FMO DATABASE

FMODB ID: YV762

Calculation Name: 3RAZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3RAZ

Chain ID: A

ChEMBL ID:

UniProt ID: Q9K1R4

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	134
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1214032.59297
FMO2-HF: Nuclear repulsion	1160696.286358
FMO2-HF: Total energy	-53336.306611
FMO2-MP2: Total energy	-53489.614867

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:24:GLU)

Summations of interaction energy for fragment #1(A:24: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.
-216.364	-203.287	4.67	-7.637	-10.107	0.06

Interaction energy analysis for fragmet #1(A:24:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.904 / q_NPA : -0.970

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	26	ALA	0	0.030	0.031	3.802	-1.115	0.876	-0.028	-0.936	-1.026	0.003
4	A	27	GLY	0	0.042	0.018	6.721	-0.701	-0.701	0.000	0.000	0.000	0.000
5	A	28	TRP	0	-0.040	-0.020	10.235	0.279	0.279	0.000	0.000	0.000	0.000
6	A	29	LYS	1	0.941	0.996	11.919	-14.720	-14.720	0.000	0.000	0.000	0.000
7	A	30	ASP	-1	-0.818	-0.924	12.193	19.384	19.384	0.000	0.000	0.000	0.000
8	A	31	ASN	0	0.008	0.007	8.225	1.599	1.599	0.000	0.000	0.000	0.000
9	A	32	THR	0	-0.034	-0.009	8.798	1.077	1.077	0.000	0.000	0.000	0.000
10	A	33	PRO	0	0.030	0.026	6.328	1.333	1.333	0.000	0.000	0.000	0.000
11	A	34	GLN	0	-0.022	-0.010	5.868	-4.048	-4.048	0.000	0.000	0.000	0.000
12	A	35	SER	0	0.036	0.006	5.086	4.238	4.228	-0.001	-0.010	0.021	0.000
13	A	36	LEU	0	0.061	0.040	6.407	-3.200	-3.200	0.000	0.000	0.000	0.000
14	A	37	GLN	0	0.032	0.022	7.728	-0.457	-0.457	0.000	0.000	0.000	0.000
15	A	38	SER	0	-0.090	-0.062	10.072	-2.067	-2.067	0.000	0.000	0.000	0.000
16	A	39	LEU	0	-0.059	-0.032	10.930	-1.016	-1.016	0.000	0.000	0.000	0.000
17	A	40	LYS	1	0.872	0.941	13.750	-16.607	-16.607	0.000	0.000	0.000	0.000
18	A	41	ALA	0	-0.029	0.020	17.121	-0.655	-0.655	0.000	0.000	0.000	0.000
19	A	42	PRO	0	-0.033	-0.011	18.312	0.494	0.494	0.000	0.000	0.000	0.000
20	A	43	VAL	0	-0.009	-0.003	19.380	0.271	0.271	0.000	0.000	0.000	0.000
21	A	44	ARG	1	0.875	0.925	11.656	-20.385	-20.385	0.000	0.000	0.000	0.000
22	A	45	ILE	0	0.019	0.004	16.271	-0.041	-0.041	0.000	0.000	0.000	0.000
23	A	46	VAL	0	-0.011	-0.006	10.416	0.481	0.481	0.000	0.000	0.000	0.000
24	A	47	ASN	0	-0.008	-0.012	13.547	-0.233	-0.233	0.000	0.000	0.000	0.000
25	A	48	LEU	0	-0.012	-0.002	9.423	1.100	1.100	0.000	0.000	0.000	0.000
26	A	49	TRP	0	-0.011	-0.024	12.729	-1.739	-1.739	0.000	0.000	0.000	0.000
27	A	50	ALA	0	0.032	0.011	13.192	1.625	1.625	0.000	0.000	0.000	0.000
28	A	51	THR	0	-0.033	-0.039	15.416	-1.376	-1.376	0.000	0.000	0.000	0.000
29	A	52	TRP	0	0.071	0.038	15.092	-1.299	-1.299	0.000	0.000	0.000	0.000
30	A	53	CYS	0	0.006	0.041	18.378	-0.578	-0.578	0.000	0.000	0.000	0.000
31	A	54	GLY	0	0.019	0.005	20.356	-0.173	-0.173	0.000	0.000	0.000	0.000
32	A	55	PRO	0	0.034	-0.003	22.367	-0.264	-0.264	0.000	0.000	0.000	0.000
33	A	57	ARG	1	0.862	0.934	20.584	-13.249	-13.249	0.000	0.000	0.000	0.000
34	A	58	LYS	1	0.932	0.982	22.562	-10.788	-10.788	0.000	0.000	0.000	0.000
35	A	59	GLU	-1	-0.852	-0.938	21.156	13.532	13.532	0.000	0.000	0.000	0.000
36	A	60	MET	0	0.000	0.014	18.064	-0.188	-0.188	0.000	0.000	0.000	0.000
37	A	61	PRO	0	0.026	-0.004	22.398	-0.040	-0.040	0.000	0.000	0.000	0.000
38	A	62	ALA	0	0.045	0.036	25.768	-0.275	-0.275	0.000	0.000	0.000	0.000
39	A	63	MET	0	-0.007	0.000	18.070	-0.179	-0.179	0.000	0.000	0.000	0.000
40	A	64	SER	0	-0.015	-0.005	22.952	-0.048	-0.048	0.000	0.000	0.000	0.000
41	A	65	LYS	1	0.946	0.958	23.835	-9.411	-9.411	0.000	0.000	0.000	0.000
42	A	66	TRP	0	0.048	0.019	21.493	-0.046	-0.046	0.000	0.000	0.000	0.000
43	A	67	TYR	0	0.033	0.005	19.302	-0.098	-0.098	0.000	0.000	0.000	0.000
44	A	68	LYS	1	0.886	0.947	23.902	-10.583	-10.583	0.000	0.000	0.000	0.000
45	A	69	ALA	0	-0.035	-0.004	26.315	-0.288	-0.288	0.000	0.000	0.000	0.000
46	A	70	GLN	0	-0.027	0.011	24.242	-0.250	-0.250	0.000	0.000	0.000	0.000
47	A	71	LYS	1	0.948	0.967	26.643	-9.274	-9.274	0.000	0.000	0.000	0.000
48	A	72	LYS	1	1.013	0.990	24.215	-10.721	-10.721	0.000	0.000	0.000	0.000
49	A	73	GLY	0	0.014	0.018	22.926	0.357	0.357	0.000	0.000	0.000	0.000
50	A	74	SER	0	-0.058	-0.037	22.917	0.242	0.242	0.000	0.000	0.000	0.000
51	A	75	VAL	0	0.015	-0.007	19.513	0.046	0.046	0.000	0.000	0.000	0.000
52	A	76	ASP	-1	-0.783	-0.878	15.548	15.364	15.364	0.000	0.000	0.000	0.000
53	A	77	MET	0	-0.034	-0.021	16.243	0.055	0.055	0.000	0.000	0.000	0.000
54	A	78	VAL	0	-0.016	-0.002	10.542	0.070	0.070	0.000	0.000	0.000	0.000
55	A	79	GLY	0	0.046	0.024	13.615	-0.090	-0.090	0.000	0.000	0.000	0.000
56	A	80	ILE	0	-0.045	-0.032	7.297	0.275	0.275	0.000	0.000	0.000	0.000
57	A	81	ALA	0	0.000	0.001	10.541	-0.117	-0.117	0.000	0.000	0.000	0.000
58	A	82	LEU	0	-0.003	-0.016	8.692	2.838	2.838	0.000	0.000	0.000	0.000
59	A	83	ASP	-1	-0.723	-0.854	10.076	17.397	17.397	0.000	0.000	0.000	0.000
60	A	84	THR	0	0.005	0.009	10.837	1.490	1.490	0.000	0.000	0.000	0.000
61	A	85	SER	0	-0.004	-0.042	12.689	-1.113	-1.113	0.000	0.000	0.000	0.000
62	A	86	ASP	-1	-0.904	-0.948	13.945	14.168	14.168	0.000	0.000	0.000	0.000
63	A	87	ASN	0	0.026	0.008	16.140	-1.554	-1.554	0.000	0.000	0.000	0.000
64	A	88	ILE	0	-0.047	-0.023	12.093	-0.590	-0.590	0.000	0.000	0.000	0.000
65	A	89	GLY	0	0.034	0.002	16.654	-0.708	-0.708	0.000	0.000	0.000	0.000
66	A	90	ASN	0	-0.072	-0.050	19.061	-1.313	-1.313	0.000	0.000	0.000	0.000
67	A	91	PHE	0	0.014	0.000	19.314	-0.581	-0.581	0.000	0.000	0.000	0.000
68	A	92	LEU	0	0.003	-0.006	17.001	-0.512	-0.512	0.000	0.000	0.000	0.000
69	A	93	LYS	1	0.923	0.981	21.466	-12.239	-12.239	0.000	0.000	0.000	0.000
70	A	94	GLN	0	-0.030	-0.012	24.499	-0.447	-0.447	0.000	0.000	0.000	0.000
71	A	95	THR	0	-0.067	-0.030	22.888	-0.407	-0.407	0.000	0.000	0.000	0.000
72	A	96	PRO	0	0.025	0.015	22.368	0.681	0.681	0.000	0.000	0.000	0.000
73	A	97	VAL	0	-0.011	-0.002	19.068	-0.343	-0.343	0.000	0.000	0.000	0.000
74	A	98	SER	0	-0.065	-0.038	21.585	0.166	0.166	0.000	0.000	0.000	0.000
75	A	99	TYR	0	0.003	0.005	16.464	-0.016	-0.016	0.000	0.000	0.000	0.000
76	A	100	PRO	0	0.017	0.003	13.916	0.063	0.063	0.000	0.000	0.000	0.000
77	A	101	ILE	0	0.024	0.028	13.526	0.379	0.379	0.000	0.000	0.000	0.000
78	A	102	TRP	0	0.000	-0.012	7.567	0.584	0.584	0.000	0.000	0.000	0.000
79	A	103	ARG	1	0.913	0.966	8.203	-29.529	-29.529	0.000	0.000	0.000	0.000
80	A	104	TYR	0	-0.024	0.012	2.430	-18.597	-13.669	2.442	-3.425	-3.945	0.042
81	A	105	THR	0	-0.024	-0.025	2.780	-5.847	-3.570	0.778	-1.105	-1.950	-0.009
82	A	106	GLY	0	0.020	0.015	2.636	-2.626	0.753	1.421	-2.479	-2.319	0.021
83	A	107	ALA	0	0.033	0.013	3.516	-13.321	-13.394	0.055	0.418	-0.400	0.003
84	A	108	ASN	0	-0.010	-0.002	4.745	-10.990	-10.933	-0.001	-0.006	-0.050	0.000
85	A	109	SER	0	0.073	0.030	5.904	1.483	1.483	0.000	0.000	0.000	0.000
86	A	110	ARG	1	0.957	0.969	7.534	-23.064	-23.064	0.000	0.000	0.000	0.000
87	A	111	ASN	0	0.000	-0.019	6.862	-4.803	-4.803	0.000	0.000	0.000	0.000
88	A	112	PHE	0	0.048	0.036	4.008	-2.425	-1.897	0.004	-0.094	-0.438	0.000
89	A	113	MET	0	-0.007	0.019	6.051	-4.258	-4.258	0.000	0.000	0.000	0.000
90	A	114	LYS	1	0.951	0.986	9.671	-26.691	-26.691	0.000	0.000	0.000	0.000
91	A	115	THR	0	-0.057	-0.028	7.449	-2.508	-2.508	0.000	0.000	0.000	0.000
92	A	116	TYR	0	0.020	0.001	6.472	-1.092	-1.092	0.000	0.000	0.000	0.000
93	A	117	GLY	0	-0.026	-0.014	11.500	-1.857	-1.857	0.000	0.000	0.000	0.000
94	A	118	ASN	0	-0.054	-0.022	12.747	-2.377	-2.377	0.000	0.000	0.000	0.000
95	A	119	THR	0	0.010	-0.013	13.421	1.626	1.626	0.000	0.000	0.000	0.000
96	A	120	VAL	0	0.027	-0.002	15.576	0.435	0.435	0.000	0.000	0.000	0.000
97	A	121	GLY	0	-0.061	-0.014	13.573	0.139	0.139	0.000	0.000	0.000	0.000
98	A	122	VAL	0	0.008	0.008	14.498	-0.185	-0.185	0.000	0.000	0.000	0.000
99	A	123	LEU	0	0.001	0.026	12.938	0.884	0.884	0.000	0.000	0.000	0.000
100	A	124	PRO	0	0.073	-0.019	16.976	-0.564	-0.564	0.000	0.000	0.000	0.000
101	A	125	PHE	0	-0.007	-0.007	13.825	-0.144	-0.144	0.000	0.000	0.000	0.000
102	A	126	THR	0	0.049	0.027	15.416	1.134	1.134	0.000	0.000	0.000	0.000
103	A	127	VAL	0	-0.024	0.002	14.016	-0.673	-0.673	0.000	0.000	0.000	0.000
104	A	128	VAL	0	0.014	0.015	16.274	0.451	0.451	0.000	0.000	0.000	0.000
105	A	129	GLU	-1	-0.861	-0.928	13.199	20.326	20.326	0.000	0.000	0.000	0.000
106	A	130	ALA	0	0.060	0.032	17.593	-0.319	-0.319	0.000	0.000	0.000	0.000
107	A	131	PRO	0	0.025	0.011	14.608	-0.173	-0.173	0.000	0.000	0.000	0.000
108	A	132	LYS	1	0.895	0.941	16.727	-14.417	-14.417	0.000	0.000	0.000	0.000
109	A	133	CYS	0	-0.006	-0.006	19.332	-0.467	-0.467	0.000	0.000	0.000	0.000
110	A	134	GLY	0	0.003	0.026	18.018	-0.266	-0.266	0.000	0.000	0.000	0.000
111	A	135	TYR	0	-0.006	-0.016	19.092	0.241	0.241	0.000	0.000	0.000	0.000
112	A	136	ARG	1	0.979	0.984	13.153	-19.691	-19.691	0.000	0.000	0.000	0.000
113	A	137	GLN	0	0.019	0.029	18.900	-0.390	-0.390	0.000	0.000	0.000	0.000
114	A	138	THR	0	-0.004	-0.011	18.550	0.411	0.411	0.000	0.000	0.000	0.000
115	A	139	ILE	0	-0.016	-0.002	19.882	-0.631	-0.631	0.000	0.000	0.000	0.000
116	A	140	THR	0	-0.029	-0.005	22.001	0.271	0.271	0.000	0.000	0.000	0.000
117	A	141	GLY	0	0.006	-0.006	24.426	-0.428	-0.428	0.000	0.000	0.000	0.000
118	A	142	GLU	-1	-0.936	-0.974	24.860	10.789	10.789	0.000	0.000	0.000	0.000
119	A	143	VAL	0	-0.013	0.002	21.080	-0.127	-0.127	0.000	0.000	0.000	0.000
120	A	144	ASN	0	0.040	0.015	24.475	-0.079	-0.079	0.000	0.000	0.000	0.000
121	A	145	GLU	-1	-0.853	-0.949	26.718	10.330	10.330	0.000	0.000	0.000	0.000
122	A	146	LYS	1	0.893	0.954	28.631	-9.226	-9.226	0.000	0.000	0.000	0.000
123	A	147	SER	0	0.013	0.018	25.972	0.071	0.071	0.000	0.000	0.000	0.000
124	A	148	LEU	0	-0.001	-0.004	21.806	0.263	0.263	0.000	0.000	0.000	0.000
125	A	149	THR	0	-0.036	-0.016	25.018	0.124	0.124	0.000	0.000	0.000	0.000
126	A	150	ASP	-1	-0.864	-0.938	27.677	9.665	9.665	0.000	0.000	0.000	0.000
127	A	151	ALA	0	0.005	0.005	23.244	0.015	0.015	0.000	0.000	0.000	0.000
128	A	152	VAL	0	-0.002	0.001	22.010	0.216	0.216	0.000	0.000	0.000	0.000
129	A	153	LYS	1	0.960	0.985	24.277	-9.063	-9.063	0.000	0.000	0.000	0.000
130	A	154	LEU	0	-0.002	0.001	26.076	-0.173	-0.173	0.000	0.000	0.000	0.000
131	A	155	ALA	0	0.000	-0.006	21.825	-0.045	-0.045	0.000	0.000	0.000	0.000
132	A	156	HIS	0	0.000	-0.014	23.942	-0.018	-0.018	0.000	0.000	0.000	0.000
133	A	157	SER	0	-0.146	-0.055	25.619	-0.217	-0.217	0.000	0.000	0.000	0.000
134	A	158	LYS	1	0.913	0.979	24.377	-11.403	-11.403	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:24:GLU)