FMO DATABASE

FMODB ID: YZ8K2

Calculation Name: 1THX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1THX

Chain ID: A

ChEMBL ID:

UniProt ID: P20857

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	107
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-856903.789779
FMO2-HF: Nuclear repulsion	815085.195521
FMO2-HF: Total energy	-41818.594258
FMO2-MP2: Total energy	-41941.441084

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:1:SER)

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

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.
-32.239	-28.595	13.996	-8.859	-8.781	-0.044

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / q_NPA : -0.024

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	GLY	0	0.025	0.004	3.319	-2.052	0.248	-0.002	-1.143	-1.156	0.001
4	A	4	VAL	0	-0.051	-0.014	3.809	-0.461	-0.169	0.005	-0.095	-0.202	0.000
5	A	5	ILE	0	0.009	0.026	4.768	0.346	0.410	-0.001	-0.003	-0.059	0.000
6	A	6	THR	0	-0.062	-0.051	7.164	-0.350	-0.350	0.000	0.000	0.000	0.000
7	A	7	ILE	0	-0.008	0.002	9.636	0.110	0.110	0.000	0.000	0.000	0.000
8	A	8	THR	0	-0.025	-0.056	12.508	-0.106	-0.106	0.000	0.000	0.000	0.000
9	A	9	ASP	-1	-0.728	-0.852	15.685	0.121	0.121	0.000	0.000	0.000	0.000
10	A	10	ALA	0	-0.061	-0.015	18.268	-0.002	-0.002	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.753	-0.847	13.200	0.464	0.464	0.000	0.000	0.000	0.000
12	A	12	PHE	0	0.030	0.017	13.011	0.051	0.051	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.820	-0.901	13.249	0.290	0.290	0.000	0.000	0.000	0.000
14	A	14	SER	0	0.014	-0.010	13.006	-0.011	-0.011	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.848	-0.917	8.045	1.441	1.441	0.000	0.000	0.000	0.000
16	A	16	VAL	0	-0.027	-0.012	8.338	0.053	0.053	0.000	0.000	0.000	0.000
17	A	17	LEU	0	-0.062	-0.026	10.481	-0.039	-0.039	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.818	0.899	12.545	-0.362	-0.362	0.000	0.000	0.000	0.000
19	A	19	ALA	0	-0.040	0.000	7.338	0.124	0.124	0.000	0.000	0.000	0.000
20	A	20	GLU	-1	-0.905	-0.952	8.371	0.274	0.274	0.000	0.000	0.000	0.000
21	A	21	GLN	0	-0.062	-0.036	2.349	-6.075	-4.649	1.283	-1.172	-1.537	0.016
22	A	22	PRO	0	-0.010	-0.008	7.719	0.085	0.085	0.000	0.000	0.000	0.000
23	A	23	VAL	0	0.012	0.002	6.678	-0.213	-0.213	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.003	0.013	7.520	0.110	0.110	0.000	0.000	0.000	0.000
25	A	25	VAL	0	0.012	0.010	8.915	-0.012	-0.012	0.000	0.000	0.000	0.000
26	A	26	TYR	0	-0.042	-0.031	11.475	-0.010	-0.010	0.000	0.000	0.000	0.000
27	A	27	PHE	0	0.030	0.012	13.544	0.082	0.082	0.000	0.000	0.000	0.000
28	A	28	TRP	0	0.031	-0.022	14.588	-0.034	-0.034	0.000	0.000	0.000	0.000
29	A	29	ALA	0	0.077	0.031	18.736	0.026	0.026	0.000	0.000	0.000	0.000
30	A	30	SER	0	-0.035	-0.033	21.416	-0.021	-0.021	0.000	0.000	0.000	0.000
31	A	31	TRP	0	-0.040	-0.032	22.723	-0.016	-0.016	0.000	0.000	0.000	0.000
32	A	32	CYS	0	-0.025	0.032	18.948	-0.052	-0.052	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.048	0.026	22.831	-0.014	-0.014	0.000	0.000	0.000	0.000
34	A	34	PRO	0	0.007	-0.016	23.544	-0.014	-0.014	0.000	0.000	0.000	0.000
35	A	36	GLN	0	-0.027	-0.015	18.463	-0.025	-0.025	0.000	0.000	0.000	0.000
36	A	37	LEU	0	-0.004	-0.001	19.379	-0.016	-0.016	0.000	0.000	0.000	0.000
37	A	38	MET	0	0.027	0.037	16.375	-0.048	-0.048	0.000	0.000	0.000	0.000
38	A	39	SER	0	0.008	0.006	13.580	-0.059	-0.059	0.000	0.000	0.000	0.000
39	A	40	PRO	0	-0.017	-0.008	13.105	-0.062	-0.062	0.000	0.000	0.000	0.000
40	A	41	LEU	0	0.020	0.028	13.375	-0.108	-0.108	0.000	0.000	0.000	0.000
41	A	42	ILE	0	0.043	0.011	9.760	-0.186	-0.186	0.000	0.000	0.000	0.000
42	A	43	ASN	0	0.027	0.007	8.494	-0.439	-0.439	0.000	0.000	0.000	0.000
43	A	44	LEU	0	-0.009	0.009	9.213	-0.248	-0.248	0.000	0.000	0.000	0.000
44	A	45	ALA	0	0.018	0.012	9.247	-0.222	-0.222	0.000	0.000	0.000	0.000
45	A	46	ALA	0	0.012	0.004	5.086	-0.363	-0.363	0.000	0.000	0.000	0.000
46	A	47	ASN	0	-0.022	-0.019	4.958	-1.346	-1.385	-0.001	-0.006	0.046	0.000
47	A	48	THR	0	-0.061	-0.031	7.538	0.045	0.045	0.000	0.000	0.000	0.000
48	A	49	TYR	0	-0.059	-0.069	6.471	0.361	0.361	0.000	0.000	0.000	0.000
49	A	50	SER	0	0.005	-0.011	2.806	0.409	1.229	0.126	-0.385	-0.560	-0.001
50	A	51	ASP	-1	-0.887	-0.897	1.744	-21.095	-24.295	10.649	-4.645	-2.803	-0.050
51	A	52	ARG	1	0.795	0.889	4.324	3.496	3.594	-0.001	-0.009	-0.088	0.000
52	A	53	LEU	0	-0.013	0.004	4.380	1.393	1.515	-0.001	-0.025	-0.096	0.000
53	A	54	LYS	1	0.797	0.893	2.437	-7.183	-5.303	1.930	-1.650	-2.161	-0.010
54	A	55	VAL	0	-0.016	-0.012	3.427	0.446	0.327	0.009	0.274	-0.165	0.000
55	A	56	VAL	0	0.025	0.011	5.371	0.405	0.405	0.000	0.000	0.000	0.000
56	A	57	LYS	1	0.872	0.942	8.064	-0.056	-0.056	0.000	0.000	0.000	0.000
57	A	58	LEU	0	0.007	0.011	11.525	0.114	0.114	0.000	0.000	0.000	0.000
58	A	59	GLU	-1	-0.850	-0.894	14.871	0.005	0.005	0.000	0.000	0.000	0.000
59	A	60	ILE	0	0.025	-0.014	18.064	0.019	0.019	0.000	0.000	0.000	0.000
60	A	61	ASP	-1	-0.841	-0.899	20.769	0.015	0.015	0.000	0.000	0.000	0.000
61	A	62	PRO	0	-0.030	-0.020	20.211	0.006	0.006	0.000	0.000	0.000	0.000
62	A	63	ASN	0	-0.033	-0.005	17.518	0.047	0.047	0.000	0.000	0.000	0.000
63	A	64	PRO	0	0.056	0.019	20.815	-0.023	-0.023	0.000	0.000	0.000	0.000
64	A	65	THR	0	-0.073	-0.050	21.439	-0.019	-0.019	0.000	0.000	0.000	0.000
65	A	66	THR	0	-0.027	-0.058	15.999	-0.013	-0.013	0.000	0.000	0.000	0.000
66	A	67	VAL	0	-0.012	0.003	19.389	-0.029	-0.029	0.000	0.000	0.000	0.000
67	A	68	LYS	1	0.931	0.967	21.354	-0.037	-0.037	0.000	0.000	0.000	0.000
68	A	69	LYS	1	0.772	0.879	17.954	-0.030	-0.030	0.000	0.000	0.000	0.000
69	A	70	TYR	0	0.009	0.008	16.355	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	71	LYS	1	0.851	0.906	20.593	0.058	0.058	0.000	0.000	0.000	0.000
71	A	72	VAL	0	0.000	0.016	19.152	-0.020	-0.020	0.000	0.000	0.000	0.000
72	A	73	GLU	-1	-0.849	-0.914	22.373	-0.063	-0.063	0.000	0.000	0.000	0.000
73	A	74	GLY	0	-0.005	0.001	24.042	0.005	0.005	0.000	0.000	0.000	0.000
74	A	75	VAL	0	-0.017	0.005	20.498	-0.009	-0.009	0.000	0.000	0.000	0.000
75	A	76	PRO	0	-0.015	-0.035	18.998	0.013	0.013	0.000	0.000	0.000	0.000
76	A	77	ALA	0	-0.012	0.008	18.591	0.001	0.001	0.000	0.000	0.000	0.000
77	A	78	LEU	0	-0.034	-0.015	13.198	-0.023	-0.023	0.000	0.000	0.000	0.000
78	A	79	ARG	1	0.761	0.826	14.503	0.261	0.261	0.000	0.000	0.000	0.000
79	A	80	LEU	0	-0.011	0.016	10.666	-0.044	-0.044	0.000	0.000	0.000	0.000
80	A	81	VAL	0	0.023	0.003	11.676	0.070	0.070	0.000	0.000	0.000	0.000
81	A	82	LYS	1	0.988	0.985	11.332	0.087	0.087	0.000	0.000	0.000	0.000
82	A	83	GLY	0	0.052	0.044	12.119	0.022	0.022	0.000	0.000	0.000	0.000
83	A	84	GLU	-1	-0.795	-0.896	14.106	-0.011	-0.011	0.000	0.000	0.000	0.000
84	A	85	GLN	0	-0.066	-0.014	16.461	-0.024	-0.024	0.000	0.000	0.000	0.000
85	A	86	ILE	0	0.011	-0.006	15.808	-0.040	-0.040	0.000	0.000	0.000	0.000
86	A	87	LEU	0	-0.076	-0.031	12.973	0.006	0.006	0.000	0.000	0.000	0.000
87	A	88	ASP	-1	-0.802	-0.891	16.442	-0.420	-0.420	0.000	0.000	0.000	0.000
88	A	89	SER	0	-0.062	-0.033	16.830	0.006	0.006	0.000	0.000	0.000	0.000
89	A	90	THR	0	-0.004	0.008	17.716	0.010	0.010	0.000	0.000	0.000	0.000
90	A	91	GLU	-1	-0.775	-0.858	19.427	-0.222	-0.222	0.000	0.000	0.000	0.000
91	A	92	GLY	0	0.005	0.007	21.957	-0.008	-0.008	0.000	0.000	0.000	0.000
92	A	93	VAL	0	-0.033	-0.033	20.614	-0.030	-0.030	0.000	0.000	0.000	0.000
93	A	94	ILE	0	-0.001	0.000	16.439	0.015	0.015	0.000	0.000	0.000	0.000
94	A	95	SER	0	0.020	-0.030	19.689	-0.022	-0.022	0.000	0.000	0.000	0.000
95	A	96	LYS	1	0.934	0.937	16.005	0.591	0.591	0.000	0.000	0.000	0.000
96	A	97	ASP	-1	-0.823	-0.908	16.509	-0.624	-0.624	0.000	0.000	0.000	0.000
97	A	98	LYN	0	0.048	0.081	18.563	-0.034	-0.034	0.000	0.000	0.000	0.000
98	A	99	LEU	0	0.025	0.012	12.211	-0.007	-0.007	0.000	0.000	0.000	0.000
99	A	100	LEU	0	0.004	-0.007	13.088	-0.072	-0.072	0.000	0.000	0.000	0.000
100	A	101	SER	0	-0.007	-0.008	14.663	-0.027	-0.027	0.000	0.000	0.000	0.000
101	A	102	PHE	0	-0.040	-0.003	13.743	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	103	LEU	0	0.013	0.007	9.488	0.002	0.002	0.000	0.000	0.000	0.000
103	A	104	ASP	-1	-0.735	-0.852	12.866	-1.165	-1.165	0.000	0.000	0.000	0.000
104	A	105	THR	0	-0.062	-0.033	14.438	0.078	0.078	0.000	0.000	0.000	0.000
105	A	106	HIS	1	0.783	0.863	13.978	0.588	0.588	0.000	0.000	0.000	0.000
106	A	107	LEU	0	-0.034	0.003	8.628	0.021	0.021	0.000	0.000	0.000	0.000
107	A	108	ASN	0	-0.072	-0.031	12.332	-0.090	-0.090	0.000	0.000	0.000	0.000

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