FMO DATABASE

FMODB ID: 98Z62

Calculation Name: 1TP6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1TP6

Chain ID: A

ChEMBL ID:

UniProt ID: Q9I430

Base Structure: X-ray

Registration Date: 2023-09-23

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	126
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1060443.45403
FMO2-HF: Nuclear repulsion	1011217.954382
FMO2-HF: Total energy	-49225.499648
FMO2-MP2: Total energy	-49369.009036

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:3:CYM)

Summations of interaction energy for fragment #1(A:3:CYM)

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.
-66.648	-84.826	38.9	-7.413	-13.308	0.068

Interaction energy analysis for fragmet #1(A:3:CYM)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.774 / q_NPA : -0.822

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	5	TYR	0	0.133	0.037	2.460	-14.338	-20.711	15.148	-2.661	-6.115	0.036
4	A	6	ARG	1	0.911	0.924	1.988	-60.815	-72.605	23.667	-6.035	-5.841	0.023
5	A	7	ARG	1	0.852	0.926	3.149	-64.528	-64.772	0.086	1.310	-1.152	0.009
6	A	8	GLU	-1	-0.679	-0.789	4.989	21.703	21.819	-0.001	-0.014	-0.100	0.000
7	A	9	ILE	0	0.000	0.000	6.698	-5.830	-5.830	0.000	0.000	0.000	0.000
8	A	10	HIS	0	-0.044	-0.028	6.942	-5.748	-5.748	0.000	0.000	0.000	0.000
9	A	11	HIS	0	-0.036	-0.031	8.852	-4.388	-4.388	0.000	0.000	0.000	0.000
10	A	12	ALA	0	0.007	0.018	10.854	-2.818	-2.818	0.000	0.000	0.000	0.000
11	A	13	HIS	1	0.839	0.906	12.275	-25.338	-25.338	0.000	0.000	0.000	0.000
12	A	14	VAL	0	-0.021	-0.001	12.726	-1.650	-1.650	0.000	0.000	0.000	0.000
13	A	15	ALA	0	0.024	0.011	14.870	-1.467	-1.467	0.000	0.000	0.000	0.000
14	A	16	ILE	0	-0.012	-0.005	16.024	-1.332	-1.332	0.000	0.000	0.000	0.000
15	A	17	ARG	1	0.833	0.894	16.152	-18.955	-18.955	0.000	0.000	0.000	0.000
16	A	18	ASP	-1	-0.793	-0.876	18.627	16.079	16.079	0.000	0.000	0.000	0.000
17	A	19	TRP	0	-0.052	-0.036	20.912	-0.914	-0.914	0.000	0.000	0.000	0.000
18	A	20	LEU	0	-0.025	-0.014	21.379	-0.755	-0.755	0.000	0.000	0.000	0.000
19	A	21	ALA	0	-0.038	-0.004	23.372	-0.609	-0.609	0.000	0.000	0.000	0.000
20	A	22	GLY	0	0.042	0.006	25.002	-0.618	-0.618	0.000	0.000	0.000	0.000
21	A	23	ASP	-1	-0.961	-0.957	23.781	12.111	12.111	0.000	0.000	0.000	0.000
22	A	24	SER	0	-0.074	-0.030	22.977	0.589	0.589	0.000	0.000	0.000	0.000
23	A	25	ARG	1	0.916	0.943	20.857	-14.769	-14.769	0.000	0.000	0.000	0.000
24	A	26	ALA	0	0.046	0.008	24.284	-0.125	-0.125	0.000	0.000	0.000	0.000
25	A	27	ASP	-1	-0.891	-0.957	25.233	12.875	12.875	0.000	0.000	0.000	0.000
26	A	28	ALA	0	-0.029	-0.001	22.336	0.471	0.471	0.000	0.000	0.000	0.000
27	A	29	LEU	0	0.015	0.020	21.763	0.711	0.711	0.000	0.000	0.000	0.000
28	A	30	ASP	-1	-0.774	-0.866	22.683	12.735	12.735	0.000	0.000	0.000	0.000
29	A	31	ALA	0	0.012	0.004	20.613	0.458	0.458	0.000	0.000	0.000	0.000
30	A	32	LEU	0	-0.053	-0.020	17.104	1.091	1.091	0.000	0.000	0.000	0.000
31	A	33	MET	0	0.000	-0.007	18.316	0.793	0.793	0.000	0.000	0.000	0.000
32	A	34	ALA	0	0.002	0.000	19.268	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	35	ARG	1	0.798	0.870	11.233	-26.056	-26.056	0.000	0.000	0.000	0.000
34	A	36	PHE	0	-0.027	0.000	15.019	1.605	1.605	0.000	0.000	0.000	0.000
35	A	37	ALA	0	0.057	0.028	17.309	-0.849	-0.849	0.000	0.000	0.000	0.000
36	A	38	GLU	-1	-0.948	-0.979	18.850	12.333	12.333	0.000	0.000	0.000	0.000
37	A	39	ASP	-1	-0.819	-0.899	21.233	14.872	14.872	0.000	0.000	0.000	0.000
38	A	40	PHE	0	-0.058	-0.023	16.790	0.202	0.202	0.000	0.000	0.000	0.000
39	A	41	SER	0	-0.012	-0.012	20.078	-0.952	-0.952	0.000	0.000	0.000	0.000
40	A	42	MET	0	-0.037	-0.017	19.559	1.082	1.082	0.000	0.000	0.000	0.000
41	A	43	VAL	0	-0.014	-0.005	20.859	-0.921	-0.921	0.000	0.000	0.000	0.000
42	A	44	THR	0	0.006	-0.013	21.453	0.574	0.574	0.000	0.000	0.000	0.000
43	A	45	PRO	0	0.001	-0.015	21.795	-0.296	-0.296	0.000	0.000	0.000	0.000
44	A	46	HIS	0	-0.014	0.001	24.077	-0.445	-0.445	0.000	0.000	0.000	0.000
45	A	47	GLY	0	0.003	0.009	26.044	-0.475	-0.475	0.000	0.000	0.000	0.000
46	A	48	VAL	0	-0.030	-0.008	27.251	-0.177	-0.177	0.000	0.000	0.000	0.000
47	A	49	VAL	0	0.011	0.008	25.303	0.590	0.590	0.000	0.000	0.000	0.000
48	A	50	LEU	0	-0.026	-0.016	23.900	-0.458	-0.458	0.000	0.000	0.000	0.000
49	A	51	ASP	-1	-0.742	-0.859	23.932	12.675	12.675	0.000	0.000	0.000	0.000
50	A	52	LYS	1	0.862	0.930	20.711	-15.402	-15.402	0.000	0.000	0.000	0.000
51	A	53	THR	0	-0.042	-0.035	23.564	0.020	0.020	0.000	0.000	0.000	0.000
52	A	54	ALA	0	0.026	0.015	27.187	-0.028	-0.028	0.000	0.000	0.000	0.000
53	A	55	LEU	0	-0.050	-0.019	19.822	-0.066	-0.066	0.000	0.000	0.000	0.000
54	A	56	GLY	0	0.067	0.022	24.479	0.161	0.161	0.000	0.000	0.000	0.000
55	A	57	GLU	-1	-0.949	-0.977	25.560	10.306	10.306	0.000	0.000	0.000	0.000
56	A	58	LEU	0	-0.031	-0.004	24.933	-0.269	-0.269	0.000	0.000	0.000	0.000
57	A	59	PHE	0	0.050	0.011	20.027	-0.162	-0.162	0.000	0.000	0.000	0.000
58	A	60	ARG	1	0.851	0.914	25.716	-11.787	-11.787	0.000	0.000	0.000	0.000
59	A	61	SER	0	-0.074	-0.034	28.660	-0.355	-0.355	0.000	0.000	0.000	0.000
60	A	62	LYS	1	0.862	0.907	26.783	-11.132	-11.132	0.000	0.000	0.000	0.000
61	A	63	GLY	0	0.048	0.054	26.589	0.267	0.267	0.000	0.000	0.000	0.000
62	A	64	GLY	0	0.020	-0.007	26.831	-0.500	-0.500	0.000	0.000	0.000	0.000
63	A	65	THR	0	-0.115	-0.064	28.227	-0.292	-0.292	0.000	0.000	0.000	0.000
64	A	66	ARG	1	0.800	0.887	22.925	-13.529	-13.529	0.000	0.000	0.000	0.000
65	A	67	PRO	0	0.060	0.037	26.201	0.491	0.491	0.000	0.000	0.000	0.000
66	A	68	GLY	0	-0.004	-0.009	25.856	-0.165	-0.165	0.000	0.000	0.000	0.000
67	A	69	LEU	0	-0.088	-0.029	21.279	0.256	0.256	0.000	0.000	0.000	0.000
68	A	70	ARG	1	0.899	0.951	20.115	-12.880	-12.880	0.000	0.000	0.000	0.000
69	A	71	ILE	0	-0.007	-0.017	15.128	-0.483	-0.483	0.000	0.000	0.000	0.000
70	A	72	GLU	-1	-0.913	-0.938	13.376	22.565	22.565	0.000	0.000	0.000	0.000
71	A	73	ILE	0	-0.058	-0.035	9.543	-0.572	-0.572	0.000	0.000	0.000	0.000
72	A	74	ASP	-1	-0.794	-0.862	10.555	22.810	22.810	0.000	0.000	0.000	0.000
73	A	75	GLY	0	0.036	0.009	11.490	-0.100	-0.100	0.000	0.000	0.000	0.000
74	A	76	GLU	-1	-0.828	-0.903	6.874	37.207	37.207	0.000	0.000	0.000	0.000
75	A	77	SER	0	-0.029	-0.009	8.428	1.632	1.632	0.000	0.000	0.000	0.000
76	A	78	LEU	0	-0.011	-0.006	5.908	0.118	0.118	0.000	0.000	0.000	0.000
77	A	79	LEU	0	-0.018	-0.008	8.109	-2.974	-2.974	0.000	0.000	0.000	0.000
78	A	80	ALA	0	0.008	-0.002	10.699	-2.328	-2.328	0.000	0.000	0.000	0.000
79	A	81	SER	0	-0.007	-0.013	8.656	3.721	3.721	0.000	0.000	0.000	0.000
80	A	82	GLY	0	-0.012	-0.007	10.677	-2.276	-2.276	0.000	0.000	0.000	0.000
81	A	83	VAL	0	0.019	0.013	11.779	1.883	1.883	0.000	0.000	0.000	0.000
82	A	84	ASP	-1	-0.808	-0.889	13.512	19.158	19.158	0.000	0.000	0.000	0.000
83	A	85	GLY	0	-0.011	0.007	10.336	0.113	0.113	0.000	0.000	0.000	0.000
84	A	86	ALA	0	-0.025	-0.019	7.496	0.844	0.844	0.000	0.000	0.000	0.000
85	A	87	THR	0	-0.030	-0.012	9.473	-2.737	-2.737	0.000	0.000	0.000	0.000
86	A	88	LEU	0	-0.011	-0.006	5.014	2.362	2.475	0.000	-0.013	-0.100	0.000
87	A	89	ALA	0	0.029	0.024	9.621	-2.722	-2.722	0.000	0.000	0.000	0.000
88	A	90	TYR	0	-0.034	-0.037	9.967	4.157	4.157	0.000	0.000	0.000	0.000
89	A	91	ARG	1	0.787	0.859	11.834	-20.926	-20.926	0.000	0.000	0.000	0.000
90	A	92	GLU	-1	-0.741	-0.862	13.500	21.319	21.319	0.000	0.000	0.000	0.000
91	A	93	ILE	0	-0.054	-0.023	15.830	-1.590	-1.590	0.000	0.000	0.000	0.000
92	A	94	GLN	0	-0.008	-0.018	18.030	-0.447	-0.447	0.000	0.000	0.000	0.000
93	A	95	SER	0	-0.034	-0.025	20.663	-0.537	-0.537	0.000	0.000	0.000	0.000
94	A	96	ASP	-1	-0.750	-0.867	23.625	12.400	12.400	0.000	0.000	0.000	0.000
95	A	97	ALA	0	0.028	0.015	26.415	-0.183	-0.183	0.000	0.000	0.000	0.000
96	A	98	ALA	0	-0.023	-0.001	29.446	-0.351	-0.351	0.000	0.000	0.000	0.000
97	A	99	GLY	0	-0.008	0.003	28.899	-0.232	-0.232	0.000	0.000	0.000	0.000
98	A	100	ARG	1	0.818	0.883	20.975	-13.872	-13.872	0.000	0.000	0.000	0.000
99	A	101	SER	0	-0.045	-0.017	23.314	-0.298	-0.298	0.000	0.000	0.000	0.000
100	A	102	GLU	-1	-0.765	-0.867	19.666	15.908	15.908	0.000	0.000	0.000	0.000
101	A	103	ARG	1	0.813	0.914	17.924	-17.384	-17.384	0.000	0.000	0.000	0.000
102	A	104	LEU	0	0.047	0.025	16.580	1.024	1.024	0.000	0.000	0.000	0.000
103	A	105	SER	0	-0.023	-0.036	14.551	-1.462	-1.462	0.000	0.000	0.000	0.000
104	A	106	THR	0	-0.049	-0.029	13.401	1.101	1.101	0.000	0.000	0.000	0.000
105	A	107	VAL	0	-0.004	0.004	9.972	-1.493	-1.493	0.000	0.000	0.000	0.000
106	A	108	VAL	0	-0.011	0.000	11.709	1.524	1.524	0.000	0.000	0.000	0.000
107	A	109	LEU	0	-0.030	-0.013	7.010	-0.448	-0.448	0.000	0.000	0.000	0.000
108	A	110	HIS	0	0.003	-0.008	10.688	1.816	1.816	0.000	0.000	0.000	0.000
109	A	111	ARG	1	0.795	0.873	9.740	-22.930	-22.930	0.000	0.000	0.000	0.000
110	A	112	ASP	-1	-0.742	-0.836	12.544	19.299	19.299	0.000	0.000	0.000	0.000
111	A	113	ASP	-1	-0.832	-0.920	12.974	21.614	21.614	0.000	0.000	0.000	0.000
112	A	114	GLU	-1	-0.945	-0.953	14.283	17.833	17.833	0.000	0.000	0.000	0.000
113	A	115	GLY	0	-0.060	-0.024	10.629	0.735	0.735	0.000	0.000	0.000	0.000
114	A	116	ARG	1	0.773	0.875	9.894	-15.641	-15.641	0.000	0.000	0.000	0.000
115	A	117	LEU	0	-0.015	-0.016	6.489	1.555	1.555	0.000	0.000	0.000	0.000
116	A	118	TYR	0	-0.048	-0.039	11.114	-1.403	-1.403	0.000	0.000	0.000	0.000
117	A	119	TRP	0	-0.070	-0.046	10.960	0.395	0.395	0.000	0.000	0.000	0.000
118	A	120	ARG	1	0.832	0.892	14.022	-17.557	-17.557	0.000	0.000	0.000	0.000
119	A	121	HIS	0	0.022	0.017	15.254	-1.537	-1.537	0.000	0.000	0.000	0.000
120	A	122	LEU	0	0.015	0.008	14.516	1.915	1.915	0.000	0.000	0.000	0.000
121	A	123	GLN	0	-0.013	0.009	16.752	-1.356	-1.356	0.000	0.000	0.000	0.000
122	A	124	GLU	-1	-0.730	-0.844	16.828	19.987	19.987	0.000	0.000	0.000	0.000
123	A	125	THR	0	-0.046	-0.030	19.502	-1.085	-1.085	0.000	0.000	0.000	0.000
124	A	126	PHE	0	0.034	0.018	21.480	0.570	0.570	0.000	0.000	0.000	0.000
125	A	127	CYS	0	-0.045	-0.015	21.875	0.054	0.054	0.000	0.000	0.000	0.000
126	A	128	GLY	0	0.011	0.013	24.136	-0.199	-0.199	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:3:CYM)