FMO DATABASE

FMODB ID: R5R88

Calculation Name: 3NFQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NFQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q06505

Base Structure: X-ray

Registration Date: 2023-06-20

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	147
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1372102.599758
FMO2-HF: Nuclear repulsion	1314876.752498
FMO2-HF: Total energy	-57225.847261
FMO2-MP2: Total energy	-57396.233798

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:8:ASP)

Summations of interaction energy for fragment #1(A:8:ASP)

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.
12.512	16.8	8.431	-5.656	-7.063	0.031

Interaction energy analysis for fragmet #1(A:8:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.892 / q_NPA : -0.960

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	10	LEU	0	-0.011	-0.016	2.924	-11.149	-7.890	0.770	-1.822	-2.207	0.013
4	A	11	GLU	-1	-0.882	-0.956	1.976	33.335	33.758	7.652	-3.723	-4.352	0.017
5	A	12	GLN	0	-0.016	0.004	3.798	-11.297	-10.691	0.009	-0.111	-0.504	0.001
6	A	13	TYR	0	-0.007	0.001	5.530	-5.730	-5.730	0.000	0.000	0.000	0.000
7	A	14	LEU	0	-0.056	-0.024	6.672	-4.819	-4.819	0.000	0.000	0.000	0.000
8	A	15	ASP	-1	-0.785	-0.900	7.390	30.254	30.254	0.000	0.000	0.000	0.000
9	A	16	GLU	-1	-0.858	-0.912	9.222	18.436	18.436	0.000	0.000	0.000	0.000
10	A	17	LYS	1	0.883	0.961	11.261	-20.247	-20.247	0.000	0.000	0.000	0.000
11	A	18	ILE	0	-0.051	-0.051	12.340	-2.193	-2.193	0.000	0.000	0.000	0.000
12	A	19	LEU	0	0.004	-0.007	11.819	-1.813	-1.813	0.000	0.000	0.000	0.000
13	A	20	ARG	1	0.920	0.960	15.091	-18.301	-18.301	0.000	0.000	0.000	0.000
14	A	21	LEU	0	-0.083	-0.034	17.018	-1.015	-1.015	0.000	0.000	0.000	0.000
15	A	22	LYS	1	0.945	0.976	17.277	-17.336	-17.336	0.000	0.000	0.000	0.000
16	A	23	ASP	-1	-0.908	-0.949	19.319	14.088	14.088	0.000	0.000	0.000	0.000
17	A	24	GLU	-1	-0.970	-0.993	21.193	11.759	11.759	0.000	0.000	0.000	0.000
18	A	25	MET	0	-0.071	-0.037	22.473	-0.451	-0.451	0.000	0.000	0.000	0.000
19	A	26	ASN	0	0.064	0.044	22.667	-0.750	-0.750	0.000	0.000	0.000	0.000
20	A	27	ILE	0	0.020	0.022	24.465	-0.563	-0.563	0.000	0.000	0.000	0.000
21	A	28	ALA	0	-0.014	-0.016	27.055	-0.488	-0.488	0.000	0.000	0.000	0.000
22	A	29	ALA	0	-0.019	-0.017	28.416	-0.427	-0.427	0.000	0.000	0.000	0.000
23	A	30	GLN	0	-0.019	0.000	29.851	-0.181	-0.181	0.000	0.000	0.000	0.000
24	A	31	LEU	0	0.044	0.013	30.850	-0.327	-0.327	0.000	0.000	0.000	0.000
25	A	32	ASP	-1	-0.778	-0.896	33.033	8.836	8.836	0.000	0.000	0.000	0.000
26	A	33	ILE	0	0.005	0.008	34.136	-0.304	-0.304	0.000	0.000	0.000	0.000
27	A	34	ASP	-1	-0.867	-0.926	35.770	8.324	8.324	0.000	0.000	0.000	0.000
28	A	35	THR	0	-0.072	-0.042	37.440	-0.300	-0.300	0.000	0.000	0.000	0.000
29	A	36	LEU	0	-0.050	-0.018	38.923	-0.247	-0.247	0.000	0.000	0.000	0.000
30	A	37	ASN	0	0.055	0.015	39.568	-0.265	-0.265	0.000	0.000	0.000	0.000
31	A	38	LYS	1	1.020	1.030	42.032	-7.387	-7.387	0.000	0.000	0.000	0.000
32	A	39	ARG	1	0.833	0.918	43.452	-7.127	-7.127	0.000	0.000	0.000	0.000
33	A	40	ILE	0	-0.052	-0.024	43.522	-0.176	-0.176	0.000	0.000	0.000	0.000
34	A	41	GLU	-1	-0.963	-0.988	45.422	6.793	6.793	0.000	0.000	0.000	0.000
35	A	42	THR	0	-0.100	-0.065	47.498	-0.157	-0.157	0.000	0.000	0.000	0.000
36	A	43	GLY	0	0.013	0.017	49.216	-0.128	-0.128	0.000	0.000	0.000	0.000
37	A	44	ASP	-1	-0.824	-0.869	48.197	6.342	6.342	0.000	0.000	0.000	0.000
38	A	45	THR	0	-0.057	-0.043	47.368	0.172	0.172	0.000	0.000	0.000	0.000
39	A	46	SER	0	-0.081	-0.078	46.947	0.127	0.127	0.000	0.000	0.000	0.000
40	A	47	LEU	0	-0.004	0.019	43.247	0.183	0.183	0.000	0.000	0.000	0.000
41	A	48	ILE	0	0.001	-0.010	40.365	-0.041	-0.041	0.000	0.000	0.000	0.000
42	A	49	ALA	0	0.017	0.016	36.311	0.094	0.094	0.000	0.000	0.000	0.000
43	A	50	MET	0	-0.001	-0.007	35.638	0.032	0.032	0.000	0.000	0.000	0.000
44	A	51	GLN	0	-0.023	-0.007	30.748	-0.030	-0.030	0.000	0.000	0.000	0.000
45	A	52	LYS	1	0.906	0.949	29.404	-9.128	-9.128	0.000	0.000	0.000	0.000
46	A	53	VAL	0	0.008	-0.001	29.727	0.271	0.271	0.000	0.000	0.000	0.000
47	A	54	LYS	1	0.913	0.958	30.950	-8.855	-8.855	0.000	0.000	0.000	0.000
48	A	55	LEU	0	-0.002	0.021	23.582	0.210	0.210	0.000	0.000	0.000	0.000
49	A	56	LEU	0	-0.012	-0.010	26.085	0.438	0.438	0.000	0.000	0.000	0.000
50	A	57	PRO	0	0.019	0.011	26.450	0.375	0.375	0.000	0.000	0.000	0.000
51	A	58	LYS	1	0.961	0.981	19.881	-13.626	-13.626	0.000	0.000	0.000	0.000
52	A	59	VAL	0	0.027	0.016	21.977	0.648	0.648	0.000	0.000	0.000	0.000
53	A	60	VAL	0	0.028	0.010	22.198	0.484	0.484	0.000	0.000	0.000	0.000
54	A	61	SER	0	-0.028	-0.011	21.655	0.529	0.529	0.000	0.000	0.000	0.000
55	A	62	VAL	0	-0.021	-0.009	16.540	0.466	0.466	0.000	0.000	0.000	0.000
56	A	63	LEU	0	-0.003	-0.008	18.090	0.643	0.643	0.000	0.000	0.000	0.000
57	A	64	SER	0	-0.049	-0.012	20.162	0.092	0.092	0.000	0.000	0.000	0.000
58	A	65	LYS	1	0.903	0.952	16.156	-15.581	-15.581	0.000	0.000	0.000	0.000
59	A	66	ALA	0	0.088	0.042	16.324	0.757	0.757	0.000	0.000	0.000	0.000
60	A	67	ASN	0	-0.046	-0.036	11.490	0.294	0.294	0.000	0.000	0.000	0.000
61	A	68	LEU	0	0.024	0.017	11.315	1.389	1.389	0.000	0.000	0.000	0.000
62	A	69	ALA	0	-0.014	-0.004	13.157	0.107	0.107	0.000	0.000	0.000	0.000
63	A	70	ASP	-1	-0.833	-0.908	10.490	25.155	25.155	0.000	0.000	0.000	0.000
64	A	71	THR	0	0.049	0.044	8.901	-0.973	-0.973	0.000	0.000	0.000	0.000
65	A	72	ILE	0	-0.074	-0.041	10.999	-1.254	-1.254	0.000	0.000	0.000	0.000
66	A	73	LEU	0	-0.083	-0.061	14.622	-1.186	-1.186	0.000	0.000	0.000	0.000
67	A	74	ASP	-1	-0.874	-0.928	10.205	26.225	26.225	0.000	0.000	0.000	0.000
68	A	75	ASN	0	-0.072	-0.044	9.777	-1.050	-1.050	0.000	0.000	0.000	0.000
69	A	76	ASN	0	0.012	-0.006	13.677	-1.632	-1.632	0.000	0.000	0.000	0.000
70	A	77	LEU	0	0.022	0.018	16.715	-1.088	-1.088	0.000	0.000	0.000	0.000
71	A	78	LEU	0	0.002	-0.016	18.352	-0.986	-0.986	0.000	0.000	0.000	0.000
72	A	79	GLN	0	-0.010	0.007	20.824	-0.548	-0.548	0.000	0.000	0.000	0.000
73	A	80	SER	0	0.015	-0.008	21.792	-0.377	-0.377	0.000	0.000	0.000	0.000
74	A	81	VAL	0	-0.021	-0.005	22.285	-0.555	-0.555	0.000	0.000	0.000	0.000
75	A	82	ARG	1	0.783	0.905	24.831	-11.789	-11.789	0.000	0.000	0.000	0.000
76	A	83	ILE	0	-0.009	-0.003	25.368	-0.452	-0.452	0.000	0.000	0.000	0.000
77	A	84	TRP	0	-0.054	-0.046	26.737	-0.447	-0.447	0.000	0.000	0.000	0.000
78	A	85	LEU	0	-0.039	-0.006	28.368	-0.384	-0.384	0.000	0.000	0.000	0.000
79	A	86	GLU	-1	-0.872	-0.917	30.962	9.741	9.741	0.000	0.000	0.000	0.000
80	A	87	PRO	0	-0.039	-0.017	32.788	-0.091	-0.091	0.000	0.000	0.000	0.000
81	A	88	LEU	0	0.031	0.022	36.140	0.108	0.108	0.000	0.000	0.000	0.000
82	A	89	PRO	0	0.033	-0.001	38.055	-0.104	-0.104	0.000	0.000	0.000	0.000
83	A	90	ASP	-1	-0.855	-0.910	40.564	7.272	7.272	0.000	0.000	0.000	0.000
84	A	91	GLY	0	-0.053	-0.033	40.918	-0.164	-0.164	0.000	0.000	0.000	0.000
85	A	92	SER	0	-0.122	-0.068	40.897	0.107	0.107	0.000	0.000	0.000	0.000
86	A	93	LEU	0	0.021	0.010	36.554	0.162	0.162	0.000	0.000	0.000	0.000
87	A	94	PRO	0	0.020	0.021	33.136	-0.173	-0.173	0.000	0.000	0.000	0.000
88	A	95	SER	0	0.055	0.029	36.053	-0.065	-0.065	0.000	0.000	0.000	0.000
89	A	96	PHE	0	0.070	0.022	35.851	0.262	0.262	0.000	0.000	0.000	0.000
90	A	97	GLU	-1	-0.889	-0.955	34.932	8.368	8.368	0.000	0.000	0.000	0.000
91	A	98	ILE	0	0.000	0.005	30.571	0.323	0.323	0.000	0.000	0.000	0.000
92	A	99	GLN	0	-0.015	-0.014	31.181	0.347	0.347	0.000	0.000	0.000	0.000
93	A	100	LYS	1	0.973	0.986	31.975	-8.388	-8.388	0.000	0.000	0.000	0.000
94	A	101	SER	0	-0.040	-0.021	29.277	0.212	0.212	0.000	0.000	0.000	0.000
95	A	102	LEU	0	-0.001	-0.004	25.877	0.397	0.397	0.000	0.000	0.000	0.000
96	A	103	PHE	0	-0.011	-0.011	27.215	0.363	0.363	0.000	0.000	0.000	0.000
97	A	104	ALA	0	-0.034	-0.017	28.749	0.135	0.135	0.000	0.000	0.000	0.000
98	A	105	ALA	0	0.018	0.008	23.843	0.213	0.213	0.000	0.000	0.000	0.000
99	A	106	LEU	0	-0.021	-0.019	23.525	0.439	0.439	0.000	0.000	0.000	0.000
100	A	107	ASN	0	-0.055	-0.033	25.027	-0.040	-0.040	0.000	0.000	0.000	0.000
101	A	108	ASP	-1	-0.913	-0.939	22.921	12.132	12.132	0.000	0.000	0.000	0.000
102	A	109	LEU	0	-0.012	-0.001	18.190	0.650	0.650	0.000	0.000	0.000	0.000
103	A	110	PRO	0	-0.016	0.005	17.950	-0.694	-0.694	0.000	0.000	0.000	0.000
104	A	111	VAL	0	-0.042	-0.024	19.966	0.543	0.543	0.000	0.000	0.000	0.000
105	A	112	LYS	1	0.945	0.976	20.020	-15.190	-15.190	0.000	0.000	0.000	0.000
106	A	113	THR	0	0.027	-0.011	22.409	-0.211	-0.211	0.000	0.000	0.000	0.000
107	A	114	GLU	-1	-0.880	-0.947	18.745	15.033	15.033	0.000	0.000	0.000	0.000
108	A	115	HIS	0	0.198	0.098	16.394	-1.186	-1.186	0.000	0.000	0.000	0.000
109	A	116	LEU	0	-0.058	-0.003	21.052	-0.458	-0.458	0.000	0.000	0.000	0.000
110	A	117	LYS	1	0.860	0.925	24.096	-11.505	-11.505	0.000	0.000	0.000	0.000
111	A	118	GLU	-1	-0.889	-0.930	17.816	16.584	16.584	0.000	0.000	0.000	0.000
112	A	119	SER	0	-0.005	-0.017	21.778	-0.408	-0.408	0.000	0.000	0.000	0.000
113	A	120	GLY	0	0.016	-0.014	23.335	-0.448	-0.448	0.000	0.000	0.000	0.000
114	A	121	LEU	0	0.034	0.011	24.491	-0.566	-0.566	0.000	0.000	0.000	0.000
115	A	122	GLY	0	0.026	0.026	27.160	-0.355	-0.355	0.000	0.000	0.000	0.000
116	A	123	ARG	1	0.910	0.942	29.158	-9.777	-9.777	0.000	0.000	0.000	0.000
117	A	124	VAL	0	0.029	0.027	30.162	-0.376	-0.376	0.000	0.000	0.000	0.000
118	A	125	VAL	0	0.061	0.029	28.986	-0.351	-0.351	0.000	0.000	0.000	0.000
119	A	126	ILE	0	0.021	0.001	32.069	-0.363	-0.363	0.000	0.000	0.000	0.000
120	A	127	PHE	0	-0.039	0.008	34.882	-0.332	-0.332	0.000	0.000	0.000	0.000
121	A	128	TYR	0	-0.021	-0.056	33.688	-0.312	-0.312	0.000	0.000	0.000	0.000
122	A	129	THR	0	-0.088	-0.047	35.772	-0.257	-0.257	0.000	0.000	0.000	0.000
123	A	130	LYS	1	0.927	0.959	38.315	-8.318	-8.318	0.000	0.000	0.000	0.000
124	A	131	SER	0	-0.026	0.007	39.977	-0.334	-0.334	0.000	0.000	0.000	0.000
125	A	132	LYS	1	0.966	0.957	41.847	-6.809	-6.809	0.000	0.000	0.000	0.000
126	A	133	ARG	1	0.948	0.980	41.834	-7.296	-7.296	0.000	0.000	0.000	0.000
127	A	134	VAL	0	-0.030	0.014	37.998	0.063	0.063	0.000	0.000	0.000	0.000
128	A	135	GLU	-1	-0.862	-0.931	40.248	7.145	7.145	0.000	0.000	0.000	0.000
129	A	136	ALA	0	0.035	0.012	40.332	0.193	0.193	0.000	0.000	0.000	0.000
130	A	137	GLN	0	-0.012	-0.020	37.964	0.288	0.288	0.000	0.000	0.000	0.000
131	A	138	LEU	0	0.017	0.006	34.547	0.202	0.202	0.000	0.000	0.000	0.000
132	A	139	ALA	0	0.018	0.024	36.001	0.214	0.214	0.000	0.000	0.000	0.000
133	A	140	ARG	1	0.851	0.902	37.477	-7.707	-7.707	0.000	0.000	0.000	0.000
134	A	141	LEU	0	0.012	0.027	31.230	0.089	0.089	0.000	0.000	0.000	0.000
135	A	142	ALA	0	0.005	-0.003	32.736	0.285	0.285	0.000	0.000	0.000	0.000
136	A	143	GLU	-1	-0.884	-0.939	33.293	8.315	8.315	0.000	0.000	0.000	0.000
137	A	144	LYS	1	0.940	0.975	30.939	-10.030	-10.030	0.000	0.000	0.000	0.000
138	A	145	LEU	0	0.005	0.007	28.038	0.166	0.166	0.000	0.000	0.000	0.000
139	A	146	ILE	0	-0.010	0.000	29.498	0.320	0.320	0.000	0.000	0.000	0.000
140	A	147	ALA	0	0.003	0.019	30.638	0.166	0.166	0.000	0.000	0.000	0.000
141	A	148	GLU	-1	-0.926	-0.967	27.461	11.494	11.494	0.000	0.000	0.000	0.000
142	A	149	TRP	0	-0.007	-0.014	25.631	0.167	0.167	0.000	0.000	0.000	0.000
143	A	150	THR	0	-0.097	-0.060	26.057	0.286	0.286	0.000	0.000	0.000	0.000
144	A	151	ARG	1	0.882	0.951	24.620	-12.432	-12.432	0.000	0.000	0.000	0.000
145	A	152	PRO	0	0.010	-0.017	28.022	0.356	0.356	0.000	0.000	0.000	0.000
146	A	153	ILE	0	-0.033	0.005	24.197	0.282	0.282	0.000	0.000	0.000	0.000
147	A	154	ILE	0	0.007	0.012	27.480	0.132	0.132	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:8:ASP)