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: 1VLRZ

Calculation Name: 1I2A-A-Xray549

Preferred Name:

Target Type:

Ligand Name: pentanal

Ligand 3-letter code: PTL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1I2A

Chain ID: A

ChEMBL ID:

UniProt ID: P54050

Base Structure: X-ray

Registration Date: 2025-10-11

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 OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 212
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230712
Total energy (hartree)
FMO2-HF: Electronic energy -2405559.58266
FMO2-HF: Nuclear repulsion 2322223.674095
FMO2-HF: Total energy -83335.908565
FMO2-MP2: Total energy -83580.181594


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.
117.369125.1786.817-4.589-10.038-0.04
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 : 0.784 / q_NPA : 0.892
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].
3A3ARG10.8640.9073.30215.99218.4090.004-1.339-1.082-0.007
5A5ALA0-0.025-0.0242.001-1.697-1.1721.802-1.123-1.205-0.016
6A6LEU0-0.060-0.0282.5492.3653.3050.412-0.225-1.128-0.001
28A28PHE00.0530.0243.807-0.955-0.8010.000-0.018-0.1360.000
182A182LEU00.000-0.0062.2990.6950.4112.291-0.268-1.738-0.003
193A193LEU0-0.008-0.0312.803-0.4190.5500.203-0.210-0.9620.001
194A194TYR0-0.038-0.0325.190-2.110-1.876-0.001-0.016-0.2170.000
196A196ILE0-0.0060.0033.7091.0001.8570.150-0.171-0.8360.000
197A197LYS10.8790.9436.26819.57919.659-0.001-0.003-0.0760.000
199A199ALA00.000-0.0054.1731.8021.9870.001-0.032-0.1540.000
211A211VAL0-0.041-0.0222.719-3.398-2.4560.322-0.377-0.887-0.004
212A212LYS00.0390.0252.336-8.713-7.9231.634-0.807-1.617-0.010
4A4GLU-1-0.857-0.9166.156-30.553-30.5530.0000.0000.0000.000
7A7LEU00.0360.0135.4695.2515.2510.0000.0000.0000.000
8A8GLN00.0370.0227.6715.0215.0210.0000.0000.0000.000
9A9ALA00.0320.0166.9142.7472.7470.0000.0000.0000.000
10A10VAL0-0.068-0.0328.6873.2943.2940.0000.0000.0000.000
11A11LYS10.8950.94411.21522.91722.9170.0000.0000.0000.000
12A12GLU-1-0.885-0.94511.864-22.307-22.3070.0000.0000.0000.000
13A13ALA0-0.064-0.03212.6811.7951.7950.0000.0000.0000.000
14A14ARG10.7460.83514.42918.96718.9670.0000.0000.0000.000
15A15GLU-1-0.870-0.91816.402-17.488-17.4880.0000.0000.0000.000
16A16LEU0-0.012-0.00315.6471.1571.1570.0000.0000.0000.000
17A17ALA0-0.058-0.02718.8190.6950.6950.0000.0000.0000.000
18A18LYS10.9560.98220.59812.16712.1670.0000.0000.0000.000
19A19PRO00.0580.02524.3670.0400.0400.0000.0000.0000.000
20A20ARG10.8930.94424.14212.79412.7940.0000.0000.0000.000
21A21ASN00.0200.01528.146-0.179-0.1790.0000.0000.0000.000
22A22PHE0-0.044-0.02923.8230.2330.2330.0000.0000.0000.000
23A23THR0-0.0250.00222.992-0.262-0.2620.0000.0000.0000.000
24A24GLN0-0.030-0.01920.626-0.024-0.0240.0000.0000.0000.000
25A25SER0-0.009-0.02018.175-0.030-0.0300.0000.0000.0000.000
26A26PHE00.0320.01113.4250.1190.1190.0000.0000.0000.000
27A27GLU-1-0.911-0.94713.406-16.511-16.5110.0000.0000.0000.000
29A29ILE0-0.019-0.0248.8442.1642.1640.0000.0000.0000.000
30A30ALA00.0360.0256.259-2.995-2.9950.0000.0000.0000.000
31A31THR00.002-0.0078.0002.1122.1120.0000.0000.0000.000
32A32LEU0-0.006-0.0048.956-1.624-1.6240.0000.0000.0000.000
33A33LYS10.9210.9808.95825.52825.5280.0000.0000.0000.000
34A34GLU-1-0.815-0.88812.233-19.368-19.3680.0000.0000.0000.000
35A35ILE0-0.012-0.00112.9190.1570.1570.0000.0000.0000.000
36A36ASP-1-0.812-0.91115.732-12.181-12.1810.0000.0000.0000.000
37A37MET0-0.0170.02114.6720.4880.4880.0000.0000.0000.000
38A38ARG10.9820.99119.48811.55711.5570.0000.0000.0000.000
39A39LYS10.9791.00421.68712.52312.5230.0000.0000.0000.000
40A40PRO00.010-0.01421.437-0.526-0.5260.0000.0000.0000.000
41A41GLU-1-0.887-0.93220.739-12.459-12.4590.0000.0000.0000.000
42A42ASN00.016-0.00417.629-0.958-0.9580.0000.0000.0000.000
43A43ARG10.8290.92516.30911.16011.1600.0000.0000.0000.000
44A44ILE0-0.026-0.01111.7510.1390.1390.0000.0000.0000.000
45A45LYS10.9510.96315.91811.86811.8680.0000.0000.0000.000
46A46THR0-0.0110.00315.1850.8170.8170.0000.0000.0000.000
47A47GLU-1-0.945-0.96316.122-12.775-12.7750.0000.0000.0000.000
48A48VAL00.009-0.00312.146-0.313-0.3130.0000.0000.0000.000
49A49VAL0-0.017-0.00515.4440.3010.3010.0000.0000.0000.000
50A50LEU0-0.0060.01112.867-0.698-0.6980.0000.0000.0000.000
51A51PRO00.0390.01813.0321.1991.1990.0000.0000.0000.000
52A52HIS00.0080.00215.0192.0312.0310.0000.0000.0000.000
53A53GLY0-0.032-0.01417.7720.7370.7370.0000.0000.0000.000
54A54ARG10.8620.90117.24612.53812.5380.0000.0000.0000.000
55A55GLY00.0660.03618.737-0.019-0.0190.0000.0000.0000.000
56A56LYS10.8690.92620.82712.16612.1660.0000.0000.0000.000
57A57GLU-1-0.835-0.91322.543-11.036-11.0360.0000.0000.0000.000
58A58ALA0-0.074-0.02922.2680.2150.2150.0000.0000.0000.000
59A59LYS10.9090.95024.26410.36110.3610.0000.0000.0000.000
60A60ILE00.0210.00526.642-0.096-0.0960.0000.0000.0000.000
61A61ALA00.0100.01429.5580.2300.2300.0000.0000.0000.000
62A62VAL0-0.009-0.01332.257-0.224-0.2240.0000.0000.0000.000
63A63ILE0-0.019-0.01434.8360.2070.2070.0000.0000.0000.000
64A64GLY0-0.003-0.01637.278-0.074-0.0740.0000.0000.0000.000
65A65THR0-0.044-0.03339.9140.1590.1590.0000.0000.0000.000
66A66GLY00.0460.01442.371-0.100-0.1000.0000.0000.0000.000
67A67ASP-1-0.792-0.89841.254-7.268-7.2680.0000.0000.0000.000
68A68LEU0-0.0050.00635.888-0.156-0.1560.0000.0000.0000.000
69A69ALA0-0.043-0.02738.324-0.174-0.1740.0000.0000.0000.000
70A70LYS10.8840.95540.6196.6326.6320.0000.0000.0000.000
71A71GLN00.0810.01436.538-0.365-0.3650.0000.0000.0000.000
72A72ALA0-0.039-0.02235.933-0.208-0.2080.0000.0000.0000.000
73A73GLU-1-0.805-0.88736.952-6.985-6.9850.0000.0000.0000.000
74A74GLU-1-0.934-0.96838.937-7.415-7.4150.0000.0000.0000.000
75A75LEU0-0.084-0.04232.562-0.193-0.1930.0000.0000.0000.000
76A76GLY0-0.0060.01034.042-0.243-0.2430.0000.0000.0000.000
77A77LEU0-0.077-0.04031.095-0.210-0.2100.0000.0000.0000.000
78A78THR0-0.047-0.04434.3850.2840.2840.0000.0000.0000.000
79A79VAL00.0160.01435.909-0.139-0.1390.0000.0000.0000.000
80A80ILE0-0.056-0.02536.4150.0400.0400.0000.0000.0000.000
81A81ARG10.9120.93939.7966.7036.7030.0000.0000.0000.000
82A82LYS10.9680.97542.7226.3756.3750.0000.0000.0000.000
83A83GLU-1-0.850-0.93844.098-6.460-6.4600.0000.0000.0000.000
84A84GLU-1-0.837-0.91042.701-6.995-6.9950.0000.0000.0000.000
85A85ILE0-0.038-0.01540.450-0.114-0.1140.0000.0000.0000.000
86A86GLU-1-0.856-0.92342.606-6.229-6.2290.0000.0000.0000.000
87A87GLU-1-0.930-0.95445.334-6.285-6.2850.0000.0000.0000.000
88A88LEU0-0.052-0.04338.985-0.045-0.0450.0000.0000.0000.000
89A89GLY00.0220.01841.873-0.093-0.0930.0000.0000.0000.000
90A90LYS10.9700.99743.0855.9575.9570.0000.0000.0000.000
91A91ASN00.0200.01443.817-0.107-0.1070.0000.0000.0000.000
92A92LYS10.9540.95140.2516.7556.7550.0000.0000.0000.000
93A93ARG10.9440.98139.4156.7936.7930.0000.0000.0000.000
94A94LYS10.9690.98739.1736.7306.7300.0000.0000.0000.000
95A95LEU00.0550.04436.621-0.195-0.1950.0000.0000.0000.000
96A96ARG10.9620.97735.1487.3507.3500.0000.0000.0000.000
97A97LYS10.9260.96834.2447.3587.3580.0000.0000.0000.000
98A98ILE00.0480.02134.348-0.214-0.2140.0000.0000.0000.000
99A99ALA00.0320.02031.707-0.233-0.2330.0000.0000.0000.000
100A100LYS10.8940.94329.9958.9158.9150.0000.0000.0000.000
101A101ALA0-0.035-0.01629.654-0.274-0.2740.0000.0000.0000.000
102A102HIS00.0240.02729.3630.0240.0240.0000.0000.0000.000
103A103ASP-1-0.844-0.88223.724-11.640-11.6400.0000.0000.0000.000
104A104PHE00.013-0.00320.685-0.086-0.0860.0000.0000.0000.000
105A105PHE00.0230.00326.8680.3240.3240.0000.0000.0000.000
106A106ILE00.0110.02229.398-0.208-0.2080.0000.0000.0000.000
107A107ALA00.004-0.00931.5180.2140.2140.0000.0000.0000.000
108A108GLN00.0640.03034.772-0.127-0.1270.0000.0000.0000.000
109A109ALA0-0.004-0.00736.3860.0610.0610.0000.0000.0000.000
110A110ASP-1-0.838-0.90437.537-7.007-7.0070.0000.0000.0000.000
111A111LEU00.010-0.00139.5440.1440.1440.0000.0000.0000.000
112A112MET00.0090.01932.6990.0130.0130.0000.0000.0000.000
113A113PRO00.0090.00137.676-0.046-0.0460.0000.0000.0000.000
114A114LEU0-0.0180.00040.2940.0970.0970.0000.0000.0000.000
115A115ILE00.0570.01035.691-0.008-0.0080.0000.0000.0000.000
116A116GLY0-0.003-0.01836.569-0.068-0.0680.0000.0000.0000.000
117A117ARG10.9050.96737.4936.6366.6360.0000.0000.0000.000
118A118TYR0-0.025-0.01340.8800.0220.0220.0000.0000.0000.000
119A119MET0-0.012-0.01436.6120.0060.0060.0000.0000.0000.000
120A120GLY00.0420.01834.863-0.207-0.2070.0000.0000.0000.000
121A121VAL0-0.0010.00734.529-0.220-0.2200.0000.0000.0000.000
122A122ILE0-0.082-0.04434.067-0.084-0.0840.0000.0000.0000.000
123A123LEU00.0520.01931.685-0.238-0.2380.0000.0000.0000.000
124A124GLY00.0310.02430.065-0.315-0.3150.0000.0000.0000.000
125A125PRO0-0.021-0.02029.198-0.343-0.3430.0000.0000.0000.000
126A126ARG10.8440.92027.7548.8118.8110.0000.0000.0000.000
127A127GLY0-0.0030.00725.115-0.336-0.3360.0000.0000.0000.000
128A128LYS10.8070.90025.68910.22910.2290.0000.0000.0000.000
129A129MET0-0.0160.00228.0920.3430.3430.0000.0000.0000.000
130A130PRO00.001-0.00128.956-0.250-0.2500.0000.0000.0000.000
131A131LYS10.9470.98626.16310.00210.0020.0000.0000.0000.000
132A132PRO0-0.0060.00229.3670.1560.1560.0000.0000.0000.000
133A133VAL0-0.017-0.02131.460-0.334-0.3340.0000.0000.0000.000
134A134PRO00.0470.01633.9230.1730.1730.0000.0000.0000.000
135A135ALA00.012-0.00137.416-0.093-0.0930.0000.0000.0000.000
136A136ASN00.0240.01839.885-0.018-0.0180.0000.0000.0000.000
137A137ALA0-0.0110.00534.571-0.048-0.0480.0000.0000.0000.000
138A138ASN00.0630.03834.289-0.006-0.0060.0000.0000.0000.000
139A139ILE00.014-0.00832.202-0.336-0.3360.0000.0000.0000.000
140A140LYS11.0141.03030.8028.8638.8630.0000.0000.0000.000
141A141PRO00.000-0.01328.278-0.354-0.3540.0000.0000.0000.000
142A142LEU0-0.061-0.02525.779-0.456-0.4560.0000.0000.0000.000
143A143VAL00.0370.01626.144-0.408-0.4080.0000.0000.0000.000
144A144GLU-1-0.868-0.94926.054-10.498-10.4980.0000.0000.0000.000
145A145ARG10.9280.97321.93010.94110.9410.0000.0000.0000.000
146A146LEU00.0200.01921.843-0.503-0.5030.0000.0000.0000.000
147A147LYS10.8800.95422.8309.9379.9370.0000.0000.0000.000
148A148LYS10.8660.93019.52913.85913.8590.0000.0000.0000.000
149A149THR0-0.035-0.02118.346-0.924-0.9240.0000.0000.0000.000
150A150VAL0-0.016-0.00113.9460.6290.6290.0000.0000.0000.000
151A151VAL00.006-0.01216.8330.0570.0570.0000.0000.0000.000
152A152ILE00.0100.02810.318-0.010-0.0100.0000.0000.0000.000
153A153ASN00.008-0.03114.2210.6860.6860.0000.0000.0000.000
154A154THR00.0400.02713.585-0.271-0.2710.0000.0000.0000.000
155A155ARG10.8750.94616.07713.72413.7240.0000.0000.0000.000
156A156ASP-1-0.885-0.94619.054-12.458-12.4580.0000.0000.0000.000
157A157LYS10.9740.98817.80512.83712.8370.0000.0000.0000.000
158A158PRO00.0200.01414.935-0.373-0.3730.0000.0000.0000.000
159A159TYR0-0.002-0.01812.012-0.531-0.5310.0000.0000.0000.000
160A160PHE0-0.001-0.0017.4191.3011.3010.0000.0000.0000.000
161A161GLN0-0.041-0.02911.105-1.318-1.3180.0000.0000.0000.000
162A162VAL0-0.067-0.03510.3151.1111.1110.0000.0000.0000.000
163A163LEU00.0160.03112.255-0.931-0.9310.0000.0000.0000.000
164A164VAL00.032-0.0069.570-0.083-0.0830.0000.0000.0000.000
165A165GLY00.0670.03012.995-0.323-0.3230.0000.0000.0000.000
166A166ASN0-0.009-0.01016.2590.1690.1690.0000.0000.0000.000
167A167GLU-1-0.774-0.89518.751-14.031-14.0310.0000.0000.0000.000
168A168LYS10.8930.95020.16612.33212.3320.0000.0000.0000.000
169A169MET0-0.0450.04016.8610.3180.3180.0000.0000.0000.000
170A170THR00.0590.02117.778-0.466-0.4660.0000.0000.0000.000
171A171ASP-1-0.763-0.89312.926-20.814-20.8140.0000.0000.0000.000
172A172GLU-1-0.785-0.89112.402-26.003-26.0030.0000.0000.0000.000
173A173GLN0-0.019-0.00112.604-0.689-0.6890.0000.0000.0000.000
174A174ILE0-0.023-0.00910.951-0.095-0.0950.0000.0000.0000.000
175A175VAL00.0170.0107.044-1.437-1.4370.0000.0000.0000.000
176A176ASP-1-0.736-0.8328.612-24.266-24.2660.0000.0000.0000.000
177A177ASN0-0.084-0.06510.5320.6300.6300.0000.0000.0000.000
178A178ILE00.0110.0054.9560.5190.5190.0000.0000.0000.000
179A179GLU-1-0.859-0.9285.789-34.979-34.9790.0000.0000.0000.000
180A180ALA0-0.027-0.0136.9311.0081.0080.0000.0000.0000.000
181A181VAL0-0.033-0.0247.2131.2961.2960.0000.0000.0000.000
183A183ASN00.0240.0086.1862.3882.3880.0000.0000.0000.000
184A184VAL0-0.003-0.0018.9221.6131.6130.0000.0000.0000.000
185A185VAL0-0.025-0.0217.0151.1301.1300.0000.0000.0000.000
186A186ALA0-0.034-0.0297.1340.5670.5670.0000.0000.0000.000
187A187LYS10.9210.9738.85218.76818.7680.0000.0000.0000.000
188A188LYS10.8010.92812.34516.28816.2880.0000.0000.0000.000
189A189TYR0-0.038-0.04311.0910.6890.6890.0000.0000.0000.000
190A190GLU-1-0.873-0.92512.620-16.312-16.3120.0000.0000.0000.000
191A191LYS10.9270.96710.60517.30217.3020.0000.0000.0000.000
192A192GLY00.0570.0348.888-1.955-1.9550.0000.0000.0000.000
195A195HIS10.8180.8946.86421.04821.0480.0000.0000.0000.000
198A198ASP-1-0.827-0.9047.374-28.279-28.2790.0000.0000.0000.000
200A200TYR0-0.007-0.0076.095-1.423-1.4230.0000.0000.0000.000
201A201VAL00.0230.0208.2170.2830.2830.0000.0000.0000.000
202A202LYS10.9170.97510.52117.21117.2110.0000.0000.0000.000
203A203LEU00.0760.05314.3220.1660.1660.0000.0000.0000.000
204A204THR0-0.016-0.01617.3350.3160.3160.0000.0000.0000.000
205A205MET0-0.074-0.04319.6330.2880.2880.0000.0000.0000.000
206A206GLY00.0520.03319.1570.5810.5810.0000.0000.0000.000
207A207PRO0-0.019-0.00616.9710.2000.2000.0000.0000.0000.000
208A208ALA0-0.051-0.03213.226-0.536-0.5360.0000.0000.0000.000
209A209VAL00.0570.0499.6950.3580.3580.0000.0000.0000.000
210A210LYS10.8510.9057.18826.95826.9580.0000.0000.0000.000