FMO DATABASE

FMODB ID: 66KNZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1289049.727742
FMO2-HF: Nuclear repulsion	1227668.023025
FMO2-HF: Total energy	-61381.704717
FMO2-MP2: Total energy	-61553.168083

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.
-15.581	-10.774	9.471	-6.56	-7.719	-0.046

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 : 0.038 / q_NPA : 0.008

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	0.025	-0.009	3.276	-1.294	0.945	0.073	-1.106	-1.206	-0.002
4	A	37	LEU	0	-0.028	-0.003	2.608	-0.810	0.222	0.171	-0.363	-0.839	0.000
5	A	38	PRO	0	0.004	-0.010	3.469	-2.135	-1.714	0.017	-0.351	-0.088	-0.002
6	A	39	GLU	-1	-0.799	-0.894	1.952	-12.851	-12.678	7.905	-3.852	-4.227	-0.046
7	A	40	ASN	0	-0.011	-0.013	4.168	0.836	0.943	-0.001	-0.010	-0.096	0.000
8	A	41	MET	0	-0.034	-0.025	5.932	0.369	0.369	0.000	0.000	0.000	0.000
9	A	42	VAL	0	0.036	0.031	2.436	-1.172	-0.337	1.306	-0.878	-1.263	0.004
10	A	43	TYR	0	0.065	0.039	5.552	0.308	0.308	0.000	0.000	0.000	0.000
11	A	44	ARG	1	0.861	0.930	7.877	0.719	0.719	0.000	0.000	0.000	0.000
12	A	45	PHE	0	0.009	0.001	8.139	0.054	0.054	0.000	0.000	0.000	0.000
13	A	46	ASP	-1	-0.818	-0.885	7.704	0.327	0.327	0.000	0.000	0.000	0.000
14	A	47	LYS	1	0.832	0.907	10.767	0.162	0.162	0.000	0.000	0.000	0.000
15	A	48	SER	0	-0.114	-0.068	13.298	0.016	0.016	0.000	0.000	0.000	0.000
16	A	49	THR	0	0.013	-0.014	12.845	0.028	0.028	0.000	0.000	0.000	0.000
17	A	50	ASN	0	0.004	-0.005	15.029	-0.015	-0.015	0.000	0.000	0.000	0.000
18	A	51	ILE	0	-0.013	-0.019	16.420	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	52	LEU	0	-0.010	-0.011	16.704	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	53	ASP	-1	-0.828	-0.892	16.991	0.139	0.139	0.000	0.000	0.000	0.000
21	A	54	TYR	0	-0.115	-0.058	19.962	-0.010	-0.010	0.000	0.000	0.000	0.000
22	A	55	LEU	0	-0.053	-0.033	22.708	-0.012	-0.012	0.000	0.000	0.000	0.000
23	A	56	SER	0	0.022	0.015	23.051	0.013	0.013	0.000	0.000	0.000	0.000
24	A	57	THR	0	-0.041	-0.043	24.492	0.003	0.003	0.000	0.000	0.000	0.000
25	A	58	GLU	-1	-0.848	-0.932	28.010	0.083	0.083	0.000	0.000	0.000	0.000
26	A	59	ARG	1	0.942	0.976	30.456	-0.050	-0.050	0.000	0.000	0.000	0.000
27	A	60	ASP	-1	-0.861	-0.909	27.571	0.060	0.060	0.000	0.000	0.000	0.000
28	A	61	HIS	0	0.075	0.038	24.365	-0.016	-0.016	0.000	0.000	0.000	0.000
29	A	62	VAL	0	0.004	0.008	29.106	-0.007	-0.007	0.000	0.000	0.000	0.000
30	A	63	MET	0	-0.044	-0.028	31.261	-0.008	-0.008	0.000	0.000	0.000	0.000
31	A	64	MET	0	-0.027	0.004	25.533	-0.010	-0.010	0.000	0.000	0.000	0.000
32	A	65	ALA	0	0.030	0.020	30.272	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	66	VAL	0	-0.002	-0.003	32.200	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	67	ARG	1	0.934	0.946	30.140	-0.031	-0.031	0.000	0.000	0.000	0.000
35	A	68	TYR	0	0.022	0.030	30.094	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	69	TYR	0	0.032	0.019	32.652	-0.005	-0.005	0.000	0.000	0.000	0.000
37	A	70	MET	0	-0.031	-0.019	35.955	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	71	SER	0	-0.025	-0.023	33.799	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	72	LYS	1	0.809	0.891	33.799	0.002	0.002	0.000	0.000	0.000	0.000
40	A	73	GLN	0	0.047	0.019	35.782	-0.004	-0.004	0.000	0.000	0.000	0.000
41	A	74	ARG	1	0.824	0.900	39.238	0.006	0.006	0.000	0.000	0.000	0.000
42	A	75	LEU	0	0.029	0.016	34.398	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	76	ASP	-1	-0.792	-0.881	37.786	-0.008	-0.008	0.000	0.000	0.000	0.000
44	A	77	ASP	-1	-0.876	-0.934	39.912	-0.006	-0.006	0.000	0.000	0.000	0.000
45	A	78	LEU	0	0.006	0.004	39.906	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	79	TYR	0	0.049	0.011	40.339	0.000	0.000	0.000	0.000	0.000	0.000
47	A	80	ARG	1	0.826	0.912	42.070	0.003	0.003	0.000	0.000	0.000	0.000
48	A	81	GLN	0	0.013	0.014	45.457	0.000	0.000	0.000	0.000	0.000	0.000
49	A	82	LEU	0	0.003	0.024	42.107	0.000	0.000	0.000	0.000	0.000	0.000
50	A	83	PRO	0	0.019	0.021	46.615	0.000	0.000	0.000	0.000	0.000	0.000
51	A	84	THR	0	0.041	-0.004	47.421	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	85	LYS	1	0.979	1.016	47.109	0.022	0.022	0.000	0.000	0.000	0.000
53	A	86	THR	0	0.056	0.025	43.317	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	87	ARG	1	0.812	0.917	42.756	0.015	0.015	0.000	0.000	0.000	0.000
55	A	88	SER	0	0.032	0.007	42.174	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	89	TYR	0	0.041	0.000	42.644	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	90	ILE	0	-0.025	-0.008	37.411	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	91	ASP	-1	-0.873	-0.944	37.920	-0.035	-0.035	0.000	0.000	0.000	0.000
59	A	92	ILE	0	-0.017	-0.004	38.494	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	93	ILE	0	-0.005	-0.006	34.304	-0.004	-0.004	0.000	0.000	0.000	0.000
61	A	94	ASN	0	-0.028	-0.009	33.956	-0.006	-0.006	0.000	0.000	0.000	0.000
62	A	95	ILE	0	0.000	-0.001	33.738	-0.005	-0.005	0.000	0.000	0.000	0.000
63	A	96	TYR	0	-0.028	-0.006	34.040	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	97	CYS	0	-0.041	-0.018	30.550	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	98	ASP	-1	-0.860	-0.918	29.148	-0.065	-0.065	0.000	0.000	0.000	0.000
66	A	99	LYS	1	0.813	0.906	29.095	0.078	0.078	0.000	0.000	0.000	0.000
67	A	100	VAL	0	0.027	0.008	26.970	-0.007	-0.007	0.000	0.000	0.000	0.000
68	A	101	SER	0	-0.062	-0.049	25.150	-0.014	-0.014	0.000	0.000	0.000	0.000
69	A	102	ASN	0	-0.102	-0.065	24.423	-0.008	-0.008	0.000	0.000	0.000	0.000
70	A	103	ASP	-1	-0.859	-0.893	25.664	-0.098	-0.098	0.000	0.000	0.000	0.000
71	A	104	TYR	0	-0.111	-0.051	21.232	-0.030	-0.030	0.000	0.000	0.000	0.000
72	A	114	MET	0	0.050	0.003	18.049	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	115	ALA	0	0.005	-0.004	19.710	0.016	0.016	0.000	0.000	0.000	0.000
74	A	116	SER	0	0.017	0.034	17.225	0.003	0.003	0.000	0.000	0.000	0.000
75	A	117	THR	0	-0.025	-0.004	20.157	0.023	0.023	0.000	0.000	0.000	0.000
76	A	118	LYS	1	0.956	0.957	21.435	-0.034	-0.034	0.000	0.000	0.000	0.000
77	A	119	SER	0	0.002	-0.010	24.617	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	120	PHE	0	-0.025	0.001	23.894	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	121	THR	0	0.064	0.023	25.560	0.007	0.007	0.000	0.000	0.000	0.000
80	A	122	VAL	0	0.011	0.004	28.429	-0.005	-0.005	0.000	0.000	0.000	0.000
81	A	123	TYR	0	-0.003	-0.009	29.717	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	124	ASP	-1	-0.823	-0.906	30.327	-0.048	-0.048	0.000	0.000	0.000	0.000
83	A	125	ILE	0	0.030	0.025	25.396	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	126	ASN	0	0.015	0.014	29.708	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	127	ASN	0	-0.011	-0.008	33.121	0.002	0.002	0.000	0.000	0.000	0.000
86	A	128	GLU	-1	-0.913	-0.950	28.750	-0.084	-0.084	0.000	0.000	0.000	0.000
87	A	129	VAL	0	-0.004	-0.010	30.798	0.000	0.000	0.000	0.000	0.000	0.000
88	A	130	ASN	0	0.004	-0.007	33.351	0.002	0.002	0.000	0.000	0.000	0.000
89	A	131	THR	0	-0.041	-0.019	35.679	0.003	0.003	0.000	0.000	0.000	0.000
90	A	132	ILE	0	0.010	0.003	31.266	0.000	0.000	0.000	0.000	0.000	0.000
91	A	133	MET	0	-0.047	-0.013	34.266	0.000	0.000	0.000	0.000	0.000	0.000
92	A	134	LEU	0	0.003	0.018	38.005	0.003	0.003	0.000	0.000	0.000	0.000
93	A	135	ASP	-1	-0.896	-0.941	38.261	-0.055	-0.055	0.000	0.000	0.000	0.000
94	A	136	ASN	0	-0.055	-0.024	35.891	0.002	0.002	0.000	0.000	0.000	0.000
95	A	137	LYS	1	0.882	0.931	38.942	0.046	0.046	0.000	0.000	0.000	0.000
96	A	138	GLY	0	0.055	0.041	38.690	0.002	0.002	0.000	0.000	0.000	0.000
97	A	139	LEU	0	0.048	0.026	38.201	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	140	GLY	0	0.010	-0.001	35.041	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	141	VAL	0	0.034	0.013	32.438	-0.004	-0.004	0.000	0.000	0.000	0.000
100	A	142	ARG	1	0.804	0.891	33.075	0.051	0.051	0.000	0.000	0.000	0.000
101	A	143	LEU	0	0.046	0.023	33.483	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	144	ALA	0	0.013	0.014	29.271	-0.003	-0.003	0.000	0.000	0.000	0.000
103	A	145	THR	0	-0.008	-0.019	28.852	-0.006	-0.006	0.000	0.000	0.000	0.000
104	A	146	ILE	0	0.022	0.013	29.805	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	147	SER	0	0.001	0.005	27.184	0.002	0.002	0.000	0.000	0.000	0.000
106	A	148	PHE	0	-0.012	-0.007	23.409	-0.005	-0.005	0.000	0.000	0.000	0.000
107	A	149	ILE	0	0.035	0.002	25.239	-0.002	-0.002	0.000	0.000	0.000	0.000
108	A	150	THR	0	-0.010	-0.016	26.503	0.007	0.007	0.000	0.000	0.000	0.000
109	A	151	GLU	-1	-0.791	-0.863	19.102	-0.134	-0.134	0.000	0.000	0.000	0.000
110	A	152	LEU	0	-0.036	-0.019	22.022	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	153	GLY	0	0.002	-0.018	23.687	0.008	0.008	0.000	0.000	0.000	0.000
112	A	154	ARG	1	0.875	0.927	21.820	0.098	0.098	0.000	0.000	0.000	0.000
113	A	155	ARG	1	0.845	0.914	17.421	0.170	0.170	0.000	0.000	0.000	0.000
114	A	156	CYS	0	-0.020	0.002	20.906	0.010	0.010	0.000	0.000	0.000	0.000
115	A	157	MET	0	0.018	0.017	18.859	0.007	0.007	0.000	0.000	0.000	0.000
116	A	158	ASN	0	-0.048	-0.033	23.836	0.007	0.007	0.000	0.000	0.000	0.000
117	A	159	PRO	0	0.077	0.039	27.489	-0.005	-0.005	0.000	0.000	0.000	0.000
118	A	160	VAL	0	0.026	0.010	30.151	-0.004	-0.004	0.000	0.000	0.000	0.000
119	A	161	LYS	1	0.834	0.927	26.532	0.022	0.022	0.000	0.000	0.000	0.000
120	A	162	THR	0	0.051	0.026	27.328	-0.004	-0.004	0.000	0.000	0.000	0.000
121	A	163	ILE	0	0.028	0.017	29.742	-0.004	-0.004	0.000	0.000	0.000	0.000
122	A	164	LYS	1	0.939	0.986	33.380	0.012	0.012	0.000	0.000	0.000	0.000
123	A	165	MET	0	0.003	0.022	26.441	-0.003	-0.003	0.000	0.000	0.000	0.000
124	A	166	PHE	0	0.007	-0.003	28.594	-0.002	-0.002	0.000	0.000	0.000	0.000
125	A	167	THR	0	-0.011	-0.006	33.395	0.000	0.000	0.000	0.000	0.000	0.000
126	A	168	LEU	0	-0.031	-0.003	34.233	0.000	0.000	0.000	0.000	0.000	0.000
127	A	169	LEU	0	0.027	-0.004	31.269	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	170	SER	0	-0.030	-0.018	34.715	-0.001	-0.001	0.000	0.000	0.000	0.000
129	A	171	HIS	0	-0.022	-0.021	36.951	0.002	0.002	0.000	0.000	0.000	0.000
130	A	172	THR	0	-0.046	-0.037	36.281	0.001	0.001	0.000	0.000	0.000	0.000
131	A	173	ILE	0	-0.023	-0.014	33.082	-0.002	-0.002	0.000	0.000	0.000	0.000
132	A	174	CYS	0	-0.108	-0.043	37.414	-0.001	-0.001	0.000	0.000	0.000	0.000
133	A	175	ASP	-1	-0.725	-0.841	40.871	-0.043	-0.043	0.000	0.000	0.000	0.000
134	A	176	ASP	-1	-0.876	-0.945	42.856	-0.033	-0.033	0.000	0.000	0.000	0.000
135	A	177	CYS	0	-0.025	0.008	43.147	-0.001	-0.001	0.000	0.000	0.000	0.000
136	A	178	PHE	0	0.023	-0.009	38.031	-0.002	-0.002	0.000	0.000	0.000	0.000
137	A	179	VAL	0	-0.005	0.000	42.262	0.000	0.000	0.000	0.000	0.000	0.000
138	A	180	ASP	-1	-0.868	-0.915	45.290	-0.033	-0.033	0.000	0.000	0.000	0.000
139	A	181	TYR	0	-0.048	-0.051	41.617	-0.001	-0.001	0.000	0.000	0.000	0.000
140	A	182	ILE	0	-0.037	-0.017	40.058	0.000	0.000	0.000	0.000	0.000	0.000
141	A	183	THR	0	-0.098	-0.059	44.185	0.002	0.002	0.000	0.000	0.000	0.000
142	A	184	ASP	-1	-0.871	-0.917	47.492	-0.032	-0.032	0.000	0.000	0.000	0.000
143	A	185	ILE	0	-0.117	-0.063	41.467	0.000	0.000	0.000	0.000	0.000	0.000
144	A	186	SER	0	-0.120	-0.066	45.480	0.002	0.002	0.000	0.000	0.000	0.000

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