FMO DATABASE

FMODB ID: 14Z7Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-508989.163749
FMO2-HF: Nuclear repulsion	471227.591026
FMO2-HF: Total energy	-37761.572723
FMO2-MP2: Total energy	-37873.115644

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.
0.632	2.68	-0.022	-1	-1.027	0.002

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 : 0.980 / q_NPA : 0.983

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	-0.008	0.005	3.871	-0.538	1.510	-0.022	-1.000	-1.027	0.002
4	A	8	ALA	0	0.025	0.017	6.593	1.517	1.517	0.000	0.000	0.000	0.000
5	A	9	ILE	0	-0.027	-0.015	9.265	0.291	0.291	0.000	0.000	0.000	0.000
6	A	10	ASP	-1	-0.894	-0.934	12.797	-15.142	-15.142	0.000	0.000	0.000	0.000
7	A	11	SER	0	-0.030	-0.030	15.161	0.953	0.953	0.000	0.000	0.000	0.000
8	A	12	TYR	0	-0.106	-0.076	17.473	-0.890	-0.890	0.000	0.000	0.000	0.000
9	A	13	GLN	0	-0.020	-0.004	19.507	0.552	0.552	0.000	0.000	0.000	0.000
10	A	14	GLU	-1	-0.862	-0.904	22.765	-12.139	-12.139	0.000	0.000	0.000	0.000
11	A	15	ASP	-1	-0.927	-0.952	24.670	-9.615	-9.615	0.000	0.000	0.000	0.000
12	A	16	PRO	0	-0.110	-0.074	26.664	-0.226	-0.226	0.000	0.000	0.000	0.000
13	A	17	SER	0	0.034	0.019	25.243	0.017	0.017	0.000	0.000	0.000	0.000
14	A	18	VAL	0	-0.017	0.001	23.079	0.308	0.308	0.000	0.000	0.000	0.000
15	A	19	VAL	0	-0.001	-0.010	26.519	0.046	0.046	0.000	0.000	0.000	0.000
16	A	20	VAL	0	0.004	0.014	22.766	-0.120	-0.120	0.000	0.000	0.000	0.000
17	A	21	SER	0	-0.025	-0.014	26.103	0.268	0.268	0.000	0.000	0.000	0.000
18	A	22	ASN	0	-0.011	-0.017	27.782	-0.493	-0.493	0.000	0.000	0.000	0.000
19	A	23	PHE	0	0.016	0.018	29.357	0.286	0.286	0.000	0.000	0.000	0.000
20	A	24	PHE	0	0.050	0.024	31.762	-0.045	-0.045	0.000	0.000	0.000	0.000
21	A	25	LYS	1	0.967	0.963	25.777	11.579	11.579	0.000	0.000	0.000	0.000
22	A	26	GLY	0	0.034	0.012	29.664	0.257	0.257	0.000	0.000	0.000	0.000
23	A	27	VAL	0	-0.021	0.013	30.517	0.258	0.258	0.000	0.000	0.000	0.000
24	A	28	ARG	1	0.908	0.946	30.174	9.419	9.419	0.000	0.000	0.000	0.000
25	A	29	VAL	0	0.033	0.019	33.425	0.211	0.211	0.000	0.000	0.000	0.000
26	A	30	PRO	0	0.011	0.015	34.873	-0.210	-0.210	0.000	0.000	0.000	0.000
27	A	31	LYS	1	0.948	0.968	33.867	8.815	8.815	0.000	0.000	0.000	0.000
28	A	32	ASP	-1	-0.895	-0.946	36.057	-7.801	-7.801	0.000	0.000	0.000	0.000
29	A	33	THR	0	-0.046	-0.029	37.045	0.175	0.175	0.000	0.000	0.000	0.000
30	A	34	GLU	-1	-0.934	-0.946	37.177	-7.563	-7.563	0.000	0.000	0.000	0.000
31	A	35	PHE	0	-0.050	-0.035	35.187	0.049	0.049	0.000	0.000	0.000	0.000
32	A	36	GLN	0	0.014	0.006	37.201	-0.057	-0.057	0.000	0.000	0.000	0.000
33	A	37	LEU	0	-0.007	0.005	31.571	-0.053	-0.053	0.000	0.000	0.000	0.000
34	A	38	TYR	0	0.013	-0.001	35.666	0.142	0.142	0.000	0.000	0.000	0.000
35	A	39	LYS	1	0.986	0.994	33.865	8.407	8.407	0.000	0.000	0.000	0.000
36	A	40	LYS	1	0.988	0.992	36.219	8.017	8.017	0.000	0.000	0.000	0.000
37	A	41	ARG	1	0.924	0.957	37.559	6.831	6.831	0.000	0.000	0.000	0.000
38	A	42	LYS	1	0.859	0.916	33.230	8.855	8.855	0.000	0.000	0.000	0.000
39	A	43	GLN	0	-0.043	-0.026	39.063	0.054	0.054	0.000	0.000	0.000	0.000
40	A	44	ASP	-1	-0.821	-0.888	35.027	-8.653	-8.653	0.000	0.000	0.000	0.000
41	A	45	GLN	0	0.031	0.012	36.874	0.302	0.302	0.000	0.000	0.000	0.000
42	A	46	PHE	0	-0.002	-0.018	36.376	-0.209	-0.209	0.000	0.000	0.000	0.000
43	A	47	VAL	0	0.040	0.016	35.973	0.162	0.162	0.000	0.000	0.000	0.000
44	A	48	LEU	0	-0.049	-0.018	37.216	-0.126	-0.126	0.000	0.000	0.000	0.000
45	A	49	HIS	1	0.837	0.880	36.626	7.785	7.785	0.000	0.000	0.000	0.000
46	A	50	GLY	0	-0.016	-0.011	38.482	-0.059	-0.059	0.000	0.000	0.000	0.000
47	A	51	GLU	-1	-0.793	-0.887	37.741	-7.695	-7.695	0.000	0.000	0.000	0.000
48	A	52	ASN	0	-0.016	-0.007	41.268	0.116	0.116	0.000	0.000	0.000	0.000
49	A	53	GLU	-1	-0.807	-0.896	41.324	-7.126	-7.126	0.000	0.000	0.000	0.000
50	A	54	ARG	1	0.890	0.952	44.372	5.847	5.847	0.000	0.000	0.000	0.000
51	A	55	LEU	0	-0.061	-0.036	45.998	0.102	0.102	0.000	0.000	0.000	0.000
52	A	56	GLU	-1	-0.829	-0.916	40.171	-7.460	-7.460	0.000	0.000	0.000	0.000
53	A	57	TYR	0	-0.046	-0.030	42.419	0.176	0.176	0.000	0.000	0.000	0.000
54	A	58	ASP	-1	-0.801	-0.877	39.540	-7.689	-7.689	0.000	0.000	0.000	0.000
55	A	59	GLY	0	0.018	0.002	41.502	0.216	0.216	0.000	0.000	0.000	0.000
56	A	60	GLU	-1	-0.877	-0.912	40.949	-7.380	-7.380	0.000	0.000	0.000	0.000
57	A	61	THR	0	0.012	0.014	41.192	0.120	0.120	0.000	0.000	0.000	0.000
58	A	62	ASP	-1	-0.770	-0.865	43.269	-6.585	-6.585	0.000	0.000	0.000	0.000
59	A	63	GLU	-1	-0.811	-0.882	41.315	-7.325	-7.325	0.000	0.000	0.000	0.000
60	A	64	LEU	0	0.037	0.014	43.615	-0.055	-0.055	0.000	0.000	0.000	0.000
61	A	65	THR	0	-0.006	-0.044	46.711	0.002	0.002	0.000	0.000	0.000	0.000
62	A	66	THR	0	-0.073	-0.024	40.789	-0.009	-0.009	0.000	0.000	0.000	0.000
63	A	67	LYS	1	0.756	0.853	41.886	7.206	7.206	0.000	0.000	0.000	0.000
64	A	68	THR	0	-0.049	-0.004	44.948	0.054	0.054	0.000	0.000	0.000	0.000
65	A	69	ASN	0	-0.057	-0.042	47.867	0.097	0.097	0.000	0.000	0.000	0.000
66	A	70	GLN	0	0.024	0.014	45.640	-0.308	-0.308	0.000	0.000	0.000	0.000
67	A	71	TYR	0	0.059	0.033	46.699	0.194	0.194	0.000	0.000	0.000	0.000
68	A	72	MET	0	-0.044	-0.020	45.773	-0.184	-0.184	0.000	0.000	0.000	0.000
69	A	73	VAL	0	0.028	0.022	47.951	0.138	0.138	0.000	0.000	0.000	0.000
70	A	74	GLY	0	0.020	-0.005	49.347	-0.085	-0.085	0.000	0.000	0.000	0.000
71	A	75	LEU	0	-0.022	0.002	49.916	0.091	0.091	0.000	0.000	0.000	0.000
72	A	76	TYR	0	0.006	-0.013	53.364	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	77	ASP	-1	-0.802	-0.862	56.684	-5.159	-5.159	0.000	0.000	0.000	0.000
74	A	78	LYS	1	0.944	0.945	58.853	4.906	4.906	0.000	0.000	0.000	0.000
75	A	79	GLN	0	-0.009	0.011	62.396	0.033	0.033	0.000	0.000	0.000	0.000
76	A	80	SER	0	-0.063	-0.065	58.754	0.011	0.011	0.000	0.000	0.000	0.000
77	A	81	GLY	0	0.004	0.007	60.819	0.001	0.001	0.000	0.000	0.000	0.000
78	A	82	LYS	1	0.932	0.975	55.416	5.396	5.396	0.000	0.000	0.000	0.000
79	A	83	ILE	0	0.002	-0.012	53.052	0.029	0.029	0.000	0.000	0.000	0.000
80	A	84	ASN	0	-0.034	0.003	49.268	-0.125	-0.125	0.000	0.000	0.000	0.000
81	A	85	LEU	0	-0.004	-0.012	48.550	0.032	0.032	0.000	0.000	0.000	0.000
82	A	86	TYR	0	0.034	0.018	44.125	-0.090	-0.090	0.000	0.000	0.000	0.000
83	A	87	ARG	1	0.889	0.937	40.408	7.366	7.366	0.000	0.000	0.000	0.000
84	A	88	ALA	0	0.000	0.000	43.252	-0.118	-0.118	0.000	0.000	0.000	0.000
85	A	89	PRO	0	-0.002	0.017	40.598	0.099	0.099	0.000	0.000	0.000	0.000
86	A	90	VAL	0	-0.011	-0.008	43.535	0.082	0.082	0.000	0.000	0.000	0.000
87	A	91	VAL	0	-0.015	-0.003	41.896	-0.049	-0.049	0.000	0.000	0.000	0.000
88	A	92	THR	0	-0.032	-0.005	45.137	0.169	0.169	0.000	0.000	0.000	0.000
89	A	93	SER	0	0.017	-0.020	45.534	-0.172	-0.172	0.000	0.000	0.000	0.000
90	A	94	LYS	1	0.849	0.923	44.027	7.000	7.000	0.000	0.000	0.000	0.000
91	A	95	ILE	0	-0.012	-0.005	46.100	-0.116	-0.116	0.000	0.000	0.000	0.000
92	A	96	VAL	0	0.009	0.007	45.349	0.128	0.128	0.000	0.000	0.000	0.000
93	A	97	SER	0	-0.020	-0.010	46.393	-0.028	-0.028	0.000	0.000	0.000	0.000
94	A	98	LYS	1	0.776	0.892	39.899	7.165	7.165	0.000	0.000	0.000	0.000

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