FMO DATABASE

FMODB ID: GN961

Calculation Name: 3NFG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NFG

Chain ID: A

ChEMBL ID:

UniProt ID: Q6FNZ9

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	94
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-509864.552319
FMO2-HF: Nuclear repulsion	472102.650483
FMO2-HF: Total energy	-37761.901836
FMO2-MP2: Total energy	-37873.455839

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:5:ARG)

Summations of interaction energy for fragment #1(A:5:ARG)

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.
0.261	2.751	-0.022	-1.352	-1.117	0.004

Interaction energy analysis for fragmet #1(A:5:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.985 / q_NPA : 0.990

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

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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	7	ILE	0	0.006	0.005	3.879	-1.718	0.772	-0.022	-1.352	-1.117	0.004
4	A	8	ALA	0	0.016	0.010	6.745	1.790	1.790	0.000	0.000	0.000	0.000
5	A	9	ILE	0	-0.018	-0.012	9.280	0.286	0.286	0.000	0.000	0.000	0.000
6	A	10	ASP	-1	-0.908	-0.925	12.718	-15.014	-15.014	0.000	0.000	0.000	0.000
7	A	11	SER	0	-0.040	-0.037	14.997	0.976	0.976	0.000	0.000	0.000	0.000
8	A	12	TYR	0	-0.089	-0.080	17.172	-0.983	-0.983	0.000	0.000	0.000	0.000
9	A	13	GLN	0	0.009	0.006	19.536	0.616	0.616	0.000	0.000	0.000	0.000
10	A	14	GLU	-1	-0.882	-0.907	22.326	-12.336	-12.336	0.000	0.000	0.000	0.000
11	A	15	ASP	-1	-0.907	-0.954	24.778	-9.354	-9.354	0.000	0.000	0.000	0.000
12	A	16	PRO	0	-0.119	-0.076	26.996	-0.239	-0.239	0.000	0.000	0.000	0.000
13	A	17	SER	0	0.005	0.010	25.637	0.048	0.048	0.000	0.000	0.000	0.000
14	A	18	VAL	0	0.002	0.009	23.254	0.130	0.130	0.000	0.000	0.000	0.000
15	A	19	VAL	0	0.004	-0.010	26.742	0.049	0.049	0.000	0.000	0.000	0.000
16	A	20	VAL	0	0.000	0.007	22.768	-0.006	-0.006	0.000	0.000	0.000	0.000
17	A	21	SER	0	-0.006	0.000	26.076	0.202	0.202	0.000	0.000	0.000	0.000
18	A	22	ASN	0	-0.021	-0.021	27.827	-0.477	-0.477	0.000	0.000	0.000	0.000
19	A	23	PHE	0	0.021	0.019	29.467	0.301	0.301	0.000	0.000	0.000	0.000
20	A	24	PHE	0	0.052	0.021	31.457	0.050	0.050	0.000	0.000	0.000	0.000
21	A	25	LYS	1	0.971	0.974	25.666	11.625	11.625	0.000	0.000	0.000	0.000
22	A	26	GLY	0	0.049	0.022	29.726	0.247	0.247	0.000	0.000	0.000	0.000
23	A	27	VAL	0	-0.038	0.006	30.443	0.209	0.209	0.000	0.000	0.000	0.000
24	A	28	ARG	1	0.874	0.925	30.155	9.464	9.464	0.000	0.000	0.000	0.000
25	A	29	VAL	0	0.042	0.016	33.579	0.145	0.145	0.000	0.000	0.000	0.000
26	A	30	PRO	0	0.019	0.028	35.105	-0.216	-0.216	0.000	0.000	0.000	0.000
27	A	31	LYS	1	0.950	0.977	34.269	8.810	8.810	0.000	0.000	0.000	0.000
28	A	32	ASP	-1	-0.886	-0.945	36.126	-7.861	-7.861	0.000	0.000	0.000	0.000
29	A	33	THR	0	-0.061	-0.038	37.322	0.220	0.220	0.000	0.000	0.000	0.000
30	A	34	GLU	-1	-0.930	-0.954	37.478	-7.569	-7.569	0.000	0.000	0.000	0.000
31	A	35	PHE	0	-0.033	-0.025	35.564	-0.012	-0.012	0.000	0.000	0.000	0.000
32	A	36	GLN	0	-0.012	-0.007	37.238	-0.040	-0.040	0.000	0.000	0.000	0.000
33	A	37	LEU	0	-0.005	0.005	31.517	-0.091	-0.091	0.000	0.000	0.000	0.000
34	A	38	TYR	0	0.022	0.009	35.567	0.165	0.165	0.000	0.000	0.000	0.000
35	A	39	LYS	1	0.976	0.988	33.106	8.723	8.723	0.000	0.000	0.000	0.000
36	A	40	LYS	1	0.969	0.986	36.327	8.069	8.069	0.000	0.000	0.000	0.000
37	A	41	ARG	1	0.922	0.949	37.712	6.866	6.866	0.000	0.000	0.000	0.000
38	A	42	LYS	1	0.847	0.898	33.428	8.788	8.788	0.000	0.000	0.000	0.000
39	A	43	GLN	0	-0.013	-0.002	39.335	0.032	0.032	0.000	0.000	0.000	0.000
40	A	44	ASP	-1	-0.808	-0.872	35.139	-8.630	-8.630	0.000	0.000	0.000	0.000
41	A	45	GLN	0	0.031	0.008	37.123	0.249	0.249	0.000	0.000	0.000	0.000
42	A	46	PHE	0	-0.004	-0.017	36.287	-0.217	-0.217	0.000	0.000	0.000	0.000
43	A	47	VAL	0	0.015	0.006	36.035	0.171	0.171	0.000	0.000	0.000	0.000
44	A	48	LEU	0	-0.041	-0.010	37.043	-0.148	-0.148	0.000	0.000	0.000	0.000
45	A	49	HIS	1	0.839	0.875	36.688	7.771	7.771	0.000	0.000	0.000	0.000
46	A	50	GLY	0	-0.009	-0.004	38.485	-0.080	-0.080	0.000	0.000	0.000	0.000
47	A	51	GLU	-1	-0.812	-0.887	37.545	-7.665	-7.665	0.000	0.000	0.000	0.000
48	A	52	ASN	0	-0.008	0.000	41.247	0.099	0.099	0.000	0.000	0.000	0.000
49	A	53	GLU	-1	-0.811	-0.901	41.056	-7.129	-7.129	0.000	0.000	0.000	0.000
50	A	54	ARG	1	0.900	0.952	44.242	5.892	5.892	0.000	0.000	0.000	0.000
51	A	55	LEU	0	-0.056	-0.016	45.989	0.088	0.088	0.000	0.000	0.000	0.000
52	A	56	GLU	-1	-0.825	-0.919	40.073	-7.461	-7.461	0.000	0.000	0.000	0.000
53	A	57	TYR	0	-0.027	-0.021	42.358	0.201	0.201	0.000	0.000	0.000	0.000
54	A	58	ASP	-1	-0.805	-0.882	39.550	-7.672	-7.672	0.000	0.000	0.000	0.000
55	A	59	GLY	0	0.004	-0.005	41.363	0.232	0.232	0.000	0.000	0.000	0.000
56	A	60	GLU	-1	-0.823	-0.887	40.853	-7.277	-7.277	0.000	0.000	0.000	0.000
57	A	61	THR	0	-0.016	0.006	40.976	0.113	0.113	0.000	0.000	0.000	0.000
58	A	62	ASP	-1	-0.750	-0.843	42.968	-6.618	-6.618	0.000	0.000	0.000	0.000
59	A	63	GLU	-1	-0.794	-0.865	41.086	-7.337	-7.337	0.000	0.000	0.000	0.000
60	A	64	LEU	0	0.033	0.021	43.546	-0.044	-0.044	0.000	0.000	0.000	0.000
61	A	65	THR	0	-0.036	-0.055	46.779	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	66	THR	0	-0.068	-0.044	40.747	-0.037	-0.037	0.000	0.000	0.000	0.000
63	A	67	LYS	1	0.759	0.856	41.918	7.188	7.188	0.000	0.000	0.000	0.000
64	A	68	THR	0	-0.065	-0.027	44.551	0.040	0.040	0.000	0.000	0.000	0.000
65	A	69	ASN	0	-0.047	-0.030	47.283	0.120	0.120	0.000	0.000	0.000	0.000
66	A	70	GLN	0	0.058	0.037	45.418	-0.341	-0.341	0.000	0.000	0.000	0.000
67	A	71	TYR	0	0.039	0.022	46.333	0.205	0.205	0.000	0.000	0.000	0.000
68	A	72	MET	0	-0.027	-0.007	45.839	-0.182	-0.182	0.000	0.000	0.000	0.000
69	A	73	VAL	0	0.050	0.042	47.585	0.143	0.143	0.000	0.000	0.000	0.000
70	A	74	GLY	0	0.009	-0.012	49.149	-0.078	-0.078	0.000	0.000	0.000	0.000
71	A	75	LEU	0	-0.028	-0.002	49.821	0.083	0.083	0.000	0.000	0.000	0.000
72	A	76	TYR	0	0.013	-0.004	53.292	-0.009	-0.009	0.000	0.000	0.000	0.000
73	A	77	ASP	-1	-0.786	-0.850	56.585	-5.129	-5.129	0.000	0.000	0.000	0.000
74	A	78	LYS	1	0.948	0.952	58.953	4.918	4.918	0.000	0.000	0.000	0.000
75	A	79	GLN	0	-0.031	-0.004	62.166	0.052	0.052	0.000	0.000	0.000	0.000
76	A	80	SER	0	-0.070	-0.073	59.014	0.009	0.009	0.000	0.000	0.000	0.000
77	A	81	GLY	0	0.010	0.014	60.678	-0.018	-0.018	0.000	0.000	0.000	0.000
78	A	82	LYS	1	0.925	0.970	55.446	5.369	5.369	0.000	0.000	0.000	0.000
79	A	83	ILE	0	0.001	-0.013	52.953	0.040	0.040	0.000	0.000	0.000	0.000
80	A	84	ASN	0	-0.037	0.008	49.309	-0.128	-0.128	0.000	0.000	0.000	0.000
81	A	85	LEU	0	-0.001	-0.018	48.586	0.068	0.068	0.000	0.000	0.000	0.000
82	A	86	TYR	0	0.030	0.008	44.345	-0.081	-0.081	0.000	0.000	0.000	0.000
83	A	87	ARG	1	0.858	0.909	40.283	7.396	7.396	0.000	0.000	0.000	0.000
84	A	88	ALA	0	-0.002	0.001	42.784	-0.141	-0.141	0.000	0.000	0.000	0.000
85	A	89	PRO	0	0.005	0.014	40.646	0.097	0.097	0.000	0.000	0.000	0.000
86	A	90	VAL	0	-0.014	-0.013	43.429	0.102	0.102	0.000	0.000	0.000	0.000
87	A	91	VAL	0	0.003	-0.001	42.144	-0.069	-0.069	0.000	0.000	0.000	0.000
88	A	92	THR	0	-0.002	0.016	45.132	0.132	0.132	0.000	0.000	0.000	0.000
89	A	93	SER	0	-0.012	-0.025	45.630	-0.185	-0.185	0.000	0.000	0.000	0.000
90	A	94	LYS	1	0.797	0.882	43.843	7.054	7.054	0.000	0.000	0.000	0.000
91	A	95	ILE	0	-0.015	-0.011	46.182	-0.105	-0.105	0.000	0.000	0.000	0.000
92	A	96	VAL	0	0.002	0.007	45.158	0.119	0.119	0.000	0.000	0.000	0.000
93	A	97	SER	0	-0.016	-0.007	46.604	0.003	0.003	0.000	0.000	0.000	0.000
94	A	98	LYS	1	0.772	0.880	39.560	7.195	7.195	0.000	0.000	0.000	0.000

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Highlights

Manual

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:ARG)