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: RL188

Calculation Name: 1KOP-A-Xray547

Preferred Name:

Target Type:

Ligand Name: sulfate ion | azide ion | beta-mercaptoethanol | zinc ion

Ligand 3-letter code: SO4 | AZI | BME | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1KOP

Chain ID: A

ChEMBL ID:

UniProt ID: Q50940

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 222
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2778754.924318
FMO2-HF: Nuclear repulsion 2691328.750874
FMO2-HF: Total energy -87426.173444
FMO2-MP2: Total energy -87682.76381


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:4:HIS)


Summations of interaction energy for fragment #1(A:4:HIS)
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.
-24.13-21.98216.595-8.217-10.525-0.061
Interaction energy analysis for fragmet #1(A:4:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.799 / q_NPA : 0.886
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].
3A6HIS0-0.044-0.0311.749-24.201-27.14112.434-5.675-3.818-0.064
4A7TRP00.0300.0032.5552.2534.3513.749-1.546-4.3010.007
5A8GLY0-0.010-0.0074.950-0.722-0.654-0.001-0.005-0.0620.000
19A22SER0-0.003-0.0224.501-1.552-1.535-0.001-0.004-0.0120.000
21A24GLU-1-0.894-0.9403.654-57.340-56.4010.009-0.375-0.573-0.002
22A25PHE0-0.005-0.0182.5070.9772.1510.319-0.379-1.114-0.001
63A66HIS10.8540.9492.85234.01534.8070.086-0.233-0.645-0.001
6A9TYR00.0460.0147.701-0.134-0.1340.0000.0000.0000.000
7A10THR00.0070.00911.2850.9580.9580.0000.0000.0000.000
8A11GLY00.0230.01411.921-1.304-1.3040.0000.0000.0000.000
9A12HIS00.0550.01912.7490.1540.1540.0000.0000.0000.000
10A13ASP-1-0.846-0.8977.767-30.327-30.3270.0000.0000.0000.000
11A14SER00.0230.0069.074-1.691-1.6910.0000.0000.0000.000
12A15PRO00.001-0.03311.699-0.402-0.4020.0000.0000.0000.000
13A16GLU-1-0.978-0.97012.678-16.261-16.2610.0000.0000.0000.000
14A17SER00.0310.01112.6110.4820.4820.0000.0000.0000.000
15A18TRP0-0.040-0.0238.892-0.997-0.9970.0000.0000.0000.000
16A19GLY0-0.0060.0009.072-2.282-2.2820.0000.0000.0000.000
17A20ASN0-0.029-0.01511.2901.2901.2900.0000.0000.0000.000
18A21LEU0-0.0110.0207.1870.0630.0630.0000.0000.0000.000
20A23GLU-1-0.923-0.9537.629-24.007-24.0070.0000.0000.0000.000
23A26ARG10.9160.9628.07521.88121.8810.0000.0000.0000.000
24A27LEU00.0210.02411.6611.7101.7100.0000.0000.0000.000
25A28CYS0-0.063-0.0227.7802.6772.6770.0000.0000.0000.000
26A29SER0-0.029-0.02012.6930.8820.8820.0000.0000.0000.000
27A30THR0-0.064-0.04315.3251.0821.0820.0000.0000.0000.000
28A31GLY0-0.0030.01416.4540.8070.8070.0000.0000.0000.000
29A32LYS10.8980.93817.93313.18513.1850.0000.0000.0000.000
30A33ASN0-0.063-0.04220.0061.1351.1350.0000.0000.0000.000
31A34GLN00.0610.02914.820-1.032-1.0320.0000.0000.0000.000
32A35SER00.0100.02916.6461.1711.1710.0000.0000.0000.000
33A36PRO00.0420.02016.166-1.079-1.0790.0000.0000.0000.000
34A37VAL00.014-0.00118.9350.0060.0060.0000.0000.0000.000
35A38ASN00.0420.01822.7080.1840.1840.0000.0000.0000.000
36A39ILE00.0040.00625.7930.1680.1680.0000.0000.0000.000
37A40THR00.0140.00228.4530.1470.1470.0000.0000.0000.000
38A41GLU-1-0.973-0.98031.696-8.457-8.4570.0000.0000.0000.000
39A42THR0-0.074-0.07131.650-0.263-0.2630.0000.0000.0000.000
40A43VAL00.0140.01433.8700.2520.2520.0000.0000.0000.000
41A44SER0-0.020-0.00335.083-0.090-0.0900.0000.0000.0000.000
42A45GLY00.0400.00135.8310.1070.1070.0000.0000.0000.000
43A46LYS10.9170.95636.8057.1787.1780.0000.0000.0000.000
44A47LEU0-0.0090.00930.917-0.056-0.0560.0000.0000.0000.000
45A48PRO0-0.0100.00731.2930.1710.1710.0000.0000.0000.000
46A49ALA00.0100.00232.233-0.218-0.2180.0000.0000.0000.000
47A50ILE00.0200.01627.236-0.112-0.1120.0000.0000.0000.000
48A51LYS10.9230.96830.4219.0759.0750.0000.0000.0000.000
49A52VAL00.002-0.00126.950-0.198-0.1980.0000.0000.0000.000
50A53ASN0-0.039-0.01928.0510.3850.3850.0000.0000.0000.000
51A54TYR0-0.025-0.03422.955-0.336-0.3360.0000.0000.0000.000
52A55LYS11.0251.01426.90810.62910.6290.0000.0000.0000.000
53A56PRO0-0.0090.01027.038-0.405-0.4050.0000.0000.0000.000
54A57SER00.006-0.00724.1100.0850.0850.0000.0000.0000.000
55A58MET0-0.0080.00624.5560.0180.0180.0000.0000.0000.000
56A59VAL00.0020.00819.884-0.350-0.3500.0000.0000.0000.000
57A60ASP-1-0.884-0.94115.886-16.300-16.3000.0000.0000.0000.000
58A61VAL00.0180.01116.639-0.284-0.2840.0000.0000.0000.000
59A62GLU-1-0.887-0.94810.718-21.988-21.9880.0000.0000.0000.000
60A63ASN0-0.045-0.01911.095-0.976-0.9760.0000.0000.0000.000
61A64ASN00.0700.0106.612-0.746-0.7460.0000.0000.0000.000
62A65GLY00.0340.0196.113-2.632-2.6320.0000.0000.0000.000
64A67THR0-0.016-0.0227.7891.5611.5610.0000.0000.0000.000
65A68ILE00.0260.02611.015-0.522-0.5220.0000.0000.0000.000
66A69GLN0-0.067-0.0559.9540.1150.1150.0000.0000.0000.000
67A70VAL00.0090.00713.6970.2050.2050.0000.0000.0000.000
68A71ASN0-0.027-0.02312.583-0.370-0.3700.0000.0000.0000.000
69A72TYR00.025-0.00515.8620.7510.7510.0000.0000.0000.000
70A73PRO0-0.047-0.02517.546-0.340-0.3400.0000.0000.0000.000
71A74GLU-1-0.943-0.95818.541-11.194-11.1940.0000.0000.0000.000
72A75GLY00.0240.00621.310-0.225-0.2250.0000.0000.0000.000
73A76GLY0-0.017-0.02522.8560.2450.2450.0000.0000.0000.000
74A77ASN0-0.0160.00422.9650.5280.5280.0000.0000.0000.000
75A78THR0-0.017-0.02323.369-0.389-0.3890.0000.0000.0000.000
76A79LEU00.0480.03423.8010.3240.3240.0000.0000.0000.000
77A80THR0-0.059-0.02926.026-0.080-0.0800.0000.0000.0000.000
78A81VAL00.0320.01026.6530.2160.2160.0000.0000.0000.000
79A82ASN0-0.001-0.00329.2040.0780.0780.0000.0000.0000.000
80A83GLY00.0130.00831.7410.0220.0220.0000.0000.0000.000
81A84ARG10.9360.98126.5009.5039.5030.0000.0000.0000.000
82A85THR0-0.006-0.01526.2400.1970.1970.0000.0000.0000.000
83A86TYR00.0470.03420.980-0.029-0.0290.0000.0000.0000.000
84A87THR0-0.008-0.01820.7000.4860.4860.0000.0000.0000.000
85A88LEU0-0.045-0.01918.913-0.611-0.6110.0000.0000.0000.000
86A89LYS10.8910.94214.62815.45715.4570.0000.0000.0000.000
87A90GLN00.0660.03810.8680.4570.4570.0000.0000.0000.000
88A91PHE00.0240.01815.6090.5050.5050.0000.0000.0000.000
89A92HIS00.0080.01212.959-0.386-0.3860.0000.0000.0000.000
90A93PHE00.0190.00414.8690.6830.6830.0000.0000.0000.000
91A94HIS10.8250.91211.64316.93116.9310.0000.0000.0000.000
92A95VAL00.0180.03516.0380.9000.9000.0000.0000.0000.000
93A96PRO00.0550.03517.013-0.510-0.5100.0000.0000.0000.000
94A97SER0-0.046-0.04218.368-0.444-0.4440.0000.0000.0000.000
95A98GLU-1-0.736-0.85614.102-17.787-17.7870.0000.0000.0000.000
96A99ASN0-0.054-0.05018.5480.2340.2340.0000.0000.0000.000
97A100GLN0-0.0060.00521.7550.3240.3240.0000.0000.0000.000
98A101ILE0-0.0130.00125.1870.0670.0670.0000.0000.0000.000
99A102LYS10.9470.96428.8238.4678.4670.0000.0000.0000.000
100A103GLY00.0090.01427.9240.2320.2320.0000.0000.0000.000
101A104ARG10.7970.89227.9429.0579.0570.0000.0000.0000.000
102A105THR00.0310.01422.577-0.371-0.3710.0000.0000.0000.000
103A106PHE0-0.036-0.02823.9900.4330.4330.0000.0000.0000.000
104A107PRO0-0.001-0.01123.140-0.441-0.4410.0000.0000.0000.000
105A108MET00.0050.01819.729-0.438-0.4380.0000.0000.0000.000
106A109GLU-1-0.741-0.83619.090-13.060-13.0600.0000.0000.0000.000
107A110ALA0-0.0200.00818.464-0.597-0.5970.0000.0000.0000.000
108A111HIS10.7550.85014.54015.84715.8470.0000.0000.0000.000
109A112PHE00.0440.01917.026-0.471-0.4710.0000.0000.0000.000
110A113VAL0-0.0080.00013.0920.2930.2930.0000.0000.0000.000
111A114HIS00.0110.01316.4160.4280.4280.0000.0000.0000.000
112A115LEU0-0.020-0.00414.284-0.559-0.5590.0000.0000.0000.000
113A116ASP-1-0.816-0.90018.384-12.233-12.2330.0000.0000.0000.000
114A117GLU-1-0.876-0.95220.695-11.638-11.6380.0000.0000.0000.000
115A118ASN0-0.070-0.02821.778-0.069-0.0690.0000.0000.0000.000
116A119LYS10.9150.96115.82115.84715.8470.0000.0000.0000.000
117A120GLN00.0380.02116.801-1.255-1.2550.0000.0000.0000.000
118A121PRO00.015-0.00414.9260.4270.4270.0000.0000.0000.000
119A122LEU0-0.0240.00717.2820.5940.5940.0000.0000.0000.000
120A123VAL0-0.017-0.00216.002-0.304-0.3040.0000.0000.0000.000
121A124LEU0-0.0010.01218.8820.5180.5180.0000.0000.0000.000
122A125ALA0-0.006-0.01520.554-0.417-0.4170.0000.0000.0000.000
123A126VAL0-0.0110.00221.8290.5600.5600.0000.0000.0000.000
124A127LEU00.0250.02422.640-0.452-0.4520.0000.0000.0000.000
125A128TYR00.009-0.01622.3830.2190.2190.0000.0000.0000.000
126A129GLU-1-0.802-0.89926.272-8.910-8.9100.0000.0000.0000.000
127A130ALA0-0.009-0.00828.662-0.084-0.0840.0000.0000.0000.000
128A131GLY00.005-0.00829.8180.2790.2790.0000.0000.0000.000
129A132LYS10.9400.98732.3268.0448.0440.0000.0000.0000.000
130A133THR00.0560.02129.635-0.142-0.1420.0000.0000.0000.000
131A134ASN0-0.058-0.04727.2100.2820.2820.0000.0000.0000.000
132A135GLY00.0480.01428.365-0.221-0.2210.0000.0000.0000.000
133A136ARG10.7480.86328.5749.3669.3660.0000.0000.0000.000
134A137LEU00.0210.01622.401-0.187-0.1870.0000.0000.0000.000
135A138SER0-0.045-0.02624.480-0.345-0.3450.0000.0000.0000.000
136A139SER00.0170.00925.917-0.245-0.2450.0000.0000.0000.000
137A140ILE00.0310.01419.689-0.200-0.2000.0000.0000.0000.000
138A141TRP0-0.026-0.04320.019-0.380-0.3800.0000.0000.0000.000
139A142ASN0-0.044-0.03322.728-0.222-0.2220.0000.0000.0000.000
140A143VAL0-0.0060.00320.6540.0340.0340.0000.0000.0000.000
141A144MET0-0.0340.01017.512-0.469-0.4690.0000.0000.0000.000
142A145PRO00.0070.00915.2030.3190.3190.0000.0000.0000.000
143A146MET0-0.0030.00215.721-0.495-0.4950.0000.0000.0000.000
144A147THR00.0100.01214.193-0.132-0.1320.0000.0000.0000.000
145A148ALA00.0070.0069.7830.1880.1880.0000.0000.0000.000
146A149GLY00.0370.02211.6110.2370.2370.0000.0000.0000.000
147A150LYS10.8480.92013.29318.22718.2270.0000.0000.0000.000
148A151VAL00.0220.02015.4050.4440.4440.0000.0000.0000.000
149A152LYS10.9580.96919.01813.19313.1930.0000.0000.0000.000
150A153LEU0-0.0280.00621.4330.2420.2420.0000.0000.0000.000
151A154ASN00.003-0.01123.547-0.112-0.1120.0000.0000.0000.000
152A155GLN00.0060.01427.0500.3140.3140.0000.0000.0000.000
153A156PRO00.0230.00526.543-0.364-0.3640.0000.0000.0000.000
154A157PHE00.019-0.00423.6820.1830.1830.0000.0000.0000.000
155A158ASP-1-0.782-0.87125.823-9.832-9.8320.0000.0000.0000.000
156A159ALA00.0100.01323.3330.0730.0730.0000.0000.0000.000
157A160SER0-0.057-0.05525.2760.0410.0410.0000.0000.0000.000
158A161THR0-0.036-0.02327.8400.1060.1060.0000.0000.0000.000
159A162LEU0-0.019-0.01122.8890.1290.1290.0000.0000.0000.000
160A163LEU00.0080.01725.358-0.163-0.1630.0000.0000.0000.000
161A164PRO0-0.0020.00427.9140.3600.3600.0000.0000.0000.000
162A165LYS10.9790.98331.1257.9617.9610.0000.0000.0000.000
163A166ARG10.8880.94533.7997.9007.9000.0000.0000.0000.000
164A167LEU00.0870.04828.954-0.142-0.1420.0000.0000.0000.000
165A168LYS10.9620.97931.6477.9487.9480.0000.0000.0000.000
166A169TYR0-0.033-0.03627.834-0.194-0.1940.0000.0000.0000.000
167A170TYR00.0650.05127.5500.2480.2480.0000.0000.0000.000
168A171ARG10.8790.93525.22210.56610.5660.0000.0000.0000.000
169A172PHE00.0530.02521.0650.3170.3170.0000.0000.0000.000
170A173ALA0-0.008-0.00122.496-0.146-0.1460.0000.0000.0000.000
171A174GLY00.0410.01519.5790.2590.2590.0000.0000.0000.000
172A175SER00.011-0.01014.5250.2180.2180.0000.0000.0000.000
173A176LEU0-0.0020.0079.1990.8030.8030.0000.0000.0000.000
174A177THR0-0.090-0.06312.745-0.270-0.2700.0000.0000.0000.000
175A178THR00.0180.0197.2150.8390.8390.0000.0000.0000.000
176A179PRO00.0540.0215.5131.5061.5060.0000.0000.0000.000
177A180PRO0-0.034-0.0106.065-0.801-0.8010.0000.0000.0000.000
178A182THR00.0340.01210.8700.9560.9560.0000.0000.0000.000
179A183GLU-1-0.726-0.85312.880-14.590-14.5900.0000.0000.0000.000
180A184GLY00.0210.01116.650-0.205-0.2050.0000.0000.0000.000
181A185VAL0-0.0390.00014.7770.2730.2730.0000.0000.0000.000
182A186SER0-0.057-0.04017.9930.7170.7170.0000.0000.0000.000
183A187TRP0-0.011-0.00316.110-0.050-0.0500.0000.0000.0000.000
184A188LEU0-0.013-0.01521.8380.5910.5910.0000.0000.0000.000
185A189VAL00.0390.02222.617-0.232-0.2320.0000.0000.0000.000
186A190LEU0-0.026-0.01525.0230.4510.4510.0000.0000.0000.000
187A191LYS10.8000.88027.8238.7008.7000.0000.0000.0000.000
188A192THR0-0.087-0.03530.9360.2470.2470.0000.0000.0000.000
189A193TYR00.0380.02128.514-0.225-0.2250.0000.0000.0000.000
190A194ASP-1-0.777-0.84827.356-9.362-9.3620.0000.0000.0000.000
191A195HIS0-0.040-0.02429.0800.0420.0420.0000.0000.0000.000
192A196ILE0-0.002-0.00823.874-0.226-0.2260.0000.0000.0000.000
193A197ASP-1-0.831-0.90427.933-8.990-8.9900.0000.0000.0000.000
194A198GLN00.0830.02726.787-0.385-0.3850.0000.0000.0000.000
195A199ALA00.0540.02725.524-0.428-0.4280.0000.0000.0000.000
196A200GLN0-0.013-0.00624.202-0.136-0.1360.0000.0000.0000.000
197A201ALA00.0780.04721.554-0.532-0.5320.0000.0000.0000.000
198A202GLU-1-0.835-0.88520.596-11.163-11.1630.0000.0000.0000.000
199A203LYS10.8740.94120.87711.76011.7600.0000.0000.0000.000
200A204PHE00.000-0.01414.112-0.461-0.4610.0000.0000.0000.000
201A205THR00.001-0.01716.459-0.772-0.7720.0000.0000.0000.000
202A206ARG10.8190.89316.33810.99010.9900.0000.0000.0000.000
203A207ALA0-0.024-0.00616.118-0.179-0.1790.0000.0000.0000.000
204A208VAL0-0.028-0.00710.679-0.884-0.8840.0000.0000.0000.000
205A209GLY0-0.0110.01211.616-1.249-1.2490.0000.0000.0000.000
206A210SER0-0.061-0.05512.598-0.093-0.0930.0000.0000.0000.000
207A211GLU-1-0.893-0.93714.558-13.280-13.2800.0000.0000.0000.000
208A212ASN0-0.014-0.02211.3740.0800.0800.0000.0000.0000.000
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