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: NLJJQ

Calculation Name: 3M6C-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3M6C

Chain ID: A

ChEMBL ID:

UniProt ID: P9WPE9

Base Structure: X-ray

Registration Date: 2025-10-05

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 194
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1990195.015622
FMO2-HF: Nuclear repulsion 1918981.079472
FMO2-HF: Total energy -71213.93615
FMO2-MP2: Total energy -71426.844533


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(A:184:GLU)


Summations of interaction energy for fragment #1(A:184:GLU)
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.
-8.822-4.3593.228-3.146-4.545-0.005
Interaction energy analysis for fragmet #1(A:184:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.083 / q_NPA : -0.035
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].
3A186GLU-1-0.905-0.9481.9161.5235.3723.199-2.939-4.109-0.001
4A187PHE0-0.060-0.0263.372-7.301-6.6870.029-0.207-0.436-0.004
5A188THR0-0.011-0.0036.1551.4021.4020.0000.0000.0000.000
6A189GLU-1-0.929-0.9759.560-1.019-1.0190.0000.0000.0000.000
7A190GLY00.0290.01612.7400.1060.1060.0000.0000.0000.000
8A191ILE0-0.048-0.01112.966-0.413-0.4130.0000.0000.0000.000
9A192GLY00.0450.02013.8770.3390.3390.0000.0000.0000.000
10A193PHE0-0.054-0.05915.086-0.360-0.3600.0000.0000.0000.000
11A194ASP-1-0.848-0.90816.970-1.517-1.5170.0000.0000.0000.000
12A195LYS10.8050.90419.6351.2121.2120.0000.0000.0000.000
13A196GLY00.0800.07922.965-0.033-0.0330.0000.0000.0000.000
14A197PHE0-0.063-0.03325.030-0.017-0.0170.0000.0000.0000.000
15A198LEU0-0.036-0.02028.4150.0250.0250.0000.0000.0000.000
16A199SER0-0.013-0.01731.2980.0470.0470.0000.0000.0000.000
17A200ALA00.0300.01632.780-0.007-0.0070.0000.0000.0000.000
18A201TYR0-0.046-0.02933.9110.0250.0250.0000.0000.0000.000
19A202PHE00.009-0.00131.6230.0030.0030.0000.0000.0000.000
20A203VAL0-0.0590.00030.354-0.014-0.0140.0000.0000.0000.000
21A204THR0-0.027-0.02730.1460.0070.0070.0000.0000.0000.000
22A205ASP-1-0.832-0.90829.059-0.083-0.0830.0000.0000.0000.000
23A206PHE0-0.005-0.01630.289-0.028-0.0280.0000.0000.0000.000
24A207ASP-1-0.942-0.95030.701-0.020-0.0200.0000.0000.0000.000
25A208ASN0-0.100-0.06625.5390.0420.0420.0000.0000.0000.000
26A209GLN0-0.067-0.03526.346-0.082-0.0820.0000.0000.0000.000
27A210GLN00.0430.01623.471-0.056-0.0560.0000.0000.0000.000
28A211ALA0-0.0170.00427.0010.0480.0480.0000.0000.0000.000
29A212VAL00.0180.02125.264-0.058-0.0580.0000.0000.0000.000
30A213LEU0-0.071-0.04526.0950.0600.0600.0000.0000.0000.000
31A214GLU-1-0.845-0.92925.744-0.355-0.3550.0000.0000.0000.000
32A215ASP-1-0.888-0.93626.766-0.493-0.4930.0000.0000.0000.000
33A216ALA0-0.0140.00426.5060.0290.0290.0000.0000.0000.000
34A217LEU00.0180.00327.618-0.052-0.0520.0000.0000.0000.000
35A218ILE0-0.010-0.01523.7720.0040.0040.0000.0000.0000.000
36A219LEU00.0090.01427.988-0.021-0.0210.0000.0000.0000.000
37A220LEU00.0010.01224.375-0.031-0.0310.0000.0000.0000.000
38A221HIS0-0.015-0.01528.2110.0500.0500.0000.0000.0000.000
39A222GLN00.0260.01527.592-0.073-0.0730.0000.0000.0000.000
40A223ASP-1-0.768-0.88330.382-0.793-0.7930.0000.0000.0000.000
41A224LYS10.8520.92332.6340.5970.5970.0000.0000.0000.000
42A225ILE00.0220.01833.1540.0330.0330.0000.0000.0000.000
43A226SER00.023-0.00336.4650.0210.0210.0000.0000.0000.000
44A227SER00.018-0.00239.7970.0340.0340.0000.0000.0000.000
45A228LEU00.0680.04041.800-0.015-0.0150.0000.0000.0000.000
46A229PRO00.004-0.01543.171-0.007-0.0070.0000.0000.0000.000
47A230ASP-1-0.859-0.92940.749-0.492-0.4920.0000.0000.0000.000
48A231LEU00.0440.02336.458-0.016-0.0160.0000.0000.0000.000
49A232LEU0-0.012-0.00439.958-0.008-0.0080.0000.0000.0000.000
50A233PRO00.0430.02042.1920.0040.0040.0000.0000.0000.000
51A234LEU00.0000.01434.8860.0030.0030.0000.0000.0000.000
52A235LEU0-0.005-0.01137.055-0.003-0.0030.0000.0000.0000.000
53A236GLU-1-0.930-0.96839.332-0.327-0.3270.0000.0000.0000.000
54A237LYS10.8590.92739.5840.4690.4690.0000.0000.0000.000
55A238VAL00.0390.01934.7570.0050.0050.0000.0000.0000.000
56A239ALA00.0010.01637.5660.0110.0110.0000.0000.0000.000
57A240GLY0-0.025-0.00539.7800.0200.0200.0000.0000.0000.000
58A241THR0-0.067-0.05636.3920.0050.0050.0000.0000.0000.000
59A242GLY0-0.035-0.01437.7530.0090.0090.0000.0000.0000.000
60A243LYS10.8200.90530.2580.5240.5240.0000.0000.0000.000
61A244PRO0-0.043-0.01430.1190.0000.0000.0000.0000.0000.000
62A245LEU0-0.004-0.00530.856-0.031-0.0310.0000.0000.0000.000
63A246LEU00.0060.00724.1050.0230.0230.0000.0000.0000.000
64A247ILE0-0.005-0.01128.452-0.009-0.0090.0000.0000.0000.000
65A248VAL00.0000.00424.1100.0000.0000.0000.0000.0000.000
66A249ALA00.0180.01827.365-0.007-0.0070.0000.0000.0000.000
67A250GLU-1-0.905-0.94828.435-0.858-0.8580.0000.0000.0000.000
68A251ASP-1-0.819-0.93730.177-0.653-0.6530.0000.0000.0000.000
69A252VAL0-0.0190.00231.7890.0060.0060.0000.0000.0000.000
70A253GLU-1-0.858-0.93234.306-0.504-0.5040.0000.0000.0000.000
71A254GLY00.0180.00037.6130.0050.0050.0000.0000.0000.000
72A255GLU-1-0.873-0.94641.187-0.320-0.3200.0000.0000.0000.000
73A256ALA0-0.031-0.00338.2970.0080.0080.0000.0000.0000.000
74A257LEU00.0110.01135.0770.0040.0040.0000.0000.0000.000
75A258ALA00.0220.02138.1710.0130.0130.0000.0000.0000.000
76A259THR0-0.011-0.01441.3370.0130.0130.0000.0000.0000.000
77A260LEU00.0220.02235.0710.0110.0110.0000.0000.0000.000
78A261VAL00.0160.00737.1830.0130.0130.0000.0000.0000.000
79A262VAL0-0.004-0.00438.7730.0190.0190.0000.0000.0000.000
80A263ASN0-0.032-0.02139.9330.0380.0380.0000.0000.0000.000
81A264ALA00.0380.04435.9480.0090.0090.0000.0000.0000.000
82A265ILE0-0.018-0.00837.7610.0210.0210.0000.0000.0000.000
83A266ARG10.8370.90540.2670.2720.2720.0000.0000.0000.000
84A267LYS10.9270.96835.8620.2440.2440.0000.0000.0000.000
85A268THR0-0.022-0.02039.8370.0000.0000.0000.0000.0000.000
86A269LEU00.0180.00435.808-0.007-0.0070.0000.0000.0000.000
87A270LYS10.8450.93230.5730.3450.3450.0000.0000.0000.000
88A271ALA00.0330.01732.546-0.026-0.0260.0000.0000.0000.000
89A272VAL0-0.011-0.00528.1180.0350.0350.0000.0000.0000.000
90A273ALA00.0110.01729.913-0.043-0.0430.0000.0000.0000.000
91A274VAL00.0100.00124.2090.0350.0350.0000.0000.0000.000
92A275LYS10.8340.92026.6800.7020.7020.0000.0000.0000.000
93A276GLY00.0700.03124.384-0.072-0.0720.0000.0000.0000.000
94A277PRO0-0.047-0.01619.8920.0750.0750.0000.0000.0000.000
95A278TYR0-0.018-0.02515.4760.0800.0800.0000.0000.0000.000
96A279PHE00.0550.01322.3480.1150.1150.0000.0000.0000.000
97A280GLY00.0260.01024.202-0.101-0.1010.0000.0000.0000.000
98A281ASP-1-0.807-0.89724.513-1.229-1.2290.0000.0000.0000.000
99A282ARG10.8190.89715.2632.6152.6150.0000.0000.0000.000
100A283ARG10.7650.87921.0950.9260.9260.0000.0000.0000.000
101A284LYS10.8920.93723.6241.1241.1240.0000.0000.0000.000
102A285ALA00.0410.01220.478-0.016-0.0160.0000.0000.0000.000
103A286PHE00.0330.01115.601-0.129-0.1290.0000.0000.0000.000
104A287LEU00.0070.00920.062-0.008-0.0080.0000.0000.0000.000
105A288GLU-1-0.820-0.90422.086-1.589-1.5890.0000.0000.0000.000
106A289ASP-1-0.789-0.85516.912-2.797-2.7970.0000.0000.0000.000
107A290LEU00.0210.00918.927-0.023-0.0230.0000.0000.0000.000
108A291ALA0-0.0280.00720.5550.0820.0820.0000.0000.0000.000
109A292VAL0-0.026-0.01518.4840.0580.0580.0000.0000.0000.000
110A293VAL0-0.018-0.01415.9940.0580.0580.0000.0000.0000.000
111A294THR0-0.041-0.04219.2650.1480.1480.0000.0000.0000.000
112A295GLY00.0140.02522.6090.1230.1230.0000.0000.0000.000
113A296GLY00.0260.02424.9250.0940.0940.0000.0000.0000.000
114A297GLN0-0.074-0.04526.589-0.045-0.0450.0000.0000.0000.000
115A298VAL0-0.023-0.00925.8930.0330.0330.0000.0000.0000.000
116A299VAL00.013-0.00328.7830.0290.0290.0000.0000.0000.000
117A300ASN00.006-0.04731.0130.0120.0120.0000.0000.0000.000
118A301PRO00.0170.01033.1980.0140.0140.0000.0000.0000.000
119A302ASP-1-0.872-0.92034.108-0.719-0.7190.0000.0000.0000.000
120A303ALA0-0.133-0.06233.508-0.001-0.0010.0000.0000.0000.000
121A304GLY0-0.015-0.00635.6320.0170.0170.0000.0000.0000.000
122A305MET0-0.0340.02933.1940.0090.0090.0000.0000.0000.000
123A306VAL00.0280.00837.7380.0050.0050.0000.0000.0000.000
124A307LEU0-0.038-0.01635.646-0.008-0.0080.0000.0000.0000.000
125A308ARG10.8300.90538.8050.4340.4340.0000.0000.0000.000
126A309GLU-1-0.962-0.98141.117-0.469-0.4690.0000.0000.0000.000
127A310VAL00.0000.02636.065-0.001-0.0010.0000.0000.0000.000
128A311GLY0-0.037-0.04537.5890.0410.0410.0000.0000.0000.000
129A312LEU0-0.004-0.01235.197-0.027-0.0270.0000.0000.0000.000
130A313GLU-1-0.845-0.91233.456-0.615-0.6150.0000.0000.0000.000
131A314VAL0-0.018-0.00532.077-0.046-0.0460.0000.0000.0000.000
132A315LEU0-0.059-0.02030.310-0.053-0.0530.0000.0000.0000.000
133A316GLY00.0650.03926.219-0.013-0.0130.0000.0000.0000.000
134A317SER0-0.085-0.05025.7750.0950.0950.0000.0000.0000.000
135A318ALA00.0570.01422.028-0.128-0.1280.0000.0000.0000.000
136A319ARG10.8490.93319.5780.6160.6160.0000.0000.0000.000
137A320ARG10.9090.95521.0450.4790.4790.0000.0000.0000.000
138A321VAL0-0.011-0.00121.806-0.132-0.1320.0000.0000.0000.000
139A322VAL0-0.0150.00020.9170.1260.1260.0000.0000.0000.000
140A323VAL0-0.0130.00421.775-0.107-0.1070.0000.0000.0000.000
141A324SER00.028-0.00521.2450.1350.1350.0000.0000.0000.000
142A325LYS10.9640.97024.2400.2910.2910.0000.0000.0000.000
143A326ASP-1-0.991-1.00322.467-0.577-0.5770.0000.0000.0000.000
144A327ASP-1-0.863-0.91018.695-0.939-0.9390.0000.0000.0000.000
145A328THR00.020-0.01119.7850.1690.1690.0000.0000.0000.000
146A329VAL00.0070.00715.832-0.232-0.2320.0000.0000.0000.000
147A330ILE0-0.042-0.01617.9400.1980.1980.0000.0000.0000.000
148A331VAL00.0250.00616.701-0.241-0.2410.0000.0000.0000.000
149A332ASP-1-0.754-0.87417.735-0.720-0.7200.0000.0000.0000.000
150A333GLY00.0220.01319.1250.1440.1440.0000.0000.0000.000
151A334GLY00.0250.00021.070-0.036-0.0360.0000.0000.0000.000
152A335GLY0-0.0010.01221.0680.0450.0450.0000.0000.0000.000
153A336THR0-0.017-0.02021.881-0.012-0.0120.0000.0000.0000.000
154A337ALA00.0610.01619.454-0.146-0.1460.0000.0000.0000.000
155A338GLU-1-0.899-0.94419.183-1.472-1.4720.0000.0000.0000.000
156A339ALA00.0100.01920.554-0.145-0.1450.0000.0000.0000.000
157A340VAL00.0640.02315.034-0.191-0.1910.0000.0000.0000.000
158A341ALA0-0.0030.00115.979-0.390-0.3900.0000.0000.0000.000
159A342ASN0-0.057-0.04816.815-0.308-0.3080.0000.0000.0000.000
160A343ARG10.7740.87716.9062.0832.0830.0000.0000.0000.000
161A344ALA00.0530.01512.548-0.285-0.2850.0000.0000.0000.000
162A345LYS10.8740.93713.8291.7571.7570.0000.0000.0000.000
163A346HIS0-0.021-0.00516.3070.0090.0090.0000.0000.0000.000
164A347LEU00.019-0.00213.1140.0280.0280.0000.0000.0000.000
165A348ARG10.9360.97610.5444.5094.5090.0000.0000.0000.000
166A349ALA0-0.024-0.00313.8720.1510.1510.0000.0000.0000.000
167A350GLU-1-0.924-0.96916.850-1.921-1.9210.0000.0000.0000.000
168A351ILE0-0.071-0.03810.6260.0280.0280.0000.0000.0000.000
169A352ASP-1-0.925-0.97114.138-3.312-3.3120.0000.0000.0000.000
170A353LYS10.8980.95016.5471.9821.9820.0000.0000.0000.000
171A354SER0-0.0310.00417.1750.2870.2870.0000.0000.0000.000
172A355ASP-1-0.933-0.96618.410-1.568-1.5680.0000.0000.0000.000
173A356SER0-0.018-0.03418.9350.1510.1510.0000.0000.0000.000
174A357ASP-1-0.841-0.91814.954-2.669-2.6690.0000.0000.0000.000
175A358TRP00.0280.02114.824-0.456-0.4560.0000.0000.0000.000
176A359ASP-1-0.815-0.90215.987-2.248-2.2480.0000.0000.0000.000
177A360ARG10.8550.92012.2592.8852.8850.0000.0000.0000.000
178A361GLU-1-0.846-0.89411.040-3.933-3.9330.0000.0000.0000.000
179A362LYS10.7240.84311.6792.4182.4180.0000.0000.0000.000
180A363LEU0-0.016-0.01213.4220.0350.0350.0000.0000.0000.000
181A364GLY00.0360.0209.189-0.335-0.3350.0000.0000.0000.000
182A365GLU-1-0.792-0.8828.665-4.264-4.2640.0000.0000.0000.000
183A366ARG10.8070.88010.2733.0693.0690.0000.0000.0000.000
184A367LEU0-0.024-0.0058.6420.2950.2950.0000.0000.0000.000
185A368ALA00.000-0.0066.440-0.117-0.1170.0000.0000.0000.000
186A369LYS10.8780.9318.0153.7593.7590.0000.0000.0000.000
187A370LEU0-0.049-0.02311.4910.5300.5300.0000.0000.0000.000
188A371ALA0-0.025-0.0199.0340.5140.5140.0000.0000.0000.000
189A372GLY00.0430.03411.0460.4480.4480.0000.0000.0000.000
190A373GLY0-0.025-0.01011.7510.5530.5530.0000.0000.0000.000
191A374VAL0-0.055-0.02315.4190.2860.2860.0000.0000.0000.000
192A375ALA0-0.0210.00016.749-0.004-0.0040.0000.0000.0000.000
193A376VAL0-0.071-0.04415.483-0.113-0.1130.0000.0000.0000.000
194A377ILE-1-0.957-0.95718.904-0.348-0.3480.0000.0000.0000.000