FMO DATABASE

FMODB ID: KG5V3

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1652292.561704
FMO2-HF: Nuclear repulsion	1586918.520103
FMO2-HF: Total energy	-65374.041601
FMO2-MP2: Total energy	-65562.852493

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.
-39.666	-37.965	13.427	-6.052	-9.074	0.021

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 : 0.009 / q_NPA : 0.010

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	0.919	0.958	3.114	-5.073	-2.363	0.153	-1.239	-1.624	-0.001
4	A	3	LEU	0	0.065	0.038	5.835	0.385	0.385	0.000	0.000	0.000	0.000
5	A	4	LEU	0	-0.109	-0.057	8.420	0.395	0.395	0.000	0.000	0.000	0.000
6	A	5	GLU	-1	-0.923	-0.954	11.878	-0.482	-0.482	0.000	0.000	0.000	0.000
7	A	6	ASN	0	0.026	0.001	15.118	0.082	0.082	0.000	0.000	0.000	0.000
8	A	7	SER	0	0.060	0.034	17.903	-0.043	-0.043	0.000	0.000	0.000	0.000
9	A	8	SER	0	0.037	0.006	21.045	-0.014	-0.014	0.000	0.000	0.000	0.000
10	A	9	PHE	0	-0.025	-0.021	15.859	-0.001	-0.001	0.000	0.000	0.000	0.000
11	A	10	GLU	-1	-0.954	-0.961	18.536	-0.480	-0.480	0.000	0.000	0.000	0.000
12	A	11	ALA	0	0.010	0.006	20.228	-0.010	-0.010	0.000	0.000	0.000	0.000
13	A	12	ILE	0	-0.023	-0.012	21.738	0.008	0.008	0.000	0.000	0.000	0.000
14	A	13	ASN	0	0.020	-0.001	17.016	0.009	0.009	0.000	0.000	0.000	0.000
15	A	14	SER	0	-0.057	-0.020	21.242	-0.012	-0.012	0.000	0.000	0.000	0.000
16	A	15	GLN	0	-0.046	-0.033	24.157	0.028	0.028	0.000	0.000	0.000	0.000
17	A	16	LEU	0	-0.059	0.005	21.355	0.025	0.025	0.000	0.000	0.000	0.000
18	A	17	THR	0	0.032	0.012	24.053	-0.039	-0.039	0.000	0.000	0.000	0.000
19	A	18	VAL	0	-0.015	0.000	26.316	0.032	0.032	0.000	0.000	0.000	0.000
20	A	19	GLU	-1	-0.869	-0.942	25.947	-0.444	-0.444	0.000	0.000	0.000	0.000
21	A	20	THR	0	-0.123	-0.094	29.705	0.024	0.024	0.000	0.000	0.000	0.000
22	A	21	GLY	0	0.035	-0.008	32.525	0.013	0.013	0.000	0.000	0.000	0.000
23	A	22	ASP	-1	-0.979	-0.969	31.170	-0.328	-0.328	0.000	0.000	0.000	0.000
24	A	23	ALA	0	-0.057	0.008	29.480	-0.005	-0.005	0.000	0.000	0.000	0.000
25	A	24	HIS	0	-0.001	0.001	25.525	-0.016	-0.016	0.000	0.000	0.000	0.000
26	A	25	ILE	0	0.004	0.003	20.478	0.019	0.019	0.000	0.000	0.000	0.000
27	A	26	ILE	0	-0.023	-0.001	23.360	-0.007	-0.007	0.000	0.000	0.000	0.000
28	A	27	GLY	0	0.058	-0.024	19.983	-0.009	-0.009	0.000	0.000	0.000	0.000
29	A	28	ARG	1	0.860	0.943	13.940	1.034	1.034	0.000	0.000	0.000	0.000
30	A	29	ILE	0	-0.026	-0.018	16.422	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	30	GLU	-1	-0.774	-0.855	11.369	-1.598	-1.598	0.000	0.000	0.000	0.000
32	A	31	SER	0	-0.014	-0.029	12.557	0.099	0.099	0.000	0.000	0.000	0.000
33	A	32	TYR	0	0.021	-0.005	6.430	-0.263	-0.263	0.000	0.000	0.000	0.000
34	A	33	SER	0	-0.045	-0.019	7.938	0.626	0.626	0.000	0.000	0.000	0.000
35	A	34	CYS	0	0.000	-0.006	5.131	0.099	0.099	0.000	0.000	0.000	0.000
36	A	35	LYS	1	0.935	0.967	2.138	-18.833	-22.367	12.998	-4.157	-5.308	0.026
37	A	36	PRO	0	0.001	0.009	4.378	-1.639	-1.410	-0.001	-0.028	-0.200	0.000
38	A	37	LEU	0	0.024	0.029	4.130	0.430	0.628	-0.001	-0.016	-0.181	0.000
39	A	38	SER	0	0.025	0.015	6.721	-0.380	-0.380	0.000	0.000	0.000	0.000
40	A	39	ASP	-1	-0.855	-0.949	9.870	1.108	1.108	0.000	0.000	0.000	0.000
41	A	40	LYS	1	0.887	0.932	12.853	-0.939	-0.939	0.000	0.000	0.000	0.000
42	A	41	CYS	0	-0.019	0.024	8.636	-0.176	-0.176	0.000	0.000	0.000	0.000
43	A	42	SER	0	0.028	0.007	11.920	0.008	0.008	0.000	0.000	0.000	0.000
44	A	43	ARG	1	0.961	0.972	12.579	-0.251	-0.251	0.000	0.000	0.000	0.000
45	A	44	LYS	1	0.941	0.968	9.009	-1.225	-1.225	0.000	0.000	0.000	0.000
46	A	45	THR	0	0.026	0.020	8.537	0.006	0.006	0.000	0.000	0.000	0.000
47	A	46	LEU	0	0.026	0.023	10.020	-0.088	-0.088	0.000	0.000	0.000	0.000
48	A	47	PHE	0	0.017	0.005	3.169	-0.615	-0.176	0.028	-0.099	-0.367	0.000
49	A	48	TYR	0	-0.025	-0.062	3.607	-0.718	-0.448	0.003	-0.038	-0.235	0.000
50	A	49	LEU	0	-0.021	0.010	6.594	-0.445	-0.445	0.000	0.000	0.000	0.000
51	A	50	ILE	0	0.062	0.037	7.847	-0.224	-0.224	0.000	0.000	0.000	0.000
52	A	51	ALA	0	-0.035	-0.018	2.670	-0.884	-0.370	0.191	-0.211	-0.494	-0.001
53	A	52	THR	0	-0.045	-0.032	4.783	-1.358	-1.277	-0.001	-0.004	-0.075	0.000
54	A	53	LEU	0	-0.006	0.013	6.803	-0.168	-0.168	0.000	0.000	0.000	0.000
55	A	54	ASN	0	0.036	0.017	6.063	0.130	0.130	0.000	0.000	0.000	0.000
56	A	55	GLU	-1	-0.965	-0.982	2.966	-10.830	-10.134	0.058	-0.258	-0.496	-0.003
57	A	56	SER	0	-0.061	-0.040	5.785	0.378	0.378	0.000	0.000	0.000	0.000
58	A	57	PHE	0	0.032	0.011	9.342	0.213	0.213	0.000	0.000	0.000	0.000
59	A	58	ARG	1	0.843	0.961	4.204	6.798	6.896	-0.001	-0.002	-0.094	0.000
60	A	59	PRO	0	-0.084	-0.063	10.157	-0.005	-0.005	0.000	0.000	0.000	0.000
61	A	60	ASP	-1	-0.897	-0.947	12.341	-1.081	-1.081	0.000	0.000	0.000	0.000
62	A	61	TYR	0	-0.009	-0.012	13.203	0.152	0.152	0.000	0.000	0.000	0.000
63	A	62	ASP	-1	-0.858	-0.904	10.838	-1.459	-1.459	0.000	0.000	0.000	0.000
64	A	63	PHE	0	0.032	-0.002	10.497	0.203	0.203	0.000	0.000	0.000	0.000
65	A	64	SER	0	-0.094	-0.081	9.941	0.171	0.171	0.000	0.000	0.000	0.000
66	A	65	THR	0	-0.067	-0.035	11.182	0.153	0.153	0.000	0.000	0.000	0.000
67	A	66	ALA	0	-0.005	0.023	13.190	0.064	0.064	0.000	0.000	0.000	0.000
68	A	67	ARG	1	0.940	0.963	14.991	0.255	0.255	0.000	0.000	0.000	0.000
69	A	68	SER	0	-0.064	-0.059	16.511	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	69	HIS	0	-0.135	-0.093	17.508	0.031	0.031	0.000	0.000	0.000	0.000
71	A	70	GLU	-1	-0.715	-0.825	17.193	-0.373	-0.373	0.000	0.000	0.000	0.000
72	A	71	PHE	0	-0.052	-0.028	12.504	-0.038	-0.038	0.000	0.000	0.000	0.000
73	A	72	SER	0	-0.002	0.008	17.444	0.049	0.049	0.000	0.000	0.000	0.000
74	A	73	ARG	1	0.822	0.903	18.642	-0.111	-0.111	0.000	0.000	0.000	0.000
75	A	74	GLU	-1	-0.859	-0.933	19.994	-0.144	-0.144	0.000	0.000	0.000	0.000
76	A	75	PRO	0	-0.044	-0.018	22.349	0.024	0.024	0.000	0.000	0.000	0.000
77	A	76	SER	0	-0.002	-0.005	25.070	0.015	0.015	0.000	0.000	0.000	0.000
78	A	77	LEU	0	0.096	0.049	23.230	-0.019	-0.019	0.000	0.000	0.000	0.000
79	A	78	SER	0	0.003	-0.012	25.423	-0.018	-0.018	0.000	0.000	0.000	0.000
80	A	79	TRP	0	-0.015	-0.001	25.768	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	80	VAL	0	0.059	0.032	21.789	-0.013	-0.013	0.000	0.000	0.000	0.000
82	A	81	VAL	0	-0.004	0.010	25.120	-0.022	-0.022	0.000	0.000	0.000	0.000
83	A	82	ASN	0	-0.027	-0.023	26.807	-0.013	-0.013	0.000	0.000	0.000	0.000
84	A	83	ALA	0	0.026	0.020	26.049	-0.007	-0.007	0.000	0.000	0.000	0.000
85	A	84	VAL	0	0.015	0.010	23.071	-0.013	-0.013	0.000	0.000	0.000	0.000
86	A	85	ASN	0	0.005	0.000	26.046	-0.020	-0.020	0.000	0.000	0.000	0.000
87	A	86	CYS	0	-0.067	-0.033	29.307	0.003	0.003	0.000	0.000	0.000	0.000
88	A	87	SER	0	0.015	0.016	26.975	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	88	LEU	0	0.022	0.000	24.464	-0.007	-0.007	0.000	0.000	0.000	0.000
90	A	89	PHE	0	-0.054	-0.012	28.503	0.003	0.003	0.000	0.000	0.000	0.000
91	A	90	SER	0	-0.052	-0.025	31.507	0.003	0.003	0.000	0.000	0.000	0.000
92	A	91	ALA	0	0.006	0.012	28.720	0.003	0.003	0.000	0.000	0.000	0.000
93	A	92	VAL	0	0.019	0.009	28.261	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	93	ARG	1	0.934	0.967	31.286	0.190	0.190	0.000	0.000	0.000	0.000
95	A	94	GLU	-1	-0.958	-0.996	34.470	-0.134	-0.134	0.000	0.000	0.000	0.000
96	A	95	ASP	-1	-0.851	-0.911	32.798	-0.189	-0.189	0.000	0.000	0.000	0.000
97	A	96	PHE	0	-0.041	-0.031	27.648	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	97	LYS	1	0.891	0.954	32.039	0.111	0.111	0.000	0.000	0.000	0.000
99	A	98	ASP	-1	-0.892	-0.958	33.347	-0.123	-0.123	0.000	0.000	0.000	0.000
100	A	99	LEU	0	0.025	0.025	25.939	0.005	0.005	0.000	0.000	0.000	0.000
101	A	100	LYS	1	0.922	0.975	28.199	0.118	0.118	0.000	0.000	0.000	0.000
102	A	101	PRO	0	-0.026	-0.031	28.468	0.003	0.003	0.000	0.000	0.000	0.000
103	A	102	GLN	0	0.048	0.040	26.320	0.009	0.009	0.000	0.000	0.000	0.000
104	A	103	LEU	0	0.021	-0.001	22.267	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	104	TRP	0	-0.039	-0.044	22.780	0.002	0.002	0.000	0.000	0.000	0.000
106	A	105	ASN	0	0.003	0.003	25.021	0.023	0.023	0.000	0.000	0.000	0.000
107	A	106	ALA	0	0.030	0.024	22.143	0.022	0.022	0.000	0.000	0.000	0.000
108	A	107	VAL	0	-0.007	-0.013	19.312	0.013	0.013	0.000	0.000	0.000	0.000
109	A	108	ASP	-1	-0.886	-0.955	20.581	0.056	0.056	0.000	0.000	0.000	0.000
110	A	109	GLU	-1	-0.966	-0.976	22.335	0.027	0.027	0.000	0.000	0.000	0.000
111	A	110	GLU	-1	-0.850	-0.889	15.785	0.057	0.057	0.000	0.000	0.000	0.000
112	A	111	ILE	0	-0.079	-0.051	14.210	0.085	0.085	0.000	0.000	0.000	0.000
113	A	112	CYS	0	-0.040	-0.008	18.149	0.046	0.046	0.000	0.000	0.000	0.000
114	A	113	LEU	0	0.089	0.027	20.304	0.018	0.018	0.000	0.000	0.000	0.000
115	A	114	ALA	0	-0.054	-0.022	22.035	0.002	0.002	0.000	0.000	0.000	0.000
116	A	115	GLU	-1	-0.804	-0.860	19.556	0.331	0.331	0.000	0.000	0.000	0.000
117	A	116	CYS	0	-0.119	-0.029	17.980	0.033	0.033	0.000	0.000	0.000	0.000
118	A	117	ASP	-1	-0.871	-0.924	16.197	0.212	0.212	0.000	0.000	0.000	0.000
119	A	118	ILE	0	0.017	0.002	16.657	-0.023	-0.023	0.000	0.000	0.000	0.000
120	A	119	TYR	0	-0.032	-0.030	14.766	0.081	0.081	0.000	0.000	0.000	0.000
121	A	120	SER	0	0.020	-0.004	17.285	-0.040	-0.040	0.000	0.000	0.000	0.000
122	A	121	TYR	0	0.007	0.003	14.793	-0.006	-0.006	0.000	0.000	0.000	0.000
123	A	122	ASN	0	-0.060	-0.042	16.928	-0.031	-0.031	0.000	0.000	0.000	0.000
124	A	123	PRO	0	0.005	0.014	18.649	0.032	0.032	0.000	0.000	0.000	0.000
125	A	124	ASP	-1	-0.783	-0.878	20.031	-0.193	-0.193	0.000	0.000	0.000	0.000
126	A	125	LEU	0	-0.023	-0.033	22.734	-0.022	-0.022	0.000	0.000	0.000	0.000
127	A	126	ASP	-1	-0.965	-0.981	24.347	-0.264	-0.264	0.000	0.000	0.000	0.000
128	A	127	SER	0	-0.077	-0.032	19.691	-0.011	-0.011	0.000	0.000	0.000	0.000
129	A	128	ASP	-1	-0.867	-0.942	19.651	-0.524	-0.524	0.000	0.000	0.000	0.000
130	A	129	PRO	0	-0.046	-0.021	16.723	0.006	0.006	0.000	0.000	0.000	0.000
131	A	130	PHE	0	-0.085	-0.043	16.408	-0.030	-0.030	0.000	0.000	0.000	0.000
132	A	131	GLY	0	0.002	0.023	21.123	0.018	0.018	0.000	0.000	0.000	0.000
133	A	132	GLU	-1	-0.976	-0.994	24.490	-0.285	-0.285	0.000	0.000	0.000	0.000
134	A	133	ASP	-1	-0.767	-0.855	24.472	-0.428	-0.428	0.000	0.000	0.000	0.000
135	A	134	GLY	0	-0.040	-0.019	27.402	0.008	0.008	0.000	0.000	0.000	0.000
136	A	135	SER	0	-0.099	-0.041	26.358	0.019	0.019	0.000	0.000	0.000	0.000
137	A	136	LEU	0	-0.050	-0.038	28.586	0.016	0.016	0.000	0.000	0.000	0.000
138	A	137	TRP	0	-0.025	-0.009	24.262	0.010	0.010	0.000	0.000	0.000	0.000
139	A	138	SER	0	0.021	-0.004	22.189	-0.033	-0.033	0.000	0.000	0.000	0.000
140	A	139	PHE	0	-0.013	-0.006	20.104	0.041	0.041	0.000	0.000	0.000	0.000
141	A	140	ASN	0	0.056	0.044	15.797	-0.133	-0.133	0.000	0.000	0.000	0.000
142	A	141	TYR	0	-0.006	0.002	17.188	0.043	0.043	0.000	0.000	0.000	0.000
143	A	142	PHE	0	0.001	-0.006	10.594	-0.048	-0.048	0.000	0.000	0.000	0.000
144	A	143	PHE	0	0.010	0.002	14.641	0.094	0.094	0.000	0.000	0.000	0.000
145	A	144	TYR	0	-0.006	-0.016	9.512	0.005	0.005	0.000	0.000	0.000	0.000
146	A	145	ASN	0	0.061	0.031	13.814	0.115	0.115	0.000	0.000	0.000	0.000
147	A	146	LYS	1	0.940	0.949	12.982	-0.257	-0.257	0.000	0.000	0.000	0.000
148	A	147	ARG	1	0.776	0.851	13.790	-0.238	-0.238	0.000	0.000	0.000	0.000
149	A	148	LEU	0	-0.047	-0.029	14.692	0.108	0.108	0.000	0.000	0.000	0.000
150	A	149	LYS	1	0.874	0.951	9.500	-1.113	-1.113	0.000	0.000	0.000	0.000
151	A	150	ARG	1	0.922	0.971	9.748	-0.113	-0.113	0.000	0.000	0.000	0.000
152	A	151	ILE	0	0.014	-0.006	8.369	-0.002	-0.002	0.000	0.000	0.000	0.000
153	A	152	VAL	0	0.015	0.020	11.534	-0.117	-0.117	0.000	0.000	0.000	0.000
154	A	153	PHE	0	-0.031	-0.016	11.476	0.062	0.062	0.000	0.000	0.000	0.000
155	A	154	PHE	0	0.023	-0.004	13.576	-0.013	-0.013	0.000	0.000	0.000	0.000
156	A	155	SER	0	-0.009	-0.016	15.820	0.039	0.039	0.000	0.000	0.000	0.000
157	A	156	CYS	0	-0.013	0.018	17.756	-0.013	-0.013	0.000	0.000	0.000	0.000
158	A	157	ARG	1	0.901	0.926	20.908	0.524	0.524	0.000	0.000	0.000	0.000
159	A	158	SER	0	0.047	0.049	23.907	0.011	0.011	0.000	0.000	0.000	0.000

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