FMO DATABASE

FMODB ID: M93NZ

Calculation Name: 2VYI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2VYI

Chain ID: A

ChEMBL ID:

UniProt ID: O43765

Base Structure: X-ray

Registration Date: 2023-09-26

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	131
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1090231.056203
FMO2-HF: Nuclear repulsion	1039206.120701
FMO2-HF: Total energy	-51024.935503
FMO2-MP2: Total energy	-51172.693295

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:80:GLY)

Summations of interaction energy for fragment #1(A:80:GLY)

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.
-2.37	1.295	0.986	-2.411	-2.237	-0.011

Interaction energy analysis for fragmet #1(A:80:GLY)

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 : 0.016

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	82	LEU	0	-0.029	0.005	3.380	0.068	1.962	0.008	-1.012	-0.890	0.001
4	A	83	GLY	0	0.021	0.012	2.516	-0.306	0.207	0.500	-0.440	-0.572	-0.001
5	A	84	SER	0	-0.087	-0.088	2.869	-1.661	-0.390	0.479	-0.953	-0.796	-0.011
6	A	85	GLU	-1	-0.835	-0.905	4.888	-0.310	-0.323	-0.001	-0.006	0.021	0.000
7	A	86	GLU	-1	-0.769	-0.820	6.000	-0.084	-0.084	0.000	0.000	0.000	0.000
8	A	87	ASP	-1	-0.854	-0.930	9.994	-0.251	-0.251	0.000	0.000	0.000	0.000
9	A	88	SER	0	-0.019	-0.046	6.759	-0.140	-0.140	0.000	0.000	0.000	0.000
10	A	89	ALA	0	-0.019	0.013	8.227	-0.143	-0.143	0.000	0.000	0.000	0.000
11	A	90	GLU	-1	-0.821	-0.897	9.580	-0.179	-0.179	0.000	0.000	0.000	0.000
12	A	91	ALA	0	0.000	0.004	11.684	0.023	0.023	0.000	0.000	0.000	0.000
13	A	92	GLU	-1	-0.768	-0.849	9.692	-1.074	-1.074	0.000	0.000	0.000	0.000
14	A	93	ARG	1	0.785	0.863	12.194	0.264	0.264	0.000	0.000	0.000	0.000
15	A	94	LEU	0	0.015	0.011	15.211	0.039	0.039	0.000	0.000	0.000	0.000
16	A	95	LYS	1	0.812	0.891	13.672	0.767	0.767	0.000	0.000	0.000	0.000
17	A	96	THR	0	-0.104	-0.066	15.501	0.007	0.007	0.000	0.000	0.000	0.000
18	A	97	GLU	-1	-0.821	-0.898	18.112	-0.177	-0.177	0.000	0.000	0.000	0.000
19	A	98	GLY	0	0.023	0.005	20.514	0.026	0.026	0.000	0.000	0.000	0.000
20	A	99	ASN	0	-0.022	-0.011	18.597	0.018	0.018	0.000	0.000	0.000	0.000
21	A	100	GLU	-1	-0.799	-0.874	22.006	-0.248	-0.248	0.000	0.000	0.000	0.000
22	A	101	GLN	0	-0.007	-0.022	24.404	0.030	0.030	0.000	0.000	0.000	0.000
23	A	102	MET	0	-0.057	-0.020	24.711	0.018	0.018	0.000	0.000	0.000	0.000
24	A	103	LYS	1	0.734	0.857	23.105	0.271	0.271	0.000	0.000	0.000	0.000
25	A	104	VAL	0	-0.039	-0.012	28.653	0.014	0.014	0.000	0.000	0.000	0.000
26	A	105	GLU	-1	-0.800	-0.898	31.026	-0.150	-0.150	0.000	0.000	0.000	0.000
27	A	106	ASN	0	0.022	0.030	29.711	0.008	0.008	0.000	0.000	0.000	0.000
28	A	107	PHE	0	0.033	-0.007	29.020	-0.017	-0.017	0.000	0.000	0.000	0.000
29	A	108	GLU	-1	-0.853	-0.931	28.595	-0.160	-0.160	0.000	0.000	0.000	0.000
30	A	109	ALA	0	-0.003	0.006	27.475	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	110	ALA	0	0.007	0.004	24.684	-0.017	-0.017	0.000	0.000	0.000	0.000
32	A	111	VAL	0	-0.039	-0.024	23.825	-0.028	-0.028	0.000	0.000	0.000	0.000
33	A	112	HIS	0	-0.017	0.002	24.198	-0.009	-0.009	0.000	0.000	0.000	0.000
34	A	113	PHE	0	0.009	0.000	21.183	-0.006	-0.006	0.000	0.000	0.000	0.000
35	A	114	TYR	0	0.014	-0.035	19.247	-0.029	-0.029	0.000	0.000	0.000	0.000
36	A	115	GLY	0	-0.028	-0.010	19.271	-0.035	-0.035	0.000	0.000	0.000	0.000
37	A	116	LYS	1	0.821	0.887	19.700	0.178	0.178	0.000	0.000	0.000	0.000
38	A	117	ALA	0	0.013	0.019	15.529	-0.009	-0.009	0.000	0.000	0.000	0.000
39	A	118	ILE	0	-0.053	-0.036	15.011	-0.062	-0.062	0.000	0.000	0.000	0.000
40	A	119	GLU	-1	-0.868	-0.924	16.448	-0.221	-0.221	0.000	0.000	0.000	0.000
41	A	120	LEU	0	-0.024	0.011	13.293	0.034	0.034	0.000	0.000	0.000	0.000
42	A	121	ASN	0	0.022	0.002	9.478	-0.009	-0.009	0.000	0.000	0.000	0.000
43	A	122	PRO	0	0.006	0.013	12.184	-0.041	-0.041	0.000	0.000	0.000	0.000
44	A	123	ALA	0	0.005	0.000	10.807	0.081	0.081	0.000	0.000	0.000	0.000
45	A	124	ASN	0	0.027	0.027	11.407	-0.020	-0.020	0.000	0.000	0.000	0.000
46	A	125	ALA	0	0.075	0.026	12.865	0.140	0.140	0.000	0.000	0.000	0.000
47	A	126	VAL	0	-0.057	-0.037	15.022	0.119	0.119	0.000	0.000	0.000	0.000
48	A	127	TYR	0	-0.037	-0.037	11.790	0.103	0.103	0.000	0.000	0.000	0.000
49	A	128	PHE	0	0.039	0.024	16.263	0.072	0.072	0.000	0.000	0.000	0.000
50	A	129	CYS	0	0.010	0.035	19.919	0.062	0.062	0.000	0.000	0.000	0.000
51	A	130	ASN	0	0.001	0.014	20.592	0.043	0.043	0.000	0.000	0.000	0.000
52	A	131	ARG	1	0.881	0.919	21.973	0.326	0.326	0.000	0.000	0.000	0.000
53	A	132	ALA	0	0.027	0.019	23.844	0.032	0.032	0.000	0.000	0.000	0.000
54	A	133	ALA	0	-0.031	-0.008	25.644	0.025	0.025	0.000	0.000	0.000	0.000
55	A	134	ALA	0	0.043	0.016	26.411	0.021	0.021	0.000	0.000	0.000	0.000
56	A	135	TYR	0	-0.002	-0.015	26.161	0.017	0.017	0.000	0.000	0.000	0.000
57	A	136	SER	0	-0.044	-0.037	29.821	0.017	0.017	0.000	0.000	0.000	0.000
58	A	137	LYS	1	0.734	0.863	31.292	0.180	0.180	0.000	0.000	0.000	0.000
59	A	138	LEU	0	-0.024	0.004	30.696	0.010	0.010	0.000	0.000	0.000	0.000
60	A	139	GLY	0	0.015	0.019	34.125	0.008	0.008	0.000	0.000	0.000	0.000
61	A	140	ASN	0	-0.020	-0.004	30.549	0.010	0.010	0.000	0.000	0.000	0.000
62	A	141	TYR	0	0.032	-0.005	31.721	-0.011	-0.011	0.000	0.000	0.000	0.000
63	A	142	ALA	0	0.021	0.015	32.058	-0.008	-0.008	0.000	0.000	0.000	0.000
64	A	143	GLY	0	0.029	0.014	29.329	-0.008	-0.008	0.000	0.000	0.000	0.000
65	A	144	ALA	0	-0.006	-0.004	27.627	-0.020	-0.020	0.000	0.000	0.000	0.000
66	A	145	VAL	0	0.029	0.005	27.405	-0.020	-0.020	0.000	0.000	0.000	0.000
67	A	146	GLN	0	0.020	0.024	25.675	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	147	ASP	-1	-0.793	-0.882	23.485	-0.322	-0.322	0.000	0.000	0.000	0.000
69	A	148	CYS	0	-0.065	-0.038	22.765	-0.042	-0.042	0.000	0.000	0.000	0.000
70	A	149	GLU	-1	-0.912	-0.956	23.888	-0.241	-0.241	0.000	0.000	0.000	0.000
71	A	150	ARG	1	0.867	0.940	16.911	0.415	0.415	0.000	0.000	0.000	0.000
72	A	151	ALA	0	-0.031	-0.020	19.109	-0.046	-0.046	0.000	0.000	0.000	0.000
73	A	152	ILE	0	0.000	-0.001	19.267	-0.048	-0.048	0.000	0.000	0.000	0.000
74	A	153	CYS	0	-0.073	-0.045	20.858	0.007	0.007	0.000	0.000	0.000	0.000
75	A	154	ILE	0	-0.086	-0.023	14.341	-0.007	-0.007	0.000	0.000	0.000	0.000
76	A	155	ASP	-1	-0.852	-0.938	16.153	-0.682	-0.682	0.000	0.000	0.000	0.000
77	A	156	PRO	0	0.018	0.004	17.890	0.043	0.043	0.000	0.000	0.000	0.000
78	A	157	ALA	0	0.002	0.025	19.447	0.051	0.051	0.000	0.000	0.000	0.000
79	A	158	TYR	0	0.095	0.034	18.074	0.032	0.032	0.000	0.000	0.000	0.000
80	A	159	SER	0	0.022	0.011	21.131	0.019	0.019	0.000	0.000	0.000	0.000
81	A	160	LYS	1	0.867	0.931	20.065	0.495	0.495	0.000	0.000	0.000	0.000
82	A	161	ALA	0	0.009	-0.001	22.189	0.020	0.020	0.000	0.000	0.000	0.000
83	A	162	TYR	0	-0.020	-0.033	23.798	0.040	0.040	0.000	0.000	0.000	0.000
84	A	163	GLY	0	0.039	0.013	27.287	0.024	0.024	0.000	0.000	0.000	0.000
85	A	164	ARG	1	0.804	0.872	23.270	0.353	0.353	0.000	0.000	0.000	0.000
86	A	165	MET	0	0.030	0.041	27.480	0.020	0.020	0.000	0.000	0.000	0.000
87	A	166	GLY	0	0.044	0.019	29.565	0.017	0.017	0.000	0.000	0.000	0.000
88	A	167	LEU	0	-0.032	-0.002	30.683	0.015	0.015	0.000	0.000	0.000	0.000
89	A	168	ALA	0	0.023	0.026	31.048	0.014	0.014	0.000	0.000	0.000	0.000
90	A	169	LEU	0	0.020	0.000	32.543	0.014	0.014	0.000	0.000	0.000	0.000
91	A	170	SER	0	-0.030	-0.014	35.153	0.014	0.014	0.000	0.000	0.000	0.000
92	A	171	SER	0	-0.062	-0.036	35.945	0.011	0.011	0.000	0.000	0.000	0.000
93	A	172	LEU	0	-0.054	-0.027	34.478	0.008	0.008	0.000	0.000	0.000	0.000
94	A	173	ASN	0	-0.039	-0.030	38.491	0.007	0.007	0.000	0.000	0.000	0.000
95	A	174	LYS	1	0.866	0.938	35.408	0.154	0.154	0.000	0.000	0.000	0.000
96	A	175	HIS	0	0.025	0.006	38.471	-0.012	-0.012	0.000	0.000	0.000	0.000
97	A	176	VAL	0	0.013	0.004	39.624	-0.004	-0.004	0.000	0.000	0.000	0.000
98	A	177	GLU	-1	-0.785	-0.878	34.522	-0.159	-0.159	0.000	0.000	0.000	0.000
99	A	178	ALA	0	0.020	0.008	34.892	-0.011	-0.011	0.000	0.000	0.000	0.000
100	A	179	VAL	0	-0.023	-0.012	35.173	-0.008	-0.008	0.000	0.000	0.000	0.000
101	A	180	ALA	0	-0.017	-0.003	34.881	-0.004	-0.004	0.000	0.000	0.000	0.000
102	A	181	TYR	0	0.037	0.015	28.114	-0.013	-0.013	0.000	0.000	0.000	0.000
103	A	182	TYR	0	-0.020	-0.031	31.064	-0.013	-0.013	0.000	0.000	0.000	0.000
104	A	183	LYS	1	0.838	0.916	32.597	0.131	0.131	0.000	0.000	0.000	0.000
105	A	184	LYS	1	0.876	0.932	26.868	0.251	0.251	0.000	0.000	0.000	0.000
106	A	185	ALA	0	0.005	-0.002	27.961	-0.016	-0.016	0.000	0.000	0.000	0.000
107	A	186	LEU	0	-0.057	-0.029	28.653	-0.009	-0.009	0.000	0.000	0.000	0.000
108	A	187	GLU	-1	-0.891	-0.924	29.068	-0.220	-0.220	0.000	0.000	0.000	0.000
109	A	188	LEU	0	-0.053	-0.018	24.041	-0.006	-0.006	0.000	0.000	0.000	0.000
110	A	189	ASP	-1	-0.852	-0.910	25.955	-0.301	-0.301	0.000	0.000	0.000	0.000
111	A	190	PRO	0	0.036	0.017	27.929	0.011	0.011	0.000	0.000	0.000	0.000
112	A	191	ASP	-1	-0.899	-0.950	30.768	-0.185	-0.185	0.000	0.000	0.000	0.000
113	A	192	ASN	0	-0.025	-0.010	28.189	0.030	0.030	0.000	0.000	0.000	0.000
114	A	193	GLU	-1	-0.779	-0.892	31.764	-0.146	-0.146	0.000	0.000	0.000	0.000
115	A	194	THR	0	-0.029	-0.002	31.497	0.011	0.011	0.000	0.000	0.000	0.000
116	A	195	TYR	0	-0.020	-0.031	27.077	0.007	0.007	0.000	0.000	0.000	0.000
117	A	196	LYS	1	0.811	0.902	33.811	0.168	0.168	0.000	0.000	0.000	0.000
118	A	197	SER	0	-0.012	-0.014	36.968	0.012	0.012	0.000	0.000	0.000	0.000
119	A	198	ASN	0	-0.031	-0.039	35.429	0.012	0.012	0.000	0.000	0.000	0.000
120	A	199	LEU	0	-0.007	0.018	36.801	0.005	0.005	0.000	0.000	0.000	0.000
121	A	200	LYS	1	0.860	0.920	38.422	0.126	0.126	0.000	0.000	0.000	0.000
122	A	201	ILE	0	0.004	0.008	40.041	0.007	0.007	0.000	0.000	0.000	0.000
123	A	202	ALA	0	0.020	0.011	39.202	0.005	0.005	0.000	0.000	0.000	0.000
124	A	203	GLU	-1	-0.798	-0.904	41.269	-0.118	-0.118	0.000	0.000	0.000	0.000
125	A	204	LEU	0	-0.061	-0.027	43.558	0.006	0.006	0.000	0.000	0.000	0.000
126	A	205	LYS	1	0.982	0.994	42.112	0.119	0.119	0.000	0.000	0.000	0.000
127	A	206	LEU	0	-0.054	-0.017	42.912	0.003	0.003	0.000	0.000	0.000	0.000
128	A	207	ARG	1	0.901	0.953	45.718	0.081	0.081	0.000	0.000	0.000	0.000
129	A	208	GLU	-1	-0.923	-0.965	48.148	-0.087	-0.087	0.000	0.000	0.000	0.000
130	A	209	ALA	0	-0.048	-0.008	47.170	0.002	0.002	0.000	0.000	0.000	0.000
131	A	210	PRO	0	-0.030	-0.010	49.333	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:80:GLY)