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: JKQM9

Calculation Name: 5FCI-A-Xray547

Preferred Name:

Target Type:

Ligand Name: osmium (iii) hexammine | magnesium ion | zinc ion

Ligand 3-letter code: OHX | MG | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5FCI

Chain ID: A

ChEMBL ID:

UniProt ID: P38011

Base Structure: X-ray

Registration Date: 2025-10-06

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 194
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1608132.115213
FMO2-HF: Nuclear repulsion 1533387.188568
FMO2-HF: Total energy -74744.926645
FMO2-MP2: Total energy -74969.494801


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:ALA)


Summations of interaction energy for fragment #1(A:2:ALA)
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.
250.148251.38-0.01-0.522-0.699-0.001
Interaction energy analysis for fragmet #1(A:2:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.866 / q_NPA : 0.925
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].
3A4SER00.0100.0043.8704.1345.366-0.010-0.522-0.699-0.001
4A5LYS10.9800.9875.83034.74134.7410.0000.0000.0000.000
5A6ASN00.0380.0319.594-2.122-2.1220.0000.0000.0000.000
6A7LEU00.0160.0098.4991.2941.2940.0000.0000.0000.000
7A8PRO00.0180.01711.666-0.803-0.8030.0000.0000.0000.000
8A9ILE00.0270.0038.767-2.125-2.1250.0000.0000.0000.000
9A10LEU0-0.0060.0069.7192.2022.2020.0000.0000.0000.000
10A11LYS10.9670.9779.88218.76618.7660.0000.0000.0000.000
11A12ASN00.0500.03310.8492.7112.7110.0000.0000.0000.000
12A13HIS0-0.045-0.03111.562-1.070-1.0700.0000.0000.0000.000
13A14PHE0-0.013-0.01012.5441.1781.1780.0000.0000.0000.000
14A15ARG10.9840.9786.85734.34434.3440.0000.0000.0000.000
15A16LYS10.9770.99813.61316.44616.4460.0000.0000.0000.000
16A17HIS00.0570.02117.4160.1920.1920.0000.0000.0000.000
17A18TRP00.003-0.00814.9471.2341.2340.0000.0000.0000.000
18A19GLN00.011-0.00217.9711.1011.1010.0000.0000.0000.000
19A20GLU-1-0.845-0.90021.334-12.829-12.8290.0000.0000.0000.000
20A21ARG10.8340.91621.13714.44814.4480.0000.0000.0000.000
21A22VAL00.0070.01722.443-0.163-0.1630.0000.0000.0000.000
22A23LYS10.9270.96124.99410.89010.8900.0000.0000.0000.000
23A24VAL00.0500.02626.435-0.235-0.2350.0000.0000.0000.000
24A25HIS00.0030.01229.0270.4290.4290.0000.0000.0000.000
25A26PHE00.0830.02229.5010.2330.2330.0000.0000.0000.000
26A27ASP-1-0.787-0.87934.261-8.736-8.7360.0000.0000.0000.000
27A28GLN0-0.046-0.01734.0730.3570.3570.0000.0000.0000.000
28A29ALA00.0260.01737.2780.2130.2130.0000.0000.0000.000
29A30GLY00.1040.04940.1690.2150.2150.0000.0000.0000.000
30A31LYS10.9050.92836.8778.7958.7950.0000.0000.0000.000
31A32LYS10.9000.95341.6247.5357.5350.0000.0000.0000.000
32A33VAL00.0320.01743.1380.1590.1590.0000.0000.0000.000
33A34SER00.018-0.00244.4480.1640.1640.0000.0000.0000.000
34A35ARG10.9060.95140.1497.9037.9030.0000.0000.0000.000
35A36ARG10.9030.96246.1676.6036.6030.0000.0000.0000.000
36A37ASN00.0440.00649.0310.1210.1210.0000.0000.0000.000
37A38ALA00.0530.04349.1400.0860.0860.0000.0000.0000.000
38A39ARG10.9110.94346.1726.7786.7780.0000.0000.0000.000
39A40ALA00.0170.01551.9380.0910.0910.0000.0000.0000.000
40A41THR00.0430.01753.9480.0910.0910.0000.0000.0000.000
41A42ARG10.8400.92153.0586.0726.0720.0000.0000.0000.000
42A43ALA00.014-0.00755.8120.0850.0850.0000.0000.0000.000
43A44ALA00.1070.08057.7910.0830.0830.0000.0000.0000.000
44A45LYS10.9751.00158.1505.5425.5420.0000.0000.0000.000
45A46ILE0-0.145-0.08257.431-0.021-0.0210.0000.0000.0000.000
46A47ALA00.0780.04660.8190.0450.0450.0000.0000.0000.000
47A48PRO00.0850.04962.960-0.093-0.0930.0000.0000.0000.000
48A49ARG10.8830.94560.9275.2405.2400.0000.0000.0000.000
49A50PRO00.0410.02459.044-0.061-0.0610.0000.0000.0000.000
50A51LEU0-0.0020.00853.622-0.159-0.1590.0000.0000.0000.000
51A52ASP-1-0.866-0.93453.129-6.008-6.0080.0000.0000.0000.000
52A53LEU0-0.037-0.01754.6440.0850.0850.0000.0000.0000.000
53A54LEU00.0520.02655.357-0.140-0.1400.0000.0000.0000.000
54A55ARG10.8490.92051.4566.1736.1730.0000.0000.0000.000
55A56PRO0-0.0200.02753.9760.0460.0460.0000.0000.0000.000
56A57VAL00.0770.01353.818-0.165-0.1650.0000.0000.0000.000
57A58VAL0-0.033-0.02349.3710.0310.0310.0000.0000.0000.000
58A59ARG10.9470.95550.4396.2106.2100.0000.0000.0000.000
59A60ALA00.0120.01845.657-0.091-0.0910.0000.0000.0000.000
60A61PRO00.0350.01743.2570.0520.0520.0000.0000.0000.000
61A62THR00.012-0.01640.224-0.208-0.2080.0000.0000.0000.000
62A63VAL00.0680.02342.5250.0980.0980.0000.0000.0000.000
63A64LYS10.9541.00235.5028.9438.9430.0000.0000.0000.000
64A65TYR0-0.004-0.02937.432-0.072-0.0720.0000.0000.0000.000
65A66ASN00.0230.03543.9190.0280.0280.0000.0000.0000.000
66A67ARG10.9720.98942.3367.5657.5650.0000.0000.0000.000
67A68LYS10.8870.95945.8446.9206.9200.0000.0000.0000.000
68A69VAL00.0140.02448.1000.0750.0750.0000.0000.0000.000
69A70ARG10.9390.97445.2436.9426.9420.0000.0000.0000.000
70A71ALA00.0730.04049.1930.0930.0930.0000.0000.0000.000
71A72GLY0-0.037-0.02549.204-0.166-0.1660.0000.0000.0000.000
72A73ARG10.9230.96148.7656.4686.4680.0000.0000.0000.000
73A74GLY00.053-0.00251.3710.0350.0350.0000.0000.0000.000
74A75PHE00.0320.00655.195-0.082-0.0820.0000.0000.0000.000
75A76THR0-0.0220.01157.1630.1030.1030.0000.0000.0000.000
76A77LEU00.0430.00759.1320.0430.0430.0000.0000.0000.000
77A78ALA0-0.0170.00362.2450.0930.0930.0000.0000.0000.000
78A79GLU-1-0.641-0.79158.927-5.542-5.5420.0000.0000.0000.000
79A80VAL00.0040.00062.3320.0500.0500.0000.0000.0000.000
80A81LYS11.0011.00364.8024.7144.7140.0000.0000.0000.000
81A82ALA0-0.016-0.00366.5410.0820.0820.0000.0000.0000.000
82A83ALA0-0.021-0.00766.4030.0350.0350.0000.0000.0000.000
83A84GLY00.0120.02168.3770.0330.0330.0000.0000.0000.000
84A85LEU0-0.030-0.00566.0810.0340.0340.0000.0000.0000.000
85A86THR00.0480.01468.123-0.065-0.0650.0000.0000.0000.000
86A87ALA00.004-0.00962.679-0.038-0.0380.0000.0000.0000.000
87A88ALA0-0.017-0.01963.678-0.067-0.0670.0000.0000.0000.000
88A89TYR00.0930.05265.394-0.046-0.0460.0000.0000.0000.000
89A90ALA00.0640.03563.462-0.039-0.0390.0000.0000.0000.000
90A91ARG10.8850.93257.2945.4545.4540.0000.0000.0000.000
91A92THR0-0.107-0.05761.530-0.034-0.0340.0000.0000.0000.000
92A93ILE0-0.0010.02564.2420.0040.0040.0000.0000.0000.000
93A94GLY00.0620.02360.716-0.023-0.0230.0000.0000.0000.000
94A95ILE0-0.0090.02159.542-0.088-0.0880.0000.0000.0000.000
95A96ALA0-0.020-0.00354.884-0.020-0.0200.0000.0000.0000.000
96A97VAL00.017-0.00556.9950.0080.0080.0000.0000.0000.000
97A98ASP-1-0.871-0.92952.696-6.284-6.2840.0000.0000.0000.000
98A99HIS00.0600.02754.6710.0900.0900.0000.0000.0000.000
99A100ARG10.8620.93551.0846.3206.3200.0000.0000.0000.000
100A101ARG10.7230.84053.2215.7935.7930.0000.0000.0000.000
101A102GLN00.0460.00354.6120.0110.0110.0000.0000.0000.000
102A103ASN0-0.009-0.02756.616-0.063-0.0630.0000.0000.0000.000
103A104ARG10.9840.97953.3625.9875.9870.0000.0000.0000.000
104A105ASN00.0090.01556.9350.0050.0050.0000.0000.0000.000
105A106GLN00.0200.00958.831-0.038-0.0380.0000.0000.0000.000
106A107GLU-1-0.834-0.91658.977-5.410-5.4100.0000.0000.0000.000
107A108ILE0-0.095-0.05254.927-0.060-0.0600.0000.0000.0000.000
108A109PHE0-0.026-0.01958.566-0.024-0.0240.0000.0000.0000.000
109A110ASP-1-0.778-0.88261.241-4.969-4.9690.0000.0000.0000.000
110A111ALA00.0020.00259.4480.0370.0370.0000.0000.0000.000
111A112ASN0-0.065-0.04056.736-0.060-0.0600.0000.0000.0000.000
112A113VAL00.015-0.00360.7810.0240.0240.0000.0000.0000.000
113A114GLN00.0040.01263.4630.0880.0880.0000.0000.0000.000
114A115ARG10.7830.88156.7665.6865.6860.0000.0000.0000.000
115A116LEU0-0.058-0.02062.1300.0030.0030.0000.0000.0000.000
116A117LYS11.0051.00964.2134.7484.7480.0000.0000.0000.000
117A118GLU-1-0.906-0.94763.302-4.965-4.9650.0000.0000.0000.000
118A119TYR00.0270.00761.6870.0370.0370.0000.0000.0000.000
119A120GLN0-0.030-0.03964.7100.0210.0210.0000.0000.0000.000
120A121SER0-0.057-0.03067.9810.0540.0540.0000.0000.0000.000
121A122LYS10.9700.99364.5725.0245.0240.0000.0000.0000.000
122A123ILE0-0.076-0.02764.465-0.068-0.0680.0000.0000.0000.000
123A124ILE00.0360.02767.6640.0570.0570.0000.0000.0000.000
124A125VAL0-0.030-0.02168.787-0.046-0.0460.0000.0000.0000.000
125A126PHE00.0200.00870.3370.0720.0720.0000.0000.0000.000
126A127PRO00.0280.02372.233-0.004-0.0040.0000.0000.0000.000
127A128ARG10.9440.96472.9824.4034.4030.0000.0000.0000.000
128A129ASN0-0.018-0.02774.6880.0290.0290.0000.0000.0000.000
129A130GLY00.0400.01973.972-0.028-0.0280.0000.0000.0000.000
130A131LYS10.9420.99474.6653.9943.9940.0000.0000.0000.000
131A132ALA00.013-0.00373.5440.0160.0160.0000.0000.0000.000
132A133PRO0-0.009-0.01674.2420.0130.0130.0000.0000.0000.000
133A134GLU-1-0.905-0.92970.607-4.600-4.6000.0000.0000.0000.000
134A135ALA0-0.053-0.04269.405-0.068-0.0680.0000.0000.0000.000
135A136GLU-1-0.868-0.92566.027-4.872-4.8720.0000.0000.0000.000
136A137GLN0-0.072-0.04160.432-0.051-0.0510.0000.0000.0000.000
137A138VAL0-0.0010.00660.429-0.090-0.0900.0000.0000.0000.000
138A139LEU0-0.009-0.01856.427-0.061-0.0610.0000.0000.0000.000
139A140SER0-0.063-0.02154.571-0.109-0.1090.0000.0000.0000.000
140A141ALA00.0410.02656.5570.0990.0990.0000.0000.0000.000
141A142ALA0-0.050-0.04652.9860.0270.0270.0000.0000.0000.000
142A143ALA0-0.025-0.02454.202-0.014-0.0140.0000.0000.0000.000
143A144THR00.0000.00855.6220.0680.0680.0000.0000.0000.000
144A145PHE0-0.0070.00258.1960.0530.0530.0000.0000.0000.000
145A146PRO00.0510.03254.720-0.097-0.0970.0000.0000.0000.000
146A147ILE0-0.055-0.02952.7680.0600.0600.0000.0000.0000.000
147A148ALA00.0360.02153.187-0.105-0.1050.0000.0000.0000.000
148A149GLN0-0.029-0.04450.062-0.099-0.0990.0000.0000.0000.000
149A150PRO00.006-0.00753.7100.0400.0400.0000.0000.0000.000
150A151ALA00.0860.05656.152-0.077-0.0770.0000.0000.0000.000
151A152THR0-0.129-0.06354.193-0.114-0.1140.0000.0000.0000.000
152A153ASP-1-0.787-0.87057.622-5.416-5.4160.0000.0000.0000.000
153A154VAL0-0.027-0.01859.6770.0130.0130.0000.0000.0000.000
154A155GLU-1-0.941-0.97459.523-5.439-5.4390.0000.0000.0000.000
155A156ALA00.0120.00860.635-0.048-0.0480.0000.0000.0000.000
156A157ARG10.8250.89959.7605.4145.4140.0000.0000.0000.000
157A158ALA00.0390.02364.492-0.012-0.0120.0000.0000.0000.000
158A159VAL0-0.014-0.01562.153-0.067-0.0670.0000.0000.0000.000
159A160GLN0-0.0030.00364.1590.0610.0610.0000.0000.0000.000
160A161ASP-1-0.924-0.95761.321-5.385-5.3850.0000.0000.0000.000
161A162ASN0-0.042-0.03861.3880.0410.0410.0000.0000.0000.000
162A163GLY00.0680.05963.2660.0560.0560.0000.0000.0000.000
163A164GLU-1-0.945-0.97259.453-5.306-5.3060.0000.0000.0000.000
164A165SER00.0150.01754.741-0.120-0.1200.0000.0000.0000.000
165A166ALA00.0900.03253.472-0.038-0.0380.0000.0000.0000.000
166A167PHE00.0110.00047.192-0.093-0.0930.0000.0000.0000.000
167A168ARG10.9930.98751.8175.6935.6930.0000.0000.0000.000
168A169THR00.0720.03054.4140.0080.0080.0000.0000.0000.000
169A170LEU0-0.021-0.01848.833-0.063-0.0630.0000.0000.0000.000
170A171ARG10.8380.92546.3126.6656.6650.0000.0000.0000.000
171A172LEU00.0120.01250.904-0.069-0.0690.0000.0000.0000.000
172A173ALA00.0960.04951.967-0.014-0.0140.0000.0000.0000.000
173A174ARG10.9060.95144.6307.0447.0440.0000.0000.0000.000
174A175SER0-0.010-0.01849.564-0.130-0.1300.0000.0000.0000.000
175A176GLU-1-0.917-0.94151.524-5.728-5.7280.0000.0000.0000.000
176A177LYS10.9470.96746.8496.7716.7710.0000.0000.0000.000
177A178LYS10.8820.94744.9057.0437.0430.0000.0000.0000.000
178A179PHE00.005-0.01549.498-0.047-0.0470.0000.0000.0000.000
179A180ARG10.8780.94352.6865.9965.9960.0000.0000.0000.000
180A181GLY00.0080.01052.4400.0840.0840.0000.0000.0000.000
181A182ILE0-0.007-0.00650.2170.0600.0600.0000.0000.0000.000
182A183ARG10.9310.96054.3615.8095.8090.0000.0000.0000.000
183A184GLU-1-0.739-0.86456.698-5.571-5.5710.0000.0000.0000.000
184A185LYS10.8590.95454.5595.9125.9120.0000.0000.0000.000
185A186ARG10.9710.97855.9805.6755.6750.0000.0000.0000.000
186A187ALA0-0.038-0.01760.2050.0910.0910.0000.0000.0000.000
187A188ARG10.7900.87657.7175.4945.4940.0000.0000.0000.000
188A189GLU-1-0.781-0.90658.936-5.500-5.5000.0000.0000.0000.000
189A190LYS10.9050.95863.2084.9614.9610.0000.0000.0000.000
190A191ALA0-0.0060.00065.9700.0690.0690.0000.0000.0000.000
191A192GLU-1-0.839-0.91462.848-5.164-5.1640.0000.0000.0000.000
192A193ALA0-0.071-0.02267.0550.0050.0050.0000.0000.0000.000
193A194GLU-1-1.020-1.01368.801-4.324-4.3240.0000.0000.0000.000
194A195ALA-1-0.917-0.93872.436-4.393-4.3930.0000.0000.0000.000