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: VZ7K1

Calculation Name: 1VIO-A-Xray549

Preferred Name:

Target Type:

Ligand Name: 1,4-butanediol

Ligand 3-letter code: BU1

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1VIO

Chain ID: A

ChEMBL ID:

UniProt ID: P45124

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 232
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2851359.206489
FMO2-HF: Nuclear repulsion 2759785.293672
FMO2-HF: Total energy -91573.912817
FMO2-MP2: Total energy -91842.261841


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:0:SER)


Summations of interaction energy for fragment #1(A:0:SER)
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.
-203.771-198.7317.727-12.22-10.55-0.115
Interaction energy analysis for fragmet #1(A:0:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.801 / q_NPA : 0.887
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].
3A2ARG10.8080.8723.33527.44429.6370.016-1.145-1.064-0.004
41A40GLN0-0.039-0.0131.762-27.870-30.74211.555-5.027-3.656-0.046
42A41ILE00.0390.0402.6971.9523.4180.410-0.718-1.158-0.009
43A42SER0-0.057-0.0722.312-31.729-27.9045.341-4.911-4.256-0.054
44A43GLN0-0.007-0.0253.9704.2714.2340.000-0.0330.0700.000
57A56TRP0-0.048-0.0342.526-4.424-3.9580.405-0.386-0.486-0.002
4A3LEU00.1030.0695.9751.2701.2700.0000.0000.0000.000
5A4ASP-1-0.799-0.8858.151-25.026-25.0260.0000.0000.0000.000
6A5LYS10.7610.8828.31931.13131.1310.0000.0000.0000.000
7A6PHE00.0760.0427.3471.1641.1640.0000.0000.0000.000
8A7ILE00.0320.0159.7702.1772.1770.0000.0000.0000.000
9A8ALA0-0.085-0.04313.0011.5271.5270.0000.0000.0000.000
10A9GLU-1-0.835-0.92711.334-25.583-25.5830.0000.0000.0000.000
11A10ASN0-0.0050.00412.1621.7011.7010.0000.0000.0000.000
12A11VAL00.0500.02214.1301.1131.1130.0000.0000.0000.000
13A12GLY00.0410.03916.8741.1021.1020.0000.0000.0000.000
14A13LEU0-0.072-0.03217.4561.1451.1450.0000.0000.0000.000
15A14THR00.004-0.02417.776-0.745-0.7450.0000.0000.0000.000
16A15ARG11.0531.00315.77016.58416.5840.0000.0000.0000.000
17A16SER0-0.040-0.00816.981-0.085-0.0850.0000.0000.0000.000
18A17GLN00.0490.02919.817-0.028-0.0280.0000.0000.0000.000
19A18ALA00.1030.07014.2980.2830.2830.0000.0000.0000.000
20A19THR0-0.054-0.04415.963-0.262-0.2620.0000.0000.0000.000
21A20LYS10.8570.93216.85713.78313.7830.0000.0000.0000.000
22A21ALA00.0880.05017.6090.3800.3800.0000.0000.0000.000
23A22ILE00.0250.02912.2150.2650.2650.0000.0000.0000.000
24A23ARG10.9200.94616.30116.12116.1210.0000.0000.0000.000
25A24GLN0-0.062-0.04719.0360.5650.5650.0000.0000.0000.000
26A25SER0-0.036-0.02318.7420.4570.4570.0000.0000.0000.000
27A26ALA00.0280.03219.4410.1100.1100.0000.0000.0000.000
28A27VAL0-0.029-0.00813.009-0.264-0.2640.0000.0000.0000.000
29A28LYS10.8390.88814.88615.00215.0020.0000.0000.0000.000
30A29ILE0-0.020-0.0108.232-1.418-1.4180.0000.0000.0000.000
31A30ASN00.007-0.00310.2050.9630.9630.0000.0000.0000.000
32A31GLY00.0800.05513.9380.9810.9810.0000.0000.0000.000
33A32GLU-1-0.957-0.97115.168-16.283-16.2830.0000.0000.0000.000
34A33ILE0-0.024-0.02015.130-0.969-0.9690.0000.0000.0000.000
35A34VAL0-0.0070.00110.737-0.129-0.1290.0000.0000.0000.000
36A35LYS10.9240.96814.15314.27514.2750.0000.0000.0000.000
37A36SER0-0.049-0.02712.1870.3920.3920.0000.0000.0000.000
38A37GLY00.0540.02510.788-1.325-1.3250.0000.0000.0000.000
39A38SER0-0.060-0.0428.623-2.296-2.2960.0000.0000.0000.000
40A39VAL00.0410.0226.771-3.480-3.4800.0000.0000.0000.000
45A44GLU-1-0.933-0.9656.539-26.084-26.0840.0000.0000.0000.000
46A45ASP-1-0.842-0.8706.336-36.368-36.3680.0000.0000.0000.000
47A46GLU-1-0.843-0.9108.989-19.931-19.9310.0000.0000.0000.000
48A47ILE0-0.060-0.0388.0290.3840.3840.0000.0000.0000.000
49A48TYR00.0360.00912.0391.2711.2710.0000.0000.0000.000
50A49PHE0-0.032-0.03115.520-0.569-0.5690.0000.0000.0000.000
51A50GLU-1-0.943-0.98417.453-12.647-12.6470.0000.0000.0000.000
52A51ASP-1-0.837-0.88519.633-13.491-13.4910.0000.0000.0000.000
53A52GLU-1-0.747-0.84019.815-12.885-12.8850.0000.0000.0000.000
54A53LEU00.0140.00814.495-0.959-0.9590.0000.0000.0000.000
55A54LEU0-0.070-0.03413.1830.2300.2300.0000.0000.0000.000
56A55THR00.0190.00912.929-1.328-1.3280.0000.0000.0000.000
58A57ILE0-0.053-0.0329.756-0.670-0.6700.0000.0000.0000.000
59A58GLU-1-0.827-0.89912.148-18.344-18.3440.0000.0000.0000.000
60A59GLU-1-0.941-0.97715.483-17.320-17.3200.0000.0000.0000.000
61A60GLY0-0.0400.00018.5670.6250.6250.0000.0000.0000.000
62A61GLN0-0.034-0.01420.6371.3501.3500.0000.0000.0000.000
63A62TYR0-0.033-0.04722.369-0.171-0.1710.0000.0000.0000.000
64A63PHE00.0040.00524.1480.4350.4350.0000.0000.0000.000
65A64MET0-0.037-0.00528.438-0.041-0.0410.0000.0000.0000.000
66A65LEU00.0000.00530.0950.0410.0410.0000.0000.0000.000
67A66ASN00.002-0.00332.418-0.036-0.0360.0000.0000.0000.000
68A67LYS10.7600.87932.4029.1409.1400.0000.0000.0000.000
69A68PRO00.1060.05634.7130.1860.1860.0000.0000.0000.000
70A69GLN0-0.091-0.05736.498-0.086-0.0860.0000.0000.0000.000
71A70GLY00.0030.00137.561-0.061-0.0610.0000.0000.0000.000
72A71CYS0-0.039-0.00332.544-0.183-0.1830.0000.0000.0000.000
73A72VAL00.0310.00629.0600.0710.0710.0000.0000.0000.000
74A73CYS0-0.033-0.00427.824-0.185-0.1850.0000.0000.0000.000
75A74SER0-0.035-0.02024.883-0.426-0.4260.0000.0000.0000.000
76A75ASN00.040-0.00920.3400.0310.0310.0000.0000.0000.000
77A76ASP-1-0.914-0.94822.600-12.410-12.4100.0000.0000.0000.000
78A77ASP-1-0.846-0.91024.665-11.184-11.1840.0000.0000.0000.000
79A78GLY00.0040.00927.9720.3750.3750.0000.0000.0000.000
80A79ASP-1-0.996-0.99729.708-9.443-9.4430.0000.0000.0000.000
81A80TYR0-0.056-0.03931.9140.4350.4350.0000.0000.0000.000
82A81PRO00.0240.03130.562-0.319-0.3190.0000.0000.0000.000
83A82THR0-0.016-0.02725.8320.1470.1470.0000.0000.0000.000
84A83ILE00.005-0.01326.7650.2840.2840.0000.0000.0000.000
85A84TYR00.005-0.00923.6840.0400.0400.0000.0000.0000.000
86A85GLN0-0.055-0.02026.6480.0910.0910.0000.0000.0000.000
87A86PHE0-0.018-0.00929.4320.2370.2370.0000.0000.0000.000
88A87PHE0-0.004-0.00725.7820.0180.0180.0000.0000.0000.000
89A88ASP-1-0.878-0.91926.957-10.757-10.7570.0000.0000.0000.000
90A89TYR0-0.0070.00020.826-0.811-0.8110.0000.0000.0000.000
91A90PRO0-0.040-0.04419.0280.3630.3630.0000.0000.0000.000
92A91LEU0-0.0030.00419.979-0.643-0.6430.0000.0000.0000.000
93A92ALA00.0450.01121.113-0.422-0.4220.0000.0000.0000.000
94A93GLY0-0.022-0.00118.881-0.060-0.0600.0000.0000.0000.000
95A94LYS10.7820.87714.40518.52918.5290.0000.0000.0000.000
96A95LEU0-0.0260.00417.736-0.241-0.2410.0000.0000.0000.000
97A96HIS10.7770.90217.82216.01016.0100.0000.0000.0000.000
98A97SER00.023-0.02521.2320.5180.5180.0000.0000.0000.000
99A98ALA0-0.055-0.02323.609-0.481-0.4810.0000.0000.0000.000
100A99GLY00.0210.00625.8880.4570.4570.0000.0000.0000.000
101A100ARG10.7980.89923.57113.17413.1740.0000.0000.0000.000
102A101LEU0-0.015-0.01829.1050.2730.2730.0000.0000.0000.000
103A102ASP-1-0.808-0.89632.040-9.179-9.1790.0000.0000.0000.000
104A103VAL00.0020.00934.2760.0580.0580.0000.0000.0000.000
105A104ASP-1-0.829-0.91035.141-8.077-8.0770.0000.0000.0000.000
106A105THR0-0.083-0.03936.4040.2440.2440.0000.0000.0000.000
107A106THR00.0510.03736.451-0.223-0.2230.0000.0000.0000.000
108A107GLY00.0550.03637.5120.0160.0160.0000.0000.0000.000
109A108LEU00.0070.00433.386-0.280-0.2800.0000.0000.0000.000
110A109VAL00.0110.01028.610-0.124-0.1240.0000.0000.0000.000
111A110LEU00.0230.02128.1330.0440.0440.0000.0000.0000.000
112A111LEU0-0.011-0.00324.821-0.271-0.2710.0000.0000.0000.000
113A112THR0-0.006-0.02921.4670.1040.1040.0000.0000.0000.000
114A113ASP-1-0.728-0.86317.396-16.878-16.8780.0000.0000.0000.000
115A114ASP-1-0.772-0.84417.301-16.137-16.1370.0000.0000.0000.000
116A115GLY00.0390.00517.1810.6650.6650.0000.0000.0000.000
117A116GLN0-0.056-0.02216.6221.7391.7390.0000.0000.0000.000
118A117TRP0-0.047-0.03320.2520.5470.5470.0000.0000.0000.000
119A118SER00.009-0.00620.9300.4020.4020.0000.0000.0000.000
120A119HIS0-0.0060.01120.9610.6060.6060.0000.0000.0000.000
121A120ARG10.8190.89223.02513.23013.2300.0000.0000.0000.000
122A121ILE00.0520.04426.0290.4460.4460.0000.0000.0000.000
123A122THR0-0.033-0.03324.9230.3390.3390.0000.0000.0000.000
124A123SER0-0.039-0.01425.5310.1580.1580.0000.0000.0000.000
125A124PRO00.019-0.00927.0580.3380.3380.0000.0000.0000.000
126A125LYS10.8220.91425.99512.01512.0150.0000.0000.0000.000
127A126HIS00.0330.02726.9100.1470.1470.0000.0000.0000.000
128A127HIS0-0.026-0.01431.1870.1950.1950.0000.0000.0000.000
129A128CYS-1-0.731-0.78831.773-9.555-9.5550.0000.0000.0000.000
130A129GLU-1-0.905-0.97033.855-7.826-7.8260.0000.0000.0000.000
131A130LYS10.7080.79731.1299.8279.8270.0000.0000.0000.000
132A131THR0-0.021-0.01036.6630.2380.2380.0000.0000.0000.000
133A132TYR0-0.008-0.01535.399-0.248-0.2480.0000.0000.0000.000
134A133LEU00.0600.04941.1640.1550.1550.0000.0000.0000.000
135A134VAL0-0.053-0.04343.367-0.177-0.1770.0000.0000.0000.000
136A135THR00.0130.00845.5910.1050.1050.0000.0000.0000.000
137A136LEU0-0.029-0.02347.786-0.158-0.1580.0000.0000.0000.000
138A137ALA0-0.042-0.02650.2010.0710.0710.0000.0000.0000.000
139A138ASP-1-0.912-0.95352.413-5.770-5.7700.0000.0000.0000.000
140A139PRO0-0.025-0.01654.168-0.085-0.0850.0000.0000.0000.000
141A140VAL0-0.0110.00052.597-0.057-0.0570.0000.0000.0000.000
142A141GLU-1-0.879-0.93854.699-5.631-5.6310.0000.0000.0000.000
143A142GLU-1-0.928-0.96955.242-5.560-5.5600.0000.0000.0000.000
144A143ASN0-0.075-0.04455.149-0.137-0.1370.0000.0000.0000.000
145A144TYR00.0420.01950.953-0.158-0.1580.0000.0000.0000.000
146A145SER00.0480.01850.474-0.183-0.1830.0000.0000.0000.000
147A146ALA00.0050.01450.789-0.095-0.0950.0000.0000.0000.000
148A147ALA00.0270.00850.097-0.101-0.1010.0000.0000.0000.000
149A148CYS0-0.073-0.03246.545-0.186-0.1860.0000.0000.0000.000
150A149ALA00.0110.01746.257-0.163-0.1630.0000.0000.0000.000
151A150GLU-1-0.978-1.00147.625-6.155-6.1550.0000.0000.0000.000
152A151GLY0-0.0250.01345.403-0.083-0.0830.0000.0000.0000.000
153A152ILE00.026-0.00244.8700.1250.1250.0000.0000.0000.000
154A153LEU0-0.038-0.01643.114-0.210-0.2100.0000.0000.0000.000
155A154LEU00.0250.02740.2000.1000.1000.0000.0000.0000.000
156A155ARG10.9830.97642.4937.0677.0670.0000.0000.0000.000
157A156GLY0-0.011-0.00539.374-0.135-0.1350.0000.0000.0000.000
158A157GLU-1-0.803-0.86137.385-8.786-8.7860.0000.0000.0000.000
159A158LYS10.9040.93736.1898.6488.6480.0000.0000.0000.000
160A159GLU-1-0.906-0.94437.951-8.311-8.3110.0000.0000.0000.000
161A160PRO00.0410.02341.026-0.132-0.1320.0000.0000.0000.000
162A161THR00.0250.01040.368-0.141-0.1410.0000.0000.0000.000
163A162LYS10.8230.90837.3618.5968.5960.0000.0000.0000.000
164A163PRO0-0.028-0.00941.299-0.018-0.0180.0000.0000.0000.000
165A164ALA0-0.0060.00642.740-0.165-0.1650.0000.0000.0000.000
166A165LYS10.9020.95343.3367.5117.5110.0000.0000.0000.000
167A166LEU0-0.004-0.00345.555-0.120-0.1200.0000.0000.0000.000
168A167GLU-1-0.892-0.93848.036-6.416-6.4160.0000.0000.0000.000
169A168ILE00.005-0.00250.154-0.087-0.0870.0000.0000.0000.000
170A169LEU0-0.064-0.01948.7610.0530.0530.0000.0000.0000.000
171A170ASP-1-0.814-0.89553.329-5.866-5.8660.0000.0000.0000.000
172A171ASP-1-0.907-0.96055.053-5.468-5.4680.0000.0000.0000.000
173A172TYR0-0.045-0.01553.2980.0260.0260.0000.0000.0000.000
174A173ASN0-0.053-0.02650.116-0.291-0.2910.0000.0000.0000.000
175A174VAL00.0260.00247.2880.1040.1040.0000.0000.0000.000
176A175ASN00.0250.01245.810-0.269-0.2690.0000.0000.0000.000
177A176LEU0-0.009-0.01642.6090.0950.0950.0000.0000.0000.000
178A177THR0-0.022-0.02040.088-0.122-0.1220.0000.0000.0000.000
179A178ILE0-0.013-0.01137.0990.1510.1510.0000.0000.0000.000
180A179SER00.0310.02236.612-0.128-0.1280.0000.0000.0000.000
181A180GLU-1-0.765-0.85534.607-8.681-8.6810.0000.0000.0000.000
182A181GLY00.0560.02032.2170.0210.0210.0000.0000.0000.000
183A182ARG10.6670.81032.0058.1488.1480.0000.0000.0000.000
184A183TYR00.0370.01531.4060.0330.0330.0000.0000.0000.000
185A184HIS0-0.002-0.01533.8310.4460.4460.0000.0000.0000.000
186A185GLN00.0130.00436.3950.0560.0560.0000.0000.0000.000
187A186VAL00.0760.03338.3490.1980.1980.0000.0000.0000.000
188A187LYS10.8900.93337.9868.4198.4190.0000.0000.0000.000
189A188ARG10.7530.84637.1388.4618.4610.0000.0000.0000.000
190A189MET0-0.0090.00342.0270.0600.0600.0000.0000.0000.000
191A190PHE00.0770.03144.3010.1280.1280.0000.0000.0000.000
192A191ALA0-0.0030.01545.1380.1360.1360.0000.0000.0000.000
193A192ALA0-0.095-0.05245.9850.1310.1310.0000.0000.0000.000
194A193LEU0-0.060-0.02047.8310.1130.1130.0000.0000.0000.000
195A194GLY0-0.0210.00150.2700.1200.1200.0000.0000.0000.000
196A195ASN00.0240.01550.3840.0160.0160.0000.0000.0000.000
197A196LYS10.9240.94546.7906.5096.5090.0000.0000.0000.000
198A197VAL00.0010.00543.3240.0530.0530.0000.0000.0000.000
199A198VAL0-0.088-0.05545.888-0.060-0.0600.0000.0000.0000.000
200A199GLY00.0290.02944.743-0.035-0.0350.0000.0000.0000.000
201A200LEU0-0.064-0.03339.1540.0260.0260.0000.0000.0000.000
202A201HIS00.0380.02939.890-0.134-0.1340.0000.0000.0000.000
203A202ARG10.7770.87631.1769.7469.7460.0000.0000.0000.000
204A203TRP00.0610.02038.064-0.157-0.1570.0000.0000.0000.000
205A204LYS10.8110.89937.9357.9997.9990.0000.0000.0000.000
206A205ILE00.0240.00931.625-0.043-0.0430.0000.0000.0000.000
207A206GLY00.0720.04734.972-0.082-0.0820.0000.0000.0000.000
208A207ASP-1-0.877-0.93235.800-7.837-7.8370.0000.0000.0000.000
209A208VAL0-0.044-0.00933.0070.1570.1570.0000.0000.0000.000
210A209VAL0-0.017-0.01236.1640.0180.0180.0000.0000.0000.000
211A210LEU00.0120.00436.495-0.225-0.2250.0000.0000.0000.000
212A211ASP-1-0.812-0.87037.509-7.877-7.8770.0000.0000.0000.000
213A212GLU-1-0.925-0.97039.279-7.385-7.3850.0000.0000.0000.000
214A213SER0-0.147-0.09140.9620.1370.1370.0000.0000.0000.000
215A214LEU0-0.051-0.00935.494-0.045-0.0450.0000.0000.0000.000
216A215GLU-1-0.875-0.93939.492-7.173-7.1730.0000.0000.0000.000
217A216GLU-1-0.941-0.99238.298-8.111-8.1110.0000.0000.0000.000
218A217GLY0-0.040-0.02534.8760.0580.0580.0000.0000.0000.000
219A218GLU-1-0.911-0.94034.379-8.383-8.3830.0000.0000.0000.000
220A219TYR0-0.024-0.02728.326-0.095-0.0950.0000.0000.0000.000
221A220ARG10.7610.83732.6239.0569.0560.0000.0000.0000.000
222A221PRO00.005-0.00429.379-0.227-0.2270.0000.0000.0000.000
223A222LEU0-0.030-0.00428.8300.4040.4040.0000.0000.0000.000
224A223THR0-0.032-0.04430.986-0.070-0.0700.0000.0000.0000.000
225A224GLN0-0.007-0.02428.273-0.184-0.1840.0000.0000.0000.000
226A225SER0-0.002-0.00131.875-0.033-0.0330.0000.0000.0000.000
227A226GLU-1-0.766-0.85532.930-9.037-9.0370.0000.0000.0000.000
228A227ILE00.0400.02926.884-0.065-0.0650.0000.0000.0000.000
229A228GLU-1-0.872-0.94029.466-10.252-10.2520.0000.0000.0000.000
230A229LYS10.7930.89331.1828.6838.6830.0000.0000.0000.000
231A230LEU0-0.050-0.01329.5560.1920.1920.0000.0000.0000.000
232A231VAL-1-0.927-0.92827.034-11.508-11.5080.0000.0000.0000.000