FMO DATABASE

FMODB ID: 1NV2Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1215849.378411
FMO2-HF: Nuclear repulsion	1162511.936999
FMO2-HF: Total energy	-53337.441413
FMO2-MP2: Total energy	-53490.691483

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.
-260.38	-262.102	31.999	-13.248	-17.027	0.14

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 : -0.836 / q_NPA : -0.908

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	0.036	0.028	3.872	-1.416	0.297	-0.019	-0.850	-0.844	0.001
4	A	27	GLY	0	0.037	0.022	7.041	-0.553	-0.553	0.000	0.000	0.000	0.000
5	A	28	TRP	0	-0.018	-0.014	10.554	0.268	0.268	0.000	0.000	0.000	0.000
6	A	29	LYS	1	0.928	0.986	12.195	-14.326	-14.326	0.000	0.000	0.000	0.000
7	A	30	ASP	-1	-0.788	-0.887	12.822	18.589	18.589	0.000	0.000	0.000	0.000
8	A	31	ASN	0	-0.021	-0.001	7.017	0.898	0.898	0.000	0.000	0.000	0.000
9	A	32	THR	0	0.010	-0.003	9.133	1.162	1.162	0.000	0.000	0.000	0.000
10	A	33	PRO	0	0.011	-0.001	6.735	1.062	1.062	0.000	0.000	0.000	0.000
11	A	34	GLN	0	-0.018	0.000	6.286	-3.330	-3.330	0.000	0.000	0.000	0.000
12	A	35	SER	0	0.029	0.009	5.508	3.684	3.659	-0.001	-0.006	0.032	0.000
13	A	36	LEU	0	0.034	0.023	6.617	-2.902	-2.902	0.000	0.000	0.000	0.000
14	A	37	GLN	0	0.026	0.006	7.666	-0.965	-0.965	0.000	0.000	0.000	0.000
15	A	38	SER	0	-0.029	-0.020	10.309	-1.844	-1.844	0.000	0.000	0.000	0.000
16	A	39	LEU	0	-0.015	0.004	11.930	-1.202	-1.202	0.000	0.000	0.000	0.000
17	A	40	LYS	1	0.793	0.872	14.225	-16.380	-16.380	0.000	0.000	0.000	0.000
18	A	41	ALA	0	-0.009	0.024	17.626	-0.596	-0.596	0.000	0.000	0.000	0.000
19	A	42	PRO	0	-0.032	-0.017	18.927	0.504	0.504	0.000	0.000	0.000	0.000
20	A	43	VAL	0	-0.004	0.006	19.768	0.265	0.265	0.000	0.000	0.000	0.000
21	A	44	ARG	1	0.839	0.904	11.853	-20.252	-20.252	0.000	0.000	0.000	0.000
22	A	45	ILE	0	0.006	0.002	16.535	-0.043	-0.043	0.000	0.000	0.000	0.000
23	A	46	VAL	0	-0.007	-0.005	10.575	0.532	0.532	0.000	0.000	0.000	0.000
24	A	47	ASN	0	-0.015	-0.015	13.739	-0.291	-0.291	0.000	0.000	0.000	0.000
25	A	48	LEU	0	-0.033	-0.004	9.225	1.247	1.247	0.000	0.000	0.000	0.000
26	A	49	TRP	0	0.002	-0.024	12.408	-1.733	-1.733	0.000	0.000	0.000	0.000
27	A	50	ALA	0	0.031	0.015	12.746	1.817	1.817	0.000	0.000	0.000	0.000
28	A	51	THR	0	-0.047	-0.050	14.876	-1.412	-1.412	0.000	0.000	0.000	0.000
29	A	52	TRP	0	0.076	0.039	14.494	-1.445	-1.445	0.000	0.000	0.000	0.000
30	A	53	CYS	0	-0.005	0.040	17.596	-0.689	-0.689	0.000	0.000	0.000	0.000
31	A	54	GLY	0	0.026	0.007	19.581	-0.224	-0.224	0.000	0.000	0.000	0.000
32	A	55	PRO	0	0.022	-0.003	21.969	-0.237	-0.237	0.000	0.000	0.000	0.000
33	A	57	ARG	1	0.878	0.932	20.273	-13.721	-13.721	0.000	0.000	0.000	0.000
34	A	58	LYS	1	0.891	0.949	22.317	-11.089	-11.089	0.000	0.000	0.000	0.000
35	A	59	GLU	-1	-0.834	-0.915	21.041	13.707	13.707	0.000	0.000	0.000	0.000
36	A	60	MET	0	-0.006	0.004	17.212	-0.231	-0.231	0.000	0.000	0.000	0.000
37	A	61	PRO	0	0.033	0.011	21.741	-0.126	-0.126	0.000	0.000	0.000	0.000
38	A	62	ALA	0	0.013	0.020	25.321	-0.308	-0.308	0.000	0.000	0.000	0.000
39	A	63	MET	0	-0.005	-0.006	17.571	-0.102	-0.102	0.000	0.000	0.000	0.000
40	A	64	SER	0	-0.021	-0.024	23.173	-0.240	-0.240	0.000	0.000	0.000	0.000
41	A	65	LYS	1	0.848	0.903	24.095	-9.721	-9.721	0.000	0.000	0.000	0.000
42	A	66	TRP	0	0.049	0.006	22.072	-0.043	-0.043	0.000	0.000	0.000	0.000
43	A	67	TYR	0	-0.017	-0.008	20.062	-0.205	-0.205	0.000	0.000	0.000	0.000
44	A	68	LYS	1	0.887	0.946	24.227	-10.981	-10.981	0.000	0.000	0.000	0.000
45	A	69	ALA	0	0.016	0.028	26.948	-0.304	-0.304	0.000	0.000	0.000	0.000
46	A	70	GLN	0	-0.051	-0.002	24.345	-0.379	-0.379	0.000	0.000	0.000	0.000
47	A	71	LYS	1	0.895	0.930	26.821	-9.819	-9.819	0.000	0.000	0.000	0.000
48	A	72	LYS	1	0.991	0.991	24.091	-10.961	-10.961	0.000	0.000	0.000	0.000
49	A	73	GLY	0	0.063	0.046	23.094	0.335	0.335	0.000	0.000	0.000	0.000
50	A	74	SER	0	-0.069	-0.044	23.628	0.095	0.095	0.000	0.000	0.000	0.000
51	A	75	VAL	0	0.008	-0.014	20.302	0.078	0.078	0.000	0.000	0.000	0.000
52	A	76	ASP	-1	-0.787	-0.879	15.867	15.060	15.060	0.000	0.000	0.000	0.000
53	A	77	MET	0	-0.035	-0.019	16.505	-0.007	-0.007	0.000	0.000	0.000	0.000
54	A	78	VAL	0	-0.023	-0.003	10.774	0.047	0.047	0.000	0.000	0.000	0.000
55	A	79	GLY	0	0.047	0.022	13.880	0.008	0.008	0.000	0.000	0.000	0.000
56	A	80	ILE	0	-0.031	-0.016	6.917	0.077	0.077	0.000	0.000	0.000	0.000
57	A	81	ALA	0	0.015	0.009	10.264	0.067	0.067	0.000	0.000	0.000	0.000
58	A	82	LEU	0	-0.016	-0.025	8.166	3.121	3.121	0.000	0.000	0.000	0.000
59	A	83	ASP	-1	-0.722	-0.822	9.618	18.212	18.212	0.000	0.000	0.000	0.000
60	A	84	THR	0	0.005	-0.016	10.405	1.501	1.501	0.000	0.000	0.000	0.000
61	A	85	SER	0	-0.023	-0.043	12.784	-0.970	-0.970	0.000	0.000	0.000	0.000
62	A	86	ASP	-1	-0.846	-0.916	13.953	14.104	14.104	0.000	0.000	0.000	0.000
63	A	87	ASN	0	0.019	0.001	15.849	-1.454	-1.454	0.000	0.000	0.000	0.000
64	A	88	ILE	0	-0.030	-0.015	11.975	-0.621	-0.621	0.000	0.000	0.000	0.000
65	A	89	GLY	0	0.017	0.004	16.536	-0.675	-0.675	0.000	0.000	0.000	0.000
66	A	90	ASN	0	-0.029	-0.025	19.183	-1.433	-1.433	0.000	0.000	0.000	0.000
67	A	91	PHE	0	-0.012	-0.005	18.756	-0.592	-0.592	0.000	0.000	0.000	0.000
68	A	92	LEU	0	-0.002	-0.014	17.229	-0.566	-0.566	0.000	0.000	0.000	0.000
69	A	93	LYS	1	0.871	0.945	21.451	-12.289	-12.289	0.000	0.000	0.000	0.000
70	A	94	GLN	0	-0.006	-0.005	24.431	-0.470	-0.470	0.000	0.000	0.000	0.000
71	A	95	THR	0	-0.076	-0.039	23.252	-0.340	-0.340	0.000	0.000	0.000	0.000
72	A	96	PRO	0	0.036	0.038	22.449	0.647	0.647	0.000	0.000	0.000	0.000
73	A	97	VAL	0	-0.013	-0.009	19.098	-0.268	-0.268	0.000	0.000	0.000	0.000
74	A	98	SER	0	-0.019	0.001	22.189	-0.100	-0.100	0.000	0.000	0.000	0.000
75	A	99	TYR	0	0.033	0.006	16.661	-0.610	-0.610	0.000	0.000	0.000	0.000
76	A	100	PRO	0	0.012	0.006	14.145	0.110	0.110	0.000	0.000	0.000	0.000
77	A	101	ILE	0	0.026	0.034	13.786	0.507	0.507	0.000	0.000	0.000	0.000
78	A	102	TRP	0	0.000	-0.013	7.883	0.409	0.409	0.000	0.000	0.000	0.000
79	A	103	ARG	1	0.869	0.941	7.835	-30.207	-30.207	0.000	0.000	0.000	0.000
80	A	104	TYR	0	-0.065	-0.052	1.614	-33.861	-39.959	23.778	-10.193	-7.486	0.099
81	A	105	THR	0	-0.047	-0.044	2.609	-5.941	-4.118	1.240	-1.130	-1.932	-0.008
82	A	106	GLY	0	0.031	0.025	2.424	-2.645	-1.069	6.626	-4.640	-3.562	0.025
83	A	107	ALA	0	0.019	0.013	2.692	-14.574	-17.743	0.303	4.619	-1.754	0.017
84	A	108	ASN	0	-0.013	-0.010	3.890	-15.867	-15.235	0.001	-0.348	-0.285	0.002
85	A	109	SER	0	0.072	0.040	5.143	0.140	0.232	-0.001	-0.001	-0.090	0.000
86	A	110	ARG	1	0.944	0.964	6.554	-25.160	-25.160	0.000	0.000	0.000	0.000
87	A	111	ASN	0	0.040	0.015	6.350	-6.213	-6.213	0.000	0.000	0.000	0.000
88	A	112	PHE	0	0.068	0.040	3.265	-6.633	-4.878	0.073	-0.697	-1.130	0.004
89	A	113	MET	0	-0.038	0.011	5.188	-6.639	-6.660	-0.001	-0.002	0.024	0.000
90	A	114	LYS	1	0.920	0.961	8.863	-29.745	-29.745	0.000	0.000	0.000	0.000
91	A	115	THR	0	-0.044	-0.018	6.857	-2.988	-2.988	0.000	0.000	0.000	0.000
92	A	116	TYR	0	0.014	0.003	5.815	-4.348	-4.348	0.000	0.000	0.000	0.000
93	A	117	GLY	0	0.029	0.010	11.537	-2.003	-2.003	0.000	0.000	0.000	0.000
94	A	118	ASN	0	-0.052	-0.012	12.065	-2.292	-2.292	0.000	0.000	0.000	0.000
95	A	119	THR	0	0.003	-0.019	12.701	1.809	1.809	0.000	0.000	0.000	0.000
96	A	120	VAL	0	0.023	0.011	14.312	0.625	0.625	0.000	0.000	0.000	0.000
97	A	121	GLY	0	-0.031	-0.019	12.525	0.263	0.263	0.000	0.000	0.000	0.000
98	A	122	VAL	0	-0.002	-0.002	13.340	-0.116	-0.116	0.000	0.000	0.000	0.000
99	A	123	LEU	0	0.016	0.005	12.356	0.998	0.998	0.000	0.000	0.000	0.000
100	A	124	PRO	0	0.063	0.002	16.488	-0.591	-0.591	0.000	0.000	0.000	0.000
101	A	125	PHE	0	-0.028	-0.008	13.731	-0.025	-0.025	0.000	0.000	0.000	0.000
102	A	126	THR	0	0.039	0.020	14.954	1.239	1.239	0.000	0.000	0.000	0.000
103	A	127	VAL	0	-0.023	0.004	13.923	-0.735	-0.735	0.000	0.000	0.000	0.000
104	A	128	VAL	0	0.019	0.011	16.684	0.338	0.338	0.000	0.000	0.000	0.000
105	A	129	GLU	-1	-0.746	-0.854	13.504	20.617	20.617	0.000	0.000	0.000	0.000
106	A	130	ALA	0	0.075	0.039	17.935	-0.363	-0.363	0.000	0.000	0.000	0.000
107	A	131	PRO	0	-0.011	-0.006	14.977	-0.173	-0.173	0.000	0.000	0.000	0.000
108	A	132	LYS	1	0.925	0.954	17.063	-13.732	-13.732	0.000	0.000	0.000	0.000
109	A	133	CYS	0	-0.005	0.001	19.788	-0.602	-0.602	0.000	0.000	0.000	0.000
110	A	134	GLY	0	0.001	0.015	18.183	-0.258	-0.258	0.000	0.000	0.000	0.000
111	A	135	TYR	0	-0.009	-0.015	18.880	0.517	0.517	0.000	0.000	0.000	0.000
112	A	136	ARG	1	0.816	0.883	11.812	-21.126	-21.126	0.000	0.000	0.000	0.000
113	A	137	GLN	0	0.030	0.035	18.953	-0.476	-0.476	0.000	0.000	0.000	0.000
114	A	138	THR	0	-0.001	-0.006	18.089	0.290	0.290	0.000	0.000	0.000	0.000
115	A	139	ILE	0	-0.010	-0.008	19.763	-0.675	-0.675	0.000	0.000	0.000	0.000
116	A	140	THR	0	-0.032	-0.010	22.076	0.318	0.318	0.000	0.000	0.000	0.000
117	A	141	GLY	0	0.017	-0.001	23.953	-0.654	-0.654	0.000	0.000	0.000	0.000
118	A	142	GLU	-1	-0.824	-0.874	24.106	11.097	11.097	0.000	0.000	0.000	0.000
119	A	143	VAL	0	-0.016	-0.011	20.460	-0.228	-0.228	0.000	0.000	0.000	0.000
120	A	144	ASN	0	0.003	-0.015	23.872	-0.057	-0.057	0.000	0.000	0.000	0.000
121	A	145	GLU	-1	-0.788	-0.909	26.628	10.295	10.295	0.000	0.000	0.000	0.000
122	A	146	LYS	1	0.842	0.919	28.425	-9.416	-9.416	0.000	0.000	0.000	0.000
123	A	147	SER	0	-0.008	-0.011	25.882	0.051	0.051	0.000	0.000	0.000	0.000
124	A	148	LEU	0	0.015	0.002	21.626	0.275	0.275	0.000	0.000	0.000	0.000
125	A	149	THR	0	-0.041	-0.028	25.067	0.116	0.116	0.000	0.000	0.000	0.000
126	A	150	ASP	-1	-0.833	-0.884	27.796	9.732	9.732	0.000	0.000	0.000	0.000
127	A	151	ALA	0	0.034	0.018	23.291	0.000	0.000	0.000	0.000	0.000	0.000
128	A	152	VAL	0	0.013	0.006	22.167	0.223	0.223	0.000	0.000	0.000	0.000
129	A	153	LYS	1	0.960	0.985	24.441	-9.137	-9.137	0.000	0.000	0.000	0.000
130	A	154	LEU	0	-0.010	0.001	26.215	-0.252	-0.252	0.000	0.000	0.000	0.000
131	A	155	ALA	0	0.000	0.004	21.945	0.001	0.001	0.000	0.000	0.000	0.000
132	A	156	HIS	0	0.008	-0.014	24.016	-0.081	-0.081	0.000	0.000	0.000	0.000
133	A	157	SER	0	-0.078	-0.015	25.936	-0.182	-0.182	0.000	0.000	0.000	0.000
134	A	158	LYS	1	0.844	0.921	24.513	-10.977	-10.977	0.000	0.000	0.000	0.000

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