FMO DATABASE

FMODB ID: N1Y3Q

Calculation Name: 3NFG-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NFG

Chain ID: H

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	120
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-843880.19157
FMO2-HF: Nuclear repulsion	797279.290783
FMO2-HF: Total energy	-46600.900787
FMO2-MP2: Total energy	-46737.857953

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(H:24:GLY)

Summations of interaction energy for fragment #1(H:24:GLY)

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.
0.036	0.996	-0.005	-0.366	-0.59	0.001

Interaction energy analysis for fragmet #1(H:24:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : -0.012

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	H	26	GLN	0	0.017	0.003	3.844	-0.298	0.662	-0.005	-0.366	-0.590	0.001
4	H	27	PRO	0	-0.038	-0.004	6.579	0.418	0.418	0.000	0.000	0.000	0.000
5	H	28	PRO	0	0.015	0.014	10.127	-0.064	-0.064	0.000	0.000	0.000	0.000
6	H	29	SER	0	0.005	-0.003	13.276	-0.021	-0.021	0.000	0.000	0.000	0.000
7	H	30	ASP	-1	-0.900	-0.948	14.751	-0.358	-0.358	0.000	0.000	0.000	0.000
8	H	31	TYR	0	-0.024	-0.001	14.213	0.066	0.066	0.000	0.000	0.000	0.000
9	H	32	LYS	1	0.963	0.975	14.034	0.246	0.246	0.000	0.000	0.000	0.000
10	H	33	GLN	0	-0.044	-0.028	11.307	-0.033	-0.033	0.000	0.000	0.000	0.000
11	H	34	CYS	0	0.003	0.006	14.258	0.037	0.037	0.000	0.000	0.000	0.000
12	H	35	LYS	1	0.999	0.982	12.902	0.335	0.335	0.000	0.000	0.000	0.000
13	H	36	HIS	0	-0.053	-0.023	17.556	0.014	0.014	0.000	0.000	0.000	0.000
14	H	37	LEU	0	0.013	0.019	17.881	0.003	0.003	0.000	0.000	0.000	0.000
15	H	38	LYS	1	0.914	0.953	21.880	0.089	0.089	0.000	0.000	0.000	0.000
16	H	39	SER	0	0.006	0.001	24.980	0.002	0.002	0.000	0.000	0.000	0.000
17	H	40	PHE	0	0.062	0.026	26.449	-0.004	-0.004	0.000	0.000	0.000	0.000
18	H	41	PRO	0	0.035	0.027	28.212	0.005	0.005	0.000	0.000	0.000	0.000
19	H	42	VAL	0	0.009	-0.010	26.190	0.004	0.004	0.000	0.000	0.000	0.000
20	H	43	SER	0	-0.052	-0.043	29.258	0.003	0.003	0.000	0.000	0.000	0.000
21	H	44	GLU	-1	-0.899	-0.952	32.553	0.006	0.006	0.000	0.000	0.000	0.000
22	H	45	LEU	0	-0.018	0.003	28.792	0.001	0.001	0.000	0.000	0.000	0.000
23	H	46	LYS	1	0.819	0.913	28.828	-0.049	-0.049	0.000	0.000	0.000	0.000
24	H	47	GLY	0	0.033	0.011	34.402	0.001	0.001	0.000	0.000	0.000	0.000
25	H	48	ASP	-1	-0.920	-0.949	38.095	0.026	0.026	0.000	0.000	0.000	0.000
26	H	49	ASN	0	-0.026	-0.020	40.420	0.000	0.000	0.000	0.000	0.000	0.000
27	H	50	LYS	1	0.887	0.958	36.912	-0.007	-0.007	0.000	0.000	0.000	0.000
28	H	51	GLU	-1	-0.720	-0.837	37.817	0.012	0.012	0.000	0.000	0.000	0.000
29	H	52	LEU	0	-0.112	-0.042	29.847	-0.004	-0.004	0.000	0.000	0.000	0.000
30	H	53	TRP	0	0.005	-0.027	34.398	-0.001	-0.001	0.000	0.000	0.000	0.000
31	H	54	LEU	0	-0.024	-0.007	29.591	-0.003	-0.003	0.000	0.000	0.000	0.000
32	H	55	MET	0	-0.012	0.003	33.023	0.001	0.001	0.000	0.000	0.000	0.000
33	H	56	LYS	1	0.951	0.994	32.743	0.021	0.021	0.000	0.000	0.000	0.000
34	H	57	VAL	0	0.034	0.005	34.335	0.003	0.003	0.000	0.000	0.000	0.000
35	H	58	PRO	0	-0.023	-0.004	35.244	-0.004	-0.004	0.000	0.000	0.000	0.000
36	H	59	ALA	0	0.017	-0.003	33.679	0.000	0.000	0.000	0.000	0.000	0.000
37	H	60	ASN	0	-0.090	-0.054	35.360	-0.001	-0.001	0.000	0.000	0.000	0.000
38	H	61	ILE	0	-0.009	0.009	38.316	0.001	0.001	0.000	0.000	0.000	0.000
39	H	62	ASP	-1	-0.818	-0.889	37.725	-0.050	-0.050	0.000	0.000	0.000	0.000
40	H	63	ILE	0	0.022	-0.013	36.030	0.003	0.003	0.000	0.000	0.000	0.000
41	H	64	SER	0	-0.071	-0.046	37.063	0.003	0.003	0.000	0.000	0.000	0.000
42	H	65	GLN	0	-0.051	-0.025	38.826	0.004	0.004	0.000	0.000	0.000	0.000
43	H	66	LEU	0	-0.042	-0.004	40.753	0.002	0.002	0.000	0.000	0.000	0.000
44	H	67	LYS	1	0.921	0.956	42.424	0.027	0.027	0.000	0.000	0.000	0.000
45	H	68	SER	0	-0.014	-0.014	44.731	0.001	0.001	0.000	0.000	0.000	0.000
46	H	69	LEU	0	0.042	0.023	39.537	-0.002	-0.002	0.000	0.000	0.000	0.000
47	H	70	PRO	0	-0.020	-0.002	44.261	0.002	0.002	0.000	0.000	0.000	0.000
48	H	71	LEU	0	-0.010	-0.013	41.007	0.000	0.000	0.000	0.000	0.000	0.000
49	H	72	ASP	-1	-0.871	-0.937	45.721	0.000	0.000	0.000	0.000	0.000	0.000
50	H	73	THR	0	-0.028	-0.033	44.665	0.000	0.000	0.000	0.000	0.000	0.000
51	H	74	ASP	-1	-0.907	-0.939	45.500	0.007	0.007	0.000	0.000	0.000	0.000
52	H	75	ALA	0	-0.033	-0.001	48.046	0.001	0.001	0.000	0.000	0.000	0.000
53	H	76	THR	0	-0.034	-0.016	44.489	0.000	0.000	0.000	0.000	0.000	0.000
54	H	77	VAL	0	0.007	-0.008	44.893	-0.001	-0.001	0.000	0.000	0.000	0.000
55	H	78	SER	0	0.014	0.009	46.909	0.000	0.000	0.000	0.000	0.000	0.000
56	H	79	THR	0	-0.052	-0.033	47.892	-0.001	-0.001	0.000	0.000	0.000	0.000
57	H	80	VAL	0	0.020	0.014	44.292	0.001	0.001	0.000	0.000	0.000	0.000
58	H	81	GLU	-1	-0.951	-0.979	47.580	-0.018	-0.018	0.000	0.000	0.000	0.000
59	H	82	LEU	0	-0.007	0.013	42.435	0.000	0.000	0.000	0.000	0.000	0.000
60	H	83	GLY	0	-0.012	-0.010	46.553	-0.002	-0.002	0.000	0.000	0.000	0.000
61	H	84	SER	0	-0.040	-0.023	47.219	0.001	0.001	0.000	0.000	0.000	0.000
62	H	85	LYS	1	0.989	0.989	45.660	0.033	0.033	0.000	0.000	0.000	0.000
63	H	86	ASN	0	0.042	0.017	47.949	0.001	0.001	0.000	0.000	0.000	0.000
64	H	87	PHE	0	-0.031	-0.010	43.244	-0.002	-0.002	0.000	0.000	0.000	0.000
65	H	88	ASN	0	0.010	0.000	44.947	0.001	0.001	0.000	0.000	0.000	0.000
66	H	89	VAL	0	0.015	0.003	42.322	-0.002	-0.002	0.000	0.000	0.000	0.000
67	H	90	LEU	0	0.021	0.013	40.189	0.001	0.001	0.000	0.000	0.000	0.000
68	H	91	GLN	0	0.007	0.012	40.433	0.001	0.001	0.000	0.000	0.000	0.000
69	H	92	ASN	0	0.019	-0.012	37.025	0.000	0.000	0.000	0.000	0.000	0.000
70	H	93	THR	0	0.050	0.026	36.629	0.001	0.001	0.000	0.000	0.000	0.000
71	H	94	SER	0	-0.014	0.020	39.216	0.002	0.002	0.000	0.000	0.000	0.000
72	H	95	THR	0	-0.023	-0.016	41.226	0.000	0.000	0.000	0.000	0.000	0.000
73	H	96	GLN	0	0.000	-0.016	41.653	0.002	0.002	0.000	0.000	0.000	0.000
74	H	97	GLU	-1	-0.978	-0.978	39.221	0.008	0.008	0.000	0.000	0.000	0.000
75	H	98	GLY	0	-0.006	-0.009	36.512	0.002	0.002	0.000	0.000	0.000	0.000
76	H	99	SER	0	0.013	0.016	36.992	0.001	0.001	0.000	0.000	0.000	0.000
77	H	100	ASP	-1	-0.875	-0.916	32.739	0.049	0.049	0.000	0.000	0.000	0.000
78	H	101	ASN	0	-0.026	-0.029	31.610	-0.006	-0.006	0.000	0.000	0.000	0.000
79	H	102	THR	0	-0.061	-0.043	29.547	0.003	0.003	0.000	0.000	0.000	0.000
80	H	103	ASN	0	0.000	0.005	26.562	0.009	0.009	0.000	0.000	0.000	0.000
81	H	104	LEU	0	-0.060	-0.023	25.197	-0.002	-0.002	0.000	0.000	0.000	0.000
82	H	105	SER	0	0.042	0.019	22.525	0.006	0.006	0.000	0.000	0.000	0.000
83	H	106	LEU	0	0.019	0.018	23.411	-0.008	-0.008	0.000	0.000	0.000	0.000
84	H	107	LEU	0	-0.023	-0.017	17.552	0.013	0.013	0.000	0.000	0.000	0.000
85	H	108	ILE	0	0.021	0.008	21.277	-0.015	-0.015	0.000	0.000	0.000	0.000
86	H	109	PRO	0	0.028	0.011	19.714	0.011	0.011	0.000	0.000	0.000	0.000
87	H	110	SER	0	-0.059	-0.021	18.315	0.016	0.016	0.000	0.000	0.000	0.000
88	H	111	GLU	-1	-0.873	-0.970	20.347	0.011	0.011	0.000	0.000	0.000	0.000
89	H	112	LYS	1	0.878	0.948	18.868	-0.136	-0.136	0.000	0.000	0.000	0.000
90	H	113	LYS	1	0.998	1.003	14.315	-0.135	-0.135	0.000	0.000	0.000	0.000
91	H	114	LYS	1	1.000	1.007	17.611	0.016	0.016	0.000	0.000	0.000	0.000
92	H	115	GLU	-1	-0.908	-0.956	12.298	-0.163	-0.163	0.000	0.000	0.000	0.000
93	H	116	THR	0	-0.038	-0.014	12.367	-0.004	-0.004	0.000	0.000	0.000	0.000
94	H	117	LEU	0	0.027	0.000	14.965	0.002	0.002	0.000	0.000	0.000	0.000
95	H	118	LYS	1	0.917	0.961	15.957	-0.070	-0.070	0.000	0.000	0.000	0.000
96	H	119	VAL	0	0.065	0.036	18.502	-0.018	-0.018	0.000	0.000	0.000	0.000
97	H	120	ALA	0	-0.009	0.008	21.285	0.009	0.009	0.000	0.000	0.000	0.000
98	H	121	THR	0	0.018	0.015	23.328	0.004	0.004	0.000	0.000	0.000	0.000
99	H	122	SER	0	-0.034	-0.032	25.950	-0.010	-0.010	0.000	0.000	0.000	0.000
100	H	123	LYS	1	0.934	0.948	28.300	-0.049	-0.049	0.000	0.000	0.000	0.000
101	H	124	ASP	-1	-0.854	-0.909	29.652	0.083	0.083	0.000	0.000	0.000	0.000
102	H	125	ASN	0	-0.045	-0.026	24.618	0.005	0.005	0.000	0.000	0.000	0.000
103	H	126	LYS	1	0.965	0.988	27.306	-0.057	-0.057	0.000	0.000	0.000	0.000
104	H	127	SER	0	-0.002	-0.014	25.425	-0.002	-0.002	0.000	0.000	0.000	0.000
105	H	128	VAL	0	-0.028	-0.016	27.517	-0.003	-0.003	0.000	0.000	0.000	0.000
106	H	129	TYR	0	0.024	0.028	28.362	0.003	0.003	0.000	0.000	0.000	0.000
107	H	130	PHE	0	-0.031	-0.025	28.134	-0.003	-0.003	0.000	0.000	0.000	0.000
108	H	131	ASP	-1	-0.830	-0.902	32.778	0.026	0.026	0.000	0.000	0.000	0.000
109	H	132	ARG	1	0.812	0.903	36.305	-0.009	-0.009	0.000	0.000	0.000	0.000
110	H	133	VAL	0	-0.022	-0.021	33.793	-0.001	-0.001	0.000	0.000	0.000	0.000
111	H	134	PHE	0	0.015	-0.002	36.181	0.000	0.000	0.000	0.000	0.000	0.000
112	H	135	THR	0	-0.039	-0.028	36.289	-0.004	-0.004	0.000	0.000	0.000	0.000
113	H	136	ILE	0	-0.018	0.004	38.321	0.001	0.001	0.000	0.000	0.000	0.000
114	H	137	SER	0	0.024	-0.005	39.259	-0.003	-0.003	0.000	0.000	0.000	0.000
115	H	138	GLU	-1	-0.882	-0.939	41.397	-0.033	-0.033	0.000	0.000	0.000	0.000
116	H	139	THR	0	0.018	0.013	43.801	0.001	0.001	0.000	0.000	0.000	0.000
117	H	140	ALA	0	0.015	0.002	46.876	-0.002	-0.002	0.000	0.000	0.000	0.000
118	H	141	ARG	1	0.904	0.959	45.263	0.028	0.028	0.000	0.000	0.000	0.000
119	H	142	ILE	0	0.002	0.008	47.819	-0.001	-0.001	0.000	0.000	0.000	0.000
120	H	143	PRO	0	-0.003	0.006	45.753	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(H:24:GLY)