FMO DATABASE

FMODB ID: 3JL5L

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1060244.696101
FMO2-HF: Nuclear repulsion	1011019.785777
FMO2-HF: Total energy	-49224.910324
FMO2-MP2: Total energy	-49368.422607

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.
-70.396	-74.868	23.69	-7.482	-11.737	0.098

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 : -0.838 / q_NPA : -0.897

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	0.097	0.036	2.741	-17.857	-18.182	7.823	-2.728	-4.771	0.028
4	A	6	ARG	1	0.958	0.969	2.205	-67.327	-72.437	15.857	-4.882	-5.866	0.061
5	A	7	ARG	1	0.899	0.944	3.361	-54.246	-53.651	0.011	0.167	-0.772	0.009
6	A	8	GLU	-1	-0.741	-0.843	5.057	21.541	21.662	-0.001	-0.008	-0.113	0.000
7	A	9	ILE	0	0.010	0.007	6.731	-5.319	-5.319	0.000	0.000	0.000	0.000
8	A	10	HIS	0	-0.069	-0.053	6.967	-5.856	-5.856	0.000	0.000	0.000	0.000
9	A	11	HIS	0	-0.022	-0.033	8.945	-3.002	-3.002	0.000	0.000	0.000	0.000
10	A	12	ALA	0	0.015	0.027	10.953	-2.375	-2.375	0.000	0.000	0.000	0.000
11	A	13	HIS	1	0.895	0.937	12.144	-24.343	-24.343	0.000	0.000	0.000	0.000
12	A	14	VAL	0	-0.007	0.016	12.698	-1.441	-1.441	0.000	0.000	0.000	0.000
13	A	15	ALA	0	0.015	0.010	15.078	-1.299	-1.299	0.000	0.000	0.000	0.000
14	A	16	ILE	0	-0.011	-0.005	16.456	-1.176	-1.176	0.000	0.000	0.000	0.000
15	A	17	ARG	1	0.830	0.892	16.792	-17.447	-17.447	0.000	0.000	0.000	0.000
16	A	18	ASP	-1	-0.810	-0.886	19.172	14.989	14.989	0.000	0.000	0.000	0.000
17	A	19	TRP	0	-0.069	-0.046	21.106	-0.845	-0.845	0.000	0.000	0.000	0.000
18	A	20	LEU	0	-0.025	-0.023	21.927	-0.704	-0.704	0.000	0.000	0.000	0.000
19	A	21	ALA	0	-0.024	-0.005	23.625	-0.580	-0.580	0.000	0.000	0.000	0.000
20	A	22	GLY	0	-0.010	-0.001	25.325	-0.473	-0.473	0.000	0.000	0.000	0.000
21	A	23	ASP	-1	-0.968	-0.954	23.354	11.782	11.782	0.000	0.000	0.000	0.000
22	A	24	SER	0	-0.032	-0.021	22.807	0.518	0.518	0.000	0.000	0.000	0.000
23	A	25	ARG	1	0.950	0.972	20.600	-14.344	-14.344	0.000	0.000	0.000	0.000
24	A	26	ALA	0	0.019	-0.009	24.191	-0.159	-0.159	0.000	0.000	0.000	0.000
25	A	27	ASP	-1	-0.911	-0.965	25.562	12.300	12.300	0.000	0.000	0.000	0.000
26	A	28	ALA	0	-0.026	-0.007	22.784	0.435	0.435	0.000	0.000	0.000	0.000
27	A	29	LEU	0	-0.007	0.002	22.361	0.566	0.566	0.000	0.000	0.000	0.000
28	A	30	ASP	-1	-0.822	-0.902	23.263	12.388	12.388	0.000	0.000	0.000	0.000
29	A	31	ALA	0	-0.026	-0.015	20.203	0.573	0.573	0.000	0.000	0.000	0.000
30	A	32	LEU	0	-0.057	-0.023	17.712	1.035	1.035	0.000	0.000	0.000	0.000
31	A	33	MET	0	0.004	-0.012	18.935	0.778	0.778	0.000	0.000	0.000	0.000
32	A	34	ALA	0	-0.015	0.002	20.112	0.107	0.107	0.000	0.000	0.000	0.000
33	A	35	ARG	1	0.848	0.927	11.812	-23.096	-23.096	0.000	0.000	0.000	0.000
34	A	36	PHE	0	-0.042	-0.015	15.744	1.392	1.392	0.000	0.000	0.000	0.000
35	A	37	ALA	0	0.058	0.032	17.645	-0.790	-0.790	0.000	0.000	0.000	0.000
36	A	38	GLU	-1	-0.957	-0.986	19.258	12.049	12.049	0.000	0.000	0.000	0.000
37	A	39	ASP	-1	-0.895	-0.955	20.913	14.923	14.923	0.000	0.000	0.000	0.000
38	A	40	PHE	0	-0.054	-0.025	17.047	0.286	0.286	0.000	0.000	0.000	0.000
39	A	41	SER	0	-0.012	-0.009	20.135	-0.961	-0.961	0.000	0.000	0.000	0.000
40	A	42	MET	0	-0.034	-0.014	19.923	0.958	0.958	0.000	0.000	0.000	0.000
41	A	43	VAL	0	0.006	0.004	21.032	-0.873	-0.873	0.000	0.000	0.000	0.000
42	A	44	THR	0	0.035	0.000	21.729	0.542	0.542	0.000	0.000	0.000	0.000
43	A	45	PRO	0	-0.002	-0.008	22.355	-0.325	-0.325	0.000	0.000	0.000	0.000
44	A	46	HIS	0	-0.034	-0.015	24.627	-0.551	-0.551	0.000	0.000	0.000	0.000
45	A	47	GLY	0	-0.012	0.001	26.392	-0.420	-0.420	0.000	0.000	0.000	0.000
46	A	48	VAL	0	-0.044	-0.011	27.142	-0.323	-0.323	0.000	0.000	0.000	0.000
47	A	49	VAL	0	0.002	-0.003	25.485	0.558	0.558	0.000	0.000	0.000	0.000
48	A	50	LEU	0	-0.047	-0.023	24.371	-0.472	-0.472	0.000	0.000	0.000	0.000
49	A	51	ASP	-1	-0.802	-0.891	24.057	12.197	12.197	0.000	0.000	0.000	0.000
50	A	52	LYS	1	0.919	0.949	21.523	-14.631	-14.631	0.000	0.000	0.000	0.000
51	A	53	THR	0	0.004	-0.001	24.121	0.142	0.142	0.000	0.000	0.000	0.000
52	A	54	ALA	0	0.036	0.025	27.329	-0.141	-0.141	0.000	0.000	0.000	0.000
53	A	55	LEU	0	-0.049	-0.012	20.387	-0.112	-0.112	0.000	0.000	0.000	0.000
54	A	56	GLY	0	0.045	0.010	24.958	0.075	0.075	0.000	0.000	0.000	0.000
55	A	57	GLU	-1	-0.937	-0.968	26.095	10.024	10.024	0.000	0.000	0.000	0.000
56	A	58	LEU	0	-0.028	-0.008	25.326	-0.316	-0.316	0.000	0.000	0.000	0.000
57	A	59	PHE	0	0.051	-0.009	20.376	-0.144	-0.144	0.000	0.000	0.000	0.000
58	A	60	ARG	1	0.943	0.997	26.146	-10.897	-10.897	0.000	0.000	0.000	0.000
59	A	61	SER	0	-0.070	-0.044	29.080	-0.272	-0.272	0.000	0.000	0.000	0.000
60	A	62	LYS	1	0.909	0.955	27.026	-10.911	-10.911	0.000	0.000	0.000	0.000
61	A	63	GLY	0	0.027	0.042	26.993	0.253	0.253	0.000	0.000	0.000	0.000
62	A	64	GLY	0	0.021	-0.007	27.066	-0.455	-0.455	0.000	0.000	0.000	0.000
63	A	65	THR	0	-0.111	-0.060	28.464	-0.268	-0.268	0.000	0.000	0.000	0.000
64	A	66	ARG	1	0.809	0.905	23.609	-13.003	-13.003	0.000	0.000	0.000	0.000
65	A	67	PRO	0	0.060	0.033	26.313	0.460	0.460	0.000	0.000	0.000	0.000
66	A	68	GLY	0	0.003	-0.008	25.886	-0.098	-0.098	0.000	0.000	0.000	0.000
67	A	69	LEU	0	-0.058	-0.008	21.432	0.294	0.294	0.000	0.000	0.000	0.000
68	A	70	ARG	1	0.903	0.953	20.014	-12.796	-12.796	0.000	0.000	0.000	0.000
69	A	71	ILE	0	-0.008	-0.018	15.324	-0.358	-0.358	0.000	0.000	0.000	0.000
70	A	72	GLU	-1	-0.951	-0.960	14.254	21.243	21.243	0.000	0.000	0.000	0.000
71	A	73	ILE	0	-0.041	-0.026	9.972	-0.302	-0.302	0.000	0.000	0.000	0.000
72	A	74	ASP	-1	-0.758	-0.831	10.631	22.080	22.080	0.000	0.000	0.000	0.000
73	A	75	GLY	0	0.034	0.003	11.648	-0.373	-0.373	0.000	0.000	0.000	0.000
74	A	76	GLU	-1	-0.862	-0.933	6.804	36.062	36.062	0.000	0.000	0.000	0.000
75	A	77	SER	0	-0.034	-0.011	8.407	0.943	0.943	0.000	0.000	0.000	0.000
76	A	78	LEU	0	-0.009	-0.003	5.404	0.098	0.202	-0.001	-0.007	-0.095	0.000
77	A	79	LEU	0	-0.022	-0.015	7.557	-3.128	-3.128	0.000	0.000	0.000	0.000
78	A	80	ALA	0	0.016	0.005	10.133	-2.468	-2.468	0.000	0.000	0.000	0.000
79	A	81	SER	0	-0.018	-0.020	8.156	4.021	4.021	0.000	0.000	0.000	0.000
80	A	82	GLY	0	-0.003	-0.002	10.152	-2.129	-2.129	0.000	0.000	0.000	0.000
81	A	83	VAL	0	0.013	0.002	11.175	2.100	2.100	0.000	0.000	0.000	0.000
82	A	84	ASP	-1	-0.849	-0.909	13.402	18.874	18.874	0.000	0.000	0.000	0.000
83	A	85	GLY	0	-0.002	0.003	10.400	-0.264	-0.264	0.000	0.000	0.000	0.000
84	A	86	ALA	0	-0.029	-0.018	7.449	0.952	0.952	0.000	0.000	0.000	0.000
85	A	87	THR	0	-0.033	0.000	9.476	-2.309	-2.309	0.000	0.000	0.000	0.000
86	A	88	LEU	0	-0.033	-0.020	4.715	2.488	2.631	0.001	-0.024	-0.120	0.000
87	A	89	ALA	0	0.029	0.021	9.333	-3.112	-3.112	0.000	0.000	0.000	0.000
88	A	90	TYR	0	-0.004	-0.001	9.885	2.906	2.906	0.000	0.000	0.000	0.000
89	A	91	ARG	1	0.776	0.868	11.848	-20.583	-20.583	0.000	0.000	0.000	0.000
90	A	92	GLU	-1	-0.818	-0.906	14.095	19.632	19.632	0.000	0.000	0.000	0.000
91	A	93	ILE	0	-0.045	-0.020	16.329	-1.441	-1.441	0.000	0.000	0.000	0.000
92	A	94	GLN	0	-0.032	-0.033	18.519	-0.544	-0.544	0.000	0.000	0.000	0.000
93	A	95	SER	0	-0.035	-0.029	21.081	-0.426	-0.426	0.000	0.000	0.000	0.000
94	A	96	ASP	-1	-0.760	-0.899	23.806	11.972	11.972	0.000	0.000	0.000	0.000
95	A	97	ALA	0	-0.004	-0.006	26.632	-0.160	-0.160	0.000	0.000	0.000	0.000
96	A	98	ALA	0	-0.037	-0.004	29.827	-0.310	-0.310	0.000	0.000	0.000	0.000
97	A	99	GLY	0	0.021	0.021	28.961	-0.228	-0.228	0.000	0.000	0.000	0.000
98	A	100	ARG	1	0.900	0.942	21.749	-13.387	-13.387	0.000	0.000	0.000	0.000
99	A	101	SER	0	-0.064	-0.021	23.342	-0.264	-0.264	0.000	0.000	0.000	0.000
100	A	102	GLU	-1	-0.819	-0.929	19.971	15.641	15.641	0.000	0.000	0.000	0.000
101	A	103	ARG	1	0.859	0.940	18.340	-16.255	-16.255	0.000	0.000	0.000	0.000
102	A	104	LEU	0	0.018	0.006	16.821	1.020	1.020	0.000	0.000	0.000	0.000
103	A	105	SER	0	0.026	-0.005	14.254	-1.357	-1.357	0.000	0.000	0.000	0.000
104	A	106	THR	0	-0.023	-0.004	13.483	1.239	1.239	0.000	0.000	0.000	0.000
105	A	107	VAL	0	-0.016	-0.011	9.977	-1.462	-1.462	0.000	0.000	0.000	0.000
106	A	108	VAL	0	0.003	0.011	11.549	1.863	1.863	0.000	0.000	0.000	0.000
107	A	109	LEU	0	-0.028	-0.024	7.407	-0.768	-0.768	0.000	0.000	0.000	0.000
108	A	110	HIS	0	0.032	0.011	11.300	1.068	1.068	0.000	0.000	0.000	0.000
109	A	111	ARG	1	0.902	0.938	9.229	-25.169	-25.169	0.000	0.000	0.000	0.000
110	A	112	ASP	-1	-0.729	-0.841	12.227	19.352	19.352	0.000	0.000	0.000	0.000
111	A	113	ASP	-1	-0.913	-0.977	13.033	20.028	20.028	0.000	0.000	0.000	0.000
112	A	114	GLU	-1	-0.971	-0.977	14.239	17.766	17.766	0.000	0.000	0.000	0.000
113	A	115	GLY	0	-0.098	-0.046	10.287	0.943	0.943	0.000	0.000	0.000	0.000
114	A	116	ARG	1	0.769	0.874	9.941	-15.612	-15.612	0.000	0.000	0.000	0.000
115	A	117	LEU	0	-0.016	-0.012	6.983	1.087	1.087	0.000	0.000	0.000	0.000
116	A	118	TYR	0	-0.018	0.007	11.644	-1.536	-1.536	0.000	0.000	0.000	0.000
117	A	119	TRP	0	-0.096	-0.057	11.362	0.939	0.939	0.000	0.000	0.000	0.000
118	A	120	ARG	1	0.947	0.968	14.569	-17.288	-17.288	0.000	0.000	0.000	0.000
119	A	121	HIS	0	-0.004	-0.002	15.521	-1.569	-1.569	0.000	0.000	0.000	0.000
120	A	122	LEU	0	0.017	0.010	14.669	1.929	1.929	0.000	0.000	0.000	0.000
121	A	123	GLN	0	-0.009	0.023	16.900	-1.111	-1.111	0.000	0.000	0.000	0.000
122	A	124	GLU	-1	-0.835	-0.926	17.634	17.677	17.677	0.000	0.000	0.000	0.000
123	A	125	THR	0	-0.033	-0.020	19.756	-1.048	-1.048	0.000	0.000	0.000	0.000
124	A	126	PHE	0	0.005	0.002	21.585	0.573	0.573	0.000	0.000	0.000	0.000
125	A	127	CYS	0	-0.017	0.002	21.183	-0.032	-0.032	0.000	0.000	0.000	0.000
126	A	128	GLY	0	0.003	0.008	24.486	-0.416	-0.416	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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