FMO DATABASE

FMODB ID: MVQMZ

Calculation Name: 1Y9W-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Y9W

Chain ID: A

ChEMBL ID:

UniProt ID: Q81CG1

Base Structure: X-ray

Registration Date: 2023-09-20

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	140
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1208801.670429
FMO2-HF: Nuclear repulsion	1150833.196672
FMO2-HF: Total energy	-57968.473757
FMO2-MP2: Total energy	-58136.751792

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:MET)

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

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.
-5.449	-1.349	0.002	-2.218	-1.884	0.007

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / q_NPA : 0.001

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	MET	0	-0.035	-0.012	3.446	-5.072	-1.004	0.003	-2.213	-1.858	0.007
4	A	4	LYS	1	0.954	0.973	5.453	-0.749	-0.717	-0.001	-0.005	-0.026	0.000
5	A	5	HIS	0	0.011	0.023	9.090	0.224	0.224	0.000	0.000	0.000	0.000
6	A	6	ILE	0	0.002	-0.005	11.830	-0.096	-0.096	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.933	-0.963	15.278	0.259	0.259	0.000	0.000	0.000	0.000
8	A	8	ASN	0	-0.055	-0.031	17.980	-0.029	-0.029	0.000	0.000	0.000	0.000
9	A	9	GLY	0	0.066	0.049	20.762	0.002	0.002	0.000	0.000	0.000	0.000
10	A	10	THR	0	-0.032	-0.037	22.332	-0.011	-0.011	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.995	0.984	24.780	-0.040	-0.040	0.000	0.000	0.000	0.000
12	A	12	ILE	0	0.036	0.004	23.512	-0.004	-0.004	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.809	-0.887	19.731	0.074	0.074	0.000	0.000	0.000	0.000
14	A	14	GLY	0	-0.011	-0.003	23.668	-0.003	-0.003	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.925	-0.967	26.127	0.006	0.006	0.000	0.000	0.000	0.000
16	A	16	TYR	0	-0.014	-0.011	19.672	-0.014	-0.014	0.000	0.000	0.000	0.000
17	A	17	ILE	0	0.006	0.001	21.151	-0.010	-0.010	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.994	1.002	24.739	-0.015	-0.015	0.000	0.000	0.000	0.000
19	A	19	ASN	0	0.029	0.004	27.522	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.796	0.899	21.928	0.057	0.057	0.000	0.000	0.000	0.000
21	A	21	VAL	0	0.022	0.016	25.651	-0.007	-0.007	0.000	0.000	0.000	0.000
22	A	22	ILE	0	0.008	0.009	27.696	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	23	GLN	0	0.060	0.037	24.827	-0.010	-0.010	0.000	0.000	0.000	0.000
24	A	24	TYR	0	0.008	0.008	25.902	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	25	ASN	0	0.047	0.047	27.871	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	26	MET	0	-0.016	-0.012	31.364	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	27	SER	0	-0.129	-0.088	28.654	-0.003	-0.003	0.000	0.000	0.000	0.000
28	A	28	ILE	0	-0.010	0.000	29.407	-0.005	-0.005	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.016	0.007	32.150	0.003	0.003	0.000	0.000	0.000	0.000
30	A	30	THR	0	0.030	0.003	35.761	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.864	-0.965	38.657	-0.034	-0.034	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.988	-0.978	40.627	-0.022	-0.022	0.000	0.000	0.000	0.000
33	A	33	VAL	0	0.020	0.006	39.556	0.002	0.002	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.812	0.910	34.971	0.040	0.040	0.000	0.000	0.000	0.000
35	A	35	GLN	0	0.009	0.033	40.899	0.000	0.000	0.000	0.000	0.000	0.000
36	A	36	PRO	0	-0.042	-0.022	41.845	0.000	0.000	0.000	0.000	0.000	0.000
37	A	37	MET	0	-0.012	-0.016	39.350	0.001	0.001	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.851	-0.916	42.469	-0.007	-0.007	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.955	-0.956	44.280	0.003	0.003	0.000	0.000	0.000	0.000
40	A	40	VAL	0	-0.011	-0.011	46.842	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	41	SER	0	-0.033	-0.025	50.526	0.001	0.001	0.000	0.000	0.000	0.000
42	A	42	LEU	0	0.001	0.013	52.856	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	43	VAL	0	-0.008	-0.014	56.156	0.001	0.001	0.000	0.000	0.000	0.000
44	A	44	VAL	0	0.023	0.024	58.654	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.947	0.952	59.297	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	46	ASN	0	0.034	0.029	63.606	0.000	0.000	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.917	-0.972	65.172	0.002	0.002	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.980	-0.984	65.898	0.005	0.005	0.000	0.000	0.000	0.000
49	A	49	GLY	0	-0.021	-0.001	62.351	0.000	0.000	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.909	0.961	61.371	-0.006	-0.006	0.000	0.000	0.000	0.000
51	A	51	ILE	0	-0.018	-0.019	57.001	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	52	PHE	0	0.021	0.000	60.967	0.001	0.001	0.000	0.000	0.000	0.000
53	A	53	GLY	0	0.038	0.020	59.470	0.000	0.000	0.000	0.000	0.000	0.000
54	A	54	GLY	0	-0.017	-0.007	56.489	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	55	VAL	0	-0.030	-0.008	53.124	0.001	0.001	0.000	0.000	0.000	0.000
56	A	56	THR	0	0.040	0.006	48.443	0.000	0.000	0.000	0.000	0.000	0.000
57	A	57	GLY	0	0.030	0.016	47.822	0.001	0.001	0.000	0.000	0.000	0.000
58	A	58	THR	0	-0.024	0.014	43.440	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	59	MET	0	-0.008	-0.017	45.710	0.000	0.000	0.000	0.000	0.000	0.000
60	A	60	TYR	0	0.070	0.015	39.568	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	61	PHE	0	-0.051	-0.010	36.549	0.001	0.001	0.000	0.000	0.000	0.000
62	A	62	TYR	0	-0.004	0.003	42.563	0.000	0.000	0.000	0.000	0.000	0.000
63	A	63	HIS	0	-0.079	-0.054	42.721	0.002	0.002	0.000	0.000	0.000	0.000
64	A	64	LEU	0	0.060	0.024	46.471	0.000	0.000	0.000	0.000	0.000	0.000
65	A	65	HIS	0	-0.043	-0.009	44.673	0.001	0.001	0.000	0.000	0.000	0.000
66	A	66	ILE	0	-0.031	-0.032	46.752	0.000	0.000	0.000	0.000	0.000	0.000
67	A	67	ASP	-1	-0.879	-0.936	44.914	0.007	0.007	0.000	0.000	0.000	0.000
68	A	68	PHE	0	-0.009	-0.011	45.232	0.002	0.002	0.000	0.000	0.000	0.000
69	A	69	LEU	0	-0.008	0.001	50.313	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	70	TRP	0	-0.029	-0.006	54.068	0.001	0.001	0.000	0.000	0.000	0.000
71	A	71	VAL	0	-0.020	-0.019	56.353	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	72	ASP	-1	-0.870	-0.932	60.088	0.009	0.009	0.000	0.000	0.000	0.000
73	A	73	GLU	-1	-0.898	-0.974	61.890	0.009	0.009	0.000	0.000	0.000	0.000
74	A	74	SER	0	-0.080	-0.024	63.589	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	75	VAL	0	-0.024	-0.011	64.867	0.000	0.000	0.000	0.000	0.000	0.000
76	A	76	ARG	1	0.902	0.956	63.086	-0.008	-0.008	0.000	0.000	0.000	0.000
77	A	77	HIS	0	-0.040	-0.042	65.143	0.000	0.000	0.000	0.000	0.000	0.000
78	A	78	ASP	-1	-0.885	-0.938	67.928	0.004	0.004	0.000	0.000	0.000	0.000
79	A	79	GLY	0	-0.034	-0.005	65.769	0.000	0.000	0.000	0.000	0.000	0.000
80	A	80	TYR	0	0.076	0.026	63.252	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	81	GLY	0	0.041	0.019	60.330	0.000	0.000	0.000	0.000	0.000	0.000
82	A	82	SER	0	-0.066	-0.070	60.177	0.000	0.000	0.000	0.000	0.000	0.000
83	A	83	GLN	0	0.025	0.006	61.894	0.000	0.000	0.000	0.000	0.000	0.000
84	A	84	LEU	0	0.009	0.016	58.112	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	85	LEU	0	-0.032	0.004	55.401	0.000	0.000	0.000	0.000	0.000	0.000
86	A	86	HIS	0	0.015	-0.002	57.834	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.937	-0.972	59.732	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	88	ILE	0	0.005	-0.007	52.082	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	89	GLU	-1	-0.802	-0.894	55.049	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	90	GLY	0	-0.068	-0.029	56.121	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	91	ILE	0	0.039	0.026	53.974	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	92	ALA	0	0.046	0.015	51.969	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	93	LYS	1	0.849	0.916	53.083	0.003	0.003	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.958	-0.972	55.498	-0.009	-0.009	0.000	0.000	0.000	0.000
95	A	95	LYS	1	0.816	0.909	51.014	0.006	0.006	0.000	0.000	0.000	0.000
96	A	96	GLY	0	0.007	0.011	50.815	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	97	CYS	0	-0.086	-0.017	49.688	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	98	ARG	1	0.970	0.974	45.873	0.012	0.012	0.000	0.000	0.000	0.000
99	A	99	LEU	0	-0.093	-0.041	46.284	0.000	0.000	0.000	0.000	0.000	0.000
100	A	100	ILE	0	0.015	0.027	49.521	0.000	0.000	0.000	0.000	0.000	0.000
101	A	101	LEU	0	-0.034	-0.031	44.037	0.000	0.000	0.000	0.000	0.000	0.000
102	A	102	LEU	0	0.050	0.042	47.507	0.000	0.000	0.000	0.000	0.000	0.000
103	A	103	ASP	-1	-0.887	-0.934	44.998	0.013	0.013	0.000	0.000	0.000	0.000
104	A	104	SER	0	0.018	0.004	47.854	0.000	0.000	0.000	0.000	0.000	0.000
105	A	105	PHE	0	0.029	0.006	44.211	0.000	0.000	0.000	0.000	0.000	0.000
106	A	106	SER	0	0.037	0.019	50.033	-0.001	-0.001	0.000	0.000	0.000	0.000
107	A	107	PHE	0	-0.093	-0.053	48.577	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	108	GLN	0	-0.002	-0.009	49.406	0.000	0.000	0.000	0.000	0.000	0.000
109	A	109	ALA	0	0.028	0.025	54.187	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	110	PRO	0	0.068	0.034	53.312	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	111	GLU	-1	-0.884	-0.958	55.259	0.008	0.008	0.000	0.000	0.000	0.000
112	A	112	PHE	0	-0.007	0.002	57.172	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	113	TYR	0	0.086	0.041	53.926	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	114	LYS	1	0.960	1.007	56.878	-0.005	-0.005	0.000	0.000	0.000	0.000
115	A	115	LYS	1	0.882	0.937	58.025	-0.004	-0.004	0.000	0.000	0.000	0.000
116	A	116	HIS	0	-0.042	0.001	58.855	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	117	GLY	0	0.011	0.009	59.107	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	118	TYR	0	-0.044	-0.028	52.557	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	119	ARG	1	0.867	0.928	49.526	0.000	0.000	0.000	0.000	0.000	0.000
120	A	120	GLU	-1	-0.887	-0.946	50.678	0.008	0.008	0.000	0.000	0.000	0.000
121	A	121	TYR	0	-0.097	-0.061	43.518	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	122	GLY	0	0.019	0.003	45.946	0.000	0.000	0.000	0.000	0.000	0.000
123	A	123	VAL	0	0.018	0.017	46.431	0.000	0.000	0.000	0.000	0.000	0.000
124	A	124	VAL	0	-0.044	0.001	42.289	0.001	0.001	0.000	0.000	0.000	0.000
125	A	125	GLU	-1	-0.909	-0.981	44.947	0.015	0.015	0.000	0.000	0.000	0.000
126	A	126	ASP	-1	-0.889	-0.941	45.487	0.026	0.026	0.000	0.000	0.000	0.000
127	A	127	HIS	0	-0.004	0.007	41.332	0.004	0.004	0.000	0.000	0.000	0.000
128	A	128	PRO	0	0.018	-0.014	44.408	-0.002	-0.002	0.000	0.000	0.000	0.000
129	A	129	LYS	1	0.977	0.985	45.196	-0.030	-0.030	0.000	0.000	0.000	0.000
130	A	130	GLY	0	-0.074	-0.042	46.856	0.000	0.000	0.000	0.000	0.000	0.000
131	A	131	HIS	1	0.808	0.902	49.093	-0.022	-0.022	0.000	0.000	0.000	0.000
132	A	132	SER	0	0.050	0.043	48.021	0.001	0.001	0.000	0.000	0.000	0.000
133	A	133	GLN	0	-0.030	-0.002	43.310	0.001	0.001	0.000	0.000	0.000	0.000
134	A	134	HIS	0	0.003	0.005	47.362	0.001	0.001	0.000	0.000	0.000	0.000
135	A	135	PHE	0	0.025	0.018	42.666	0.000	0.000	0.000	0.000	0.000	0.000
136	A	136	PHE	0	0.006	-0.008	47.679	-0.001	-0.001	0.000	0.000	0.000	0.000
137	A	137	GLU	-1	-0.825	-0.926	48.781	-0.002	-0.002	0.000	0.000	0.000	0.000
138	A	138	LYS	1	0.836	0.921	50.590	0.000	0.000	0.000	0.000	0.000	0.000
139	A	139	ARG	1	0.841	0.934	47.221	0.005	0.005	0.000	0.000	0.000	0.000
140	A	140	LEU	0	-0.005	-0.008	52.853	0.000	0.000	0.000	0.000	0.000	0.000

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