FMO DATABASE

FMODB ID: QVM4Y

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1041885.873465
FMO2-HF: Nuclear repulsion	989416.282039
FMO2-HF: Total energy	-52469.591425
FMO2-MP2: Total energy	-52619.616608

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.
28.189	32.032	0.07	-2.105	-1.807	0.011

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 : -0.888 / q_NPA : -0.958

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

Sort

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	-0.929	-0.983	3.542	17.051	20.894	0.070	-2.105	-1.807	0.011
4	A	6	LEU	0	0.024	0.014	5.508	-4.968	-4.968	0.000	0.000	0.000	0.000
5	A	7	MET	0	0.001	-0.001	5.235	-5.835	-5.835	0.000	0.000	0.000	0.000
6	A	8	ARG	1	0.871	0.929	8.578	-28.139	-28.139	0.000	0.000	0.000	0.000
7	A	9	LEU	0	0.038	0.021	9.738	-3.461	-3.461	0.000	0.000	0.000	0.000
8	A	10	MET	0	-0.032	-0.026	11.596	-2.727	-2.727	0.000	0.000	0.000	0.000
9	A	11	LYS	1	0.876	0.907	12.322	-25.524	-25.524	0.000	0.000	0.000	0.000
10	A	12	ARG	1	0.798	0.864	14.160	-19.318	-19.318	0.000	0.000	0.000	0.000
11	A	13	ARG	1	0.942	0.966	14.324	-20.512	-20.512	0.000	0.000	0.000	0.000
12	A	14	ILE	0	-0.042	-0.004	17.150	-1.060	-1.060	0.000	0.000	0.000	0.000
13	A	15	LEU	0	0.005	0.001	18.566	-0.980	-0.980	0.000	0.000	0.000	0.000
14	A	16	GLU	-1	-0.807	-0.877	18.764	15.748	15.748	0.000	0.000	0.000	0.000
15	A	17	SER	0	-0.072	-0.017	21.857	-0.794	-0.794	0.000	0.000	0.000	0.000
16	A	18	TYR	0	-0.032	-0.040	23.885	-0.176	-0.176	0.000	0.000	0.000	0.000
17	A	19	ARG	1	0.931	0.952	25.072	-12.504	-12.504	0.000	0.000	0.000	0.000
18	A	20	TRP	0	0.004	0.008	22.831	-0.173	-0.173	0.000	0.000	0.000	0.000
19	A	21	GLN	0	-0.036	-0.025	23.659	-0.651	-0.651	0.000	0.000	0.000	0.000
20	A	22	GLU	-1	-0.783	-0.865	27.395	9.801	9.801	0.000	0.000	0.000	0.000
21	A	23	ASP	-1	-0.822	-0.881	30.326	9.822	9.822	0.000	0.000	0.000	0.000
22	A	24	VAL	0	-0.071	-0.041	26.641	-0.088	-0.088	0.000	0.000	0.000	0.000
23	A	25	VAL	0	-0.033	-0.039	24.024	-0.093	-0.093	0.000	0.000	0.000	0.000
24	A	26	LYS	1	0.915	0.952	27.036	-10.399	-10.399	0.000	0.000	0.000	0.000
25	A	27	PRO	0	0.007	0.006	30.161	-0.261	-0.261	0.000	0.000	0.000	0.000
26	A	28	LEU	0	-0.045	0.001	28.300	-0.317	-0.317	0.000	0.000	0.000	0.000
27	A	29	SER	0	0.046	0.008	30.585	0.198	0.198	0.000	0.000	0.000	0.000
28	A	30	ARG	1	0.852	0.930	32.913	-8.856	-8.856	0.000	0.000	0.000	0.000
29	A	31	GLU	-1	-0.897	-0.959	30.686	9.643	9.643	0.000	0.000	0.000	0.000
30	A	32	LEU	0	-0.043	-0.030	32.479	0.070	0.070	0.000	0.000	0.000	0.000
31	A	33	GLH	0	0.003	0.005	28.713	0.005	0.005	0.000	0.000	0.000	0.000
32	A	34	ILE	0	-0.067	-0.032	25.808	0.372	0.372	0.000	0.000	0.000	0.000
33	A	35	ASP	-1	-0.810	-0.900	27.230	11.208	11.208	0.000	0.000	0.000	0.000
34	A	36	VAL	0	-0.021	-0.017	25.502	0.387	0.387	0.000	0.000	0.000	0.000
35	A	37	GLU	-1	-0.971	-0.977	21.394	14.261	14.261	0.000	0.000	0.000	0.000
36	A	38	GLU	-1	-0.912	-0.951	21.625	13.242	13.242	0.000	0.000	0.000	0.000
37	A	39	PHE	0	-0.011	-0.002	21.941	0.733	0.733	0.000	0.000	0.000	0.000
38	A	40	GLN	0	0.008	-0.011	19.191	-0.120	-0.120	0.000	0.000	0.000	0.000
39	A	41	ASP	-1	-0.714	-0.858	15.923	20.217	20.217	0.000	0.000	0.000	0.000
40	A	42	ILE	0	-0.002	0.008	17.765	0.998	0.998	0.000	0.000	0.000	0.000
41	A	43	LEU	0	-0.043	-0.016	19.619	0.466	0.466	0.000	0.000	0.000	0.000
42	A	44	MET	0	-0.102	-0.029	13.553	0.793	0.793	0.000	0.000	0.000	0.000
43	A	45	ASP	-1	-0.897	-0.917	14.607	20.907	20.907	0.000	0.000	0.000	0.000
44	A	46	LYS	1	0.825	0.898	15.870	-15.960	-15.960	0.000	0.000	0.000	0.000
45	A	47	LEU	0	-0.006	0.018	17.750	-0.441	-0.441	0.000	0.000	0.000	0.000
46	A	48	ASP	-1	-0.787	-0.860	14.422	20.836	20.836	0.000	0.000	0.000	0.000
47	A	49	MET	0	0.016	0.007	12.218	-0.391	-0.391	0.000	0.000	0.000	0.000
48	A	50	SER	0	-0.004	-0.025	15.337	-1.095	-1.095	0.000	0.000	0.000	0.000
49	A	51	SER	0	-0.066	-0.056	18.063	-1.461	-1.461	0.000	0.000	0.000	0.000
50	A	52	LEU	0	0.006	-0.002	16.599	-0.999	-0.999	0.000	0.000	0.000	0.000
51	A	53	GLU	-1	-0.927	-0.973	16.610	17.799	17.799	0.000	0.000	0.000	0.000
52	A	54	ALA	0	-0.024	-0.001	20.643	-0.717	-0.717	0.000	0.000	0.000	0.000
53	A	55	LEU	0	-0.054	-0.029	22.202	-0.710	-0.710	0.000	0.000	0.000	0.000
54	A	56	HIS	0	0.007	0.010	24.985	-0.291	-0.291	0.000	0.000	0.000	0.000
55	A	57	PRO	0	0.030	-0.003	26.595	-0.420	-0.420	0.000	0.000	0.000	0.000
56	A	58	ARG	1	0.919	0.972	23.944	-13.312	-13.312	0.000	0.000	0.000	0.000
57	A	59	PHE	0	0.001	0.021	28.717	-0.279	-0.279	0.000	0.000	0.000	0.000
58	A	60	GLU	-1	-0.771	-0.882	30.555	9.308	9.308	0.000	0.000	0.000	0.000
59	A	61	SER	0	-0.114	-0.061	32.670	-0.347	-0.347	0.000	0.000	0.000	0.000
60	A	62	ALA	0	-0.033	-0.027	33.129	-0.251	-0.251	0.000	0.000	0.000	0.000
61	A	63	ARG	1	0.843	0.907	34.624	-9.525	-9.525	0.000	0.000	0.000	0.000
62	A	64	PRO	0	0.041	0.016	36.247	-0.163	-0.163	0.000	0.000	0.000	0.000
63	A	65	ARG	1	0.864	0.920	34.504	-9.226	-9.226	0.000	0.000	0.000	0.000
64	A	66	CYS	0	-0.024	-0.031	35.895	-0.047	-0.047	0.000	0.000	0.000	0.000
65	A	67	ILE	0	0.005	0.022	38.274	-0.089	-0.089	0.000	0.000	0.000	0.000
66	A	68	ARG	1	0.772	0.850	40.855	-7.227	-7.227	0.000	0.000	0.000	0.000
67	A	69	GLU	-1	-0.820	-0.894	38.426	8.423	8.423	0.000	0.000	0.000	0.000
68	A	70	LYS	1	0.834	0.900	39.473	-8.074	-8.074	0.000	0.000	0.000	0.000
69	A	71	LEU	0	0.011	0.008	42.224	-0.153	-0.153	0.000	0.000	0.000	0.000
70	A	72	HIS	0	0.006	-0.016	45.457	-0.129	-0.129	0.000	0.000	0.000	0.000
71	A	73	SER	0	-0.025	-0.007	43.786	-0.120	-0.120	0.000	0.000	0.000	0.000
72	A	74	ASP	-1	-0.779	-0.862	44.019	7.444	7.444	0.000	0.000	0.000	0.000
73	A	75	LEU	0	-0.058	-0.034	46.852	-0.143	-0.143	0.000	0.000	0.000	0.000
74	A	76	GLN	0	-0.063	-0.038	48.428	-0.175	-0.175	0.000	0.000	0.000	0.000
75	A	77	LEU	0	0.051	0.030	49.834	-0.120	-0.120	0.000	0.000	0.000	0.000
76	A	78	CYS	0	-0.052	-0.016	48.536	-0.063	-0.063	0.000	0.000	0.000	0.000
77	A	79	TRP	0	-0.003	-0.013	50.657	-0.120	-0.120	0.000	0.000	0.000	0.000
78	A	80	LEU	0	-0.026	-0.031	53.875	-0.114	-0.114	0.000	0.000	0.000	0.000
79	A	81	VAL	0	0.002	0.014	53.296	-0.095	-0.095	0.000	0.000	0.000	0.000
80	A	82	ASP	-1	-0.798	-0.888	49.791	6.496	6.496	0.000	0.000	0.000	0.000
81	A	83	VAL	0	-0.058	-0.019	52.855	-0.029	-0.029	0.000	0.000	0.000	0.000
82	A	84	MET	0	-0.078	-0.047	55.579	-0.128	-0.128	0.000	0.000	0.000	0.000
83	A	85	GLU	-1	-0.962	-0.970	57.811	5.384	5.384	0.000	0.000	0.000	0.000
84	A	86	ILE	0	-0.075	-0.023	58.964	-0.075	-0.075	0.000	0.000	0.000	0.000
85	A	87	ILE	0	-0.032	-0.010	56.345	-0.054	-0.054	0.000	0.000	0.000	0.000
86	A	88	SER	0	0.010	-0.015	57.834	0.078	0.078	0.000	0.000	0.000	0.000
87	A	89	VAL	0	0.043	-0.006	52.840	0.090	0.090	0.000	0.000	0.000	0.000
88	A	90	ASP	-1	-0.918	-0.955	54.198	5.828	5.828	0.000	0.000	0.000	0.000
89	A	91	ASP	-1	-0.845	-0.894	55.548	5.594	5.594	0.000	0.000	0.000	0.000
90	A	92	ALA	0	-0.001	-0.002	52.657	0.084	0.084	0.000	0.000	0.000	0.000
91	A	93	GLU	-1	-0.811	-0.880	48.114	7.034	7.034	0.000	0.000	0.000	0.000
92	A	94	ALA	0	0.038	0.023	50.692	0.125	0.125	0.000	0.000	0.000	0.000
93	A	95	LEU	0	-0.003	0.003	51.833	0.080	0.080	0.000	0.000	0.000	0.000
94	A	96	LYS	1	0.742	0.843	46.614	-6.799	-6.799	0.000	0.000	0.000	0.000
95	A	97	ASP	-1	-0.804	-0.852	47.383	7.000	7.000	0.000	0.000	0.000	0.000
96	A	98	GLU	-1	-0.821	-0.895	48.160	6.180	6.180	0.000	0.000	0.000	0.000
97	A	99	ILE	0	-0.033	-0.020	47.037	0.047	0.047	0.000	0.000	0.000	0.000
98	A	100	THR	0	-0.015	-0.042	42.820	0.227	0.227	0.000	0.000	0.000	0.000
99	A	101	GLU	-1	-0.984	-0.984	44.329	6.815	6.815	0.000	0.000	0.000	0.000
100	A	102	LEU	0	-0.023	-0.007	45.757	0.095	0.095	0.000	0.000	0.000	0.000
101	A	103	VAL	0	-0.025	-0.016	40.980	0.092	0.092	0.000	0.000	0.000	0.000
102	A	104	LEU	0	-0.037	-0.019	40.097	0.240	0.240	0.000	0.000	0.000	0.000
103	A	105	ALA	0	-0.061	-0.014	41.668	0.128	0.128	0.000	0.000	0.000	0.000
104	A	106	GLY	0	-0.008	-0.004	41.118	-0.044	-0.044	0.000	0.000	0.000	0.000
105	A	107	ARG	1	0.756	0.868	42.124	-6.845	-6.845	0.000	0.000	0.000	0.000
106	A	108	GLU	-1	-0.752	-0.870	41.129	7.998	7.998	0.000	0.000	0.000	0.000
107	A	109	TYR	0	0.029	-0.010	41.251	-0.200	-0.200	0.000	0.000	0.000	0.000
108	A	110	SER	0	-0.041	-0.045	42.714	-0.169	-0.169	0.000	0.000	0.000	0.000
109	A	111	GLU	-1	-0.864	-0.906	45.006	6.645	6.645	0.000	0.000	0.000	0.000
110	A	112	ALA	0	-0.006	0.003	45.766	-0.181	-0.181	0.000	0.000	0.000	0.000
111	A	113	LEU	0	0.006	0.008	45.317	-0.167	-0.167	0.000	0.000	0.000	0.000
112	A	114	SER	0	-0.057	-0.046	47.990	-0.183	-0.183	0.000	0.000	0.000	0.000
113	A	115	GLU	-1	-0.828	-0.889	50.793	5.853	5.853	0.000	0.000	0.000	0.000
114	A	116	GLY	0	0.068	0.031	50.942	-0.125	-0.125	0.000	0.000	0.000	0.000
115	A	117	ARG	1	0.883	0.946	48.625	-6.659	-6.659	0.000	0.000	0.000	0.000
116	A	118	ARG	1	0.809	0.881	53.688	-6.115	-6.115	0.000	0.000	0.000	0.000
117	A	119	ARG	1	0.903	0.932	54.888	-6.113	-6.113	0.000	0.000	0.000	0.000
118	A	120	LEU	0	0.025	0.025	53.598	-0.070	-0.070	0.000	0.000	0.000	0.000
119	A	121	HIS	0	-0.010	-0.007	56.534	-0.191	-0.191	0.000	0.000	0.000	0.000
120	A	122	GLU	-1	-0.965	-0.981	59.493	5.316	5.316	0.000	0.000	0.000	0.000
121	A	123	ILE	0	0.045	0.031	57.018	-0.095	-0.095	0.000	0.000	0.000	0.000
122	A	124	LEU	0	-0.019	-0.016	57.979	-0.080	-0.080	0.000	0.000	0.000	0.000
123	A	125	ARG	1	0.766	0.892	61.663	-5.332	-5.332	0.000	0.000	0.000	0.000
124	A	126	SER	0	-0.040	-0.010	64.128	-0.105	-0.105	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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