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

tag_button

FMODB ID: 2MM5R

Calculation Name: 2PTH-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2PTH

Chain ID: A

ChEMBL ID:

UniProt ID: P0A7D1

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 193
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2098929.575438
FMO2-HF: Nuclear repulsion 2026341.109829
FMO2-HF: Total energy -72588.465609
FMO2-MP2: Total energy -72803.299782


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:1:THR)


Summations of interaction energy for fragment #1(A:1: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.
-44.984-37.4740.674-3.145-5.04-0.016
Interaction energy analysis for fragmet #1(A:1:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.858 / q_NPA : 0.922
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].
3A3LYS10.8870.9262.83449.51152.4990.371-1.410-1.949-0.007
4A4LEU0-0.035-0.0104.5295.5515.668-0.001-0.014-0.1020.000
56A56GLU-1-0.921-0.9552.566-51.580-49.9020.144-0.762-1.061-0.006
87A87GLU-1-0.837-0.9042.821-72.614-71.0470.073-0.643-0.997-0.004
88A88ILE0-0.015-0.0084.9492.8502.893-0.001-0.012-0.0300.000
175A175TRP0-0.036-0.0204.0330.5670.730-0.001-0.018-0.1440.000
176A176PHE0-0.052-0.0353.052-3.866-2.9120.089-0.286-0.7570.001
5A5ILE00.0260.0218.160-1.311-1.3110.0000.0000.0000.000
6A6VAL0-0.022-0.02110.6161.6981.6980.0000.0000.0000.000
7A7GLY00.0410.01614.046-0.207-0.2070.0000.0000.0000.000
8A8LEU0-0.071-0.04617.3960.6670.6670.0000.0000.0000.000
9A9ALA00.0170.00120.3510.2590.2590.0000.0000.0000.000
10A10ASN0-0.0250.00323.822-0.076-0.0760.0000.0000.0000.000
11A11PRO00.0410.02826.511-0.073-0.0730.0000.0000.0000.000
12A12GLY00.0530.02327.5740.3820.3820.0000.0000.0000.000
13A13ALA0-0.002-0.02330.160-0.135-0.1350.0000.0000.0000.000
14A14GLU-1-0.913-0.92732.388-8.872-8.8720.0000.0000.0000.000
15A15TYR0-0.008-0.03129.406-0.040-0.0400.0000.0000.0000.000
16A16ALA00.0060.02828.178-0.283-0.2830.0000.0000.0000.000
17A17ALA0-0.022-0.00928.300-0.279-0.2790.0000.0000.0000.000
18A18THR0-0.055-0.03829.7170.1250.1250.0000.0000.0000.000
19A19ARG10.8860.92427.7999.3999.3990.0000.0000.0000.000
20A20HIS0-0.086-0.07525.990-0.352-0.3520.0000.0000.0000.000
21A21ASN00.0160.00424.532-0.426-0.4260.0000.0000.0000.000
22A22ALA00.0320.01723.017-0.380-0.3800.0000.0000.0000.000
23A23GLY0-0.011-0.00519.163-0.540-0.5400.0000.0000.0000.000
24A24ALA0-0.023-0.01118.720-0.875-0.8750.0000.0000.0000.000
25A25TRP00.0360.02120.010-0.400-0.4000.0000.0000.0000.000
26A26PHE00.006-0.00512.805-0.069-0.0690.0000.0000.0000.000
27A27VAL0-0.017-0.00814.916-0.631-0.6310.0000.0000.0000.000
28A28ASP-1-0.878-0.94416.950-13.914-13.9140.0000.0000.0000.000
29A29LEU0-0.034-0.01218.8380.2200.2200.0000.0000.0000.000
30A30LEU0-0.021-0.01012.599-0.061-0.0610.0000.0000.0000.000
31A31ALA00.0150.00316.215-0.010-0.0100.0000.0000.0000.000
32A32GLU-1-0.897-0.93817.955-12.312-12.3120.0000.0000.0000.000
33A33ARG10.8420.90218.05014.63514.6350.0000.0000.0000.000
34A34LEU0-0.007-0.00213.0720.2310.2310.0000.0000.0000.000
35A35ARG10.7900.88417.36912.59712.5970.0000.0000.0000.000
36A36ALA00.0290.02716.9090.3360.3360.0000.0000.0000.000
37A37PRO0-0.019-0.01118.424-0.516-0.5160.0000.0000.0000.000
38A38LEU00.0070.01516.998-0.398-0.3980.0000.0000.0000.000
39A39ARG10.8930.93620.08814.24914.2490.0000.0000.0000.000
40A40GLU-1-0.882-0.91220.909-12.374-12.3740.0000.0000.0000.000
41A41GLU-1-0.865-0.90818.619-14.842-14.8420.0000.0000.0000.000
42A42ALA00.0450.01322.002-0.336-0.3360.0000.0000.0000.000
43A43LYS10.8520.94119.52614.72714.7270.0000.0000.0000.000
44A44PHE00.000-0.01617.135-0.547-0.5470.0000.0000.0000.000
45A45PHE0-0.004-0.01019.693-0.190-0.1900.0000.0000.0000.000
46A46GLY00.1210.05520.332-0.040-0.0400.0000.0000.0000.000
47A47TYR0-0.0090.00620.2380.1790.1790.0000.0000.0000.000
48A48THR0-0.036-0.04115.978-0.766-0.7660.0000.0000.0000.000
49A49SER00.010-0.00915.1140.6760.6760.0000.0000.0000.000
50A50ARG10.7560.83510.90920.80220.8020.0000.0000.0000.000
51A51VAL00.0210.01610.6241.4631.4630.0000.0000.0000.000
52A52THR00.0030.0149.625-1.368-1.3680.0000.0000.0000.000
53A53LEU0-0.004-0.0067.7961.8471.8470.0000.0000.0000.000
54A54GLY00.0370.0106.912-2.875-2.8750.0000.0000.0000.000
55A55GLY0-0.028-0.0048.013-0.237-0.2370.0000.0000.0000.000
57A57ASP-1-0.832-0.8825.714-22.406-22.4060.0000.0000.0000.000
58A58VAL0-0.014-0.0025.354-3.936-3.9360.0000.0000.0000.000
59A59ARG10.9110.9577.43827.32427.3240.0000.0000.0000.000
60A60LEU00.0200.01210.026-1.345-1.3450.0000.0000.0000.000
61A61LEU0-0.016-0.01912.8580.7270.7270.0000.0000.0000.000
62A62VAL00.0420.02815.350-0.345-0.3450.0000.0000.0000.000
63A63PRO0-0.049-0.02118.1840.5370.5370.0000.0000.0000.000
64A64THR0-0.004-0.03220.8490.2030.2030.0000.0000.0000.000
65A65THR0-0.096-0.05722.8210.3550.3550.0000.0000.0000.000
66A66PHE00.0540.02325.3310.3410.3410.0000.0000.0000.000
67A67MET00.0650.06823.605-0.710-0.7100.0000.0000.0000.000
68A68ASN0-0.035-0.02924.137-0.817-0.8170.0000.0000.0000.000
69A69LEU0-0.0110.00425.2370.0820.0820.0000.0000.0000.000
70A70SER00.013-0.00620.081-0.284-0.2840.0000.0000.0000.000
71A71GLY00.0000.00019.164-0.841-0.8410.0000.0000.0000.000
72A72LYS10.8740.94719.40811.50211.5020.0000.0000.0000.000
73A73ALA00.0120.01619.005-0.110-0.1100.0000.0000.0000.000
74A74VAL00.0170.00413.757-0.656-0.6560.0000.0000.0000.000
75A75ALA00.0350.02214.825-1.243-1.2430.0000.0000.0000.000
76A76ALA0-0.0050.01616.451-0.471-0.4710.0000.0000.0000.000
77A77MET0-0.009-0.00512.485-0.061-0.0610.0000.0000.0000.000
78A78ALA00.0070.00111.501-0.890-0.8900.0000.0000.0000.000
79A79SER0-0.017-0.01712.367-0.909-0.9090.0000.0000.0000.000
80A80PHE0-0.027-0.02414.9220.3290.3290.0000.0000.0000.000
81A81PHE0-0.022-0.02410.2600.5400.5400.0000.0000.0000.000
82A82ARG10.9090.96610.09720.01620.0160.0000.0000.0000.000
83A83ILE0-0.0230.0016.533-2.281-2.2810.0000.0000.0000.000
84A84ASN00.0300.0196.4756.6486.6480.0000.0000.0000.000
85A85PRO00.026-0.0087.671-2.725-2.7250.0000.0000.0000.000
86A86ASP-1-0.876-0.9345.963-44.170-44.1700.0000.0000.0000.000
89A89LEU0-0.006-0.0048.192-0.105-0.1050.0000.0000.0000.000
90A90VAL0-0.024-0.0189.9191.7131.7130.0000.0000.0000.000
91A91ALA00.0110.01913.7720.5140.5140.0000.0000.0000.000
92A92HIS0-0.052-0.05215.8390.0190.0190.0000.0000.0000.000
93A93ASP-1-0.712-0.81819.295-13.081-13.0810.0000.0000.0000.000
94A94GLU-1-0.818-0.89621.355-14.180-14.1800.0000.0000.0000.000
95A95LEU00.0210.01323.4040.4350.4350.0000.0000.0000.000
96A96ASP-1-0.950-0.97924.718-11.424-11.4240.0000.0000.0000.000
97A97LEU0-0.058-0.03220.681-0.202-0.2020.0000.0000.0000.000
98A98PRO00.0120.01425.2230.1040.1040.0000.0000.0000.000
99A99PRO00.0340.00625.909-0.420-0.4200.0000.0000.0000.000
100A100GLY0-0.0040.01325.6250.3250.3250.0000.0000.0000.000
101A101VAL0-0.020-0.01222.190-0.299-0.2990.0000.0000.0000.000
102A102ALA00.0400.01418.213-0.021-0.0210.0000.0000.0000.000
103A103LYS10.8880.94416.96614.82814.8280.0000.0000.0000.000
104A104PHE00.0550.03711.647-0.452-0.4520.0000.0000.0000.000
105A105LYS10.8810.93613.10119.03619.0360.0000.0000.0000.000
106A106LEU00.0370.0368.699-0.644-0.6440.0000.0000.0000.000
107A107GLY00.0170.02211.8131.7251.7250.0000.0000.0000.000
108A108GLY0-0.016-0.01814.1570.8810.8810.0000.0000.0000.000
109A109GLY00.0200.00317.859-0.377-0.3770.0000.0000.0000.000
110A110HIS00.0640.02819.437-0.634-0.6340.0000.0000.0000.000
111A111GLY00.0420.02921.5210.0640.0640.0000.0000.0000.000
112A112GLY0-0.023-0.00824.2210.4430.4430.0000.0000.0000.000
113A113HIS00.002-0.01422.4860.2360.2360.0000.0000.0000.000
114A114ASN0-0.004-0.03723.325-0.526-0.5260.0000.0000.0000.000
115A115GLY00.0510.03922.524-0.009-0.0090.0000.0000.0000.000
116A116LEU00.0060.00317.215-0.661-0.6610.0000.0000.0000.000
117A117LYS10.9140.95619.49411.00311.0030.0000.0000.0000.000
118A118ASP-1-0.785-0.88621.793-13.665-13.6650.0000.0000.0000.000
119A119ILE00.0300.01615.438-0.171-0.1710.0000.0000.0000.000
120A120ILE0-0.028-0.00717.381-0.490-0.4900.0000.0000.0000.000
121A121SER0-0.049-0.01318.393-0.109-0.1090.0000.0000.0000.000
122A122LYS10.8320.90019.75313.34213.3420.0000.0000.0000.000
123A123LEU0-0.0090.01213.039-0.387-0.3870.0000.0000.0000.000
124A124GLY0-0.018-0.00416.451-0.653-0.6530.0000.0000.0000.000
125A125ASN0-0.067-0.04219.2500.1340.1340.0000.0000.0000.000
126A126ASN00.0610.04213.293-0.190-0.1900.0000.0000.0000.000
127A127PRO00.013-0.00215.333-0.696-0.6960.0000.0000.0000.000
128A128ASN0-0.059-0.01711.331-0.095-0.0950.0000.0000.0000.000
129A129PHE00.0630.0289.419-2.093-2.0930.0000.0000.0000.000
130A130HIS00.007-0.0115.1626.8036.8030.0000.0000.0000.000
131A131ARG10.7610.87810.00720.92620.9260.0000.0000.0000.000
132A132LEU00.0010.00113.066-0.591-0.5910.0000.0000.0000.000
133A133ARG10.8340.90414.59115.86015.8600.0000.0000.0000.000
134A134ILE00.0490.01017.9170.1040.1040.0000.0000.0000.000
135A135GLY00.006-0.00120.4450.3720.3720.0000.0000.0000.000
136A136ILE0-0.055-0.02523.8250.2670.2670.0000.0000.0000.000
137A137GLY00.0250.01326.8770.4890.4890.0000.0000.0000.000
138A138HIS00.0490.01229.3740.0400.0400.0000.0000.0000.000
139A139PRO0-0.037-0.00431.6970.2370.2370.0000.0000.0000.000
140A140GLY00.0210.01834.7310.3240.3240.0000.0000.0000.000
141A141ASP-1-0.826-0.91836.416-8.066-8.0660.0000.0000.0000.000
142A142LYS10.9940.97132.9679.2469.2460.0000.0000.0000.000
143A143ASN0-0.059-0.02435.655-0.092-0.0920.0000.0000.0000.000
144A144LYS10.9100.95237.2727.8827.8820.0000.0000.0000.000
145A145VAL00.0040.00830.962-0.082-0.0820.0000.0000.0000.000
146A146VAL00.0190.01332.956-0.209-0.2090.0000.0000.0000.000
147A147GLY00.0360.01234.076-0.110-0.1100.0000.0000.0000.000
148A148PHE0-0.018-0.00230.1470.0990.0990.0000.0000.0000.000
149A149VAL00.015-0.00128.816-0.097-0.0970.0000.0000.0000.000
150A150LEU0-0.001-0.00230.335-0.247-0.2470.0000.0000.0000.000
151A151GLY00.0340.03432.6770.2480.2480.0000.0000.0000.000
152A152LYS10.9390.97032.2308.6788.6780.0000.0000.0000.000
153A153PRO00.0040.00629.7050.2620.2620.0000.0000.0000.000
154A154PRO0-0.0090.00032.8440.1670.1670.0000.0000.0000.000
155A155VAL00.0170.00133.704-0.264-0.2640.0000.0000.0000.000
156A156SER00.0140.00333.263-0.228-0.2280.0000.0000.0000.000
157A157GLU-1-0.804-0.89730.858-9.789-9.7890.0000.0000.0000.000
158A158GLN0-0.048-0.03827.386-0.100-0.1000.0000.0000.0000.000
159A159LYS10.9520.97928.2719.1919.1910.0000.0000.0000.000
160A160LEU00.0320.02427.858-0.302-0.3020.0000.0000.0000.000
161A161ILE00.000-0.00423.870-0.478-0.4780.0000.0000.0000.000
162A162ASP-1-0.865-0.92923.546-11.883-11.8830.0000.0000.0000.000
163A163GLU-1-0.863-0.92923.283-11.585-11.5850.0000.0000.0000.000
164A164ALA0-0.036-0.00921.647-0.508-0.5080.0000.0000.0000.000
165A165ILE0-0.0030.00519.101-0.972-0.9720.0000.0000.0000.000
166A166ASP-1-0.756-0.82718.324-14.874-14.8740.0000.0000.0000.000
167A167GLU-1-0.767-0.85418.184-15.889-15.8890.0000.0000.0000.000
168A168ALA00.0260.01115.643-0.976-0.9760.0000.0000.0000.000
169A169ALA0-0.0070.01514.052-1.707-1.7070.0000.0000.0000.000
170A170ARG10.8460.90013.34712.86512.8650.0000.0000.0000.000
171A171CYS0-0.064-0.02813.399-0.622-0.6220.0000.0000.0000.000
172A172THR0-0.035-0.0439.234-2.103-2.1030.0000.0000.0000.000
173A173GLU-1-0.955-0.9758.677-22.633-22.6330.0000.0000.0000.000
174A174MET00.0180.0108.968-1.120-1.1200.0000.0000.0000.000
177A177THR0-0.0060.0005.798-1.141-1.1410.0000.0000.0000.000
178A178ASP-1-0.861-0.9208.930-20.035-20.0350.0000.0000.0000.000
179A179GLY00.0180.0206.9540.6150.6150.0000.0000.0000.000
180A180LEU00.003-0.0066.6852.6482.6480.0000.0000.0000.000
181A181THR00.0110.0088.3641.6931.6930.0000.0000.0000.000
182A182LYS10.9120.96211.59321.40921.4090.0000.0000.0000.000
183A183ALA00.0350.02910.1291.4521.4520.0000.0000.0000.000
184A184THR0-0.031-0.03911.3681.1351.1350.0000.0000.0000.000
185A185ASN0-0.041-0.02713.6621.0581.0580.0000.0000.0000.000
186A186ARG10.8390.89815.65017.32717.3270.0000.0000.0000.000
187A187LEU00.0390.01114.7370.8480.8480.0000.0000.0000.000
188A188HIS0-0.097-0.06516.1380.3980.3980.0000.0000.0000.000
189A189ALA00.0630.04219.0730.5690.5690.0000.0000.0000.000
190A190PHE00.0250.01820.7400.7310.7310.0000.0000.0000.000
191A191LYS10.7600.86322.47911.55911.5590.0000.0000.0000.000
192A192ALA0-0.048-0.01924.1620.3500.3500.0000.0000.0000.000
193A193GLN-1-0.954-0.95325.618-10.931-10.9310.0000.0000.0000.000