FMO DATABASE

FMODB ID: 85G4Y

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1650498.636048
FMO2-HF: Nuclear repulsion	1586712.187896
FMO2-HF: Total energy	-63786.448152
FMO2-MP2: Total energy	-63972.686375

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.
-7.228	-3.128	10.302	-4.765	-9.637	-0.034

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 : -0.029 / q_NPA : -0.026

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	-0.015	0.002	3.633	-1.544	-0.074	0.004	-0.662	-0.812	0.003
4	A	4	ARG	1	0.907	0.935	5.990	1.026	1.026	0.000	0.000	0.000	0.000
5	A	5	ALA	0	-0.003	-0.013	8.852	0.198	0.198	0.000	0.000	0.000	0.000
6	A	6	ASP	-1	-0.816	-0.910	6.236	-0.698	-0.698	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.038	-0.007	8.625	0.236	0.236	0.000	0.000	0.000	0.000
8	A	8	PHE	0	-0.035	-0.027	9.852	0.059	0.059	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.052	0.036	11.660	0.038	0.038	0.000	0.000	0.000	0.000
10	A	10	PHE	0	-0.007	-0.007	10.184	0.066	0.066	0.000	0.000	0.000	0.000
11	A	11	PHE	0	-0.017	-0.038	12.308	-0.006	-0.006	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.833	-0.899	15.085	0.024	0.024	0.000	0.000	0.000	0.000
13	A	13	ALA	0	-0.058	-0.021	15.180	0.000	0.000	0.000	0.000	0.000	0.000
14	A	14	HIS	0	-0.029	-0.010	13.847	0.013	0.013	0.000	0.000	0.000	0.000
15	A	15	GLY	0	-0.012	0.004	17.800	-0.014	-0.014	0.000	0.000	0.000	0.000
16	A	16	VAL	0	-0.073	-0.023	16.221	-0.016	-0.016	0.000	0.000	0.000	0.000
17	A	17	ASP	-1	-0.804	-0.878	18.730	0.004	0.004	0.000	0.000	0.000	0.000
18	A	18	HIS	1	0.870	0.905	17.237	0.042	0.042	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.904	0.958	19.332	0.090	0.090	0.000	0.000	0.000	0.000
20	A	20	THR	0	-0.029	-0.035	15.739	0.006	0.006	0.000	0.000	0.000	0.000
21	A	21	LEU	0	-0.009	0.009	18.713	0.009	0.009	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.788	-0.896	16.908	-0.321	-0.321	0.000	0.000	0.000	0.000
23	A	23	HIS	0	-0.049	-0.007	18.254	0.035	0.035	0.000	0.000	0.000	0.000
24	A	24	PRO	0	0.031	0.008	18.504	-0.033	-0.033	0.000	0.000	0.000	0.000
25	A	25	PRO	0	-0.001	0.013	16.465	0.019	0.019	0.000	0.000	0.000	0.000
26	A	26	VAL	0	0.014	0.019	18.855	0.020	0.020	0.000	0.000	0.000	0.000
27	A	27	PHE	0	-0.030	-0.025	18.934	-0.010	-0.010	0.000	0.000	0.000	0.000
28	A	28	ARG	1	0.831	0.904	23.402	0.150	0.150	0.000	0.000	0.000	0.000
29	A	29	VAL	0	0.029	0.003	26.589	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.915	-0.963	28.753	-0.118	-0.118	0.000	0.000	0.000	0.000
31	A	31	GLU	-1	-0.755	-0.870	25.525	-0.149	-0.149	0.000	0.000	0.000	0.000
32	A	32	GLY	0	-0.016	-0.008	25.134	-0.004	-0.004	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.034	-0.019	26.155	0.005	0.005	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.869	-0.932	26.958	-0.104	-0.104	0.000	0.000	0.000	0.000
35	A	35	ILE	0	-0.043	-0.013	21.603	0.004	0.004	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.907	0.944	24.687	0.135	0.135	0.000	0.000	0.000	0.000
37	A	37	ALA	0	-0.003	0.015	26.645	0.009	0.009	0.000	0.000	0.000	0.000
38	A	38	ALA	0	-0.025	-0.002	25.678	0.007	0.007	0.000	0.000	0.000	0.000
39	A	39	MET	0	-0.110	-0.036	20.530	0.007	0.007	0.000	0.000	0.000	0.000
40	A	40	PRO	0	0.078	0.051	25.220	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	41	GLY	0	0.046	0.027	25.536	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	42	GLY	0	0.017	0.012	24.735	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	43	HIS	0	-0.035	-0.040	21.832	-0.016	-0.016	0.000	0.000	0.000	0.000
44	A	44	THR	0	-0.007	-0.019	18.350	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.855	0.962	18.899	0.100	0.100	0.000	0.000	0.000	0.000
46	A	46	ASN	0	0.017	-0.007	14.954	0.049	0.049	0.000	0.000	0.000	0.000
47	A	47	LEU	0	-0.016	-0.004	16.188	-0.036	-0.036	0.000	0.000	0.000	0.000
48	A	48	PHE	0	0.064	0.044	9.990	0.028	0.028	0.000	0.000	0.000	0.000
49	A	49	LEU	0	-0.029	-0.014	14.225	-0.007	-0.007	0.000	0.000	0.000	0.000
50	A	50	LYS	1	1.011	1.001	14.975	0.165	0.165	0.000	0.000	0.000	0.000
51	A	51	ASP	-1	-0.763	-0.882	16.896	-0.061	-0.061	0.000	0.000	0.000	0.000
52	A	52	ALA	0	-0.066	-0.045	19.830	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	53	LYS	1	0.906	0.951	21.344	0.029	0.029	0.000	0.000	0.000	0.000
54	A	54	GLY	0	-0.047	-0.012	17.780	0.011	0.011	0.000	0.000	0.000	0.000
55	A	55	GLN	0	-0.037	-0.002	14.246	0.008	0.008	0.000	0.000	0.000	0.000
56	A	56	LEU	0	-0.010	-0.005	10.211	-0.013	-0.013	0.000	0.000	0.000	0.000
57	A	57	TRP	0	-0.001	-0.018	13.887	0.048	0.048	0.000	0.000	0.000	0.000
58	A	58	LEU	0	0.013	0.015	10.973	-0.049	-0.049	0.000	0.000	0.000	0.000
59	A	59	ILE	0	-0.013	0.001	14.172	0.037	0.037	0.000	0.000	0.000	0.000
60	A	60	SER	0	0.007	-0.003	16.029	-0.019	-0.019	0.000	0.000	0.000	0.000
61	A	61	ALA	0	-0.011	-0.026	18.201	0.020	0.020	0.000	0.000	0.000	0.000
62	A	62	LEU	0	0.017	0.023	21.723	-0.014	-0.014	0.000	0.000	0.000	0.000
63	A	63	GLY	0	-0.023	-0.015	23.447	-0.006	-0.006	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.895	-0.966	24.252	-0.087	-0.087	0.000	0.000	0.000	0.000
65	A	65	THR	0	-0.033	-0.020	25.709	0.006	0.006	0.000	0.000	0.000	0.000
66	A	66	THR	0	-0.037	-0.029	26.509	-0.013	-0.013	0.000	0.000	0.000	0.000
67	A	67	ILE	0	0.008	0.005	21.680	0.006	0.006	0.000	0.000	0.000	0.000
68	A	68	ASP	-1	-0.844	-0.917	25.807	-0.078	-0.078	0.000	0.000	0.000	0.000
69	A	69	LEU	0	0.017	-0.008	21.710	0.006	0.006	0.000	0.000	0.000	0.000
70	A	70	LYS	1	0.873	0.936	25.341	0.108	0.108	0.000	0.000	0.000	0.000
71	A	71	LYS	1	0.964	0.968	28.071	0.054	0.054	0.000	0.000	0.000	0.000
72	A	72	LEU	0	0.074	0.048	22.474	0.005	0.005	0.000	0.000	0.000	0.000
73	A	73	HIS	0	-0.009	0.005	24.720	0.002	0.002	0.000	0.000	0.000	0.000
74	A	74	HIS	0	-0.035	-0.025	25.686	0.009	0.009	0.000	0.000	0.000	0.000
75	A	75	VAL	0	0.007	0.028	26.713	0.005	0.005	0.000	0.000	0.000	0.000
76	A	76	ILE	0	0.011	-0.007	20.719	0.006	0.006	0.000	0.000	0.000	0.000
77	A	77	GLY	0	0.009	0.022	23.633	0.007	0.007	0.000	0.000	0.000	0.000
78	A	78	SER	0	-0.033	-0.016	21.373	0.005	0.005	0.000	0.000	0.000	0.000
79	A	79	GLY	0	-0.067	-0.033	22.428	0.005	0.005	0.000	0.000	0.000	0.000
80	A	80	ARG	1	0.870	0.936	23.395	0.062	0.062	0.000	0.000	0.000	0.000
81	A	81	LEU	0	0.062	0.026	19.898	-0.007	-0.007	0.000	0.000	0.000	0.000
82	A	82	SER	0	-0.050	-0.025	20.486	0.010	0.010	0.000	0.000	0.000	0.000
83	A	83	PHE	0	0.041	0.014	17.745	0.002	0.002	0.000	0.000	0.000	0.000
84	A	84	GLY	0	-0.023	-0.008	14.468	0.014	0.014	0.000	0.000	0.000	0.000
85	A	85	PRO	0	-0.016	-0.011	13.193	-0.013	-0.013	0.000	0.000	0.000	0.000
86	A	86	GLN	0	0.063	0.018	11.190	-0.118	-0.118	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.858	-0.938	9.975	-0.612	-0.612	0.000	0.000	0.000	0.000
88	A	88	MET	0	0.015	0.010	8.304	-0.153	-0.153	0.000	0.000	0.000	0.000
89	A	89	MET	0	-0.038	0.012	7.726	-0.149	-0.149	0.000	0.000	0.000	0.000
90	A	90	LEU	0	-0.005	-0.003	4.305	-0.177	-0.058	-0.001	-0.009	-0.109	0.000
91	A	91	GLU	-1	-0.962	-0.981	3.913	-1.767	-1.418	0.004	-0.085	-0.268	0.000
92	A	92	THR	0	-0.058	-0.054	2.876	-2.684	-1.734	0.370	-0.544	-0.775	-0.006
93	A	93	LEU	0	-0.004	-0.010	4.483	0.087	0.243	-0.001	-0.015	-0.141	0.000
94	A	94	GLY	0	-0.008	0.019	2.830	0.342	1.153	0.585	-0.649	-0.747	0.003
95	A	95	VAL	0	-0.039	-0.011	3.440	-1.744	-1.521	0.004	0.136	-0.363	-0.001
96	A	96	THR	0	0.031	0.011	6.271	-0.044	-0.044	0.000	0.000	0.000	0.000
97	A	97	PRO	0	0.023	-0.019	9.240	0.097	0.097	0.000	0.000	0.000	0.000
98	A	98	GLY	0	-0.005	0.006	12.859	-0.014	-0.014	0.000	0.000	0.000	0.000
99	A	99	SER	0	-0.009	0.006	9.749	0.034	0.034	0.000	0.000	0.000	0.000
100	A	100	VAL	0	-0.006	0.001	10.251	-0.006	-0.006	0.000	0.000	0.000	0.000
101	A	101	THR	0	-0.032	-0.032	9.800	0.058	0.058	0.000	0.000	0.000	0.000
102	A	102	ALA	0	0.086	0.051	11.248	0.020	0.020	0.000	0.000	0.000	0.000
103	A	103	PHE	0	0.003	-0.012	10.553	0.061	0.061	0.000	0.000	0.000	0.000
104	A	104	GLY	0	0.050	0.016	7.293	0.152	0.152	0.000	0.000	0.000	0.000
105	A	105	LEU	0	0.018	0.007	6.048	0.106	0.106	0.000	0.000	0.000	0.000
106	A	106	ILE	0	-0.026	0.003	5.414	0.083	0.083	0.000	0.000	0.000	0.000
107	A	107	ASN	0	-0.034	-0.043	1.999	2.503	1.417	7.185	-1.856	-4.243	-0.012
108	A	108	ASP	-1	-0.743	-0.852	2.364	-3.628	-2.949	2.124	-0.996	-1.807	-0.021
109	A	109	THR	0	-0.069	-0.046	3.714	0.037	0.466	0.028	-0.085	-0.372	0.000
110	A	110	GLU	-1	-0.931	-0.967	6.071	0.909	0.909	0.000	0.000	0.000	0.000
111	A	111	LYS	1	0.804	0.912	7.999	-0.775	-0.775	0.000	0.000	0.000	0.000
112	A	112	ARG	1	0.944	0.969	5.607	0.279	0.279	0.000	0.000	0.000	0.000
113	A	113	VAL	0	-0.073	-0.036	8.531	-0.032	-0.032	0.000	0.000	0.000	0.000
114	A	114	ARG	1	0.939	0.980	11.110	0.045	0.045	0.000	0.000	0.000	0.000
115	A	115	PHE	0	0.039	0.008	13.664	-0.029	-0.029	0.000	0.000	0.000	0.000
116	A	116	VAL	0	-0.010	-0.013	15.273	0.016	0.016	0.000	0.000	0.000	0.000
117	A	117	LEU	0	-0.019	-0.011	18.361	-0.014	-0.014	0.000	0.000	0.000	0.000
118	A	118	ASP	-1	-0.735	-0.865	20.323	-0.048	-0.048	0.000	0.000	0.000	0.000
119	A	119	LYS	1	0.893	0.946	23.536	0.001	0.001	0.000	0.000	0.000	0.000
120	A	120	ALA	0	0.046	0.021	26.344	0.005	0.005	0.000	0.000	0.000	0.000
121	A	121	LEU	0	-0.046	-0.008	20.114	-0.002	-0.002	0.000	0.000	0.000	0.000
122	A	122	ALA	0	-0.039	-0.032	23.557	0.006	0.006	0.000	0.000	0.000	0.000
123	A	123	ASP	-1	-0.817	-0.907	24.408	0.007	0.007	0.000	0.000	0.000	0.000
124	A	124	SER	0	-0.075	-0.035	25.525	-0.005	-0.005	0.000	0.000	0.000	0.000
125	A	125	ASP	-1	-0.846	-0.909	26.076	0.008	0.008	0.000	0.000	0.000	0.000
126	A	126	PRO	0	-0.034	-0.007	23.501	-0.001	-0.001	0.000	0.000	0.000	0.000
127	A	127	VAL	0	-0.015	-0.018	19.946	-0.006	-0.006	0.000	0.000	0.000	0.000
128	A	128	ASN	0	0.000	-0.015	19.228	-0.004	-0.004	0.000	0.000	0.000	0.000
129	A	129	PHE	0	0.014	0.011	14.376	0.001	0.001	0.000	0.000	0.000	0.000
130	A	130	HIS	0	0.004	-0.001	12.088	-0.003	-0.003	0.000	0.000	0.000	0.000
131	A	131	PRO	0	-0.038	0.005	11.127	0.048	0.048	0.000	0.000	0.000	0.000
132	A	132	LEU	0	-0.021	-0.020	5.049	-0.081	-0.081	0.000	0.000	0.000	0.000
133	A	133	LYS	1	0.949	0.964	7.435	0.527	0.527	0.000	0.000	0.000	0.000
134	A	134	ASN	0	0.021	0.003	10.065	0.049	0.049	0.000	0.000	0.000	0.000
135	A	135	ASP	-1	-0.934	-0.965	13.107	-0.528	-0.528	0.000	0.000	0.000	0.000
136	A	136	ALA	0	0.043	0.020	14.072	0.027	0.027	0.000	0.000	0.000	0.000
137	A	137	THR	0	-0.029	-0.028	15.210	-0.013	-0.013	0.000	0.000	0.000	0.000
138	A	138	THR	0	-0.021	-0.016	14.839	0.003	0.003	0.000	0.000	0.000	0.000
139	A	139	ALA	0	0.011	0.019	17.164	0.009	0.009	0.000	0.000	0.000	0.000
140	A	140	VAL	0	-0.017	-0.014	17.307	0.005	0.005	0.000	0.000	0.000	0.000
141	A	141	SER	0	0.011	-0.013	20.491	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	142	GLN	0	0.033	0.017	22.076	0.023	0.023	0.000	0.000	0.000	0.000
143	A	143	ALA	0	-0.014	-0.014	22.464	0.014	0.014	0.000	0.000	0.000	0.000
144	A	144	GLY	0	0.032	0.014	20.792	0.020	0.020	0.000	0.000	0.000	0.000
145	A	145	LEU	0	0.006	0.005	16.615	0.027	0.027	0.000	0.000	0.000	0.000
146	A	146	ARG	1	0.841	0.898	17.784	-0.022	-0.022	0.000	0.000	0.000	0.000
147	A	147	ARG	1	0.929	0.965	19.015	-0.071	-0.071	0.000	0.000	0.000	0.000
148	A	148	PHE	0	-0.003	0.007	10.445	0.037	0.037	0.000	0.000	0.000	0.000
149	A	149	LEU	0	-0.034	-0.021	13.962	0.057	0.057	0.000	0.000	0.000	0.000
150	A	150	ALA	0	0.023	0.010	15.093	0.035	0.035	0.000	0.000	0.000	0.000
151	A	151	ALA	0	-0.014	0.006	14.767	0.025	0.025	0.000	0.000	0.000	0.000
152	A	152	LEU	0	-0.083	-0.031	9.101	0.114	0.114	0.000	0.000	0.000	0.000
153	A	153	GLY	0	0.017	0.018	12.318	0.038	0.038	0.000	0.000	0.000	0.000
154	A	154	VAL	0	-0.057	-0.028	11.734	-0.029	-0.029	0.000	0.000	0.000	0.000
155	A	155	GLU	-1	-0.892	-0.954	14.760	0.135	0.135	0.000	0.000	0.000	0.000
156	A	156	PRO	0	-0.109	-0.041	17.955	-0.016	-0.016	0.000	0.000	0.000	0.000
157	A	157	MET	0	0.003	0.010	18.840	-0.004	-0.004	0.000	0.000	0.000	0.000
158	A	158	ILE	0	0.006	-0.002	21.265	-0.013	-0.013	0.000	0.000	0.000	0.000
159	A	159	VAL	0	-0.014	-0.005	23.359	0.001	0.001	0.000	0.000	0.000	0.000
160	A	160	ASP	-1	-0.816	-0.896	25.509	-0.030	-0.030	0.000	0.000	0.000	0.000
161	A	161	PHE	0	-0.009	-0.040	22.423	-0.003	-0.003	0.000	0.000	0.000	0.000
162	A	162	ALA	0	-0.042	-0.005	28.463	-0.004	-0.004	0.000	0.000	0.000	0.000
163	A	163	ALA	0	-0.001	0.003	32.160	-0.001	-0.001	0.000	0.000	0.000	0.000
164	A	164	MET	0	-0.114	-0.048	27.884	-0.001	-0.001	0.000	0.000	0.000	0.000
165	A	165	GLU	-1	-0.894	-0.946	29.938	-0.006	-0.006	0.000	0.000	0.000	0.000
166	A	166	VAL	0	-0.041	-0.026	25.584	-0.002	-0.002	0.000	0.000	0.000	0.000
167	A	167	VAL	0	-0.022	-0.012	27.270	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)