FMO DATABASE

FMODB ID: 9QQ92

Calculation Name: 2WKF-B-Xray547

Preferred Name: Macrophage migration inhibitory factor homologue

Target Type: SINGLE PROTEIN

Ligand Name: s,s-(2-hydroxyethyl)thiocysteine | glycerol

Ligand 3-letter code: CME | GOL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2WKF

Chain ID: B

ChEMBL ID: CHEMBL2176864

UniProt ID: Q8I5C5

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	105
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-783004.569473
FMO2-HF: Nuclear repulsion	741018.479915
FMO2-HF: Total energy	-41986.089558
FMO2-MP2: Total energy	-42105.123299

3D Structure Molmil

Snapshot

Ligand structure

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/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(B:1:PRO)

Summations of interaction energy for fragment #1(B:1:PRO)

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.
-93.508	-82.478	7.002	-7.688	-10.343	-0.077

Interaction energy analysis for fragmet #1(B:1:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.838 / q_NPA : 0.908

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 ES EX CT+mix DI(MP2)

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].
3	B	3	CYS	0	0.015	0.027	3.857	3.805	5.733	-0.024	-0.966	-0.937	-0.003
37	B	37	TYR	0	-0.023	-0.020	3.396	0.249	0.542	0.009	-0.047	-0.255	0.000
38	B	38	ILE	0	0.009	-0.006	2.835	-17.843	-15.596	0.387	-1.157	-1.476	-0.012
39	B	39	MET	0	-0.011	0.013	2.998	7.257	8.134	0.022	-0.284	-0.616	-0.002
63	B	63	THR	0	0.005	0.003	4.455	5.431	5.627	-0.001	-0.054	-0.141	0.000
64	B	64	SER	0	0.042	0.009	2.343	-20.384	-18.093	2.512	-2.438	-2.364	-0.028
65	B	65	ILE	0	-0.012	-0.007	2.327	-21.120	-17.850	4.075	-2.914	-4.432	-0.031
66	B	66	GLY	0	0.020	0.004	3.324	6.948	6.876	0.022	0.172	-0.122	-0.001
4	B	4	GLU	-1	-0.801	-0.870	7.201	-30.005	-30.005	0.000	0.000	0.000	0.000
5	B	5	VAL	0	0.009	-0.003	10.034	1.197	1.197	0.000	0.000	0.000	0.000
6	B	6	ILE	0	0.011	0.016	12.766	0.955	0.955	0.000	0.000	0.000	0.000
7	B	7	THR	0	-0.022	-0.044	15.738	0.949	0.949	0.000	0.000	0.000	0.000
8	B	8	ASN	0	-0.003	0.001	19.358	-0.296	-0.296	0.000	0.000	0.000	0.000
9	B	9	VAL	0	0.005	-0.002	22.256	0.683	0.683	0.000	0.000	0.000	0.000
10	B	10	ASN	0	-0.021	-0.004	22.391	-0.973	-0.973	0.000	0.000	0.000	0.000
11	B	11	LEU	0	0.015	0.006	20.073	0.405	0.405	0.000	0.000	0.000	0.000
12	B	12	PRO	0	0.016	0.007	22.563	-0.351	-0.351	0.000	0.000	0.000	0.000
13	B	13	ASP	-1	-0.844	-0.922	20.600	-14.540	-14.540	0.000	0.000	0.000	0.000
14	B	14	ASP	-1	-0.895	-0.946	19.873	-13.780	-13.780	0.000	0.000	0.000	0.000
15	B	15	ASN	0	-0.023	-0.017	20.567	-0.196	-0.196	0.000	0.000	0.000	0.000
16	B	16	VAL	0	-0.017	0.010	16.614	-0.578	-0.578	0.000	0.000	0.000	0.000
17	B	17	GLN	0	0.028	0.007	15.031	-1.476	-1.476	0.000	0.000	0.000	0.000
18	B	18	SER	0	-0.004	0.006	15.938	-0.907	-0.907	0.000	0.000	0.000	0.000
19	B	19	THR	0	-0.024	-0.029	16.229	-0.092	-0.092	0.000	0.000	0.000	0.000
20	B	20	LEU	0	-0.041	-0.016	11.534	-0.497	-0.497	0.000	0.000	0.000	0.000
21	B	21	SER	0	0.039	0.032	12.056	-0.905	-0.905	0.000	0.000	0.000	0.000
22	B	22	GLN	0	0.001	0.000	13.631	-0.072	-0.072	0.000	0.000	0.000	0.000
23	B	23	ILE	0	0.011	-0.004	9.990	-0.142	-0.142	0.000	0.000	0.000	0.000
24	B	24	GLU	-1	-0.848	-0.901	8.286	-27.941	-27.941	0.000	0.000	0.000	0.000
25	B	25	ASN	0	-0.026	0.001	10.095	-1.202	-1.202	0.000	0.000	0.000	0.000
26	B	26	ALA	0	0.048	0.029	13.030	-0.045	-0.045	0.000	0.000	0.000	0.000
27	B	27	ILE	0	-0.034	-0.040	6.403	-0.464	-0.464	0.000	0.000	0.000	0.000
28	B	28	SER	0	-0.024	-0.030	9.882	-0.536	-0.536	0.000	0.000	0.000	0.000
29	B	29	ASP	-1	-0.969	-0.982	11.012	-16.860	-16.860	0.000	0.000	0.000	0.000
30	B	30	VAL	0	-0.097	-0.042	12.256	1.039	1.039	0.000	0.000	0.000	0.000
31	B	31	MET	0	-0.073	-0.032	7.132	-1.076	-1.076	0.000	0.000	0.000	0.000
32	B	32	GLY	0	-0.015	-0.001	10.724	0.444	0.444	0.000	0.000	0.000	0.000
33	B	33	LYS	1	0.958	0.965	11.972	15.424	15.424	0.000	0.000	0.000	0.000
34	B	34	PRO	0	-0.022	-0.007	10.480	0.355	0.355	0.000	0.000	0.000	0.000
35	B	35	LEU	0	0.056	0.042	9.540	-1.761	-1.761	0.000	0.000	0.000	0.000
36	B	36	GLY	0	0.003	0.002	6.269	0.073	0.073	0.000	0.000	0.000	0.000
40	B	40	SER	0	-0.046	-0.055	5.250	-2.957	-2.957	0.000	0.000	0.000	0.000
41	B	41	ASN	0	0.035	0.002	8.082	1.798	1.798	0.000	0.000	0.000	0.000
42	B	42	TYR	0	0.014	-0.009	11.263	0.087	0.087	0.000	0.000	0.000	0.000
43	B	43	ASP	-1	-0.867	-0.914	14.340	-18.757	-18.757	0.000	0.000	0.000	0.000
44	B	44	TYR	0	0.009	0.002	16.121	0.852	0.852	0.000	0.000	0.000	0.000
45	B	45	GLN	0	-0.022	-0.017	18.109	1.468	1.468	0.000	0.000	0.000	0.000
46	B	46	LYS	1	0.971	0.985	21.111	11.889	11.889	0.000	0.000	0.000	0.000
47	B	47	ASN	0	-0.010	-0.007	24.666	0.578	0.578	0.000	0.000	0.000	0.000
48	B	48	LEU	0	0.008	0.024	19.279	0.296	0.296	0.000	0.000	0.000	0.000
49	B	49	ARG	1	0.897	0.947	23.144	11.335	11.335	0.000	0.000	0.000	0.000
50	B	50	PHE	0	0.056	0.033	22.112	-0.303	-0.303	0.000	0.000	0.000	0.000
51	B	51	GLY	0	0.027	0.019	24.886	0.420	0.420	0.000	0.000	0.000	0.000
52	B	52	GLY	0	-0.005	-0.001	27.891	0.359	0.359	0.000	0.000	0.000	0.000
53	B	53	SER	0	-0.009	-0.004	28.756	0.204	0.204	0.000	0.000	0.000	0.000
54	B	54	ASN	0	-0.031	-0.043	26.331	-0.151	-0.151	0.000	0.000	0.000	0.000
55	B	55	GLU	-1	-0.873	-0.925	27.636	-10.283	-10.283	0.000	0.000	0.000	0.000
56	B	56	ALA	0	0.037	0.039	25.622	-0.454	-0.454	0.000	0.000	0.000	0.000
57	B	57	TYR	0	-0.021	-0.029	19.605	0.092	0.092	0.000	0.000	0.000	0.000
58	B	58	CYS	0	-0.014	0.030	17.521	-0.137	-0.137	0.000	0.000	0.000	0.000
59	B	59	PHE	0	-0.013	-0.002	13.982	0.167	0.167	0.000	0.000	0.000	0.000
60	B	60	VAL	0	0.028	0.012	11.370	-0.848	-0.848	0.000	0.000	0.000	0.000
61	B	61	ARG	1	0.807	0.889	9.056	27.449	27.449	0.000	0.000	0.000	0.000
62	B	62	ILE	0	0.036	0.012	6.100	-3.350	-3.350	0.000	0.000	0.000	0.000
67	B	67	GLY	0	0.017	0.019	5.939	3.474	3.474	0.000	0.000	0.000	0.000
68	B	68	ILE	0	-0.042	-0.001	7.352	2.804	2.804	0.000	0.000	0.000	0.000
69	B	69	ASN	0	0.057	0.027	9.013	-1.607	-1.607	0.000	0.000	0.000	0.000
70	B	70	ARG	1	0.914	0.936	12.064	16.732	16.732	0.000	0.000	0.000	0.000
71	B	71	SER	0	-0.029	-0.023	15.267	0.926	0.926	0.000	0.000	0.000	0.000
72	B	72	ASN	0	0.028	0.019	12.408	0.132	0.132	0.000	0.000	0.000	0.000
73	B	73	ASN	0	0.096	0.049	12.114	1.220	1.220	0.000	0.000	0.000	0.000
74	B	74	SER	0	0.004	-0.003	13.223	0.018	0.018	0.000	0.000	0.000	0.000
75	B	75	ALA	0	0.016	0.017	16.277	0.499	0.499	0.000	0.000	0.000	0.000
76	B	76	LEU	0	0.031	0.031	9.401	0.338	0.338	0.000	0.000	0.000	0.000
77	B	77	ALA	0	0.026	0.007	13.891	0.030	0.030	0.000	0.000	0.000	0.000
78	B	78	ASP	-1	-0.836	-0.887	15.415	-13.416	-13.416	0.000	0.000	0.000	0.000
79	B	79	GLN	0	0.027	0.011	15.824	0.251	0.251	0.000	0.000	0.000	0.000
80	B	80	ILE	0	0.042	0.019	11.212	0.434	0.434	0.000	0.000	0.000	0.000
81	B	81	THR	0	-0.023	-0.027	15.804	0.629	0.629	0.000	0.000	0.000	0.000
82	B	82	LYS	1	0.808	0.878	19.080	13.876	13.876	0.000	0.000	0.000	0.000
83	B	83	LEU	0	0.024	0.028	15.553	0.574	0.574	0.000	0.000	0.000	0.000
84	B	84	LEU	0	0.017	0.002	15.795	0.382	0.382	0.000	0.000	0.000	0.000
85	B	85	VAL	0	-0.067	-0.041	19.835	0.523	0.523	0.000	0.000	0.000	0.000
86	B	86	SER	0	-0.080	-0.038	22.546	0.698	0.698	0.000	0.000	0.000	0.000
87	B	87	ASN	0	-0.031	-0.040	19.494	0.944	0.944	0.000	0.000	0.000	0.000
88	B	88	LEU	0	-0.030	-0.004	19.176	0.046	0.046	0.000	0.000	0.000	0.000
89	B	89	ASN	0	-0.019	0.000	23.324	0.462	0.462	0.000	0.000	0.000	0.000
90	B	90	VAL	0	-0.025	0.003	22.280	0.407	0.407	0.000	0.000	0.000	0.000
91	B	91	LYS	1	0.970	0.972	25.045	10.248	10.248	0.000	0.000	0.000	0.000
92	B	92	SER	0	0.115	0.046	23.334	-0.221	-0.221	0.000	0.000	0.000	0.000
93	B	93	ARG	1	0.920	0.958	23.150	9.946	9.946	0.000	0.000	0.000	0.000
94	B	94	ARG	1	0.707	0.827	23.600	11.978	11.978	0.000	0.000	0.000	0.000
95	B	95	ILE	0	0.048	0.037	18.130	-0.266	-0.266	0.000	0.000	0.000	0.000
96	B	96	TYR	0	-0.062	-0.016	16.295	0.634	0.634	0.000	0.000	0.000	0.000
97	B	97	VAL	0	0.006	0.000	12.859	-0.796	-0.796	0.000	0.000	0.000	0.000
98	B	98	GLU	-1	-0.896	-0.955	11.584	-21.336	-21.336	0.000	0.000	0.000	0.000
99	B	99	PHE	0	-0.013	-0.015	8.808	-1.726	-1.726	0.000	0.000	0.000	0.000
100	B	100	ARG	1	0.906	0.949	7.717	33.689	33.689	0.000	0.000	0.000	0.000
101	B	101	ASP	-1	-0.869	-0.925	6.892	-34.819	-34.819	0.000	0.000	0.000	0.000
102	B	102	CYS	0	-0.083	-0.065	6.904	1.861	1.861	0.000	0.000	0.000	0.000
103	B	103	SER	0	-0.009	0.004	8.408	-0.697	-0.697	0.000	0.000	0.000	0.000
104	B	104	ALA	0	-0.048	-0.037	7.242	-1.247	-1.247	0.000	0.000	0.000	0.000
105	B	105	GLN	-1	-0.917	-0.936	9.343	-22.058	-22.058	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:1:PRO)