FMO DATABASE

FMODB ID: 8GR8Y

Calculation Name: 1N2F-A-Xray547

Preferred Name:

Target Type:

Ligand Name: 2,3-dihydroxy-1,4-dithiobutane

Ligand 3-letter code: DTT

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1N2F

Chain ID: A

ChEMBL ID:

UniProt ID: Q9HZZ3

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	142
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1025014.859486
FMO2-HF: Nuclear repulsion	973181.987625
FMO2-HF: Total energy	-51832.871861
FMO2-MP2: Total energy	-51981.466182

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(A:1:MET)

Summations of interaction energy for fragment #1(A:1:MET)

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.
-5.155	-2.787	0.257	-0.858	-1.767	-0.003

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.872 / q_NPA : 0.932

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	A	3	THR	0	0.006	0.014	3.444	4.802	7.124	0.258	-0.853	-1.727	-0.003
4	A	4	ILE	0	0.036	0.017	5.397	1.011	1.057	-0.001	-0.005	-0.040	0.000
5	A	5	LYS	1	0.933	0.959	8.985	23.707	23.707	0.000	0.000	0.000	0.000
6	A	6	ALA	0	0.016	0.013	11.897	-0.017	-0.017	0.000	0.000	0.000	0.000
7	A	7	LEU	0	0.027	0.011	13.433	0.850	0.850	0.000	0.000	0.000	0.000
8	A	8	TYR	0	0.053	0.021	16.022	0.756	0.756	0.000	0.000	0.000	0.000
9	A	9	THR	0	-0.061	-0.041	13.862	-1.455	-1.455	0.000	0.000	0.000	0.000
10	A	10	ALA	0	0.021	0.039	15.966	0.741	0.741	0.000	0.000	0.000	0.000
11	A	11	THR	0	0.017	0.001	16.253	-0.786	-0.786	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.005	-0.006	18.226	0.570	0.570	0.000	0.000	0.000	0.000
13	A	13	THR	0	-0.022	0.008	19.050	-0.454	-0.454	0.000	0.000	0.000	0.000
14	A	14	ALA	0	0.009	-0.002	20.690	0.247	0.247	0.000	0.000	0.000	0.000
15	A	15	THR	0	-0.023	-0.015	22.439	0.160	0.160	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.031	0.016	25.437	0.115	0.115	0.000	0.000	0.000	0.000
17	A	17	GLY	0	0.003	0.002	23.349	-0.114	-0.114	0.000	0.000	0.000	0.000
18	A	18	ARG	1	0.805	0.851	20.833	13.102	13.102	0.000	0.000	0.000	0.000
19	A	19	ASP	-1	-0.810	-0.870	25.607	-9.551	-9.551	0.000	0.000	0.000	0.000
20	A	20	GLY	0	-0.009	-0.010	27.854	0.019	0.019	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.840	0.907	27.311	9.569	9.569	0.000	0.000	0.000	0.000
22	A	22	ALA	0	-0.016	0.001	22.607	-0.276	-0.276	0.000	0.000	0.000	0.000
23	A	23	VAL	0	0.011	0.018	24.020	0.215	0.215	0.000	0.000	0.000	0.000
24	A	24	SER	0	-0.013	-0.030	22.369	-0.345	-0.345	0.000	0.000	0.000	0.000
25	A	25	SER	0	-0.010	-0.023	21.864	0.200	0.200	0.000	0.000	0.000	0.000
26	A	26	ASP	-1	-0.880	-0.913	23.693	-11.188	-11.188	0.000	0.000	0.000	0.000
27	A	27	GLY	0	-0.006	-0.001	26.329	0.359	0.359	0.000	0.000	0.000	0.000
28	A	28	VAL	0	-0.047	-0.015	26.409	0.263	0.263	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.023	-0.009	23.012	0.107	0.107	0.000	0.000	0.000	0.000
30	A	30	ASP	-1	-0.802	-0.892	26.107	-9.854	-9.854	0.000	0.000	0.000	0.000
31	A	31	VAL	0	-0.007	-0.005	25.668	0.336	0.336	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.873	0.925	27.823	9.030	9.030	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.015	-0.004	24.545	-0.186	-0.186	0.000	0.000	0.000	0.000
34	A	34	SER	0	-0.003	-0.008	28.197	0.406	0.406	0.000	0.000	0.000	0.000
35	A	35	THR	0	-0.009	-0.022	28.127	-0.439	-0.439	0.000	0.000	0.000	0.000
36	A	36	PRO	0	-0.007	-0.006	28.331	0.366	0.366	0.000	0.000	0.000	0.000
37	A	37	ARG	1	0.924	0.968	31.208	8.222	8.222	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.883	-0.950	30.858	-9.406	-9.406	0.000	0.000	0.000	0.000
39	A	39	MET	0	-0.065	-0.033	24.651	-0.363	-0.363	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.004	0.010	29.931	-0.083	-0.083	0.000	0.000	0.000	0.000
41	A	41	GLY	0	0.000	0.000	31.921	0.151	0.151	0.000	0.000	0.000	0.000
42	A	42	GLN	0	-0.024	-0.018	32.642	0.364	0.364	0.000	0.000	0.000	0.000
43	A	43	GLY	0	0.007	0.000	33.929	0.307	0.307	0.000	0.000	0.000	0.000
44	A	44	GLY	0	-0.023	-0.008	33.192	-0.119	-0.119	0.000	0.000	0.000	0.000
45	A	45	ALA	0	0.002	-0.014	33.663	0.270	0.270	0.000	0.000	0.000	0.000
46	A	46	ALA	0	-0.042	-0.006	31.173	0.105	0.105	0.000	0.000	0.000	0.000
47	A	47	THR	0	0.030	0.006	26.095	-0.227	-0.227	0.000	0.000	0.000	0.000
48	A	48	ASN	0	0.023	-0.006	25.493	-0.242	-0.242	0.000	0.000	0.000	0.000
49	A	49	PRO	0	0.037	0.007	19.906	-0.081	-0.081	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.700	-0.811	20.997	-14.068	-14.068	0.000	0.000	0.000	0.000
51	A	51	GLN	0	0.030	0.037	22.548	-0.095	-0.095	0.000	0.000	0.000	0.000
52	A	52	LEU	0	-0.006	-0.004	21.611	0.007	0.007	0.000	0.000	0.000	0.000
53	A	53	PHE	0	-0.005	-0.003	14.574	-0.326	-0.326	0.000	0.000	0.000	0.000
54	A	54	ALA	0	0.022	0.010	19.958	-0.397	-0.397	0.000	0.000	0.000	0.000
55	A	55	ALA	0	0.007	0.023	22.281	-0.019	-0.019	0.000	0.000	0.000	0.000
56	A	56	GLY	0	0.017	0.007	20.082	0.045	0.045	0.000	0.000	0.000	0.000
57	A	57	TYR	0	0.000	-0.029	14.574	-0.437	-0.437	0.000	0.000	0.000	0.000
58	A	58	SER	0	0.024	-0.012	19.012	-0.056	-0.056	0.000	0.000	0.000	0.000
59	A	59	ALA	0	0.005	0.005	22.489	0.164	0.164	0.000	0.000	0.000	0.000
60	A	60	CYS	0	-0.052	-0.016	17.293	-0.392	-0.392	0.000	0.000	0.000	0.000
61	A	61	PHE	0	0.050	0.012	17.112	-0.256	-0.256	0.000	0.000	0.000	0.000
62	A	62	ILE	0	0.025	0.012	19.918	0.280	0.280	0.000	0.000	0.000	0.000
63	A	63	GLY	0	-0.013	0.000	21.714	0.361	0.361	0.000	0.000	0.000	0.000
64	A	64	ALA	0	-0.010	-0.009	17.815	0.131	0.131	0.000	0.000	0.000	0.000
65	A	65	MET	0	0.002	0.005	19.669	0.117	0.117	0.000	0.000	0.000	0.000
66	A	66	LYS	1	0.939	0.973	22.680	11.607	11.607	0.000	0.000	0.000	0.000
67	A	67	PHE	0	-0.027	-0.001	18.919	0.301	0.301	0.000	0.000	0.000	0.000
68	A	68	VAL	0	0.020	0.007	19.478	0.285	0.285	0.000	0.000	0.000	0.000
69	A	69	ALA	0	0.012	0.010	22.438	0.345	0.345	0.000	0.000	0.000	0.000
70	A	70	GLY	0	0.024	0.015	25.854	0.424	0.424	0.000	0.000	0.000	0.000
71	A	71	GLN	0	-0.067	-0.042	20.052	0.157	0.157	0.000	0.000	0.000	0.000
72	A	72	ARG	1	0.837	0.916	21.891	13.420	13.420	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.914	0.964	27.343	10.113	10.113	0.000	0.000	0.000	0.000
74	A	74	GLN	0	0.020	0.012	27.391	0.010	0.010	0.000	0.000	0.000	0.000
75	A	75	THR	0	-0.009	-0.017	30.022	-0.119	-0.119	0.000	0.000	0.000	0.000
76	A	76	LEU	0	0.030	0.012	26.629	0.040	0.040	0.000	0.000	0.000	0.000
77	A	77	PRO	0	-0.001	0.010	30.227	0.112	0.112	0.000	0.000	0.000	0.000
78	A	78	ALA	0	-0.026	-0.019	31.777	-0.265	-0.265	0.000	0.000	0.000	0.000
79	A	79	ASP	-1	-0.897	-0.950	33.447	-8.908	-8.908	0.000	0.000	0.000	0.000
80	A	80	ALA	0	-0.039	-0.008	28.977	-0.074	-0.074	0.000	0.000	0.000	0.000
81	A	81	SER	0	-0.059	-0.029	28.775	-0.086	-0.086	0.000	0.000	0.000	0.000
82	A	82	ILE	0	-0.011	-0.012	22.655	-0.164	-0.164	0.000	0.000	0.000	0.000
83	A	83	THR	0	-0.033	-0.004	26.459	0.214	0.214	0.000	0.000	0.000	0.000
84	A	84	GLY	0	0.022	0.003	23.520	-0.135	-0.135	0.000	0.000	0.000	0.000
85	A	85	LYS	1	0.888	0.951	23.798	11.291	11.291	0.000	0.000	0.000	0.000
86	A	86	VAL	0	-0.012	-0.007	19.791	-0.631	-0.631	0.000	0.000	0.000	0.000
87	A	87	GLY	0	0.024	0.025	21.848	0.663	0.663	0.000	0.000	0.000	0.000
88	A	88	ILE	0	-0.035	-0.035	21.134	-0.788	-0.788	0.000	0.000	0.000	0.000
89	A	89	GLY	0	0.034	0.023	21.917	0.712	0.712	0.000	0.000	0.000	0.000
90	A	90	GLN	0	-0.031	-0.018	22.112	-0.899	-0.899	0.000	0.000	0.000	0.000
91	A	91	ILE	0	0.000	0.011	16.901	-0.154	-0.154	0.000	0.000	0.000	0.000
92	A	92	PRO	0	0.019	-0.011	19.831	0.311	0.311	0.000	0.000	0.000	0.000
93	A	93	GLY	0	0.011	0.015	19.513	-0.733	-0.733	0.000	0.000	0.000	0.000
94	A	94	GLY	0	-0.029	-0.017	19.907	-0.221	-0.221	0.000	0.000	0.000	0.000
95	A	95	PHE	0	-0.020	-0.011	19.473	0.647	0.647	0.000	0.000	0.000	0.000
96	A	96	GLY	0	0.014	0.016	17.336	-1.066	-1.066	0.000	0.000	0.000	0.000
97	A	97	LEU	0	-0.038	-0.028	15.849	0.879	0.879	0.000	0.000	0.000	0.000
98	A	98	GLU	-1	-0.909	-0.941	17.747	-14.110	-14.110	0.000	0.000	0.000	0.000
99	A	99	VAL	0	-0.028	-0.029	17.075	0.306	0.306	0.000	0.000	0.000	0.000
100	A	100	GLU	-1	-0.915	-0.951	19.627	-12.427	-12.427	0.000	0.000	0.000	0.000
101	A	101	LEU	0	-0.027	-0.002	19.005	0.398	0.398	0.000	0.000	0.000	0.000
102	A	102	HIS	0	-0.019	-0.017	22.888	-0.019	-0.019	0.000	0.000	0.000	0.000
103	A	103	ILE	0	-0.025	-0.025	21.795	0.052	0.052	0.000	0.000	0.000	0.000
104	A	104	ASN	0	0.029	0.029	26.470	0.215	0.215	0.000	0.000	0.000	0.000
105	A	105	LEU	0	0.012	-0.022	26.309	-0.165	-0.165	0.000	0.000	0.000	0.000
106	A	106	PRO	0	0.037	0.021	30.794	0.131	0.131	0.000	0.000	0.000	0.000
107	A	107	GLY	0	0.013	-0.001	34.650	0.067	0.067	0.000	0.000	0.000	0.000
108	A	108	MET	0	-0.068	-0.022	28.412	-0.085	-0.085	0.000	0.000	0.000	0.000
109	A	109	GLU	-1	-0.886	-0.941	32.854	-9.243	-9.243	0.000	0.000	0.000	0.000
110	A	110	ARG	1	0.984	0.985	30.424	9.124	9.124	0.000	0.000	0.000	0.000
111	A	111	GLU	-1	-0.876	-0.920	29.192	-10.868	-10.868	0.000	0.000	0.000	0.000
112	A	112	ALA	0	-0.024	-0.015	27.870	-0.525	-0.525	0.000	0.000	0.000	0.000
113	A	113	ALA	0	-0.010	-0.007	27.024	-0.484	-0.484	0.000	0.000	0.000	0.000
114	A	114	GLU	-1	-0.874	-0.956	25.046	-11.567	-11.567	0.000	0.000	0.000	0.000
115	A	115	ALA	0	0.033	0.017	23.308	-0.783	-0.783	0.000	0.000	0.000	0.000
116	A	116	LEU	0	-0.071	-0.016	22.646	-0.655	-0.655	0.000	0.000	0.000	0.000
117	A	117	VAL	0	0.032	0.011	21.246	-0.848	-0.848	0.000	0.000	0.000	0.000
118	A	118	ALA	0	0.016	0.006	18.998	-0.958	-0.958	0.000	0.000	0.000	0.000
119	A	119	ALA	0	-0.012	-0.009	17.382	-1.143	-1.143	0.000	0.000	0.000	0.000
120	A	120	ALA	0	0.019	0.008	16.897	-1.066	-1.066	0.000	0.000	0.000	0.000
121	A	121	HIS	0	0.064	0.047	14.565	-1.360	-1.360	0.000	0.000	0.000	0.000
122	A	122	GLN	0	-0.019	-0.005	12.112	-3.485	-3.485	0.000	0.000	0.000	0.000
123	A	123	VAL	0	-0.004	0.011	12.239	-1.730	-1.730	0.000	0.000	0.000	0.000
124	A	124	CYS	0	-0.028	0.004	13.983	-0.621	-0.621	0.000	0.000	0.000	0.000
125	A	125	PRO	0	0.012	0.001	11.258	-1.678	-1.678	0.000	0.000	0.000	0.000
126	A	126	TYR	0	0.043	0.004	10.468	-2.505	-2.505	0.000	0.000	0.000	0.000
127	A	127	SER	0	0.034	0.031	11.634	-0.547	-0.547	0.000	0.000	0.000	0.000
128	A	128	ASN	0	-0.062	-0.019	7.390	-2.942	-2.942	0.000	0.000	0.000	0.000
129	A	129	ALA	0	-0.053	-0.026	6.684	-4.789	-4.789	0.000	0.000	0.000	0.000
130	A	130	THR	0	-0.017	-0.030	7.995	-1.064	-1.064	0.000	0.000	0.000	0.000
131	A	131	ARG	1	0.830	0.902	6.531	29.508	29.508	0.000	0.000	0.000	0.000
132	A	132	GLY	0	-0.007	-0.004	7.599	-3.336	-3.336	0.000	0.000	0.000	0.000
133	A	133	ASN	0	-0.051	-0.016	7.161	0.769	0.769	0.000	0.000	0.000	0.000
134	A	134	ILE	0	-0.021	-0.006	10.961	1.418	1.418	0.000	0.000	0.000	0.000
135	A	135	ASP	-1	-0.825	-0.895	14.314	-16.047	-16.047	0.000	0.000	0.000	0.000
136	A	136	VAL	0	-0.027	-0.022	14.053	0.035	0.035	0.000	0.000	0.000	0.000
137	A	137	ARG	1	0.870	0.935	17.097	13.349	13.349	0.000	0.000	0.000	0.000
138	A	138	LEU	0	-0.005	-0.013	17.738	0.009	0.009	0.000	0.000	0.000	0.000
139	A	139	ASN	0	0.010	0.020	21.746	0.468	0.468	0.000	0.000	0.000	0.000
140	A	140	VAL	0	0.029	0.011	24.942	0.029	0.029	0.000	0.000	0.000	0.000
141	A	141	SER	0	-0.049	-0.029	27.255	0.222	0.222	0.000	0.000	0.000	0.000
142	A	142	VAL	-1	-0.893	-0.938	30.948	-9.716	-9.716	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1:MET)