FMO DATABASE

FMODB ID: 2JMVR

Calculation Name: 5WFB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5WFB

Chain ID: A

ChEMBL ID:

UniProt ID: Q96N21

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	132
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1110792.054901
FMO2-HF: Nuclear repulsion	1061002.887977
FMO2-HF: Total energy	-49789.166925
FMO2-MP2: Total energy	-49936.312693

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:ALA)

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

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.
-1.14	0.993	0.006	-1.023	-1.116	0.002

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / q_NPA : -0.013

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	A	4	ALA	0	-0.002	0.013	3.193	-1.325	0.683	0.008	-0.997	-1.019	0.002
4	A	5	PRO	0	-0.019	-0.012	4.372	-0.930	-0.905	-0.001	-0.020	-0.004	0.000
5	A	6	PRO	0	0.040	0.025	4.434	0.085	0.185	-0.001	-0.006	-0.093	0.000
6	A	7	LEU	0	0.043	0.015	5.946	0.210	0.210	0.000	0.000	0.000	0.000
7	A	8	ARG	1	0.878	0.916	8.992	0.797	0.797	0.000	0.000	0.000	0.000
8	A	9	ASP	-1	-0.746	-0.820	8.861	-0.741	-0.741	0.000	0.000	0.000	0.000
9	A	10	ARG	1	0.825	0.874	9.489	0.337	0.337	0.000	0.000	0.000	0.000
10	A	11	LEU	0	-0.007	0.000	11.937	0.059	0.059	0.000	0.000	0.000	0.000
11	A	12	SER	0	0.028	0.006	14.146	0.028	0.028	0.000	0.000	0.000	0.000
12	A	13	PHE	0	0.041	0.014	14.715	0.040	0.040	0.000	0.000	0.000	0.000
13	A	14	LEU	0	-0.009	-0.010	16.015	0.034	0.034	0.000	0.000	0.000	0.000
14	A	15	HIS	0	0.002	-0.007	18.263	0.017	0.017	0.000	0.000	0.000	0.000
15	A	16	ARG	1	0.784	0.861	18.749	0.227	0.227	0.000	0.000	0.000	0.000
16	A	17	LEU	0	0.011	0.019	19.430	0.015	0.015	0.000	0.000	0.000	0.000
17	A	18	PRO	0	0.007	-0.003	22.283	0.012	0.012	0.000	0.000	0.000	0.000
18	A	19	ILE	0	-0.013	0.001	23.281	0.009	0.009	0.000	0.000	0.000	0.000
19	A	20	LEU	0	0.032	0.017	20.086	0.008	0.008	0.000	0.000	0.000	0.000
20	A	21	LEU	0	-0.016	0.012	24.636	0.011	0.011	0.000	0.000	0.000	0.000
21	A	22	LYS	1	0.906	0.954	26.945	0.065	0.065	0.000	0.000	0.000	0.000
22	A	23	GLY	0	0.030	0.009	28.223	0.004	0.004	0.000	0.000	0.000	0.000
23	A	24	THR	0	-0.065	-0.065	25.724	0.004	0.004	0.000	0.000	0.000	0.000
24	A	25	SER	0	-0.024	-0.028	28.798	0.004	0.004	0.000	0.000	0.000	0.000
25	A	26	ASP	-1	-0.740	-0.837	31.411	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	27	ASP	-1	-0.797	-0.870	33.213	-0.023	-0.023	0.000	0.000	0.000	0.000
27	A	28	ASP	-1	-0.895	-0.958	36.298	-0.016	-0.016	0.000	0.000	0.000	0.000
28	A	29	VAL	0	0.006	0.010	37.335	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	30	PRO	0	-0.038	-0.031	36.352	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	31	CYS	0	0.006	0.026	31.202	-0.004	-0.004	0.000	0.000	0.000	0.000
31	A	32	PRO	0	0.006	-0.008	33.079	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	33	GLY	0	0.043	0.017	32.758	-0.004	-0.004	0.000	0.000	0.000	0.000
33	A	34	TYR	0	0.064	0.028	30.626	0.000	0.000	0.000	0.000	0.000	0.000
34	A	35	LEU	0	0.004	-0.005	28.494	-0.007	-0.007	0.000	0.000	0.000	0.000
35	A	36	PHE	0	-0.009	0.005	27.418	-0.007	-0.007	0.000	0.000	0.000	0.000
36	A	37	GLU	-1	-0.807	-0.877	27.033	-0.101	-0.101	0.000	0.000	0.000	0.000
37	A	38	GLU	-1	-0.854	-0.907	25.786	-0.128	-0.128	0.000	0.000	0.000	0.000
38	A	39	ILE	0	0.006	-0.015	22.444	-0.015	-0.015	0.000	0.000	0.000	0.000
39	A	40	ALA	0	0.000	0.001	22.015	-0.014	-0.014	0.000	0.000	0.000	0.000
40	A	41	LYS	1	0.843	0.910	21.869	0.111	0.111	0.000	0.000	0.000	0.000
41	A	42	ILE	0	0.026	0.024	17.551	-0.023	-0.023	0.000	0.000	0.000	0.000
42	A	43	SER	0	-0.077	-0.049	17.319	-0.034	-0.034	0.000	0.000	0.000	0.000
43	A	44	HIS	0	-0.016	-0.024	17.319	-0.041	-0.041	0.000	0.000	0.000	0.000
44	A	45	GLU	-1	-0.825	-0.846	16.219	-0.267	-0.267	0.000	0.000	0.000	0.000
45	A	46	SER	0	-0.019	-0.044	11.412	-0.034	-0.034	0.000	0.000	0.000	0.000
46	A	47	PRO	0	0.037	0.012	9.624	0.045	0.045	0.000	0.000	0.000	0.000
47	A	48	GLY	0	0.069	0.034	9.294	0.034	0.034	0.000	0.000	0.000	0.000
48	A	49	SER	0	0.019	0.006	9.830	0.104	0.104	0.000	0.000	0.000	0.000
49	A	50	SER	0	0.001	0.000	13.516	0.079	0.079	0.000	0.000	0.000	0.000
50	A	51	GLN	0	-0.030	-0.032	7.492	-0.088	-0.088	0.000	0.000	0.000	0.000
51	A	52	CYS	0	-0.040	-0.013	11.521	0.068	0.068	0.000	0.000	0.000	0.000
52	A	53	LEU	0	0.012	0.006	14.010	0.049	0.049	0.000	0.000	0.000	0.000
53	A	54	LEU	0	-0.007	0.001	15.627	0.030	0.030	0.000	0.000	0.000	0.000
54	A	55	GLU	-1	-0.810	-0.872	11.694	-0.103	-0.103	0.000	0.000	0.000	0.000
55	A	56	TYR	0	-0.020	-0.015	16.546	0.025	0.025	0.000	0.000	0.000	0.000
56	A	57	LEU	0	0.009	-0.005	19.546	0.016	0.016	0.000	0.000	0.000	0.000
57	A	58	LEU	0	0.016	0.009	18.113	0.010	0.010	0.000	0.000	0.000	0.000
58	A	59	SER	0	0.037	0.028	19.903	0.015	0.015	0.000	0.000	0.000	0.000
59	A	60	ARG	1	0.853	0.961	21.739	0.037	0.037	0.000	0.000	0.000	0.000
60	A	61	LEU	0	-0.004	0.018	24.452	0.004	0.004	0.000	0.000	0.000	0.000
61	A	62	HIS	0	-0.037	-0.022	24.205	0.008	0.008	0.000	0.000	0.000	0.000
62	A	63	SER	0	-0.067	-0.068	25.266	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	64	SER	0	-0.077	-0.037	27.302	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	65	SER	0	0.010	-0.036	29.877	0.005	0.005	0.000	0.000	0.000	0.000
65	A	66	GLY	0	0.024	-0.014	32.664	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	67	HIS	0	0.003	0.010	34.558	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	68	GLY	0	0.050	0.021	30.788	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	69	LYS	1	0.785	0.888	29.102	-0.021	-0.021	0.000	0.000	0.000	0.000
69	A	70	LEU	0	0.003	0.002	30.496	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	71	LYS	1	0.759	0.892	30.849	0.024	0.024	0.000	0.000	0.000	0.000
71	A	72	VAL	0	0.008	-0.002	25.367	-0.006	-0.006	0.000	0.000	0.000	0.000
72	A	73	LEU	0	-0.009	-0.003	27.493	-0.005	-0.005	0.000	0.000	0.000	0.000
73	A	74	LYS	1	0.972	0.991	29.424	0.021	0.021	0.000	0.000	0.000	0.000
74	A	75	ILE	0	-0.002	0.006	25.034	-0.005	-0.005	0.000	0.000	0.000	0.000
75	A	76	LEU	0	-0.006	-0.009	22.745	-0.009	-0.009	0.000	0.000	0.000	0.000
76	A	77	LEU	0	0.038	0.033	26.068	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	78	TYR	0	-0.052	-0.056	27.642	0.001	0.001	0.000	0.000	0.000	0.000
78	A	79	LEU	0	0.009	0.003	21.957	-0.006	-0.006	0.000	0.000	0.000	0.000
79	A	80	CYS	0	-0.045	-0.027	25.059	-0.006	-0.006	0.000	0.000	0.000	0.000
80	A	81	SER	0	-0.032	-0.003	26.593	0.004	0.004	0.000	0.000	0.000	0.000
81	A	82	HIS	1	0.824	0.914	26.454	0.077	0.077	0.000	0.000	0.000	0.000
82	A	83	GLY	0	0.033	0.027	22.353	-0.011	-0.011	0.000	0.000	0.000	0.000
83	A	84	SER	0	-0.023	-0.010	17.344	0.010	0.010	0.000	0.000	0.000	0.000
84	A	85	SER	0	0.059	0.003	19.458	0.007	0.007	0.000	0.000	0.000	0.000
85	A	86	PHE	0	-0.027	-0.002	10.668	0.012	0.012	0.000	0.000	0.000	0.000
86	A	87	PHE	0	0.048	0.013	16.288	0.023	0.023	0.000	0.000	0.000	0.000
87	A	88	LEU	0	0.047	0.025	17.597	0.029	0.029	0.000	0.000	0.000	0.000
88	A	89	LEU	0	-0.024	0.005	15.294	0.027	0.027	0.000	0.000	0.000	0.000
89	A	90	ILE	0	-0.057	-0.033	12.982	0.038	0.038	0.000	0.000	0.000	0.000
90	A	91	LEU	0	0.028	0.022	16.324	0.031	0.031	0.000	0.000	0.000	0.000
91	A	92	LYS	1	0.928	0.960	19.784	0.032	0.032	0.000	0.000	0.000	0.000
92	A	93	ARG	1	0.899	0.966	11.803	-0.089	-0.089	0.000	0.000	0.000	0.000
93	A	94	ASN	0	-0.023	-0.020	16.175	0.043	0.043	0.000	0.000	0.000	0.000
94	A	95	SER	0	0.026	-0.008	20.266	-0.010	-0.010	0.000	0.000	0.000	0.000
95	A	96	ALA	0	0.018	0.018	23.230	-0.006	-0.006	0.000	0.000	0.000	0.000
96	A	97	PHE	0	0.048	0.019	19.762	-0.005	-0.005	0.000	0.000	0.000	0.000
97	A	98	ILE	0	0.001	0.006	24.551	-0.007	-0.007	0.000	0.000	0.000	0.000
98	A	99	GLN	0	0.007	0.000	27.294	-0.002	-0.002	0.000	0.000	0.000	0.000
99	A	100	GLU	-1	-0.872	-0.921	27.285	0.048	0.048	0.000	0.000	0.000	0.000
100	A	101	ALA	0	-0.008	-0.008	28.943	-0.004	-0.004	0.000	0.000	0.000	0.000
101	A	102	ALA	0	-0.006	-0.020	30.716	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	103	ALA	0	-0.027	-0.015	32.828	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	104	PHE	0	0.006	0.012	32.926	0.000	0.000	0.000	0.000	0.000	0.000
104	A	105	ALA	0	0.004	-0.014	34.658	-0.004	-0.004	0.000	0.000	0.000	0.000
105	A	106	GLY	0	0.033	0.016	37.154	0.002	0.002	0.000	0.000	0.000	0.000
106	A	107	PRO	0	0.000	0.017	39.746	-0.001	-0.001	0.000	0.000	0.000	0.000
107	A	108	PRO	0	0.000	0.004	42.558	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	109	ASP	-1	-0.771	-0.881	43.311	0.003	0.003	0.000	0.000	0.000	0.000
109	A	110	PRO	0	-0.031	-0.029	45.081	0.000	0.000	0.000	0.000	0.000	0.000
110	A	111	LEU	0	-0.010	0.009	47.516	0.000	0.000	0.000	0.000	0.000	0.000
111	A	112	HIS	0	-0.057	-0.031	44.685	-0.002	-0.002	0.000	0.000	0.000	0.000
112	A	113	GLY	0	0.055	0.043	46.084	0.000	0.000	0.000	0.000	0.000	0.000
113	A	114	ASN	0	0.011	-0.017	43.496	0.001	0.001	0.000	0.000	0.000	0.000
114	A	115	SER	0	-0.023	-0.019	42.410	0.000	0.000	0.000	0.000	0.000	0.000
115	A	116	LEU	0	0.001	-0.003	37.662	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	117	TYR	0	0.006	-0.004	37.370	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	118	GLN	0	-0.029	-0.012	38.043	0.000	0.000	0.000	0.000	0.000	0.000
118	A	119	LYS	1	0.953	0.982	38.592	0.006	0.006	0.000	0.000	0.000	0.000
119	A	120	VAL	0	-0.032	0.007	32.866	-0.002	-0.002	0.000	0.000	0.000	0.000
120	A	121	ARG	1	0.907	0.951	34.329	-0.017	-0.017	0.000	0.000	0.000	0.000
121	A	122	ALA	0	-0.015	-0.004	35.534	0.000	0.000	0.000	0.000	0.000	0.000
122	A	123	ALA	0	0.008	-0.002	33.472	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	124	ALA	0	0.006	0.011	31.189	-0.003	-0.003	0.000	0.000	0.000	0.000
124	A	125	GLN	0	0.009	0.004	31.670	0.001	0.001	0.000	0.000	0.000	0.000
125	A	126	ASP	-1	-0.921	-0.937	34.070	-0.019	-0.019	0.000	0.000	0.000	0.000
126	A	127	LEU	0	-0.009	-0.010	26.544	-0.002	-0.002	0.000	0.000	0.000	0.000
127	A	128	GLY	0	0.024	-0.001	29.399	-0.002	-0.002	0.000	0.000	0.000	0.000
128	A	129	SER	0	-0.033	-0.027	30.446	0.002	0.002	0.000	0.000	0.000	0.000
129	A	130	THR	0	-0.028	-0.005	29.475	-0.002	-0.002	0.000	0.000	0.000	0.000
130	A	131	LEU	0	-0.034	-0.011	23.494	-0.004	-0.004	0.000	0.000	0.000	0.000
131	A	132	PHE	0	-0.051	-0.037	26.233	0.002	0.002	0.000	0.000	0.000	0.000
132	A	133	SER	0	-0.045	-0.008	28.757	0.001	0.001	0.000	0.000	0.000	0.000

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