FMO DATABASE

FMODB ID: 2J3JR

Calculation Name: 1NYU-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NYU

Chain ID: B

ChEMBL ID:

UniProt ID: P38444

Base Structure: X-ray

Registration Date: 2023-09-19

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	83
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-550759.372794
FMO2-HF: Nuclear repulsion	513299.120109
FMO2-HF: Total energy	-37460.252685
FMO2-MP2: Total energy	-37560.007209

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(B:2:LEU)

Summations of interaction energy for fragment #1(B:2:LEU)

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.
-6.337	2.254	3.674	-4.216	-8.051	-0.03

Interaction energy analysis for fragmet #1(B:2:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : 0.015

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	B	4	CYS	0	-0.018	0.036	2.496	-7.907	-2.124	3.567	-3.657	-5.693	-0.027
4	B	5	ASP	-1	-0.827	-0.903	4.399	-0.762	-0.630	-0.001	-0.019	-0.112	0.000
5	B	6	GLY	0	-0.042	-0.031	7.541	-0.015	-0.015	0.000	0.000	0.000	0.000
6	B	7	LYS	1	0.753	0.865	7.831	0.772	0.772	0.000	0.000	0.000	0.000
7	B	8	VAL	0	0.035	0.027	6.019	0.154	0.154	0.000	0.000	0.000	0.000
8	B	9	ASN	0	-0.092	-0.059	8.559	0.011	0.011	0.000	0.000	0.000	0.000
9	B	10	ILE	0	0.009	-0.003	3.229	-0.609	0.092	0.069	-0.138	-0.633	0.000
10	B	11	CYS	0	-0.070	-0.013	4.310	-0.480	-0.225	-0.002	-0.044	-0.209	0.000
11	B	13	LYS	1	0.835	0.886	3.359	3.049	3.498	0.021	0.116	-0.587	0.000
12	B	14	LYS	1	0.806	0.891	5.765	1.462	1.462	0.000	0.000	0.000	0.000
13	B	15	GLN	0	0.017	-0.008	7.522	0.206	0.206	0.000	0.000	0.000	0.000
14	B	16	PHE	0	-0.007	-0.003	10.284	0.098	0.098	0.000	0.000	0.000	0.000
15	B	17	PHE	0	-0.031	-0.018	14.018	0.026	0.026	0.000	0.000	0.000	0.000
16	B	18	VAL	0	-0.010	0.015	16.979	0.010	0.010	0.000	0.000	0.000	0.000
17	B	19	SER	0	0.025	0.021	20.494	0.019	0.019	0.000	0.000	0.000	0.000
18	B	20	PHE	0	0.060	-0.008	22.225	-0.006	-0.006	0.000	0.000	0.000	0.000
19	B	21	LYS	1	0.850	0.930	25.572	0.147	0.147	0.000	0.000	0.000	0.000
20	B	22	ASP	-1	-0.866	-0.942	24.351	-0.240	-0.240	0.000	0.000	0.000	0.000
21	B	23	ILE	0	-0.056	-0.025	23.193	-0.007	-0.007	0.000	0.000	0.000	0.000
22	B	24	GLY	0	-0.007	0.012	27.005	0.010	0.010	0.000	0.000	0.000	0.000
23	B	25	TRP	0	0.008	-0.022	24.197	0.004	0.004	0.000	0.000	0.000	0.000
24	B	26	ASN	0	-0.049	-0.036	28.809	0.001	0.001	0.000	0.000	0.000	0.000
25	B	27	ASP	-1	-0.856	-0.918	29.666	-0.116	-0.116	0.000	0.000	0.000	0.000
26	B	28	TRP	0	-0.001	0.010	27.515	0.010	0.010	0.000	0.000	0.000	0.000
27	B	29	ILE	0	-0.032	-0.010	25.496	0.007	0.007	0.000	0.000	0.000	0.000
28	B	30	ILE	0	-0.010	0.012	29.274	-0.004	-0.004	0.000	0.000	0.000	0.000
29	B	31	ALA	0	-0.029	-0.008	26.462	-0.003	-0.003	0.000	0.000	0.000	0.000
30	B	32	PRO	0	0.019	0.005	21.257	0.009	0.009	0.000	0.000	0.000	0.000
31	B	33	SER	0	0.042	-0.004	24.202	-0.001	-0.001	0.000	0.000	0.000	0.000
32	B	34	GLY	0	0.011	0.013	22.059	-0.001	-0.001	0.000	0.000	0.000	0.000
33	B	35	TYR	0	-0.021	-0.006	16.978	0.005	0.005	0.000	0.000	0.000	0.000
34	B	36	HIS	0	0.036	0.008	12.915	-0.061	-0.061	0.000	0.000	0.000	0.000
35	B	37	ALA	0	0.006	0.020	13.945	-0.020	-0.020	0.000	0.000	0.000	0.000
36	B	38	ASN	0	-0.033	-0.031	9.328	-0.034	-0.034	0.000	0.000	0.000	0.000
37	B	39	TYR	0	0.001	0.001	10.407	0.126	0.126	0.000	0.000	0.000	0.000
38	B	40	CYS	0	-0.076	-0.011	3.274	0.158	0.465	0.003	-0.083	-0.227	0.000
39	B	41	GLU	-1	-0.854	-0.953	7.585	-0.775	-0.775	0.000	0.000	0.000	0.000
40	B	42	GLY	0	0.114	0.041	6.676	-0.362	-0.362	0.000	0.000	0.000	0.000
41	B	43	GLU	-1	-0.843	-0.891	8.063	-0.567	-0.567	0.000	0.000	0.000	0.000
42	B	44	CYS	0	-0.021	-0.010	6.005	-0.423	-0.423	0.000	0.000	0.000	0.000
43	B	45	PRO	0	0.017	-0.007	8.039	0.017	0.017	0.000	0.000	0.000	0.000
44	B	46	SER	0	0.006	-0.019	11.239	-0.032	-0.032	0.000	0.000	0.000	0.000
45	B	47	HIS	0	0.039	0.017	14.869	-0.013	-0.013	0.000	0.000	0.000	0.000
46	B	48	ILE	0	-0.049	0.018	14.041	0.008	0.008	0.000	0.000	0.000	0.000
47	B	77	LEU	0	0.001	-0.002	18.526	-0.001	-0.001	0.000	0.000	0.000	0.000
48	B	78	LYS	1	0.879	0.921	13.137	0.185	0.185	0.000	0.000	0.000	0.000
49	B	79	SER	0	0.000	0.005	11.440	-0.026	-0.026	0.000	0.000	0.000	0.000
50	B	80	CYS	0	0.001	-0.008	11.911	-0.026	-0.026	0.000	0.000	0.000	0.000
51	B	82	VAL	0	0.001	-0.003	8.672	0.067	0.067	0.000	0.000	0.000	0.000
52	B	83	PRO	0	0.060	-0.001	7.995	-0.127	-0.127	0.000	0.000	0.000	0.000
53	B	84	THR	0	-0.059	-0.018	6.546	0.218	0.218	0.000	0.000	0.000	0.000
54	B	85	LYS	1	0.806	0.889	7.884	-0.372	-0.372	0.000	0.000	0.000	0.000
55	B	86	LEU	0	-0.021	-0.004	9.217	-0.220	-0.220	0.000	0.000	0.000	0.000
56	B	87	ARG	1	0.884	0.935	10.134	0.426	0.426	0.000	0.000	0.000	0.000
57	B	88	PRO	0	-0.010	-0.013	13.992	-0.041	-0.041	0.000	0.000	0.000	0.000
58	B	89	MET	0	-0.010	-0.002	16.595	-0.031	-0.031	0.000	0.000	0.000	0.000
59	B	90	SER	0	-0.058	-0.043	18.962	0.012	0.012	0.000	0.000	0.000	0.000
60	B	91	MET	0	-0.027	-0.003	22.386	-0.023	-0.023	0.000	0.000	0.000	0.000
61	B	92	LEU	0	-0.019	-0.021	24.932	0.016	0.016	0.000	0.000	0.000	0.000
62	B	93	TYR	0	-0.023	-0.018	27.426	-0.009	-0.009	0.000	0.000	0.000	0.000
63	B	94	TYR	0	0.031	0.016	30.547	0.010	0.010	0.000	0.000	0.000	0.000
64	B	95	ASP	-1	-0.814	-0.903	33.059	-0.063	-0.063	0.000	0.000	0.000	0.000
65	B	96	ASP	-1	-0.888	-0.962	34.878	-0.075	-0.075	0.000	0.000	0.000	0.000
66	B	97	GLY	0	-0.058	-0.020	37.557	0.002	0.002	0.000	0.000	0.000	0.000
67	B	98	GLN	0	-0.093	-0.050	37.574	0.002	0.002	0.000	0.000	0.000	0.000
68	B	99	ASN	0	-0.031	-0.013	36.884	0.004	0.004	0.000	0.000	0.000	0.000
69	B	100	ILE	0	-0.023	-0.006	33.466	-0.005	-0.005	0.000	0.000	0.000	0.000
70	B	101	ILE	0	-0.017	-0.002	30.183	0.007	0.007	0.000	0.000	0.000	0.000
71	B	102	LYS	1	0.863	0.931	25.477	0.041	0.041	0.000	0.000	0.000	0.000
72	B	103	LYS	1	0.901	0.939	24.905	0.072	0.072	0.000	0.000	0.000	0.000
73	B	104	ASP	-1	-0.787	-0.861	22.030	-0.064	-0.064	0.000	0.000	0.000	0.000
74	B	105	ILE	0	-0.013	-0.003	21.228	0.016	0.016	0.000	0.000	0.000	0.000
75	B	106	GLN	0	0.062	0.005	18.626	-0.025	-0.025	0.000	0.000	0.000	0.000
76	B	107	ASN	0	-0.027	-0.022	15.816	0.003	0.003	0.000	0.000	0.000	0.000
77	B	108	MET	0	0.020	0.026	15.796	-0.027	-0.027	0.000	0.000	0.000	0.000
78	B	109	ILE	0	-0.025	0.004	11.605	-0.037	-0.037	0.000	0.000	0.000	0.000
79	B	110	VAL	0	0.058	0.022	7.883	0.085	0.085	0.000	0.000	0.000	0.000
80	B	111	GLU	-1	-0.847	-0.891	7.266	-0.152	-0.152	0.000	0.000	0.000	0.000
81	B	112	GLU	-1	-0.795	-0.898	3.623	0.568	0.806	0.002	-0.037	-0.203	0.000
82	B	114	GLY	0	0.062	0.030	3.390	-0.779	-0.053	0.015	-0.354	-0.387	-0.003
83	B	116	SER	0	0.043	0.045	8.849	0.161	0.161	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:2:LEU)