FMO DATABASE

FMODB ID: R8MK8

Calculation Name: 1NXH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NXH

Chain ID: A

ChEMBL ID:

UniProt ID: O26496

Base Structure: X-ray

Registration Date: 2023-09-23

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	124
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1040676.332049
FMO2-HF: Nuclear repulsion	988207.68861
FMO2-HF: Total energy	-52468.643439
FMO2-MP2: Total energy	-52618.907656

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:3:GLU)

Summations of interaction energy for fragment #1(A:3:GLU)

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.
29.601	34.504	0.085	-2.34	-2.648	0.017

Interaction energy analysis for fragmet #1(A:3:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.913 / q_NPA : -0.979

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	5	GLU	-1	-0.985	-1.028	3.072	17.322	22.046	0.086	-2.321	-2.489	0.017
4	A	6	LEU	0	0.050	0.025	4.782	-5.110	-4.931	-0.001	-0.019	-0.159	0.000
5	A	7	MET	0	0.004	0.001	5.566	-5.761	-5.761	0.000	0.000	0.000	0.000
6	A	8	ARG	1	0.957	0.979	7.934	-28.482	-28.482	0.000	0.000	0.000	0.000
7	A	9	LEU	0	0.053	0.031	9.478	-3.472	-3.472	0.000	0.000	0.000	0.000
8	A	10	MET	0	-0.035	-0.033	11.359	-2.490	-2.490	0.000	0.000	0.000	0.000
9	A	11	LYS	1	0.887	0.939	12.575	-24.785	-24.785	0.000	0.000	0.000	0.000
10	A	12	ARG	1	0.818	0.883	13.570	-19.297	-19.297	0.000	0.000	0.000	0.000
11	A	13	ARG	1	0.919	0.954	14.526	-20.213	-20.213	0.000	0.000	0.000	0.000
12	A	14	ILE	0	-0.029	0.000	17.238	-1.059	-1.059	0.000	0.000	0.000	0.000
13	A	15	LEU	0	0.006	0.014	18.057	-0.947	-0.947	0.000	0.000	0.000	0.000
14	A	16	GLU	-1	-0.849	-0.913	18.021	15.838	15.838	0.000	0.000	0.000	0.000
15	A	17	SER	0	-0.076	-0.037	21.117	-0.749	-0.749	0.000	0.000	0.000	0.000
16	A	18	TYR	0	-0.036	-0.041	23.335	-0.178	-0.178	0.000	0.000	0.000	0.000
17	A	19	ARG	1	0.930	0.949	25.245	-12.363	-12.363	0.000	0.000	0.000	0.000
18	A	20	TRP	0	0.015	0.014	22.825	-0.138	-0.138	0.000	0.000	0.000	0.000
19	A	21	GLN	0	-0.032	-0.026	22.791	-0.771	-0.771	0.000	0.000	0.000	0.000
20	A	22	GLU	-1	-0.807	-0.885	26.740	9.618	9.618	0.000	0.000	0.000	0.000
21	A	23	ASP	-1	-0.842	-0.901	29.686	9.927	9.927	0.000	0.000	0.000	0.000
22	A	24	VAL	0	-0.096	-0.067	26.572	-0.035	-0.035	0.000	0.000	0.000	0.000
23	A	25	VAL	0	-0.024	-0.020	23.499	-0.130	-0.130	0.000	0.000	0.000	0.000
24	A	26	LYS	1	0.942	0.979	26.460	-10.329	-10.329	0.000	0.000	0.000	0.000
25	A	27	PRO	0	0.038	0.036	29.349	-0.212	-0.212	0.000	0.000	0.000	0.000
26	A	28	LEU	0	-0.049	0.013	28.080	-0.325	-0.325	0.000	0.000	0.000	0.000
27	A	29	SER	0	0.027	-0.044	30.098	0.173	0.173	0.000	0.000	0.000	0.000
28	A	30	ARG	1	0.849	0.916	32.272	-8.769	-8.769	0.000	0.000	0.000	0.000
29	A	31	GLU	-1	-0.876	-0.939	30.622	9.821	9.821	0.000	0.000	0.000	0.000
30	A	32	LEU	0	-0.066	-0.040	31.989	0.081	0.081	0.000	0.000	0.000	0.000
31	A	33	GLH	0	-0.036	-0.010	28.518	0.121	0.121	0.000	0.000	0.000	0.000
32	A	34	ILE	0	-0.026	0.001	25.768	0.247	0.247	0.000	0.000	0.000	0.000
33	A	35	ASP	-1	-0.896	-0.948	26.647	11.112	11.112	0.000	0.000	0.000	0.000
34	A	36	VAL	0	0.040	0.023	24.644	0.422	0.422	0.000	0.000	0.000	0.000
35	A	37	GLU	-1	-0.980	-0.978	21.229	13.958	13.958	0.000	0.000	0.000	0.000
36	A	38	GLU	-1	-0.888	-0.952	21.481	12.931	12.931	0.000	0.000	0.000	0.000
37	A	39	PHE	0	0.009	0.016	21.274	0.852	0.852	0.000	0.000	0.000	0.000
38	A	40	GLN	0	0.013	-0.001	18.496	-0.053	-0.053	0.000	0.000	0.000	0.000
39	A	41	ASP	-1	-0.750	-0.883	15.816	19.542	19.542	0.000	0.000	0.000	0.000
40	A	42	ILE	0	0.012	0.023	17.364	0.989	0.989	0.000	0.000	0.000	0.000
41	A	43	LEU	0	-0.058	-0.018	19.105	0.601	0.601	0.000	0.000	0.000	0.000
42	A	44	MET	0	-0.117	-0.055	13.029	0.810	0.810	0.000	0.000	0.000	0.000
43	A	45	ASP	-1	-0.903	-0.929	14.554	20.058	20.058	0.000	0.000	0.000	0.000
44	A	46	LYS	1	0.777	0.888	15.910	-15.679	-15.679	0.000	0.000	0.000	0.000
45	A	47	LEU	0	-0.007	0.005	17.444	0.312	0.312	0.000	0.000	0.000	0.000
46	A	48	ASP	-1	-0.793	-0.869	14.370	20.534	20.534	0.000	0.000	0.000	0.000
47	A	49	MET	0	0.019	-0.006	11.910	-0.481	-0.481	0.000	0.000	0.000	0.000
48	A	50	SER	0	-0.002	-0.020	14.905	-0.797	-0.797	0.000	0.000	0.000	0.000
49	A	51	SER	0	-0.078	-0.051	17.680	-1.436	-1.436	0.000	0.000	0.000	0.000
50	A	52	LEU	0	0.030	-0.001	16.376	-0.925	-0.925	0.000	0.000	0.000	0.000
51	A	53	GLU	-1	-0.965	-0.964	17.068	17.480	17.480	0.000	0.000	0.000	0.000
52	A	54	ALA	0	-0.022	-0.030	20.660	-0.337	-0.337	0.000	0.000	0.000	0.000
53	A	55	LEU	0	-0.071	-0.037	22.307	-0.760	-0.760	0.000	0.000	0.000	0.000
54	A	56	HIS	0	0.030	0.019	24.967	-0.340	-0.340	0.000	0.000	0.000	0.000
55	A	57	PRO	0	0.052	0.031	26.646	-0.408	-0.408	0.000	0.000	0.000	0.000
56	A	58	ARG	1	0.960	0.978	24.326	-13.013	-13.013	0.000	0.000	0.000	0.000
57	A	59	PHE	0	-0.018	-0.002	28.572	-0.263	-0.263	0.000	0.000	0.000	0.000
58	A	60	GLU	-1	-0.800	-0.905	30.451	9.238	9.238	0.000	0.000	0.000	0.000
59	A	61	SER	0	-0.123	-0.050	32.879	-0.342	-0.342	0.000	0.000	0.000	0.000
60	A	62	ALA	0	-0.018	-0.023	33.233	-0.238	-0.238	0.000	0.000	0.000	0.000
61	A	63	ARG	1	0.923	0.971	34.791	-9.311	-9.311	0.000	0.000	0.000	0.000
62	A	64	PRO	0	0.036	0.009	36.084	-0.163	-0.163	0.000	0.000	0.000	0.000
63	A	65	ARG	1	0.881	0.928	34.487	-9.178	-9.178	0.000	0.000	0.000	0.000
64	A	66	CYS	0	-0.025	-0.026	35.564	-0.014	-0.014	0.000	0.000	0.000	0.000
65	A	67	ILE	0	0.013	0.019	38.021	-0.068	-0.068	0.000	0.000	0.000	0.000
66	A	68	ARG	1	0.751	0.842	40.664	-7.206	-7.206	0.000	0.000	0.000	0.000
67	A	69	GLU	-1	-0.847	-0.903	38.320	8.414	8.414	0.000	0.000	0.000	0.000
68	A	70	LYS	1	0.840	0.909	39.247	-8.038	-8.038	0.000	0.000	0.000	0.000
69	A	71	LEU	0	0.012	0.006	42.095	-0.162	-0.162	0.000	0.000	0.000	0.000
70	A	72	HIS	0	0.049	0.013	45.546	-0.119	-0.119	0.000	0.000	0.000	0.000
71	A	73	SER	0	-0.020	-0.003	43.860	-0.147	-0.147	0.000	0.000	0.000	0.000
72	A	74	ASP	-1	-0.805	-0.876	43.914	7.383	7.383	0.000	0.000	0.000	0.000
73	A	75	LEU	0	-0.084	-0.042	46.714	-0.156	-0.156	0.000	0.000	0.000	0.000
74	A	76	GLN	0	-0.061	-0.039	48.442	-0.162	-0.162	0.000	0.000	0.000	0.000
75	A	77	LEU	0	0.063	0.021	49.935	-0.145	-0.145	0.000	0.000	0.000	0.000
76	A	78	CYS	0	-0.072	-0.010	48.529	-0.051	-0.051	0.000	0.000	0.000	0.000
77	A	79	TRP	0	0.015	-0.009	50.559	-0.115	-0.115	0.000	0.000	0.000	0.000
78	A	80	LEU	0	-0.011	-0.011	53.934	-0.112	-0.112	0.000	0.000	0.000	0.000
79	A	81	VAL	0	-0.017	0.005	53.229	-0.097	-0.097	0.000	0.000	0.000	0.000
80	A	82	ASP	-1	-0.814	-0.915	49.893	6.470	6.470	0.000	0.000	0.000	0.000
81	A	83	VAL	0	-0.083	-0.028	53.243	-0.065	-0.065	0.000	0.000	0.000	0.000
82	A	84	MET	0	-0.062	-0.049	55.843	-0.123	-0.123	0.000	0.000	0.000	0.000
83	A	85	GLU	-1	-0.967	-0.962	57.712	5.382	5.382	0.000	0.000	0.000	0.000
84	A	86	ILE	0	-0.076	-0.032	59.147	-0.091	-0.091	0.000	0.000	0.000	0.000
85	A	87	ILE	0	-0.047	-0.030	56.534	-0.053	-0.053	0.000	0.000	0.000	0.000
86	A	88	SER	0	0.008	-0.007	57.611	0.092	0.092	0.000	0.000	0.000	0.000
87	A	89	VAL	0	0.075	0.013	53.094	0.081	0.081	0.000	0.000	0.000	0.000
88	A	90	ASP	-1	-0.933	-0.954	54.489	5.776	5.776	0.000	0.000	0.000	0.000
89	A	91	ASP	-1	-0.854	-0.900	55.607	5.578	5.578	0.000	0.000	0.000	0.000
90	A	92	ALA	0	-0.021	-0.015	52.548	0.098	0.098	0.000	0.000	0.000	0.000
91	A	93	GLU	-1	-0.814	-0.888	48.371	6.939	6.939	0.000	0.000	0.000	0.000
92	A	94	ALA	0	0.053	0.033	50.896	0.121	0.121	0.000	0.000	0.000	0.000
93	A	95	LEU	0	0.019	0.009	52.017	0.093	0.093	0.000	0.000	0.000	0.000
94	A	96	LYS	1	0.756	0.852	47.067	-6.713	-6.713	0.000	0.000	0.000	0.000
95	A	97	ASP	-1	-0.804	-0.848	47.666	6.979	6.979	0.000	0.000	0.000	0.000
96	A	98	GLU	-1	-0.798	-0.888	48.141	6.160	6.160	0.000	0.000	0.000	0.000
97	A	99	ILE	0	-0.030	-0.013	46.905	0.070	0.070	0.000	0.000	0.000	0.000
98	A	100	THR	0	-0.014	-0.043	42.897	0.216	0.216	0.000	0.000	0.000	0.000
99	A	101	GLU	-1	-1.001	-0.993	44.508	6.781	6.781	0.000	0.000	0.000	0.000
100	A	102	LEU	0	-0.024	-0.015	45.726	0.092	0.092	0.000	0.000	0.000	0.000
101	A	103	VAL	0	-0.050	-0.015	40.927	0.114	0.114	0.000	0.000	0.000	0.000
102	A	104	LEU	0	-0.033	-0.023	39.970	0.239	0.239	0.000	0.000	0.000	0.000
103	A	105	ALA	0	-0.066	-0.022	41.391	0.141	0.141	0.000	0.000	0.000	0.000
104	A	106	GLY	0	-0.019	-0.012	40.902	-0.070	-0.070	0.000	0.000	0.000	0.000
105	A	107	ARG	1	0.780	0.898	41.985	-6.808	-6.808	0.000	0.000	0.000	0.000
106	A	108	GLU	-1	-0.763	-0.858	40.495	8.064	8.064	0.000	0.000	0.000	0.000
107	A	109	TYR	0	0.025	-0.015	40.969	-0.185	-0.185	0.000	0.000	0.000	0.000
108	A	110	SER	0	-0.019	-0.035	42.122	-0.198	-0.198	0.000	0.000	0.000	0.000
109	A	111	GLU	-1	-0.865	-0.939	44.499	6.681	6.681	0.000	0.000	0.000	0.000
110	A	112	ALA	0	-0.026	-0.028	45.617	-0.184	-0.184	0.000	0.000	0.000	0.000
111	A	113	LEU	0	-0.009	0.000	45.440	-0.160	-0.160	0.000	0.000	0.000	0.000
112	A	114	SER	0	-0.057	-0.030	47.926	-0.179	-0.179	0.000	0.000	0.000	0.000
113	A	115	GLU	-1	-0.819	-0.885	50.705	5.826	5.826	0.000	0.000	0.000	0.000
114	A	116	GLY	0	0.080	0.037	50.900	-0.114	-0.114	0.000	0.000	0.000	0.000
115	A	117	ARG	1	0.911	0.959	48.502	-6.617	-6.617	0.000	0.000	0.000	0.000
116	A	118	ARG	1	0.778	0.868	53.531	-6.063	-6.063	0.000	0.000	0.000	0.000
117	A	119	ARG	1	0.917	0.947	54.253	-6.088	-6.088	0.000	0.000	0.000	0.000
118	A	120	LEU	0	0.026	0.032	53.665	-0.072	-0.072	0.000	0.000	0.000	0.000
119	A	121	HIS	0	-0.016	-0.021	56.699	-0.187	-0.187	0.000	0.000	0.000	0.000
120	A	122	GLU	-1	-0.969	-0.978	59.421	5.285	5.285	0.000	0.000	0.000	0.000
121	A	123	ILE	0	0.058	0.030	57.236	-0.088	-0.088	0.000	0.000	0.000	0.000
122	A	124	LEU	0	-0.034	-0.022	58.075	-0.079	-0.079	0.000	0.000	0.000	0.000
123	A	125	ARG	1	0.766	0.898	61.353	-5.337	-5.337	0.000	0.000	0.000	0.000
124	A	126	SER	0	-0.016	0.004	64.357	-0.056	-0.056	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:GLU)