FMO DATABASE

FMODB ID: 2JQVR

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	OptHSide
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	-810297.127771
FMO2-HF: Nuclear repulsion	769042.975251
FMO2-HF: Total energy	-41254.15252
FMO2-MP2: Total energy	-41372.881112

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.
-0.921	1.216	-0.005	-1.014	-1.117	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 : 0.026 / q_NPA : 0.004

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	-0.019	-0.003	3.810	-0.765	1.282	-0.004	-1.009	-1.033	0.003
4	A	5	LYS	1	0.866	0.930	5.462	-0.153	-0.153	0.000	0.000	0.000	0.000
5	A	6	PRO	0	0.005	0.001	6.588	0.432	0.432	0.000	0.000	0.000	0.000
6	A	7	VAL	0	-0.029	-0.011	9.648	0.120	0.120	0.000	0.000	0.000	0.000
7	A	8	GLY	0	0.006	-0.010	12.610	-0.010	-0.010	0.000	0.000	0.000	0.000
8	A	9	SER	0	0.017	-0.012	14.358	0.029	0.029	0.000	0.000	0.000	0.000
9	A	10	ASP	-1	-0.723	-0.855	17.334	-0.150	-0.150	0.000	0.000	0.000	0.000
10	A	11	PRO	0	-0.034	-0.012	19.374	0.006	0.006	0.000	0.000	0.000	0.000
11	A	12	ASP	-1	-0.851	-0.901	14.291	-0.071	-0.071	0.000	0.000	0.000	0.000
12	A	13	PHE	0	0.009	-0.013	14.711	0.005	0.005	0.000	0.000	0.000	0.000
13	A	14	GLN	0	0.044	0.013	15.824	0.017	0.017	0.000	0.000	0.000	0.000
14	A	15	PRO	0	0.008	0.011	14.810	0.020	0.020	0.000	0.000	0.000	0.000
15	A	16	GLU	-1	-0.825	-0.897	9.603	-0.058	-0.058	0.000	0.000	0.000	0.000
16	A	17	LEU	0	-0.007	-0.007	12.785	0.024	0.024	0.000	0.000	0.000	0.000
17	A	18	SER	0	-0.072	-0.040	15.231	0.014	0.014	0.000	0.000	0.000	0.000
18	A	19	GLY	0	0.003	0.002	12.425	0.024	0.024	0.000	0.000	0.000	0.000
19	A	20	ALA	0	0.015	0.017	11.507	0.084	0.084	0.000	0.000	0.000	0.000
20	A	21	GLY	0	-0.018	-0.001	12.540	0.024	0.024	0.000	0.000	0.000	0.000
21	A	22	SER	0	-0.033	-0.025	15.550	-0.025	-0.025	0.000	0.000	0.000	0.000
22	A	23	ARG	1	0.855	0.933	7.943	-0.424	-0.424	0.000	0.000	0.000	0.000
23	A	24	LEU	0	0.010	0.013	14.358	-0.019	-0.019	0.000	0.000	0.000	0.000
24	A	25	ALA	0	0.022	0.009	12.538	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	26	VAL	0	-0.009	0.003	12.367	0.018	0.018	0.000	0.000	0.000	0.000
26	A	27	VAL	0	0.001	-0.001	12.254	-0.100	-0.100	0.000	0.000	0.000	0.000
27	A	28	LYS	1	0.847	0.930	13.113	0.852	0.852	0.000	0.000	0.000	0.000
28	A	29	PHE	0	0.012	-0.002	15.202	-0.043	-0.043	0.000	0.000	0.000	0.000
29	A	30	THR	0	0.011	-0.032	15.425	0.041	0.041	0.000	0.000	0.000	0.000
30	A	31	MET	0	0.035	0.031	18.412	0.033	0.033	0.000	0.000	0.000	0.000
31	A	32	ARG	1	0.978	0.981	18.295	0.330	0.330	0.000	0.000	0.000	0.000
32	A	33	GLY	0	0.006	0.013	21.057	0.020	0.020	0.000	0.000	0.000	0.000
33	A	34	CYS	0	0.050	0.036	18.848	0.013	0.013	0.000	0.000	0.000	0.000
34	A	35	GLY	0	0.039	0.016	21.923	-0.026	-0.026	0.000	0.000	0.000	0.000
35	A	36	PRO	0	0.002	-0.007	22.092	-0.022	-0.022	0.000	0.000	0.000	0.000
36	A	38	LEU	0	-0.011	-0.006	17.580	-0.056	-0.056	0.000	0.000	0.000	0.000
37	A	39	ARG	1	0.917	0.958	17.836	0.211	0.211	0.000	0.000	0.000	0.000
38	A	40	ILE	0	0.026	0.023	16.376	-0.008	-0.008	0.000	0.000	0.000	0.000
39	A	41	ALA	0	-0.017	0.001	13.617	-0.043	-0.043	0.000	0.000	0.000	0.000
40	A	42	PRO	0	0.048	0.019	12.053	-0.127	-0.127	0.000	0.000	0.000	0.000
41	A	43	ALA	0	0.045	0.029	11.673	-0.054	-0.054	0.000	0.000	0.000	0.000
42	A	44	PHE	0	0.010	0.000	11.248	-0.012	-0.012	0.000	0.000	0.000	0.000
43	A	45	SER	0	0.042	0.015	7.146	-0.209	-0.209	0.000	0.000	0.000	0.000
44	A	46	SER	0	-0.018	-0.008	7.588	-0.066	-0.066	0.000	0.000	0.000	0.000
45	A	47	MET	0	-0.059	-0.024	9.836	0.088	0.088	0.000	0.000	0.000	0.000
46	A	48	SER	0	-0.015	-0.009	6.278	-0.106	-0.106	0.000	0.000	0.000	0.000
47	A	49	ASN	0	-0.068	-0.043	4.643	0.143	0.233	-0.001	-0.005	-0.084	0.000
48	A	50	LYS	1	0.820	0.896	6.963	0.369	0.369	0.000	0.000	0.000	0.000
49	A	51	TYR	0	-0.060	-0.057	9.217	0.087	0.087	0.000	0.000	0.000	0.000
50	A	52	PRO	0	0.027	0.020	6.249	-0.008	-0.008	0.000	0.000	0.000	0.000
51	A	53	GLN	0	0.020	0.013	7.530	0.112	0.112	0.000	0.000	0.000	0.000
52	A	54	ALA	0	-0.033	-0.012	9.645	0.016	0.016	0.000	0.000	0.000	0.000
53	A	55	VAL	0	-0.030	-0.018	8.109	0.021	0.021	0.000	0.000	0.000	0.000
54	A	56	PHE	0	-0.005	0.006	7.535	-0.009	-0.009	0.000	0.000	0.000	0.000
55	A	57	LEU	0	0.029	0.017	7.644	-0.287	-0.287	0.000	0.000	0.000	0.000
56	A	58	GLU	-1	-0.850	-0.926	10.072	-0.883	-0.883	0.000	0.000	0.000	0.000
57	A	59	VAL	0	0.042	0.015	12.260	0.015	0.015	0.000	0.000	0.000	0.000
58	A	60	ASP	-1	-0.801	-0.909	15.342	-0.323	-0.323	0.000	0.000	0.000	0.000
59	A	61	VAL	0	-0.008	-0.040	17.513	0.028	0.028	0.000	0.000	0.000	0.000
60	A	62	HIS	0	-0.020	-0.011	20.851	0.038	0.038	0.000	0.000	0.000	0.000
61	A	63	GLN	0	-0.055	-0.024	16.039	0.009	0.009	0.000	0.000	0.000	0.000
62	A	64	CYS	0	-0.054	0.011	17.428	0.019	0.019	0.000	0.000	0.000	0.000
63	A	65	GLN	0	0.020	0.007	20.197	0.011	0.011	0.000	0.000	0.000	0.000
64	A	66	GLY	0	0.018	0.019	23.806	0.006	0.006	0.000	0.000	0.000	0.000
65	A	67	THR	0	-0.039	-0.047	18.372	0.011	0.011	0.000	0.000	0.000	0.000
66	A	68	ALA	0	0.004	0.006	21.745	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	69	ALA	0	0.021	0.013	22.933	0.006	0.006	0.000	0.000	0.000	0.000
68	A	70	THR	0	-0.047	-0.031	24.344	0.006	0.006	0.000	0.000	0.000	0.000
69	A	71	ASN	0	-0.078	-0.035	21.330	0.008	0.008	0.000	0.000	0.000	0.000
70	A	72	ASN	0	-0.071	-0.046	24.253	0.000	0.000	0.000	0.000	0.000	0.000
71	A	73	ILE	0	-0.047	-0.018	21.512	-0.006	-0.006	0.000	0.000	0.000	0.000
72	A	74	SER	0	0.028	0.019	25.039	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	75	ALA	0	0.005	0.002	25.736	0.003	0.003	0.000	0.000	0.000	0.000
74	A	76	THR	0	-0.006	0.045	21.285	-0.011	-0.011	0.000	0.000	0.000	0.000
75	A	77	PRO	0	-0.036	-0.044	19.197	0.010	0.010	0.000	0.000	0.000	0.000
76	A	78	THR	0	0.005	-0.018	20.054	0.033	0.033	0.000	0.000	0.000	0.000
77	A	79	PHE	0	-0.027	-0.015	15.045	-0.039	-0.039	0.000	0.000	0.000	0.000
78	A	80	GLN	0	-0.003	0.010	17.615	0.058	0.058	0.000	0.000	0.000	0.000
79	A	81	PHE	0	0.029	0.005	17.038	-0.036	-0.036	0.000	0.000	0.000	0.000
80	A	82	PHE	0	0.031	-0.001	16.530	0.021	0.021	0.000	0.000	0.000	0.000
81	A	83	ARG	1	0.872	0.904	17.138	0.038	0.038	0.000	0.000	0.000	0.000
82	A	84	ASN	0	0.008	-0.004	18.347	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	85	LYS	1	0.918	0.960	18.088	-0.041	-0.041	0.000	0.000	0.000	0.000
84	A	86	VAL	0	0.011	0.026	19.639	-0.008	-0.008	0.000	0.000	0.000	0.000
85	A	87	ARG	1	0.865	0.944	21.015	0.122	0.122	0.000	0.000	0.000	0.000
86	A	88	ILE	0	-0.012	-0.023	20.431	0.010	0.010	0.000	0.000	0.000	0.000
87	A	89	ASP	-1	-0.770	-0.845	21.619	-0.119	-0.119	0.000	0.000	0.000	0.000
88	A	90	GLN	0	-0.049	-0.044	21.788	-0.021	-0.021	0.000	0.000	0.000	0.000
89	A	91	TYR	0	-0.003	-0.009	20.708	0.022	0.022	0.000	0.000	0.000	0.000
90	A	92	GLN	0	-0.011	0.001	21.588	-0.018	-0.018	0.000	0.000	0.000	0.000
91	A	93	GLY	0	0.024	0.012	23.019	0.011	0.011	0.000	0.000	0.000	0.000
92	A	94	ALA	0	-0.027	-0.042	20.621	-0.024	-0.024	0.000	0.000	0.000	0.000
93	A	95	ASP	-1	-0.848	-0.900	21.301	-0.208	-0.208	0.000	0.000	0.000	0.000
94	A	96	ALA	0	0.040	0.002	17.799	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	97	VAL	0	0.018	0.013	19.126	-0.006	-0.006	0.000	0.000	0.000	0.000
96	A	98	GLY	0	0.060	0.030	21.524	0.008	0.008	0.000	0.000	0.000	0.000
97	A	99	LEU	0	-0.052	-0.018	16.026	0.006	0.006	0.000	0.000	0.000	0.000
98	A	100	GLU	-1	-0.764	-0.861	15.539	-0.228	-0.228	0.000	0.000	0.000	0.000
99	A	101	GLU	-1	-0.820	-0.874	17.913	-0.129	-0.129	0.000	0.000	0.000	0.000
100	A	102	LYS	1	0.817	0.887	20.638	0.153	0.153	0.000	0.000	0.000	0.000
101	A	103	ILE	0	-0.005	-0.005	13.894	0.009	0.009	0.000	0.000	0.000	0.000
102	A	104	LYS	1	0.816	0.887	17.451	0.174	0.174	0.000	0.000	0.000	0.000
103	A	105	GLN	0	-0.024	-0.008	18.805	0.011	0.011	0.000	0.000	0.000	0.000
104	A	106	HIS	0	-0.008	-0.010	18.755	0.022	0.022	0.000	0.000	0.000	0.000
105	A	107	LEU	0	-0.088	-0.025	13.841	0.019	0.019	0.000	0.000	0.000	0.000
106	A	108	GLU	-1	-0.903	-0.909	18.007	-0.001	-0.001	0.000	0.000	0.000	0.000

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