FMO DATABASE

FMODB ID: 89NYY

Calculation Name: 1YUD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YUD

Chain ID: A

ChEMBL ID:

UniProt ID: Q8EIN8

Base Structure: X-ray

Registration Date: 2023-09-22

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	158
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1575423.529973
FMO2-HF: Nuclear repulsion	1511663.468723
FMO2-HF: Total energy	-63760.06125
FMO2-MP2: Total energy	-63943.430853

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.
-6.285	-3.572	1.348	-1.721	-2.339	-0.013

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 : -0.054 / q_NPA : -0.037

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	ASN	0	-0.001	-0.018	2.522	-5.383	-2.977	1.344	-1.686	-2.063	-0.013
4	A	4	ALA	0	0.048	0.015	5.036	0.885	0.960	-0.001	-0.006	-0.068	0.000
5	A	5	ASP	-1	-0.856	-0.927	8.410	-1.353	-1.353	0.000	0.000	0.000	0.000
6	A	6	ASP	-1	-0.835	-0.911	6.808	-2.092	-2.092	0.000	0.000	0.000	0.000
7	A	7	PHE	0	0.018	0.001	6.118	0.331	0.331	0.000	0.000	0.000	0.000
8	A	8	ILE	0	-0.002	-0.004	11.019	0.133	0.133	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.914	0.980	11.873	0.774	0.774	0.000	0.000	0.000	0.000
10	A	10	PHE	0	-0.051	-0.050	9.524	0.088	0.088	0.000	0.000	0.000	0.000
11	A	11	LEU	0	-0.027	-0.005	13.353	0.092	0.092	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.858	-0.912	16.173	-0.131	-0.131	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.084	-0.023	13.702	0.025	0.025	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.770	-0.885	17.620	-0.355	-0.355	0.000	0.000	0.000	0.000
15	A	15	GLN	0	-0.085	-0.044	20.151	0.004	0.004	0.000	0.000	0.000	0.000
16	A	16	HIS	0	0.004	0.006	21.453	0.025	0.025	0.000	0.000	0.000	0.000
17	A	17	VAL	0	-0.001	0.001	23.203	-0.010	-0.010	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.804	-0.876	22.613	-0.119	-0.119	0.000	0.000	0.000	0.000
19	A	19	GLY	0	-0.021	0.011	21.598	0.002	0.002	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.017	-0.006	17.439	0.014	0.014	0.000	0.000	0.000	0.000
21	A	21	PHE	0	-0.068	-0.035	15.747	-0.011	-0.011	0.000	0.000	0.000	0.000
22	A	22	TYR	0	-0.030	-0.025	17.402	0.025	0.025	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.840	0.911	19.318	0.108	0.108	0.000	0.000	0.000	0.000
24	A	24	SER	0	-0.014	-0.010	20.950	0.020	0.020	0.000	0.000	0.000	0.000
25	A	25	SER	0	-0.023	0.000	19.826	-0.006	-0.006	0.000	0.000	0.000	0.000
26	A	26	TYR	0	-0.008	-0.007	22.404	0.013	0.013	0.000	0.000	0.000	0.000
27	A	27	ARG	1	0.848	0.916	26.003	0.029	0.029	0.000	0.000	0.000	0.000
28	A	28	SER	0	0.014	0.018	29.449	0.006	0.006	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.901	-0.952	32.287	0.011	0.011	0.000	0.000	0.000	0.000
30	A	30	THR	0	-0.081	-0.027	35.067	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	31	ALA	0	0.035	0.014	36.522	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	32	PHE	0	-0.057	-0.029	37.934	0.006	0.006	0.000	0.000	0.000	0.000
33	A	33	ASP	-1	-0.813	-0.878	39.778	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	34	PRO	0	-0.062	-0.061	41.239	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	35	SER	0	-0.004	-0.004	40.672	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	36	ARG	1	0.818	0.890	36.021	0.014	0.014	0.000	0.000	0.000	0.000
37	A	37	GLN	0	-0.025	-0.018	33.707	0.002	0.002	0.000	0.000	0.000	0.000
38	A	38	LEU	0	-0.003	-0.005	34.849	0.000	0.000	0.000	0.000	0.000	0.000
39	A	39	TRP	0	0.047	0.035	27.395	0.004	0.004	0.000	0.000	0.000	0.000
40	A	40	SER	0	-0.052	-0.024	28.335	-0.008	-0.008	0.000	0.000	0.000	0.000
41	A	41	SER	0	0.019	0.005	22.402	0.010	0.010	0.000	0.000	0.000	0.000
42	A	42	ILE	0	-0.028	-0.012	21.018	-0.006	-0.006	0.000	0.000	0.000	0.000
43	A	43	TYR	0	0.041	0.029	16.276	0.018	0.018	0.000	0.000	0.000	0.000
44	A	44	PHE	0	0.019	-0.008	16.724	-0.024	-0.024	0.000	0.000	0.000	0.000
45	A	45	LEU	0	-0.017	-0.008	10.179	-0.014	-0.014	0.000	0.000	0.000	0.000
46	A	46	LEU	0	-0.001	0.016	12.950	0.015	0.015	0.000	0.000	0.000	0.000
47	A	47	ARG	1	0.942	0.942	10.570	0.729	0.729	0.000	0.000	0.000	0.000
48	A	48	THR	0	0.014	-0.038	11.308	0.048	0.048	0.000	0.000	0.000	0.000
49	A	49	GLY	0	-0.057	-0.015	13.111	0.069	0.069	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.931	-0.956	15.454	-0.340	-0.340	0.000	0.000	0.000	0.000
51	A	51	VAL	0	-0.022	-0.017	16.554	0.002	0.002	0.000	0.000	0.000	0.000
52	A	52	SER	0	-0.082	-0.044	19.026	0.005	0.005	0.000	0.000	0.000	0.000
53	A	53	HIS	0	-0.043	-0.052	21.333	0.019	0.019	0.000	0.000	0.000	0.000
54	A	54	PHE	0	-0.012	-0.024	24.678	0.006	0.006	0.000	0.000	0.000	0.000
55	A	55	HIS	1	0.861	0.934	24.158	0.088	0.088	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.825	0.913	29.108	0.042	0.042	0.000	0.000	0.000	0.000
57	A	57	LEU	0	-0.010	0.000	28.008	-0.007	-0.007	0.000	0.000	0.000	0.000
58	A	58	THR	0	-0.025	-0.017	31.760	0.006	0.006	0.000	0.000	0.000	0.000
59	A	59	ALA	0	-0.016	-0.007	32.415	0.006	0.006	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.799	-0.882	30.947	0.008	0.008	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.813	-0.918	24.764	-0.044	-0.044	0.000	0.000	0.000	0.000
62	A	62	MET	0	-0.021	0.008	24.527	0.002	0.002	0.000	0.000	0.000	0.000
63	A	63	TRP	0	-0.031	-0.038	18.284	-0.014	-0.014	0.000	0.000	0.000	0.000
64	A	64	TYR	0	-0.017	-0.024	19.024	0.024	0.024	0.000	0.000	0.000	0.000
65	A	65	PHE	0	0.004	0.000	10.601	-0.027	-0.027	0.000	0.000	0.000	0.000
66	A	66	HIS	0	-0.029	-0.004	12.732	0.098	0.098	0.000	0.000	0.000	0.000
67	A	67	ALA	0	-0.012	-0.019	7.668	0.199	0.199	0.000	0.000	0.000	0.000
68	A	68	GLY	0	0.020	0.027	6.130	-0.232	-0.232	0.000	0.000	0.000	0.000
69	A	69	GLN	0	0.011	-0.005	5.576	0.006	0.006	0.000	0.000	0.000	0.000
70	A	70	SER	0	-0.020	-0.012	9.296	-0.038	-0.038	0.000	0.000	0.000	0.000
71	A	71	LEU	0	-0.003	0.003	12.935	-0.063	-0.063	0.000	0.000	0.000	0.000
72	A	72	THR	0	0.004	-0.007	15.790	0.053	0.053	0.000	0.000	0.000	0.000
73	A	73	ILE	0	-0.035	0.008	19.392	-0.028	-0.028	0.000	0.000	0.000	0.000
74	A	74	TYR	0	0.020	-0.010	20.882	0.020	0.020	0.000	0.000	0.000	0.000
75	A	75	MET	0	0.003	-0.004	25.170	-0.007	-0.007	0.000	0.000	0.000	0.000
76	A	76	ILE	0	-0.013	0.008	28.532	0.007	0.007	0.000	0.000	0.000	0.000
77	A	77	SER	0	0.002	-0.020	31.946	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	78	PRO	0	0.027	0.008	34.887	-0.004	-0.004	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.844	-0.903	37.870	-0.005	-0.005	0.000	0.000	0.000	0.000
80	A	80	GLY	0	-0.010	-0.013	36.628	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	81	GLU	-1	-0.968	-0.977	34.249	0.014	0.014	0.000	0.000	0.000	0.000
82	A	82	LEU	0	-0.060	-0.022	27.975	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	83	THR	0	0.015	0.007	29.782	0.006	0.006	0.000	0.000	0.000	0.000
84	A	84	THR	0	-0.022	-0.030	24.461	-0.006	-0.006	0.000	0.000	0.000	0.000
85	A	85	ALA	0	0.007	0.019	23.541	0.011	0.011	0.000	0.000	0.000	0.000
86	A	86	GLN	0	-0.062	-0.036	19.354	-0.004	-0.004	0.000	0.000	0.000	0.000
87	A	87	LEU	0	0.000	0.018	16.928	0.023	0.023	0.000	0.000	0.000	0.000
88	A	88	GLY	0	0.025	-0.007	14.250	-0.037	-0.037	0.000	0.000	0.000	0.000
89	A	89	LEU	0	-0.038	-0.026	11.280	0.026	0.026	0.000	0.000	0.000	0.000
90	A	90	ASP	-1	-0.841	-0.914	14.969	0.368	0.368	0.000	0.000	0.000	0.000
91	A	91	LEU	0	-0.055	-0.044	16.503	-0.048	-0.048	0.000	0.000	0.000	0.000
92	A	92	ALA	0	-0.064	-0.014	19.487	-0.028	-0.028	0.000	0.000	0.000	0.000
93	A	93	ALA	0	0.018	0.014	18.834	-0.032	-0.032	0.000	0.000	0.000	0.000
94	A	94	GLY	0	-0.011	-0.018	20.879	0.001	0.001	0.000	0.000	0.000	0.000
95	A	95	GLU	-1	-0.775	-0.853	14.949	0.212	0.212	0.000	0.000	0.000	0.000
96	A	96	ARG	1	0.830	0.917	19.096	-0.163	-0.163	0.000	0.000	0.000	0.000
97	A	97	PRO	0	0.054	0.023	17.346	-0.023	-0.023	0.000	0.000	0.000	0.000
98	A	98	GLN	0	-0.032	-0.021	18.374	-0.027	-0.027	0.000	0.000	0.000	0.000
99	A	99	PHE	0	0.009	-0.001	21.236	0.003	0.003	0.000	0.000	0.000	0.000
100	A	100	LEU	0	0.010	0.006	23.552	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	101	VAL	0	0.029	0.023	25.647	0.002	0.002	0.000	0.000	0.000	0.000
102	A	102	PRO	0	-0.027	-0.012	27.605	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	103	LYS	1	0.881	0.915	31.415	-0.016	-0.016	0.000	0.000	0.000	0.000
104	A	104	GLY	0	-0.020	-0.010	33.306	0.003	0.003	0.000	0.000	0.000	0.000
105	A	105	CYS	0	-0.084	-0.029	30.720	-0.003	-0.003	0.000	0.000	0.000	0.000
106	A	106	ILE	0	0.003	0.008	30.570	-0.005	-0.005	0.000	0.000	0.000	0.000
107	A	107	PHE	0	-0.007	-0.023	24.556	0.004	0.004	0.000	0.000	0.000	0.000
108	A	108	GLY	0	0.076	0.041	23.921	-0.010	-0.010	0.000	0.000	0.000	0.000
109	A	109	SER	0	-0.082	-0.055	18.884	0.013	0.013	0.000	0.000	0.000	0.000
110	A	110	ALA	0	0.050	0.020	17.436	-0.029	-0.029	0.000	0.000	0.000	0.000
111	A	111	MET	0	-0.018	0.015	10.972	0.005	0.005	0.000	0.000	0.000	0.000
112	A	112	ASN	0	-0.021	0.012	14.013	-0.021	-0.021	0.000	0.000	0.000	0.000
113	A	113	GLN	0	-0.072	-0.046	10.941	0.088	0.088	0.000	0.000	0.000	0.000
114	A	114	ASP	-1	-0.818	-0.885	10.480	-0.420	-0.420	0.000	0.000	0.000	0.000
115	A	115	GLY	0	-0.021	-0.003	6.981	0.025	0.025	0.000	0.000	0.000	0.000
116	A	116	PHE	0	-0.035	-0.035	3.601	-0.111	0.121	0.005	-0.029	-0.208	0.000
117	A	117	SER	0	0.020	0.003	8.085	0.055	0.055	0.000	0.000	0.000	0.000
118	A	118	LEU	0	-0.060	-0.016	10.219	-0.017	-0.017	0.000	0.000	0.000	0.000
119	A	119	VAL	0	0.034	0.004	11.793	0.114	0.114	0.000	0.000	0.000	0.000
120	A	120	GLY	0	-0.029	-0.008	15.298	-0.021	-0.021	0.000	0.000	0.000	0.000
121	A	121	CYS	0	0.003	0.007	18.569	0.011	0.011	0.000	0.000	0.000	0.000
122	A	122	MET	0	0.001	-0.008	21.939	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	123	VAL	0	0.012	0.025	25.323	0.006	0.006	0.000	0.000	0.000	0.000
124	A	124	SER	0	-0.044	-0.042	28.562	0.004	0.004	0.000	0.000	0.000	0.000
125	A	125	PRO	0	0.005	-0.008	31.942	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	126	GLY	0	-0.006	0.002	31.837	-0.005	-0.005	0.000	0.000	0.000	0.000
127	A	127	PHE	0	0.003	-0.003	28.711	-0.003	-0.003	0.000	0.000	0.000	0.000
128	A	128	THR	0	-0.001	-0.006	31.181	-0.006	-0.006	0.000	0.000	0.000	0.000
129	A	129	PHE	0	0.011	-0.020	27.904	-0.002	-0.002	0.000	0.000	0.000	0.000
130	A	130	ASP	-1	-0.869	-0.928	33.234	-0.050	-0.050	0.000	0.000	0.000	0.000
131	A	131	ASP	-1	-0.870	-0.883	33.191	-0.023	-0.023	0.000	0.000	0.000	0.000
132	A	132	PHE	0	-0.011	-0.015	27.113	0.001	0.001	0.000	0.000	0.000	0.000
133	A	133	GLU	-1	-0.795	-0.872	31.841	-0.047	-0.047	0.000	0.000	0.000	0.000
134	A	134	LEU	0	-0.021	-0.011	27.417	0.000	0.000	0.000	0.000	0.000	0.000
135	A	135	PHE	0	-0.014	-0.010	30.534	0.003	0.003	0.000	0.000	0.000	0.000
136	A	136	SER	0	0.017	0.028	30.915	-0.006	-0.006	0.000	0.000	0.000	0.000
137	A	137	GLN	0	0.029	-0.007	31.490	0.005	0.005	0.000	0.000	0.000	0.000
138	A	138	GLU	-1	-0.791	-0.893	33.008	-0.081	-0.081	0.000	0.000	0.000	0.000
139	A	139	ALA	0	0.011	0.006	36.057	0.006	0.006	0.000	0.000	0.000	0.000
140	A	140	LEU	0	0.012	0.006	30.912	0.005	0.005	0.000	0.000	0.000	0.000
141	A	141	LEU	0	-0.058	-0.028	33.607	0.002	0.002	0.000	0.000	0.000	0.000
142	A	142	ALA	0	-0.040	-0.010	36.810	0.004	0.004	0.000	0.000	0.000	0.000
143	A	143	MET	0	-0.064	-0.029	37.909	0.004	0.004	0.000	0.000	0.000	0.000
144	A	144	TYR	0	0.014	0.005	35.079	-0.004	-0.004	0.000	0.000	0.000	0.000
145	A	145	PRO	0	0.039	0.029	35.680	-0.002	-0.002	0.000	0.000	0.000	0.000
146	A	146	GLN	0	-0.033	-0.023	35.909	-0.005	-0.005	0.000	0.000	0.000	0.000
147	A	147	HIS	0	0.021	0.004	31.478	-0.001	-0.001	0.000	0.000	0.000	0.000
148	A	148	LYS	1	0.942	0.971	31.079	0.053	0.053	0.000	0.000	0.000	0.000
149	A	149	ALA	0	-0.036	-0.021	29.599	-0.008	-0.008	0.000	0.000	0.000	0.000
150	A	150	VAL	0	0.051	0.026	24.942	-0.007	-0.007	0.000	0.000	0.000	0.000
151	A	151	VAL	0	0.065	0.034	26.687	-0.012	-0.012	0.000	0.000	0.000	0.000
152	A	152	GLN	0	-0.051	-0.020	28.370	-0.002	-0.002	0.000	0.000	0.000	0.000
153	A	153	LYS	1	0.824	0.909	22.957	0.080	0.080	0.000	0.000	0.000	0.000
154	A	154	LEU	0	0.005	0.031	21.655	-0.017	-0.017	0.000	0.000	0.000	0.000
155	A	155	SER	0	0.026	0.005	24.972	0.006	0.006	0.000	0.000	0.000	0.000
156	A	156	ARG	1	0.944	0.973	22.921	0.196	0.196	0.000	0.000	0.000	0.000
157	A	157	PRO	0	-0.042	-0.020	29.329	0.007	0.007	0.000	0.000	0.000	0.000
158	A	158	GLU	-1	-1.017	-1.011	32.893	-0.098	-0.098	0.000	0.000	0.000	0.000

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