FMO DATABASE

FMODB ID: 2N83R

Calculation Name: 3NX6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NX6

Chain ID: A

ChEMBL ID:

UniProt ID: Q5GUT0

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	75
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-421254.651483
FMO2-HF: Nuclear repulsion	394096.646895
FMO2-HF: Total energy	-27158.004588
FMO2-MP2: Total energy	-27239.625069

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:SER)

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

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.
-7.44	-4.067	0.213	-1.629	-1.954	-0.001

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.002 / q_NPA : -0.006

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	LYS	1	0.950	0.973	3.875	-0.830	0.456	-0.006	-0.628	-0.651	0.002
4	A	5	PRO	0	0.021	0.022	6.475	-0.260	-0.260	0.000	0.000	0.000	0.000
5	A	6	LEU	0	-0.012	-0.022	9.821	-0.122	-0.122	0.000	0.000	0.000	0.000
6	A	7	HIS	0	0.031	0.003	13.257	0.061	0.061	0.000	0.000	0.000	0.000
7	A	8	ASP	-1	-0.751	-0.840	16.275	0.402	0.402	0.000	0.000	0.000	0.000
8	A	9	ARG	1	0.893	0.959	12.899	-0.423	-0.423	0.000	0.000	0.000	0.000
9	A	10	VAL	0	0.038	0.016	12.614	0.083	0.083	0.000	0.000	0.000	0.000
10	A	11	VAL	0	-0.029	-0.005	6.634	-0.083	-0.083	0.000	0.000	0.000	0.000
11	A	12	VAL	0	0.037	0.019	9.959	0.058	0.058	0.000	0.000	0.000	0.000
12	A	13	LYS	1	0.952	0.978	9.938	-0.456	-0.456	0.000	0.000	0.000	0.000
13	A	14	PRO	0	0.018	0.019	11.561	-0.060	-0.060	0.000	0.000	0.000	0.000
14	A	15	ILE	0	-0.044	-0.009	14.777	-0.025	-0.025	0.000	0.000	0.000	0.000
15	A	35	SER	0	-0.020	-0.015	23.588	-0.003	-0.003	0.000	0.000	0.000	0.000
16	A	36	THR	0	-0.040	-0.032	20.037	-0.006	-0.006	0.000	0.000	0.000	0.000
17	A	37	LYS	1	1.005	1.000	20.073	-0.206	-0.206	0.000	0.000	0.000	0.000
18	A	38	GLY	0	0.027	0.004	15.886	-0.008	-0.008	0.000	0.000	0.000	0.000
19	A	39	GLU	-1	-0.871	-0.915	13.790	0.543	0.543	0.000	0.000	0.000	0.000
20	A	40	VAL	0	-0.014	0.003	12.320	0.124	0.124	0.000	0.000	0.000	0.000
21	A	41	VAL	0	-0.003	-0.004	6.307	-0.032	-0.032	0.000	0.000	0.000	0.000
22	A	42	ALA	0	0.000	-0.010	7.039	0.336	0.336	0.000	0.000	0.000	0.000
23	A	43	ILE	0	0.014	0.012	9.131	-0.199	-0.199	0.000	0.000	0.000	0.000
24	A	44	GLY	0	-0.024	-0.001	11.722	0.073	0.073	0.000	0.000	0.000	0.000
25	A	45	ALA	0	-0.027	-0.031	13.396	-0.019	-0.019	0.000	0.000	0.000	0.000
26	A	46	GLY	0	0.089	0.055	15.880	-0.039	-0.039	0.000	0.000	0.000	0.000
27	A	47	LYS	1	0.852	0.920	18.754	-0.215	-0.215	0.000	0.000	0.000	0.000
28	A	48	PRO	0	0.011	0.000	19.601	-0.014	-0.014	0.000	0.000	0.000	0.000
29	A	49	LEU	0	-0.038	-0.009	22.693	-0.007	-0.007	0.000	0.000	0.000	0.000
30	A	50	ASP	-1	-0.866	-0.945	26.381	0.136	0.136	0.000	0.000	0.000	0.000
31	A	51	ASN	0	-0.029	0.004	29.166	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	52	GLY	0	0.016	0.020	27.988	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	53	SER	0	-0.045	-0.035	25.601	0.007	0.007	0.000	0.000	0.000	0.000
34	A	54	LEU	0	-0.026	-0.019	19.114	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	55	HIS	0	-0.042	-0.028	21.499	-0.025	-0.025	0.000	0.000	0.000	0.000
36	A	56	ALA	0	-0.004	-0.001	20.779	0.034	0.034	0.000	0.000	0.000	0.000
37	A	57	PRO	0	-0.002	-0.005	16.714	-0.018	-0.018	0.000	0.000	0.000	0.000
38	A	58	VAL	0	-0.027	-0.008	19.643	-0.010	-0.010	0.000	0.000	0.000	0.000
39	A	59	VAL	0	-0.048	-0.015	16.255	-0.009	-0.009	0.000	0.000	0.000	0.000
40	A	60	LYS	1	0.882	0.918	15.693	-0.422	-0.422	0.000	0.000	0.000	0.000
41	A	61	VAL	0	0.009	-0.009	10.876	-0.016	-0.016	0.000	0.000	0.000	0.000
42	A	62	GLY	0	0.028	0.027	13.337	-0.098	-0.098	0.000	0.000	0.000	0.000
43	A	63	ASP	-1	-0.800	-0.863	15.092	0.379	0.379	0.000	0.000	0.000	0.000
44	A	64	LYS	1	0.829	0.895	16.473	-0.416	-0.416	0.000	0.000	0.000	0.000
45	A	65	VAL	0	0.012	0.002	16.530	-0.029	-0.029	0.000	0.000	0.000	0.000
46	A	66	ILE	0	-0.035	-0.019	19.493	-0.012	-0.012	0.000	0.000	0.000	0.000
47	A	67	TYR	0	0.076	0.038	17.025	0.033	0.033	0.000	0.000	0.000	0.000
48	A	68	GLY	0	0.054	0.023	20.787	-0.026	-0.026	0.000	0.000	0.000	0.000
49	A	69	GLN	0	0.043	0.035	20.424	0.048	0.048	0.000	0.000	0.000	0.000
50	A	70	TYR	0	-0.032	-0.037	19.995	0.011	0.011	0.000	0.000	0.000	0.000
51	A	71	ALA	0	0.014	0.031	19.828	-0.013	-0.013	0.000	0.000	0.000	0.000
52	A	72	GLY	0	0.042	0.020	16.637	0.026	0.026	0.000	0.000	0.000	0.000
53	A	73	SER	0	-0.060	-0.027	13.730	-0.063	-0.063	0.000	0.000	0.000	0.000
54	A	74	SER	0	-0.036	-0.030	12.622	0.127	0.127	0.000	0.000	0.000	0.000
55	A	75	TYR	0	-0.010	-0.008	3.056	-0.746	-0.008	0.046	-0.347	-0.437	0.003
56	A	76	LYS	1	0.883	0.911	8.090	0.176	0.176	0.000	0.000	0.000	0.000
57	A	77	SER	0	-0.005	-0.024	2.817	-0.749	0.200	0.172	-0.483	-0.637	-0.005
58	A	78	GLU	-1	-0.878	-0.917	3.674	-5.591	-5.191	0.001	-0.171	-0.229	-0.001
59	A	79	GLY	0	-0.001	0.012	7.220	0.312	0.312	0.000	0.000	0.000	0.000
60	A	80	VAL	0	-0.058	-0.018	8.462	0.164	0.164	0.000	0.000	0.000	0.000
61	A	81	GLU	-1	-0.853	-0.900	8.804	0.093	0.093	0.000	0.000	0.000	0.000
62	A	82	TYR	0	-0.026	-0.022	6.384	0.314	0.314	0.000	0.000	0.000	0.000
63	A	83	LYS	1	0.867	0.932	10.003	-0.418	-0.418	0.000	0.000	0.000	0.000
64	A	84	VAL	0	-0.005	-0.006	9.350	0.156	0.156	0.000	0.000	0.000	0.000
65	A	85	LEU	0	-0.010	0.002	11.917	-0.146	-0.146	0.000	0.000	0.000	0.000
66	A	86	ARG	1	0.803	0.852	14.777	-0.245	-0.245	0.000	0.000	0.000	0.000
67	A	87	GLU	-1	-0.775	-0.894	17.574	0.418	0.418	0.000	0.000	0.000	0.000
68	A	88	ASP	-1	-0.918	-0.959	19.072	0.231	0.231	0.000	0.000	0.000	0.000
69	A	89	ASP	-1	-0.843	-0.914	18.555	0.337	0.337	0.000	0.000	0.000	0.000
70	A	90	ILE	0	-0.089	-0.051	16.667	0.001	0.001	0.000	0.000	0.000	0.000
71	A	91	LEU	0	-0.005	0.000	20.812	-0.022	-0.022	0.000	0.000	0.000	0.000
72	A	92	ALA	0	0.013	0.002	22.870	-0.020	-0.020	0.000	0.000	0.000	0.000
73	A	93	VAL	0	0.009	0.008	20.421	0.031	0.031	0.000	0.000	0.000	0.000
74	A	94	ILE	0	-0.074	-0.039	21.821	-0.032	-0.032	0.000	0.000	0.000	0.000
75	A	95	GLY	0	-0.032	-0.021	20.362	-0.010	-0.010	0.000	0.000	0.000	0.000

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