FMO DATABASE

FMODB ID: Q1QVY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1373008.800325
FMO2-HF: Nuclear repulsion	1315781.904017
FMO2-HF: Total energy	-57226.896308
FMO2-MP2: Total energy	-57397.220038

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.
8.891	14.114	7.133	-5.455	-6.902	0.035

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 : -0.894 / 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	-0.025	-0.023	2.818	-10.780	-7.389	0.772	-1.852	-2.311	0.012
4	A	11	GLU	-1	-0.874	-0.954	2.070	32.869	33.827	6.350	-3.304	-4.005	0.022
5	A	12	GLN	0	-0.035	-0.015	3.841	-12.192	-11.318	0.011	-0.299	-0.586	0.001
6	A	13	TYR	0	-0.027	-0.008	5.582	-5.784	-5.784	0.000	0.000	0.000	0.000
7	A	14	LEU	0	-0.026	-0.013	6.949	-4.860	-4.860	0.000	0.000	0.000	0.000
8	A	15	ASP	-1	-0.772	-0.879	7.245	29.913	29.913	0.000	0.000	0.000	0.000
9	A	16	GLU	-1	-0.841	-0.884	9.266	17.844	17.844	0.000	0.000	0.000	0.000
10	A	17	LYS	1	0.886	0.949	11.311	-20.375	-20.375	0.000	0.000	0.000	0.000
11	A	18	ILE	0	-0.049	-0.039	12.385	-2.319	-2.319	0.000	0.000	0.000	0.000
12	A	19	LEU	0	0.026	0.006	12.025	-1.768	-1.768	0.000	0.000	0.000	0.000
13	A	20	ARG	1	0.847	0.909	15.135	-18.609	-18.609	0.000	0.000	0.000	0.000
14	A	21	LEU	0	-0.053	-0.019	17.066	-0.987	-0.987	0.000	0.000	0.000	0.000
15	A	22	LYS	1	0.900	0.956	17.387	-17.209	-17.209	0.000	0.000	0.000	0.000
16	A	23	ASP	-1	-0.889	-0.943	19.363	13.832	13.832	0.000	0.000	0.000	0.000
17	A	24	GLU	-1	-0.863	-0.928	21.235	12.682	12.682	0.000	0.000	0.000	0.000
18	A	25	MET	0	-0.055	-0.029	22.515	-0.470	-0.470	0.000	0.000	0.000	0.000
19	A	26	ASN	0	0.041	0.043	22.300	-0.755	-0.755	0.000	0.000	0.000	0.000
20	A	27	ILE	0	0.019	0.019	24.607	-0.560	-0.560	0.000	0.000	0.000	0.000
21	A	28	ALA	0	-0.016	-0.012	27.099	-0.490	-0.490	0.000	0.000	0.000	0.000
22	A	29	ALA	0	-0.012	-0.015	28.460	-0.434	-0.434	0.000	0.000	0.000	0.000
23	A	30	GLN	0	-0.030	-0.010	29.894	-0.196	-0.196	0.000	0.000	0.000	0.000
24	A	31	LEU	0	0.044	0.013	30.829	-0.324	-0.324	0.000	0.000	0.000	0.000
25	A	32	ASP	-1	-0.770	-0.874	33.075	8.849	8.849	0.000	0.000	0.000	0.000
26	A	33	ILE	0	0.009	0.012	34.224	-0.300	-0.300	0.000	0.000	0.000	0.000
27	A	34	ASP	-1	-0.852	-0.914	35.503	8.312	8.312	0.000	0.000	0.000	0.000
28	A	35	THR	0	-0.078	-0.046	37.297	-0.288	-0.288	0.000	0.000	0.000	0.000
29	A	36	LEU	0	-0.049	-0.017	38.965	-0.250	-0.250	0.000	0.000	0.000	0.000
30	A	37	ASN	0	0.040	0.010	39.300	-0.266	-0.266	0.000	0.000	0.000	0.000
31	A	38	LYS	1	1.035	1.036	42.075	-7.303	-7.303	0.000	0.000	0.000	0.000
32	A	39	ARG	1	0.823	0.916	43.496	-7.159	-7.159	0.000	0.000	0.000	0.000
33	A	40	ILE	0	-0.065	-0.035	43.518	-0.174	-0.174	0.000	0.000	0.000	0.000
34	A	41	GLU	-1	-0.966	-0.982	45.039	6.789	6.789	0.000	0.000	0.000	0.000
35	A	42	THR	0	-0.082	-0.074	47.451	-0.147	-0.147	0.000	0.000	0.000	0.000
36	A	43	GLY	0	0.006	0.016	49.262	-0.128	-0.128	0.000	0.000	0.000	0.000
37	A	44	ASP	-1	-0.827	-0.876	48.299	6.368	6.368	0.000	0.000	0.000	0.000
38	A	45	THR	0	-0.025	-0.029	47.414	0.135	0.135	0.000	0.000	0.000	0.000
39	A	46	SER	0	-0.117	-0.086	46.992	0.127	0.127	0.000	0.000	0.000	0.000
40	A	47	LEU	0	0.004	0.021	43.359	0.187	0.187	0.000	0.000	0.000	0.000
41	A	48	ILE	0	0.013	0.001	40.312	-0.046	-0.046	0.000	0.000	0.000	0.000
42	A	49	ALA	0	0.011	0.018	36.423	0.092	0.092	0.000	0.000	0.000	0.000
43	A	50	MET	0	0.005	-0.008	35.684	0.022	0.022	0.000	0.000	0.000	0.000
44	A	51	GLN	0	-0.022	-0.009	30.886	-0.020	-0.020	0.000	0.000	0.000	0.000
45	A	52	LYS	1	0.901	0.937	29.368	-9.201	-9.201	0.000	0.000	0.000	0.000
46	A	53	VAL	0	0.008	0.000	29.770	0.269	0.269	0.000	0.000	0.000	0.000
47	A	54	LYS	1	0.888	0.944	30.945	-8.833	-8.833	0.000	0.000	0.000	0.000
48	A	55	LEU	0	-0.007	0.013	23.746	0.197	0.197	0.000	0.000	0.000	0.000
49	A	56	LEU	0	0.005	-0.001	26.128	0.440	0.440	0.000	0.000	0.000	0.000
50	A	57	PRO	0	0.014	0.008	26.489	0.372	0.372	0.000	0.000	0.000	0.000
51	A	58	LYS	1	0.826	0.907	20.645	-13.170	-13.170	0.000	0.000	0.000	0.000
52	A	59	VAL	0	0.027	0.012	22.075	0.634	0.634	0.000	0.000	0.000	0.000
53	A	60	VAL	0	0.029	0.012	22.243	0.476	0.476	0.000	0.000	0.000	0.000
54	A	61	SER	0	0.003	0.009	22.088	0.538	0.538	0.000	0.000	0.000	0.000
55	A	62	VAL	0	-0.017	-0.008	16.732	0.440	0.440	0.000	0.000	0.000	0.000
56	A	63	LEU	0	0.005	-0.002	18.414	0.627	0.627	0.000	0.000	0.000	0.000
57	A	64	SER	0	-0.052	-0.019	20.361	0.031	0.031	0.000	0.000	0.000	0.000
58	A	65	LYS	1	0.852	0.927	16.474	-15.273	-15.273	0.000	0.000	0.000	0.000
59	A	66	ALA	0	0.086	0.038	16.617	0.732	0.732	0.000	0.000	0.000	0.000
60	A	67	ASN	0	-0.031	-0.026	11.826	-0.201	-0.201	0.000	0.000	0.000	0.000
61	A	68	LEU	0	0.023	0.018	11.596	1.492	1.492	0.000	0.000	0.000	0.000
62	A	69	ALA	0	-0.018	-0.008	13.466	0.079	0.079	0.000	0.000	0.000	0.000
63	A	70	ASP	-1	-0.843	-0.917	10.751	24.197	24.197	0.000	0.000	0.000	0.000
64	A	71	THR	0	0.059	0.049	8.982	-0.976	-0.976	0.000	0.000	0.000	0.000
65	A	72	ILE	0	-0.065	-0.040	11.021	-1.255	-1.255	0.000	0.000	0.000	0.000
66	A	73	LEU	0	-0.089	-0.059	14.641	-1.176	-1.176	0.000	0.000	0.000	0.000
67	A	74	ASP	-1	-0.886	-0.933	10.441	25.818	25.818	0.000	0.000	0.000	0.000
68	A	75	ASN	0	-0.089	-0.063	9.723	-1.047	-1.047	0.000	0.000	0.000	0.000
69	A	76	ASN	0	-0.021	-0.033	13.701	-1.740	-1.740	0.000	0.000	0.000	0.000
70	A	77	LEU	0	0.036	0.021	16.736	-1.083	-1.083	0.000	0.000	0.000	0.000
71	A	78	LEU	0	0.001	-0.015	18.382	-0.987	-0.987	0.000	0.000	0.000	0.000
72	A	79	GLN	0	0.008	0.009	20.856	-0.515	-0.515	0.000	0.000	0.000	0.000
73	A	80	SER	0	0.008	-0.018	21.821	-0.397	-0.397	0.000	0.000	0.000	0.000
74	A	81	VAL	0	-0.025	-0.009	22.278	-0.563	-0.563	0.000	0.000	0.000	0.000
75	A	82	ARG	1	0.770	0.859	24.861	-11.598	-11.598	0.000	0.000	0.000	0.000
76	A	83	ILE	0	-0.010	-0.004	25.374	-0.463	-0.463	0.000	0.000	0.000	0.000
77	A	84	TRP	0	-0.061	-0.049	26.576	-0.463	-0.463	0.000	0.000	0.000	0.000
78	A	85	LEU	0	-0.039	-0.004	28.413	-0.386	-0.386	0.000	0.000	0.000	0.000
79	A	86	GLU	-1	-0.806	-0.862	30.790	9.842	9.842	0.000	0.000	0.000	0.000
80	A	87	PRO	0	-0.044	-0.014	32.816	-0.092	-0.092	0.000	0.000	0.000	0.000
81	A	88	LEU	0	0.025	0.019	35.988	0.112	0.112	0.000	0.000	0.000	0.000
82	A	89	PRO	0	0.055	0.011	38.092	-0.105	-0.105	0.000	0.000	0.000	0.000
83	A	90	ASP	-1	-0.793	-0.864	40.593	7.261	7.261	0.000	0.000	0.000	0.000
84	A	91	GLY	0	-0.037	-0.019	40.945	-0.163	-0.163	0.000	0.000	0.000	0.000
85	A	92	SER	0	-0.123	-0.087	40.988	0.100	0.100	0.000	0.000	0.000	0.000
86	A	93	LEU	0	0.005	-0.003	36.256	0.170	0.170	0.000	0.000	0.000	0.000
87	A	94	PRO	0	0.012	0.020	33.182	-0.172	-0.172	0.000	0.000	0.000	0.000
88	A	95	SER	0	0.021	-0.013	36.088	-0.049	-0.049	0.000	0.000	0.000	0.000
89	A	96	PHE	0	0.059	0.018	35.884	0.262	0.262	0.000	0.000	0.000	0.000
90	A	97	GLU	-1	-0.830	-0.904	35.053	8.404	8.404	0.000	0.000	0.000	0.000
91	A	98	ILE	0	0.007	0.018	30.579	0.333	0.333	0.000	0.000	0.000	0.000
92	A	99	GLN	0	-0.036	-0.022	31.212	0.325	0.325	0.000	0.000	0.000	0.000
93	A	100	LYS	1	0.946	0.963	32.002	-8.297	-8.297	0.000	0.000	0.000	0.000
94	A	101	SER	0	-0.054	-0.034	29.458	0.207	0.207	0.000	0.000	0.000	0.000
95	A	102	LEU	0	0.010	0.000	25.889	0.400	0.400	0.000	0.000	0.000	0.000
96	A	103	PHE	0	-0.017	-0.014	27.240	0.368	0.368	0.000	0.000	0.000	0.000
97	A	104	ALA	0	-0.033	-0.015	28.872	0.137	0.137	0.000	0.000	0.000	0.000
98	A	105	ALA	0	0.008	0.005	24.071	0.222	0.222	0.000	0.000	0.000	0.000
99	A	106	LEU	0	-0.018	-0.016	23.455	0.445	0.445	0.000	0.000	0.000	0.000
100	A	107	ASN	0	-0.071	-0.044	25.145	-0.124	-0.124	0.000	0.000	0.000	0.000
101	A	108	ASP	-1	-0.871	-0.922	23.435	11.975	11.975	0.000	0.000	0.000	0.000
102	A	109	LEU	0	-0.001	0.011	18.527	0.660	0.660	0.000	0.000	0.000	0.000
103	A	110	PRO	0	-0.007	0.007	18.164	-0.711	-0.711	0.000	0.000	0.000	0.000
104	A	111	VAL	0	-0.047	-0.031	20.288	0.531	0.531	0.000	0.000	0.000	0.000
105	A	112	LYS	1	0.945	0.987	20.160	-15.441	-15.441	0.000	0.000	0.000	0.000
106	A	113	THR	0	0.026	-0.011	22.812	-0.199	-0.199	0.000	0.000	0.000	0.000
107	A	114	GLU	-1	-0.857	-0.943	19.089	14.910	14.910	0.000	0.000	0.000	0.000
108	A	115	HIS	0	0.169	0.081	16.773	-1.066	-1.066	0.000	0.000	0.000	0.000
109	A	116	LEU	0	-0.037	0.008	21.160	-0.426	-0.426	0.000	0.000	0.000	0.000
110	A	117	LYS	1	0.863	0.928	24.400	-11.445	-11.445	0.000	0.000	0.000	0.000
111	A	118	GLU	-1	-0.830	-0.898	18.362	16.318	16.318	0.000	0.000	0.000	0.000
112	A	119	SER	0	-0.011	-0.011	21.860	-0.361	-0.361	0.000	0.000	0.000	0.000
113	A	120	GLY	0	-0.009	-0.019	23.353	-0.431	-0.431	0.000	0.000	0.000	0.000
114	A	121	LEU	0	0.039	0.010	24.552	-0.566	-0.566	0.000	0.000	0.000	0.000
115	A	122	GLY	0	0.027	0.027	27.178	-0.351	-0.351	0.000	0.000	0.000	0.000
116	A	123	ARG	1	0.904	0.939	29.169	-9.702	-9.702	0.000	0.000	0.000	0.000
117	A	124	VAL	0	0.027	0.030	30.191	-0.378	-0.378	0.000	0.000	0.000	0.000
118	A	125	VAL	0	0.058	0.025	28.994	-0.346	-0.346	0.000	0.000	0.000	0.000
119	A	126	ILE	0	0.016	0.001	32.086	-0.368	-0.368	0.000	0.000	0.000	0.000
120	A	127	PHE	0	-0.023	0.008	34.895	-0.327	-0.327	0.000	0.000	0.000	0.000
121	A	128	TYR	0	0.001	-0.033	33.920	-0.294	-0.294	0.000	0.000	0.000	0.000
122	A	129	THR	0	-0.077	-0.034	35.781	-0.255	-0.255	0.000	0.000	0.000	0.000
123	A	130	LYS	1	0.928	0.954	38.330	-8.335	-8.335	0.000	0.000	0.000	0.000
124	A	131	SER	0	-0.022	0.003	40.189	-0.333	-0.333	0.000	0.000	0.000	0.000
125	A	132	LYS	1	0.958	0.956	41.867	-6.865	-6.865	0.000	0.000	0.000	0.000
126	A	133	ARG	1	0.866	0.942	41.889	-7.332	-7.332	0.000	0.000	0.000	0.000
127	A	134	VAL	0	-0.027	0.013	38.004	0.063	0.063	0.000	0.000	0.000	0.000
128	A	135	GLU	-1	-0.855	-0.929	40.295	7.134	7.134	0.000	0.000	0.000	0.000
129	A	136	ALA	0	0.031	0.010	40.353	0.196	0.196	0.000	0.000	0.000	0.000
130	A	137	GLN	0	0.026	0.003	38.363	0.303	0.303	0.000	0.000	0.000	0.000
131	A	138	LEU	0	0.012	0.004	34.741	0.199	0.199	0.000	0.000	0.000	0.000
132	A	139	ALA	0	0.024	0.025	36.018	0.214	0.214	0.000	0.000	0.000	0.000
133	A	140	ARG	1	0.824	0.892	37.491	-7.725	-7.725	0.000	0.000	0.000	0.000
134	A	141	LEU	0	0.024	0.034	31.705	0.103	0.103	0.000	0.000	0.000	0.000
135	A	142	ALA	0	-0.002	-0.008	32.751	0.287	0.287	0.000	0.000	0.000	0.000
136	A	143	GLU	-1	-0.900	-0.944	33.304	8.288	8.288	0.000	0.000	0.000	0.000
137	A	144	LYS	1	0.853	0.926	29.846	-10.542	-10.542	0.000	0.000	0.000	0.000
138	A	145	LEU	0	-0.010	-0.005	28.018	0.177	0.177	0.000	0.000	0.000	0.000
139	A	146	ILE	0	0.002	0.004	29.656	0.315	0.315	0.000	0.000	0.000	0.000
140	A	147	ALA	0	-0.001	0.019	30.969	0.168	0.168	0.000	0.000	0.000	0.000
141	A	148	GLU	-1	-0.858	-0.925	27.637	11.550	11.550	0.000	0.000	0.000	0.000
142	A	149	TRP	0	-0.011	-0.011	25.564	0.114	0.114	0.000	0.000	0.000	0.000
143	A	150	THR	0	-0.089	-0.054	26.463	0.271	0.271	0.000	0.000	0.000	0.000
144	A	151	ARG	1	0.869	0.942	25.945	-12.247	-12.247	0.000	0.000	0.000	0.000
145	A	152	PRO	0	0.008	-0.020	28.395	0.342	0.342	0.000	0.000	0.000	0.000
146	A	153	ILE	0	-0.037	0.003	24.416	0.267	0.267	0.000	0.000	0.000	0.000
147	A	154	ILE	0	0.013	0.017	27.817	0.123	0.123	0.000	0.000	0.000	0.000

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