FMO DATABASE

FMODB ID: 229JR

Calculation Name: 2VTY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2VTY

Chain ID: A

ChEMBL ID:

UniProt ID: O57173

Base Structure: X-ray

Registration Date: 2023-06-19

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	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	144
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1284966.503054
FMO2-HF: Nuclear repulsion	1223585.198388
FMO2-HF: Total energy	-61381.304666
FMO2-MP2: Total energy	-61552.793226

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:34:VAL)

Summations of interaction energy for fragment #1(A:34:VAL)

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.
-13.171	-5.798	2.446	-4.354	-5.466	-0.027

Interaction energy analysis for fragmet #1(A:34:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.031 / q_NPA : 0.009

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	36	PRO	0	-0.013	0.007	3.814	-1.541	1.091	-0.026	-1.278	-1.328	-0.001
4	A	37	LEU	0	0.002	-0.005	3.209	-0.502	0.053	0.015	-0.129	-0.442	0.000
5	A	38	PRO	0	0.017	0.003	3.967	-1.603	-1.595	0.000	-0.104	0.096	0.000
6	A	39	GLU	-1	-0.808	-0.900	2.569	-12.219	-8.862	1.918	-2.400	-2.875	-0.028
7	A	40	ASN	0	-0.019	-0.018	4.633	0.712	0.801	-0.001	-0.003	-0.085	0.000
8	A	41	MET	0	-0.035	-0.023	6.329	0.424	0.424	0.000	0.000	0.000	0.000
9	A	42	VAL	0	0.058	0.033	2.459	-0.557	0.175	0.540	-0.440	-0.832	0.002
10	A	43	TYR	0	0.076	0.055	5.643	0.535	0.535	0.000	0.000	0.000	0.000
11	A	44	ARG	1	0.861	0.923	7.841	1.045	1.045	0.000	0.000	0.000	0.000
12	A	45	PHE	0	-0.007	-0.011	8.490	0.135	0.135	0.000	0.000	0.000	0.000
13	A	46	ASP	-1	-0.821	-0.896	7.455	-0.062	-0.062	0.000	0.000	0.000	0.000
14	A	47	LYS	1	0.874	0.941	10.489	0.400	0.400	0.000	0.000	0.000	0.000
15	A	48	SER	0	-0.133	-0.074	13.307	0.057	0.057	0.000	0.000	0.000	0.000
16	A	49	THR	0	0.012	-0.009	12.821	0.045	0.045	0.000	0.000	0.000	0.000
17	A	50	ASN	0	0.028	0.011	15.279	0.009	0.009	0.000	0.000	0.000	0.000
18	A	51	ILE	0	0.002	-0.011	16.457	0.015	0.015	0.000	0.000	0.000	0.000
19	A	52	LEU	0	-0.009	-0.007	16.727	0.007	0.007	0.000	0.000	0.000	0.000
20	A	53	ASP	-1	-0.848	-0.900	16.630	0.025	0.025	0.000	0.000	0.000	0.000
21	A	54	TYR	0	-0.111	-0.069	19.599	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	55	LEU	0	-0.072	-0.033	22.433	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	56	SER	0	0.033	0.024	23.070	0.014	0.014	0.000	0.000	0.000	0.000
24	A	57	THR	0	-0.059	-0.053	24.412	0.010	0.010	0.000	0.000	0.000	0.000
25	A	58	GLU	-1	-0.840	-0.934	27.988	0.051	0.051	0.000	0.000	0.000	0.000
26	A	59	ARG	1	0.942	0.970	30.329	-0.019	-0.019	0.000	0.000	0.000	0.000
27	A	60	ASP	-1	-0.849	-0.906	27.361	0.019	0.019	0.000	0.000	0.000	0.000
28	A	61	HIS	0	0.064	0.035	24.297	-0.018	-0.018	0.000	0.000	0.000	0.000
29	A	62	VAL	0	0.017	0.012	28.947	-0.007	-0.007	0.000	0.000	0.000	0.000
30	A	63	MET	0	-0.069	-0.035	31.161	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	64	MET	0	-0.004	0.008	25.609	-0.009	-0.009	0.000	0.000	0.000	0.000
32	A	65	ALA	0	0.017	0.016	30.279	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	66	VAL	0	-0.013	-0.011	32.329	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	67	ARG	1	0.968	0.965	30.810	0.015	0.015	0.000	0.000	0.000	0.000
35	A	68	TYR	0	0.022	0.036	30.290	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	69	TYR	0	0.041	0.020	32.809	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	70	MET	0	-0.035	-0.022	36.194	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	71	SER	0	-0.022	-0.025	33.959	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	72	LYS	1	0.817	0.899	34.210	0.034	0.034	0.000	0.000	0.000	0.000
40	A	73	GLN	0	0.019	0.009	36.094	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	74	ARG	1	0.814	0.898	39.270	0.034	0.034	0.000	0.000	0.000	0.000
42	A	75	LEU	0	0.028	0.016	34.858	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	76	ASP	-1	-0.807	-0.891	38.153	-0.037	-0.037	0.000	0.000	0.000	0.000
44	A	77	ASP	-1	-0.909	-0.966	40.340	-0.028	-0.028	0.000	0.000	0.000	0.000
45	A	78	LEU	0	0.011	0.009	40.312	0.000	0.000	0.000	0.000	0.000	0.000
46	A	79	TYR	0	0.050	0.022	40.658	0.001	0.001	0.000	0.000	0.000	0.000
47	A	80	ARG	1	0.896	0.949	42.567	0.029	0.029	0.000	0.000	0.000	0.000
48	A	81	GLN	0	0.002	0.017	45.790	0.001	0.001	0.000	0.000	0.000	0.000
49	A	82	LEU	0	-0.042	-0.004	42.552	0.000	0.000	0.000	0.000	0.000	0.000
50	A	83	PRO	0	0.025	0.024	46.959	0.001	0.001	0.000	0.000	0.000	0.000
51	A	84	THR	0	0.054	-0.006	47.723	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	85	LYS	1	0.976	1.012	47.652	0.041	0.041	0.000	0.000	0.000	0.000
53	A	86	THR	0	0.059	0.020	43.628	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	87	ARG	1	0.860	0.933	43.237	0.037	0.037	0.000	0.000	0.000	0.000
55	A	88	SER	0	0.034	0.030	42.814	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	89	TYR	0	0.026	-0.003	42.892	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	90	ILE	0	-0.035	-0.023	37.956	-0.004	-0.004	0.000	0.000	0.000	0.000
58	A	91	ASP	-1	-0.891	-0.942	38.336	-0.063	-0.063	0.000	0.000	0.000	0.000
59	A	92	ILE	0	0.003	0.005	38.733	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	93	ILE	0	-0.019	-0.021	34.626	-0.005	-0.005	0.000	0.000	0.000	0.000
61	A	94	ASN	0	0.002	0.002	34.192	-0.009	-0.009	0.000	0.000	0.000	0.000
62	A	95	ILE	0	-0.001	0.005	34.108	-0.006	-0.006	0.000	0.000	0.000	0.000
63	A	96	TYR	0	-0.021	-0.011	34.739	-0.006	-0.006	0.000	0.000	0.000	0.000
64	A	97	CYS	0	-0.059	-0.024	30.749	-0.007	-0.007	0.000	0.000	0.000	0.000
65	A	98	ASP	-1	-0.847	-0.921	29.635	-0.114	-0.114	0.000	0.000	0.000	0.000
66	A	99	LYS	1	0.801	0.904	29.666	0.112	0.112	0.000	0.000	0.000	0.000
67	A	100	VAL	0	0.012	0.008	27.263	-0.008	-0.008	0.000	0.000	0.000	0.000
68	A	101	SER	0	-0.012	-0.021	25.547	-0.018	-0.018	0.000	0.000	0.000	0.000
69	A	102	ASN	0	-0.084	-0.009	24.706	-0.017	-0.017	0.000	0.000	0.000	0.000
70	A	103	ASP	-1	-0.860	-0.905	25.771	-0.138	-0.138	0.000	0.000	0.000	0.000
71	A	104	TYR	0	-0.150	-0.104	21.848	-0.033	-0.033	0.000	0.000	0.000	0.000
72	A	114	MET	0	0.049	0.002	18.211	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	115	ALA	0	-0.001	-0.004	19.928	0.022	0.022	0.000	0.000	0.000	0.000
74	A	116	SER	0	-0.010	0.015	17.091	0.011	0.011	0.000	0.000	0.000	0.000
75	A	117	THR	0	-0.011	0.007	20.233	0.022	0.022	0.000	0.000	0.000	0.000
76	A	118	LYS	1	0.947	0.956	21.216	0.060	0.060	0.000	0.000	0.000	0.000
77	A	119	SER	0	-0.040	-0.024	24.239	0.008	0.008	0.000	0.000	0.000	0.000
78	A	120	PHE	0	-0.013	-0.018	24.392	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	121	THR	0	0.021	0.017	26.194	0.010	0.010	0.000	0.000	0.000	0.000
80	A	122	VAL	0	0.047	0.023	28.680	-0.006	-0.006	0.000	0.000	0.000	0.000
81	A	123	TYR	0	-0.024	-0.010	30.048	0.000	0.000	0.000	0.000	0.000	0.000
82	A	124	ASP	-1	-0.816	-0.917	30.237	-0.098	-0.098	0.000	0.000	0.000	0.000
83	A	125	ILE	0	0.026	0.023	25.801	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	126	ASN	0	0.024	0.012	30.097	0.000	0.000	0.000	0.000	0.000	0.000
85	A	127	ASN	0	0.012	0.008	33.485	0.004	0.004	0.000	0.000	0.000	0.000
86	A	128	GLU	-1	-0.909	-0.945	29.124	-0.142	-0.142	0.000	0.000	0.000	0.000
87	A	129	VAL	0	-0.015	-0.019	31.271	0.000	0.000	0.000	0.000	0.000	0.000
88	A	130	ASN	0	-0.004	-0.013	33.759	0.005	0.005	0.000	0.000	0.000	0.000
89	A	131	THR	0	-0.050	-0.030	35.970	0.005	0.005	0.000	0.000	0.000	0.000
90	A	132	ILE	0	0.018	0.015	31.491	0.001	0.001	0.000	0.000	0.000	0.000
91	A	133	MET	0	-0.065	-0.013	34.857	0.002	0.002	0.000	0.000	0.000	0.000
92	A	134	LEU	0	0.021	0.006	38.548	0.005	0.005	0.000	0.000	0.000	0.000
93	A	135	ASP	-1	-0.897	-0.921	38.748	-0.087	-0.087	0.000	0.000	0.000	0.000
94	A	136	ASN	0	-0.052	-0.024	36.252	0.005	0.005	0.000	0.000	0.000	0.000
95	A	137	LYS	1	0.899	0.935	39.390	0.076	0.076	0.000	0.000	0.000	0.000
96	A	138	GLY	0	0.042	0.037	39.318	0.003	0.003	0.000	0.000	0.000	0.000
97	A	139	LEU	0	0.060	0.030	38.445	-0.003	-0.003	0.000	0.000	0.000	0.000
98	A	140	GLY	0	0.016	-0.001	35.469	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	141	VAL	0	0.034	0.013	33.083	-0.008	-0.008	0.000	0.000	0.000	0.000
100	A	142	ARG	1	0.783	0.870	33.694	0.082	0.082	0.000	0.000	0.000	0.000
101	A	143	LEU	0	0.016	0.009	33.865	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	144	ALA	0	0.006	0.003	29.843	-0.006	-0.006	0.000	0.000	0.000	0.000
103	A	145	THR	0	-0.003	-0.016	29.444	-0.010	-0.010	0.000	0.000	0.000	0.000
104	A	146	ILE	0	0.034	0.029	30.321	-0.004	-0.004	0.000	0.000	0.000	0.000
105	A	147	SER	0	-0.009	0.001	27.490	0.000	0.000	0.000	0.000	0.000	0.000
106	A	148	PHE	0	-0.006	0.000	23.678	-0.011	-0.011	0.000	0.000	0.000	0.000
107	A	149	ILE	0	0.036	0.002	25.730	-0.008	-0.008	0.000	0.000	0.000	0.000
108	A	150	THR	0	-0.020	-0.024	27.182	0.005	0.005	0.000	0.000	0.000	0.000
109	A	151	GLU	-1	-0.793	-0.865	19.798	-0.245	-0.245	0.000	0.000	0.000	0.000
110	A	152	LEU	0	-0.038	-0.020	22.646	-0.008	-0.008	0.000	0.000	0.000	0.000
111	A	153	GLY	0	-0.026	-0.030	24.044	0.005	0.005	0.000	0.000	0.000	0.000
112	A	154	ARG	1	0.875	0.927	22.337	0.172	0.172	0.000	0.000	0.000	0.000
113	A	155	ARG	1	0.822	0.899	17.749	0.301	0.301	0.000	0.000	0.000	0.000
114	A	156	CYS	0	-0.054	-0.004	20.959	0.006	0.006	0.000	0.000	0.000	0.000
115	A	157	MET	0	0.035	0.025	19.147	0.016	0.016	0.000	0.000	0.000	0.000
116	A	158	ASN	0	-0.045	-0.029	24.009	0.015	0.015	0.000	0.000	0.000	0.000
117	A	159	PRO	0	0.078	0.029	27.526	-0.005	-0.005	0.000	0.000	0.000	0.000
118	A	160	VAL	0	0.033	0.006	30.317	-0.002	-0.002	0.000	0.000	0.000	0.000
119	A	161	LYS	1	0.889	0.946	26.763	0.086	0.086	0.000	0.000	0.000	0.000
120	A	162	THR	0	0.057	0.041	27.448	-0.005	-0.005	0.000	0.000	0.000	0.000
121	A	163	ILE	0	0.032	0.022	29.893	-0.003	-0.003	0.000	0.000	0.000	0.000
122	A	164	LYS	1	0.936	0.977	33.448	0.057	0.057	0.000	0.000	0.000	0.000
123	A	165	MET	0	0.006	0.025	26.728	-0.002	-0.002	0.000	0.000	0.000	0.000
124	A	166	PHE	0	0.010	0.005	28.936	0.000	0.000	0.000	0.000	0.000	0.000
125	A	167	THR	0	0.004	0.000	33.628	0.002	0.002	0.000	0.000	0.000	0.000
126	A	168	LEU	0	-0.039	-0.008	34.655	0.001	0.001	0.000	0.000	0.000	0.000
127	A	169	LEU	0	0.045	0.004	31.695	0.000	0.000	0.000	0.000	0.000	0.000
128	A	170	SER	0	-0.035	-0.014	35.128	0.000	0.000	0.000	0.000	0.000	0.000
129	A	171	HIS	0	-0.039	-0.030	37.435	0.005	0.005	0.000	0.000	0.000	0.000
130	A	172	THR	0	-0.049	-0.040	36.548	0.003	0.003	0.000	0.000	0.000	0.000
131	A	173	ILE	0	-0.032	-0.017	33.423	-0.002	-0.002	0.000	0.000	0.000	0.000
132	A	174	CYS	0	-0.103	-0.043	37.776	0.000	0.000	0.000	0.000	0.000	0.000
133	A	175	ASP	-1	-0.685	-0.814	41.233	-0.073	-0.073	0.000	0.000	0.000	0.000
134	A	176	ASP	-1	-0.864	-0.948	43.265	-0.056	-0.056	0.000	0.000	0.000	0.000
135	A	177	CYS	0	-0.049	-0.004	43.348	-0.001	-0.001	0.000	0.000	0.000	0.000
136	A	178	PHE	0	0.022	-0.008	38.422	-0.001	-0.001	0.000	0.000	0.000	0.000
137	A	179	VAL	0	-0.008	-0.007	42.504	0.001	0.001	0.000	0.000	0.000	0.000
138	A	180	ASP	-1	-0.874	-0.924	45.348	-0.054	-0.054	0.000	0.000	0.000	0.000
139	A	181	TYR	0	-0.040	-0.044	42.184	0.000	0.000	0.000	0.000	0.000	0.000
140	A	182	ILE	0	-0.039	-0.015	40.221	0.001	0.001	0.000	0.000	0.000	0.000
141	A	183	THR	0	-0.098	-0.066	44.355	0.003	0.003	0.000	0.000	0.000	0.000
142	A	184	ASP	-1	-0.875	-0.917	47.719	-0.052	-0.052	0.000	0.000	0.000	0.000
143	A	185	ILE	0	-0.121	-0.052	41.979	0.001	0.001	0.000	0.000	0.000	0.000
144	A	186	SER	0	-0.122	-0.060	45.916	0.003	0.003	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:34:VAL)