FMO DATABASE

FMODB ID: N9ZJQ

Calculation Name: 5VXB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5VXB

Chain ID: A

ChEMBL ID:

UniProt ID: Q9ABV9

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	OptHSide
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	167
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1651470.120386
FMO2-HF: Nuclear repulsion	1587683.263926
FMO2-HF: Total energy	-63786.85646
FMO2-MP2: Total energy	-63973.132377

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:1:MET)

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

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.
-5.754	1.23	4.222	-3.64	-7.567	-0.018

Interaction energy analysis for fragmet #1(A:1:MET)

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 : -0.022

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	3	THR	0	-0.038	-0.018	3.590	-1.660	-0.206	0.000	-0.662	-0.792	0.002
4	A	4	ARG	1	0.872	0.906	5.981	0.996	0.996	0.000	0.000	0.000	0.000
5	A	5	ALA	0	0.000	-0.008	8.843	0.202	0.202	0.000	0.000	0.000	0.000
6	A	6	ASP	-1	-0.784	-0.895	6.204	-0.489	-0.489	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.038	-0.006	8.581	0.240	0.240	0.000	0.000	0.000	0.000
8	A	8	PHE	0	-0.031	-0.030	9.739	0.040	0.040	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.049	0.035	11.788	0.025	0.025	0.000	0.000	0.000	0.000
10	A	10	PHE	0	0.007	0.000	10.215	0.058	0.058	0.000	0.000	0.000	0.000
11	A	11	PHE	0	-0.004	-0.026	12.331	-0.018	-0.018	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.830	-0.892	15.002	0.099	0.099	0.000	0.000	0.000	0.000
13	A	13	ALA	0	-0.054	-0.015	15.233	-0.011	-0.011	0.000	0.000	0.000	0.000
14	A	14	HIS	0	-0.046	-0.026	13.552	0.010	0.010	0.000	0.000	0.000	0.000
15	A	15	GLY	0	-0.002	0.011	17.783	-0.021	-0.021	0.000	0.000	0.000	0.000
16	A	16	VAL	0	-0.075	-0.024	15.915	-0.024	-0.024	0.000	0.000	0.000	0.000
17	A	17	ASP	-1	-0.803	-0.884	18.592	0.073	0.073	0.000	0.000	0.000	0.000
18	A	18	HIS	1	0.846	0.888	16.742	-0.045	-0.045	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.917	0.963	19.320	0.049	0.049	0.000	0.000	0.000	0.000
20	A	20	THR	0	-0.021	-0.031	15.596	0.008	0.008	0.000	0.000	0.000	0.000
21	A	21	LEU	0	-0.009	0.009	18.705	0.005	0.005	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.786	-0.879	16.511	-0.283	-0.283	0.000	0.000	0.000	0.000
23	A	23	HIS	0	-0.038	-0.013	18.181	0.035	0.035	0.000	0.000	0.000	0.000
24	A	24	PRO	0	0.040	0.010	18.502	-0.032	-0.032	0.000	0.000	0.000	0.000
25	A	25	PRO	0	-0.003	0.013	16.415	0.020	0.020	0.000	0.000	0.000	0.000
26	A	26	VAL	0	0.004	0.015	18.856	0.017	0.017	0.000	0.000	0.000	0.000
27	A	27	PHE	0	-0.022	-0.019	18.976	-0.010	-0.010	0.000	0.000	0.000	0.000
28	A	28	ARG	1	0.776	0.855	23.403	0.140	0.140	0.000	0.000	0.000	0.000
29	A	29	VAL	0	0.030	0.007	26.588	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.859	-0.927	28.752	-0.110	-0.110	0.000	0.000	0.000	0.000
31	A	31	GLU	-1	-0.765	-0.864	25.519	-0.138	-0.138	0.000	0.000	0.000	0.000
32	A	32	GLY	0	-0.009	-0.007	25.132	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.044	-0.020	26.152	0.007	0.007	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.880	-0.938	27.015	-0.085	-0.085	0.000	0.000	0.000	0.000
35	A	35	ILE	0	-0.036	-0.013	21.613	0.006	0.006	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.918	0.948	24.562	0.109	0.109	0.000	0.000	0.000	0.000
37	A	37	ALA	0	-0.006	0.014	26.639	0.009	0.009	0.000	0.000	0.000	0.000
38	A	38	ALA	0	-0.022	0.000	25.703	0.008	0.008	0.000	0.000	0.000	0.000
39	A	39	MET	0	-0.107	-0.031	20.460	0.009	0.009	0.000	0.000	0.000	0.000
40	A	40	PRO	0	0.070	0.044	25.212	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	41	GLY	0	0.046	0.030	25.527	0.002	0.002	0.000	0.000	0.000	0.000
42	A	42	GLY	0	0.018	0.008	24.723	-0.009	-0.009	0.000	0.000	0.000	0.000
43	A	43	HIS	0	-0.034	-0.035	21.833	-0.013	-0.013	0.000	0.000	0.000	0.000
44	A	44	THR	0	-0.003	-0.022	18.347	-0.003	-0.003	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.776	0.912	18.908	0.079	0.079	0.000	0.000	0.000	0.000
46	A	46	ASN	0	0.010	0.002	14.947	0.058	0.058	0.000	0.000	0.000	0.000
47	A	47	LEU	0	-0.009	-0.001	16.186	-0.040	-0.040	0.000	0.000	0.000	0.000
48	A	48	PHE	0	0.066	0.043	9.893	0.033	0.033	0.000	0.000	0.000	0.000
49	A	49	LEU	0	-0.027	-0.014	14.258	-0.017	-0.017	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.953	0.980	14.859	0.226	0.226	0.000	0.000	0.000	0.000
51	A	51	ASP	-1	-0.763	-0.882	16.825	-0.076	-0.076	0.000	0.000	0.000	0.000
52	A	52	ALA	0	-0.053	-0.035	19.959	-0.008	-0.008	0.000	0.000	0.000	0.000
53	A	53	LYS	1	0.898	0.954	21.266	0.039	0.039	0.000	0.000	0.000	0.000
54	A	54	GLY	0	-0.024	-0.007	17.971	0.006	0.006	0.000	0.000	0.000	0.000
55	A	55	GLN	0	-0.031	-0.013	14.246	-0.004	-0.004	0.000	0.000	0.000	0.000
56	A	56	LEU	0	-0.014	-0.003	10.144	-0.008	-0.008	0.000	0.000	0.000	0.000
57	A	57	TRP	0	0.010	-0.009	13.886	0.054	0.054	0.000	0.000	0.000	0.000
58	A	58	LEU	0	0.014	0.018	11.098	-0.050	-0.050	0.000	0.000	0.000	0.000
59	A	59	ILE	0	-0.012	0.002	14.357	0.038	0.038	0.000	0.000	0.000	0.000
60	A	60	SER	0	0.012	-0.006	16.529	-0.016	-0.016	0.000	0.000	0.000	0.000
61	A	61	ALA	0	-0.017	-0.029	18.482	0.018	0.018	0.000	0.000	0.000	0.000
62	A	62	LEU	0	0.030	0.030	21.718	-0.011	-0.011	0.000	0.000	0.000	0.000
63	A	63	GLY	0	0.012	-0.003	23.435	-0.008	-0.008	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.899	-0.963	24.248	-0.070	-0.070	0.000	0.000	0.000	0.000
65	A	65	THR	0	-0.030	-0.015	25.935	0.004	0.004	0.000	0.000	0.000	0.000
66	A	66	THR	0	-0.018	-0.006	26.546	-0.014	-0.014	0.000	0.000	0.000	0.000
67	A	67	ILE	0	0.017	0.009	21.741	0.006	0.006	0.000	0.000	0.000	0.000
68	A	68	ASP	-1	-0.820	-0.916	25.953	-0.078	-0.078	0.000	0.000	0.000	0.000
69	A	69	LEU	0	0.015	-0.011	21.769	0.005	0.005	0.000	0.000	0.000	0.000
70	A	70	LYS	1	0.836	0.916	25.125	0.118	0.118	0.000	0.000	0.000	0.000
71	A	71	LYS	1	0.950	0.976	28.089	0.055	0.055	0.000	0.000	0.000	0.000
72	A	72	LEU	0	0.082	0.046	22.596	0.005	0.005	0.000	0.000	0.000	0.000
73	A	73	HIS	0	0.001	0.014	24.810	0.002	0.002	0.000	0.000	0.000	0.000
74	A	74	HIS	0	-0.046	-0.027	25.769	0.009	0.009	0.000	0.000	0.000	0.000
75	A	75	VAL	0	0.003	0.026	26.834	0.006	0.006	0.000	0.000	0.000	0.000
76	A	76	ILE	0	0.011	-0.007	20.799	0.007	0.007	0.000	0.000	0.000	0.000
77	A	77	GLY	0	0.021	0.027	23.808	0.007	0.007	0.000	0.000	0.000	0.000
78	A	78	SER	0	-0.046	-0.027	21.408	0.004	0.004	0.000	0.000	0.000	0.000
79	A	79	GLY	0	-0.059	-0.036	22.454	0.004	0.004	0.000	0.000	0.000	0.000
80	A	80	ARG	1	0.878	0.933	23.404	0.071	0.071	0.000	0.000	0.000	0.000
81	A	81	LEU	0	0.059	0.028	19.911	-0.011	-0.011	0.000	0.000	0.000	0.000
82	A	82	SER	0	-0.040	-0.022	20.462	0.012	0.012	0.000	0.000	0.000	0.000
83	A	83	PHE	0	0.045	0.016	18.062	0.002	0.002	0.000	0.000	0.000	0.000
84	A	84	GLY	0	-0.021	-0.007	14.441	0.009	0.009	0.000	0.000	0.000	0.000
85	A	85	PRO	0	-0.013	-0.010	13.199	-0.010	-0.010	0.000	0.000	0.000	0.000
86	A	86	GLN	0	0.042	0.006	11.290	-0.068	-0.068	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.847	-0.928	9.974	-0.714	-0.714	0.000	0.000	0.000	0.000
88	A	88	MET	0	0.022	0.011	8.214	-0.174	-0.174	0.000	0.000	0.000	0.000
89	A	89	MET	0	-0.037	0.011	7.781	-0.138	-0.138	0.000	0.000	0.000	0.000
90	A	90	LEU	0	0.005	0.002	4.231	-0.143	-0.017	-0.001	-0.010	-0.114	0.000
91	A	91	GLU	-1	-0.874	-0.922	3.830	-1.953	-1.661	0.002	-0.040	-0.253	0.000
92	A	92	THR	0	-0.051	-0.048	3.195	-2.346	-1.452	0.222	-0.455	-0.662	-0.004
93	A	93	LEU	0	-0.014	-0.014	4.667	0.232	0.361	-0.001	-0.009	-0.120	0.000
94	A	94	GLY	0	-0.004	0.022	2.827	0.430	1.196	0.577	-0.628	-0.715	0.003
95	A	95	VAL	0	-0.045	-0.014	3.441	-1.766	-1.556	0.003	0.143	-0.357	-0.001
96	A	96	THR	0	0.040	0.019	6.274	-0.093	-0.093	0.000	0.000	0.000	0.000
97	A	97	PRO	0	0.026	-0.015	9.246	0.109	0.109	0.000	0.000	0.000	0.000
98	A	98	GLY	0	-0.011	0.003	12.864	-0.017	-0.017	0.000	0.000	0.000	0.000
99	A	99	SER	0	-0.006	0.005	9.735	0.037	0.037	0.000	0.000	0.000	0.000
100	A	100	VAL	0	-0.001	0.004	10.249	0.009	0.009	0.000	0.000	0.000	0.000
101	A	101	THR	0	-0.030	-0.041	9.741	0.055	0.055	0.000	0.000	0.000	0.000
102	A	102	ALA	0	0.078	0.049	11.286	0.036	0.036	0.000	0.000	0.000	0.000
103	A	103	PHE	0	0.009	-0.011	10.634	0.078	0.078	0.000	0.000	0.000	0.000
104	A	104	GLY	0	0.053	0.017	7.298	0.203	0.203	0.000	0.000	0.000	0.000
105	A	105	LEU	0	0.015	0.006	6.435	0.202	0.202	0.000	0.000	0.000	0.000
106	A	106	ILE	0	-0.018	0.009	5.399	0.099	0.099	0.000	0.000	0.000	0.000
107	A	107	ASN	0	-0.037	-0.040	2.326	2.544	4.002	2.887	-1.213	-3.132	-0.009
108	A	108	ASP	-1	-0.760	-0.858	2.754	-3.106	-1.842	0.517	-0.691	-1.090	-0.009
109	A	109	THR	0	-0.090	-0.078	4.248	-0.016	0.375	0.016	-0.075	-0.332	0.000
110	A	110	GLU	-1	-0.891	-0.924	5.832	0.824	0.824	0.000	0.000	0.000	0.000
111	A	111	LYS	1	0.803	0.906	7.971	-0.901	-0.901	0.000	0.000	0.000	0.000
112	A	112	ARG	1	0.841	0.903	5.356	0.824	0.824	0.000	0.000	0.000	0.000
113	A	113	VAL	0	-0.074	-0.041	8.619	-0.040	-0.040	0.000	0.000	0.000	0.000
114	A	114	ARG	1	0.944	0.988	11.272	0.051	0.051	0.000	0.000	0.000	0.000
115	A	115	PHE	0	0.040	0.005	13.928	-0.028	-0.028	0.000	0.000	0.000	0.000
116	A	116	VAL	0	-0.014	-0.012	15.573	0.011	0.011	0.000	0.000	0.000	0.000
117	A	117	LEU	0	-0.015	-0.010	18.657	-0.010	-0.010	0.000	0.000	0.000	0.000
118	A	118	ASP	-1	-0.737	-0.861	20.662	-0.027	-0.027	0.000	0.000	0.000	0.000
119	A	119	LYS	1	0.881	0.918	23.853	-0.017	-0.017	0.000	0.000	0.000	0.000
120	A	120	ALA	0	0.043	0.017	26.701	0.006	0.006	0.000	0.000	0.000	0.000
121	A	121	LEU	0	-0.043	-0.011	20.376	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	122	ALA	0	-0.029	-0.025	23.980	0.009	0.009	0.000	0.000	0.000	0.000
123	A	123	ASP	-1	-0.813	-0.884	24.820	0.034	0.034	0.000	0.000	0.000	0.000
124	A	124	SER	0	-0.062	-0.024	25.510	-0.006	-0.006	0.000	0.000	0.000	0.000
125	A	125	ASP	-1	-0.828	-0.899	26.057	0.054	0.054	0.000	0.000	0.000	0.000
126	A	126	PRO	0	-0.042	-0.009	23.483	-0.004	-0.004	0.000	0.000	0.000	0.000
127	A	127	VAL	0	-0.017	-0.022	20.100	-0.009	-0.009	0.000	0.000	0.000	0.000
128	A	128	ASN	0	-0.007	-0.016	19.232	0.002	0.002	0.000	0.000	0.000	0.000
129	A	129	PHE	0	0.014	0.006	14.473	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	130	HIS	0	0.016	0.016	12.155	-0.003	-0.003	0.000	0.000	0.000	0.000
131	A	131	PRO	0	-0.035	0.010	11.110	0.067	0.067	0.000	0.000	0.000	0.000
132	A	132	LEU	0	-0.023	-0.020	4.839	-0.087	-0.087	0.000	0.000	0.000	0.000
133	A	133	LYS	1	0.878	0.913	7.432	0.431	0.431	0.000	0.000	0.000	0.000
134	A	134	ASN	0	-0.006	-0.007	10.064	0.064	0.064	0.000	0.000	0.000	0.000
135	A	135	ASP	-1	-0.843	-0.907	12.948	-0.519	-0.519	0.000	0.000	0.000	0.000
136	A	136	ALA	0	0.032	0.018	14.008	0.026	0.026	0.000	0.000	0.000	0.000
137	A	137	THR	0	-0.026	-0.023	15.206	-0.008	-0.008	0.000	0.000	0.000	0.000
138	A	138	THR	0	-0.028	-0.018	14.777	0.004	0.004	0.000	0.000	0.000	0.000
139	A	139	ALA	0	0.011	0.018	17.155	0.011	0.011	0.000	0.000	0.000	0.000
140	A	140	VAL	0	-0.014	-0.015	17.234	0.009	0.009	0.000	0.000	0.000	0.000
141	A	141	SER	0	0.019	-0.005	20.480	-0.005	-0.005	0.000	0.000	0.000	0.000
142	A	142	GLN	0	0.020	0.005	22.128	0.032	0.032	0.000	0.000	0.000	0.000
143	A	143	ALA	0	-0.014	-0.015	22.771	0.017	0.017	0.000	0.000	0.000	0.000
144	A	144	GLY	0	0.042	0.017	20.677	0.024	0.024	0.000	0.000	0.000	0.000
145	A	145	LEU	0	0.005	0.004	17.009	0.038	0.038	0.000	0.000	0.000	0.000
146	A	146	ARG	1	0.833	0.899	18.282	-0.059	-0.059	0.000	0.000	0.000	0.000
147	A	147	ARG	1	0.901	0.957	19.319	-0.124	-0.124	0.000	0.000	0.000	0.000
148	A	148	PHE	0	-0.003	0.003	10.464	0.043	0.043	0.000	0.000	0.000	0.000
149	A	149	LEU	0	-0.032	-0.021	14.351	0.070	0.070	0.000	0.000	0.000	0.000
150	A	150	ALA	0	0.025	0.010	15.588	0.037	0.037	0.000	0.000	0.000	0.000
151	A	151	ALA	0	-0.016	0.006	14.802	0.022	0.022	0.000	0.000	0.000	0.000
152	A	152	LEU	0	-0.077	-0.028	9.590	0.128	0.128	0.000	0.000	0.000	0.000
153	A	153	GLY	0	0.026	0.025	12.776	0.031	0.031	0.000	0.000	0.000	0.000
154	A	154	VAL	0	-0.063	-0.032	12.146	-0.039	-0.039	0.000	0.000	0.000	0.000
155	A	155	GLU	-1	-0.910	-0.956	15.194	0.159	0.159	0.000	0.000	0.000	0.000
156	A	156	PRO	0	-0.090	-0.038	18.332	-0.019	-0.019	0.000	0.000	0.000	0.000
157	A	157	MET	0	-0.005	0.008	19.227	-0.009	-0.009	0.000	0.000	0.000	0.000
158	A	158	ILE	0	0.005	-0.001	21.596	-0.011	-0.011	0.000	0.000	0.000	0.000
159	A	159	VAL	0	-0.007	-0.003	23.728	-0.002	-0.002	0.000	0.000	0.000	0.000
160	A	160	ASP	-1	-0.815	-0.892	25.806	-0.013	-0.013	0.000	0.000	0.000	0.000
161	A	161	PHE	0	-0.004	-0.039	22.669	-0.005	-0.005	0.000	0.000	0.000	0.000
162	A	162	ALA	0	-0.043	-0.006	28.705	-0.006	-0.006	0.000	0.000	0.000	0.000
163	A	163	ALA	0	-0.002	-0.004	32.404	-0.002	-0.002	0.000	0.000	0.000	0.000
164	A	164	MET	0	-0.114	-0.048	28.239	-0.002	-0.002	0.000	0.000	0.000	0.000
165	A	165	GLU	-1	-0.893	-0.941	30.181	0.002	0.002	0.000	0.000	0.000	0.000
166	A	166	VAL	0	-0.045	-0.030	25.751	0.000	0.000	0.000	0.000	0.000	0.000
167	A	167	VAL	0	-0.020	-0.009	27.629	0.005	0.005	0.000	0.000	0.000	0.000

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