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: LV6V9

Calculation Name: 3EFP-A-Xray547

Preferred Name:

Target Type:

Ligand Name: 2-amino-2-hydroxymethyl-propane-1,3-diol

Ligand 3-letter code: TRS

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3EFP

Chain ID: A

ChEMBL ID:

UniProt ID: P69853

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 204
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2486006.553632
FMO2-HF: Nuclear repulsion 2404753.514428
FMO2-HF: Total energy -81253.039203
FMO2-MP2: Total energy -81492.42301


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-167.616-164.8330.041-1.571-1.254-0.009
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.823 / q_NPA : 0.898
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].
3A3HIS00.0530.0533.059-13.318-10.5350.041-1.571-1.254-0.009
4A4PHE00.0470.0155.7272.3422.3420.0000.0000.0000.000
5A5SER0-0.012-0.0277.9732.5432.5430.0000.0000.0000.000
6A6GLN0-0.092-0.0548.0662.5382.5380.0000.0000.0000.000
7A7GLN0-0.077-0.0455.461-7.741-7.7410.0000.0000.0000.000
8A8ASP-1-0.849-0.9219.280-29.922-29.9220.0000.0000.0000.000
9A9ASN0-0.023-0.02411.8900.7430.7430.0000.0000.0000.000
10A10PHE00.0210.02612.4511.5891.5890.0000.0000.0000.000
11A11SER00.017-0.01214.4781.0811.0810.0000.0000.0000.000
12A12VAL0-0.0080.00017.0851.2561.2560.0000.0000.0000.000
13A13ALA00.0570.02717.6420.9440.9440.0000.0000.0000.000
14A14ALA0-0.023-0.00517.8850.8670.8670.0000.0000.0000.000
15A15ARG10.8520.89219.81716.17116.1710.0000.0000.0000.000
16A16VAL0-0.0080.00522.5180.6970.6970.0000.0000.0000.000
17A17LEU00.0060.00520.8580.6210.6210.0000.0000.0000.000
18A18GLY00.012-0.00423.6510.5360.5360.0000.0000.0000.000
19A19ALA0-0.012-0.01425.2510.5210.5210.0000.0000.0000.000
20A20LEU0-0.008-0.00327.7270.5050.5050.0000.0000.0000.000
21A21PHE00.014-0.00227.1400.3650.3650.0000.0000.0000.000
22A22TYR0-0.055-0.03229.5010.2670.2670.0000.0000.0000.000
23A23TYR0-0.068-0.03229.6400.3590.3590.0000.0000.0000.000
24A24ALA00.0520.03933.642-0.070-0.0700.0000.0000.0000.000
25A25PRO0-0.0090.00134.907-0.035-0.0350.0000.0000.0000.000
26A26GLU-1-0.935-0.97035.935-7.690-7.6900.0000.0000.0000.000
27A27SER0-0.074-0.04135.4110.0700.0700.0000.0000.0000.000
28A28ALA0-0.003-0.01535.855-0.113-0.1130.0000.0000.0000.000
29A29GLU-1-0.896-0.96031.255-9.483-9.4830.0000.0000.0000.000
30A30ALA0-0.0030.00930.660-0.400-0.4000.0000.0000.0000.000
31A31ALA00.0350.02932.194-0.176-0.1760.0000.0000.0000.000
32A32PRO0-0.013-0.02031.062-0.010-0.0100.0000.0000.0000.000
33A33LEU0-0.0020.00026.850-0.255-0.2550.0000.0000.0000.000
34A34VAL00.0140.00729.767-0.147-0.1470.0000.0000.0000.000
35A35ALA0-0.0050.02132.4960.0460.0460.0000.0000.0000.000
36A36VAL0-0.029-0.00326.665-0.010-0.0100.0000.0000.0000.000
37A37LEU0-0.006-0.00726.036-0.080-0.0800.0000.0000.0000.000
38A38THR0-0.107-0.06729.8770.1840.1840.0000.0000.0000.000
39A39SER0-0.031-0.01231.5240.4170.4170.0000.0000.0000.000
40A40ASP-1-0.877-0.93331.117-9.740-9.7400.0000.0000.0000.000
41A41GLY00.001-0.00527.681-0.007-0.0070.0000.0000.0000.000
42A42TRP00.0000.00823.793-0.887-0.8870.0000.0000.0000.000
43A43GLU-1-0.837-0.93723.563-12.264-12.2640.0000.0000.0000.000
44A44THR0-0.060-0.03122.373-0.654-0.6540.0000.0000.0000.000
45A45GLN0-0.083-0.04620.204-0.926-0.9260.0000.0000.0000.000
46A46TRP00.009-0.00119.122-0.744-0.7440.0000.0000.0000.000
47A47PRO0-0.0120.00914.573-0.051-0.0510.0000.0000.0000.000
48A48LEU0-0.045-0.03716.117-0.420-0.4200.0000.0000.0000.000
49A49PRO00.0090.00418.0000.3230.3230.0000.0000.0000.000
50A50GLU-1-0.803-0.91220.250-12.728-12.7280.0000.0000.0000.000
51A51ALA0-0.044-0.02623.5980.5520.5520.0000.0000.0000.000
52A52SER0-0.048-0.03122.5520.2630.2630.0000.0000.0000.000
53A53LEU0-0.0040.01421.4650.2790.2790.0000.0000.0000.000
54A54ALA00.0260.02725.5790.4100.4100.0000.0000.0000.000
55A55PRO0-0.017-0.01028.0640.4010.4010.0000.0000.0000.000
56A56LEU00.0150.00625.5190.2920.2920.0000.0000.0000.000
57A57VAL00.0150.01628.1080.1970.1970.0000.0000.0000.000
58A58THR0-0.014-0.01030.5340.3630.3630.0000.0000.0000.000
59A59ALA0-0.026-0.00432.2990.3110.3110.0000.0000.0000.000
60A60PHE0-0.011-0.01827.4530.2090.2090.0000.0000.0000.000
61A61GLN0-0.041-0.02732.9720.4340.4340.0000.0000.0000.000
62A62THR0-0.101-0.04136.0240.3410.3410.0000.0000.0000.000
63A63GLN0-0.012-0.01138.494-0.143-0.1430.0000.0000.0000.000
64A64CYS0-0.063-0.02341.0950.0990.0990.0000.0000.0000.000
65A65GLU-1-0.937-0.96043.057-6.413-6.4130.0000.0000.0000.000
66A66GLU-1-0.770-0.85841.692-7.622-7.6220.0000.0000.0000.000
67A67THR00.043-0.00142.357-0.204-0.2040.0000.0000.0000.000
68A68HIS00.0860.02837.008-0.043-0.0430.0000.0000.0000.000
69A69ALA00.0470.02138.578-0.137-0.1370.0000.0000.0000.000
70A70GLN0-0.0070.00740.490-0.046-0.0460.0000.0000.0000.000
71A71ALA00.0460.03238.3930.0110.0110.0000.0000.0000.000
72A72TRP00.0100.00133.1480.1530.1530.0000.0000.0000.000
73A73GLN0-0.021-0.02837.798-0.117-0.1170.0000.0000.0000.000
74A74ARG10.7320.82039.6287.9037.9030.0000.0000.0000.000
75A75LEU0-0.072-0.02535.3470.0200.0200.0000.0000.0000.000
76A76PHE0-0.046-0.02631.739-0.199-0.1990.0000.0000.0000.000
77A77VAL0-0.049-0.00837.051-0.011-0.0110.0000.0000.0000.000
78A78GLY00.0490.04640.4440.1210.1210.0000.0000.0000.000
79A79PRO0-0.071-0.04243.4350.0200.0200.0000.0000.0000.000
80A80TRP0-0.034-0.02545.6130.0750.0750.0000.0000.0000.000
81A81ALA00.0240.00242.989-0.140-0.1400.0000.0000.0000.000
82A82LEU00.0300.02937.1890.0140.0140.0000.0000.0000.000
83A83PRO0-0.011-0.00737.884-0.036-0.0360.0000.0000.0000.000
84A84SER0-0.022-0.02432.5260.0200.0200.0000.0000.0000.000
85A85PRO0-0.011-0.00234.606-0.117-0.1170.0000.0000.0000.000
86A86PRO00.0450.02931.302-0.201-0.2010.0000.0000.0000.000
87A87TRP00.0240.00930.439-0.270-0.2700.0000.0000.0000.000
88A88GLY00.0760.02629.2980.1700.1700.0000.0000.0000.000
89A89SER0-0.066-0.04930.0390.0500.0500.0000.0000.0000.000
90A90VAL0-0.008-0.00533.1700.2510.2510.0000.0000.0000.000
91A91TRP0-0.051-0.02630.7900.2290.2290.0000.0000.0000.000
92A92LEU0-0.020-0.01927.379-0.028-0.0280.0000.0000.0000.000
93A93ASP-1-0.808-0.89231.845-8.527-8.5270.0000.0000.0000.000
94A94ARG10.8940.94435.1568.3168.3160.0000.0000.0000.000
95A95GLU-1-0.934-0.97137.891-7.401-7.4010.0000.0000.0000.000
96A96SER0-0.081-0.04037.0350.1960.1960.0000.0000.0000.000
97A97VAL0-0.0060.00938.1400.0550.0550.0000.0000.0000.000
98A98LEU00.0240.02936.238-0.282-0.2820.0000.0000.0000.000
99A99PHE0-0.041-0.03435.4660.1450.1450.0000.0000.0000.000
100A100GLY00.0420.03435.5070.1420.1420.0000.0000.0000.000
101A101ASP-1-0.902-0.96433.738-9.652-9.6520.0000.0000.0000.000
102A102SER00.004-0.00529.259-0.147-0.1470.0000.0000.0000.000
103A103THR0-0.028-0.02729.557-0.237-0.2370.0000.0000.0000.000
104A104LEU0-0.069-0.02731.228-0.103-0.1030.0000.0000.0000.000
105A105ALA00.0050.00128.255-0.122-0.1220.0000.0000.0000.000
106A106LEU00.0230.01925.091-0.350-0.3500.0000.0000.0000.000
107A107ARG10.8330.88527.2579.2539.2530.0000.0000.0000.000
108A108GLN0-0.078-0.04729.415-0.170-0.1700.0000.0000.0000.000
109A109TRP00.010-0.00219.4190.2180.2180.0000.0000.0000.000
110A110MET00.0100.00124.716-0.302-0.3020.0000.0000.0000.000
111A111ARG10.9200.96626.0639.6629.6620.0000.0000.0000.000
112A112GLU-1-0.978-0.98923.464-13.012-13.0120.0000.0000.0000.000
113A113LYS10.8410.91119.13915.25015.2500.0000.0000.0000.000
114A114GLY0-0.0080.00922.444-0.429-0.4290.0000.0000.0000.000
115A115ILE0-0.060-0.03121.158-0.132-0.1320.0000.0000.0000.000
116A116GLN0-0.019-0.00925.0280.3230.3230.0000.0000.0000.000
117A117PHE00.006-0.00924.818-0.246-0.2460.0000.0000.0000.000
118A118GLU-1-0.953-0.96327.981-9.510-9.5100.0000.0000.0000.000
119A119MET0-0.019-0.02029.287-0.214-0.2140.0000.0000.0000.000
120A120LYS10.8960.97532.7369.4749.4740.0000.0000.0000.000
121A121GLN00.002-0.01636.217-0.068-0.0680.0000.0000.0000.000
122A122ASN0-0.039-0.02739.2150.0640.0640.0000.0000.0000.000
123A123GLU-1-0.841-0.90935.373-8.840-8.8400.0000.0000.0000.000
124A124PRO0-0.039-0.00933.633-0.087-0.0870.0000.0000.0000.000
125A125GLU-1-0.707-0.84329.394-9.945-9.9450.0000.0000.0000.000
126A126ASP-1-0.821-0.90928.108-10.574-10.5740.0000.0000.0000.000
127A127HIS00.0420.03329.096-0.318-0.3180.0000.0000.0000.000
128A128PHE00.0360.00424.261-0.467-0.4670.0000.0000.0000.000
129A129GLY00.0140.00425.183-0.540-0.5400.0000.0000.0000.000
130A130SER00.0300.00825.719-0.320-0.3200.0000.0000.0000.000
131A131LEU0-0.012-0.00123.219-0.451-0.4510.0000.0000.0000.000
132A132LEU00.0030.00920.196-0.822-0.8220.0000.0000.0000.000
133A133LEU0-0.017-0.00621.040-0.671-0.6710.0000.0000.0000.000
134A134MET0-0.032-0.00122.210-0.450-0.4500.0000.0000.0000.000
135A135ALA00.0320.00517.568-0.572-0.5720.0000.0000.0000.000
136A136ALA00.009-0.00517.478-1.082-1.0820.0000.0000.0000.000
137A137TRP00.0020.00118.479-0.694-0.6940.0000.0000.0000.000
138A138LEU0-0.020-0.00517.276-0.200-0.2000.0000.0000.0000.000
139A139ALA0-0.0060.00214.349-0.740-0.7400.0000.0000.0000.000
140A140GLU-1-0.780-0.85714.956-18.702-18.7020.0000.0000.0000.000
141A141ASN0-0.123-0.06517.4020.6500.6500.0000.0000.0000.000
142A142GLY00.0260.02112.9140.1750.1750.0000.0000.0000.000
143A143ARG10.7510.86912.34914.58514.5850.0000.0000.0000.000
144A144GLN00.034-0.0056.530-1.169-1.1690.0000.0000.0000.000
145A145THR0-0.004-0.00311.765-0.879-0.8790.0000.0000.0000.000
146A146GLU-1-0.781-0.87613.040-17.954-17.9540.0000.0000.0000.000
147A147CYS0-0.011-0.00413.8900.9790.9790.0000.0000.0000.000
148A148GLU-1-0.776-0.87910.641-27.705-27.7050.0000.0000.0000.000
149A149GLU-1-0.813-0.88314.243-15.850-15.8500.0000.0000.0000.000
150A150LEU0-0.049-0.01117.5230.8950.8950.0000.0000.0000.000
151A151LEU00.004-0.00614.5680.7690.7690.0000.0000.0000.000
152A152ALA00.0270.01315.9870.7950.7950.0000.0000.0000.000
153A153TRP0-0.033-0.03517.9980.8300.8300.0000.0000.0000.000
154A154HIS00.0150.00921.3960.9950.9950.0000.0000.0000.000
155A155LEU0-0.0090.02320.4140.5330.5330.0000.0000.0000.000
156A156PHE00.042-0.00515.3700.4600.4600.0000.0000.0000.000
157A157PRO0-0.073-0.01921.3360.3770.3770.0000.0000.0000.000
158A158TRP0-0.015-0.01224.0550.6080.6080.0000.0000.0000.000
159A159SER0-0.0080.00322.3710.3290.3290.0000.0000.0000.000
160A160THR00.0260.00723.2000.1110.1110.0000.0000.0000.000
161A161ARG10.8390.90325.4909.6979.6970.0000.0000.0000.000
162A162PHE00.0290.02527.5460.2830.2830.0000.0000.0000.000
163A163LEU00.0300.01724.4660.3430.3430.0000.0000.0000.000
164A164ASP-1-0.882-0.93228.554-10.840-10.8400.0000.0000.0000.000
165A165VAL0-0.035-0.01830.4500.3160.3160.0000.0000.0000.000
166A166PHE0-0.020-0.01831.0170.2790.2790.0000.0000.0000.000
167A167ILE0-0.054-0.02328.0420.2110.2110.0000.0000.0000.000
168A168GLU-1-0.922-0.95332.645-8.171-8.1710.0000.0000.0000.000
169A169LYS10.8350.90835.5728.4488.4480.0000.0000.0000.000
170A170ALA00.0340.04334.4580.1660.1660.0000.0000.0000.000
171A171GLU-1-0.896-0.96336.577-7.738-7.7380.0000.0000.0000.000
172A172HIS0-0.0030.00137.422-0.037-0.0370.0000.0000.0000.000
173A173PRO0-0.038-0.01136.309-0.247-0.2470.0000.0000.0000.000
174A174PHE00.0600.03631.404-0.296-0.2960.0000.0000.0000.000
175A175TYR00.0420.00232.248-0.264-0.2640.0000.0000.0000.000
176A176ARG10.8950.95231.8828.3588.3580.0000.0000.0000.000
177A177ALA00.0610.03230.223-0.322-0.3220.0000.0000.0000.000
178A178LEU00.0030.00527.385-0.488-0.4880.0000.0000.0000.000
179A179GLY00.0220.00426.907-0.489-0.4890.0000.0000.0000.000
180A180GLU-1-0.939-0.97726.561-10.836-10.8360.0000.0000.0000.000
181A181LEU00.0210.01723.019-0.505-0.5050.0000.0000.0000.000
182A182ALA0-0.0030.01222.444-0.856-0.8560.0000.0000.0000.000
183A183ARG10.8790.92621.83210.56010.5600.0000.0000.0000.000
184A184LEU0-0.002-0.00621.151-0.514-0.5140.0000.0000.0000.000
185A185THR00.013-0.00617.662-0.940-0.9400.0000.0000.0000.000
186A186LEU0-0.016-0.01316.958-1.135-1.1350.0000.0000.0000.000
187A187ALA0-0.0050.01017.314-0.718-0.7180.0000.0000.0000.000
188A188GLN0-0.037-0.01512.0010.2770.2770.0000.0000.0000.000
189A189TRP00.0290.00712.537-0.972-0.9720.0000.0000.0000.000
190A190GLN0-0.018-0.00212.606-1.066-1.0660.0000.0000.0000.000
191A191SER0-0.097-0.05813.124-0.636-0.6360.0000.0000.0000.000
192A192GLN0-0.029-0.0137.6910.9410.9410.0000.0000.0000.000
193A193LEU0-0.051-0.0068.670-2.933-2.9330.0000.0000.0000.000
194A194LEU0-0.038-0.0285.826-1.479-1.4790.0000.0000.0000.000
195A195ILE0-0.044-0.00810.1281.3681.3680.0000.0000.0000.000
196A196PRO0-0.028-0.02713.8230.1210.1210.0000.0000.0000.000
197A197VAL00.0320.02817.0690.0930.0930.0000.0000.0000.000
198A198ALA0-0.041-0.01518.7610.5430.5430.0000.0000.0000.000
199A199VAL00.007-0.00222.2770.1590.1590.0000.0000.0000.000
200A200LYS10.9360.95725.15011.39411.3940.0000.0000.0000.000
201A201PRO0-0.041-0.00628.501-0.072-0.0720.0000.0000.0000.000
202A202LEU00.007-0.00628.395-0.132-0.1320.0000.0000.0000.000
203A203PHE0-0.031-0.01932.5630.2620.2620.0000.0000.0000.000
204A204ARG00.1510.13934.310-0.577-0.5770.0000.0000.0000.000