FMO DATABASE

FMODB ID: ZVLGN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1041239.60856
FMO2-HF: Nuclear repulsion	988772.564911
FMO2-HF: Total energy	-52467.043648
FMO2-MP2: Total energy	-52617.43782

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.
21.615	22.509	0.379	2.017	-3.29	0.027

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 : -0.917 / q_NPA : -0.972

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	-0.988	-1.036	2.980	18.535	19.068	0.381	2.046	-2.960	0.027
4	A	6	LEU	0	0.072	0.039	4.824	-5.846	-5.655	-0.001	-0.016	-0.174	0.000
5	A	7	MET	0	0.004	-0.005	4.441	-7.557	-7.387	-0.001	-0.013	-0.156	0.000
6	A	8	ARG	1	0.981	0.990	7.939	-29.658	-29.658	0.000	0.000	0.000	0.000
7	A	9	LEU	0	0.069	0.036	9.506	-3.744	-3.744	0.000	0.000	0.000	0.000
8	A	10	MET	0	-0.044	-0.036	10.802	-2.685	-2.685	0.000	0.000	0.000	0.000
9	A	11	LYS	1	0.938	0.973	11.404	-27.110	-27.110	0.000	0.000	0.000	0.000
10	A	12	ARG	1	0.850	0.901	13.510	-19.928	-19.928	0.000	0.000	0.000	0.000
11	A	13	ARG	1	0.926	0.962	14.998	-20.779	-20.779	0.000	0.000	0.000	0.000
12	A	14	ILE	0	-0.015	0.003	17.221	-1.086	-1.086	0.000	0.000	0.000	0.000
13	A	15	LEU	0	0.008	0.015	17.642	-0.943	-0.943	0.000	0.000	0.000	0.000
14	A	16	GLU	-1	-0.900	-0.949	18.041	16.125	16.125	0.000	0.000	0.000	0.000
15	A	17	SER	0	-0.090	-0.037	21.165	-0.753	-0.753	0.000	0.000	0.000	0.000
16	A	18	TYR	0	0.022	0.004	23.371	-0.193	-0.193	0.000	0.000	0.000	0.000
17	A	19	ARG	1	0.987	0.981	24.185	-12.617	-12.617	0.000	0.000	0.000	0.000
18	A	20	TRP	0	0.019	0.011	22.015	-0.111	-0.111	0.000	0.000	0.000	0.000
19	A	21	GLN	0	-0.031	-0.059	22.726	-0.904	-0.904	0.000	0.000	0.000	0.000
20	A	22	GLU	-1	-0.859	-0.955	26.796	9.607	9.607	0.000	0.000	0.000	0.000
21	A	23	ASP	-1	-0.890	-0.930	29.630	9.956	9.956	0.000	0.000	0.000	0.000
22	A	24	VAL	0	-0.105	-0.069	26.053	-0.046	-0.046	0.000	0.000	0.000	0.000
23	A	25	VAL	0	-0.033	-0.005	23.299	-0.128	-0.128	0.000	0.000	0.000	0.000
24	A	26	LYS	1	0.959	1.016	26.527	-10.482	-10.482	0.000	0.000	0.000	0.000
25	A	27	PRO	0	0.037	0.060	29.414	-0.247	-0.247	0.000	0.000	0.000	0.000
26	A	28	LEU	0	-0.045	0.016	27.991	-0.361	-0.361	0.000	0.000	0.000	0.000
27	A	29	SER	0	0.043	-0.080	30.098	0.182	0.182	0.000	0.000	0.000	0.000
28	A	30	ARG	1	0.797	0.885	32.280	-8.748	-8.748	0.000	0.000	0.000	0.000
29	A	31	GLU	-1	-0.852	-0.928	30.613	10.052	10.052	0.000	0.000	0.000	0.000
30	A	32	LEU	0	-0.083	-0.048	31.989	0.052	0.052	0.000	0.000	0.000	0.000
31	A	33	GLH	0	-0.056	-0.010	28.404	0.077	0.077	0.000	0.000	0.000	0.000
32	A	34	ILE	0	-0.066	0.007	26.602	0.200	0.200	0.000	0.000	0.000	0.000
33	A	35	ASP	-1	-0.864	-0.926	26.600	10.984	10.984	0.000	0.000	0.000	0.000
34	A	36	VAL	0	0.027	0.017	24.559	0.398	0.398	0.000	0.000	0.000	0.000
35	A	37	GLU	-1	-0.999	-0.990	21.325	13.738	13.738	0.000	0.000	0.000	0.000
36	A	38	GLU	-1	-0.809	-0.928	21.555	12.517	12.517	0.000	0.000	0.000	0.000
37	A	39	PHE	0	-0.012	0.014	21.274	0.808	0.808	0.000	0.000	0.000	0.000
38	A	40	GLN	0	0.022	0.009	18.520	0.004	0.004	0.000	0.000	0.000	0.000
39	A	41	ASP	-1	-0.806	-0.913	17.324	17.475	17.475	0.000	0.000	0.000	0.000
40	A	42	ILE	0	0.013	0.017	17.364	0.911	0.911	0.000	0.000	0.000	0.000
41	A	43	LEU	0	-0.079	-0.028	19.105	0.569	0.569	0.000	0.000	0.000	0.000
42	A	44	MET	0	-0.138	-0.068	12.798	0.904	0.904	0.000	0.000	0.000	0.000
43	A	45	ASP	-1	-1.021	-0.990	14.412	19.840	19.840	0.000	0.000	0.000	0.000
44	A	46	LYS	1	0.901	0.959	15.955	-14.377	-14.377	0.000	0.000	0.000	0.000
45	A	47	LEU	0	-0.025	-0.011	17.515	0.223	0.223	0.000	0.000	0.000	0.000
46	A	48	ASP	-1	-0.760	-0.817	14.159	20.270	20.270	0.000	0.000	0.000	0.000
47	A	49	MET	0	-0.005	-0.025	11.112	-0.267	-0.267	0.000	0.000	0.000	0.000
48	A	50	SER	0	0.002	0.003	14.212	-0.572	-0.572	0.000	0.000	0.000	0.000
49	A	51	SER	0	-0.108	-0.117	16.984	-1.248	-1.248	0.000	0.000	0.000	0.000
50	A	52	LEU	0	0.054	0.011	15.741	-0.891	-0.891	0.000	0.000	0.000	0.000
51	A	53	GLU	-1	-0.988	-0.974	16.303	17.863	17.863	0.000	0.000	0.000	0.000
52	A	54	ALA	0	-0.036	-0.031	19.708	-0.346	-0.346	0.000	0.000	0.000	0.000
53	A	55	LEU	0	-0.048	-0.029	21.927	-0.782	-0.782	0.000	0.000	0.000	0.000
54	A	56	HIS	0	0.032	0.029	24.268	-0.382	-0.382	0.000	0.000	0.000	0.000
55	A	57	PRO	0	0.052	0.037	25.775	-0.434	-0.434	0.000	0.000	0.000	0.000
56	A	58	ARG	1	0.969	0.980	23.874	-13.063	-13.063	0.000	0.000	0.000	0.000
57	A	59	PHE	0	-0.048	-0.020	27.906	-0.280	-0.280	0.000	0.000	0.000	0.000
58	A	60	GLU	-1	-0.844	-0.933	29.784	9.581	9.581	0.000	0.000	0.000	0.000
59	A	61	SER	0	-0.140	-0.057	32.220	-0.371	-0.371	0.000	0.000	0.000	0.000
60	A	62	ALA	0	-0.015	-0.024	32.757	-0.253	-0.253	0.000	0.000	0.000	0.000
61	A	63	ARG	1	1.008	1.024	34.181	-9.142	-9.142	0.000	0.000	0.000	0.000
62	A	64	PRO	0	0.044	0.017	35.472	-0.178	-0.178	0.000	0.000	0.000	0.000
63	A	65	ARG	1	0.984	0.987	33.702	-9.303	-9.303	0.000	0.000	0.000	0.000
64	A	66	CYS	0	-0.006	-0.021	34.970	-0.052	-0.052	0.000	0.000	0.000	0.000
65	A	67	ILE	0	0.008	0.018	37.618	-0.065	-0.065	0.000	0.000	0.000	0.000
66	A	68	ARG	1	0.773	0.859	40.209	-7.269	-7.269	0.000	0.000	0.000	0.000
67	A	69	GLU	-1	-0.955	-0.964	38.750	8.296	8.296	0.000	0.000	0.000	0.000
68	A	70	LYS	1	0.916	0.968	38.078	-8.434	-8.434	0.000	0.000	0.000	0.000
69	A	71	LEU	0	-0.001	0.004	41.909	-0.161	-0.161	0.000	0.000	0.000	0.000
70	A	72	HIS	0	0.055	0.012	45.212	-0.121	-0.121	0.000	0.000	0.000	0.000
71	A	73	SER	0	-0.023	-0.005	43.897	-0.160	-0.160	0.000	0.000	0.000	0.000
72	A	74	ASP	-1	-0.811	-0.885	43.982	7.315	7.315	0.000	0.000	0.000	0.000
73	A	75	LEU	0	-0.112	-0.057	46.714	-0.154	-0.154	0.000	0.000	0.000	0.000
74	A	76	GLN	0	-0.050	-0.029	48.915	-0.168	-0.168	0.000	0.000	0.000	0.000
75	A	77	LEU	0	0.061	0.023	49.548	-0.144	-0.144	0.000	0.000	0.000	0.000
76	A	78	CYS	0	-0.049	-0.002	48.607	-0.062	-0.062	0.000	0.000	0.000	0.000
77	A	79	TRP	0	0.027	-0.005	50.510	-0.120	-0.120	0.000	0.000	0.000	0.000
78	A	80	LEU	0	-0.004	-0.010	53.984	-0.111	-0.111	0.000	0.000	0.000	0.000
79	A	81	VAL	0	-0.018	0.000	53.038	-0.095	-0.095	0.000	0.000	0.000	0.000
80	A	82	ASP	-1	-0.872	-0.938	49.823	6.413	6.413	0.000	0.000	0.000	0.000
81	A	83	VAL	0	-0.091	-0.030	53.348	-0.067	-0.067	0.000	0.000	0.000	0.000
82	A	84	MET	0	-0.067	-0.055	55.837	-0.121	-0.121	0.000	0.000	0.000	0.000
83	A	85	GLU	-1	-0.958	-0.958	57.624	5.361	5.361	0.000	0.000	0.000	0.000
84	A	86	ILE	0	-0.080	-0.030	58.994	-0.090	-0.090	0.000	0.000	0.000	0.000
85	A	87	ILE	0	-0.037	-0.025	56.164	-0.054	-0.054	0.000	0.000	0.000	0.000
86	A	88	SER	0	0.013	0.030	57.350	0.098	0.098	0.000	0.000	0.000	0.000
87	A	89	VAL	0	0.081	0.020	52.844	0.072	0.072	0.000	0.000	0.000	0.000
88	A	90	ASP	-1	-0.927	-0.959	54.092	5.790	5.790	0.000	0.000	0.000	0.000
89	A	91	ASP	-1	-0.869	-0.937	55.130	5.591	5.591	0.000	0.000	0.000	0.000
90	A	92	ALA	0	-0.028	-0.023	52.181	0.102	0.102	0.000	0.000	0.000	0.000
91	A	93	GLU	-1	-0.883	-0.931	48.134	6.901	6.901	0.000	0.000	0.000	0.000
92	A	94	ALA	0	0.065	0.041	50.378	0.124	0.124	0.000	0.000	0.000	0.000
93	A	95	LEU	0	0.009	0.006	51.485	0.095	0.095	0.000	0.000	0.000	0.000
94	A	96	LYS	1	0.839	0.910	46.718	-6.718	-6.718	0.000	0.000	0.000	0.000
95	A	97	ASP	-1	-0.830	-0.891	47.113	6.912	6.912	0.000	0.000	0.000	0.000
96	A	98	GLU	-1	-0.811	-0.906	47.489	6.198	6.198	0.000	0.000	0.000	0.000
97	A	99	ILE	0	-0.053	-0.002	46.380	0.073	0.073	0.000	0.000	0.000	0.000
98	A	100	THR	0	0.001	-0.033	42.509	0.231	0.231	0.000	0.000	0.000	0.000
99	A	101	GLU	-1	-0.969	-0.982	43.816	6.835	6.835	0.000	0.000	0.000	0.000
100	A	102	LEU	0	-0.016	-0.018	44.976	0.102	0.102	0.000	0.000	0.000	0.000
101	A	103	VAL	0	-0.069	-0.008	40.676	0.121	0.121	0.000	0.000	0.000	0.000
102	A	104	LEU	0	-0.071	-0.047	38.973	0.260	0.260	0.000	0.000	0.000	0.000
103	A	105	ALA	0	-0.055	-0.016	40.702	0.149	0.149	0.000	0.000	0.000	0.000
104	A	106	GLY	0	-0.013	-0.009	40.712	-0.067	-0.067	0.000	0.000	0.000	0.000
105	A	107	ARG	1	0.844	0.946	41.780	-6.824	-6.824	0.000	0.000	0.000	0.000
106	A	108	GLU	-1	-0.816	-0.905	40.504	8.100	8.100	0.000	0.000	0.000	0.000
107	A	109	TYR	0	-0.034	-0.061	40.855	-0.171	-0.171	0.000	0.000	0.000	0.000
108	A	110	SER	0	0.060	0.015	42.659	-0.143	-0.143	0.000	0.000	0.000	0.000
109	A	111	GLU	-1	-0.928	-0.971	44.568	6.848	6.848	0.000	0.000	0.000	0.000
110	A	112	ALA	0	-0.065	-0.042	45.425	-0.183	-0.183	0.000	0.000	0.000	0.000
111	A	113	LEU	0	0.008	0.008	45.274	-0.164	-0.164	0.000	0.000	0.000	0.000
112	A	114	SER	0	-0.078	-0.039	47.873	-0.186	-0.186	0.000	0.000	0.000	0.000
113	A	115	GLU	-1	-0.868	-0.942	50.677	5.837	5.837	0.000	0.000	0.000	0.000
114	A	116	GLY	0	0.102	0.035	50.707	-0.111	-0.111	0.000	0.000	0.000	0.000
115	A	117	ARG	1	0.909	0.958	48.679	-6.565	-6.565	0.000	0.000	0.000	0.000
116	A	118	ARG	1	0.808	0.894	53.368	-6.089	-6.089	0.000	0.000	0.000	0.000
117	A	119	ARG	1	0.943	0.983	53.157	-6.121	-6.121	0.000	0.000	0.000	0.000
118	A	120	LEU	0	0.032	0.035	53.821	-0.073	-0.073	0.000	0.000	0.000	0.000
119	A	121	HIS	0	-0.043	-0.038	56.438	-0.161	-0.161	0.000	0.000	0.000	0.000
120	A	122	GLU	-1	-0.976	-0.982	59.330	5.287	5.287	0.000	0.000	0.000	0.000
121	A	123	ILE	0	0.056	0.030	56.715	-0.089	-0.089	0.000	0.000	0.000	0.000
122	A	124	LEU	0	-0.042	-0.024	58.117	-0.083	-0.083	0.000	0.000	0.000	0.000
123	A	125	ARG	1	0.808	0.919	61.642	-5.304	-5.304	0.000	0.000	0.000	0.000
124	A	126	SER	0	-0.015	0.004	63.869	-0.052	-0.052	0.000	0.000	0.000	0.000

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