FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: Q5JQY

Calculation Name: 6GYB-L-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6GYB

Chain ID: L

ChEMBL ID:

UniProt ID: Q8PJB3

Base Structure: ElectronMicroscopy

Registration Date: 2025-10-06

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 218
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1867429.776213
FMO2-HF: Nuclear repulsion 1785592.915768
FMO2-HF: Total energy -81836.860444
FMO2-MP2: Total energy -82076.683088


3D Structure Molmil
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(L:150:PRO)


Summations of interaction energy for fragment #1(L:150: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.
-13.525-7.4341.674-2.848-4.914-0.023
Interaction energy analysis for fragmet #1(L:150:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.882 / q_NPA : 0.926
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].
3L152LEU00.0290.0012.828-6.890-4.4830.266-1.308-1.364-0.008
5L154GLU-1-0.870-0.9492.660-40.964-40.3340.700-0.396-0.933-0.003
6L155ARG10.9050.9532.59237.73740.0740.638-0.981-1.994-0.010
7L156ARG10.9470.9723.42129.95530.1390.048-0.023-0.208-0.001
9L158LEU0-0.008-0.0053.200-1.155-0.6220.022-0.140-0.415-0.001
4L153LEU00.0080.0125.6011.9231.9230.0000.0000.0000.000
8L157ILE00.0500.0286.6361.9531.9530.0000.0000.0000.000
10L159ALA0-0.075-0.0416.4591.4281.4280.0000.0000.0000.000
11L160GLU-1-1.005-0.9947.995-20.291-20.2910.0000.0000.0000.000
12L161SER-1-0.982-0.96610.185-22.424-22.4240.0000.0000.0000.000
13L183GLY10.8440.91549.0136.3746.3740.0000.0000.0000.000
14L184PRO00.1160.06548.491-0.123-0.1230.0000.0000.0000.000
15L185VAL00.0230.00844.4440.0090.0090.0000.0000.0000.000
16L186THR00.0020.00047.6120.1100.1100.0000.0000.0000.000
17L187LEU0-0.004-0.00845.198-0.119-0.1190.0000.0000.0000.000
18L188ALA00.0120.00748.0100.1390.1390.0000.0000.0000.000
19L189LYS10.9540.98146.9876.2436.2430.0000.0000.0000.000
20L190PRO00.0360.01946.7350.1390.1390.0000.0000.0000.000
21L191ILE0-0.001-0.00249.537-0.064-0.0640.0000.0000.0000.000
22L192SER00.0160.00449.062-0.051-0.0510.0000.0000.0000.000
23L193ASN0-0.014-0.01749.6150.0620.0620.0000.0000.0000.000
24L194PRO00.0230.01352.7650.0880.0880.0000.0000.0000.000
25L195ASP-1-0.782-0.87355.887-5.450-5.4500.0000.0000.0000.000
26L196GLY00.0280.00256.6250.1010.1010.0000.0000.0000.000
27L197LEU0-0.0240.00954.510-0.007-0.0070.0000.0000.0000.000
28L198LEU00.0360.01657.7420.0880.0880.0000.0000.0000.000
29L199VAL0-0.029-0.01157.996-0.049-0.0490.0000.0000.0000.000
30L200ARG10.9210.94858.3295.4445.4440.0000.0000.0000.000
31L201GLY0-0.023-0.01960.709-0.009-0.0090.0000.0000.0000.000
32L202THR0-0.042-0.01263.5990.0800.0800.0000.0000.0000.000
33L203TYR0-0.024-0.02265.8480.0070.0070.0000.0000.0000.000
34L204ILE00.0100.00465.9060.0360.0360.0000.0000.0000.000
35L205ARG10.8550.91470.2624.2484.2480.0000.0000.0000.000
36L206CYS0-0.048-0.02374.0170.0400.0400.0000.0000.0000.000
37L207ILE00.0310.01475.9040.0360.0360.0000.0000.0000.000
38L208LEU0-0.050-0.02778.059-0.042-0.0420.0000.0000.0000.000
39L209GLU-1-0.845-0.90878.417-4.032-4.0320.0000.0000.0000.000
40L210THR0-0.008-0.01778.2190.0330.0330.0000.0000.0000.000
41L211ARG10.9530.97380.6433.6503.6500.0000.0000.0000.000
42L212ILE00.0140.02377.502-0.003-0.0030.0000.0000.0000.000
43L213ILE0-0.011-0.01981.2970.0600.0600.0000.0000.0000.000
44L214SER0-0.0370.00180.198-0.058-0.0580.0000.0000.0000.000
45L215ASP-1-0.896-0.94581.358-3.759-3.7590.0000.0000.0000.000
46L216PHE0-0.017-0.03279.256-0.021-0.0210.0000.0000.0000.000
47L217GLY0-0.0060.01875.736-0.049-0.0490.0000.0000.0000.000
48L218GLY0-0.002-0.00574.7960.0260.0260.0000.0000.0000.000
49L219TYR0-0.002-0.00169.516-0.019-0.0190.0000.0000.0000.000
50L220THR0-0.028-0.01973.6220.0580.0580.0000.0000.0000.000
51L221SER0-0.019-0.02673.924-0.063-0.0630.0000.0000.0000.000
52L223ILE00.0230.03074.689-0.066-0.0660.0000.0000.0000.000
53L224VAL0-0.017-0.00871.1140.0320.0320.0000.0000.0000.000
54L225THR0-0.011-0.01274.5640.0640.0640.0000.0000.0000.000
55L226GLU-1-0.883-0.92573.855-4.193-4.1930.0000.0000.0000.000
56L227PRO0-0.060-0.02070.835-0.033-0.0330.0000.0000.0000.000
57L228VAL00.0180.01466.2050.0060.0060.0000.0000.0000.000
58L229TYR00.0370.00765.708-0.031-0.0310.0000.0000.0000.000
59L230SER0-0.005-0.01359.565-0.032-0.0320.0000.0000.0000.000
60L231ILE0-0.047-0.01657.8920.0680.0680.0000.0000.0000.000
61L232ASN0-0.004-0.01558.6580.0880.0880.0000.0000.0000.000
62L233GLY0-0.008-0.00562.0780.0390.0390.0000.0000.0000.000
63L234HIS0-0.089-0.04859.2450.1140.1140.0000.0000.0000.000
64L235ASN0-0.004-0.00359.9410.0620.0620.0000.0000.0000.000
65L236LEU0-0.046-0.02263.4910.0290.0290.0000.0000.0000.000
66L237LEU0-0.0190.00360.954-0.045-0.0450.0000.0000.0000.000
67L238LEU00.0030.00064.2680.0010.0010.0000.0000.0000.000
68L239PRO00.0270.00467.3110.0700.0700.0000.0000.0000.000
69L240LYS10.9690.98570.3594.1324.1320.0000.0000.0000.000
70L241GLY00.0250.02473.8870.0260.0260.0000.0000.0000.000
71L242SER0-0.003-0.01670.039-0.019-0.0190.0000.0000.0000.000
72L243LYS10.8580.93171.6404.2944.2940.0000.0000.0000.000
73L244MET0-0.0010.00568.276-0.070-0.0700.0000.0000.0000.000
74L245LEU0-0.005-0.01569.2720.0830.0830.0000.0000.0000.000
75L246GLY00.0610.02169.298-0.070-0.0700.0000.0000.0000.000
76L247GLN0-0.054-0.00966.7540.0970.0970.0000.0000.0000.000
77L248TYR0-0.029-0.03271.128-0.036-0.0360.0000.0000.0000.000
78L249SER00.0070.00371.819-0.008-0.0080.0000.0000.0000.000
79L250ALA00.0100.01773.7620.0410.0410.0000.0000.0000.000
80L251GLY00.021-0.00675.719-0.066-0.0660.0000.0000.0000.000
81L252GLU-1-0.815-0.90678.032-3.764-3.7640.0000.0000.0000.000
82L253PRO0-0.035-0.00179.957-0.043-0.0430.0000.0000.0000.000
83L254THR0-0.025-0.02778.9940.0400.0400.0000.0000.0000.000
84L255SER00.0050.01478.8030.0500.0500.0000.0000.0000.000
85L256HIS00.000-0.00980.951-0.006-0.0060.0000.0000.0000.000
86L257ARG10.8100.87177.2924.1054.1050.0000.0000.0000.000
87L258LEU00.0080.01475.715-0.011-0.0110.0000.0000.0000.000
88L259GLN0-0.026-0.02069.967-0.054-0.0540.0000.0000.0000.000
89L260VAL0-0.0080.01071.698-0.008-0.0080.0000.0000.0000.000
90L261VAL0-0.028-0.01465.402-0.040-0.0400.0000.0000.0000.000
91L262TRP0-0.022-0.03168.3790.0420.0420.0000.0000.0000.000
92L263ASP-1-0.875-0.94264.146-4.854-4.8540.0000.0000.0000.000
93L264ARG10.8200.87563.8994.7854.7850.0000.0000.0000.000
94L265VAL0-0.017-0.01265.4410.0930.0930.0000.0000.0000.000
95L266THR00.0160.02065.890-0.061-0.0610.0000.0000.0000.000
96L267THR0-0.018-0.02466.3520.0820.0820.0000.0000.0000.000
97L268PRO00.017-0.00668.901-0.010-0.0100.0000.0000.0000.000
98L269THR0-0.019-0.00366.2050.0290.0290.0000.0000.0000.000
99L270GLY00.0130.02766.094-0.054-0.0540.0000.0000.0000.000
100L271LEU0-0.017-0.00861.266-0.098-0.0980.0000.0000.0000.000
101L272ASP-1-0.778-0.86162.670-4.867-4.8670.0000.0000.0000.000
102L273VAL0-0.0130.00560.828-0.108-0.1080.0000.0000.0000.000
103L274THR00.0220.00358.4420.0840.0840.0000.0000.0000.000
104L275LEU0-0.0240.00560.119-0.092-0.0920.0000.0000.0000.000
105L276MET00.0230.00759.5370.0010.0010.0000.0000.0000.000
106L277GLY00.0560.02162.323-0.024-0.0240.0000.0000.0000.000
107L278PRO0-0.028-0.00564.9410.0630.0630.0000.0000.0000.000
108L279GLY00.0300.00967.8720.0130.0130.0000.0000.0000.000
109L280ILE0-0.077-0.02670.5190.0080.0080.0000.0000.0000.000
110L281ASP-1-0.766-0.88873.313-4.012-4.0120.0000.0000.0000.000
111L282THR0-0.020-0.01175.325-0.058-0.0580.0000.0000.0000.000
112L283LEU0-0.024-0.01576.710-0.014-0.0140.0000.0000.0000.000
113L284GLY00.0080.00472.907-0.026-0.0260.0000.0000.0000.000
114L285SER0-0.037-0.01072.414-0.040-0.0400.0000.0000.0000.000
115L286SER00.000-0.00570.6360.0050.0050.0000.0000.0000.000
116L287GLY00.0500.03672.7990.0500.0500.0000.0000.0000.000
117L288HIS00.0020.01574.0350.0090.0090.0000.0000.0000.000
118L289PRO00.0320.01277.4850.0110.0110.0000.0000.0000.000
119L290GLY00.0110.00081.048-0.006-0.0060.0000.0000.0000.000
120L291ASN0-0.062-0.02383.7460.0350.0350.0000.0000.0000.000
121L292TYR00.0370.00985.1780.0160.0160.0000.0000.0000.000
122L293ASN0-0.030-0.01687.3610.0660.0660.0000.0000.0000.000
123L294ALA00.0600.04289.234-0.029-0.0290.0000.0000.0000.000
124L295HIS00.0200.00588.9450.0860.0860.0000.0000.0000.000
125L296TRP00.044-0.01092.3450.0310.0310.0000.0000.0000.000
126L297GLY00.0230.02596.2900.0330.0330.0000.0000.0000.000
127L298ASN0-0.014-0.01895.513-0.006-0.0060.0000.0000.0000.000
128L299LYS10.8800.96089.9143.5643.5640.0000.0000.0000.000
129L300ILE00.0200.02596.8870.0130.0130.0000.0000.0000.000
130L301ALA0-0.004-0.001100.4640.0240.0240.0000.0000.0000.000
131L302SER0-0.046-0.04298.5440.0240.0240.0000.0000.0000.000
132L303ALA00.0150.01299.8220.0070.0070.0000.0000.0000.000
133L304LEU0-0.0060.003101.7910.0260.0260.0000.0000.0000.000
134L305PHE00.015-0.005105.0460.0260.0260.0000.0000.0000.000
135L306ILE00.0270.018103.2640.0290.0290.0000.0000.0000.000
136L307SER00.0490.024105.0290.0120.0120.0000.0000.0000.000
137L308LEU0-0.0210.007106.9580.0220.0220.0000.0000.0000.000
138L309LEU0-0.011-0.006109.8660.0280.0280.0000.0000.0000.000
139L310SER0-0.069-0.051108.7200.0180.0180.0000.0000.0000.000
140L311ASP-1-0.893-0.954110.775-2.851-2.8510.0000.0000.0000.000
141L312ALA0-0.011-0.001112.6470.0290.0290.0000.0000.0000.000
142L313PHE0-0.028-0.034112.8160.0260.0260.0000.0000.0000.000
143L314LYS10.9550.990110.3392.9202.9200.0000.0000.0000.000
144L315TYR00.000-0.002115.6170.0140.0140.0000.0000.0000.000
145L316ALA0-0.011-0.015118.3410.0210.0210.0000.0000.0000.000
146L317ALA0-0.0190.004118.1580.0140.0140.0000.0000.0000.000
147L318ALA0-0.060-0.029118.4210.0080.0080.0000.0000.0000.000
148L319GLU-1-0.888-0.945120.351-2.575-2.5750.0000.0000.0000.000
149L320TYR0-0.042-0.030123.1910.0030.0030.0000.0000.0000.000
150L321GLY00.0300.036123.3650.0040.0040.0000.0000.0000.000
151L322PRO0-0.057-0.037124.2500.0130.0130.0000.0000.0000.000
152L323GLU-1-0.794-0.880125.648-2.559-2.5590.0000.0000.0000.000
153L324THR0-0.069-0.047126.823-0.003-0.0030.0000.0000.0000.000
154L325THR0-0.011-0.022120.747-0.011-0.0110.0000.0000.0000.000
155L326THR0-0.016-0.024122.442-0.031-0.0310.0000.0000.0000.000
156L327ILE0-0.024-0.005123.530-0.012-0.0120.0000.0000.0000.000
157L328GLY00.0200.020121.445-0.003-0.0030.0000.0000.0000.000
158L329VAL00.0140.002119.194-0.033-0.0330.0000.0000.0000.000
159L330GLY00.0070.007115.920-0.009-0.0090.0000.0000.0000.000
160L331SER0-0.125-0.067114.845-0.026-0.0260.0000.0000.0000.000
161L332GLY00.0070.006116.666-0.005-0.0050.0000.0000.0000.000
162L333ILE0-0.0020.014118.5720.0070.0070.0000.0000.0000.000
163L334VAL0-0.005-0.003112.753-0.019-0.0190.0000.0000.0000.000
164L335THR00.008-0.035115.1830.0060.0060.0000.0000.0000.000
165L336GLN0-0.041-0.001113.9210.0160.0160.0000.0000.0000.000
166L337GLN0-0.013-0.018117.1740.0180.0180.0000.0000.0000.000
167L338PRO0-0.0070.025115.6270.0190.0190.0000.0000.0000.000
168L339PHE00.0250.023118.215-0.009-0.0090.0000.0000.0000.000
169L340GLU-1-0.883-0.957112.080-2.888-2.8880.0000.0000.0000.000
170L341SER00.0590.044115.0870.0080.0080.0000.0000.0000.000
171L342ASN00.020-0.019112.415-0.049-0.0490.0000.0000.0000.000
172L343THR0-0.0290.003111.241-0.031-0.0310.0000.0000.0000.000
173L344ALA00.0410.027110.867-0.028-0.0280.0000.0000.0000.000
174L345ARG10.9290.978107.5722.9292.9290.0000.0000.0000.000
175L346SER0-0.026-0.032106.705-0.030-0.0300.0000.0000.0000.000
176L347MET0-0.0070.000105.869-0.027-0.0270.0000.0000.0000.000
177L348GLN0-0.009-0.010103.200-0.009-0.0090.0000.0000.0000.000
178L349GLN00.0350.015102.222-0.025-0.0250.0000.0000.0000.000
179L350LEU0-0.015-0.009101.065-0.039-0.0390.0000.0000.0000.000
180L351ALA00.0010.006101.171-0.028-0.0280.0000.0000.0000.000
181L352GLU-1-0.881-0.92998.777-3.227-3.2270.0000.0000.0000.000
182L353GLN00.000-0.00596.792-0.043-0.0430.0000.0000.0000.000
183L354ALA0-0.042-0.01196.390-0.041-0.0410.0000.0000.0000.000
184L355VAL0-0.008-0.01295.953-0.033-0.0330.0000.0000.0000.000
185L356GLU-1-0.870-0.92191.675-3.523-3.5230.0000.0000.0000.000
186L357LYS10.9130.94892.0823.3333.3330.0000.0000.0000.000
187L358SER0-0.001-0.01191.937-0.029-0.0290.0000.0000.0000.000
188L359GLY0-0.002-0.00491.836-0.016-0.0160.0000.0000.0000.000
189L360ARG10.8520.92087.1823.5433.5430.0000.0000.0000.000
190L361ARG10.8710.96087.1763.4913.4910.0000.0000.0000.000
191L362PRO00.0520.03984.1630.0330.0330.0000.0000.0000.000
192L363ALA0-0.066-0.03886.0030.0500.0500.0000.0000.0000.000
193L364THR00.0080.01084.756-0.032-0.0320.0000.0000.0000.000
194L365LEU0-0.0020.00080.9250.0250.0250.0000.0000.0000.000
195L366THR0-0.010-0.01183.704-0.031-0.0310.0000.0000.0000.000
196L367ILE00.0360.01979.3930.0100.0100.0000.0000.0000.000
197L368ASN00.008-0.00483.499-0.012-0.0120.0000.0000.0000.000
198L369GLN00.0580.02183.650-0.050-0.0500.0000.0000.0000.000
199L370GLY00.0210.01183.8690.0190.0190.0000.0000.0000.000
200L371THR0-0.058-0.01581.2680.0110.0110.0000.0000.0000.000
201L372VAL00.0170.00278.969-0.043-0.0430.0000.0000.0000.000
202L373LEU0-0.029-0.00576.1610.0100.0100.0000.0000.0000.000
203L374ASN00.025-0.00872.526-0.048-0.0480.0000.0000.0000.000
204L375VAL00.0270.02967.891-0.003-0.0030.0000.0000.0000.000
205L376TYR00.0170.03763.423-0.021-0.0210.0000.0000.0000.000
206L377VAL00.0150.01661.934-0.036-0.0360.0000.0000.0000.000
207L378ALA00.029-0.00461.954-0.042-0.0420.0000.0000.0000.000
208L379LYS10.8460.89655.7445.5085.5080.0000.0000.0000.000
209L380ASP-1-0.805-0.89355.233-5.567-5.5670.0000.0000.0000.000
210L381VAL0-0.030-0.01656.664-0.045-0.0450.0000.0000.0000.000
211L382ASP-1-0.815-0.87352.054-5.929-5.9290.0000.0000.0000.000
212L383PHE00.0290.00455.435-0.001-0.0010.0000.0000.0000.000
213L384SER0-0.015-0.02752.5950.0050.0050.0000.0000.0000.000
214L385ALA0-0.018-0.01452.309-0.025-0.0250.0000.0000.0000.000
215L386VAL0-0.052-0.02353.7290.0110.0110.0000.0000.0000.000
216L387LEU0-0.0180.00057.4990.0620.0620.0000.0000.0000.000
217L388PRO0-0.011-0.00457.270-0.099-0.0990.0000.0000.0000.000
218L389LYS0-0.067-0.02953.0550.2580.2580.0000.0000.0000.000