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: 3Z33L

Calculation Name: 2LM3-A-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2LM3

Chain ID: A

ChEMBL ID:

UniProt ID: Q0PF16

Base Structure: SolutionNMR

Registration Date: 2025-10-04

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 205
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2425040.192462
FMO2-HF: Nuclear repulsion 2343193.785411
FMO2-HF: Total energy -81846.407051
FMO2-MP2: Total energy -82082.500021


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:291:THR)


Summations of interaction energy for fragment #1(A:291:THR)
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.
11.59916.2334.421-3.941-5.113-0.039
Interaction energy analysis for fragmet #1(A:291:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.844 / q_NPA : 0.908
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].
3A293LEU00.0610.0513.5961.9743.7280.006-0.673-1.0870.000
4A294THR0-0.040-0.0272.008-16.752-14.5884.410-3.006-3.568-0.038
5A295ASP-1-0.833-0.9223.581-24.182-23.4660.005-0.262-0.458-0.001
6A296ALA00.0250.0216.1055.5215.5210.0000.0000.0000.000
7A297ARG10.8490.8976.43538.30338.3030.0000.0000.0000.000
8A298ARG10.8540.9357.94330.89930.8990.0000.0000.0000.000
9A299TYR0-0.043-0.0199.9023.4413.4410.0000.0000.0000.000
10A300TRP00.013-0.00110.432-0.004-0.0040.0000.0000.0000.000
11A301VAL0-0.049-0.01513.7840.9810.9810.0000.0000.0000.000
12A302ASP-1-0.776-0.85117.544-14.253-14.2530.0000.0000.0000.000
13A303VAL0-0.049-0.02118.9980.5030.5030.0000.0000.0000.000
14A304THR00.0630.04821.5370.1950.1950.0000.0000.0000.000
15A305LEU0-0.036-0.02324.329-0.039-0.0390.0000.0000.0000.000
16A306ALA00.002-0.00927.0970.3710.3710.0000.0000.0000.000
17A307THR0-0.015-0.01030.345-0.028-0.0280.0000.0000.0000.000
18A308ASN0-0.0140.00131.9420.3560.3560.0000.0000.0000.000
19A309ASN00.006-0.00435.193-0.067-0.0670.0000.0000.0000.000
20A310ILE0-0.020-0.01235.2210.2310.2310.0000.0000.0000.000
21A311SER0-0.023-0.00433.674-0.147-0.1470.0000.0000.0000.000
22A312HIS00.0140.00535.7070.0510.0510.0000.0000.0000.000
23A313ALA0-0.029-0.01231.296-0.057-0.0570.0000.0000.0000.000
24A314VAL0-0.012-0.01132.9070.1810.1810.0000.0000.0000.000
25A315ILE0-0.016-0.01429.102-0.331-0.3310.0000.0000.0000.000
26A316ALA00.0000.01229.2510.3700.3700.0000.0000.0000.000
27A317GLU-1-0.927-0.97731.282-8.905-8.9050.0000.0000.0000.000
28A318ASP-1-0.826-0.92227.329-11.433-11.4330.0000.0000.0000.000
29A319LYS10.8390.93628.1549.5249.5240.0000.0000.0000.000
30A320ARG10.8560.89122.23612.87412.8740.0000.0000.0000.000
31A321GLN0-0.024-0.02223.934-0.146-0.1460.0000.0000.0000.000
32A322VAL00.0090.01325.8660.4690.4690.0000.0000.0000.000
33A323SER0-0.0030.00727.565-0.236-0.2360.0000.0000.0000.000
34A324SER00.0270.00930.1900.1980.1980.0000.0000.0000.000
35A325ARG10.9380.95832.8188.6018.6010.0000.0000.0000.000
36A326ASN00.0460.01936.5840.1150.1150.0000.0000.0000.000
37A327PRO00.0200.01338.613-0.006-0.0060.0000.0000.0000.000
38A328GLN0-0.042-0.03941.3060.1490.1490.0000.0000.0000.000
39A329ILE0-0.0090.01642.293-0.125-0.1250.0000.0000.0000.000
40A330MET00.0290.03241.6400.0760.0760.0000.0000.0000.000
41A331TYR0-0.031-0.03144.1800.1240.1240.0000.0000.0000.000
42A332GLN00.0220.01844.9480.0180.0180.0000.0000.0000.000
43A333ALA0-0.0050.00148.0150.1020.1020.0000.0000.0000.000
44A334PRO00.0210.03047.0830.1490.1490.0000.0000.0000.000
45A335GLY00.0290.01450.2320.0590.0590.0000.0000.0000.000
46A336THR0-0.013-0.01847.8460.0260.0260.0000.0000.0000.000
47A337LEU0-0.020-0.02346.790-0.190-0.1900.0000.0000.0000.000
48A338PHE00.0990.03041.969-0.044-0.0440.0000.0000.0000.000
49A339THR0-0.127-0.04343.569-0.062-0.0620.0000.0000.0000.000
50A340PHE00.0410.00742.580-0.136-0.1360.0000.0000.0000.000
51A341PRO00.0530.02941.3900.1040.1040.0000.0000.0000.000
52A342SER00.0240.00443.399-0.108-0.1080.0000.0000.0000.000
53A343LEU0-0.038-0.01644.041-0.021-0.0210.0000.0000.0000.000
54A344THR00.0130.00540.3290.0290.0290.0000.0000.0000.000
55A345ASN0-0.0030.00140.306-0.324-0.3240.0000.0000.0000.000
56A346PHE0-0.088-0.03934.510-0.047-0.0470.0000.0000.0000.000
57A347ASN00.0660.03933.994-0.236-0.2360.0000.0000.0000.000
58A348TYR0-0.055-0.04934.7840.2400.2400.0000.0000.0000.000
59A349CYS0-0.0170.02134.4560.1590.1590.0000.0000.0000.000
60A350THR0-0.040-0.02930.7780.1850.1850.0000.0000.0000.000
61A351GLY00.0630.03729.221-0.377-0.3770.0000.0000.0000.000
62A352VAL0-0.037-0.02826.8710.3550.3550.0000.0000.0000.000
63A353LEU00.0210.00626.400-0.411-0.4110.0000.0000.0000.000
64A354GLY00.0100.00924.5280.1410.1410.0000.0000.0000.000
65A355SER0-0.057-0.04725.4410.2650.2650.0000.0000.0000.000
66A356GLN0-0.017-0.00123.6900.5470.5470.0000.0000.0000.000
67A357SER0-0.034-0.00924.820-0.400-0.4000.0000.0000.0000.000
68A358ILE0-0.051-0.02219.523-0.382-0.3820.0000.0000.0000.000
69A359THR00.021-0.01023.4980.1210.1210.0000.0000.0000.000
70A360SER00.0470.03322.8400.2430.2430.0000.0000.0000.000
71A361GLY0-0.010-0.00519.012-0.300-0.3000.0000.0000.0000.000
72A362LYS10.8550.94811.51123.33823.3380.0000.0000.0000.000
73A363HIS10.8400.90515.34416.99216.9920.0000.0000.0000.000
74A364TYR00.003-0.0269.863-1.716-1.7160.0000.0000.0000.000
75A365TRP00.0500.02813.5161.0491.0490.0000.0000.0000.000
76A366GLU-1-0.767-0.84710.578-29.038-29.0380.0000.0000.0000.000
77A367VAL00.0030.00314.7541.2741.2740.0000.0000.0000.000
78A368ASP-1-0.826-0.88417.051-17.078-17.0780.0000.0000.0000.000
79A369VAL00.009-0.01618.3540.9270.9270.0000.0000.0000.000
80A370SER00.030-0.00920.2400.2560.2560.0000.0000.0000.000
81A371LYS10.8900.93721.64713.13813.1380.0000.0000.0000.000
82A372LYS10.7420.84923.54412.50612.5060.0000.0000.0000.000
83A373SER0-0.014-0.04324.653-0.178-0.1780.0000.0000.0000.000
84A374ALA0-0.004-0.02326.1510.0140.0140.0000.0000.0000.000
85A375TRP00.0540.01118.447-0.140-0.1400.0000.0000.0000.000
86A376ILE0-0.0140.00023.425-0.152-0.1520.0000.0000.0000.000
87A377LEU0-0.017-0.01017.3950.0850.0850.0000.0000.0000.000
88A378GLY00.020-0.00618.743-0.434-0.4340.0000.0000.0000.000
89A379VAL0-0.0050.01119.0940.0180.0180.0000.0000.0000.000
90A380CYS00.0150.04021.8420.4120.4120.0000.0000.0000.000
91A381ALA00.0430.01025.647-0.115-0.1150.0000.0000.0000.000
92A382GLY0-0.026-0.02128.0290.3570.3570.0000.0000.0000.000
93A383PHE00.0300.00230.4330.0160.0160.0000.0000.0000.000
94A384GLN0-0.011-0.00932.7530.1040.1040.0000.0000.0000.000
95A385SER0-0.021-0.00932.1960.2750.2750.0000.0000.0000.000
96A386ASP-1-0.844-0.92534.465-9.004-9.0040.0000.0000.0000.000
97A387ALA00.0400.01135.6920.0920.0920.0000.0000.0000.000
98A388MET0-0.054-0.01538.0290.2260.2260.0000.0000.0000.000
99A389TYR0-0.003-0.01035.2270.0870.0870.0000.0000.0000.000
100A390ASN00.0490.02836.376-0.128-0.1280.0000.0000.0000.000
101A391ILE0-0.0350.00431.068-0.101-0.1010.0000.0000.0000.000
102A392GLU-1-0.689-0.83930.445-10.806-10.8060.0000.0000.0000.000
103A393GLN0-0.054-0.03133.6760.0770.0770.0000.0000.0000.000
104A394ASN0-0.021-0.01335.8310.1590.1590.0000.0000.0000.000
105A395GLU-1-0.796-0.85730.372-10.628-10.6280.0000.0000.0000.000
106A396ASN0-0.032-0.01530.529-0.528-0.5280.0000.0000.0000.000
107A397TYR0-0.042-0.06026.839-0.044-0.0440.0000.0000.0000.000
108A398GLN00.0460.00227.062-0.183-0.1830.0000.0000.0000.000
109A399PRO00.0140.02023.5970.1140.1140.0000.0000.0000.000
110A400LYS10.8530.94025.7059.9089.9080.0000.0000.0000.000
111A401TYR0-0.058-0.02429.0790.3070.3070.0000.0000.0000.000
112A402GLY0-0.0090.00927.0720.1710.1710.0000.0000.0000.000
113A403TYR0-0.032-0.03825.360-0.127-0.1270.0000.0000.0000.000
114A404TRP00.0040.00020.0950.0050.0050.0000.0000.0000.000
115A405VAL0-0.010-0.00420.567-0.697-0.6970.0000.0000.0000.000
116A406ILE00.0180.00716.3150.1220.1220.0000.0000.0000.000
117A407GLY00.012-0.00920.5340.2350.2350.0000.0000.0000.000
118A408LEU0-0.0320.01222.030-0.203-0.2030.0000.0000.0000.000
119A409GLN0-0.004-0.00723.8650.5220.5220.0000.0000.0000.000
120A410GLU-1-0.821-0.90627.073-10.274-10.2740.0000.0000.0000.000
121A411GLY00.0200.01825.8840.1270.1270.0000.0000.0000.000
122A412VAL0-0.030-0.01724.055-0.511-0.5110.0000.0000.0000.000
123A413LYS10.8370.91124.0329.9449.9440.0000.0000.0000.000
124A414TYR00.0770.02019.595-0.185-0.1850.0000.0000.0000.000
125A415SER0-0.039-0.03522.0980.5060.5060.0000.0000.0000.000
126A416VAL0-0.020-0.00519.174-0.424-0.4240.0000.0000.0000.000
127A417PHE0-0.0110.00721.4020.4950.4950.0000.0000.0000.000
128A418GLN00.039-0.00620.5530.0620.0620.0000.0000.0000.000
129A419ASP-1-0.790-0.89924.911-10.609-10.6090.0000.0000.0000.000
130A420GLY00.0080.01828.0120.0250.0250.0000.0000.0000.000
131A421SER0-0.025-0.02531.2410.0890.0890.0000.0000.0000.000
132A422SER00.0260.00134.247-0.008-0.0080.0000.0000.0000.000
133A423HIS0-0.023-0.01136.7130.2470.2470.0000.0000.0000.000
134A424THR0-0.025-0.01535.4960.1780.1780.0000.0000.0000.000
135A425PRO00.0170.02035.580-0.228-0.2280.0000.0000.0000.000
136A426PHE0-0.010-0.01035.405-0.169-0.1690.0000.0000.0000.000
137A427ALA00.0100.01234.063-0.009-0.0090.0000.0000.0000.000
138A428PRO0-0.0120.00728.6070.0010.0010.0000.0000.0000.000
139A429PHE0-0.028-0.01025.9650.2290.2290.0000.0000.0000.000
140A430ILE0-0.016-0.00726.051-0.503-0.5030.0000.0000.0000.000
141A431VAL0-0.0050.00422.1240.2390.2390.0000.0000.0000.000
142A432PRO00.0120.00022.690-0.519-0.5190.0000.0000.0000.000
143A433LEU0-0.027-0.00616.978-0.465-0.4650.0000.0000.0000.000
144A434SER0-0.005-0.00117.2350.5250.5250.0000.0000.0000.000
145A435VAL0-0.040-0.02316.393-1.141-1.1410.0000.0000.0000.000
146A436ILE00.0050.00915.2420.6900.6900.0000.0000.0000.000
147A437ILE0-0.0030.00314.6780.5750.5750.0000.0000.0000.000
148A438CYS00.0040.00615.998-0.712-0.7120.0000.0000.0000.000
149A439PRO0-0.0020.00614.265-0.616-0.6160.0000.0000.0000.000
150A440ASP-1-0.873-0.93015.919-15.790-15.7900.0000.0000.0000.000
151A441ARG10.8470.90113.81020.02120.0210.0000.0000.0000.000
152A442VAL0-0.0110.00513.214-1.501-1.5010.0000.0000.0000.000
153A443GLY00.0240.01810.8370.9320.9320.0000.0000.0000.000
154A444VAL0-0.037-0.01911.907-0.168-0.1680.0000.0000.0000.000
155A445PHE00.001-0.01010.877-0.614-0.6140.0000.0000.0000.000
156A446VAL00.0150.00413.0230.9050.9050.0000.0000.0000.000
157A447ASP-1-0.871-0.93613.955-20.315-20.3150.0000.0000.0000.000
158A448TYR00.018-0.01415.9950.5310.5310.0000.0000.0000.000
159A449GLU-1-0.795-0.89118.549-13.645-13.6450.0000.0000.0000.000
160A450ALA0-0.048-0.02115.5960.4730.4730.0000.0000.0000.000
161A451CYS0-0.042-0.00317.5920.3190.3190.0000.0000.0000.000
162A452THR0-0.053-0.02414.089-0.544-0.5440.0000.0000.0000.000
163A453VAL00.0380.01215.538-0.156-0.1560.0000.0000.0000.000
164A454SER0-0.042-0.01910.362-0.071-0.0710.0000.0000.0000.000
165A455PHE00.0190.02012.1430.0280.0280.0000.0000.0000.000
166A456PHE0-0.007-0.0086.460-1.507-1.5070.0000.0000.0000.000
167A457ASN00.0410.0049.7241.7721.7720.0000.0000.0000.000
168A458ILE0-0.027-0.0218.936-2.654-2.6540.0000.0000.0000.000
169A459THR00.0260.02610.366-1.131-1.1310.0000.0000.0000.000
170A460ASN0-0.012-0.00411.0320.4040.4040.0000.0000.0000.000
171A461HIS00.005-0.0076.961-3.519-3.5190.0000.0000.0000.000
172A462GLY00.007-0.0015.424-8.134-8.1340.0000.0000.0000.000
173A463PHE0-0.062-0.0275.287-5.582-5.5820.0000.0000.0000.000
174A464LEU0-0.029-0.0136.9802.5952.5950.0000.0000.0000.000
175A465ILE0-0.040-0.0148.8531.6151.6150.0000.0000.0000.000
176A466TYR00.0460.01012.6441.4661.4660.0000.0000.0000.000
177A467LYS10.9450.9749.53524.12924.1290.0000.0000.0000.000
178A468PHE00.0120.02213.7860.7890.7890.0000.0000.0000.000
179A469SER00.020-0.01015.428-1.272-1.2720.0000.0000.0000.000
180A470GLN0-0.010-0.00617.4700.3940.3940.0000.0000.0000.000
181A471CYS0-0.0420.00118.8560.4620.4620.0000.0000.0000.000
182A472SER00.0380.01421.8060.3260.3260.0000.0000.0000.000
183A473PHE0-0.049-0.02319.3030.2190.2190.0000.0000.0000.000
184A474SER00.0080.00725.1270.0130.0130.0000.0000.0000.000
185A475LYS10.8960.94627.83910.64410.6440.0000.0000.0000.000
186A476PRO00.0040.01327.135-0.457-0.4570.0000.0000.0000.000
187A477VAL0-0.036-0.00122.3990.2300.2300.0000.0000.0000.000
188A478PHE00.017-0.00124.066-0.076-0.0760.0000.0000.0000.000
189A479PRO00.0230.00920.539-0.167-0.1670.0000.0000.0000.000
190A480TYR0-0.060-0.05121.9720.6060.6060.0000.0000.0000.000
191A481LEU00.010-0.00821.565-0.752-0.7520.0000.0000.0000.000
192A482ASN00.0830.06024.2240.7150.7150.0000.0000.0000.000
193A483PRO00.0050.00026.070-0.389-0.3890.0000.0000.0000.000
194A484ARG10.8100.86626.50111.38311.3830.0000.0000.0000.000
195A485LYS10.9780.99129.4448.8058.8050.0000.0000.0000.000
196A486CYS-1-0.886-0.82328.499-11.011-11.0110.0000.0000.0000.000
197A487THR00.006-0.01830.3000.0720.0720.0000.0000.0000.000
198A488VAL00.0050.01326.3150.1250.1250.0000.0000.0000.000
199A489PRO00.013-0.00327.065-0.211-0.2110.0000.0000.0000.000
200A490MET0-0.0310.01822.364-0.223-0.2230.0000.0000.0000.000
201A491THR0-0.010-0.01021.9610.6990.6990.0000.0000.0000.000
202A492LEU00.0030.00619.064-0.855-0.8550.0000.0000.0000.000
203A493CYS0-0.091-0.03415.967-0.018-0.0180.0000.0000.0000.000
204A494SER0-0.010-0.01817.1340.7560.7560.0000.0000.0000.000
205A495PRO-1-0.924-0.93914.066-16.613-16.6130.0000.0000.0000.000