.0000.0000.0000.000
198R200GLU-1-0.822-0.88545.3960.0340.0340.0000.0000.0000.000
199R201GLU-1-0.836-0.90048.6580.0170.0170.0000.0000.0000.000
200R203ILE0-0.062-0.04655.239-0.002-0.0020.0000.0000.0000.000