FMO DATABASE

FMODB ID: 76G4K

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1014166.82294
FMO2-HF: Nuclear repulsion	967768.407286
FMO2-HF: Total energy	-46398.415654
FMO2-MP2: Total energy	-46534.708664

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.
-215.152	-203.041	5.84	-7.334	-10.614	-0.058

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 : 0.924 / q_NPA : 0.962

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	4	ILE	0	-0.038	-0.024	3.812	-2.597	-0.223	-0.016	-1.154	-1.203	0.003
4	A	5	LEU	0	0.002	0.016	6.230	1.966	1.966	0.000	0.000	0.000	0.000
5	A	6	ILE	0	-0.053	-0.039	9.709	0.227	0.227	0.000	0.000	0.000	0.000
6	A	7	VAL	0	-0.008	-0.017	12.238	0.673	0.673	0.000	0.000	0.000	0.000
7	A	8	ASP	-1	-0.782	-0.907	15.554	-14.367	-14.367	0.000	0.000	0.000	0.000
8	A	9	ASP	-1	-0.865	-0.928	18.478	-12.550	-12.550	0.000	0.000	0.000	0.000
9	A	10	GLU	-1	-0.870	-0.913	21.682	-11.928	-11.928	0.000	0.000	0.000	0.000
10	A	11	LYS	1	0.851	0.909	20.059	12.936	12.936	0.000	0.000	0.000	0.000
11	A	12	PRO	0	0.002	-0.018	20.575	-0.416	-0.416	0.000	0.000	0.000	0.000
12	A	13	ILE	0	0.000	0.014	18.241	-0.232	-0.232	0.000	0.000	0.000	0.000
13	A	14	SER	0	0.054	0.029	16.600	-0.991	-0.991	0.000	0.000	0.000	0.000
14	A	15	ASP	-1	-0.865	-0.933	15.726	-14.928	-14.928	0.000	0.000	0.000	0.000
15	A	16	ILE	0	-0.020	-0.001	16.450	-0.444	-0.444	0.000	0.000	0.000	0.000
16	A	17	ILE	0	0.020	0.003	11.847	-0.582	-0.582	0.000	0.000	0.000	0.000
17	A	18	LYS	1	1.008	1.017	11.834	16.140	16.140	0.000	0.000	0.000	0.000
18	A	19	PHE	0	-0.021	-0.008	11.533	-0.960	-0.960	0.000	0.000	0.000	0.000
19	A	20	ASN	0	-0.051	-0.037	12.703	-0.045	-0.045	0.000	0.000	0.000	0.000
20	A	21	MET	0	0.014	0.011	7.716	-1.304	-1.304	0.000	0.000	0.000	0.000
21	A	22	THR	0	-0.028	-0.019	7.659	-1.780	-1.780	0.000	0.000	0.000	0.000
22	A	23	LYS	1	0.863	0.931	8.816	16.050	16.050	0.000	0.000	0.000	0.000
23	A	24	GLU	-1	-0.953	-0.974	7.502	-21.394	-21.394	0.000	0.000	0.000	0.000
24	A	25	GLY	0	-0.046	-0.010	5.979	-1.096	-1.096	0.000	0.000	0.000	0.000
25	A	26	TYR	0	-0.061	-0.030	2.186	-4.610	-3.279	1.408	-0.648	-2.091	-0.002
26	A	27	GLU	-1	-0.937	-0.964	3.572	-26.710	-26.195	0.000	-0.117	-0.398	0.000
27	A	28	VAL	0	-0.048	-0.031	5.634	-1.410	-1.410	0.000	0.000	0.000	0.000
28	A	29	VAL	0	0.011	0.027	8.725	1.841	1.841	0.000	0.000	0.000	0.000
29	A	30	THR	0	-0.020	-0.022	11.119	-0.474	-0.474	0.000	0.000	0.000	0.000
30	A	31	ALA	0	-0.014	0.002	14.245	0.290	0.290	0.000	0.000	0.000	0.000
31	A	32	PHE	0	-0.026	-0.025	16.819	-0.194	-0.194	0.000	0.000	0.000	0.000
32	A	33	ASN	0	0.032	0.015	19.847	0.487	0.487	0.000	0.000	0.000	0.000
33	A	34	GLY	0	0.121	0.060	19.710	-0.744	-0.744	0.000	0.000	0.000	0.000
34	A	35	ARG	1	0.919	0.962	20.276	11.368	11.368	0.000	0.000	0.000	0.000
35	A	36	GLU	-1	-0.845	-0.932	18.966	-14.419	-14.419	0.000	0.000	0.000	0.000
36	A	37	ALA	0	-0.035	-0.017	16.009	-0.930	-0.930	0.000	0.000	0.000	0.000
37	A	38	LEU	0	0.003	-0.011	15.612	-1.189	-1.189	0.000	0.000	0.000	0.000
38	A	39	GLU	-1	-0.931	-0.955	17.310	-14.338	-14.338	0.000	0.000	0.000	0.000
39	A	40	GLN	0	0.034	-0.006	13.353	-1.610	-1.610	0.000	0.000	0.000	0.000
40	A	41	PHE	0	-0.049	-0.020	11.944	-1.864	-1.864	0.000	0.000	0.000	0.000
41	A	42	GLU	-1	-0.970	-0.987	12.748	-18.044	-18.044	0.000	0.000	0.000	0.000
42	A	43	ALA	0	-0.042	-0.024	14.298	-0.577	-0.577	0.000	0.000	0.000	0.000
43	A	44	GLU	-1	-0.869	-0.919	9.445	-25.215	-25.215	0.000	0.000	0.000	0.000
44	A	45	GLN	0	-0.100	-0.034	8.622	-2.481	-2.481	0.000	0.000	0.000	0.000
45	A	46	PRO	0	-0.013	-0.009	6.525	-3.924	-3.924	0.000	0.000	0.000	0.000
46	A	47	ASP	-1	-0.865	-0.923	2.554	-90.164	-83.291	2.861	-4.972	-4.761	-0.055
47	A	48	ILE	0	-0.051	-0.030	4.284	0.792	0.981	-0.001	-0.012	-0.175	0.000
48	A	49	ILE	0	0.013	0.019	6.603	0.610	0.610	0.000	0.000	0.000	0.000
49	A	50	ILE	0	-0.058	-0.019	9.825	0.562	0.562	0.000	0.000	0.000	0.000
50	A	51	LEU	0	0.004	0.003	12.079	0.309	0.309	0.000	0.000	0.000	0.000
51	A	52	ASP	-1	-0.787	-0.873	15.329	-14.148	-14.148	0.000	0.000	0.000	0.000
52	A	53	LEU	0	-0.016	-0.059	18.577	0.112	0.112	0.000	0.000	0.000	0.000
53	A	54	MET	0	-0.114	-0.058	21.576	0.684	0.684	0.000	0.000	0.000	0.000
54	A	55	LEU	0	0.070	0.053	18.989	-0.203	-0.203	0.000	0.000	0.000	0.000
55	A	56	PRO	0	-0.011	-0.012	23.480	0.410	0.410	0.000	0.000	0.000	0.000
56	A	57	GLU	-1	-0.978	-0.978	24.540	-11.295	-11.295	0.000	0.000	0.000	0.000
57	A	58	ILE	0	-0.051	-0.035	22.398	0.306	0.306	0.000	0.000	0.000	0.000
58	A	59	ASP	-1	-0.838	-0.903	23.098	-12.635	-12.635	0.000	0.000	0.000	0.000
59	A	60	GLY	0	0.099	0.035	20.100	-0.426	-0.426	0.000	0.000	0.000	0.000
60	A	61	LEU	0	-0.012	-0.004	20.146	-0.660	-0.660	0.000	0.000	0.000	0.000
61	A	62	GLU	-1	-0.931	-0.977	21.947	-12.838	-12.838	0.000	0.000	0.000	0.000
62	A	63	VAL	0	0.014	0.014	17.130	-0.421	-0.421	0.000	0.000	0.000	0.000
63	A	64	ALA	0	0.017	0.005	17.379	-0.705	-0.705	0.000	0.000	0.000	0.000
64	A	65	LYS	1	0.888	0.955	18.411	12.483	12.483	0.000	0.000	0.000	0.000
65	A	66	THR	0	-0.112	-0.067	20.772	-0.291	-0.291	0.000	0.000	0.000	0.000
66	A	67	ILE	0	0.050	0.027	14.057	-0.180	-0.180	0.000	0.000	0.000	0.000
67	A	68	ARG	1	0.811	0.893	12.548	21.584	21.584	0.000	0.000	0.000	0.000
68	A	69	LYS	1	0.866	0.946	17.288	13.498	13.498	0.000	0.000	0.000	0.000
69	A	70	THR	0	-0.022	-0.013	17.002	0.127	0.127	0.000	0.000	0.000	0.000
70	A	71	SER	0	0.017	0.031	11.602	-1.471	-1.471	0.000	0.000	0.000	0.000
71	A	72	SER	0	-0.024	-0.020	10.961	0.611	0.611	0.000	0.000	0.000	0.000
72	A	73	VAL	0	0.003	0.021	7.885	-1.365	-1.365	0.000	0.000	0.000	0.000
73	A	74	PRO	0	0.032	0.020	6.945	3.209	3.209	0.000	0.000	0.000	0.000
74	A	75	ILE	0	0.016	0.011	9.765	-0.851	-0.851	0.000	0.000	0.000	0.000
75	A	76	LEU	0	-0.046	-0.014	11.866	0.829	0.829	0.000	0.000	0.000	0.000
76	A	77	MET	0	0.006	0.000	13.379	0.498	0.498	0.000	0.000	0.000	0.000
77	A	78	LEU	0	0.015	-0.004	15.628	0.175	0.175	0.000	0.000	0.000	0.000
78	A	79	SER	0	0.014	0.005	18.096	0.503	0.503	0.000	0.000	0.000	0.000
79	A	80	ALA	0	0.033	0.024	21.815	0.000	0.000	0.000	0.000	0.000	0.000
80	A	81	LYS	1	0.882	0.956	25.017	10.742	10.742	0.000	0.000	0.000	0.000
81	A	82	ASP	-1	-0.875	-0.938	25.013	-11.122	-11.122	0.000	0.000	0.000	0.000
82	A	83	SER	0	-0.048	-0.015	26.947	0.188	0.188	0.000	0.000	0.000	0.000
83	A	84	GLU	-1	-0.934	-0.983	27.720	-10.256	-10.256	0.000	0.000	0.000	0.000
84	A	85	PHE	0	0.015	0.008	27.926	-0.293	-0.293	0.000	0.000	0.000	0.000
85	A	86	ASP	-1	-0.827	-0.920	25.712	-11.138	-11.138	0.000	0.000	0.000	0.000
86	A	87	LYS	1	0.931	0.964	23.311	11.746	11.746	0.000	0.000	0.000	0.000
87	A	88	VAL	0	-0.004	0.000	23.186	-0.587	-0.587	0.000	0.000	0.000	0.000
88	A	89	ILE	0	0.029	0.030	24.598	-0.313	-0.313	0.000	0.000	0.000	0.000
89	A	90	GLY	0	0.035	0.003	21.709	-0.357	-0.357	0.000	0.000	0.000	0.000
90	A	91	LEU	0	-0.055	-0.033	18.525	-0.619	-0.619	0.000	0.000	0.000	0.000
91	A	92	GLU	-1	-0.976	-0.974	20.566	-11.940	-11.940	0.000	0.000	0.000	0.000
92	A	93	LEU	0	-0.082	-0.067	22.258	-0.046	-0.046	0.000	0.000	0.000	0.000
93	A	94	GLY	0	-0.017	0.008	18.358	-0.331	-0.331	0.000	0.000	0.000	0.000
94	A	95	ALA	0	-0.029	-0.015	15.987	-1.226	-1.226	0.000	0.000	0.000	0.000
95	A	96	ASP	-1	-0.850	-0.935	12.836	-23.308	-23.308	0.000	0.000	0.000	0.000
96	A	97	ASP	-1	-0.884	-0.951	14.236	-17.988	-17.988	0.000	0.000	0.000	0.000
97	A	98	TYR	0	-0.014	-0.023	15.996	-0.057	-0.057	0.000	0.000	0.000	0.000
98	A	99	VAL	0	-0.059	-0.020	15.993	0.369	0.369	0.000	0.000	0.000	0.000
99	A	100	THR	0	0.012	-0.001	18.946	0.067	0.067	0.000	0.000	0.000	0.000
100	A	101	LYS	1	0.726	0.890	20.229	13.452	13.452	0.000	0.000	0.000	0.000
101	A	102	PRO	0	0.007	-0.016	22.546	0.374	0.374	0.000	0.000	0.000	0.000
102	A	103	PHE	0	0.056	0.025	16.480	0.050	0.050	0.000	0.000	0.000	0.000
103	A	104	SER	0	0.004	0.009	19.254	0.135	0.135	0.000	0.000	0.000	0.000
104	A	105	ASN	0	0.082	0.013	15.888	-0.914	-0.914	0.000	0.000	0.000	0.000
105	A	106	ARG	1	0.979	0.974	14.665	13.479	13.479	0.000	0.000	0.000	0.000
106	A	107	GLU	-1	-0.848	-0.907	14.812	-15.796	-15.796	0.000	0.000	0.000	0.000
107	A	108	LEU	0	0.026	0.004	12.054	-0.947	-0.947	0.000	0.000	0.000	0.000
108	A	109	GLN	0	-0.003	0.014	10.337	-0.461	-0.461	0.000	0.000	0.000	0.000
109	A	110	ALA	0	-0.059	-0.018	10.122	-1.813	-1.813	0.000	0.000	0.000	0.000
110	A	111	ARG	1	0.818	0.891	11.742	15.721	15.721	0.000	0.000	0.000	0.000
111	A	112	VAL	0	0.059	0.033	6.404	-1.235	-1.235	0.000	0.000	0.000	0.000
112	A	113	LYS	1	0.966	0.981	7.128	20.605	20.605	0.000	0.000	0.000	0.000
113	A	114	ALA	0	-0.089	-0.051	7.779	-2.194	-2.194	0.000	0.000	0.000	0.000
114	A	115	LEU	0	0.053	0.016	8.392	-0.732	-0.732	0.000	0.000	0.000	0.000
115	A	116	LEU	0	0.023	0.021	2.139	-3.993	-3.300	1.590	-0.431	-1.852	-0.004
116	A	117	ARG	1	0.842	0.933	5.164	21.142	21.207	-0.001	0.000	-0.064	0.000
117	A	118	ARG	1	0.896	0.956	6.962	24.535	24.535	0.000	0.000	0.000	0.000
118	A	119	SER	0	0.042	0.035	4.631	2.629	2.700	-0.001	0.000	-0.070	0.000

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