FMO DATABASE

FMODB ID: L7JN9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1088929.359634
FMO2-HF: Nuclear repulsion	1037905.426552
FMO2-HF: Total energy	-51023.933082
FMO2-MP2: Total energy	-51171.742493

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.
-0.928	2.06	0.347	-1.602	-1.734	-0.006

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 : 0.011 / 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	82	LEU	0	-0.028	0.018	3.382	0.344	1.581	0.010	-0.547	-0.700	-0.001
4	A	83	GLY	0	0.009	-0.010	3.533	-1.778	-1.033	0.080	-0.359	-0.467	0.001
5	A	84	SER	0	-0.101	-0.103	3.018	-1.817	-0.811	0.257	-0.696	-0.567	-0.006
6	A	85	GLU	-1	-0.804	-0.922	5.609	0.047	0.047	0.000	0.000	0.000	0.000
7	A	86	GLU	-1	-0.841	-0.868	6.555	3.167	3.167	0.000	0.000	0.000	0.000
8	A	87	ASP	-1	-0.840	-0.931	10.869	0.392	0.392	0.000	0.000	0.000	0.000
9	A	88	SER	0	-0.016	-0.018	7.013	-0.381	-0.381	0.000	0.000	0.000	0.000
10	A	89	ALA	0	-0.031	0.024	8.841	-0.237	-0.237	0.000	0.000	0.000	0.000
11	A	90	GLU	-1	-0.818	-0.911	9.869	0.093	0.093	0.000	0.000	0.000	0.000
12	A	91	ALA	0	-0.017	-0.004	11.576	-0.092	-0.092	0.000	0.000	0.000	0.000
13	A	92	GLU	-1	-0.760	-0.851	10.085	-0.497	-0.497	0.000	0.000	0.000	0.000
14	A	93	ARG	1	0.781	0.881	12.602	-0.431	-0.431	0.000	0.000	0.000	0.000
15	A	94	LEU	0	0.034	0.023	15.513	-0.030	-0.030	0.000	0.000	0.000	0.000
16	A	95	LYS	1	0.872	0.939	14.098	0.258	0.258	0.000	0.000	0.000	0.000
17	A	96	THR	0	-0.120	-0.070	15.650	-0.033	-0.033	0.000	0.000	0.000	0.000
18	A	97	GLU	-1	-0.820	-0.895	18.223	0.002	0.002	0.000	0.000	0.000	0.000
19	A	98	GLY	0	0.038	0.006	20.595	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	99	ASN	0	-0.029	0.007	18.719	-0.006	-0.006	0.000	0.000	0.000	0.000
21	A	100	GLU	-1	-0.906	-0.949	22.111	-0.056	-0.056	0.000	0.000	0.000	0.000
22	A	101	GLN	0	-0.059	-0.041	24.486	0.001	0.001	0.000	0.000	0.000	0.000
23	A	102	MET	0	-0.074	-0.023	24.744	0.002	0.002	0.000	0.000	0.000	0.000
24	A	103	LYS	1	0.861	0.940	23.232	0.086	0.086	0.000	0.000	0.000	0.000
25	A	104	VAL	0	-0.039	-0.003	28.473	0.002	0.002	0.000	0.000	0.000	0.000
26	A	105	GLU	-1	-0.968	-0.997	30.666	-0.045	-0.045	0.000	0.000	0.000	0.000
27	A	106	ASN	0	0.030	0.043	29.965	0.002	0.002	0.000	0.000	0.000	0.000
28	A	107	PHE	0	0.057	-0.018	28.995	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	108	GLU	-1	-0.861	-0.933	28.654	-0.037	-0.037	0.000	0.000	0.000	0.000
30	A	109	ALA	0	0.004	0.007	27.865	0.002	0.002	0.000	0.000	0.000	0.000
31	A	110	ALA	0	-0.007	-0.008	24.879	0.002	0.002	0.000	0.000	0.000	0.000
32	A	111	VAL	0	-0.038	-0.021	23.790	-0.008	-0.008	0.000	0.000	0.000	0.000
33	A	112	HIS	0	-0.030	-0.004	24.107	0.004	0.004	0.000	0.000	0.000	0.000
34	A	113	PHE	0	0.015	0.000	21.153	0.008	0.008	0.000	0.000	0.000	0.000
35	A	114	TYR	0	-0.015	-0.065	19.116	0.000	0.000	0.000	0.000	0.000	0.000
36	A	115	GLY	0	-0.011	-0.008	19.037	-0.011	-0.011	0.000	0.000	0.000	0.000
37	A	116	LYS	1	0.886	0.952	19.713	-0.042	-0.042	0.000	0.000	0.000	0.000
38	A	117	ALA	0	0.012	0.009	15.288	0.025	0.025	0.000	0.000	0.000	0.000
39	A	118	ILE	0	-0.074	-0.043	14.782	-0.005	-0.005	0.000	0.000	0.000	0.000
40	A	119	GLU	-1	-0.939	-0.970	16.111	0.044	0.044	0.000	0.000	0.000	0.000
41	A	120	LEU	0	-0.021	0.009	13.401	0.013	0.013	0.000	0.000	0.000	0.000
42	A	121	ASN	0	0.056	0.020	8.685	0.058	0.058	0.000	0.000	0.000	0.000
43	A	122	PRO	0	-0.025	-0.013	11.998	-0.096	-0.096	0.000	0.000	0.000	0.000
44	A	123	ALA	0	-0.017	-0.003	9.905	-0.013	-0.013	0.000	0.000	0.000	0.000
45	A	124	ASN	0	0.036	0.026	10.716	-0.152	-0.152	0.000	0.000	0.000	0.000
46	A	125	ALA	0	0.073	0.025	12.270	0.104	0.104	0.000	0.000	0.000	0.000
47	A	126	VAL	0	-0.029	-0.017	14.400	0.083	0.083	0.000	0.000	0.000	0.000
48	A	127	TYR	0	-0.036	-0.060	11.906	0.061	0.061	0.000	0.000	0.000	0.000
49	A	128	PHE	0	-0.003	0.016	15.905	0.049	0.049	0.000	0.000	0.000	0.000
50	A	129	CYS	0	0.000	0.029	19.265	0.037	0.037	0.000	0.000	0.000	0.000
51	A	130	ASN	0	-0.042	-0.026	19.355	0.006	0.006	0.000	0.000	0.000	0.000
52	A	131	ARG	1	0.885	0.932	21.375	0.115	0.115	0.000	0.000	0.000	0.000
53	A	132	ALA	0	0.015	0.020	23.295	0.016	0.016	0.000	0.000	0.000	0.000
54	A	133	ALA	0	-0.047	-0.029	24.839	0.012	0.012	0.000	0.000	0.000	0.000
55	A	134	ALA	0	0.037	0.013	25.922	0.010	0.010	0.000	0.000	0.000	0.000
56	A	135	TYR	0	-0.009	-0.016	25.858	0.011	0.011	0.000	0.000	0.000	0.000
57	A	136	SER	0	-0.016	-0.021	29.240	0.007	0.007	0.000	0.000	0.000	0.000
58	A	137	LYS	1	0.855	0.954	30.551	0.086	0.086	0.000	0.000	0.000	0.000
59	A	138	LEU	0	0.001	0.007	30.490	0.005	0.005	0.000	0.000	0.000	0.000
60	A	139	GLY	0	0.009	0.022	33.728	0.005	0.005	0.000	0.000	0.000	0.000
61	A	140	ASN	0	-0.021	-0.002	30.855	0.000	0.000	0.000	0.000	0.000	0.000
62	A	141	TYR	0	0.050	0.000	31.310	-0.006	-0.006	0.000	0.000	0.000	0.000
63	A	142	ALA	0	0.024	0.015	31.317	-0.008	-0.008	0.000	0.000	0.000	0.000
64	A	143	GLY	0	0.019	0.009	29.162	-0.006	-0.006	0.000	0.000	0.000	0.000
65	A	144	ALA	0	0.001	-0.005	27.164	-0.010	-0.010	0.000	0.000	0.000	0.000
66	A	145	VAL	0	0.021	0.000	26.690	-0.015	-0.015	0.000	0.000	0.000	0.000
67	A	146	GLN	0	0.043	0.026	25.355	-0.008	-0.008	0.000	0.000	0.000	0.000
68	A	147	ASP	-1	-0.776	-0.875	22.711	-0.136	-0.136	0.000	0.000	0.000	0.000
69	A	148	CYS	0	-0.075	-0.046	22.044	-0.028	-0.028	0.000	0.000	0.000	0.000
70	A	149	GLU	-1	-0.905	-0.944	23.057	-0.154	-0.154	0.000	0.000	0.000	0.000
71	A	150	ARG	1	0.953	0.984	17.556	0.156	0.156	0.000	0.000	0.000	0.000
72	A	151	ALA	0	-0.032	-0.029	18.298	-0.035	-0.035	0.000	0.000	0.000	0.000
73	A	152	ILE	0	-0.003	0.003	18.525	-0.044	-0.044	0.000	0.000	0.000	0.000
74	A	153	CYS	0	-0.045	-0.026	20.193	-0.011	-0.011	0.000	0.000	0.000	0.000
75	A	154	ILE	0	-0.091	-0.027	13.852	-0.016	-0.016	0.000	0.000	0.000	0.000
76	A	155	ASP	-1	-0.878	-0.949	15.222	-0.600	-0.600	0.000	0.000	0.000	0.000
77	A	156	PRO	0	0.014	0.005	16.931	0.039	0.039	0.000	0.000	0.000	0.000
78	A	157	ALA	0	0.002	0.011	18.761	0.044	0.044	0.000	0.000	0.000	0.000
79	A	158	TYR	0	0.049	0.021	18.206	0.009	0.009	0.000	0.000	0.000	0.000
80	A	159	SER	0	0.029	0.002	20.008	0.029	0.029	0.000	0.000	0.000	0.000
81	A	160	LYS	1	0.913	0.952	20.160	0.290	0.290	0.000	0.000	0.000	0.000
82	A	161	ALA	0	0.001	-0.002	21.227	0.023	0.023	0.000	0.000	0.000	0.000
83	A	162	TYR	0	-0.015	-0.015	22.921	0.033	0.033	0.000	0.000	0.000	0.000
84	A	163	GLY	0	0.039	0.015	26.257	0.018	0.018	0.000	0.000	0.000	0.000
85	A	164	ARG	1	0.823	0.885	22.354	0.197	0.197	0.000	0.000	0.000	0.000
86	A	165	MET	0	0.030	0.041	26.720	0.017	0.017	0.000	0.000	0.000	0.000
87	A	166	GLY	0	0.023	0.009	28.691	0.012	0.012	0.000	0.000	0.000	0.000
88	A	167	LEU	0	-0.038	-0.021	30.221	0.010	0.010	0.000	0.000	0.000	0.000
89	A	168	ALA	0	0.001	0.013	30.503	0.010	0.010	0.000	0.000	0.000	0.000
90	A	169	LEU	0	0.040	0.005	31.630	0.010	0.010	0.000	0.000	0.000	0.000
91	A	170	SER	0	-0.031	-0.004	34.369	0.009	0.009	0.000	0.000	0.000	0.000
92	A	171	SER	0	-0.049	-0.019	35.540	0.007	0.007	0.000	0.000	0.000	0.000
93	A	172	LEU	0	-0.067	-0.020	34.214	0.006	0.006	0.000	0.000	0.000	0.000
94	A	173	ASN	0	-0.057	-0.039	38.090	0.003	0.003	0.000	0.000	0.000	0.000
95	A	174	LYS	1	0.955	0.993	35.916	0.081	0.081	0.000	0.000	0.000	0.000
96	A	175	HIS	0	0.077	0.013	37.396	-0.010	-0.010	0.000	0.000	0.000	0.000
97	A	176	VAL	0	0.011	0.015	38.700	-0.004	-0.004	0.000	0.000	0.000	0.000
98	A	177	GLU	-1	-0.909	-0.966	33.017	-0.109	-0.109	0.000	0.000	0.000	0.000
99	A	178	ALA	0	0.005	0.011	34.010	-0.008	-0.008	0.000	0.000	0.000	0.000
100	A	179	VAL	0	-0.005	-0.001	34.085	-0.008	-0.008	0.000	0.000	0.000	0.000
101	A	180	ALA	0	-0.037	-0.013	33.919	-0.006	-0.006	0.000	0.000	0.000	0.000
102	A	181	TYR	0	0.044	0.016	27.219	-0.014	-0.014	0.000	0.000	0.000	0.000
103	A	182	TYR	0	0.020	0.002	30.127	-0.009	-0.009	0.000	0.000	0.000	0.000
104	A	183	LYS	1	0.939	0.972	31.715	0.098	0.098	0.000	0.000	0.000	0.000
105	A	184	LYS	1	0.921	0.975	25.780	0.212	0.212	0.000	0.000	0.000	0.000
106	A	185	ALA	0	0.025	-0.007	27.089	-0.013	-0.013	0.000	0.000	0.000	0.000
107	A	186	LEU	0	-0.044	-0.025	27.913	-0.008	-0.008	0.000	0.000	0.000	0.000
108	A	187	GLU	-1	-0.922	-0.943	28.452	-0.177	-0.177	0.000	0.000	0.000	0.000
109	A	188	LEU	0	-0.077	-0.028	23.495	-0.009	-0.009	0.000	0.000	0.000	0.000
110	A	189	ASP	-1	-0.909	-0.958	25.510	-0.218	-0.218	0.000	0.000	0.000	0.000
111	A	190	PRO	0	-0.026	-0.016	27.251	0.013	0.013	0.000	0.000	0.000	0.000
112	A	191	ASP	-1	-0.901	-0.945	29.592	-0.149	-0.149	0.000	0.000	0.000	0.000
113	A	192	ASN	0	-0.055	-0.035	27.761	0.027	0.027	0.000	0.000	0.000	0.000
114	A	193	GLU	-1	-0.791	-0.904	31.060	-0.096	-0.096	0.000	0.000	0.000	0.000
115	A	194	THR	0	-0.014	-0.002	31.243	0.011	0.011	0.000	0.000	0.000	0.000
116	A	195	TYR	0	0.007	-0.003	25.937	0.010	0.010	0.000	0.000	0.000	0.000
117	A	196	LYS	1	0.909	0.956	32.924	0.115	0.115	0.000	0.000	0.000	0.000
118	A	197	SER	0	0.006	0.006	36.173	0.008	0.008	0.000	0.000	0.000	0.000
119	A	198	ASN	0	-0.029	-0.036	34.512	0.010	0.010	0.000	0.000	0.000	0.000
120	A	199	LEU	0	-0.003	0.025	35.775	0.003	0.003	0.000	0.000	0.000	0.000
121	A	200	LYS	1	0.931	0.971	37.336	0.091	0.091	0.000	0.000	0.000	0.000
122	A	201	ILE	0	0.001	0.000	39.226	0.005	0.005	0.000	0.000	0.000	0.000
123	A	202	ALA	0	-0.001	0.003	38.078	0.004	0.004	0.000	0.000	0.000	0.000
124	A	203	GLU	-1	-0.919	-0.987	40.184	-0.084	-0.084	0.000	0.000	0.000	0.000
125	A	204	LEU	0	-0.072	-0.035	42.477	0.004	0.004	0.000	0.000	0.000	0.000
126	A	205	LYS	1	0.978	0.981	41.588	0.067	0.067	0.000	0.000	0.000	0.000
127	A	206	LEU	0	-0.042	-0.003	41.821	0.002	0.002	0.000	0.000	0.000	0.000
128	A	207	ARG	1	0.898	0.953	44.730	0.053	0.053	0.000	0.000	0.000	0.000
129	A	208	GLU	-1	-0.936	-0.973	47.396	-0.051	-0.051	0.000	0.000	0.000	0.000
130	A	209	ALA	0	-0.040	-0.003	46.700	0.002	0.002	0.000	0.000	0.000	0.000
131	A	210	PRO	0	-0.017	-0.004	48.780	-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)