FMO DATABASE

FMODB ID: 7271K

Calculation Name: 1GH2-A-Xray372

Preferred Name: Thioredoxin-like protein 1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1GH2

Chain ID: A

ChEMBL ID: CHEMBL4295663

UniProt ID: O43396

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	106
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-810132.327084
FMO2-HF: Nuclear repulsion	768878.923238
FMO2-HF: Total energy	-41253.403846
FMO2-MP2: Total energy	-41372.199854

3D Structure

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:2:VAL)

Summations of interaction energy for fragment #1(A:2:VAL)

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.
-0.755	1.292	-0.008	-1.026	-1.013	0.003

Interaction energy analysis for fragmet #1(A:2:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.029 / q_NPA : 0.008

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

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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	4	VAL	0	-0.016	-0.003	3.798	-0.766	1.281	-0.008	-1.026	-1.013	0.003
4	A	5	LYS	1	0.945	0.984	5.482	-0.333	-0.333	0.000	0.000	0.000	0.000
5	A	6	PRO	0	0.006	-0.003	6.417	0.401	0.401	0.000	0.000	0.000	0.000
6	A	7	VAL	0	-0.033	-0.009	9.659	0.132	0.132	0.000	0.000	0.000	0.000
7	A	8	GLY	0	0.010	-0.008	12.642	-0.016	-0.016	0.000	0.000	0.000	0.000
8	A	9	SER	0	0.017	0.002	14.388	0.023	0.023	0.000	0.000	0.000	0.000
9	A	10	ASP	-1	-0.722	-0.860	17.378	-0.118	-0.118	0.000	0.000	0.000	0.000
10	A	11	PRO	0	-0.042	-0.018	19.402	0.006	0.006	0.000	0.000	0.000	0.000
11	A	12	ASP	-1	-0.859	-0.917	14.301	0.000	0.000	0.000	0.000	0.000	0.000
12	A	13	PHE	0	-0.004	-0.018	14.737	0.011	0.011	0.000	0.000	0.000	0.000
13	A	14	GLN	0	0.040	0.012	15.839	0.014	0.014	0.000	0.000	0.000	0.000
14	A	15	PRO	0	0.000	0.008	14.940	0.019	0.019	0.000	0.000	0.000	0.000
15	A	16	GLU	-1	-0.865	-0.931	9.589	0.102	0.102	0.000	0.000	0.000	0.000
16	A	17	LEU	0	-0.013	-0.010	12.789	0.020	0.020	0.000	0.000	0.000	0.000
17	A	18	SER	0	-0.085	-0.050	15.232	0.008	0.008	0.000	0.000	0.000	0.000
18	A	19	GLY	0	-0.021	-0.006	12.427	0.021	0.021	0.000	0.000	0.000	0.000
19	A	20	ALA	0	0.010	0.013	11.492	0.085	0.085	0.000	0.000	0.000	0.000
20	A	21	GLY	0	-0.025	-0.008	12.524	0.018	0.018	0.000	0.000	0.000	0.000
21	A	22	SER	0	-0.037	-0.030	15.246	-0.026	-0.026	0.000	0.000	0.000	0.000
22	A	23	ARG	1	0.872	0.948	7.664	-0.427	-0.427	0.000	0.000	0.000	0.000
23	A	24	LEU	0	0.013	0.010	14.413	-0.016	-0.016	0.000	0.000	0.000	0.000
24	A	25	ALA	0	0.016	0.007	12.516	0.000	0.000	0.000	0.000	0.000	0.000
25	A	26	VAL	0	-0.018	0.001	12.342	0.017	0.017	0.000	0.000	0.000	0.000
26	A	27	VAL	0	0.017	0.004	12.241	-0.094	-0.094	0.000	0.000	0.000	0.000
27	A	28	LYS	1	0.854	0.935	12.673	0.842	0.842	0.000	0.000	0.000	0.000
28	A	29	PHE	0	0.006	-0.004	15.212	-0.038	-0.038	0.000	0.000	0.000	0.000
29	A	30	THR	0	0.008	-0.033	15.288	0.027	0.027	0.000	0.000	0.000	0.000
30	A	31	MET	0	0.041	0.034	18.382	0.033	0.033	0.000	0.000	0.000	0.000
31	A	32	ARG	1	0.977	0.980	18.316	0.306	0.306	0.000	0.000	0.000	0.000
32	A	33	GLY	0	-0.002	0.005	21.014	0.019	0.019	0.000	0.000	0.000	0.000
33	A	34	CYS	0	0.054	0.043	18.772	0.011	0.011	0.000	0.000	0.000	0.000
34	A	35	GLY	0	0.032	0.010	21.861	-0.026	-0.026	0.000	0.000	0.000	0.000
35	A	36	PRO	0	0.000	-0.011	22.241	-0.022	-0.022	0.000	0.000	0.000	0.000
36	A	38	LEU	0	-0.007	-0.005	17.618	-0.055	-0.055	0.000	0.000	0.000	0.000
37	A	39	ARG	1	0.926	0.965	17.971	0.212	0.212	0.000	0.000	0.000	0.000
38	A	40	ILE	0	0.020	0.022	16.750	-0.010	-0.010	0.000	0.000	0.000	0.000
39	A	41	ALA	0	-0.012	0.000	13.707	-0.043	-0.043	0.000	0.000	0.000	0.000
40	A	42	PRO	0	0.022	0.008	12.247	-0.129	-0.129	0.000	0.000	0.000	0.000
41	A	43	ALA	0	0.060	0.029	11.979	-0.055	-0.055	0.000	0.000	0.000	0.000
42	A	44	PHE	0	-0.001	-0.001	11.088	-0.014	-0.014	0.000	0.000	0.000	0.000
43	A	45	SER	0	0.017	0.002	7.675	-0.170	-0.170	0.000	0.000	0.000	0.000
44	A	46	SER	0	0.037	0.025	8.037	-0.051	-0.051	0.000	0.000	0.000	0.000
45	A	47	MET	0	-0.061	-0.023	10.108	0.087	0.087	0.000	0.000	0.000	0.000
46	A	48	SER	0	-0.019	-0.009	6.180	-0.090	-0.090	0.000	0.000	0.000	0.000
47	A	49	ASN	0	-0.057	-0.033	5.305	0.253	0.253	0.000	0.000	0.000	0.000
48	A	50	LYS	1	0.818	0.886	6.991	0.365	0.365	0.000	0.000	0.000	0.000
49	A	51	TYR	0	-0.071	-0.063	9.109	0.095	0.095	0.000	0.000	0.000	0.000
50	A	52	PRO	0	0.021	0.015	6.265	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	53	GLN	0	0.036	0.022	7.575	0.123	0.123	0.000	0.000	0.000	0.000
52	A	54	ALA	0	-0.047	-0.021	9.719	0.022	0.022	0.000	0.000	0.000	0.000
53	A	55	VAL	0	-0.028	-0.015	8.115	0.015	0.015	0.000	0.000	0.000	0.000
54	A	56	PHE	0	-0.004	0.004	7.512	-0.013	-0.013	0.000	0.000	0.000	0.000
55	A	57	LEU	0	0.022	0.011	7.641	-0.273	-0.273	0.000	0.000	0.000	0.000
56	A	58	GLU	-1	-0.879	-0.940	10.077	-0.877	-0.877	0.000	0.000	0.000	0.000
57	A	59	VAL	0	0.046	0.019	12.276	0.023	0.023	0.000	0.000	0.000	0.000
58	A	60	ASP	-1	-0.808	-0.903	15.343	-0.303	-0.303	0.000	0.000	0.000	0.000
59	A	61	VAL	0	-0.015	-0.048	17.503	0.031	0.031	0.000	0.000	0.000	0.000
60	A	62	HIS	0	-0.024	-0.013	20.855	0.035	0.035	0.000	0.000	0.000	0.000
61	A	63	GLN	0	-0.057	-0.028	15.874	0.000	0.000	0.000	0.000	0.000	0.000
62	A	64	CYS	0	-0.053	0.003	17.348	0.024	0.024	0.000	0.000	0.000	0.000
63	A	65	GLN	0	0.047	0.018	20.217	0.006	0.006	0.000	0.000	0.000	0.000
64	A	66	GLY	0	0.012	0.016	23.837	0.004	0.004	0.000	0.000	0.000	0.000
65	A	67	THR	0	-0.039	-0.044	18.382	0.011	0.011	0.000	0.000	0.000	0.000
66	A	68	ALA	0	0.011	0.010	21.765	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	69	ALA	0	0.023	0.016	22.950	0.005	0.005	0.000	0.000	0.000	0.000
68	A	70	THR	0	-0.048	-0.021	24.284	0.006	0.006	0.000	0.000	0.000	0.000
69	A	71	ASN	0	-0.073	-0.031	21.225	0.009	0.009	0.000	0.000	0.000	0.000
70	A	72	ASN	0	-0.060	-0.044	24.260	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	73	ILE	0	-0.051	-0.016	21.545	-0.006	-0.006	0.000	0.000	0.000	0.000
72	A	74	SER	0	0.019	0.012	25.048	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	75	ALA	0	0.010	0.005	25.741	0.003	0.003	0.000	0.000	0.000	0.000
74	A	76	THR	0	0.003	0.055	21.201	-0.010	-0.010	0.000	0.000	0.000	0.000
75	A	77	PRO	0	-0.049	-0.050	19.156	0.010	0.010	0.000	0.000	0.000	0.000
76	A	78	THR	0	0.019	-0.024	20.049	0.030	0.030	0.000	0.000	0.000	0.000
77	A	79	PHE	0	-0.033	-0.015	15.078	-0.037	-0.037	0.000	0.000	0.000	0.000
78	A	80	GLN	0	-0.011	-0.002	17.600	0.057	0.057	0.000	0.000	0.000	0.000
79	A	81	PHE	0	0.016	0.000	17.024	-0.035	-0.035	0.000	0.000	0.000	0.000
80	A	82	PHE	0	0.030	0.002	16.575	0.020	0.020	0.000	0.000	0.000	0.000
81	A	83	ARG	1	0.938	0.970	17.114	0.026	0.026	0.000	0.000	0.000	0.000
82	A	84	ASN	0	0.027	0.015	18.341	0.004	0.004	0.000	0.000	0.000	0.000
83	A	85	LYS	1	0.947	0.970	18.230	-0.056	-0.056	0.000	0.000	0.000	0.000
84	A	86	VAL	0	0.009	0.026	19.630	-0.008	-0.008	0.000	0.000	0.000	0.000
85	A	87	ARG	1	0.877	0.958	20.999	0.112	0.112	0.000	0.000	0.000	0.000
86	A	88	ILE	0	-0.021	-0.026	20.706	0.009	0.009	0.000	0.000	0.000	0.000
87	A	89	ASP	-1	-0.733	-0.831	21.666	-0.113	-0.113	0.000	0.000	0.000	0.000
88	A	90	GLN	0	-0.071	-0.050	21.778	-0.020	-0.020	0.000	0.000	0.000	0.000
89	A	91	TYR	0	-0.016	-0.013	20.798	0.021	0.021	0.000	0.000	0.000	0.000
90	A	92	GLN	0	0.028	0.026	21.577	-0.022	-0.022	0.000	0.000	0.000	0.000
91	A	93	GLY	0	0.016	0.007	23.015	0.010	0.010	0.000	0.000	0.000	0.000
92	A	94	ALA	0	-0.034	-0.045	20.950	-0.024	-0.024	0.000	0.000	0.000	0.000
93	A	95	ASP	-1	-0.876	-0.909	21.663	-0.206	-0.206	0.000	0.000	0.000	0.000
94	A	96	ALA	0	0.054	0.000	18.149	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	97	VAL	0	0.013	0.024	19.173	-0.007	-0.007	0.000	0.000	0.000	0.000
96	A	98	GLY	0	0.062	0.027	21.360	0.008	0.008	0.000	0.000	0.000	0.000
97	A	99	LEU	0	-0.051	-0.020	15.978	0.007	0.007	0.000	0.000	0.000	0.000
98	A	100	GLU	-1	-0.735	-0.838	16.376	-0.241	-0.241	0.000	0.000	0.000	0.000
99	A	101	GLU	-1	-0.876	-0.936	17.774	-0.143	-0.143	0.000	0.000	0.000	0.000
100	A	102	LYS	1	0.785	0.857	20.636	0.150	0.150	0.000	0.000	0.000	0.000
101	A	103	ILE	0	0.009	0.007	13.705	0.009	0.009	0.000	0.000	0.000	0.000
102	A	104	LYS	1	0.876	0.944	17.413	0.169	0.169	0.000	0.000	0.000	0.000
103	A	105	GLN	0	-0.037	-0.007	18.758	0.021	0.021	0.000	0.000	0.000	0.000
104	A	106	HIS	0	-0.042	-0.038	18.703	0.024	0.024	0.000	0.000	0.000	0.000
105	A	107	LEU	0	-0.085	-0.031	14.106	0.020	0.020	0.000	0.000	0.000	0.000
106	A	108	GLU	-1	-0.935	-0.946	18.058	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:VAL)