FMO DATABASE

FMODB ID: 6N21Z

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	OptAll
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	-810242.722129
FMO2-HF: Nuclear repulsion	768988.321078
FMO2-HF: Total energy	-41254.401051
FMO2-MP2: Total energy	-41373.072378

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.
-1.034	1.002	-0.014	-0.979	-1.043	0.004

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 : 0.026 / q_NPA : 0.007

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	4	VAL	0	-0.024	-0.013	3.874	-0.676	1.276	-0.013	-0.974	-0.965	0.004
4	A	5	LYS	1	0.822	0.895	4.869	-0.590	-0.590	0.000	0.000	0.000	0.000
5	A	6	PRO	0	-0.015	-0.017	6.110	0.473	0.473	0.000	0.000	0.000	0.000
6	A	7	VAL	0	-0.019	-0.006	9.222	0.158	0.158	0.000	0.000	0.000	0.000
7	A	8	GLY	0	-0.001	0.006	12.046	-0.038	-0.038	0.000	0.000	0.000	0.000
8	A	9	SER	0	0.024	-0.018	13.957	0.008	0.008	0.000	0.000	0.000	0.000
9	A	10	ASP	-1	-0.749	-0.857	17.044	-0.098	-0.098	0.000	0.000	0.000	0.000
10	A	11	PRO	0	-0.028	-0.015	19.306	0.007	0.007	0.000	0.000	0.000	0.000
11	A	12	ASP	-1	-0.829	-0.891	13.830	0.041	0.041	0.000	0.000	0.000	0.000
12	A	13	PHE	0	0.021	-0.001	14.954	0.028	0.028	0.000	0.000	0.000	0.000
13	A	14	GLN	0	0.027	0.002	15.666	0.026	0.026	0.000	0.000	0.000	0.000
14	A	15	PRO	0	-0.002	-0.001	14.920	0.021	0.021	0.000	0.000	0.000	0.000
15	A	16	GLU	-1	-0.802	-0.883	9.530	0.252	0.252	0.000	0.000	0.000	0.000
16	A	17	LEU	0	-0.018	-0.012	12.288	0.032	0.032	0.000	0.000	0.000	0.000
17	A	18	SER	0	-0.064	-0.025	14.743	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	19	GLY	0	0.014	0.016	11.695	0.025	0.025	0.000	0.000	0.000	0.000
19	A	20	ALA	0	0.014	0.012	11.385	0.086	0.086	0.000	0.000	0.000	0.000
20	A	21	GLY	0	0.002	0.015	12.361	0.029	0.029	0.000	0.000	0.000	0.000
21	A	22	SER	0	-0.038	-0.035	15.554	-0.030	-0.030	0.000	0.000	0.000	0.000
22	A	23	ARG	1	0.856	0.935	7.860	-0.563	-0.563	0.000	0.000	0.000	0.000
23	A	24	LEU	0	0.013	0.016	14.590	-0.017	-0.017	0.000	0.000	0.000	0.000
24	A	25	ALA	0	0.018	0.003	12.281	0.010	0.010	0.000	0.000	0.000	0.000
25	A	26	VAL	0	-0.014	-0.003	12.084	0.012	0.012	0.000	0.000	0.000	0.000
26	A	27	VAL	0	0.015	0.005	12.023	-0.097	-0.097	0.000	0.000	0.000	0.000
27	A	28	LYS	1	0.824	0.925	13.163	0.835	0.835	0.000	0.000	0.000	0.000
28	A	29	PHE	0	0.050	0.013	15.092	-0.043	-0.043	0.000	0.000	0.000	0.000
29	A	30	THR	0	0.000	-0.027	15.164	0.028	0.028	0.000	0.000	0.000	0.000
30	A	31	MET	0	0.057	0.041	18.292	0.039	0.039	0.000	0.000	0.000	0.000
31	A	32	ARG	1	0.978	0.983	18.287	0.319	0.319	0.000	0.000	0.000	0.000
32	A	33	GLY	0	0.031	0.019	21.057	0.021	0.021	0.000	0.000	0.000	0.000
33	A	34	CYS	0	0.016	0.041	18.309	0.008	0.008	0.000	0.000	0.000	0.000
34	A	35	GLY	0	0.033	0.013	21.728	-0.029	-0.029	0.000	0.000	0.000	0.000
35	A	36	PRO	0	-0.023	-0.029	22.751	-0.019	-0.019	0.000	0.000	0.000	0.000
36	A	38	LEU	0	-0.003	0.004	17.561	-0.059	-0.059	0.000	0.000	0.000	0.000
37	A	39	ARG	1	0.934	0.966	17.776	0.218	0.218	0.000	0.000	0.000	0.000
38	A	40	ILE	0	0.037	0.035	16.914	-0.017	-0.017	0.000	0.000	0.000	0.000
39	A	41	ALA	0	-0.020	0.003	13.780	-0.053	-0.053	0.000	0.000	0.000	0.000
40	A	42	PRO	0	0.046	0.020	12.291	-0.139	-0.139	0.000	0.000	0.000	0.000
41	A	43	ALA	0	0.016	0.027	12.096	-0.065	-0.065	0.000	0.000	0.000	0.000
42	A	44	PHE	0	0.040	-0.001	11.208	-0.024	-0.024	0.000	0.000	0.000	0.000
43	A	45	SER	0	0.006	0.007	7.664	-0.218	-0.218	0.000	0.000	0.000	0.000
44	A	46	SER	0	-0.005	0.001	8.178	-0.109	-0.109	0.000	0.000	0.000	0.000
45	A	47	MET	0	-0.057	-0.026	10.207	0.063	0.063	0.000	0.000	0.000	0.000
46	A	48	SER	0	-0.030	-0.028	6.570	-0.178	-0.178	0.000	0.000	0.000	0.000
47	A	49	ASN	0	-0.055	-0.043	4.621	0.137	0.221	-0.001	-0.005	-0.078	0.000
48	A	50	LYS	1	0.815	0.905	7.095	0.485	0.485	0.000	0.000	0.000	0.000
49	A	51	TYR	0	-0.058	-0.050	9.337	0.113	0.113	0.000	0.000	0.000	0.000
50	A	52	PRO	0	0.054	0.023	6.115	0.002	0.002	0.000	0.000	0.000	0.000
51	A	53	GLN	0	0.008	0.008	7.703	0.156	0.156	0.000	0.000	0.000	0.000
52	A	54	ALA	0	-0.038	-0.014	10.002	0.035	0.035	0.000	0.000	0.000	0.000
53	A	55	VAL	0	-0.044	-0.015	7.711	0.035	0.035	0.000	0.000	0.000	0.000
54	A	56	PHE	0	0.033	0.017	7.324	-0.025	-0.025	0.000	0.000	0.000	0.000
55	A	57	LEU	0	0.019	0.021	7.462	-0.292	-0.292	0.000	0.000	0.000	0.000
56	A	58	GLU	-1	-0.834	-0.922	9.967	-0.877	-0.877	0.000	0.000	0.000	0.000
57	A	59	VAL	0	0.036	0.010	11.890	0.030	0.030	0.000	0.000	0.000	0.000
58	A	60	ASP	-1	-0.810	-0.913	14.940	-0.282	-0.282	0.000	0.000	0.000	0.000
59	A	61	VAL	0	0.017	-0.010	17.364	0.032	0.032	0.000	0.000	0.000	0.000
60	A	62	HIS	0	-0.027	-0.024	20.770	0.038	0.038	0.000	0.000	0.000	0.000
61	A	63	GLN	0	-0.082	-0.033	16.414	0.018	0.018	0.000	0.000	0.000	0.000
62	A	64	CYS	0	-0.040	0.002	16.967	0.013	0.013	0.000	0.000	0.000	0.000
63	A	65	GLN	0	0.025	0.009	19.665	0.007	0.007	0.000	0.000	0.000	0.000
64	A	66	GLY	0	0.018	0.005	23.370	0.004	0.004	0.000	0.000	0.000	0.000
65	A	67	THR	0	-0.051	-0.040	18.428	0.010	0.010	0.000	0.000	0.000	0.000
66	A	68	ALA	0	-0.007	-0.003	21.718	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	69	ALA	0	-0.002	0.005	22.750	0.002	0.002	0.000	0.000	0.000	0.000
68	A	70	THR	0	-0.036	-0.040	24.093	0.003	0.003	0.000	0.000	0.000	0.000
69	A	71	ASN	0	-0.082	-0.046	20.798	0.006	0.006	0.000	0.000	0.000	0.000
70	A	72	ASN	0	-0.058	-0.034	23.872	0.000	0.000	0.000	0.000	0.000	0.000
71	A	73	ILE	0	-0.032	-0.011	21.244	-0.007	-0.007	0.000	0.000	0.000	0.000
72	A	74	SER	0	0.018	0.020	24.839	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	75	ALA	0	0.021	0.013	25.718	0.004	0.004	0.000	0.000	0.000	0.000
74	A	76	THR	0	0.006	0.030	21.146	-0.011	-0.011	0.000	0.000	0.000	0.000
75	A	77	PRO	0	-0.039	-0.040	19.338	0.007	0.007	0.000	0.000	0.000	0.000
76	A	78	THR	0	-0.013	-0.018	19.971	0.030	0.030	0.000	0.000	0.000	0.000
77	A	79	PHE	0	-0.016	-0.009	15.102	-0.031	-0.031	0.000	0.000	0.000	0.000
78	A	80	GLN	0	0.012	0.017	17.427	0.062	0.062	0.000	0.000	0.000	0.000
79	A	81	PHE	0	0.031	0.016	16.769	-0.036	-0.036	0.000	0.000	0.000	0.000
80	A	82	PHE	0	0.007	-0.013	16.354	0.021	0.021	0.000	0.000	0.000	0.000
81	A	83	ARG	1	0.868	0.907	16.926	0.023	0.023	0.000	0.000	0.000	0.000
82	A	84	ASN	0	0.014	0.005	18.085	-0.005	-0.005	0.000	0.000	0.000	0.000
83	A	85	LYS	1	0.905	0.951	17.621	-0.113	-0.113	0.000	0.000	0.000	0.000
84	A	86	VAL	0	0.015	0.023	19.224	-0.015	-0.015	0.000	0.000	0.000	0.000
85	A	87	ARG	1	0.865	0.935	20.793	0.100	0.100	0.000	0.000	0.000	0.000
86	A	88	ILE	0	-0.031	-0.027	20.404	0.006	0.006	0.000	0.000	0.000	0.000
87	A	89	ASP	-1	-0.768	-0.845	21.597	-0.115	-0.115	0.000	0.000	0.000	0.000
88	A	90	GLN	0	-0.039	-0.037	21.510	-0.018	-0.018	0.000	0.000	0.000	0.000
89	A	91	TYR	0	-0.010	-0.018	20.689	0.017	0.017	0.000	0.000	0.000	0.000
90	A	92	GLN	0	-0.021	-0.016	21.854	-0.009	-0.009	0.000	0.000	0.000	0.000
91	A	93	GLY	0	0.013	0.022	23.091	0.012	0.012	0.000	0.000	0.000	0.000
92	A	94	ALA	0	-0.024	-0.044	21.172	-0.025	-0.025	0.000	0.000	0.000	0.000
93	A	95	ASP	-1	-0.800	-0.876	21.780	-0.235	-0.235	0.000	0.000	0.000	0.000
94	A	96	ALA	0	0.037	0.004	18.150	-0.008	-0.008	0.000	0.000	0.000	0.000
95	A	97	VAL	0	0.005	0.006	19.463	-0.009	-0.009	0.000	0.000	0.000	0.000
96	A	98	GLY	0	0.035	0.012	21.520	0.005	0.005	0.000	0.000	0.000	0.000
97	A	99	LEU	0	-0.041	-0.009	16.159	0.006	0.006	0.000	0.000	0.000	0.000
98	A	100	GLU	-1	-0.758	-0.853	15.840	-0.299	-0.299	0.000	0.000	0.000	0.000
99	A	101	GLU	-1	-0.827	-0.894	18.219	-0.155	-0.155	0.000	0.000	0.000	0.000
100	A	102	LYS	1	0.805	0.888	20.751	0.156	0.156	0.000	0.000	0.000	0.000
101	A	103	ILE	0	-0.006	-0.009	13.932	0.011	0.011	0.000	0.000	0.000	0.000
102	A	104	LYS	1	0.817	0.887	17.479	0.213	0.213	0.000	0.000	0.000	0.000
103	A	105	GLN	0	-0.008	-0.002	19.095	0.013	0.013	0.000	0.000	0.000	0.000
104	A	106	HIS	0	-0.008	-0.009	18.951	0.024	0.024	0.000	0.000	0.000	0.000
105	A	107	LEU	0	-0.063	-0.014	13.934	0.021	0.021	0.000	0.000	0.000	0.000
106	A	108	GLU	-1	-0.923	-0.924	18.072	0.007	0.007	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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