FMO DATABASE

FMODB ID: G5641

Calculation Name: 2YQY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YQY

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SLJ0

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	127
LigandCharge	DGL=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1077648.314818
FMO2-HF: Nuclear repulsion	1028825.035731
FMO2-HF: Total energy	-48823.279087
FMO2-MP2: Total energy	-48969.925042

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:9:THR)

Summations of interaction energy for fragment #1(A:9:THR)

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.
-48.639	-51.22	30.891	-15.404	-12.907	-0.077

Interaction energy analysis for fragmet #1(A:9:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.034 / q_NPA : -0.064

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

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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	11	ASP	-1	-0.857	-0.935	3.224	-0.206	2.115	0.039	-0.913	-1.447	0.002
4	A	12	GLU	-1	-0.886	-0.908	1.669	-44.874	-51.643	30.739	-13.821	-10.149	-0.081
5	A	13	ALA	0	-0.041	-0.020	3.264	0.162	0.803	0.009	-0.228	-0.422	0.000
6	A	14	LEU	0	0.046	0.029	4.997	0.157	0.269	-0.001	-0.008	-0.102	0.000
7	A	15	LYS	1	0.851	0.908	7.168	0.096	0.096	0.000	0.000	0.000	0.000
8	A	16	ARG	1	0.941	0.957	5.538	1.825	1.825	0.000	0.000	0.000	0.000
9	A	17	LEU	0	0.051	0.044	8.987	0.091	0.091	0.000	0.000	0.000	0.000
10	A	18	GLU	-1	-0.860	-0.906	11.106	-0.008	-0.008	0.000	0.000	0.000	0.000
11	A	19	ALA	0	-0.053	-0.025	12.235	0.030	0.030	0.000	0.000	0.000	0.000
12	A	20	SER	0	-0.017	-0.039	13.116	0.010	0.010	0.000	0.000	0.000	0.000
13	A	21	ARG	1	0.818	0.900	14.887	-0.007	-0.007	0.000	0.000	0.000	0.000
14	A	22	LYS	1	0.926	0.959	15.339	0.168	0.168	0.000	0.000	0.000	0.000
15	A	23	ALA	0	0.010	0.013	17.836	0.010	0.010	0.000	0.000	0.000	0.000
16	A	24	LEU	0	0.004	0.001	18.909	0.011	0.011	0.000	0.000	0.000	0.000
17	A	25	LEU	0	-0.014	-0.019	20.747	0.009	0.009	0.000	0.000	0.000	0.000
18	A	26	ALA	0	-0.019	-0.004	22.601	0.007	0.007	0.000	0.000	0.000	0.000
19	A	27	LEU	0	0.034	0.018	23.125	0.004	0.004	0.000	0.000	0.000	0.000
20	A	28	LEU	0	-0.030	-0.031	24.302	0.007	0.007	0.000	0.000	0.000	0.000
21	A	29	ARG	1	0.899	0.942	25.006	0.025	0.025	0.000	0.000	0.000	0.000
22	A	30	GLU	-1	-0.941	-0.959	27.313	-0.072	-0.072	0.000	0.000	0.000	0.000
23	A	31	ALA	0	-0.054	-0.003	29.321	0.000	0.000	0.000	0.000	0.000	0.000
24	A	32	ASP	-1	-0.809	-0.916	31.064	-0.013	-0.013	0.000	0.000	0.000	0.000
25	A	33	PRO	0	-0.003	-0.024	34.063	0.003	0.003	0.000	0.000	0.000	0.000
26	A	34	ALA	0	-0.045	-0.018	35.729	0.004	0.004	0.000	0.000	0.000	0.000
27	A	35	TRP	0	0.010	-0.002	27.043	0.004	0.004	0.000	0.000	0.000	0.000
28	A	36	LEU	0	-0.014	-0.006	29.404	0.004	0.004	0.000	0.000	0.000	0.000
29	A	37	SER	0	-0.031	-0.022	31.899	0.004	0.004	0.000	0.000	0.000	0.000
30	A	38	ALA	0	0.015	0.019	34.263	0.003	0.003	0.000	0.000	0.000	0.000
31	A	39	PRO	0	-0.040	-0.031	33.174	0.000	0.000	0.000	0.000	0.000	0.000
32	A	40	LEU	0	0.006	0.006	27.114	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	41	ARG	1	0.853	0.908	31.574	-0.023	-0.023	0.000	0.000	0.000	0.000
34	A	42	DGL	-1	-0.801	-0.901	34.047	0.015	0.015	0.000	0.000	0.000	0.000
35	A	43	GLY	0	-0.040	-0.007	35.491	0.003	0.003	0.000	0.000	0.000	0.000
36	A	44	ALA	0	-0.081	-0.022	30.963	0.005	0.005	0.000	0.000	0.000	0.000
37	A	45	TRP	0	0.031	0.009	24.035	0.000	0.000	0.000	0.000	0.000	0.000
38	A	46	THR	0	0.031	-0.008	30.912	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	47	PRO	0	0.052	0.019	27.376	0.007	0.007	0.000	0.000	0.000	0.000
40	A	48	LEU	0	-0.013	-0.001	26.798	0.003	0.003	0.000	0.000	0.000	0.000
41	A	49	MET	0	0.011	0.038	27.914	0.006	0.006	0.000	0.000	0.000	0.000
42	A	50	VAL	0	-0.016	0.010	22.920	0.010	0.010	0.000	0.000	0.000	0.000
43	A	51	ALA	0	-0.006	-0.013	23.038	0.010	0.010	0.000	0.000	0.000	0.000
44	A	52	GLU	-1	-0.895	-0.948	23.256	0.067	0.067	0.000	0.000	0.000	0.000
45	A	53	HIS	0	0.030	0.002	21.707	0.023	0.023	0.000	0.000	0.000	0.000
46	A	54	VAL	0	-0.005	-0.009	17.862	0.019	0.019	0.000	0.000	0.000	0.000
47	A	55	ALA	0	0.020	0.019	19.406	0.018	0.018	0.000	0.000	0.000	0.000
48	A	56	LEU	0	-0.001	-0.001	21.307	0.017	0.017	0.000	0.000	0.000	0.000
49	A	57	VAL	0	0.003	0.005	17.041	0.021	0.021	0.000	0.000	0.000	0.000
50	A	58	GLU	-1	-0.786	-0.857	15.460	0.132	0.132	0.000	0.000	0.000	0.000
51	A	59	ASP	-1	-0.752	-0.842	17.839	0.160	0.160	0.000	0.000	0.000	0.000
52	A	60	SER	0	0.013	0.005	20.236	0.008	0.008	0.000	0.000	0.000	0.000
53	A	61	THR	0	-0.058	-0.049	13.710	0.033	0.033	0.000	0.000	0.000	0.000
54	A	62	ALA	0	0.021	0.024	16.511	0.037	0.037	0.000	0.000	0.000	0.000
55	A	63	ARG	1	0.771	0.845	17.834	-0.140	-0.140	0.000	0.000	0.000	0.000
56	A	64	VAL	0	-0.022	0.007	16.061	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	65	LEU	0	0.005	0.008	11.974	0.017	0.017	0.000	0.000	0.000	0.000
58	A	66	ARG	1	0.922	0.982	15.926	-0.178	-0.178	0.000	0.000	0.000	0.000
59	A	67	ARG	1	0.895	0.944	19.197	-0.247	-0.247	0.000	0.000	0.000	0.000
60	A	68	LEU	0	0.004	-0.007	14.242	-0.011	-0.011	0.000	0.000	0.000	0.000
61	A	69	ARG	1	0.832	0.902	16.806	-0.240	-0.240	0.000	0.000	0.000	0.000
62	A	70	ARG	1	0.900	0.938	17.936	-0.186	-0.186	0.000	0.000	0.000	0.000
63	A	71	LEU	0	-0.040	-0.019	19.705	-0.016	-0.016	0.000	0.000	0.000	0.000
64	A	72	ALA	0	-0.048	0.008	17.254	-0.024	-0.024	0.000	0.000	0.000	0.000
65	A	104	LEU	0	0.012	-0.001	31.930	0.000	0.000	0.000	0.000	0.000	0.000
66	A	105	SER	0	0.039	0.019	33.681	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	106	LEU	0	0.054	0.022	28.732	0.004	0.004	0.000	0.000	0.000	0.000
68	A	107	DGL	-1	-0.912	-0.970	30.057	0.009	0.009	0.000	0.000	0.000	0.000
69	A	108	GLU	-1	-0.843	-0.891	30.789	0.046	0.046	0.000	0.000	0.000	0.000
70	A	109	VAL	0	0.018	-0.002	26.405	0.006	0.006	0.000	0.000	0.000	0.000
71	A	110	LEU	0	-0.017	-0.020	25.789	0.004	0.004	0.000	0.000	0.000	0.000
72	A	111	ALA	0	0.078	0.054	25.751	0.002	0.002	0.000	0.000	0.000	0.000
73	A	112	LEU	0	-0.062	-0.007	25.261	0.008	0.008	0.000	0.000	0.000	0.000
74	A	113	LEU	0	-0.015	-0.014	20.877	0.011	0.011	0.000	0.000	0.000	0.000
75	A	114	ASP	-1	-0.920	-0.958	21.443	0.027	0.027	0.000	0.000	0.000	0.000
76	A	115	ARG	1	0.777	0.851	22.281	-0.046	-0.046	0.000	0.000	0.000	0.000
77	A	116	ALA	0	0.024	0.020	20.713	0.011	0.011	0.000	0.000	0.000	0.000
78	A	117	ARG	1	0.770	0.858	14.311	-0.012	-0.012	0.000	0.000	0.000	0.000
79	A	118	ALA	0	-0.007	-0.007	17.845	0.013	0.013	0.000	0.000	0.000	0.000
80	A	119	PHE	0	-0.052	-0.024	19.593	0.018	0.018	0.000	0.000	0.000	0.000
81	A	120	LEU	0	0.010	-0.012	13.451	0.026	0.026	0.000	0.000	0.000	0.000
82	A	121	LEU	0	-0.002	-0.008	13.504	0.032	0.032	0.000	0.000	0.000	0.000
83	A	122	GLU	-1	-0.815	-0.885	15.428	0.188	0.188	0.000	0.000	0.000	0.000
84	A	123	GLU	-1	-0.772	-0.881	16.333	0.251	0.251	0.000	0.000	0.000	0.000
85	A	124	VAL	0	-0.062	-0.033	10.307	0.044	0.044	0.000	0.000	0.000	0.000
86	A	125	ALA	0	-0.033	-0.015	11.972	0.046	0.046	0.000	0.000	0.000	0.000
87	A	126	LYS	1	0.780	0.872	14.007	-0.174	-0.174	0.000	0.000	0.000	0.000
88	A	127	ALA	0	-0.052	-0.005	11.597	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	128	ASP	-1	-0.797	-0.901	11.101	0.531	0.531	0.000	0.000	0.000	0.000
90	A	129	PRO	0	-0.050	-0.030	6.102	0.046	0.046	0.000	0.000	0.000	0.000
91	A	130	GLN	0	-0.035	-0.031	6.490	0.260	0.260	0.000	0.000	0.000	0.000
92	A	131	ASN	0	0.026	0.018	9.452	-0.083	-0.083	0.000	0.000	0.000	0.000
93	A	132	PRO	0	0.003	-0.001	11.790	0.098	0.098	0.000	0.000	0.000	0.000
94	A	133	ALA	0	-0.022	0.006	13.771	-0.009	-0.009	0.000	0.000	0.000	0.000
95	A	134	THR	0	-0.032	-0.053	14.243	0.064	0.064	0.000	0.000	0.000	0.000
96	A	135	PHE	0	-0.032	-0.023	16.080	-0.070	-0.070	0.000	0.000	0.000	0.000
97	A	136	PRO	0	0.036	0.028	16.957	0.049	0.049	0.000	0.000	0.000	0.000
98	A	137	HIS	0	0.001	0.006	15.557	-0.028	-0.028	0.000	0.000	0.000	0.000
99	A	138	PRO	0	-0.012	-0.020	18.217	-0.005	-0.005	0.000	0.000	0.000	0.000
100	A	139	PHE	0	-0.046	-0.012	16.868	-0.026	-0.026	0.000	0.000	0.000	0.000
101	A	140	PHE	0	-0.019	-0.036	13.982	0.016	0.016	0.000	0.000	0.000	0.000
102	A	141	GLY	0	0.045	0.044	16.119	0.041	0.041	0.000	0.000	0.000	0.000
103	A	142	GLU	-1	-0.838	-0.906	16.895	0.385	0.385	0.000	0.000	0.000	0.000
104	A	143	LEU	0	-0.023	-0.002	11.332	0.110	0.110	0.000	0.000	0.000	0.000
105	A	144	ASN	0	0.046	0.017	8.569	0.065	0.065	0.000	0.000	0.000	0.000
106	A	145	PRO	0	0.037	0.010	10.253	0.060	0.060	0.000	0.000	0.000	0.000
107	A	146	LEU	0	0.009	0.015	3.113	-0.402	0.000	0.095	-0.101	-0.397	0.000
108	A	147	GLY	0	-0.038	-0.017	7.083	0.226	0.226	0.000	0.000	0.000	0.000
109	A	148	TRP	0	0.005	-0.019	9.106	-0.107	-0.107	0.000	0.000	0.000	0.000
110	A	149	LEU	0	0.004	0.023	6.629	-0.096	-0.096	0.000	0.000	0.000	0.000
111	A	150	ARG	1	0.953	0.956	3.873	-6.619	-5.907	0.010	-0.333	-0.390	0.002
112	A	151	ALA	0	-0.018	0.009	7.607	-0.228	-0.228	0.000	0.000	0.000	0.000
113	A	152	ALA	0	0.034	0.016	11.347	-0.112	-0.112	0.000	0.000	0.000	0.000
114	A	153	ALA	0	0.005	-0.006	8.117	-0.094	-0.094	0.000	0.000	0.000	0.000
115	A	154	TYR	0	-0.030	-0.020	10.100	-0.105	-0.105	0.000	0.000	0.000	0.000
116	A	155	HIS	0	-0.018	-0.005	11.593	-0.068	-0.068	0.000	0.000	0.000	0.000
117	A	156	GLU	-1	-0.662	-0.797	13.918	-0.046	-0.046	0.000	0.000	0.000	0.000
118	A	157	ALA	0	-0.032	-0.017	12.468	-0.036	-0.036	0.000	0.000	0.000	0.000
119	A	158	HIS	0	-0.049	-0.022	14.532	-0.022	-0.022	0.000	0.000	0.000	0.000
120	A	159	HIS	0	-0.003	-0.010	16.962	-0.030	-0.030	0.000	0.000	0.000	0.000
121	A	160	LEU	0	-0.002	0.013	16.540	-0.012	-0.012	0.000	0.000	0.000	0.000
122	A	161	LYS	1	0.941	0.971	16.366	0.116	0.116	0.000	0.000	0.000	0.000
123	A	162	ALA	0	-0.002	0.003	19.969	-0.004	-0.004	0.000	0.000	0.000	0.000
124	A	163	LEU	0	0.022	0.018	22.694	-0.002	-0.002	0.000	0.000	0.000	0.000
125	A	164	GLN	0	0.004	-0.016	19.847	-0.007	-0.007	0.000	0.000	0.000	0.000
126	A	165	ALA	0	-0.066	-0.021	24.092	-0.003	-0.003	0.000	0.000	0.000	0.000
127	A	166	SER	0	-0.057	-0.006	25.852	0.008	0.008	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:9:THR)