FMO DATABASE

FMODB ID: 1NJ4Z

Calculation Name: 3DWM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DWM

Chain ID: A

ChEMBL ID:

UniProt ID: P9WP33

Base Structure: X-ray

Registration Date: 2023-09-20

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	89
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-547355.897267
FMO2-HF: Nuclear repulsion	515190.863331
FMO2-HF: Total energy	-32165.033936
FMO2-MP2: Total energy	-32260.180299

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:ASN)

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

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.
-26.364	-18.928	3.872	-5.277	-6.031	-0.043

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.039 / q_NPA : -0.028

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	THR	0	-0.033	-0.011	3.924	3.696	5.129	-0.013	-0.635	-0.786	0.001
4	A	5	VAL	0	0.004	-0.006	6.060	-1.153	-1.153	0.000	0.000	0.000	0.000
5	A	6	SER	0	-0.045	-0.009	9.452	0.201	0.201	0.000	0.000	0.000	0.000
6	A	7	ILE	0	0.070	0.025	12.259	-0.124	-0.124	0.000	0.000	0.000	0.000
7	A	8	PRO	0	0.027	0.023	14.975	-0.077	-0.077	0.000	0.000	0.000	0.000
8	A	9	THR	0	-0.026	-0.061	18.618	0.051	0.051	0.000	0.000	0.000	0.000
9	A	10	ILE	0	0.001	-0.007	20.996	0.047	0.047	0.000	0.000	0.000	0.000
10	A	11	LEU	0	0.057	0.021	17.913	-0.011	-0.011	0.000	0.000	0.000	0.000
11	A	12	ARG	1	0.886	0.977	16.980	-0.663	-0.663	0.000	0.000	0.000	0.000
12	A	13	PRO	0	-0.038	0.006	18.524	0.068	0.068	0.000	0.000	0.000	0.000
13	A	14	HIS	0	-0.023	-0.013	17.726	-0.036	-0.036	0.000	0.000	0.000	0.000
14	A	15	THR	0	0.035	0.030	13.530	0.013	0.013	0.000	0.000	0.000	0.000
15	A	16	GLY	0	0.010	0.009	15.514	0.106	0.106	0.000	0.000	0.000	0.000
16	A	17	GLY	0	-0.044	-0.044	18.175	-0.038	-0.038	0.000	0.000	0.000	0.000
17	A	18	GLN	0	-0.045	-0.020	11.765	0.208	0.208	0.000	0.000	0.000	0.000
18	A	19	LYS	1	0.920	0.943	14.300	-0.664	-0.664	0.000	0.000	0.000	0.000
19	A	20	SER	0	-0.006	-0.011	9.525	-0.117	-0.117	0.000	0.000	0.000	0.000
20	A	21	VAL	0	0.007	0.021	8.511	-0.036	-0.036	0.000	0.000	0.000	0.000
21	A	22	SER	0	0.016	0.015	2.818	-3.295	-2.143	0.135	-0.486	-0.801	0.005
22	A	23	ALA	0	-0.007	-0.008	4.284	-1.717	-1.591	-0.001	-0.015	-0.109	0.000
23	A	24	SER	0	-0.039	-0.016	3.400	1.353	2.415	0.078	-0.563	-0.577	0.000
24	A	25	GLY	0	0.036	0.002	5.357	-0.974	-0.927	-0.001	-0.003	-0.042	0.000
25	A	26	ASP	-1	-0.852	-0.915	7.499	-0.177	-0.177	0.000	0.000	0.000	0.000
26	A	27	THR	0	-0.031	-0.027	9.616	-0.207	-0.207	0.000	0.000	0.000	0.000
27	A	28	LEU	0	0.056	0.034	11.472	0.249	0.249	0.000	0.000	0.000	0.000
28	A	29	GLY	0	-0.031	-0.032	13.213	0.180	0.180	0.000	0.000	0.000	0.000
29	A	30	ALA	0	-0.052	-0.003	11.002	0.096	0.096	0.000	0.000	0.000	0.000
30	A	31	VAL	0	0.052	0.032	7.848	0.256	0.256	0.000	0.000	0.000	0.000
31	A	32	ILE	0	-0.023	-0.018	10.174	0.213	0.213	0.000	0.000	0.000	0.000
32	A	33	SER	0	-0.070	-0.042	13.307	0.013	0.013	0.000	0.000	0.000	0.000
33	A	34	ASP	-1	-0.793	-0.895	7.692	3.563	3.563	0.000	0.000	0.000	0.000
34	A	35	LEU	0	-0.018	-0.023	9.319	0.067	0.067	0.000	0.000	0.000	0.000
35	A	36	GLU	-1	-0.812	-0.897	11.527	0.846	0.846	0.000	0.000	0.000	0.000
36	A	37	ALA	0	-0.035	-0.011	12.441	-0.117	-0.117	0.000	0.000	0.000	0.000
37	A	38	ASN	0	-0.032	-0.017	9.252	-0.389	-0.389	0.000	0.000	0.000	0.000
38	A	39	TYR	0	-0.080	-0.042	10.109	0.105	0.105	0.000	0.000	0.000	0.000
39	A	40	SER	0	0.051	0.035	15.361	-0.114	-0.114	0.000	0.000	0.000	0.000
40	A	41	GLY	0	0.021	-0.010	18.508	-0.035	-0.035	0.000	0.000	0.000	0.000
41	A	42	ILE	0	-0.043	-0.032	14.829	-0.108	-0.108	0.000	0.000	0.000	0.000
42	A	43	SER	0	0.008	0.012	17.158	-0.112	-0.112	0.000	0.000	0.000	0.000
43	A	44	GLU	-1	-0.918	-0.960	18.482	0.474	0.474	0.000	0.000	0.000	0.000
44	A	45	ARG	1	0.817	0.917	20.967	-0.610	-0.610	0.000	0.000	0.000	0.000
45	A	46	LEU	0	-0.005	-0.005	15.886	-0.052	-0.052	0.000	0.000	0.000	0.000
46	A	47	MET	0	-0.022	0.006	20.274	-0.053	-0.053	0.000	0.000	0.000	0.000
47	A	48	ASP	-1	-0.880	-0.961	22.649	0.211	0.211	0.000	0.000	0.000	0.000
48	A	49	PRO	0	-0.035	0.002	26.266	0.004	0.004	0.000	0.000	0.000	0.000
49	A	50	SER	0	-0.061	-0.021	28.401	-0.010	-0.010	0.000	0.000	0.000	0.000
50	A	51	SER	0	-0.008	-0.011	29.413	-0.007	-0.007	0.000	0.000	0.000	0.000
51	A	52	PRO	0	0.072	0.019	26.005	0.013	0.013	0.000	0.000	0.000	0.000
52	A	53	GLY	0	-0.001	0.010	22.288	-0.024	-0.024	0.000	0.000	0.000	0.000
53	A	54	LYS	1	0.850	0.934	22.303	-0.207	-0.207	0.000	0.000	0.000	0.000
54	A	55	LEU	0	0.076	0.031	18.664	0.024	0.024	0.000	0.000	0.000	0.000
55	A	56	HIS	0	0.037	0.027	22.829	-0.057	-0.057	0.000	0.000	0.000	0.000
56	A	57	ARG	1	0.945	0.953	24.812	-0.162	-0.162	0.000	0.000	0.000	0.000
57	A	58	PHE	0	-0.046	-0.023	26.797	-0.026	-0.026	0.000	0.000	0.000	0.000
58	A	59	VAL	0	0.002	0.029	20.264	0.017	0.017	0.000	0.000	0.000	0.000
59	A	60	ASN	0	0.010	0.008	21.310	-0.043	-0.043	0.000	0.000	0.000	0.000
60	A	61	ILE	0	0.014	-0.021	15.259	0.086	0.086	0.000	0.000	0.000	0.000
61	A	62	TYR	0	-0.006	0.024	16.642	-0.008	-0.008	0.000	0.000	0.000	0.000
62	A	63	VAL	0	0.026	0.003	11.568	0.145	0.145	0.000	0.000	0.000	0.000
63	A	64	ASN	0	-0.039	-0.026	10.792	-0.039	-0.039	0.000	0.000	0.000	0.000
64	A	65	ASP	-1	-0.962	-0.976	13.883	-0.570	-0.570	0.000	0.000	0.000	0.000
65	A	66	GLU	-1	-0.828	-0.904	16.902	-0.246	-0.246	0.000	0.000	0.000	0.000
66	A	67	ASP	-1	-0.932	-0.969	17.761	0.075	0.075	0.000	0.000	0.000	0.000
67	A	68	VAL	0	0.078	0.035	16.185	-0.007	-0.007	0.000	0.000	0.000	0.000
68	A	69	ARG	1	0.742	0.865	19.044	-0.149	-0.149	0.000	0.000	0.000	0.000
69	A	70	PHE	0	-0.064	-0.040	21.805	0.012	0.012	0.000	0.000	0.000	0.000
70	A	71	SER	0	0.032	0.006	17.829	-0.034	-0.034	0.000	0.000	0.000	0.000
71	A	72	GLY	0	0.023	0.016	19.084	-0.012	-0.012	0.000	0.000	0.000	0.000
72	A	73	GLY	0	-0.029	-0.022	19.848	0.047	0.047	0.000	0.000	0.000	0.000
73	A	74	LEU	0	0.009	-0.014	16.942	-0.008	-0.008	0.000	0.000	0.000	0.000
74	A	75	ALA	0	-0.014	-0.001	16.011	0.051	0.051	0.000	0.000	0.000	0.000
75	A	76	THR	0	-0.030	0.011	14.097	-0.071	-0.071	0.000	0.000	0.000	0.000
76	A	77	ALA	0	0.018	-0.007	12.860	0.093	0.093	0.000	0.000	0.000	0.000
77	A	78	ILE	0	-0.055	-0.015	6.948	0.029	0.029	0.000	0.000	0.000	0.000
78	A	79	ALA	0	-0.025	-0.004	7.752	0.121	0.121	0.000	0.000	0.000	0.000
79	A	80	ASP	-1	-0.875	-0.963	2.123	-27.500	-24.352	3.676	-3.498	-3.326	-0.049
80	A	81	GLY	0	-0.059	-0.026	3.881	1.164	1.415	-0.001	-0.068	-0.183	0.000
81	A	82	ASP	-1	-0.811	-0.884	4.965	-0.390	-0.173	-0.001	-0.009	-0.207	0.000
82	A	83	SER	0	-0.079	-0.033	7.037	0.098	0.098	0.000	0.000	0.000	0.000
83	A	84	VAL	0	0.057	0.021	9.157	0.037	0.037	0.000	0.000	0.000	0.000
84	A	85	THR	0	-0.058	-0.038	11.408	0.168	0.168	0.000	0.000	0.000	0.000
85	A	86	ILE	0	0.019	0.031	13.791	-0.088	-0.088	0.000	0.000	0.000	0.000
86	A	87	LEU	0	-0.009	-0.026	16.820	0.022	0.022	0.000	0.000	0.000	0.000
87	A	88	PRO	0	-0.026	-0.003	20.412	-0.019	-0.019	0.000	0.000	0.000	0.000
88	A	89	ALA	0	0.009	-0.002	23.799	-0.030	-0.030	0.000	0.000	0.000	0.000
89	A	90	VAL	0	-0.043	-0.016	25.959	0.000	0.000	0.000	0.000	0.000	0.000

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