FMO DATABASE

FMODB ID: 1NYKZ

Calculation Name: 1TY4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1TY4

Chain ID: A

ChEMBL ID:

UniProt ID: P41958

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	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	164
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1766553.979956
FMO2-HF: Nuclear repulsion	1697599.402335
FMO2-HF: Total energy	-68954.577621
FMO2-MP2: Total energy	-69149.546222

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:74:GLU)

Summations of interaction energy for fragment #1(A:74:GLU)

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.
-164.715	-169.066	31.063	-13.506	-13.206	0.147

Interaction energy analysis for fragmet #1(A:74:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.848 / q_NPA : -0.917

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	76	PRO	0	0.017	0.009	3.473	2.256	4.044	0.014	-0.746	-1.056	0.002
4	A	77	ARG	1	0.724	0.806	4.886	-32.323	-32.148	-0.001	-0.009	-0.165	0.000
5	A	78	LEU	0	-0.080	-0.040	4.163	-2.697	-2.276	0.000	-0.057	-0.365	0.000
6	A	79	ASP	-1	-0.786	-0.875	4.130	51.917	52.341	0.001	-0.076	-0.349	0.000
7	A	80	ILE	0	0.032	0.002	4.043	-8.549	-8.170	0.000	-0.055	-0.323	0.000
8	A	81	GLU	-1	-0.902	-0.949	6.343	21.588	21.588	0.000	0.000	0.000	0.000
9	A	82	GLY	0	-0.002	-0.006	8.466	-3.476	-3.476	0.000	0.000	0.000	0.000
10	A	83	PHE	0	-0.017	-0.012	6.910	-3.524	-3.524	0.000	0.000	0.000	0.000
11	A	84	VAL	0	-0.053	-0.021	10.588	-2.623	-2.623	0.000	0.000	0.000	0.000
12	A	85	VAL	0	0.034	0.023	12.715	-2.008	-2.008	0.000	0.000	0.000	0.000
13	A	86	ASP	-1	-0.776	-0.841	13.791	17.659	17.659	0.000	0.000	0.000	0.000
14	A	87	TYR	0	0.021	0.018	14.794	-1.446	-1.446	0.000	0.000	0.000	0.000
15	A	88	PHE	0	0.004	-0.014	16.493	-1.183	-1.183	0.000	0.000	0.000	0.000
16	A	89	THR	0	-0.014	-0.023	18.116	-1.292	-1.292	0.000	0.000	0.000	0.000
17	A	90	HIS	0	-0.026	-0.003	19.313	-0.942	-0.942	0.000	0.000	0.000	0.000
18	A	91	ARG	1	0.779	0.854	20.645	-13.412	-13.412	0.000	0.000	0.000	0.000
19	A	92	ILE	0	0.017	-0.001	21.773	-0.712	-0.712	0.000	0.000	0.000	0.000
20	A	93	ARG	1	0.827	0.898	22.174	-13.859	-13.859	0.000	0.000	0.000	0.000
21	A	94	GLN	0	-0.062	-0.012	25.018	-0.711	-0.711	0.000	0.000	0.000	0.000
22	A	95	ASN	0	-0.091	-0.054	26.854	-0.172	-0.172	0.000	0.000	0.000	0.000
23	A	96	GLY	0	0.003	0.009	28.911	-0.374	-0.374	0.000	0.000	0.000	0.000
24	A	97	MET	0	-0.060	-0.009	28.099	-0.314	-0.314	0.000	0.000	0.000	0.000
25	A	98	GLU	-1	-0.791	-0.896	26.503	12.148	12.148	0.000	0.000	0.000	0.000
26	A	99	TRP	0	-0.006	-0.005	17.903	-0.006	-0.006	0.000	0.000	0.000	0.000
27	A	100	PHE	0	0.020	-0.006	23.887	0.358	0.358	0.000	0.000	0.000	0.000
28	A	101	GLY	0	-0.031	-0.009	23.398	-0.139	-0.139	0.000	0.000	0.000	0.000
29	A	102	ALA	0	-0.034	-0.002	19.365	0.535	0.535	0.000	0.000	0.000	0.000
30	A	103	PRO	0	-0.005	0.006	15.644	-0.304	-0.304	0.000	0.000	0.000	0.000
31	A	104	GLY	0	0.022	0.006	16.690	0.065	0.065	0.000	0.000	0.000	0.000
32	A	105	LEU	0	0.000	0.004	12.175	1.297	1.297	0.000	0.000	0.000	0.000
33	A	106	PRO	0	-0.006	-0.011	10.781	-0.748	-0.748	0.000	0.000	0.000	0.000
34	A	107	CYS	0	-0.021	-0.014	10.321	-0.150	-0.150	0.000	0.000	0.000	0.000
35	A	108	GLY	0	0.014	0.021	12.745	-0.530	-0.530	0.000	0.000	0.000	0.000
36	A	109	VAL	0	-0.031	-0.013	13.559	1.550	1.550	0.000	0.000	0.000	0.000
37	A	110	GLN	0	0.016	0.015	10.320	-0.091	-0.091	0.000	0.000	0.000	0.000
38	A	111	PRO	0	0.032	0.011	13.159	-0.806	-0.806	0.000	0.000	0.000	0.000
39	A	112	GLU	-1	-0.740	-0.889	9.348	28.947	28.947	0.000	0.000	0.000	0.000
40	A	113	HIS	0	0.014	-0.001	9.719	-2.119	-2.119	0.000	0.000	0.000	0.000
41	A	114	GLU	-1	-0.799	-0.904	13.682	15.577	15.577	0.000	0.000	0.000	0.000
42	A	115	MET	0	-0.049	-0.001	14.518	-1.493	-1.493	0.000	0.000	0.000	0.000
43	A	116	MET	0	-0.001	0.000	11.076	-1.226	-1.226	0.000	0.000	0.000	0.000
44	A	117	ARG	1	0.752	0.855	15.085	-18.572	-18.572	0.000	0.000	0.000	0.000
45	A	118	VAL	0	-0.009	0.014	18.298	-1.051	-1.051	0.000	0.000	0.000	0.000
46	A	119	MET	0	-0.011	-0.005	16.573	-0.828	-0.828	0.000	0.000	0.000	0.000
47	A	120	GLY	0	0.026	0.012	18.313	-0.573	-0.573	0.000	0.000	0.000	0.000
48	A	121	THR	0	0.003	-0.013	19.346	-0.999	-0.999	0.000	0.000	0.000	0.000
49	A	122	ILE	0	-0.042	-0.022	22.380	-0.772	-0.772	0.000	0.000	0.000	0.000
50	A	123	PHE	0	-0.032	-0.018	20.620	-0.568	-0.568	0.000	0.000	0.000	0.000
51	A	124	GLU	-1	-0.795	-0.879	22.779	12.480	12.480	0.000	0.000	0.000	0.000
52	A	125	LYS	1	0.940	0.961	24.666	-12.310	-12.310	0.000	0.000	0.000	0.000
53	A	126	LYS	1	0.858	0.936	25.078	-12.675	-12.675	0.000	0.000	0.000	0.000
54	A	127	HIS	1	0.882	0.949	24.721	-12.656	-12.656	0.000	0.000	0.000	0.000
55	A	128	ALA	0	0.056	0.049	28.094	-0.006	-0.006	0.000	0.000	0.000	0.000
56	A	129	GLU	-1	-0.887	-0.942	29.335	9.098	9.098	0.000	0.000	0.000	0.000
57	A	130	ASN	0	-0.018	-0.018	28.585	0.132	0.132	0.000	0.000	0.000	0.000
58	A	131	PHE	0	-0.003	-0.006	22.151	0.191	0.191	0.000	0.000	0.000	0.000
59	A	132	GLU	-1	-0.845	-0.929	27.840	10.416	10.416	0.000	0.000	0.000	0.000
60	A	133	THR	0	-0.006	0.002	31.003	-0.219	-0.219	0.000	0.000	0.000	0.000
61	A	134	PHE	0	-0.048	-0.030	25.960	0.006	0.006	0.000	0.000	0.000	0.000
62	A	135	CYS	0	0.001	0.001	28.545	0.118	0.118	0.000	0.000	0.000	0.000
63	A	136	GLU	-1	-0.940	-0.959	29.451	8.712	8.712	0.000	0.000	0.000	0.000
64	A	137	GLN	0	-0.004	-0.019	31.234	0.118	0.118	0.000	0.000	0.000	0.000
65	A	138	LEU	0	-0.038	-0.030	25.415	0.015	0.015	0.000	0.000	0.000	0.000
66	A	139	LEU	0	-0.024	-0.011	30.092	-0.022	-0.022	0.000	0.000	0.000	0.000
67	A	140	ALA	0	-0.006	0.016	32.636	-0.282	-0.282	0.000	0.000	0.000	0.000
68	A	141	VAL	0	-0.040	-0.002	30.379	-0.205	-0.205	0.000	0.000	0.000	0.000
69	A	142	PRO	0	0.039	0.001	33.644	0.007	0.007	0.000	0.000	0.000	0.000
70	A	143	ARG	1	0.882	0.925	34.098	-8.378	-8.378	0.000	0.000	0.000	0.000
71	A	144	ILE	0	0.031	0.039	29.871	0.163	0.163	0.000	0.000	0.000	0.000
72	A	145	SER	0	-0.011	-0.001	29.328	0.406	0.406	0.000	0.000	0.000	0.000
73	A	146	PHE	0	0.084	0.038	19.991	0.248	0.248	0.000	0.000	0.000	0.000
74	A	147	SER	0	0.018	-0.002	24.427	0.363	0.363	0.000	0.000	0.000	0.000
75	A	148	PRO	0	0.033	0.020	24.853	0.407	0.407	0.000	0.000	0.000	0.000
76	A	149	TYR	0	0.023	0.011	17.954	0.092	0.092	0.000	0.000	0.000	0.000
77	A	150	GLN	0	-0.047	-0.031	19.942	0.118	0.118	0.000	0.000	0.000	0.000
78	A	151	ASP	-1	-0.796	-0.883	20.939	13.073	13.073	0.000	0.000	0.000	0.000
79	A	152	VAL	0	-0.007	0.024	21.508	0.236	0.236	0.000	0.000	0.000	0.000
80	A	153	VAL	0	0.007	-0.007	16.185	0.411	0.411	0.000	0.000	0.000	0.000
81	A	154	ARG	1	0.811	0.881	18.013	-13.297	-13.297	0.000	0.000	0.000	0.000
82	A	155	THR	0	-0.021	-0.026	19.301	0.086	0.086	0.000	0.000	0.000	0.000
83	A	156	VAL	0	-0.018	-0.008	17.399	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	157	GLY	0	-0.018	-0.011	16.290	0.416	0.416	0.000	0.000	0.000	0.000
85	A	158	ASN	0	-0.017	0.005	16.924	1.428	1.428	0.000	0.000	0.000	0.000
86	A	159	ALA	0	0.030	0.040	19.842	-0.753	-0.753	0.000	0.000	0.000	0.000
87	A	160	GLN	0	0.000	-0.011	20.776	0.735	0.735	0.000	0.000	0.000	0.000
88	A	161	THR	0	-0.079	-0.062	19.408	0.096	0.096	0.000	0.000	0.000	0.000
89	A	162	ASP	-1	-0.880	-0.921	21.503	14.564	14.564	0.000	0.000	0.000	0.000
90	A	163	GLN	0	0.015	0.000	18.075	1.201	1.201	0.000	0.000	0.000	0.000
91	A	164	CYS	0	-0.041	0.004	12.358	0.572	0.572	0.000	0.000	0.000	0.000
92	A	165	PRO	0	0.018	0.012	14.122	-0.358	-0.358	0.000	0.000	0.000	0.000
93	A	166	MET	0	-0.018	-0.016	10.236	-1.222	-1.222	0.000	0.000	0.000	0.000
94	A	167	SER	0	0.043	0.029	11.710	2.301	2.301	0.000	0.000	0.000	0.000
95	A	168	TYR	0	0.035	-0.043	10.645	0.982	0.982	0.000	0.000	0.000	0.000
96	A	169	GLY	0	0.006	0.012	13.942	-0.262	-0.262	0.000	0.000	0.000	0.000
97	A	170	ARG	1	0.858	0.945	15.160	-18.375	-18.375	0.000	0.000	0.000	0.000
98	A	171	LEU	0	0.023	0.024	9.271	-0.329	-0.329	0.000	0.000	0.000	0.000
99	A	172	ILE	0	0.005	-0.008	13.055	-0.342	-0.342	0.000	0.000	0.000	0.000
100	A	173	GLY	0	0.005	0.009	15.603	-0.822	-0.822	0.000	0.000	0.000	0.000
101	A	174	LEU	0	-0.023	-0.019	14.281	-0.789	-0.789	0.000	0.000	0.000	0.000
102	A	175	ILE	0	0.008	0.002	10.940	-0.463	-0.463	0.000	0.000	0.000	0.000
103	A	176	SER	0	-0.043	-0.022	15.583	-1.045	-1.045	0.000	0.000	0.000	0.000
104	A	177	PHE	0	0.012	0.000	18.986	-0.674	-0.674	0.000	0.000	0.000	0.000
105	A	178	GLY	0	0.027	0.015	18.292	-0.635	-0.635	0.000	0.000	0.000	0.000
106	A	179	GLY	0	0.015	-0.002	18.976	-0.391	-0.391	0.000	0.000	0.000	0.000
107	A	180	PHE	0	-0.031	-0.010	20.046	-0.563	-0.563	0.000	0.000	0.000	0.000
108	A	181	VAL	0	-0.007	-0.015	22.524	-0.572	-0.572	0.000	0.000	0.000	0.000
109	A	182	ALA	0	0.003	-0.002	20.814	-0.487	-0.487	0.000	0.000	0.000	0.000
110	A	183	ALA	0	-0.022	-0.018	22.981	-0.429	-0.429	0.000	0.000	0.000	0.000
111	A	184	LYS	1	0.943	0.988	25.465	-10.896	-10.896	0.000	0.000	0.000	0.000
112	A	185	MET	0	-0.047	-0.022	24.840	-0.199	-0.199	0.000	0.000	0.000	0.000
113	A	186	MET	0	-0.022	-0.010	25.096	-0.134	-0.134	0.000	0.000	0.000	0.000
114	A	187	GLU	-1	-0.873	-0.919	28.018	9.966	9.966	0.000	0.000	0.000	0.000
115	A	188	SER	0	0.004	-0.003	30.837	-0.479	-0.479	0.000	0.000	0.000	0.000
116	A	189	VAL	0	0.025	-0.001	31.166	0.286	0.286	0.000	0.000	0.000	0.000
117	A	190	GLU	-1	-0.940	-0.962	32.071	9.226	9.226	0.000	0.000	0.000	0.000
118	A	191	LEU	0	-0.022	-0.014	28.755	0.160	0.160	0.000	0.000	0.000	0.000
119	A	192	GLN	0	-0.023	-0.018	27.325	0.535	0.535	0.000	0.000	0.000	0.000
120	A	193	GLY	0	0.010	0.015	26.055	0.470	0.470	0.000	0.000	0.000	0.000
121	A	194	GLN	0	-0.040	-0.030	25.000	0.812	0.812	0.000	0.000	0.000	0.000
122	A	195	VAL	0	0.048	0.030	21.506	0.671	0.671	0.000	0.000	0.000	0.000
123	A	196	ARG	1	0.951	0.975	19.984	-13.457	-13.457	0.000	0.000	0.000	0.000
124	A	197	ASN	0	-0.028	-0.014	19.128	0.821	0.821	0.000	0.000	0.000	0.000
125	A	198	LEU	0	0.033	0.020	18.817	0.967	0.967	0.000	0.000	0.000	0.000
126	A	199	PHE	0	0.048	0.029	14.601	0.782	0.782	0.000	0.000	0.000	0.000
127	A	200	VAL	0	0.013	0.015	14.471	1.579	1.579	0.000	0.000	0.000	0.000
128	A	201	TYR	0	0.015	0.005	14.010	1.434	1.434	0.000	0.000	0.000	0.000
129	A	202	THR	0	0.008	-0.011	13.741	0.700	0.700	0.000	0.000	0.000	0.000
130	A	203	SER	0	0.012	0.014	10.151	2.729	2.729	0.000	0.000	0.000	0.000
131	A	204	LEU	0	0.037	0.010	9.619	2.993	2.993	0.000	0.000	0.000	0.000
132	A	205	PHE	0	-0.020	0.012	10.762	1.345	1.345	0.000	0.000	0.000	0.000
133	A	206	ILE	0	0.032	-0.001	8.028	0.883	0.883	0.000	0.000	0.000	0.000
134	A	207	LYS	1	0.809	0.908	5.664	-34.744	-34.744	0.000	0.000	0.000	0.000
135	A	208	THR	0	-0.076	-0.044	7.023	2.336	2.336	0.000	0.000	0.000	0.000
136	A	209	ARG	1	0.811	0.898	9.627	-21.930	-21.930	0.000	0.000	0.000	0.000
137	A	210	ILE	0	0.033	0.011	4.739	-1.092	-0.987	-0.001	-0.006	-0.098	0.000
138	A	211	ARG	1	0.796	0.872	1.773	-136.310	-144.108	31.051	-12.524	-10.729	0.145
139	A	212	ASN	0	-0.049	-0.002	6.786	-2.498	-2.498	0.000	0.000	0.000	0.000
140	A	213	ASN	0	-0.011	-0.022	9.640	-4.121	-4.121	0.000	0.000	0.000	0.000
141	A	214	TRP	0	0.030	0.012	6.939	0.335	0.335	0.000	0.000	0.000	0.000
142	A	215	LYS	1	0.900	0.969	7.846	-29.528	-29.528	0.000	0.000	0.000	0.000
143	A	216	GLU	-1	-0.800	-0.938	9.940	28.515	28.515	0.000	0.000	0.000	0.000
144	A	217	HIS	0	-0.010	-0.005	12.699	-2.171	-2.171	0.000	0.000	0.000	0.000
145	A	218	ASN	0	-0.052	-0.021	12.875	0.374	0.374	0.000	0.000	0.000	0.000
146	A	219	ARG	1	0.924	0.987	10.644	-23.273	-23.273	0.000	0.000	0.000	0.000
147	A	220	SER	0	0.001	-0.015	7.799	3.488	3.488	0.000	0.000	0.000	0.000
148	A	221	TRP	0	0.079	0.014	4.347	-8.148	-7.993	-0.001	-0.033	-0.121	0.000
149	A	222	ASP	-1	-0.899	-0.931	8.552	21.223	21.223	0.000	0.000	0.000	0.000
150	A	223	ASP	-1	-0.777	-0.859	11.338	19.986	19.986	0.000	0.000	0.000	0.000
151	A	224	PHE	0	-0.042	-0.025	10.997	-1.525	-1.525	0.000	0.000	0.000	0.000
152	A	225	MET	0	-0.001	0.007	11.941	-1.817	-1.817	0.000	0.000	0.000	0.000
153	A	226	THR	0	0.019	0.017	14.350	-1.970	-1.970	0.000	0.000	0.000	0.000
154	A	227	LEU	0	-0.013	-0.007	16.337	-1.270	-1.270	0.000	0.000	0.000	0.000
155	A	228	GLY	0	0.029	0.004	16.714	-1.038	-1.038	0.000	0.000	0.000	0.000
156	A	229	LYS	1	0.790	0.865	18.034	-14.631	-14.631	0.000	0.000	0.000	0.000
157	A	230	GLN	0	-0.027	-0.019	20.030	-0.310	-0.310	0.000	0.000	0.000	0.000
158	A	231	MET	0	0.012	0.015	21.014	-0.440	-0.440	0.000	0.000	0.000	0.000
159	A	232	LYS	1	0.874	0.940	21.397	-14.769	-14.769	0.000	0.000	0.000	0.000
160	A	233	GLU	-1	-0.776	-0.868	23.246	12.513	12.513	0.000	0.000	0.000	0.000
161	A	234	ASP	-1	-0.908	-0.944	26.177	11.543	11.543	0.000	0.000	0.000	0.000
162	A	235	TYR	0	-0.053	-0.037	25.976	-0.522	-0.522	0.000	0.000	0.000	0.000
163	A	236	GLU	-1	-0.935	-0.961	25.932	12.512	12.512	0.000	0.000	0.000	0.000
164	A	237	ARG	1	0.878	0.956	29.087	-10.561	-10.561	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:74:GLU)