FMO DATABASE

FMODB ID: 4J8VN

Calculation Name: 3N3W-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3N3W

Chain ID: A

ChEMBL ID:

UniProt ID: Q9PM40

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	144
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1328539.252906
FMO2-HF: Nuclear repulsion	1272936.742505
FMO2-HF: Total energy	-55602.510401
FMO2-MP2: Total energy	-55767.972413

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:1:MET)

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

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.
-15.396	-5.728	10.63	-5.326	-14.974	-0.019

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.035 / q_NPA : 0.031

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	3	ASN	0	0.018	0.014	3.097	-2.087	0.684	0.138	-1.384	-1.525	0.000
4	A	4	ILE	0	0.028	0.031	2.484	-0.821	0.054	4.165	-1.227	-3.813	-0.004
5	A	5	GLU	-1	-0.727	-0.886	4.027	-1.822	-1.559	0.005	-0.071	-0.197	0.000
6	A	6	LYS	1	0.862	0.929	7.250	1.109	1.109	0.000	0.000	0.000	0.000
7	A	7	LEU	0	0.002	0.042	5.519	-0.080	0.038	-0.001	-0.008	-0.109	0.000
8	A	8	GLU	-1	-0.804	-0.917	7.135	0.167	0.167	0.000	0.000	0.000	0.000
9	A	9	GLN	0	-0.012	-0.012	9.910	-0.020	-0.020	0.000	0.000	0.000	0.000
10	A	10	SER	0	-0.059	-0.032	11.427	-0.015	-0.015	0.000	0.000	0.000	0.000
11	A	11	LEU	0	-0.014	-0.010	9.699	-0.027	-0.027	0.000	0.000	0.000	0.000
12	A	12	THR	0	-0.098	-0.052	13.438	-0.028	-0.028	0.000	0.000	0.000	0.000
13	A	13	TYR	0	-0.038	-0.052	12.321	-0.036	-0.036	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.938	-0.965	10.526	-0.036	-0.036	0.000	0.000	0.000	0.000
15	A	15	PHE	0	-0.038	-0.023	9.047	0.019	0.019	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.780	0.877	10.990	-0.260	-0.260	0.000	0.000	0.000	0.000
17	A	17	ASP	-1	-0.817	-0.904	10.436	0.874	0.874	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.944	0.950	5.268	-2.020	-2.020	0.000	0.000	0.000	0.000
19	A	19	ASN	0	-0.078	-0.045	6.170	1.134	1.134	0.000	0.000	0.000	0.000
20	A	20	LEU	0	0.037	0.028	7.740	-0.070	-0.070	0.000	0.000	0.000	0.000
21	A	21	LEU	0	0.010	0.025	5.354	-0.233	-0.121	-0.001	-0.012	-0.099	0.000
22	A	22	ILE	0	0.016	-0.010	2.563	-1.787	-0.027	0.862	-0.415	-2.208	0.001
23	A	23	HIS	0	-0.073	-0.022	4.413	-1.048	-0.967	-0.001	-0.004	-0.076	0.000
24	A	24	ALA	0	0.007	-0.007	7.304	-0.261	-0.261	0.000	0.000	0.000	0.000
25	A	25	LEU	0	0.015	0.011	2.473	-1.030	-0.243	1.659	-0.512	-1.934	-0.005
26	A	26	THR	0	-0.049	-0.033	4.698	-0.447	-0.365	-0.001	-0.001	-0.080	0.000
27	A	27	HIS	0	0.142	0.084	6.333	0.314	0.314	0.000	0.000	0.000	0.000
28	A	28	LYS	1	0.809	0.862	9.355	0.148	0.148	0.000	0.000	0.000	0.000
29	A	29	SER	0	-0.061	-0.030	11.957	0.041	0.041	0.000	0.000	0.000	0.000
30	A	30	PHE	0	-0.028	0.001	6.677	0.014	0.014	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.909	0.956	7.944	-0.620	-0.620	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.973	0.990	12.051	-0.113	-0.113	0.000	0.000	0.000	0.000
33	A	33	SER	0	-0.051	-0.044	14.837	0.030	0.030	0.000	0.000	0.000	0.000
34	A	34	TYR	0	0.028	0.019	7.531	0.114	0.114	0.000	0.000	0.000	0.000
35	A	35	ASN	0	0.014	0.003	10.115	-0.020	-0.020	0.000	0.000	0.000	0.000
36	A	36	ASN	0	0.066	0.039	8.607	0.106	0.106	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.764	-0.856	10.676	-0.056	-0.056	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.920	0.955	14.397	-0.059	-0.059	0.000	0.000	0.000	0.000
39	A	39	LEU	0	-0.001	0.012	10.242	0.013	0.013	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.901	-0.957	13.114	-0.017	-0.017	0.000	0.000	0.000	0.000
41	A	41	PHE	0	0.022	0.028	14.432	0.015	0.015	0.000	0.000	0.000	0.000
42	A	42	LEU	0	-0.054	-0.022	16.802	0.004	0.004	0.000	0.000	0.000	0.000
43	A	43	GLY	0	0.046	0.006	15.832	0.004	0.004	0.000	0.000	0.000	0.000
44	A	44	ASP	-1	-0.871	-0.903	16.814	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	45	ALA	0	0.020	0.008	19.313	0.001	0.001	0.000	0.000	0.000	0.000
46	A	46	VAL	0	-0.046	-0.019	19.130	0.000	0.000	0.000	0.000	0.000	0.000
47	A	47	LEU	0	0.012	-0.005	16.671	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.828	-0.904	21.077	0.009	0.009	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.002	0.008	24.337	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	50	VAL	0	-0.031	-0.008	21.600	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	51	VAL	0	0.003	-0.003	23.293	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.014	0.009	25.996	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.785	-0.867	28.417	0.030	0.030	0.000	0.000	0.000	0.000
54	A	54	TYR	0	0.022	0.015	27.513	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	55	LEU	0	-0.032	-0.019	29.370	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	56	PHE	0	-0.006	-0.004	31.729	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	57	HIS	0	-0.030	-0.034	31.453	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	58	LYS	1	0.847	0.928	30.761	0.003	0.003	0.000	0.000	0.000	0.000
59	A	59	PHE	0	0.008	-0.005	33.544	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.008	0.024	37.502	0.000	0.000	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.849	0.915	39.399	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.857	-0.921	41.006	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	63	ALA	0	-0.054	-0.026	42.225	0.001	0.001	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.945	-0.960	43.150	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	65	GLY	0	-0.008	0.000	39.169	0.000	0.000	0.000	0.000	0.000	0.000
66	A	66	ASP	-1	-0.828	-0.920	35.539	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	67	LEU	0	0.053	0.008	33.272	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	68	SER	0	0.002	0.016	31.637	0.001	0.001	0.000	0.000	0.000	0.000
69	A	69	LYS	1	0.870	0.921	30.678	0.009	0.009	0.000	0.000	0.000	0.000
70	A	70	LEU	0	-0.016	-0.009	30.723	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	71	ARG	1	0.849	0.922	26.556	-0.012	-0.012	0.000	0.000	0.000	0.000
72	A	72	ALA	0	0.023	0.018	26.431	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	73	ALA	0	-0.031	-0.018	26.225	-0.005	-0.005	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.040	-0.026	24.562	-0.004	-0.004	0.000	0.000	0.000	0.000
75	A	75	VAL	0	0.017	0.008	21.757	0.001	0.001	0.000	0.000	0.000	0.000
76	A	76	ASN	0	-0.065	-0.018	21.864	-0.009	-0.009	0.000	0.000	0.000	0.000
77	A	77	GLU	-1	-0.809	-0.927	18.374	-0.088	-0.088	0.000	0.000	0.000	0.000
78	A	78	LYS	1	0.958	0.982	18.957	0.052	0.052	0.000	0.000	0.000	0.000
79	A	79	SER	0	-0.039	-0.036	20.615	-0.006	-0.006	0.000	0.000	0.000	0.000
80	A	80	PHE	0	0.059	0.032	16.526	0.005	0.005	0.000	0.000	0.000	0.000
81	A	81	ALA	0	0.029	0.014	15.646	0.000	0.000	0.000	0.000	0.000	0.000
82	A	82	LYS	1	0.808	0.911	16.241	0.038	0.038	0.000	0.000	0.000	0.000
83	A	83	ILE	0	0.015	0.011	15.578	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	84	ALA	0	0.028	0.034	12.207	0.018	0.018	0.000	0.000	0.000	0.000
85	A	85	ASN	0	0.020	0.000	12.402	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	86	SER	0	-0.107	-0.053	14.561	0.001	0.001	0.000	0.000	0.000	0.000
87	A	87	LEU	0	-0.018	-0.010	10.771	0.001	0.001	0.000	0.000	0.000	0.000
88	A	88	ASN	0	-0.025	-0.020	10.040	0.055	0.055	0.000	0.000	0.000	0.000
89	A	89	LEU	0	0.025	0.013	7.375	0.023	0.023	0.000	0.000	0.000	0.000
90	A	90	GLY	0	0.076	0.045	7.486	-0.160	-0.160	0.000	0.000	0.000	0.000
91	A	91	ASP	-1	-0.930	-0.946	7.578	-0.535	-0.535	0.000	0.000	0.000	0.000
92	A	92	PHE	0	-0.052	-0.039	3.322	-1.195	-0.098	0.621	-0.342	-1.376	0.001
93	A	93	ILE	0	-0.028	-0.010	2.723	-4.939	-3.570	0.989	-0.975	-1.384	-0.012
94	A	94	LEU	0	-0.031	0.003	2.447	-0.468	-0.149	2.196	-0.372	-2.143	0.000
95	A	95	MET	0	0.001	0.004	4.965	0.497	0.531	-0.001	-0.003	-0.030	0.000
96	A	96	SER	0	-0.005	-0.005	8.731	0.044	0.044	0.000	0.000	0.000	0.000
97	A	97	VAL	0	0.081	0.023	11.572	-0.026	-0.026	0.000	0.000	0.000	0.000
98	A	98	ALA	0	-0.031	-0.013	13.092	0.000	0.000	0.000	0.000	0.000	0.000
99	A	99	GLU	-1	-0.786	-0.880	12.538	-0.186	-0.186	0.000	0.000	0.000	0.000
100	A	100	GLU	-1	-0.893	-0.960	9.798	-0.543	-0.543	0.000	0.000	0.000	0.000
101	A	101	ASN	0	-0.033	-0.019	12.936	0.013	0.013	0.000	0.000	0.000	0.000
102	A	102	ASN	0	-0.119	-0.053	16.383	0.031	0.031	0.000	0.000	0.000	0.000
103	A	103	GLY	0	0.045	0.024	16.023	0.015	0.015	0.000	0.000	0.000	0.000
104	A	104	GLY	0	-0.024	-0.034	13.024	0.009	0.009	0.000	0.000	0.000	0.000
105	A	105	LYS	1	0.801	0.890	9.069	0.499	0.499	0.000	0.000	0.000	0.000
106	A	106	GLU	-1	-0.866	-0.950	11.707	-0.227	-0.227	0.000	0.000	0.000	0.000
107	A	107	LYS	1	0.777	0.893	14.885	0.218	0.218	0.000	0.000	0.000	0.000
108	A	108	PRO	0	-0.024	-0.008	14.868	-0.016	-0.016	0.000	0.000	0.000	0.000
109	A	109	SER	0	0.034	0.019	15.988	-0.002	-0.002	0.000	0.000	0.000	0.000
110	A	110	ILE	0	-0.016	0.010	10.495	0.002	0.002	0.000	0.000	0.000	0.000
111	A	111	LEU	0	-0.011	-0.005	11.026	-0.034	-0.034	0.000	0.000	0.000	0.000
112	A	112	SER	0	0.003	-0.004	12.262	0.032	0.032	0.000	0.000	0.000	0.000
113	A	113	ASP	-1	-0.859	-0.947	12.178	-0.127	-0.127	0.000	0.000	0.000	0.000
114	A	114	ALA	0	-0.026	-0.015	7.846	0.020	0.020	0.000	0.000	0.000	0.000
115	A	115	LEU	0	-0.005	-0.001	9.680	0.083	0.083	0.000	0.000	0.000	0.000
116	A	116	GLH	0	-0.041	-0.046	11.841	0.040	0.040	0.000	0.000	0.000	0.000
117	A	117	ALA	0	0.008	0.010	9.937	0.039	0.039	0.000	0.000	0.000	0.000
118	A	118	ILE	0	-0.027	-0.017	7.286	0.082	0.082	0.000	0.000	0.000	0.000
119	A	119	ILE	0	0.013	0.008	10.601	0.043	0.043	0.000	0.000	0.000	0.000
120	A	120	GLY	0	0.042	0.019	14.134	0.005	0.005	0.000	0.000	0.000	0.000
121	A	121	ALA	0	-0.048	-0.025	10.976	0.014	0.014	0.000	0.000	0.000	0.000
122	A	122	ILE	0	0.004	0.000	12.816	0.015	0.015	0.000	0.000	0.000	0.000
123	A	123	HIS	0	0.000	0.000	14.889	-0.016	-0.016	0.000	0.000	0.000	0.000
124	A	124	LEU	0	-0.047	-0.029	14.849	-0.008	-0.008	0.000	0.000	0.000	0.000
125	A	125	GLU	-1	-0.761	-0.841	12.976	0.351	0.351	0.000	0.000	0.000	0.000
126	A	126	ALA	0	-0.037	-0.016	16.937	-0.011	-0.011	0.000	0.000	0.000	0.000
127	A	127	GLY	0	0.035	0.038	19.426	-0.018	-0.018	0.000	0.000	0.000	0.000
128	A	128	PHE	0	0.015	0.001	20.706	0.003	0.003	0.000	0.000	0.000	0.000
129	A	129	GLU	-1	-0.869	-0.945	22.421	0.065	0.065	0.000	0.000	0.000	0.000
130	A	130	PHE	0	0.007	0.010	18.717	-0.006	-0.006	0.000	0.000	0.000	0.000
131	A	131	ALA	0	0.035	0.016	17.958	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	132	LYS	1	0.831	0.895	18.941	-0.044	-0.044	0.000	0.000	0.000	0.000
133	A	133	THR	0	-0.035	-0.021	21.423	-0.011	-0.011	0.000	0.000	0.000	0.000
134	A	134	ILE	0	-0.045	-0.020	14.963	-0.010	-0.010	0.000	0.000	0.000	0.000
135	A	135	ALA	0	0.027	0.006	18.139	-0.008	-0.008	0.000	0.000	0.000	0.000
136	A	136	LEU	0	-0.016	-0.012	19.036	-0.012	-0.012	0.000	0.000	0.000	0.000
137	A	137	ARG	1	0.909	0.974	16.023	-0.042	-0.042	0.000	0.000	0.000	0.000
138	A	138	LEU	0	-0.035	-0.021	14.844	-0.010	-0.010	0.000	0.000	0.000	0.000
139	A	139	ILE	0	0.039	0.024	18.921	-0.013	-0.013	0.000	0.000	0.000	0.000
140	A	140	GLU	-1	-0.910	-0.963	21.852	-0.005	-0.005	0.000	0.000	0.000	0.000
141	A	141	LYS	1	0.877	0.935	18.241	0.019	0.019	0.000	0.000	0.000	0.000
142	A	142	ASN	0	-0.071	-0.044	18.394	-0.018	-0.018	0.000	0.000	0.000	0.000
143	A	143	PHE	0	-0.043	-0.013	21.770	-0.008	-0.008	0.000	0.000	0.000	0.000
144	A	144	PRO	0	0.007	0.024	25.725	0.003	0.003	0.000	0.000	0.000	0.000

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