FMO DATABASE

FMODB ID: QVJGY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1323066.733703
FMO2-HF: Nuclear repulsion	1267465.336914
FMO2-HF: Total energy	-55601.396789
FMO2-MP2: Total energy	-55766.797701

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.
-10.133	-7.316	18.357	-5.698	-15.474	-0.022

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 : -0.006 / q_NPA : -0.011

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	0.017	0.006	3.047	-2.716	-0.338	0.156	-1.165	-1.369	-0.002
4	A	4	ILE	0	0.053	0.042	2.318	-0.059	-0.547	5.878	-1.374	-4.015	-0.007
5	A	5	GLU	-1	-0.813	-0.916	3.743	-1.780	-1.540	0.011	-0.069	-0.182	0.000
6	A	6	LYS	1	0.918	0.951	6.892	0.872	0.872	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.013	0.025	5.712	0.054	0.165	-0.001	-0.007	-0.102	0.000
8	A	8	GLU	-1	-0.799	-0.920	7.779	-0.695	-0.695	0.000	0.000	0.000	0.000
9	A	9	GLN	0	-0.036	-0.020	9.980	0.122	0.122	0.000	0.000	0.000	0.000
10	A	10	SER	0	-0.061	-0.027	11.190	0.057	0.057	0.000	0.000	0.000	0.000
11	A	11	LEU	0	-0.008	0.004	9.992	0.030	0.030	0.000	0.000	0.000	0.000
12	A	12	THR	0	-0.126	-0.063	13.869	0.024	0.024	0.000	0.000	0.000	0.000
13	A	13	TYR	0	-0.047	-0.071	12.556	0.020	0.020	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.951	-0.963	10.836	-0.367	-0.367	0.000	0.000	0.000	0.000
15	A	15	PHE	0	-0.030	-0.026	8.988	0.072	0.072	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.901	0.948	10.852	0.111	0.111	0.000	0.000	0.000	0.000
17	A	17	ASP	-1	-0.881	-0.934	10.606	-0.273	-0.273	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.995	0.980	5.449	0.305	0.305	0.000	0.000	0.000	0.000
19	A	19	ASN	0	-0.042	-0.042	6.317	-0.088	-0.088	0.000	0.000	0.000	0.000
20	A	20	LEU	0	0.014	0.031	7.969	-0.036	-0.036	0.000	0.000	0.000	0.000
21	A	21	LEU	0	0.027	0.022	5.339	-0.123	-0.004	-0.001	-0.014	-0.104	0.000
22	A	22	ILE	0	-0.001	-0.013	2.651	-1.789	-0.122	0.415	-0.368	-1.714	0.000
23	A	23	HIS	0	-0.066	-0.011	4.631	-0.642	-0.569	-0.001	-0.004	-0.069	0.000
24	A	24	ALA	0	0.021	0.000	7.563	-0.082	-0.082	0.000	0.000	0.000	0.000
25	A	25	LEU	0	0.016	0.015	3.053	-0.715	-0.051	1.209	-0.393	-1.480	-0.003
26	A	26	THR	0	-0.066	-0.031	4.840	-0.585	-0.508	-0.001	-0.002	-0.074	0.000
27	A	27	HIS	0	0.153	0.099	6.234	0.306	0.306	0.000	0.000	0.000	0.000
28	A	28	LYS	1	0.950	0.948	9.183	0.230	0.230	0.000	0.000	0.000	0.000
29	A	29	SER	0	-0.088	-0.057	11.660	0.039	0.039	0.000	0.000	0.000	0.000
30	A	30	PHE	0	-0.043	0.000	6.390	0.009	0.009	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.992	0.992	7.321	0.370	0.370	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.970	0.979	11.747	0.058	0.058	0.000	0.000	0.000	0.000
33	A	33	SER	0	-0.043	-0.034	14.831	0.013	0.013	0.000	0.000	0.000	0.000
34	A	34	TYR	0	-0.001	0.004	7.534	0.007	0.007	0.000	0.000	0.000	0.000
35	A	35	ASN	0	-0.031	-0.014	9.759	-0.045	-0.045	0.000	0.000	0.000	0.000
36	A	36	ASN	0	0.050	0.020	8.879	0.087	0.087	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.869	-0.928	10.862	-0.200	-0.200	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.927	0.954	14.521	0.168	0.168	0.000	0.000	0.000	0.000
39	A	39	LEU	0	-0.004	0.004	10.775	0.020	0.020	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.895	-0.939	13.762	-0.167	-0.167	0.000	0.000	0.000	0.000
41	A	41	PHE	0	0.027	0.026	15.097	0.025	0.025	0.000	0.000	0.000	0.000
42	A	42	LEU	0	-0.065	-0.033	17.294	0.014	0.014	0.000	0.000	0.000	0.000
43	A	43	GLY	0	0.040	-0.004	16.524	0.012	0.012	0.000	0.000	0.000	0.000
44	A	44	ASP	-1	-0.884	-0.919	17.473	-0.114	-0.114	0.000	0.000	0.000	0.000
45	A	45	ALA	0	0.041	0.023	19.889	0.011	0.011	0.000	0.000	0.000	0.000
46	A	46	VAL	0	-0.052	-0.021	19.247	0.008	0.008	0.000	0.000	0.000	0.000
47	A	47	LEU	0	0.000	-0.012	17.496	0.008	0.008	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.846	-0.914	21.890	-0.089	-0.089	0.000	0.000	0.000	0.000
49	A	49	LEU	0	-0.064	-0.029	24.891	0.008	0.008	0.000	0.000	0.000	0.000
50	A	50	VAL	0	-0.033	-0.012	22.097	0.005	0.005	0.000	0.000	0.000	0.000
51	A	51	VAL	0	0.003	-0.010	24.188	0.005	0.005	0.000	0.000	0.000	0.000
52	A	52	GLY	0	-0.006	-0.002	26.873	0.005	0.005	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.917	-0.960	28.813	-0.070	-0.070	0.000	0.000	0.000	0.000
54	A	54	TYR	0	-0.016	-0.018	28.325	0.005	0.005	0.000	0.000	0.000	0.000
55	A	55	LEU	0	-0.030	-0.021	30.283	0.003	0.003	0.000	0.000	0.000	0.000
56	A	56	PHE	0	-0.016	0.003	32.677	0.004	0.004	0.000	0.000	0.000	0.000
57	A	57	HIS	0	-0.004	-0.013	32.567	0.005	0.005	0.000	0.000	0.000	0.000
58	A	58	LYS	1	0.889	0.958	32.463	0.065	0.065	0.000	0.000	0.000	0.000
59	A	59	PHE	0	-0.016	-0.019	34.219	0.001	0.001	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.044	0.043	38.095	0.002	0.002	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.828	0.903	40.143	0.040	0.040	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.874	-0.948	41.282	-0.042	-0.042	0.000	0.000	0.000	0.000
63	A	63	ALA	0	-0.037	-0.012	42.353	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.950	-0.946	43.848	-0.038	-0.038	0.000	0.000	0.000	0.000
65	A	65	GLY	0	0.031	0.006	39.825	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	66	ASP	-1	-0.897	-0.952	36.882	-0.054	-0.054	0.000	0.000	0.000	0.000
67	A	67	LEU	0	0.037	-0.008	34.123	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	68	SER	0	0.012	0.014	32.582	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	69	LYS	1	0.934	0.974	31.711	0.052	0.052	0.000	0.000	0.000	0.000
70	A	70	LEU	0	-0.016	-0.013	31.720	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	71	ARG	1	0.952	0.979	27.123	0.075	0.075	0.000	0.000	0.000	0.000
72	A	72	ALA	0	-0.004	0.009	27.243	-0.005	-0.005	0.000	0.000	0.000	0.000
73	A	73	ALA	0	-0.061	-0.037	27.044	-0.004	-0.004	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.033	-0.030	25.542	-0.002	-0.002	0.000	0.000	0.000	0.000
75	A	75	VAL	0	0.029	0.003	22.531	-0.004	-0.004	0.000	0.000	0.000	0.000
76	A	76	ASN	0	-0.021	0.027	22.317	-0.009	-0.009	0.000	0.000	0.000	0.000
77	A	77	GLU	-1	-0.808	-0.928	19.087	-0.137	-0.137	0.000	0.000	0.000	0.000
78	A	78	LYS	1	0.935	0.964	19.789	0.082	0.082	0.000	0.000	0.000	0.000
79	A	79	SER	0	-0.041	-0.033	21.276	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	80	PHE	0	0.085	0.044	17.270	0.001	0.001	0.000	0.000	0.000	0.000
81	A	81	ALA	0	0.041	0.033	16.239	-0.006	-0.006	0.000	0.000	0.000	0.000
82	A	82	LYS	1	0.875	0.957	16.794	0.092	0.092	0.000	0.000	0.000	0.000
83	A	83	ILE	0	0.022	0.011	15.807	0.001	0.001	0.000	0.000	0.000	0.000
84	A	84	ALA	0	0.030	0.042	12.725	0.002	0.002	0.000	0.000	0.000	0.000
85	A	85	ASN	0	0.004	-0.017	12.854	0.001	0.001	0.000	0.000	0.000	0.000
86	A	86	SER	0	-0.111	-0.064	14.840	0.001	0.001	0.000	0.000	0.000	0.000
87	A	87	LEU	0	-0.032	-0.023	11.080	-0.009	-0.009	0.000	0.000	0.000	0.000
88	A	88	ASN	0	-0.010	0.001	10.373	0.029	0.029	0.000	0.000	0.000	0.000
89	A	89	LEU	0	0.026	0.004	7.836	0.048	0.048	0.000	0.000	0.000	0.000
90	A	90	GLY	0	0.049	0.028	7.810	-0.015	-0.015	0.000	0.000	0.000	0.000
91	A	91	ASP	-1	-0.993	-0.999	7.856	-0.281	-0.281	0.000	0.000	0.000	0.000
92	A	92	PHE	0	-0.053	-0.043	3.257	-1.297	-0.126	0.531	-0.337	-1.365	0.001
93	A	93	ILE	0	-0.037	-0.001	3.028	-3.463	-1.922	0.467	-0.831	-1.177	-0.010
94	A	94	LEU	0	-0.018	0.007	2.039	2.274	-2.507	9.695	-1.127	-3.786	-0.001
95	A	95	MET	0	0.005	0.002	4.822	0.356	0.401	-0.001	-0.007	-0.037	0.000
96	A	96	SER	0	-0.032	-0.006	8.643	0.079	0.079	0.000	0.000	0.000	0.000
97	A	97	VAL	0	0.095	0.032	11.570	-0.010	-0.010	0.000	0.000	0.000	0.000
98	A	98	ALA	0	-0.007	0.000	13.275	0.003	0.003	0.000	0.000	0.000	0.000
99	A	99	GLU	-1	-0.834	-0.910	12.540	-0.204	-0.204	0.000	0.000	0.000	0.000
100	A	100	GLU	-1	-0.894	-0.960	9.124	-0.318	-0.318	0.000	0.000	0.000	0.000
101	A	101	ASN	0	-0.043	-0.024	13.321	0.016	0.016	0.000	0.000	0.000	0.000
102	A	102	ASN	0	-0.086	-0.030	16.683	0.028	0.028	0.000	0.000	0.000	0.000
103	A	103	GLY	0	0.034	0.012	16.537	0.004	0.004	0.000	0.000	0.000	0.000
104	A	104	GLY	0	-0.008	-0.020	13.258	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	105	LYS	1	0.903	0.933	9.645	0.227	0.227	0.000	0.000	0.000	0.000
106	A	106	GLU	-1	-0.897	-0.938	12.225	-0.134	-0.134	0.000	0.000	0.000	0.000
107	A	107	LYS	1	0.781	0.886	14.895	0.201	0.201	0.000	0.000	0.000	0.000
108	A	108	PRO	0	0.027	-0.002	15.189	-0.018	-0.018	0.000	0.000	0.000	0.000
109	A	109	SER	0	0.054	0.031	16.535	-0.007	-0.007	0.000	0.000	0.000	0.000
110	A	110	ILE	0	-0.035	0.000	10.921	-0.015	-0.015	0.000	0.000	0.000	0.000
111	A	111	LEU	0	-0.025	-0.011	11.243	-0.035	-0.035	0.000	0.000	0.000	0.000
112	A	112	SER	0	0.005	-0.010	12.710	0.007	0.007	0.000	0.000	0.000	0.000
113	A	113	ASP	-1	-0.847	-0.918	13.141	-0.228	-0.228	0.000	0.000	0.000	0.000
114	A	114	ALA	0	-0.044	-0.024	8.505	-0.013	-0.013	0.000	0.000	0.000	0.000
115	A	115	LEU	0	-0.013	-0.011	10.429	0.026	0.026	0.000	0.000	0.000	0.000
116	A	116	GLH	0	-0.029	-0.027	12.647	0.006	0.006	0.000	0.000	0.000	0.000
117	A	117	ALA	0	-0.003	0.006	10.435	0.010	0.010	0.000	0.000	0.000	0.000
118	A	118	ILE	0	-0.034	-0.023	8.214	0.014	0.014	0.000	0.000	0.000	0.000
119	A	119	ILE	0	0.007	0.006	11.407	0.007	0.007	0.000	0.000	0.000	0.000
120	A	120	GLY	0	0.044	0.017	14.902	0.009	0.009	0.000	0.000	0.000	0.000
121	A	121	ALA	0	-0.030	-0.015	11.800	0.008	0.008	0.000	0.000	0.000	0.000
122	A	122	ILE	0	0.001	0.005	13.168	0.006	0.006	0.000	0.000	0.000	0.000
123	A	123	HIS	0	0.012	0.011	15.460	0.007	0.007	0.000	0.000	0.000	0.000
124	A	124	LEU	0	-0.055	-0.029	15.456	0.009	0.009	0.000	0.000	0.000	0.000
125	A	125	GLU	-1	-0.806	-0.844	13.501	-0.222	-0.222	0.000	0.000	0.000	0.000
126	A	126	ALA	0	-0.083	-0.051	17.225	0.008	0.008	0.000	0.000	0.000	0.000
127	A	127	GLY	0	0.020	0.024	19.290	0.010	0.010	0.000	0.000	0.000	0.000
128	A	128	PHE	0	0.035	0.004	21.318	-0.005	-0.005	0.000	0.000	0.000	0.000
129	A	129	GLU	-1	-0.911	-0.961	22.894	-0.086	-0.086	0.000	0.000	0.000	0.000
130	A	130	PHE	0	-0.004	-0.001	18.796	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	131	ALA	0	0.046	0.014	18.546	-0.003	-0.003	0.000	0.000	0.000	0.000
132	A	132	LYS	1	0.931	0.968	19.522	0.078	0.078	0.000	0.000	0.000	0.000
133	A	133	THR	0	-0.023	-0.007	22.109	0.004	0.004	0.000	0.000	0.000	0.000
134	A	134	ILE	0	-0.015	0.004	15.454	0.000	0.000	0.000	0.000	0.000	0.000
135	A	135	ALA	0	0.025	0.003	18.659	0.000	0.000	0.000	0.000	0.000	0.000
136	A	136	LEU	0	-0.007	-0.017	19.542	0.003	0.003	0.000	0.000	0.000	0.000
137	A	137	ARG	1	0.942	0.987	16.543	0.147	0.147	0.000	0.000	0.000	0.000
138	A	138	LEU	0	-0.046	-0.027	15.105	0.001	0.001	0.000	0.000	0.000	0.000
139	A	139	ILE	0	0.037	0.023	19.291	0.002	0.002	0.000	0.000	0.000	0.000
140	A	140	GLU	-1	-0.932	-0.975	22.272	-0.084	-0.084	0.000	0.000	0.000	0.000
141	A	141	LYS	1	0.852	0.925	18.725	0.124	0.124	0.000	0.000	0.000	0.000
142	A	142	ASN	0	-0.086	-0.045	18.563	0.001	0.001	0.000	0.000	0.000	0.000
143	A	143	PHE	0	-0.079	-0.026	22.126	0.003	0.003	0.000	0.000	0.000	0.000
144	A	144	PRO	0	0.013	0.025	26.103	0.004	0.004	0.000	0.000	0.000	0.000

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