FMO DATABASE

FMODB ID: 6Y65Z

Calculation Name: 1NXV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NXV

Chain ID: A

ChEMBL ID:

UniProt ID: Q9S1K0

Base Structure: X-ray

Registration Date: 2023-09-21

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	118
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1019112.472621
FMO2-HF: Nuclear repulsion	972712.623018
FMO2-HF: Total energy	-46399.849603
FMO2-MP2: Total energy	-46536.209616

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:2:LYS)

Summations of interaction energy for fragment #1(A:2:LYS)

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.
-261.517	-258.338	26.226	-14.209	-15.195	-0.141

Interaction energy analysis for fragmet #1(A:2:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.859 / q_NPA : 0.919

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	4	ILE	0	-0.021	-0.020	3.893	-2.932	-0.952	-0.014	-0.947	-1.019	0.003
4	A	5	LEU	0	0.011	0.009	6.154	1.992	1.992	0.000	0.000	0.000	0.000
5	A	6	ILE	0	-0.038	-0.014	9.763	0.296	0.296	0.000	0.000	0.000	0.000
6	A	7	VAL	0	0.018	0.001	12.306	0.662	0.662	0.000	0.000	0.000	0.000
7	A	8	ASP	-1	-0.792	-0.901	15.618	-14.653	-14.653	0.000	0.000	0.000	0.000
8	A	9	ASP	-1	-0.854	-0.933	18.327	-12.825	-12.825	0.000	0.000	0.000	0.000
9	A	10	GLU	-1	-0.819	-0.887	21.527	-11.933	-11.933	0.000	0.000	0.000	0.000
10	A	11	LYS	1	0.787	0.872	19.829	13.394	13.394	0.000	0.000	0.000	0.000
11	A	12	PRO	0	0.016	-0.005	20.261	-0.445	-0.445	0.000	0.000	0.000	0.000
12	A	13	ILE	0	0.020	0.015	18.391	-0.312	-0.312	0.000	0.000	0.000	0.000
13	A	14	SER	0	0.046	0.022	16.418	-1.151	-1.151	0.000	0.000	0.000	0.000
14	A	15	ASP	-1	-0.816	-0.888	15.517	-15.331	-15.331	0.000	0.000	0.000	0.000
15	A	16	ILE	0	-0.032	-0.013	16.418	-0.504	-0.504	0.000	0.000	0.000	0.000
16	A	17	ILE	0	0.014	0.012	11.812	-0.585	-0.585	0.000	0.000	0.000	0.000
17	A	18	LYS	1	0.946	0.986	11.955	18.348	18.348	0.000	0.000	0.000	0.000
18	A	19	PHE	0	-0.018	0.002	11.943	-0.878	-0.878	0.000	0.000	0.000	0.000
19	A	20	ASN	0	-0.063	-0.050	12.797	-0.142	-0.142	0.000	0.000	0.000	0.000
20	A	21	MET	0	0.003	0.011	8.037	-1.429	-1.429	0.000	0.000	0.000	0.000
21	A	22	THR	0	0.014	-0.007	7.661	-1.923	-1.923	0.000	0.000	0.000	0.000
22	A	23	LYS	1	0.852	0.925	9.415	16.403	16.403	0.000	0.000	0.000	0.000
23	A	24	GLU	-1	-0.826	-0.858	6.939	-24.617	-24.617	0.000	0.000	0.000	0.000
24	A	25	GLY	0	-0.039	-0.007	6.718	-0.624	-0.624	0.000	0.000	0.000	0.000
25	A	26	TYR	0	-0.069	-0.051	2.313	-3.902	-2.875	0.824	-0.413	-1.437	-0.002
26	A	27	GLU	-1	-0.867	-0.939	3.729	-29.251	-28.685	-0.001	-0.159	-0.406	0.000
27	A	28	VAL	0	-0.044	-0.027	5.698	-1.869	-1.869	0.000	0.000	0.000	0.000
28	A	29	VAL	0	0.032	0.028	8.833	2.791	2.791	0.000	0.000	0.000	0.000
29	A	30	THR	0	-0.035	-0.036	11.087	-0.470	-0.470	0.000	0.000	0.000	0.000
30	A	31	ALA	0	0.004	0.021	14.199	0.355	0.355	0.000	0.000	0.000	0.000
31	A	32	PHE	0	-0.030	-0.033	17.082	-0.242	-0.242	0.000	0.000	0.000	0.000
32	A	33	ASN	0	0.002	-0.021	20.159	0.662	0.662	0.000	0.000	0.000	0.000
33	A	34	GLY	0	0.091	0.038	20.180	-0.803	-0.803	0.000	0.000	0.000	0.000
34	A	35	ARG	1	0.779	0.883	20.920	11.714	11.714	0.000	0.000	0.000	0.000
35	A	36	GLU	-1	-0.776	-0.888	18.791	-14.988	-14.988	0.000	0.000	0.000	0.000
36	A	37	ALA	0	-0.038	-0.018	16.397	-1.081	-1.081	0.000	0.000	0.000	0.000
37	A	38	LEU	0	-0.005	0.001	15.870	-1.412	-1.412	0.000	0.000	0.000	0.000
38	A	39	GLU	-1	-0.895	-0.954	17.046	-14.770	-14.770	0.000	0.000	0.000	0.000
39	A	40	GLN	0	-0.007	-0.018	13.419	-0.956	-0.956	0.000	0.000	0.000	0.000
40	A	41	PHE	0	-0.033	-0.020	11.836	-1.945	-1.945	0.000	0.000	0.000	0.000
41	A	42	GLU	-1	-0.947	-0.976	12.658	-19.045	-19.045	0.000	0.000	0.000	0.000
42	A	43	ALA	0	-0.053	-0.020	14.589	-0.321	-0.321	0.000	0.000	0.000	0.000
43	A	44	GLU	-1	-0.882	-0.942	9.938	-24.643	-24.643	0.000	0.000	0.000	0.000
44	A	45	GLN	0	-0.094	-0.029	8.848	-4.024	-4.024	0.000	0.000	0.000	0.000
45	A	46	PRO	0	-0.028	0.001	6.271	-3.703	-3.703	0.000	0.000	0.000	0.000
46	A	47	ASP	-1	-0.797	-0.892	1.687	-129.663	-131.870	24.338	-12.216	-9.916	-0.139
47	A	48	ILE	0	-0.053	-0.035	4.406	0.206	0.430	-0.001	-0.021	-0.202	0.000
48	A	49	ILE	0	0.005	0.012	6.699	1.410	1.410	0.000	0.000	0.000	0.000
49	A	50	ILE	0	-0.046	-0.018	9.312	0.591	0.591	0.000	0.000	0.000	0.000
50	A	51	LEU	0	0.005	-0.003	12.045	0.618	0.618	0.000	0.000	0.000	0.000
51	A	52	ASP	-1	-0.797	-0.895	15.499	-13.632	-13.632	0.000	0.000	0.000	0.000
52	A	53	LEU	0	0.011	-0.007	18.844	0.034	0.034	0.000	0.000	0.000	0.000
53	A	54	MET	0	-0.095	-0.060	21.817	0.624	0.624	0.000	0.000	0.000	0.000
54	A	55	LEU	0	0.006	0.027	18.866	0.344	0.344	0.000	0.000	0.000	0.000
55	A	56	PRO	0	0.026	0.011	23.336	0.366	0.366	0.000	0.000	0.000	0.000
56	A	57	GLU	-1	-0.870	-0.903	24.576	-11.667	-11.667	0.000	0.000	0.000	0.000
57	A	58	ILE	0	-0.065	-0.038	22.665	0.310	0.310	0.000	0.000	0.000	0.000
58	A	59	ASP	-1	-0.799	-0.885	23.506	-13.082	-13.082	0.000	0.000	0.000	0.000
59	A	60	GLY	0	0.060	0.014	20.475	-0.473	-0.473	0.000	0.000	0.000	0.000
60	A	61	LEU	0	0.004	0.000	20.433	-0.759	-0.759	0.000	0.000	0.000	0.000
61	A	62	GLU	-1	-0.792	-0.876	22.497	-13.365	-13.365	0.000	0.000	0.000	0.000
62	A	63	VAL	0	0.009	0.028	17.309	-0.450	-0.450	0.000	0.000	0.000	0.000
63	A	64	ALA	0	0.022	0.013	17.000	-0.804	-0.804	0.000	0.000	0.000	0.000
64	A	65	LYS	1	0.854	0.915	17.773	12.684	12.684	0.000	0.000	0.000	0.000
65	A	66	THR	0	-0.047	-0.049	20.179	0.109	0.109	0.000	0.000	0.000	0.000
66	A	67	ILE	0	0.023	0.029	13.280	-0.165	-0.165	0.000	0.000	0.000	0.000
67	A	68	ARG	1	0.784	0.868	11.726	22.913	22.913	0.000	0.000	0.000	0.000
68	A	69	LYS	1	0.735	0.866	16.887	14.629	14.629	0.000	0.000	0.000	0.000
69	A	70	THR	0	-0.029	-0.018	16.508	0.204	0.204	0.000	0.000	0.000	0.000
70	A	71	SER	0	0.008	0.012	10.815	-1.581	-1.581	0.000	0.000	0.000	0.000
71	A	72	SER	0	0.003	0.004	9.832	1.622	1.622	0.000	0.000	0.000	0.000
72	A	73	VAL	0	-0.008	0.014	7.015	-1.888	-1.888	0.000	0.000	0.000	0.000
73	A	74	PRO	0	0.015	0.018	6.172	3.873	3.873	0.000	0.000	0.000	0.000
74	A	75	ILE	0	0.004	-0.012	9.093	-0.940	-0.940	0.000	0.000	0.000	0.000
75	A	76	LEU	0	-0.041	-0.007	11.865	1.277	1.277	0.000	0.000	0.000	0.000
76	A	77	MET	0	-0.008	0.003	13.425	0.488	0.488	0.000	0.000	0.000	0.000
77	A	78	LEU	0	-0.023	-0.009	15.482	0.127	0.127	0.000	0.000	0.000	0.000
78	A	79	SER	0	0.062	0.029	18.306	0.490	0.490	0.000	0.000	0.000	0.000
79	A	80	ALA	0	0.028	0.028	22.080	0.010	0.010	0.000	0.000	0.000	0.000
80	A	81	LYS	1	0.798	0.901	25.184	11.268	11.268	0.000	0.000	0.000	0.000
81	A	82	ASP	-1	-0.826	-0.922	25.190	-11.596	-11.596	0.000	0.000	0.000	0.000
82	A	83	SER	0	-0.030	-0.026	26.925	0.144	0.144	0.000	0.000	0.000	0.000
83	A	84	GLU	-1	-0.923	-0.971	28.027	-10.440	-10.440	0.000	0.000	0.000	0.000
84	A	85	PHE	0	0.037	0.015	27.719	-0.354	-0.354	0.000	0.000	0.000	0.000
85	A	86	ASP	-1	-0.774	-0.847	25.858	-11.350	-11.350	0.000	0.000	0.000	0.000
86	A	87	LYS	1	0.831	0.909	23.420	11.394	11.394	0.000	0.000	0.000	0.000
87	A	88	VAL	0	0.000	0.009	22.864	-0.601	-0.601	0.000	0.000	0.000	0.000
88	A	89	ILE	0	0.001	0.005	23.704	-0.435	-0.435	0.000	0.000	0.000	0.000
89	A	90	GLY	0	0.046	-0.002	21.508	-0.319	-0.319	0.000	0.000	0.000	0.000
90	A	91	LEU	0	-0.040	-0.015	18.085	-0.718	-0.718	0.000	0.000	0.000	0.000
91	A	92	GLU	-1	-0.956	-0.977	19.712	-12.399	-12.399	0.000	0.000	0.000	0.000
92	A	93	LEU	0	-0.107	-0.055	21.584	0.078	0.078	0.000	0.000	0.000	0.000
93	A	94	GLY	0	-0.017	-0.002	17.741	-0.330	-0.330	0.000	0.000	0.000	0.000
94	A	95	ALA	0	-0.011	0.004	15.362	-1.435	-1.435	0.000	0.000	0.000	0.000
95	A	96	ASP	-1	-0.833	-0.920	11.670	-24.915	-24.915	0.000	0.000	0.000	0.000
96	A	97	ASP	-1	-0.845	-0.926	14.095	-18.679	-18.679	0.000	0.000	0.000	0.000
97	A	98	TYR	0	-0.014	-0.022	15.835	-0.061	-0.061	0.000	0.000	0.000	0.000
98	A	99	VAL	0	-0.057	-0.021	15.868	0.483	0.483	0.000	0.000	0.000	0.000
99	A	100	THR	0	0.028	0.009	18.824	0.115	0.115	0.000	0.000	0.000	0.000
100	A	101	LYS	1	0.706	0.831	19.683	13.797	13.797	0.000	0.000	0.000	0.000
101	A	102	PRO	0	-0.011	-0.017	22.297	0.433	0.433	0.000	0.000	0.000	0.000
102	A	103	PHE	0	0.059	0.024	17.268	-0.032	-0.032	0.000	0.000	0.000	0.000
103	A	104	SER	0	-0.006	-0.001	19.540	0.122	0.122	0.000	0.000	0.000	0.000
104	A	105	ASN	0	0.044	0.006	15.825	-1.058	-1.058	0.000	0.000	0.000	0.000
105	A	106	ARG	1	0.994	0.989	14.615	13.408	13.408	0.000	0.000	0.000	0.000
106	A	107	GLU	-1	-0.859	-0.908	14.836	-16.121	-16.121	0.000	0.000	0.000	0.000
107	A	108	LEU	0	0.057	0.029	11.750	-1.041	-1.041	0.000	0.000	0.000	0.000
108	A	109	GLN	0	-0.059	-0.044	10.368	-0.511	-0.511	0.000	0.000	0.000	0.000
109	A	110	ALA	0	-0.036	-0.016	10.131	-2.070	-2.070	0.000	0.000	0.000	0.000
110	A	111	ARG	1	0.796	0.873	11.426	16.083	16.083	0.000	0.000	0.000	0.000
111	A	112	VAL	0	0.066	0.031	6.355	-1.430	-1.430	0.000	0.000	0.000	0.000
112	A	113	LYS	1	0.837	0.904	6.549	22.013	22.013	0.000	0.000	0.000	0.000
113	A	114	ALA	0	-0.086	-0.052	7.580	-2.170	-2.170	0.000	0.000	0.000	0.000
114	A	115	LEU	0	0.040	0.017	8.538	-0.496	-0.496	0.000	0.000	0.000	0.000
115	A	116	LEU	0	0.026	0.025	2.340	-5.457	-4.066	1.082	-0.441	-2.031	-0.003
116	A	117	ARG	1	0.876	0.946	4.651	21.162	21.260	-0.001	-0.006	-0.091	0.000
117	A	118	ARG	1	0.891	0.957	6.783	27.621	27.621	0.000	0.000	0.000	0.000
118	A	119	SER	0	0.005	0.002	4.686	-2.988	-2.888	-0.001	-0.006	-0.093	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:2:LYS)