FMO DATABASE

FMODB ID: VR751

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

Total energy (hartree)

FMO2-HF: Electronic energy	-507599.490814
FMO2-HF: Nuclear repulsion	469838.579294
FMO2-HF: Total energy	-37760.911519
FMO2-MP2: Total energy	-37872.42493

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.
1.018	2.643	-0.021	-0.727	-0.877	-0.001

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 : 0.952 / q_NPA : 0.950

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	0.000	0.005	3.871	-0.204	1.421	-0.021	-0.727	-0.877	-0.001
4	A	8	ALA	0	0.034	0.021	6.554	1.547	1.547	0.000	0.000	0.000	0.000
5	A	9	ILE	0	-0.036	-0.019	9.225	0.178	0.178	0.000	0.000	0.000	0.000
6	A	10	ASP	-1	-0.922	-0.955	12.756	-15.099	-15.099	0.000	0.000	0.000	0.000
7	A	11	SER	0	-0.028	-0.017	15.124	1.014	1.014	0.000	0.000	0.000	0.000
8	A	12	TYR	0	-0.052	-0.027	17.530	-0.814	-0.814	0.000	0.000	0.000	0.000
9	A	13	GLN	0	-0.027	-0.010	19.572	0.667	0.667	0.000	0.000	0.000	0.000
10	A	14	GLU	-1	-0.872	-0.941	23.067	-11.901	-11.901	0.000	0.000	0.000	0.000
11	A	15	ASP	-1	-0.955	-0.957	25.082	-9.592	-9.592	0.000	0.000	0.000	0.000
12	A	16	PRO	0	-0.099	-0.067	27.057	-0.227	-0.227	0.000	0.000	0.000	0.000
13	A	17	SER	0	0.044	0.027	25.241	0.062	0.062	0.000	0.000	0.000	0.000
14	A	18	VAL	0	-0.019	-0.007	23.458	0.294	0.294	0.000	0.000	0.000	0.000
15	A	19	VAL	0	0.000	-0.010	26.857	0.052	0.052	0.000	0.000	0.000	0.000
16	A	20	VAL	0	0.004	0.014	23.223	-0.125	-0.125	0.000	0.000	0.000	0.000
17	A	21	SER	0	-0.021	-0.008	26.564	0.265	0.265	0.000	0.000	0.000	0.000
18	A	22	ASN	0	-0.022	-0.021	28.334	-0.417	-0.417	0.000	0.000	0.000	0.000
19	A	23	PHE	0	0.020	0.018	29.873	0.288	0.288	0.000	0.000	0.000	0.000
20	A	24	PHE	0	0.053	0.022	32.327	-0.043	-0.043	0.000	0.000	0.000	0.000
21	A	25	LYS	1	0.963	0.958	25.766	11.540	11.540	0.000	0.000	0.000	0.000
22	A	26	GLY	0	0.033	0.014	30.171	0.255	0.255	0.000	0.000	0.000	0.000
23	A	27	VAL	0	-0.028	0.010	31.068	0.254	0.254	0.000	0.000	0.000	0.000
24	A	28	ARG	1	0.928	0.953	30.566	9.319	9.319	0.000	0.000	0.000	0.000
25	A	29	VAL	0	0.025	0.015	33.827	0.209	0.209	0.000	0.000	0.000	0.000
26	A	30	PRO	0	0.013	0.015	35.191	-0.206	-0.206	0.000	0.000	0.000	0.000
27	A	31	LYS	1	0.950	0.960	33.487	8.850	8.850	0.000	0.000	0.000	0.000
28	A	32	ASP	-1	-0.904	-0.947	36.200	-7.693	-7.693	0.000	0.000	0.000	0.000
29	A	33	THR	0	-0.036	-0.015	37.351	0.178	0.178	0.000	0.000	0.000	0.000
30	A	34	GLU	-1	-0.939	-0.951	37.415	-7.484	-7.484	0.000	0.000	0.000	0.000
31	A	35	PHE	0	-0.048	-0.030	35.233	0.047	0.047	0.000	0.000	0.000	0.000
32	A	36	GLN	0	0.015	0.006	37.520	-0.044	-0.044	0.000	0.000	0.000	0.000
33	A	37	LEU	0	-0.007	0.004	31.907	-0.049	-0.049	0.000	0.000	0.000	0.000
34	A	38	TYR	0	0.012	-0.002	36.101	0.148	0.148	0.000	0.000	0.000	0.000
35	A	39	LYS	1	0.986	0.998	34.817	8.073	8.073	0.000	0.000	0.000	0.000
36	A	40	LYS	1	0.990	0.991	36.809	7.912	7.912	0.000	0.000	0.000	0.000
37	A	41	ARG	1	0.924	0.956	38.152	6.737	6.737	0.000	0.000	0.000	0.000
38	A	42	LYS	1	0.909	0.957	33.792	8.647	8.647	0.000	0.000	0.000	0.000
39	A	43	GLN	0	-0.018	-0.016	39.494	0.130	0.130	0.000	0.000	0.000	0.000
40	A	44	ASP	-1	-0.868	-0.927	35.137	-8.550	-8.550	0.000	0.000	0.000	0.000
41	A	45	GLN	0	0.013	0.001	36.969	0.358	0.358	0.000	0.000	0.000	0.000
42	A	46	PHE	0	0.007	-0.011	36.399	-0.194	-0.194	0.000	0.000	0.000	0.000
43	A	47	VAL	0	0.052	0.024	36.178	0.150	0.150	0.000	0.000	0.000	0.000
44	A	48	LEU	0	-0.050	-0.019	37.430	-0.120	-0.120	0.000	0.000	0.000	0.000
45	A	49	HIS	1	0.838	0.896	36.866	7.671	7.671	0.000	0.000	0.000	0.000
46	A	50	GLY	0	-0.012	-0.011	38.837	-0.056	-0.056	0.000	0.000	0.000	0.000
47	A	51	GLU	-1	-0.839	-0.930	38.281	-7.516	-7.516	0.000	0.000	0.000	0.000
48	A	52	ASN	0	0.001	-0.004	41.653	0.165	0.165	0.000	0.000	0.000	0.000
49	A	53	GLU	-1	-0.860	-0.932	41.593	-7.041	-7.041	0.000	0.000	0.000	0.000
50	A	54	ARG	1	0.909	0.964	44.797	5.769	5.769	0.000	0.000	0.000	0.000
51	A	55	LEU	0	-0.068	-0.036	46.388	0.094	0.094	0.000	0.000	0.000	0.000
52	A	56	GLU	-1	-0.858	-0.921	40.393	-7.387	-7.387	0.000	0.000	0.000	0.000
53	A	57	TYR	0	-0.056	-0.032	42.670	0.173	0.173	0.000	0.000	0.000	0.000
54	A	58	ASP	-1	-0.800	-0.875	39.749	-7.526	-7.526	0.000	0.000	0.000	0.000
55	A	59	GLY	0	0.030	0.007	41.644	0.209	0.209	0.000	0.000	0.000	0.000
56	A	60	GLU	-1	-0.946	-0.951	40.944	-7.403	-7.403	0.000	0.000	0.000	0.000
57	A	61	THR	0	-0.019	-0.002	41.231	0.112	0.112	0.000	0.000	0.000	0.000
58	A	62	ASP	-1	-0.832	-0.917	43.269	-6.485	-6.485	0.000	0.000	0.000	0.000
59	A	63	GLU	-1	-0.849	-0.917	41.071	-7.233	-7.233	0.000	0.000	0.000	0.000
60	A	64	LEU	0	0.013	0.003	43.532	-0.053	-0.053	0.000	0.000	0.000	0.000
61	A	65	THR	0	0.016	0.003	46.696	0.008	0.008	0.000	0.000	0.000	0.000
62	A	66	THR	0	-0.011	0.008	41.028	0.062	0.062	0.000	0.000	0.000	0.000
63	A	67	LYS	1	0.794	0.875	41.545	7.152	7.152	0.000	0.000	0.000	0.000
64	A	68	THR	0	-0.051	-0.009	45.135	0.048	0.048	0.000	0.000	0.000	0.000
65	A	69	ASN	0	-0.062	-0.047	48.064	0.108	0.108	0.000	0.000	0.000	0.000
66	A	70	GLN	0	0.006	0.006	46.300	-0.248	-0.248	0.000	0.000	0.000	0.000
67	A	71	TYR	0	0.050	0.026	46.876	0.133	0.133	0.000	0.000	0.000	0.000
68	A	72	MET	0	-0.048	-0.021	45.824	-0.170	-0.170	0.000	0.000	0.000	0.000
69	A	73	VAL	0	0.025	0.020	47.973	0.133	0.133	0.000	0.000	0.000	0.000
70	A	74	GLY	0	0.017	-0.005	49.304	-0.083	-0.083	0.000	0.000	0.000	0.000
71	A	75	LEU	0	-0.020	0.002	49.915	0.089	0.089	0.000	0.000	0.000	0.000
72	A	76	TYR	0	0.007	-0.013	53.321	-0.024	-0.024	0.000	0.000	0.000	0.000
73	A	77	ASP	-1	-0.865	-0.924	56.642	-5.134	-5.134	0.000	0.000	0.000	0.000
74	A	78	LYS	1	0.938	0.943	58.811	4.846	4.846	0.000	0.000	0.000	0.000
75	A	79	GLN	0	0.001	0.012	62.377	0.026	0.026	0.000	0.000	0.000	0.000
76	A	80	SER	0	-0.027	-0.013	58.749	0.007	0.007	0.000	0.000	0.000	0.000
77	A	81	GLY	0	0.033	0.026	60.777	0.001	0.001	0.000	0.000	0.000	0.000
78	A	82	LYS	1	0.924	0.967	55.374	5.380	5.380	0.000	0.000	0.000	0.000
79	A	83	ILE	0	-0.001	-0.010	53.095	0.030	0.030	0.000	0.000	0.000	0.000
80	A	84	ASN	0	-0.023	0.007	49.185	-0.144	-0.144	0.000	0.000	0.000	0.000
81	A	85	LEU	0	-0.010	-0.016	48.594	0.032	0.032	0.000	0.000	0.000	0.000
82	A	86	TYR	0	0.030	0.020	43.974	-0.087	-0.087	0.000	0.000	0.000	0.000
83	A	87	ARG	1	0.921	0.960	40.851	7.234	7.234	0.000	0.000	0.000	0.000
84	A	88	ALA	0	0.001	-0.005	43.209	-0.115	-0.115	0.000	0.000	0.000	0.000
85	A	89	PRO	0	-0.007	0.015	40.542	0.093	0.093	0.000	0.000	0.000	0.000
86	A	90	VAL	0	-0.007	-0.010	43.535	0.079	0.079	0.000	0.000	0.000	0.000
87	A	91	VAL	0	-0.016	-0.002	42.032	-0.047	-0.047	0.000	0.000	0.000	0.000
88	A	92	THR	0	-0.036	-0.013	45.228	0.166	0.166	0.000	0.000	0.000	0.000
89	A	93	SER	0	0.028	-0.012	45.532	-0.166	-0.166	0.000	0.000	0.000	0.000
90	A	94	LYS	1	0.935	0.973	45.383	6.696	6.696	0.000	0.000	0.000	0.000
91	A	95	ILE	0	-0.011	-0.006	46.254	-0.109	-0.109	0.000	0.000	0.000	0.000
92	A	96	VAL	0	0.011	0.008	45.374	0.126	0.126	0.000	0.000	0.000	0.000
93	A	97	SER	0	-0.014	-0.006	46.568	-0.030	-0.030	0.000	0.000	0.000	0.000
94	A	98	LYS	1	0.841	0.931	40.469	7.021	7.021	0.000	0.000	0.000	0.000

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