FMO DATABASE

FMODB ID: K98N3

Calculation Name: 3NXA-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NXA

Chain ID: C

ChEMBL ID:

UniProt ID: Q96FQ6

Base Structure: X-ray

Registration Date: 2023-06-22

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	97
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-695087.316105
FMO2-HF: Nuclear repulsion	656180.966081
FMO2-HF: Total energy	-38906.350024
FMO2-MP2: Total energy	-39021.029698

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(C:5:TYR)

Summations of interaction energy for fragment #1(C:5:TYR)

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.
-1.87	-5.292	0.258	5.171	-2.008	0

Interaction energy analysis for fragmet #1(C:5:TYR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.045 / q_NPA : -0.035

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	C	7	GLU	-1	-0.828	-0.923	2.683	12.504	7.467	0.110	5.792	-0.865	-0.006
4	C	8	LEU	0	0.021	0.012	4.876	-0.169	-0.131	-0.001	-0.003	-0.034	0.000
5	C	9	GLU	-1	-0.810	-0.877	4.765	-3.899	-3.760	-0.001	-0.025	-0.113	0.000
6	C	10	LYS	1	0.870	0.914	3.262	-9.237	-7.799	0.150	-0.593	-0.996	0.006
7	C	11	ALA	0	0.002	0.008	5.752	-0.541	-0.541	0.000	0.000	0.000	0.000
8	C	12	VAL	0	0.013	0.003	9.211	-0.244	-0.244	0.000	0.000	0.000	0.000
9	C	13	ILE	0	-0.001	0.000	6.633	-0.099	-0.099	0.000	0.000	0.000	0.000
10	C	14	VAL	0	0.002	0.004	9.295	-0.156	-0.156	0.000	0.000	0.000	0.000
11	C	15	LEU	0	0.005	0.003	11.372	-0.154	-0.154	0.000	0.000	0.000	0.000
12	C	16	VAL	0	0.009	0.021	12.646	-0.083	-0.083	0.000	0.000	0.000	0.000
13	C	17	GLU	-1	-0.896	-0.958	11.915	0.032	0.032	0.000	0.000	0.000	0.000
14	C	18	ASN	0	-0.044	-0.047	14.558	-0.033	-0.033	0.000	0.000	0.000	0.000
15	C	19	PHE	0	-0.037	-0.003	16.972	-0.038	-0.038	0.000	0.000	0.000	0.000
16	C	20	TYR	0	0.020	-0.019	16.788	-0.028	-0.028	0.000	0.000	0.000	0.000
17	C	21	LYS	1	0.796	0.911	18.011	-0.343	-0.343	0.000	0.000	0.000	0.000
18	C	22	TYR	0	-0.087	-0.071	20.158	-0.009	-0.009	0.000	0.000	0.000	0.000
19	C	23	VAL	0	-0.018	0.009	22.519	-0.018	-0.018	0.000	0.000	0.000	0.000
20	C	24	SER	0	-0.041	-0.016	24.630	0.002	0.002	0.000	0.000	0.000	0.000
21	C	25	LYS	1	0.968	0.969	25.145	-0.084	-0.084	0.000	0.000	0.000	0.000
22	C	26	TYR	0	0.003	-0.012	28.838	-0.001	-0.001	0.000	0.000	0.000	0.000
23	C	27	SER	0	0.002	0.022	27.902	-0.007	-0.007	0.000	0.000	0.000	0.000
24	C	28	LEU	0	0.025	0.003	29.717	-0.010	-0.010	0.000	0.000	0.000	0.000
25	C	29	VAL	0	0.014	0.012	28.605	-0.011	-0.011	0.000	0.000	0.000	0.000
26	C	30	LYS	1	0.940	0.961	24.815	0.078	0.078	0.000	0.000	0.000	0.000
27	C	31	ASN	0	0.027	0.024	22.395	-0.006	-0.006	0.000	0.000	0.000	0.000
28	C	32	LYS	1	0.813	0.890	24.218	0.009	0.009	0.000	0.000	0.000	0.000
29	C	33	ILE	0	0.022	0.033	23.454	0.000	0.000	0.000	0.000	0.000	0.000
30	C	34	SER	0	0.002	-0.004	26.638	-0.008	-0.008	0.000	0.000	0.000	0.000
31	C	35	LYS	1	0.907	0.915	29.017	-0.043	-0.043	0.000	0.000	0.000	0.000
32	C	36	SER	0	-0.033	0.007	30.941	0.007	0.007	0.000	0.000	0.000	0.000
33	C	37	SER	0	0.037	0.014	26.738	0.006	0.006	0.000	0.000	0.000	0.000
34	C	38	PHE	0	0.038	0.026	23.688	0.015	0.015	0.000	0.000	0.000	0.000
35	C	39	ARG	1	0.924	0.947	26.702	-0.076	-0.076	0.000	0.000	0.000	0.000
36	C	40	GLU	-1	-0.895	-0.961	27.836	0.135	0.135	0.000	0.000	0.000	0.000
37	C	41	MET	0	-0.026	0.017	21.802	0.021	0.021	0.000	0.000	0.000	0.000
38	C	42	LEU	0	-0.027	-0.019	23.892	0.031	0.031	0.000	0.000	0.000	0.000
39	C	43	GLN	0	-0.022	-0.015	25.793	0.027	0.027	0.000	0.000	0.000	0.000
40	C	44	LYS	1	0.828	0.920	22.050	-0.353	-0.353	0.000	0.000	0.000	0.000
41	C	45	GLU	-1	-0.772	-0.861	19.855	0.395	0.395	0.000	0.000	0.000	0.000
42	C	46	LEU	0	0.001	-0.001	20.264	0.038	0.038	0.000	0.000	0.000	0.000
43	C	47	ASN	0	0.013	0.002	23.235	0.006	0.006	0.000	0.000	0.000	0.000
44	C	48	HIS	0	0.024	0.015	22.378	-0.035	-0.035	0.000	0.000	0.000	0.000
45	C	49	MET	0	0.010	0.025	19.456	-0.023	-0.023	0.000	0.000	0.000	0.000
46	C	50	LEU	0	-0.031	-0.006	24.430	-0.027	-0.027	0.000	0.000	0.000	0.000
47	C	51	SER	0	0.044	0.016	27.640	-0.025	-0.025	0.000	0.000	0.000	0.000
48	C	52	ASP	-1	-0.765	-0.858	29.713	0.147	0.147	0.000	0.000	0.000	0.000
49	C	53	THR	0	0.007	-0.017	31.822	0.003	0.003	0.000	0.000	0.000	0.000
50	C	54	GLY	0	-0.005	0.007	34.408	-0.007	-0.007	0.000	0.000	0.000	0.000
51	C	55	ASN	0	-0.012	-0.039	28.880	-0.007	-0.007	0.000	0.000	0.000	0.000
52	C	56	ARG	1	0.839	0.922	30.464	-0.176	-0.176	0.000	0.000	0.000	0.000
53	C	57	LYS	1	0.819	0.896	31.428	-0.108	-0.108	0.000	0.000	0.000	0.000
54	C	58	ALA	0	-0.018	-0.008	31.334	-0.010	-0.010	0.000	0.000	0.000	0.000
55	C	59	ALA	0	0.050	0.025	28.335	-0.008	-0.008	0.000	0.000	0.000	0.000
56	C	60	ASP	-1	-0.831	-0.903	30.048	0.100	0.100	0.000	0.000	0.000	0.000
57	C	61	LYS	1	0.969	0.980	32.735	-0.083	-0.083	0.000	0.000	0.000	0.000
58	C	62	LEU	0	0.012	0.008	28.274	-0.012	-0.012	0.000	0.000	0.000	0.000
59	C	63	ILE	0	0.017	0.018	28.091	-0.011	-0.011	0.000	0.000	0.000	0.000
60	C	64	GLN	0	-0.027	-0.006	31.577	-0.008	-0.008	0.000	0.000	0.000	0.000
61	C	65	ASN	0	-0.072	-0.051	34.392	-0.005	-0.005	0.000	0.000	0.000	0.000
62	C	66	LEU	0	0.006	0.026	28.830	-0.006	-0.006	0.000	0.000	0.000	0.000
63	C	67	ASP	-1	-0.828	-0.905	32.828	0.012	0.012	0.000	0.000	0.000	0.000
64	C	68	ALA	0	-0.061	-0.031	33.617	0.001	0.001	0.000	0.000	0.000	0.000
65	C	69	ASN	0	-0.013	-0.011	30.799	-0.014	-0.014	0.000	0.000	0.000	0.000
66	C	70	HIS	0	0.057	0.019	31.502	0.007	0.007	0.000	0.000	0.000	0.000
67	C	71	ASP	-1	-0.818	-0.901	33.345	-0.006	-0.006	0.000	0.000	0.000	0.000
68	C	72	GLY	0	-0.030	-0.015	34.465	0.006	0.006	0.000	0.000	0.000	0.000
69	C	73	ARG	1	0.763	0.891	29.891	-0.003	-0.003	0.000	0.000	0.000	0.000
70	C	74	ILE	0	0.000	0.017	25.469	-0.009	-0.009	0.000	0.000	0.000	0.000
71	C	75	SER	0	-0.029	-0.049	24.609	0.000	0.000	0.000	0.000	0.000	0.000
72	C	76	PHE	0	0.087	0.029	15.924	0.020	0.020	0.000	0.000	0.000	0.000
73	C	77	ASP	-1	-0.830	-0.916	21.217	-0.039	-0.039	0.000	0.000	0.000	0.000
74	C	78	GLU	-1	-0.773	-0.831	22.717	0.025	0.025	0.000	0.000	0.000	0.000
75	C	79	TYR	0	-0.045	-0.044	17.251	0.024	0.024	0.000	0.000	0.000	0.000
76	C	80	TRP	0	0.028	0.016	14.511	0.033	0.033	0.000	0.000	0.000	0.000
77	C	81	THR	0	-0.030	-0.027	20.848	0.016	0.016	0.000	0.000	0.000	0.000
78	C	82	LEU	0	-0.031	-0.019	24.151	0.009	0.009	0.000	0.000	0.000	0.000
79	C	83	ILE	0	0.008	0.006	18.970	0.013	0.013	0.000	0.000	0.000	0.000
80	C	84	GLY	0	0.016	0.020	21.717	0.024	0.024	0.000	0.000	0.000	0.000
81	C	85	GLY	0	-0.034	-0.021	22.528	0.003	0.003	0.000	0.000	0.000	0.000
82	C	86	ILE	0	-0.028	-0.022	24.217	-0.003	-0.003	0.000	0.000	0.000	0.000
83	C	87	THR	0	0.000	-0.016	19.449	0.020	0.020	0.000	0.000	0.000	0.000
84	C	88	GLY	0	-0.009	-0.003	22.864	0.005	0.005	0.000	0.000	0.000	0.000
85	C	89	PRO	0	-0.051	-0.034	24.564	0.000	0.000	0.000	0.000	0.000	0.000
86	C	90	ILE	0	0.011	0.013	23.763	-0.003	-0.003	0.000	0.000	0.000	0.000
87	C	91	ALA	0	0.014	0.020	21.282	0.022	0.022	0.000	0.000	0.000	0.000
88	C	92	LYS	1	0.798	0.880	21.866	-0.153	-0.153	0.000	0.000	0.000	0.000
89	C	93	LEU	0	0.046	0.023	24.105	0.009	0.009	0.000	0.000	0.000	0.000
90	C	94	ILE	0	0.006	0.009	18.969	0.013	0.013	0.000	0.000	0.000	0.000
91	C	95	HIS	0	-0.001	0.005	18.850	0.045	0.045	0.000	0.000	0.000	0.000
92	C	96	GLU	-1	-0.801	-0.904	20.801	0.198	0.198	0.000	0.000	0.000	0.000
93	C	97	GLN	0	-0.059	-0.024	22.599	-0.019	-0.019	0.000	0.000	0.000	0.000
94	C	98	GLU	-1	-0.918	-0.966	17.266	0.561	0.561	0.000	0.000	0.000	0.000
95	C	99	GLN	0	-0.056	-0.027	20.095	-0.004	-0.004	0.000	0.000	0.000	0.000
96	C	100	GLN	0	-0.093	-0.048	22.068	-0.028	-0.028	0.000	0.000	0.000	0.000
97	C	101	SER	0	-0.057	-0.005	20.049	-0.010	-0.010	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:5:TYR)