FMO DATABASE

FMODB ID: 5J65Z

Calculation Name: 3NR5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NR5

Chain ID: A

ChEMBL ID:

UniProt ID: Q9H063

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	159
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1656990.147439
FMO2-HF: Nuclear repulsion	1591614.672138
FMO2-HF: Total energy	-65375.475301
FMO2-MP2: Total energy	-65564.375429

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:0:HIS)

Summations of interaction energy for fragment #1(A:0:HIS)

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.
-95.646	-95.303	33.57	-14.94	-18.966	-0.036

Interaction energy analysis for fragmet #1(A:0:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.004 / q_NPA : -0.005

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	2	LYS	1	0.854	0.914	3.443	1.450	4.190	0.316	-1.403	-1.652	0.002
4	A	3	LEU	0	0.062	0.049	5.898	0.281	0.281	0.000	0.000	0.000	0.000
5	A	4	LEU	0	-0.093	-0.045	8.098	0.653	0.653	0.000	0.000	0.000	0.000
6	A	5	GLU	-1	-0.850	-0.923	11.763	-0.467	-0.467	0.000	0.000	0.000	0.000
7	A	6	ASN	0	-0.007	-0.011	14.671	0.126	0.126	0.000	0.000	0.000	0.000
8	A	7	SER	0	0.031	-0.007	17.627	-0.049	-0.049	0.000	0.000	0.000	0.000
9	A	8	SER	0	-0.009	0.004	20.572	-0.001	-0.001	0.000	0.000	0.000	0.000
10	A	9	PHE	0	0.001	-0.002	15.663	-0.004	-0.004	0.000	0.000	0.000	0.000
11	A	10	GLU	-1	-0.865	-0.910	17.400	-0.664	-0.664	0.000	0.000	0.000	0.000
12	A	11	ALA	0	0.022	0.019	19.520	-0.007	-0.007	0.000	0.000	0.000	0.000
13	A	12	ILE	0	-0.017	0.010	21.207	0.008	0.008	0.000	0.000	0.000	0.000
14	A	13	ASN	0	-0.019	-0.039	16.680	-0.054	-0.054	0.000	0.000	0.000	0.000
15	A	14	SER	0	-0.055	-0.028	20.501	-0.008	-0.008	0.000	0.000	0.000	0.000
16	A	15	GLN	0	-0.079	-0.060	23.306	0.067	0.067	0.000	0.000	0.000	0.000
17	A	16	LEU	0	-0.050	-0.002	20.310	0.034	0.034	0.000	0.000	0.000	0.000
18	A	17	THR	0	0.020	-0.002	23.295	-0.049	-0.049	0.000	0.000	0.000	0.000
19	A	18	VAL	0	0.016	0.019	25.676	0.044	0.044	0.000	0.000	0.000	0.000
20	A	19	GLU	-1	-0.950	-0.972	24.220	-0.641	-0.641	0.000	0.000	0.000	0.000
21	A	20	THR	0	-0.093	-0.042	28.668	0.031	0.031	0.000	0.000	0.000	0.000
22	A	21	GLY	0	0.041	0.002	32.133	0.019	0.019	0.000	0.000	0.000	0.000
23	A	22	ASP	-1	-0.961	-0.968	31.209	-0.442	-0.442	0.000	0.000	0.000	0.000
24	A	23	ALA	0	-0.074	-0.031	28.787	-0.019	-0.019	0.000	0.000	0.000	0.000
25	A	24	HIS	0	0.034	0.005	24.779	-0.030	-0.030	0.000	0.000	0.000	0.000
26	A	25	ILE	0	0.010	0.009	19.599	0.023	0.023	0.000	0.000	0.000	0.000
27	A	26	ILE	0	-0.020	-0.002	22.855	-0.015	-0.015	0.000	0.000	0.000	0.000
28	A	27	GLY	0	0.027	-0.023	19.329	-0.015	-0.015	0.000	0.000	0.000	0.000
29	A	28	ARG	1	0.857	0.922	12.121	1.784	1.784	0.000	0.000	0.000	0.000
30	A	29	ILE	0	-0.012	-0.007	15.604	-0.018	-0.018	0.000	0.000	0.000	0.000
31	A	30	GLU	-1	-0.764	-0.820	10.447	-2.810	-2.810	0.000	0.000	0.000	0.000
32	A	31	SER	0	-0.001	-0.045	12.145	0.114	0.114	0.000	0.000	0.000	0.000
33	A	32	TYR	0	0.007	-0.024	5.797	-0.475	-0.475	0.000	0.000	0.000	0.000
34	A	33	SER	0	-0.007	0.006	7.526	0.065	0.065	0.000	0.000	0.000	0.000
35	A	34	CYS	0	-0.037	-0.023	5.348	0.600	0.600	0.000	0.000	0.000	0.000
36	A	35	LYS	1	0.850	0.926	1.969	-51.700	-55.412	18.318	-5.503	-9.102	0.058
37	A	36	PRO	0	0.002	-0.006	4.000	-1.494	-1.354	-0.001	-0.006	-0.133	0.000
38	A	37	LEU	0	0.023	0.024	3.299	0.060	0.465	0.019	-0.092	-0.332	0.000
39	A	38	SER	0	0.006	-0.001	6.528	-0.240	-0.240	0.000	0.000	0.000	0.000
40	A	39	ASP	-1	-0.787	-0.909	9.846	0.638	0.638	0.000	0.000	0.000	0.000
41	A	40	LYS	1	0.897	0.945	12.588	-0.789	-0.789	0.000	0.000	0.000	0.000
42	A	41	CYS	0	-0.005	0.026	8.241	-0.158	-0.158	0.000	0.000	0.000	0.000
43	A	42	SER	0	0.031	0.011	11.528	-0.026	-0.026	0.000	0.000	0.000	0.000
44	A	43	ARG	1	0.940	0.963	12.242	0.082	0.082	0.000	0.000	0.000	0.000
45	A	44	LYS	1	0.862	0.923	8.590	-0.780	-0.780	0.000	0.000	0.000	0.000
46	A	45	THR	0	0.022	0.013	8.170	-0.086	-0.086	0.000	0.000	0.000	0.000
47	A	46	LEU	0	0.038	0.031	9.836	-0.158	-0.158	0.000	0.000	0.000	0.000
48	A	47	PHE	0	0.008	0.009	3.248	-0.746	-0.281	0.028	-0.120	-0.372	0.000
49	A	48	TYR	0	-0.020	-0.044	3.816	-0.741	-0.430	0.001	-0.036	-0.275	0.000
50	A	49	LEU	0	-0.029	0.015	6.403	-0.655	-0.655	0.000	0.000	0.000	0.000
51	A	50	ILE	0	0.064	0.032	7.372	-0.333	-0.333	0.000	0.000	0.000	0.000
52	A	51	ALA	0	-0.025	-0.015	2.513	-1.302	-0.652	0.449	-0.310	-0.788	-0.002
53	A	52	THR	0	-0.055	-0.049	3.987	-2.617	-2.328	0.000	-0.149	-0.139	-0.001
54	A	53	LEU	0	-0.015	0.012	6.105	-0.118	-0.118	0.000	0.000	0.000	0.000
55	A	54	ASN	0	0.021	-0.006	5.178	0.331	0.331	0.000	0.000	0.000	0.000
56	A	55	GLU	-1	-0.868	-0.923	1.772	-40.418	-41.605	14.442	-7.293	-5.961	-0.093
57	A	56	SER	0	-0.047	-0.037	5.378	0.994	1.026	-0.001	-0.001	-0.030	0.000
58	A	57	PHE	0	0.002	-0.002	8.864	0.518	0.518	0.000	0.000	0.000	0.000
59	A	58	ARG	1	0.849	0.951	3.554	10.144	10.354	-0.001	-0.027	-0.182	0.000
60	A	59	PRO	0	-0.083	-0.060	9.475	-0.045	-0.045	0.000	0.000	0.000	0.000
61	A	60	ASP	-1	-0.903	-0.950	11.616	-1.436	-1.436	0.000	0.000	0.000	0.000
62	A	61	TYR	0	-0.023	-0.017	12.553	0.208	0.208	0.000	0.000	0.000	0.000
63	A	62	ASP	-1	-0.824	-0.880	9.811	-2.135	-2.135	0.000	0.000	0.000	0.000
64	A	63	PHE	0	0.048	0.017	9.902	0.271	0.271	0.000	0.000	0.000	0.000
65	A	64	SER	0	-0.101	-0.087	9.586	0.185	0.185	0.000	0.000	0.000	0.000
66	A	65	THR	0	-0.065	-0.038	10.864	0.218	0.218	0.000	0.000	0.000	0.000
67	A	66	ALA	0	-0.015	0.020	13.128	0.094	0.094	0.000	0.000	0.000	0.000
68	A	67	ARG	1	0.804	0.874	14.542	0.494	0.494	0.000	0.000	0.000	0.000
69	A	68	SER	0	-0.047	-0.051	15.969	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	69	HIS	0	-0.110	-0.071	16.913	0.034	0.034	0.000	0.000	0.000	0.000
71	A	70	GLU	-1	-0.715	-0.819	17.093	-0.706	-0.706	0.000	0.000	0.000	0.000
72	A	71	PHE	0	-0.024	-0.014	12.118	-0.072	-0.072	0.000	0.000	0.000	0.000
73	A	72	SER	0	0.006	0.007	16.997	0.086	0.086	0.000	0.000	0.000	0.000
74	A	73	ARG	1	0.815	0.892	18.770	0.154	0.154	0.000	0.000	0.000	0.000
75	A	74	GLU	-1	-0.789	-0.881	19.720	-0.396	-0.396	0.000	0.000	0.000	0.000
76	A	75	PRO	0	-0.053	-0.036	22.267	0.029	0.029	0.000	0.000	0.000	0.000
77	A	76	SER	0	-0.027	-0.019	25.249	0.025	0.025	0.000	0.000	0.000	0.000
78	A	77	LEU	0	0.088	0.049	23.214	-0.028	-0.028	0.000	0.000	0.000	0.000
79	A	78	SER	0	0.012	-0.006	25.371	-0.024	-0.024	0.000	0.000	0.000	0.000
80	A	79	TRP	0	-0.050	-0.005	25.532	0.010	0.010	0.000	0.000	0.000	0.000
81	A	80	VAL	0	0.053	0.033	21.277	-0.009	-0.009	0.000	0.000	0.000	0.000
82	A	81	VAL	0	0.001	0.004	24.651	-0.023	-0.023	0.000	0.000	0.000	0.000
83	A	82	ASN	0	-0.023	-0.020	26.174	-0.008	-0.008	0.000	0.000	0.000	0.000
84	A	83	ALA	0	0.049	0.035	25.573	0.000	0.000	0.000	0.000	0.000	0.000
85	A	84	VAL	0	0.008	0.021	22.107	-0.009	-0.009	0.000	0.000	0.000	0.000
86	A	85	ASN	0	0.013	0.002	25.137	-0.015	-0.015	0.000	0.000	0.000	0.000
87	A	86	CYS	0	-0.072	-0.039	28.347	0.017	0.017	0.000	0.000	0.000	0.000
88	A	87	SER	0	-0.006	-0.009	25.859	0.006	0.006	0.000	0.000	0.000	0.000
89	A	88	LEU	0	0.017	0.008	23.434	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	89	PHE	0	-0.014	-0.003	27.422	0.013	0.013	0.000	0.000	0.000	0.000
91	A	90	SER	0	-0.056	-0.037	30.437	0.018	0.018	0.000	0.000	0.000	0.000
92	A	91	ALA	0	-0.037	-0.011	27.917	0.004	0.004	0.000	0.000	0.000	0.000
93	A	92	VAL	0	0.012	0.012	27.286	-0.005	-0.005	0.000	0.000	0.000	0.000
94	A	93	ARG	1	0.826	0.886	30.487	0.292	0.292	0.000	0.000	0.000	0.000
95	A	94	GLU	-1	-0.812	-0.897	33.573	-0.258	-0.258	0.000	0.000	0.000	0.000
96	A	95	ASP	-1	-0.862	-0.912	32.595	-0.291	-0.291	0.000	0.000	0.000	0.000
97	A	96	PHE	0	-0.025	-0.020	26.756	-0.005	-0.005	0.000	0.000	0.000	0.000
98	A	97	LYS	1	0.745	0.857	31.313	0.215	0.215	0.000	0.000	0.000	0.000
99	A	98	ASP	-1	-0.822	-0.907	32.732	-0.216	-0.216	0.000	0.000	0.000	0.000
100	A	99	LEU	0	0.048	0.038	25.214	0.004	0.004	0.000	0.000	0.000	0.000
101	A	100	LYS	1	0.942	0.985	27.523	0.251	0.251	0.000	0.000	0.000	0.000
102	A	101	PRO	0	-0.024	-0.028	27.893	-0.004	-0.004	0.000	0.000	0.000	0.000
103	A	102	GLN	0	0.046	0.036	25.740	-0.021	-0.021	0.000	0.000	0.000	0.000
104	A	103	LEU	0	0.017	0.009	21.571	-0.010	-0.010	0.000	0.000	0.000	0.000
105	A	104	TRP	0	-0.025	-0.039	22.235	-0.021	-0.021	0.000	0.000	0.000	0.000
106	A	105	ASN	0	-0.063	-0.028	24.502	0.012	0.012	0.000	0.000	0.000	0.000
107	A	106	ALA	0	0.044	0.028	21.942	0.016	0.016	0.000	0.000	0.000	0.000
108	A	107	VAL	0	0.015	0.001	18.861	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	108	ASP	-1	-0.866	-0.934	20.196	-0.151	-0.151	0.000	0.000	0.000	0.000
110	A	109	GLU	-1	-0.896	-0.949	22.342	-0.155	-0.155	0.000	0.000	0.000	0.000
111	A	110	GLU	-1	-0.817	-0.861	15.506	-0.237	-0.237	0.000	0.000	0.000	0.000
112	A	111	ILE	0	-0.062	-0.037	14.564	0.045	0.045	0.000	0.000	0.000	0.000
113	A	112	CYS	0	-0.030	-0.004	18.463	0.042	0.042	0.000	0.000	0.000	0.000
114	A	113	LEU	0	0.069	0.017	20.282	0.001	0.001	0.000	0.000	0.000	0.000
115	A	114	ALA	0	-0.042	-0.020	22.165	-0.002	-0.002	0.000	0.000	0.000	0.000
116	A	115	GLU	-1	-0.804	-0.856	19.670	0.114	0.114	0.000	0.000	0.000	0.000
117	A	116	CYS	0	-0.113	-0.028	17.932	0.005	0.005	0.000	0.000	0.000	0.000
118	A	117	ASP	-1	-0.801	-0.873	16.132	-0.104	-0.104	0.000	0.000	0.000	0.000
119	A	118	ILE	0	-0.005	-0.006	17.057	-0.057	-0.057	0.000	0.000	0.000	0.000
120	A	119	TYR	0	-0.059	-0.042	14.813	0.087	0.087	0.000	0.000	0.000	0.000
121	A	120	SER	0	0.020	-0.010	17.200	-0.047	-0.047	0.000	0.000	0.000	0.000
122	A	121	TYR	0	-0.062	-0.045	14.464	-0.042	-0.042	0.000	0.000	0.000	0.000
123	A	122	ASN	0	-0.028	-0.023	16.575	-0.045	-0.045	0.000	0.000	0.000	0.000
124	A	123	PRO	0	0.028	0.028	18.283	0.044	0.044	0.000	0.000	0.000	0.000
125	A	124	ASP	-1	-0.760	-0.850	19.664	-0.377	-0.377	0.000	0.000	0.000	0.000
126	A	125	LEU	0	-0.014	-0.027	22.288	-0.027	-0.027	0.000	0.000	0.000	0.000
127	A	126	ASP	-1	-0.892	-0.911	23.327	-0.429	-0.429	0.000	0.000	0.000	0.000
128	A	127	SER	0	-0.049	-0.053	19.188	0.002	0.002	0.000	0.000	0.000	0.000
129	A	128	ASP	-1	-0.840	-0.913	18.999	-0.888	-0.888	0.000	0.000	0.000	0.000
130	A	129	PRO	0	-0.007	-0.002	15.412	0.041	0.041	0.000	0.000	0.000	0.000
131	A	130	PHE	0	-0.066	-0.030	15.100	-0.024	-0.024	0.000	0.000	0.000	0.000
132	A	131	GLY	0	0.002	0.016	20.132	0.046	0.046	0.000	0.000	0.000	0.000
133	A	132	GLU	-1	-0.986	-0.996	23.494	-0.412	-0.412	0.000	0.000	0.000	0.000
134	A	133	ASP	-1	-0.798	-0.865	23.417	-0.636	-0.636	0.000	0.000	0.000	0.000
135	A	134	GLY	0	-0.012	-0.002	26.419	0.017	0.017	0.000	0.000	0.000	0.000
136	A	135	SER	0	-0.110	-0.069	25.267	0.023	0.023	0.000	0.000	0.000	0.000
137	A	136	LEU	0	-0.030	-0.019	27.537	0.021	0.021	0.000	0.000	0.000	0.000
138	A	137	TRP	0	-0.037	-0.020	23.075	0.004	0.004	0.000	0.000	0.000	0.000
139	A	138	SER	0	0.026	0.003	21.293	-0.049	-0.049	0.000	0.000	0.000	0.000
140	A	139	PHE	0	-0.006	-0.004	19.179	0.055	0.055	0.000	0.000	0.000	0.000
141	A	140	ASN	0	0.022	0.009	15.048	-0.165	-0.165	0.000	0.000	0.000	0.000
142	A	141	TYR	0	0.006	0.007	16.228	0.024	0.024	0.000	0.000	0.000	0.000
143	A	142	PHE	0	0.000	-0.011	10.126	-0.104	-0.104	0.000	0.000	0.000	0.000
144	A	143	PHE	0	0.003	-0.006	14.546	0.150	0.150	0.000	0.000	0.000	0.000
145	A	144	TYR	0	-0.001	-0.013	9.243	-0.018	-0.018	0.000	0.000	0.000	0.000
146	A	145	ASN	0	0.040	0.011	14.071	0.158	0.158	0.000	0.000	0.000	0.000
147	A	146	LYS	1	0.902	0.926	13.095	0.109	0.109	0.000	0.000	0.000	0.000
148	A	147	ARG	1	0.787	0.866	13.972	-0.048	-0.048	0.000	0.000	0.000	0.000
149	A	148	LEU	0	-0.012	-0.019	14.902	0.137	0.137	0.000	0.000	0.000	0.000
150	A	149	LYS	1	0.838	0.931	9.583	-0.611	-0.611	0.000	0.000	0.000	0.000
151	A	150	ARG	1	0.864	0.946	9.839	0.225	0.225	0.000	0.000	0.000	0.000
152	A	151	ILE	0	0.007	-0.014	8.447	0.032	0.032	0.000	0.000	0.000	0.000
153	A	152	VAL	0	0.028	0.032	11.105	-0.189	-0.189	0.000	0.000	0.000	0.000
154	A	153	PHE	0	-0.028	-0.026	10.839	0.027	0.027	0.000	0.000	0.000	0.000
155	A	154	PHE	0	0.033	-0.001	12.866	0.035	0.035	0.000	0.000	0.000	0.000
156	A	155	SER	0	-0.018	-0.001	15.128	0.058	0.058	0.000	0.000	0.000	0.000
157	A	156	CYS	0	-0.023	0.003	16.858	0.017	0.017	0.000	0.000	0.000	0.000
158	A	157	ARG	1	0.850	0.907	20.282	0.775	0.775	0.000	0.000	0.000	0.000
159	A	158	SER	0	0.026	0.041	23.013	0.032	0.032	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:HIS)