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: J47Y9

Calculation Name: 1KNC-A-Xray547

Preferred Name:

Target Type:

Ligand Name: sulfate ion

Ligand 3-letter code: SO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1KNC

Chain ID: A

ChEMBL ID:

UniProt ID: P9WQB5

Base Structure: X-ray

Registration Date: 2025-10-03

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 174
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1628515.363402
FMO2-HF: Nuclear repulsion 1563886.935408
FMO2-HF: Total energy -64628.427994
FMO2-MP2: Total energy -64817.49613


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:2:SER)


Summations of interaction energy for fragment #1(A:2: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.
-105.199-105.74437.21-19.792-16.874-0.194
Interaction energy analysis for fragmet #1(A:2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.707 / q_NPA : 0.821
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].
3A4GLU-1-0.833-0.9083.311-33.654-31.6610.000-0.872-1.122-0.003
4A5LYS10.9450.9862.54061.21763.5980.830-1.243-1.9680.005
35A36TRP00.033-0.0043.975-1.196-1.039-0.001-0.021-0.1350.000
53A54ASP-1-0.864-0.9342.374-47.569-46.4320.555-0.530-1.162-0.001
54A55ILE0-0.039-0.0151.761-33.927-36.09112.089-5.930-3.995-0.071
55A56GLY00.0300.0104.510-0.497-0.392-0.001-0.005-0.0980.000
56A57ALA0-0.0190.0072.8023.3254.0440.082-0.304-0.4970.001
57A58GLU-1-0.744-0.8631.689-129.454-134.39323.646-10.843-7.865-0.125
58A59ALA00.0080.0053.9165.8195.8850.010-0.044-0.0320.000
5A6LEU00.0710.0394.8246.0216.0210.0000.0000.0000.000
6A7LYS10.7820.8616.99040.64840.6480.0000.0000.0000.000
7A8ALA0-0.028-0.0168.0823.2793.2790.0000.0000.0000.000
8A9ALA00.0180.0229.1292.3242.3240.0000.0000.0000.000
9A10LEU0-0.033-0.01410.9472.0982.0980.0000.0000.0000.000
10A11PRO00.0350.03613.0660.3310.3310.0000.0000.0000.000
11A12GLU-1-0.893-0.96116.611-17.147-17.1470.0000.0000.0000.000
12A13TYR0-0.007-0.01418.8130.0210.0210.0000.0000.0000.000
13A14ALA00.0230.01116.4750.3920.3920.0000.0000.0000.000
14A15LYS10.9530.98616.37314.26114.2610.0000.0000.0000.000
15A16ASP-1-0.859-0.93916.562-16.431-16.4310.0000.0000.0000.000
16A17ILE0-0.0170.00713.400-0.666-0.6660.0000.0000.0000.000
17A18LYS10.9871.00611.51119.59519.5950.0000.0000.0000.000
18A19LEU0-0.029-0.01212.297-2.067-2.0670.0000.0000.0000.000
19A20ASN0-0.001-0.01514.151-0.407-0.4070.0000.0000.0000.000
20A21LEU00.0250.0207.411-0.386-0.3860.0000.0000.0000.000
21A22SER0-0.053-0.0399.736-3.137-3.1370.0000.0000.0000.000
22A23SER0-0.040-0.00910.795-0.075-0.0750.0000.0000.0000.000
23A24ILE00.0150.00711.194-0.153-0.1530.0000.0000.0000.000
24A25THR0-0.049-0.0537.369-0.521-0.5210.0000.0000.0000.000
25A26ARG10.8820.9469.40626.47326.4730.0000.0000.0000.000
26A27SER0-0.038-0.03711.8411.9221.9220.0000.0000.0000.000
27A28SER0-0.017-0.01314.234-0.856-0.8560.0000.0000.0000.000
28A29VAL0-0.0080.01416.9910.7050.7050.0000.0000.0000.000
29A30LEU0-0.039-0.01215.8740.5790.5790.0000.0000.0000.000
30A31ASP-1-0.802-0.89316.005-19.077-19.0770.0000.0000.0000.000
31A32GLN00.007-0.02011.675-2.863-2.8630.0000.0000.0000.000
32A33GLU-1-0.807-0.90912.313-19.084-19.0840.0000.0000.0000.000
33A34GLN0-0.022-0.01614.189-0.796-0.7960.0000.0000.0000.000
34A35LEU00.0430.04110.745-0.008-0.0080.0000.0000.0000.000
36A37GLY00.0300.01610.350-0.849-0.8490.0000.0000.0000.000
37A38THR0-0.021-0.02613.1591.0711.0710.0000.0000.0000.000
38A39LEU0-0.0240.0047.6890.4560.4560.0000.0000.0000.000
39A40LEU00.0190.0138.790-0.141-0.1410.0000.0000.0000.000
40A41ALA0-0.006-0.00310.5430.9530.9530.0000.0000.0000.000
41A42SER0-0.006-0.03112.5751.5641.5640.0000.0000.0000.000
42A43ALA00.0130.0089.1140.9120.9120.0000.0000.0000.000
43A44ALA0-0.0030.01211.0641.0011.0010.0000.0000.0000.000
44A45ALA0-0.0080.00013.4141.1291.1290.0000.0000.0000.000
45A46THR0-0.051-0.03312.7870.9020.9020.0000.0000.0000.000
46A47ARG10.8140.89115.15115.37115.3710.0000.0000.0000.000
47A48ASN00.0290.02311.512-0.418-0.4180.0000.0000.0000.000
48A49PRO00.0210.00411.044-1.571-1.5710.0000.0000.0000.000
49A50GLN00.0350.0257.920-2.999-2.9990.0000.0000.0000.000
50A51VAL00.0200.0066.595-3.886-3.8860.0000.0000.0000.000
51A52LEU0-0.042-0.0216.450-3.636-3.6360.0000.0000.0000.000
52A53ALA00.0070.0106.283-1.638-1.6380.0000.0000.0000.000
59A60THR0-0.059-0.0447.0285.3565.3560.0000.0000.0000.000
60A61ASP-1-0.926-0.9516.143-39.804-39.8040.0000.0000.0000.000
61A62HIS10.7800.8835.55743.42743.4270.0000.0000.0000.000
62A63LEU0-0.0210.00610.4282.2812.2810.0000.0000.0000.000
63A64SER00.0510.04212.7300.2540.2540.0000.0000.0000.000
64A65ALA00.030-0.00515.377-0.407-0.4070.0000.0000.0000.000
65A66ALA00.0000.00516.5550.1110.1110.0000.0000.0000.000
66A67ALA00.0480.02615.5980.3070.3070.0000.0000.0000.000
67A68ARG10.9070.9508.66327.08127.0810.0000.0000.0000.000
68A69HIS00.007-0.00314.425-0.218-0.2180.0000.0000.0000.000
69A70ALA0-0.0010.00717.4910.4930.4930.0000.0000.0000.000
70A71ALA00.0120.00714.2880.5840.5840.0000.0000.0000.000
71A72LEU00.001-0.00412.2760.3180.3180.0000.0000.0000.000
72A73GLY00.0160.00216.1180.7320.7320.0000.0000.0000.000
73A74ALA0-0.014-0.00618.7750.7620.7620.0000.0000.0000.000
74A75ALA00.0140.00116.6020.6110.6110.0000.0000.0000.000
75A76ALA0-0.0060.00318.6780.6020.6020.0000.0000.0000.000
76A77ILE0-0.038-0.02220.9050.6580.6580.0000.0000.0000.000
77A78MET0-0.0120.03421.7860.8770.8770.0000.0000.0000.000
78A79GLY00.0270.02322.2550.3180.3180.0000.0000.0000.000
79A80MET0-0.0260.00923.1600.4450.4450.0000.0000.0000.000
80A81ASN00.000-0.05026.7270.5190.5190.0000.0000.0000.000
81A82ASN00.032-0.02423.755-0.093-0.0930.0000.0000.0000.000
82A83VAL00.0290.02726.7250.2100.2100.0000.0000.0000.000
83A84PHE00.0140.00529.1950.2970.2970.0000.0000.0000.000
84A85TYR00.018-0.01130.5550.3330.3330.0000.0000.0000.000
85A86ARG10.8590.93826.62210.91910.9190.0000.0000.0000.000
86A87GLY0-0.0040.00432.4360.2100.2100.0000.0000.0000.000
87A88ARG10.8350.89735.0428.3828.3820.0000.0000.0000.000
88A89GLY00.0130.00935.6560.1950.1950.0000.0000.0000.000
89A90PHE00.011-0.00732.8530.0820.0820.0000.0000.0000.000
90A91LEU0-0.035-0.00438.0410.2180.2180.0000.0000.0000.000
91A92GLU-1-0.934-0.96740.512-7.497-7.4970.0000.0000.0000.000
92A93GLY00.0230.02141.1910.1810.1810.0000.0000.0000.000
93A94ARG10.8570.91442.6837.0437.0430.0000.0000.0000.000
94A95TYR00.0260.00841.2520.1080.1080.0000.0000.0000.000
95A96ASP-1-0.864-0.92540.197-8.078-8.0780.0000.0000.0000.000
96A97ASP-1-0.901-0.94541.909-6.931-6.9310.0000.0000.0000.000
97A98LEU0-0.034-0.00241.9320.0110.0110.0000.0000.0000.000
98A99ARG10.9380.95540.9707.0927.0920.0000.0000.0000.000
99A100PRO00.0270.01136.069-0.001-0.0010.0000.0000.0000.000
100A101GLY0-0.0050.00637.102-0.068-0.0680.0000.0000.0000.000
101A102LEU0-0.0010.00231.605-0.097-0.0970.0000.0000.0000.000
102A103ARG10.9310.96730.5419.5469.5460.0000.0000.0000.000
103A104MET00.0580.04829.017-0.351-0.3510.0000.0000.0000.000
104A105ASN0-0.022-0.02729.579-0.030-0.0300.0000.0000.0000.000
105A106ILE00.0320.03822.2580.1160.1160.0000.0000.0000.000
106A107ILE00.0390.01626.292-0.237-0.2370.0000.0000.0000.000
107A108ALA00.0030.00727.6200.0210.0210.0000.0000.0000.000
108A109ASN0-0.066-0.04227.9100.3020.3020.0000.0000.0000.000
109A110PRO00.0200.02022.848-0.014-0.0140.0000.0000.0000.000
110A111GLY0-0.0090.00122.753-0.556-0.5560.0000.0000.0000.000
111A112ILE00.0050.01019.244-0.230-0.2300.0000.0000.0000.000
112A113PRO00.0360.00222.6270.5260.5260.0000.0000.0000.000
113A114LYS10.9060.94323.40110.24010.2400.0000.0000.0000.000
114A115ALA00.0570.04024.203-0.224-0.2240.0000.0000.0000.000
115A116ASN00.0240.00818.9860.1840.1840.0000.0000.0000.000
116A117PHE00.0550.01619.731-0.366-0.3660.0000.0000.0000.000
117A118GLU-1-0.820-0.89821.154-11.845-11.8450.0000.0000.0000.000
118A119LEU00.0280.02618.4130.1610.1610.0000.0000.0000.000
119A120TRP0-0.017-0.00616.120-0.174-0.1740.0000.0000.0000.000
120A121SER0-0.006-0.01318.5700.0500.0500.0000.0000.0000.000
121A122PHE0-0.029-0.00621.2380.4560.4560.0000.0000.0000.000
122A123ALA00.0170.01317.3380.2210.2210.0000.0000.0000.000
123A124VAL00.007-0.00317.4150.0500.0500.0000.0000.0000.000
124A125SER0-0.015-0.02419.7710.5960.5960.0000.0000.0000.000
125A126ALA0-0.0300.00020.9730.5900.5900.0000.0000.0000.000
126A127ILE0-0.0290.00316.0260.3250.3250.0000.0000.0000.000
127A128ASN0-0.009-0.01020.3120.0850.0850.0000.0000.0000.000
128A129GLY00.0350.03922.8080.5610.5610.0000.0000.0000.000
129A130CYS0-0.110-0.04225.7030.6380.6380.0000.0000.0000.000
130A131SER00.0500.02728.091-0.180-0.1800.0000.0000.0000.000
131A132HIS00.0730.03730.3660.1220.1220.0000.0000.0000.000
132A133CYS0-0.044-0.01927.0790.0510.0510.0000.0000.0000.000
133A134LEU00.0200.01824.326-0.138-0.1380.0000.0000.0000.000
134A135VAL00.0360.01327.216-0.139-0.1390.0000.0000.0000.000
135A136ALA00.0070.01330.4170.0540.0540.0000.0000.0000.000
136A137HIS10.7590.83625.48411.87911.8790.0000.0000.0000.000
137A138GLU-1-0.837-0.89027.203-10.833-10.8330.0000.0000.0000.000
138A139HIS00.0590.02428.079-0.040-0.0400.0000.0000.0000.000
139A140THR0-0.027-0.02328.8430.2110.2110.0000.0000.0000.000
140A141LEU0-0.018-0.01123.7350.0380.0380.0000.0000.0000.000
141A142ARG10.8390.91227.67710.33610.3360.0000.0000.0000.000
142A143THR0-0.084-0.04430.4640.2650.2650.0000.0000.0000.000
143A144VAL0-0.089-0.04027.7480.1740.1740.0000.0000.0000.000
144A145GLY00.0090.00829.551-0.200-0.2000.0000.0000.0000.000
145A146VAL0-0.033-0.00323.995-0.237-0.2370.0000.0000.0000.000
146A147ASP-1-0.778-0.88825.787-12.214-12.2140.0000.0000.0000.000
147A148ARG10.9530.93725.94810.30710.3070.0000.0000.0000.000
148A149GLU-1-0.963-0.96623.162-13.304-13.3040.0000.0000.0000.000
149A150ALA00.0670.02421.218-0.692-0.6920.0000.0000.0000.000
150A151ILE0-0.009-0.00820.743-0.697-0.6970.0000.0000.0000.000
151A152PHE0-0.031-0.01921.862-0.414-0.4140.0000.0000.0000.000
152A153GLU-1-0.742-0.83016.992-18.103-18.1030.0000.0000.0000.000
153A154ALA00.0170.00417.090-1.099-1.0990.0000.0000.0000.000
154A155LEU0-0.016-0.01317.628-0.491-0.4910.0000.0000.0000.000
155A156LYS10.8530.91817.86716.12316.1230.0000.0000.0000.000
156A157ALA00.0040.00013.370-0.675-0.6750.0000.0000.0000.000
157A158ALA00.0020.00414.015-1.037-1.0370.0000.0000.0000.000
158A159ALA0-0.013-0.01116.122-0.213-0.2130.0000.0000.0000.000
159A160ILE0-0.020-0.00912.382-0.117-0.1170.0000.0000.0000.000
160A161VAL00.002-0.00210.061-0.828-0.8280.0000.0000.0000.000
161A162SER0-0.0040.00212.452-0.202-0.2020.0000.0000.0000.000
162A163GLY00.0190.01215.5240.3920.3920.0000.0000.0000.000
163A164VAL0-0.025-0.0289.1160.1090.1090.0000.0000.0000.000
164A165ALA0-0.0040.00312.2500.0140.0140.0000.0000.0000.000
165A166GLN00.0300.01713.0600.4770.4770.0000.0000.0000.000
166A167ALA00.0070.00014.6610.5300.5300.0000.0000.0000.000
167A168LEU00.006-0.0129.2080.0300.0300.0000.0000.0000.000
168A169ALA0-0.022-0.00813.3460.3290.3290.0000.0000.0000.000
169A170THR0-0.048-0.02315.7400.9760.9760.0000.0000.0000.000
170A171ILE0-0.035-0.02713.1350.5560.5560.0000.0000.0000.000
171A172GLU-1-0.903-0.93812.970-19.422-19.4220.0000.0000.0000.000
172A173ALA0-0.045-0.01416.2530.5940.5940.0000.0000.0000.000
173A174LEU0-0.114-0.06019.4670.8700.8700.0000.0000.0000.000
174A175SER-1-0.950-0.95318.206-14.085-14.0850.0000.0000.0000.000