FMO DATABASE

FMODB ID: R8578

Calculation Name: 1YVI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YVI

Chain ID: A

ChEMBL ID:

UniProt ID: Q6VAK4

Base Structure: X-ray

Registration Date: 2023-09-21

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	143
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1272886.335936
FMO2-HF: Nuclear repulsion	1215321.755004
FMO2-HF: Total energy	-57564.580932
FMO2-MP2: Total energy	-57727.736265

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:SER)

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

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.
-10.754	-6.079	4.865	-3.983	-5.557	0.025

Interaction energy analysis for fragmet #1(A:1:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.037 / q_NPA : 0.018

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	ALA	0	0.056	0.027	2.990	-2.055	0.886	0.164	-1.480	-1.625	0.007
4	A	4	ALA	0	-0.041	-0.031	2.159	-6.586	-5.611	4.678	-2.303	-3.350	0.017
5	A	5	ALA	0	0.064	0.037	3.637	-0.660	-0.056	0.024	-0.188	-0.440	0.001
6	A	6	LEU	0	0.017	0.014	5.410	0.520	0.520	0.000	0.000	0.000	0.000
7	A	7	ARG	1	0.998	0.996	4.254	-2.214	-2.059	-0.001	-0.012	-0.142	0.000
8	A	8	ASP	-1	-0.898	-0.929	7.048	-1.278	-1.278	0.000	0.000	0.000	0.000
9	A	9	GLN	0	-0.039	-0.027	9.422	-0.018	-0.018	0.000	0.000	0.000	0.000
10	A	10	LEU	0	0.017	0.014	11.516	0.058	0.058	0.000	0.000	0.000	0.000
11	A	11	THR	0	-0.006	-0.013	11.625	0.057	0.057	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.031	-0.012	13.411	0.032	0.032	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.021	0.000	15.261	0.036	0.036	0.000	0.000	0.000	0.000
14	A	14	LEU	0	0.073	0.029	15.933	0.021	0.021	0.000	0.000	0.000	0.000
15	A	15	SER	0	-0.006	0.005	17.942	0.023	0.023	0.000	0.000	0.000	0.000
16	A	16	SER	0	-0.057	-0.028	19.516	0.013	0.013	0.000	0.000	0.000	0.000
17	A	17	MET	0	0.003	0.004	21.434	0.010	0.010	0.000	0.000	0.000	0.000
18	A	18	PHE	0	0.012	0.016	21.167	0.010	0.010	0.000	0.000	0.000	0.000
19	A	19	SER	0	-0.076	-0.051	22.774	0.000	0.000	0.000	0.000	0.000	0.000
20	A	20	GLN	0	-0.062	-0.038	23.755	0.010	0.010	0.000	0.000	0.000	0.000
21	A	21	GLY	0	0.003	0.011	27.266	0.005	0.005	0.000	0.000	0.000	0.000
22	A	22	LEU	0	-0.044	-0.015	25.638	0.009	0.009	0.000	0.000	0.000	0.000
23	A	23	VAL	0	-0.027	-0.014	24.495	0.008	0.008	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.816	-0.916	27.925	-0.012	-0.012	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.918	-0.979	27.601	0.010	0.010	0.000	0.000	0.000	0.000
26	A	26	GLN	0	-0.018	-0.010	27.952	0.007	0.007	0.000	0.000	0.000	0.000
27	A	27	PHE	0	0.027	0.015	21.534	0.008	0.008	0.000	0.000	0.000	0.000
28	A	28	GLN	0	-0.003	-0.008	23.330	0.019	0.019	0.000	0.000	0.000	0.000
29	A	29	GLN	0	0.031	0.006	23.886	0.019	0.019	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.005	0.016	24.596	0.012	0.012	0.000	0.000	0.000	0.000
31	A	31	GLN	0	-0.016	-0.017	18.135	0.000	0.000	0.000	0.000	0.000	0.000
32	A	32	MET	0	-0.006	0.006	21.194	0.028	0.028	0.000	0.000	0.000	0.000
33	A	33	LEU	0	0.028	0.010	23.543	0.012	0.012	0.000	0.000	0.000	0.000
34	A	34	GLN	0	0.004	0.020	17.531	-0.019	-0.019	0.000	0.000	0.000	0.000
35	A	35	ASP	-1	-0.926	-0.925	18.499	0.269	0.269	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-1.064	-1.051	21.203	0.120	0.120	0.000	0.000	0.000	0.000
37	A	37	GLY	0	-0.082	-0.051	25.087	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	38	GLY	0	-0.009	0.003	22.397	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	39	THR	0	-0.046	-0.023	21.613	0.029	0.029	0.000	0.000	0.000	0.000
40	A	40	PRO	0	0.042	-0.001	17.409	-0.009	-0.009	0.000	0.000	0.000	0.000
41	A	41	GLY	0	0.063	0.045	18.043	0.013	0.013	0.000	0.000	0.000	0.000
42	A	42	PHE	0	-0.035	-0.021	19.911	-0.034	-0.034	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.043	0.005	20.234	-0.024	-0.024	0.000	0.000	0.000	0.000
44	A	44	SER	0	-0.022	-0.041	18.885	-0.028	-0.028	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.927	-0.955	21.568	0.074	0.074	0.000	0.000	0.000	0.000
46	A	46	VAL	0	-0.034	-0.002	24.840	-0.016	-0.016	0.000	0.000	0.000	0.000
47	A	47	VAL	0	-0.027	-0.014	23.320	-0.013	-0.013	0.000	0.000	0.000	0.000
48	A	48	THR	0	0.007	0.001	24.281	-0.017	-0.017	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.031	0.023	26.733	-0.008	-0.008	0.000	0.000	0.000	0.000
50	A	50	PHE	0	0.011	0.006	29.019	-0.008	-0.008	0.000	0.000	0.000	0.000
51	A	51	CYS	0	-0.104	-0.063	27.570	-0.011	-0.011	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.884	-0.939	30.417	0.004	0.004	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.837	-0.919	32.739	0.015	0.015	0.000	0.000	0.000	0.000
54	A	54	ALA	0	-0.053	-0.027	33.599	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	55	ASP	-1	-0.847	-0.932	34.109	-0.027	-0.027	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.870	0.922	36.036	-0.011	-0.011	0.000	0.000	0.000	0.000
57	A	57	ILE	0	-0.036	-0.029	38.140	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	58	ILE	0	-0.003	-0.003	36.620	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	59	ASN	0	-0.023	-0.008	38.696	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.850	-0.883	42.132	0.000	0.000	0.000	0.000	0.000	0.000
61	A	61	ILE	0	-0.032	-0.025	42.432	0.000	0.000	0.000	0.000	0.000	0.000
62	A	62	ALA	0	-0.018	-0.017	44.215	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	63	THR	0	0.048	0.028	46.120	0.000	0.000	0.000	0.000	0.000	0.000
64	A	64	LEU	0	-0.058	-0.024	48.378	0.001	0.001	0.000	0.000	0.000	0.000
65	A	65	LEU	0	-0.050	-0.032	47.467	0.000	0.000	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.922	-0.949	47.960	-0.020	-0.020	0.000	0.000	0.000	0.000
67	A	67	GLN	0	-0.087	-0.028	52.087	0.001	0.001	0.000	0.000	0.000	0.000
68	A	68	PRO	0	0.023	0.009	55.150	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	69	VAL	0	-0.008	-0.002	58.587	0.000	0.000	0.000	0.000	0.000	0.000
70	A	70	VAL	0	0.013	0.020	53.063	0.001	0.001	0.000	0.000	0.000	0.000
71	A	71	ASN	0	-0.002	-0.001	53.854	0.001	0.001	0.000	0.000	0.000	0.000
72	A	72	PHE	0	0.066	-0.001	52.864	0.000	0.000	0.000	0.000	0.000	0.000
73	A	73	ASP	-1	-0.863	-0.929	52.150	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	74	LYS	1	0.903	0.964	48.583	0.000	0.000	0.000	0.000	0.000	0.000
75	A	75	VAL	0	0.025	0.009	47.805	0.000	0.000	0.000	0.000	0.000	0.000
76	A	76	ASP	-1	-0.781	-0.864	47.116	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	77	ALA	0	-0.017	-0.014	46.858	0.001	0.001	0.000	0.000	0.000	0.000
78	A	78	TYR	0	-0.037	-0.066	44.026	0.002	0.002	0.000	0.000	0.000	0.000
79	A	79	VAL	0	0.033	0.024	42.658	0.000	0.000	0.000	0.000	0.000	0.000
80	A	80	HIS	0	-0.019	-0.011	42.140	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	81	GLN	0	-0.009	-0.013	40.862	0.001	0.001	0.000	0.000	0.000	0.000
82	A	82	LEU	0	0.020	0.030	36.182	0.002	0.002	0.000	0.000	0.000	0.000
83	A	83	LYS	1	0.928	0.983	37.348	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	84	GLY	0	-0.028	-0.015	37.618	0.000	0.000	0.000	0.000	0.000	0.000
85	A	85	SER	0	0.061	0.021	34.562	0.002	0.002	0.000	0.000	0.000	0.000
86	A	86	SER	0	0.010	-0.012	33.183	0.001	0.001	0.000	0.000	0.000	0.000
87	A	87	ALA	0	-0.051	-0.036	32.710	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	88	SER	0	-0.055	-0.027	32.736	0.002	0.002	0.000	0.000	0.000	0.000
89	A	89	VAL	0	-0.001	0.004	28.195	0.006	0.006	0.000	0.000	0.000	0.000
90	A	90	GLY	0	0.044	0.032	28.002	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	91	ALA	0	0.015	0.021	29.884	-0.009	-0.009	0.000	0.000	0.000	0.000
92	A	92	GLN	0	-0.045	-0.056	31.090	0.005	0.005	0.000	0.000	0.000	0.000
93	A	93	LYS	1	0.882	0.939	31.690	0.064	0.064	0.000	0.000	0.000	0.000
94	A	94	VAL	0	0.072	0.044	33.357	0.001	0.001	0.000	0.000	0.000	0.000
95	A	95	LYS	1	0.879	0.964	34.309	0.013	0.013	0.000	0.000	0.000	0.000
96	A	96	PHE	0	-0.015	-0.039	35.649	0.003	0.003	0.000	0.000	0.000	0.000
97	A	97	THR	0	0.019	0.013	38.433	0.002	0.002	0.000	0.000	0.000	0.000
98	A	98	CYS	0	-0.048	-0.033	39.143	0.002	0.002	0.000	0.000	0.000	0.000
99	A	99	MET	0	-0.068	-0.033	41.429	0.002	0.002	0.000	0.000	0.000	0.000
100	A	100	GLN	0	-0.006	0.012	43.674	0.000	0.000	0.000	0.000	0.000	0.000
101	A	101	PHE	0	0.007	-0.002	43.422	0.001	0.001	0.000	0.000	0.000	0.000
102	A	102	ARG	1	0.846	0.882	46.259	0.005	0.005	0.000	0.000	0.000	0.000
103	A	103	GLN	0	-0.065	-0.028	48.708	0.001	0.001	0.000	0.000	0.000	0.000
104	A	104	PHE	0	0.060	0.028	47.209	0.000	0.000	0.000	0.000	0.000	0.000
105	A	105	CYS	0	-0.060	-0.011	49.314	0.000	0.000	0.000	0.000	0.000	0.000
106	A	106	GLN	0	-0.020	-0.003	52.449	0.000	0.000	0.000	0.000	0.000	0.000
107	A	107	ASP	-1	-0.888	-0.942	54.485	-0.015	-0.015	0.000	0.000	0.000	0.000
108	A	108	LYS	1	0.813	0.916	55.624	0.006	0.006	0.000	0.000	0.000	0.000
109	A	109	SER	0	0.052	0.039	54.020	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	110	ARG	1	0.867	0.907	52.921	0.015	0.015	0.000	0.000	0.000	0.000
111	A	111	ASP	-1	-0.877	-0.945	51.603	-0.023	-0.023	0.000	0.000	0.000	0.000
112	A	112	GLY	0	0.034	0.020	50.629	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	113	CYS	0	-0.023	-0.010	48.442	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	114	LEU	0	-0.011	-0.001	46.962	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	115	MET	0	-0.035	-0.014	46.081	-0.002	-0.002	0.000	0.000	0.000	0.000
116	A	116	ALA	0	0.023	0.007	44.619	-0.003	-0.003	0.000	0.000	0.000	0.000
117	A	117	LEU	0	-0.009	-0.004	41.902	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	118	ALA	0	-0.017	-0.008	41.305	-0.002	-0.002	0.000	0.000	0.000	0.000
119	A	119	VAL	0	0.012	0.011	39.443	-0.004	-0.004	0.000	0.000	0.000	0.000
120	A	120	VAL	0	0.018	0.003	38.168	-0.002	-0.002	0.000	0.000	0.000	0.000
121	A	121	ARG	1	0.930	0.980	36.754	0.029	0.029	0.000	0.000	0.000	0.000
122	A	122	ASN	0	-0.026	-0.009	35.380	-0.004	-0.004	0.000	0.000	0.000	0.000
123	A	123	ASP	-1	-0.797	-0.901	33.707	-0.053	-0.053	0.000	0.000	0.000	0.000
124	A	124	PHE	0	-0.046	-0.014	31.541	-0.003	-0.003	0.000	0.000	0.000	0.000
125	A	125	TYR	0	-0.036	-0.037	31.088	-0.003	-0.003	0.000	0.000	0.000	0.000
126	A	126	ASP	-1	-0.877	-0.929	28.947	-0.098	-0.098	0.000	0.000	0.000	0.000
127	A	127	LEU	0	0.027	0.017	26.149	-0.010	-0.010	0.000	0.000	0.000	0.000
128	A	128	ARG	1	0.922	0.959	26.378	0.033	0.033	0.000	0.000	0.000	0.000
129	A	129	ASN	0	-0.020	-0.010	24.390	-0.006	-0.006	0.000	0.000	0.000	0.000
130	A	130	LYS	1	0.855	0.931	22.536	0.107	0.107	0.000	0.000	0.000	0.000
131	A	131	PHE	0	0.071	0.016	21.549	-0.003	-0.003	0.000	0.000	0.000	0.000
132	A	132	GLN	0	0.026	0.024	21.840	0.015	0.015	0.000	0.000	0.000	0.000
133	A	133	THR	0	-0.023	-0.011	17.824	-0.005	-0.005	0.000	0.000	0.000	0.000
134	A	134	MET	0	-0.003	-0.005	17.483	-0.015	-0.015	0.000	0.000	0.000	0.000
135	A	135	LEU	0	0.011	0.020	17.009	0.025	0.025	0.000	0.000	0.000	0.000
136	A	136	GLN	0	-0.009	0.016	16.732	0.035	0.035	0.000	0.000	0.000	0.000
137	A	137	LEU	0	-0.017	-0.024	12.428	0.003	0.003	0.000	0.000	0.000	0.000
138	A	138	GLU	-1	-0.821	-0.904	12.872	0.257	0.257	0.000	0.000	0.000	0.000
139	A	139	GLN	0	-0.064	-0.029	14.018	0.072	0.072	0.000	0.000	0.000	0.000
140	A	140	GLN	0	-0.049	-0.032	11.076	0.025	0.025	0.000	0.000	0.000	0.000
141	A	141	ILE	0	-0.068	-0.027	8.953	0.154	0.154	0.000	0.000	0.000	0.000
142	A	142	GLN	0	-0.033	-0.028	10.347	0.191	0.191	0.000	0.000	0.000	0.000
143	A	143	ALA	0	-0.065	-0.007	10.364	0.067	0.067	0.000	0.000	0.000	0.000

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