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: NLZ7Q

Calculation Name: 2FO5-A-Xray547

Preferred Name:

Target Type:

Ligand Name: amino{[(4s)-4-amino-5,5-dihydroxypentyl]amino}methaniminium | acetyl group

Ligand 3-letter code: AR7 | ACE

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2FO5

Chain ID: A

ChEMBL ID:

UniProt ID: P25250

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 224
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2527005.666614
FMO2-HF: Nuclear repulsion 2442626.32704
FMO2-HF: Total energy -84379.339574
FMO2-MP2: Total energy -84621.047494


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:3:ASP)


Summations of interaction energy for fragment #1(A:3:ASP)
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.
8.36510.475-0.001-1.005-1.1040.002
Interaction energy analysis for fragmet #1(A:3:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.067 / q_NPA : -0.039
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].
3A5PRO0-0.0180.0163.7321.6053.715-0.001-1.005-1.1040.002
4A6PRO00.0360.0136.0331.8531.8530.0000.0000.0000.000
5A7SER0-0.017-0.0158.3110.0080.0080.0000.0000.0000.000
6A8VAL0-0.027-0.00810.477-0.906-0.9060.0000.0000.0000.000
7A9ASP-1-0.746-0.85912.8620.1010.1010.0000.0000.0000.000
8A10TRP0-0.004-0.01412.506-0.275-0.2750.0000.0000.0000.000
9A11ARG10.8210.89318.001-0.018-0.0180.0000.0000.0000.000
10A12GLN0-0.041-0.01417.834-0.137-0.1370.0000.0000.0000.000
11A13LYS10.8980.95512.0772.9342.9340.0000.0000.0000.000
12A14GLY00.0030.01619.061-0.089-0.0890.0000.0000.0000.000
13A15ALA0-0.004-0.01019.1510.0020.0020.0000.0000.0000.000
14A16VAL00.011-0.00620.8280.0360.0360.0000.0000.0000.000
15A17THR0-0.060-0.04523.4910.0530.0530.0000.0000.0000.000
16A18GLY00.0270.01027.1730.0430.0430.0000.0000.0000.000
17A19VAL0-0.023-0.00228.207-0.026-0.0260.0000.0000.0000.000
18A20LYS10.8270.92229.7630.3310.3310.0000.0000.0000.000
19A21ASP-1-0.853-0.93933.0460.0400.0400.0000.0000.0000.000
20A22GLN00.0570.04533.517-0.021-0.0210.0000.0000.0000.000
21A23GLY00.0150.00636.547-0.010-0.0100.0000.0000.0000.000
22A24LYS10.8830.91739.0080.0110.0110.0000.0000.0000.000
23A25CYS00.0160.08838.9490.0040.0040.0000.0000.0000.000
24A26GLY00.0680.05037.1040.0090.0090.0000.0000.0000.000
25A27SER00.049-0.01335.5210.0030.0030.0000.0000.0000.000
26A28CYS0-0.0620.00030.942-0.041-0.0410.0000.0000.0000.000
27A29TRP00.0840.05129.711-0.030-0.0300.0000.0000.0000.000
28A30ALA00.0110.02929.559-0.049-0.0490.0000.0000.0000.000
29A31PHE0-0.007-0.01730.023-0.047-0.0470.0000.0000.0000.000
30A32SER0-0.036-0.02925.274-0.072-0.0720.0000.0000.0000.000
31A33THR00.0000.00125.206-0.060-0.0600.0000.0000.0000.000
32A34VAL00.0140.00225.633-0.097-0.0970.0000.0000.0000.000
33A35VAL0-0.033-0.00922.793-0.084-0.0840.0000.0000.0000.000
34A36SER00.017-0.01621.185-0.107-0.1070.0000.0000.0000.000
35A37VAL0-0.006-0.00121.655-0.168-0.1680.0000.0000.0000.000
36A38GLU-1-0.763-0.87024.262-0.548-0.5480.0000.0000.0000.000
37A39GLY00.0310.01920.913-0.079-0.0790.0000.0000.0000.000
38A40ILE0-0.023-0.01417.327-0.191-0.1910.0000.0000.0000.000
39A41ASN00.0280.00720.159-0.145-0.1450.0000.0000.0000.000
40A42ALA0-0.0080.02421.618-0.069-0.0690.0000.0000.0000.000
41A43ILE0-0.040-0.02315.610-0.099-0.0990.0000.0000.0000.000
42A44ARG10.8540.92914.9712.2252.2250.0000.0000.0000.000
43A45THR0-0.045-0.04420.2870.0680.0680.0000.0000.0000.000
44A46GLY0-0.0120.01022.0430.0520.0520.0000.0000.0000.000
45A47SER0-0.053-0.02523.2670.1210.1210.0000.0000.0000.000
46A48LEU0-0.005-0.00224.141-0.008-0.0080.0000.0000.0000.000
47A49VAL0-0.028-0.00826.3390.0810.0810.0000.0000.0000.000
48A50SER0-0.018-0.01228.3340.0090.0090.0000.0000.0000.000
49A51LEU0-0.066-0.04027.7670.0080.0080.0000.0000.0000.000
50A52SER00.009-0.00231.4720.0380.0380.0000.0000.0000.000
51A53GLU-1-0.764-0.89131.275-0.296-0.2960.0000.0000.0000.000
52A54GLN0-0.047-0.04134.0260.0300.0300.0000.0000.0000.000
53A55GLU-1-0.770-0.88135.407-0.383-0.3830.0000.0000.0000.000
54A56LEU0-0.008-0.00230.6590.0100.0100.0000.0000.0000.000
55A57ILE0-0.0190.00035.3160.0240.0240.0000.0000.0000.000
56A58ASP-1-0.758-0.86538.273-0.168-0.1680.0000.0000.0000.000
57A59CYS0-0.098-0.04337.9210.0130.0130.0000.0000.0000.000
58A60ASP-1-0.835-0.90133.833-0.249-0.2490.0000.0000.0000.000
59A61THR0-0.066-0.04437.0630.0240.0240.0000.0000.0000.000
60A62ALA0-0.054-0.00737.8840.0140.0140.0000.0000.0000.000
61A63ASP-1-0.889-0.95035.734-0.139-0.1390.0000.0000.0000.000
62A64ASN0-0.077-0.02532.5490.0560.0560.0000.0000.0000.000
63A65ASP-1-0.783-0.89436.973-0.058-0.0580.0000.0000.0000.000
64A66GLY0-0.004-0.00838.6410.0140.0140.0000.0000.0000.000
65A67CYS0-0.113-0.09838.1410.0030.0030.0000.0000.0000.000
66A68GLN0-0.090-0.05440.3560.0260.0260.0000.0000.0000.000
67A69GLY00.0310.02536.3740.0270.0270.0000.0000.0000.000
68A70GLY0-0.013-0.01134.438-0.026-0.0260.0000.0000.0000.000
69A71LEU00.0340.02329.8430.0320.0320.0000.0000.0000.000
70A72MET00.0280.00825.736-0.035-0.0350.0000.0000.0000.000
71A73ASP-1-0.860-0.93225.971-0.237-0.2370.0000.0000.0000.000
72A74ASN0-0.014-0.01327.184-0.070-0.0700.0000.0000.0000.000
73A75ALA00.0270.02229.433-0.036-0.0360.0000.0000.0000.000
74A76PHE0-0.042-0.03923.248-0.073-0.0730.0000.0000.0000.000
75A77GLU-1-0.810-0.87527.662-0.569-0.5690.0000.0000.0000.000
76A78TYR0-0.033-0.04429.891-0.007-0.0070.0000.0000.0000.000
77A79ILE00.004-0.00428.201-0.022-0.0220.0000.0000.0000.000
78A80LYS10.8040.91027.6350.5750.5750.0000.0000.0000.000
79A81ASN0-0.076-0.05329.618-0.048-0.0480.0000.0000.0000.000
80A82ASN0-0.093-0.04733.1320.0410.0410.0000.0000.0000.000
81A83GLY0-0.030-0.00133.4600.0130.0130.0000.0000.0000.000
82A84GLY0-0.005-0.00830.424-0.018-0.0180.0000.0000.0000.000
83A85LEU0-0.012-0.00229.4750.0420.0420.0000.0000.0000.000
84A86ILE0-0.0240.00532.178-0.038-0.0380.0000.0000.0000.000
85A87THR00.010-0.00933.1020.0120.0120.0000.0000.0000.000
86A88GLU-1-0.808-0.91234.092-0.242-0.2420.0000.0000.0000.000
87A89ALA0-0.059-0.03935.8680.0260.0260.0000.0000.0000.000
88A90ALA0-0.0150.00438.0210.0200.0200.0000.0000.0000.000
89A91TYR0-0.100-0.08438.3390.0180.0180.0000.0000.0000.000
90A92PRO00.0330.04238.5990.0010.0010.0000.0000.0000.000
91A93TYR0-0.018-0.03537.5870.0160.0160.0000.0000.0000.000
92A94ARG10.8690.91939.6490.1860.1860.0000.0000.0000.000
93A95ALA0-0.051-0.00440.7000.0160.0160.0000.0000.0000.000
94A96ALA0-0.003-0.01341.7150.0210.0210.0000.0000.0000.000
95A97ARG10.9250.96841.5580.0850.0850.0000.0000.0000.000
96A98GLY0-0.036-0.01143.6460.0120.0120.0000.0000.0000.000
97A99THR0-0.038-0.02944.7500.0010.0010.0000.0000.0000.000
98A100CYS00.0620.04942.003-0.013-0.0130.0000.0000.0000.000
99A101ASN0-0.073-0.06143.3210.0020.0020.0000.0000.0000.000
100A102VAL00.0840.04338.5410.0000.0000.0000.0000.0000.000
101A103ALA00.0190.02241.445-0.016-0.0160.0000.0000.0000.000
102A104ARG10.9220.95043.2480.2010.2010.0000.0000.0000.000
103A105ALA0-0.0120.01341.7510.0050.0050.0000.0000.0000.000
104A106ALA00.0540.01540.044-0.009-0.0090.0000.0000.0000.000
105A107GLN0-0.096-0.03841.442-0.008-0.0080.0000.0000.0000.000
106A108ASN0-0.016-0.01644.393-0.004-0.0040.0000.0000.0000.000
107A109SER0-0.043-0.02939.820-0.002-0.0020.0000.0000.0000.000
108A110PRO00.0120.01939.045-0.003-0.0030.0000.0000.0000.000
109A111VAL0-0.044-0.01233.263-0.029-0.0290.0000.0000.0000.000
110A112VAL00.0360.00932.9990.0280.0280.0000.0000.0000.000
111A113VAL0-0.053-0.01926.528-0.051-0.0510.0000.0000.0000.000
112A114HIS00.0260.01728.4810.0190.0190.0000.0000.0000.000
113A115ILE0-0.043-0.02324.223-0.098-0.0980.0000.0000.0000.000
114A116ASP-1-0.775-0.87922.256-1.268-1.2680.0000.0000.0000.000
115A117GLY00.000-0.00924.2790.0660.0660.0000.0000.0000.000
116A118HIS10.8420.93621.9760.4220.4220.0000.0000.0000.000
117A119GLN0-0.052-0.01616.930-0.093-0.0930.0000.0000.0000.000
118A120ASP-1-0.817-0.91720.106-0.268-0.2680.0000.0000.0000.000
119A121VAL0-0.029-0.02215.233-0.142-0.1420.0000.0000.0000.000
120A122PRO0-0.034-0.01915.3200.0550.0550.0000.0000.0000.000
121A123ALA00.0590.03417.8300.1800.1800.0000.0000.0000.000
122A124ASN0-0.035-0.03519.3800.0470.0470.0000.0000.0000.000
123A125SER0-0.016-0.00713.6210.4280.4280.0000.0000.0000.000
124A126GLU-1-0.687-0.86413.6651.9571.9570.0000.0000.0000.000
125A127GLU-1-0.927-0.9699.0745.2525.2520.0000.0000.0000.000
126A128ASP-1-0.882-0.9219.5320.8040.8040.0000.0000.0000.000
127A129LEU00.0190.02111.925-0.628-0.6280.0000.0000.0000.000
128A130ALA0-0.0130.0038.756-0.417-0.4170.0000.0000.0000.000
129A131ARG10.9010.9256.022-2.619-2.6190.0000.0000.0000.000
130A132ALA00.0070.0268.880-1.273-1.2730.0000.0000.0000.000
131A133VAL00.0530.02412.517-0.488-0.4880.0000.0000.0000.000
132A134ALA0-0.051-0.0238.109-0.304-0.3040.0000.0000.0000.000
133A135ASN0-0.123-0.0658.380-1.693-1.6930.0000.0000.0000.000
134A136GLN0-0.044-0.03811.405-0.173-0.1730.0000.0000.0000.000
135A137PRO0-0.040-0.01715.1750.1950.1950.0000.0000.0000.000
136A138VAL0-0.0050.00515.731-0.117-0.1170.0000.0000.0000.000
137A139SER00.0070.00218.9340.0860.0860.0000.0000.0000.000
138A140VAL0-0.028-0.01619.5650.0080.0080.0000.0000.0000.000
139A141ALA00.0490.03322.837-0.033-0.0330.0000.0000.0000.000
140A142VAL0-0.028-0.02223.8450.0870.0870.0000.0000.0000.000
141A143GLU-1-0.789-0.86326.3480.4840.4840.0000.0000.0000.000
142A144ALA0-0.048-0.04628.5500.0430.0430.0000.0000.0000.000
143A145SER0-0.044-0.04730.7600.0000.0000.0000.0000.0000.000
144A146GLY00.0600.03532.494-0.004-0.0040.0000.0000.0000.000
145A147LYS10.9160.93233.276-0.312-0.3120.0000.0000.0000.000
146A148ALA00.0040.00431.283-0.022-0.0220.0000.0000.0000.000
147A149PHE00.0530.04025.8700.0080.0080.0000.0000.0000.000
148A150MET0-0.022-0.01830.537-0.029-0.0290.0000.0000.0000.000
149A151PHE0-0.088-0.04133.724-0.043-0.0430.0000.0000.0000.000
150A152TYR00.0020.01125.174-0.023-0.0230.0000.0000.0000.000
151A153SER0-0.060-0.03131.142-0.036-0.0360.0000.0000.0000.000
152A154GLU-1-0.918-0.96627.9520.4170.4170.0000.0000.0000.000
153A155GLY00.0020.00325.1040.0420.0420.0000.0000.0000.000
154A156VAL0-0.036-0.01120.088-0.033-0.0330.0000.0000.0000.000
155A157PHE00.010-0.00322.9350.0000.0000.0000.0000.0000.000
156A158THR00.009-0.01322.9220.0490.0490.0000.0000.0000.000
157A159GLY00.0220.02724.5990.0420.0420.0000.0000.0000.000
158A160GLU-1-1.013-1.00727.6530.6210.6210.0000.0000.0000.000
159A161CYS0-0.133-0.10726.249-0.019-0.0190.0000.0000.0000.000
160A162GLY0-0.0060.00128.5630.0700.0700.0000.0000.0000.000
161A163THR0-0.041-0.04225.8260.0490.0490.0000.0000.0000.000
162A164GLU-1-0.977-0.98328.4980.3430.3430.0000.0000.0000.000
163A165LEU0-0.053-0.03026.364-0.007-0.0070.0000.0000.0000.000
164A166ASP-1-0.764-0.85829.9070.2690.2690.0000.0000.0000.000
165A167HIS0-0.043-0.03729.350-0.060-0.0600.0000.0000.0000.000
166A168GLY00.0390.02127.5920.0260.0260.0000.0000.0000.000
167A169VAL0-0.011-0.01123.671-0.020-0.0200.0000.0000.0000.000
168A170ALA00.0410.03722.529-0.040-0.0400.0000.0000.0000.000
169A171VAL0-0.0050.01616.5430.0430.0430.0000.0000.0000.000
170A172VAL00.000-0.01518.533-0.205-0.2050.0000.0000.0000.000
171A173GLY00.009-0.02515.072-0.267-0.2670.0000.0000.0000.000
172A174TYR0-0.030-0.0247.449-0.154-0.1540.0000.0000.0000.000
173A175GLY0-0.0080.00513.077-0.279-0.2790.0000.0000.0000.000
174A176VAL0-0.0130.00212.3360.3480.3480.0000.0000.0000.000
175A177ALA0-0.021-0.00515.163-0.308-0.3080.0000.0000.0000.000
176A178GLU-1-0.956-0.98518.4891.1641.1640.0000.0000.0000.000
177A179ASP-1-0.898-0.95220.7331.5791.5790.0000.0000.0000.000
178A180GLY0-0.027-0.01017.1760.0750.0750.0000.0000.0000.000
179A181LYS10.8350.91216.610-1.271-1.2710.0000.0000.0000.000
180A182ALA00.0300.02013.395-0.102-0.1020.0000.0000.0000.000
181A183TYR00.008-0.01415.173-0.231-0.2310.0000.0000.0000.000
182A184TRP00.012-0.00712.2200.0070.0070.0000.0000.0000.000
183A185THR0-0.031-0.03117.0380.0060.0060.0000.0000.0000.000
184A186VAL0-0.0060.00219.079-0.161-0.1610.0000.0000.0000.000
185A187LYS10.8420.92021.7790.2910.2910.0000.0000.0000.000
186A188ASN00.0450.03124.695-0.028-0.0280.0000.0000.0000.000
187A189SER0-0.014-0.02627.954-0.050-0.0500.0000.0000.0000.000
188A190TRP0-0.0150.00031.2630.0040.0040.0000.0000.0000.000
189A191GLY00.0380.02233.3820.0110.0110.0000.0000.0000.000
190A192PRO0-0.019-0.03031.9760.0270.0270.0000.0000.0000.000
191A193SER0-0.059-0.03233.0490.0130.0130.0000.0000.0000.000
192A194TRP00.0090.01927.8290.0130.0130.0000.0000.0000.000
193A195GLY00.0400.02829.374-0.016-0.0160.0000.0000.0000.000
194A196GLU-1-0.737-0.82224.3490.5550.5550.0000.0000.0000.000
195A197GLN0-0.066-0.04927.388-0.040-0.0400.0000.0000.0000.000
196A198GLY0-0.0020.00129.424-0.063-0.0630.0000.0000.0000.000
197A199TYR0-0.056-0.03823.338-0.071-0.0710.0000.0000.0000.000
198A200ILE00.0150.00824.1520.0230.0230.0000.0000.0000.000
199A201ARG10.7770.86920.197-0.791-0.7910.0000.0000.0000.000
200A202VAL00.0210.02320.5470.0440.0440.0000.0000.0000.000
201A203GLU-1-0.848-0.92419.0341.7771.7770.0000.0000.0000.000
202A204LYS10.7690.8749.790-4.268-4.2680.0000.0000.0000.000
203A205ASP-1-0.875-0.92211.4564.8204.8200.0000.0000.0000.000
204A206SER0-0.0160.01114.664-0.052-0.0520.0000.0000.0000.000
205A207GLY0-0.003-0.01518.3600.0710.0710.0000.0000.0000.000
206A208ALA0-0.030-0.00920.832-0.095-0.0950.0000.0000.0000.000
207A209SER0-0.008-0.01320.1990.0860.0860.0000.0000.0000.000
208A210GLY00.0690.03219.6820.0630.0630.0000.0000.0000.000
209A211GLY00.0340.02118.985-0.084-0.0840.0000.0000.0000.000
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216A218GLU-1-0.912-0.95922.2820.1680.1680.0000.0000.0000.000
217A219ALA00.0050.00918.791-0.054-0.0540.0000.0000.0000.000
218A220SER00.0000.00420.199-0.070-0.0700.0000.0000.0000.000
219A221TYR00.001-0.01114.6400.0640.0640.0000.0000.0000.000
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222A224LYS10.8710.92819.5461.2891.2890.0000.0000.0000.000
223A225THR0-0.104-0.06318.656-0.236-0.2360.0000.0000.0000.000
224A226TYR-1-0.910-0.94020.885-1.424-1.4240.0000.0000.0000.000