FMO DATABASE

FMODB ID: K3NG3

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1375398.072
FMO2-HF: Nuclear repulsion	1318170.715818
FMO2-HF: Total energy	-57227.356182
FMO2-MP2: Total energy	-57397.632339

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.
7.784	15.018	2.16	-3.913	-5.479	0.026

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 : -0.881 / q_NPA : -0.952

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	-0.028	-0.016	2.756	-10.447	-7.162	0.464	-1.623	-2.126	0.011
4	A	11	GLU	-1	-0.868	-0.940	2.472	34.883	37.426	1.690	-1.631	-2.601	0.013
5	A	12	GLN	0	-0.003	-0.011	3.503	-12.879	-11.473	0.006	-0.659	-0.752	0.002
6	A	13	TYR	0	-0.032	-0.010	5.799	-5.730	-5.730	0.000	0.000	0.000	0.000
7	A	14	LEU	0	-0.031	-0.017	7.269	-4.739	-4.739	0.000	0.000	0.000	0.000
8	A	15	ASP	-1	-0.784	-0.885	7.209	29.938	29.938	0.000	0.000	0.000	0.000
9	A	16	GLU	-1	-0.851	-0.889	9.509	17.577	17.577	0.000	0.000	0.000	0.000
10	A	17	LYS	1	0.876	0.943	11.440	-20.043	-20.043	0.000	0.000	0.000	0.000
11	A	18	ILE	0	-0.035	-0.025	12.282	-2.244	-2.244	0.000	0.000	0.000	0.000
12	A	19	LEU	0	0.024	0.008	12.426	-1.801	-1.801	0.000	0.000	0.000	0.000
13	A	20	ARG	1	0.811	0.877	15.188	-18.743	-18.743	0.000	0.000	0.000	0.000
14	A	21	LEU	0	-0.039	-0.012	17.216	-1.008	-1.008	0.000	0.000	0.000	0.000
15	A	22	LYS	1	0.902	0.942	17.894	-16.736	-16.736	0.000	0.000	0.000	0.000
16	A	23	ASP	-1	-0.832	-0.913	19.683	13.507	13.507	0.000	0.000	0.000	0.000
17	A	24	GLU	-1	-0.869	-0.911	21.093	12.732	12.732	0.000	0.000	0.000	0.000
18	A	25	MET	0	-0.045	-0.026	22.779	-0.472	-0.472	0.000	0.000	0.000	0.000
19	A	26	ASN	0	0.016	0.032	22.308	-0.814	-0.814	0.000	0.000	0.000	0.000
20	A	27	ILE	0	0.009	0.004	24.883	-0.572	-0.572	0.000	0.000	0.000	0.000
21	A	28	ALA	0	-0.021	-0.021	27.248	-0.483	-0.483	0.000	0.000	0.000	0.000
22	A	29	ALA	0	-0.022	-0.017	28.541	-0.411	-0.411	0.000	0.000	0.000	0.000
23	A	30	GLN	0	-0.015	-0.014	30.168	-0.171	-0.171	0.000	0.000	0.000	0.000
24	A	31	LEU	0	0.040	0.011	31.068	-0.336	-0.336	0.000	0.000	0.000	0.000
25	A	32	ASP	-1	-0.728	-0.836	33.411	8.787	8.787	0.000	0.000	0.000	0.000
26	A	33	ILE	0	-0.011	0.006	34.353	-0.282	-0.282	0.000	0.000	0.000	0.000
27	A	34	ASP	-1	-0.808	-0.896	35.979	8.239	8.239	0.000	0.000	0.000	0.000
28	A	35	THR	0	-0.091	-0.053	37.462	-0.287	-0.287	0.000	0.000	0.000	0.000
29	A	36	LEU	0	-0.045	-0.020	39.224	-0.226	-0.226	0.000	0.000	0.000	0.000
30	A	37	ASN	0	-0.004	-0.001	39.162	-0.249	-0.249	0.000	0.000	0.000	0.000
31	A	38	LYS	1	1.031	1.025	42.287	-7.216	-7.216	0.000	0.000	0.000	0.000
32	A	39	ARG	1	0.829	0.913	43.744	-7.102	-7.102	0.000	0.000	0.000	0.000
33	A	40	ILE	0	-0.053	-0.030	43.773	-0.183	-0.183	0.000	0.000	0.000	0.000
34	A	41	GLU	-1	-0.949	-0.977	44.782	6.825	6.825	0.000	0.000	0.000	0.000
35	A	42	THR	0	-0.079	-0.061	47.778	-0.140	-0.140	0.000	0.000	0.000	0.000
36	A	43	GLY	0	-0.002	0.012	49.675	-0.134	-0.134	0.000	0.000	0.000	0.000
37	A	44	ASP	-1	-0.830	-0.891	48.023	6.417	6.417	0.000	0.000	0.000	0.000
38	A	45	THR	0	-0.004	-0.018	47.410	0.132	0.132	0.000	0.000	0.000	0.000
39	A	46	SER	0	-0.112	-0.071	47.063	0.115	0.115	0.000	0.000	0.000	0.000
40	A	47	LEU	0	0.011	0.017	43.512	0.195	0.195	0.000	0.000	0.000	0.000
41	A	48	ILE	0	-0.003	0.003	40.540	-0.048	-0.048	0.000	0.000	0.000	0.000
42	A	49	ALA	0	0.016	0.015	36.501	0.117	0.117	0.000	0.000	0.000	0.000
43	A	50	MET	0	-0.024	-0.024	35.680	-0.043	-0.043	0.000	0.000	0.000	0.000
44	A	51	GLN	0	-0.020	-0.005	31.017	-0.014	-0.014	0.000	0.000	0.000	0.000
45	A	52	LYS	1	0.896	0.940	29.529	-9.143	-9.143	0.000	0.000	0.000	0.000
46	A	53	VAL	0	0.012	0.000	29.844	0.262	0.262	0.000	0.000	0.000	0.000
47	A	54	LYS	1	0.860	0.922	31.066	-8.721	-8.721	0.000	0.000	0.000	0.000
48	A	55	LEU	0	0.003	0.018	23.828	0.171	0.171	0.000	0.000	0.000	0.000
49	A	56	LEU	0	0.019	0.009	26.012	0.474	0.474	0.000	0.000	0.000	0.000
50	A	57	PRO	0	0.007	0.003	26.540	0.342	0.342	0.000	0.000	0.000	0.000
51	A	58	LYS	1	0.795	0.881	20.996	-13.066	-13.066	0.000	0.000	0.000	0.000
52	A	59	VAL	0	0.032	0.015	22.011	0.625	0.625	0.000	0.000	0.000	0.000
53	A	60	VAL	0	0.033	0.016	22.206	0.483	0.483	0.000	0.000	0.000	0.000
54	A	61	SER	0	-0.018	0.014	22.249	0.513	0.513	0.000	0.000	0.000	0.000
55	A	62	VAL	0	-0.005	-0.005	16.685	0.490	0.490	0.000	0.000	0.000	0.000
56	A	63	LEU	0	0.012	-0.005	18.406	0.589	0.589	0.000	0.000	0.000	0.000
57	A	64	SER	0	-0.024	-0.015	20.199	0.255	0.255	0.000	0.000	0.000	0.000
58	A	65	LYS	1	0.828	0.916	16.852	-15.266	-15.266	0.000	0.000	0.000	0.000
59	A	66	ALA	0	0.076	0.028	16.717	0.837	0.837	0.000	0.000	0.000	0.000
60	A	67	ASN	0	-0.021	-0.018	12.704	-0.518	-0.518	0.000	0.000	0.000	0.000
61	A	68	LEU	0	0.017	0.015	11.932	1.448	1.448	0.000	0.000	0.000	0.000
62	A	69	ALA	0	-0.004	-0.003	13.395	-0.089	-0.089	0.000	0.000	0.000	0.000
63	A	70	ASP	-1	-0.869	-0.930	11.113	22.811	22.811	0.000	0.000	0.000	0.000
64	A	71	THR	0	0.044	0.032	9.101	-1.058	-1.058	0.000	0.000	0.000	0.000
65	A	72	ILE	0	-0.043	-0.028	11.262	-1.150	-1.150	0.000	0.000	0.000	0.000
66	A	73	LEU	0	-0.072	-0.035	14.852	-1.391	-1.391	0.000	0.000	0.000	0.000
67	A	74	ASP	-1	-0.870	-0.930	11.203	23.894	23.894	0.000	0.000	0.000	0.000
68	A	75	ASN	0	-0.097	-0.066	9.994	-0.633	-0.633	0.000	0.000	0.000	0.000
69	A	76	ASN	0	-0.045	-0.060	13.891	-1.757	-1.757	0.000	0.000	0.000	0.000
70	A	77	LEU	0	0.021	0.020	17.012	-0.969	-0.969	0.000	0.000	0.000	0.000
71	A	78	LEU	0	0.013	-0.009	18.595	-0.995	-0.995	0.000	0.000	0.000	0.000
72	A	79	GLN	0	0.021	0.016	21.123	-0.477	-0.477	0.000	0.000	0.000	0.000
73	A	80	SER	0	-0.006	-0.021	22.183	-0.405	-0.405	0.000	0.000	0.000	0.000
74	A	81	VAL	0	-0.018	-0.014	22.412	-0.549	-0.549	0.000	0.000	0.000	0.000
75	A	82	ARG	1	0.733	0.835	25.069	-11.556	-11.556	0.000	0.000	0.000	0.000
76	A	83	ILE	0	0.007	0.013	25.685	-0.455	-0.455	0.000	0.000	0.000	0.000
77	A	84	TRP	0	-0.074	-0.047	26.836	-0.414	-0.414	0.000	0.000	0.000	0.000
78	A	85	LEU	0	-0.035	-0.011	28.462	-0.317	-0.317	0.000	0.000	0.000	0.000
79	A	86	GLU	-1	-0.808	-0.867	30.718	9.811	9.811	0.000	0.000	0.000	0.000
80	A	87	PRO	0	-0.045	-0.017	33.105	-0.077	-0.077	0.000	0.000	0.000	0.000
81	A	88	LEU	0	0.027	0.021	36.361	0.091	0.091	0.000	0.000	0.000	0.000
82	A	89	PRO	0	0.027	-0.004	38.581	-0.115	-0.115	0.000	0.000	0.000	0.000
83	A	90	ASP	-1	-0.741	-0.824	41.163	7.171	7.171	0.000	0.000	0.000	0.000
84	A	91	GLY	0	-0.047	-0.027	41.224	-0.155	-0.155	0.000	0.000	0.000	0.000
85	A	92	SER	0	-0.113	-0.083	41.273	0.067	0.067	0.000	0.000	0.000	0.000
86	A	93	LEU	0	-0.008	-0.011	36.632	0.162	0.162	0.000	0.000	0.000	0.000
87	A	94	PRO	0	0.029	0.029	33.360	-0.167	-0.167	0.000	0.000	0.000	0.000
88	A	95	SER	0	0.009	-0.022	36.054	-0.049	-0.049	0.000	0.000	0.000	0.000
89	A	96	PHE	0	0.037	0.012	36.065	0.259	0.259	0.000	0.000	0.000	0.000
90	A	97	GLU	-1	-0.804	-0.890	35.407	8.316	8.316	0.000	0.000	0.000	0.000
91	A	98	ILE	0	0.004	0.018	30.865	0.324	0.324	0.000	0.000	0.000	0.000
92	A	99	GLN	0	-0.036	-0.024	31.451	0.308	0.308	0.000	0.000	0.000	0.000
93	A	100	LYS	1	0.939	0.956	32.115	-8.179	-8.179	0.000	0.000	0.000	0.000
94	A	101	SER	0	-0.041	-0.027	29.586	0.204	0.204	0.000	0.000	0.000	0.000
95	A	102	LEU	0	0.001	0.002	26.152	0.399	0.399	0.000	0.000	0.000	0.000
96	A	103	PHE	0	0.003	-0.014	27.369	0.351	0.351	0.000	0.000	0.000	0.000
97	A	104	ALA	0	-0.032	-0.011	29.097	0.112	0.112	0.000	0.000	0.000	0.000
98	A	105	ALA	0	-0.012	-0.012	24.233	0.236	0.236	0.000	0.000	0.000	0.000
99	A	106	LEU	0	-0.007	-0.008	23.618	0.510	0.510	0.000	0.000	0.000	0.000
100	A	107	ASN	0	-0.043	-0.035	24.972	-0.036	-0.036	0.000	0.000	0.000	0.000
101	A	108	ASP	-1	-0.866	-0.911	24.157	11.726	11.726	0.000	0.000	0.000	0.000
102	A	109	LEU	0	0.006	0.015	18.598	0.648	0.648	0.000	0.000	0.000	0.000
103	A	110	PRO	0	0.012	0.018	18.132	-0.727	-0.727	0.000	0.000	0.000	0.000
104	A	111	VAL	0	-0.036	-0.014	20.478	0.453	0.453	0.000	0.000	0.000	0.000
105	A	112	LYS	1	0.867	0.937	20.936	-15.155	-15.155	0.000	0.000	0.000	0.000
106	A	113	THR	0	0.038	-0.001	23.168	-0.143	-0.143	0.000	0.000	0.000	0.000
107	A	114	GLU	-1	-0.844	-0.932	19.863	14.575	14.575	0.000	0.000	0.000	0.000
108	A	115	HIS	0	0.156	0.071	17.053	-1.099	-1.099	0.000	0.000	0.000	0.000
109	A	116	LEU	0	-0.038	0.010	21.330	-0.411	-0.411	0.000	0.000	0.000	0.000
110	A	117	LYS	1	0.873	0.937	24.727	-11.390	-11.390	0.000	0.000	0.000	0.000
111	A	118	GLU	-1	-0.808	-0.888	18.568	15.955	15.955	0.000	0.000	0.000	0.000
112	A	119	SER	0	-0.024	-0.015	22.338	-0.347	-0.347	0.000	0.000	0.000	0.000
113	A	120	GLY	0	0.019	0.009	23.564	-0.445	-0.445	0.000	0.000	0.000	0.000
114	A	121	LEU	0	0.016	-0.006	24.957	-0.574	-0.574	0.000	0.000	0.000	0.000
115	A	122	GLY	0	0.040	0.024	27.522	-0.377	-0.377	0.000	0.000	0.000	0.000
116	A	123	ARG	1	0.929	0.954	29.438	-9.574	-9.574	0.000	0.000	0.000	0.000
117	A	124	VAL	0	0.011	0.022	30.756	-0.386	-0.386	0.000	0.000	0.000	0.000
118	A	125	VAL	0	0.044	0.025	29.146	-0.326	-0.326	0.000	0.000	0.000	0.000
119	A	126	ILE	0	0.014	0.001	32.421	-0.355	-0.355	0.000	0.000	0.000	0.000
120	A	127	PHE	0	-0.023	-0.002	35.227	-0.314	-0.314	0.000	0.000	0.000	0.000
121	A	128	TYR	0	0.018	-0.024	34.123	-0.308	-0.308	0.000	0.000	0.000	0.000
122	A	129	THR	0	-0.053	-0.007	36.073	-0.248	-0.248	0.000	0.000	0.000	0.000
123	A	130	LYS	1	0.932	0.968	38.609	-8.303	-8.303	0.000	0.000	0.000	0.000
124	A	131	SER	0	0.002	0.003	40.251	-0.351	-0.351	0.000	0.000	0.000	0.000
125	A	132	LYS	1	0.894	0.932	42.023	-7.001	-7.001	0.000	0.000	0.000	0.000
126	A	133	ARG	1	0.845	0.931	42.066	-7.261	-7.261	0.000	0.000	0.000	0.000
127	A	134	VAL	0	-0.017	0.014	37.932	0.078	0.078	0.000	0.000	0.000	0.000
128	A	135	GLU	-1	-0.776	-0.883	40.272	7.250	7.250	0.000	0.000	0.000	0.000
129	A	136	ALA	0	0.030	0.013	40.252	0.208	0.208	0.000	0.000	0.000	0.000
130	A	137	GLN	0	-0.018	-0.027	38.607	0.305	0.305	0.000	0.000	0.000	0.000
131	A	138	LEU	0	-0.020	-0.007	34.962	0.210	0.210	0.000	0.000	0.000	0.000
132	A	139	ALA	0	0.010	0.009	36.060	0.224	0.224	0.000	0.000	0.000	0.000
133	A	140	ARG	1	0.821	0.884	37.768	-7.704	-7.704	0.000	0.000	0.000	0.000
134	A	141	LEU	0	0.007	0.025	31.673	0.088	0.088	0.000	0.000	0.000	0.000
135	A	142	ALA	0	0.014	-0.003	32.710	0.293	0.293	0.000	0.000	0.000	0.000
136	A	143	GLU	-1	-0.911	-0.946	33.311	8.212	8.212	0.000	0.000	0.000	0.000
137	A	144	LYS	1	0.853	0.923	29.556	-10.525	-10.525	0.000	0.000	0.000	0.000
138	A	145	LEU	0	-0.001	0.006	27.895	0.170	0.170	0.000	0.000	0.000	0.000
139	A	146	ILE	0	-0.017	-0.005	29.567	0.309	0.309	0.000	0.000	0.000	0.000
140	A	147	ALA	0	0.006	0.018	31.010	0.163	0.163	0.000	0.000	0.000	0.000
141	A	148	GLU	-1	-0.835	-0.911	27.676	11.575	11.575	0.000	0.000	0.000	0.000
142	A	149	TRP	0	-0.022	-0.025	25.204	0.073	0.073	0.000	0.000	0.000	0.000
143	A	150	THR	0	-0.059	-0.042	26.505	0.267	0.267	0.000	0.000	0.000	0.000
144	A	151	ARG	1	0.853	0.937	26.587	-11.898	-11.898	0.000	0.000	0.000	0.000
145	A	152	PRO	0	0.009	-0.018	28.881	0.382	0.382	0.000	0.000	0.000	0.000
146	A	153	ILE	0	-0.055	-0.018	24.691	0.084	0.084	0.000	0.000	0.000	0.000
147	A	154	ILE	0	0.002	0.023	28.108	0.039	0.039	0.000	0.000	0.000	0.000

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