FMO DATABASE

FMODB ID: 6G31Z

Calculation Name: 1Y5H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Y5H

Chain ID: A

ChEMBL ID:

UniProt ID: P9WJA3

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	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	122
LigandCharge	DAS=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-981490.889489
FMO2-HF: Nuclear repulsion	933330.104445
FMO2-HF: Total energy	-48160.785045
FMO2-MP2: Total energy	-48297.534286

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:2:THR)

Summations of interaction energy for fragment #1(A:2: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.
-12.055	-5.489	4.378	-4.028	-6.918	-0.022

Interaction energy analysis for fragmet #1(A:2:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.047 / q_NPA : -0.029

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	4	ALA	0	0.056	0.002	2.963	-3.322	-1.113	0.189	-1.160	-1.237	-0.005
4	A	5	ARG	1	0.859	0.904	5.492	0.203	0.203	0.000	0.000	0.000	0.000
5	A	6	ASP	-1	-0.877	-0.902	2.498	-1.775	0.098	1.010	-1.377	-1.507	-0.010
6	A	7	ILE	0	-0.051	-0.029	2.444	-0.443	-0.336	1.711	-0.395	-1.423	-0.002
7	A	8	MET	0	-0.076	-0.012	5.154	0.329	0.341	-0.001	-0.002	-0.009	0.000
8	A	9	ASN	0	-0.066	-0.045	8.351	0.219	0.219	0.000	0.000	0.000	0.000
9	A	10	ALA	0	0.010	-0.009	11.437	0.070	0.070	0.000	0.000	0.000	0.000
10	A	11	GLY	0	-0.035	-0.016	12.906	0.039	0.039	0.000	0.000	0.000	0.000
11	A	12	VAL	0	-0.043	-0.012	15.365	0.036	0.036	0.000	0.000	0.000	0.000
12	A	13	THR	0	0.002	-0.003	17.838	0.004	0.004	0.000	0.000	0.000	0.000
13	A	14	CYS	0	-0.030	0.022	20.753	-0.038	-0.038	0.000	0.000	0.000	0.000
14	A	15	VAL	0	-0.004	0.010	21.841	0.024	0.024	0.000	0.000	0.000	0.000
15	A	16	GLY	0	0.044	0.018	25.222	-0.001	-0.001	0.000	0.000	0.000	0.000
16	A	17	GLU	-1	-0.809	-0.924	27.896	-0.140	-0.140	0.000	0.000	0.000	0.000
17	A	18	HIS	0	-0.026	-0.010	29.029	0.004	0.004	0.000	0.000	0.000	0.000
18	A	19	GLU	-1	-0.844	-0.883	28.897	-0.175	-0.175	0.000	0.000	0.000	0.000
19	A	20	THR	0	0.008	0.004	32.105	-0.008	-0.008	0.000	0.000	0.000	0.000
20	A	21	LEU	0	0.027	0.021	31.183	-0.012	-0.012	0.000	0.000	0.000	0.000
21	A	22	THR	0	-0.031	-0.042	32.182	-0.013	-0.013	0.000	0.000	0.000	0.000
22	A	23	ALA	0	-0.014	0.014	31.900	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	24	ALA	0	0.060	0.025	28.019	-0.011	-0.011	0.000	0.000	0.000	0.000
24	A	25	ALA	0	0.026	0.000	28.017	-0.017	-0.017	0.000	0.000	0.000	0.000
25	A	26	GLN	0	-0.129	-0.066	29.652	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	27	TYR	0	-0.002	-0.021	25.769	-0.007	-0.007	0.000	0.000	0.000	0.000
27	A	28	MET	0	-0.048	-0.012	24.865	-0.014	-0.014	0.000	0.000	0.000	0.000
28	A	29	ARG	1	0.915	0.959	25.570	0.177	0.177	0.000	0.000	0.000	0.000
29	A	30	GLU	-1	-0.967	-0.971	26.693	-0.231	-0.231	0.000	0.000	0.000	0.000
30	A	31	HIS	0	-0.071	-0.047	21.674	-0.025	-0.025	0.000	0.000	0.000	0.000
31	A	32	ASP	-1	-0.969	-0.971	22.032	-0.375	-0.375	0.000	0.000	0.000	0.000
32	A	33	ILE	0	-0.041	-0.023	19.174	-0.052	-0.052	0.000	0.000	0.000	0.000
33	A	34	GLY	0	0.068	0.032	22.158	0.023	0.023	0.000	0.000	0.000	0.000
34	A	35	ALA	0	-0.053	-0.043	19.627	0.004	0.004	0.000	0.000	0.000	0.000
35	A	36	LEU	0	-0.002	0.010	19.968	-0.043	-0.043	0.000	0.000	0.000	0.000
36	A	37	PRO	0	0.056	0.010	18.017	0.008	0.008	0.000	0.000	0.000	0.000
37	A	38	ILE	0	-0.005	-0.002	20.336	0.024	0.024	0.000	0.000	0.000	0.000
38	A	40	GLY	0	0.047	0.032	24.386	0.009	0.009	0.000	0.000	0.000	0.000
39	A	41	ASP	-1	-0.975	-0.984	26.857	-0.105	-0.105	0.000	0.000	0.000	0.000
40	A	42	DAS	-1	-0.844	-0.924	25.079	-0.093	-0.093	0.000	0.000	0.000	0.000
41	A	43	ASP	-1	-0.856	-0.935	21.406	-0.247	-0.247	0.000	0.000	0.000	0.000
42	A	44	ARG	1	0.849	0.926	20.774	0.162	0.162	0.000	0.000	0.000	0.000
43	A	45	LEU	0	-0.002	-0.019	17.746	0.001	0.001	0.000	0.000	0.000	0.000
44	A	46	HIS	0	-0.032	-0.019	21.644	0.013	0.013	0.000	0.000	0.000	0.000
45	A	47	GLY	0	0.005	0.002	21.584	0.007	0.007	0.000	0.000	0.000	0.000
46	A	48	MET	0	-0.052	0.015	18.051	-0.021	-0.021	0.000	0.000	0.000	0.000
47	A	49	LEU	0	0.015	0.010	21.681	0.026	0.026	0.000	0.000	0.000	0.000
48	A	50	THR	0	-0.027	-0.044	22.460	-0.019	-0.019	0.000	0.000	0.000	0.000
49	A	51	ASP	-1	-0.805	-0.917	24.919	-0.285	-0.285	0.000	0.000	0.000	0.000
50	A	52	ARG	1	0.926	0.949	27.230	0.259	0.259	0.000	0.000	0.000	0.000
51	A	53	ASP	-1	-0.774	-0.851	25.917	-0.258	-0.258	0.000	0.000	0.000	0.000
52	A	54	ILE	0	0.046	0.022	29.010	0.019	0.019	0.000	0.000	0.000	0.000
53	A	55	VAL	0	-0.039	-0.019	31.440	0.016	0.016	0.000	0.000	0.000	0.000
54	A	56	ILE	0	-0.075	-0.044	31.801	0.013	0.013	0.000	0.000	0.000	0.000
55	A	57	LYS	1	0.838	0.909	27.676	0.236	0.236	0.000	0.000	0.000	0.000
56	A	58	GLY	0	0.051	0.036	33.598	0.008	0.008	0.000	0.000	0.000	0.000
57	A	59	LEU	0	-0.044	-0.022	35.324	0.010	0.010	0.000	0.000	0.000	0.000
58	A	60	ALA	0	-0.064	-0.036	36.805	0.009	0.009	0.000	0.000	0.000	0.000
59	A	61	ALA	0	-0.026	0.001	37.057	0.006	0.006	0.000	0.000	0.000	0.000
60	A	62	GLY	0	-0.046	-0.017	38.992	0.007	0.007	0.000	0.000	0.000	0.000
61	A	63	LEU	0	-0.030	-0.006	36.056	0.006	0.006	0.000	0.000	0.000	0.000
62	A	64	ASP	-1	-0.769	-0.865	39.146	-0.121	-0.121	0.000	0.000	0.000	0.000
63	A	65	PRO	0	-0.009	-0.002	36.082	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	66	ASN	0	-0.065	-0.045	36.287	-0.009	-0.009	0.000	0.000	0.000	0.000
65	A	67	THR	0	-0.086	-0.069	38.860	0.004	0.004	0.000	0.000	0.000	0.000
66	A	68	ALA	0	0.035	0.042	35.809	0.001	0.001	0.000	0.000	0.000	0.000
67	A	69	THR	0	-0.056	-0.052	32.927	-0.006	-0.006	0.000	0.000	0.000	0.000
68	A	70	ALA	0	0.028	0.001	27.818	-0.006	-0.006	0.000	0.000	0.000	0.000
69	A	71	GLY	0	0.043	-0.001	28.092	-0.013	-0.013	0.000	0.000	0.000	0.000
70	A	72	GLU	-1	-0.956	-0.973	29.160	-0.136	-0.136	0.000	0.000	0.000	0.000
71	A	73	LEU	0	0.003	0.005	29.660	0.003	0.003	0.000	0.000	0.000	0.000
72	A	74	ALA	0	0.009	0.012	24.799	-0.011	-0.011	0.000	0.000	0.000	0.000
73	A	75	ARG	1	0.831	0.902	25.211	0.138	0.138	0.000	0.000	0.000	0.000
74	A	76	ASP	-1	-0.887	-0.929	26.868	-0.185	-0.185	0.000	0.000	0.000	0.000
75	A	77	SER	0	-0.066	-0.025	23.025	0.000	0.000	0.000	0.000	0.000	0.000
76	A	78	ILE	0	-0.008	-0.007	21.625	-0.035	-0.035	0.000	0.000	0.000	0.000
77	A	79	TYR	0	0.028	0.023	16.568	-0.007	-0.007	0.000	0.000	0.000	0.000
78	A	80	TYR	0	-0.011	-0.030	14.974	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	81	VAL	0	-0.006	0.008	9.377	0.007	0.007	0.000	0.000	0.000	0.000
80	A	82	ASP	-1	-0.803	-0.898	11.814	-0.081	-0.081	0.000	0.000	0.000	0.000
81	A	83	ALA	0	0.020	-0.010	9.323	-0.197	-0.197	0.000	0.000	0.000	0.000
82	A	84	ASN	0	-0.070	-0.049	7.584	-0.173	-0.173	0.000	0.000	0.000	0.000
83	A	85	ALA	0	-0.007	0.012	7.408	0.395	0.395	0.000	0.000	0.000	0.000
84	A	86	SER	0	-0.015	-0.045	4.295	-0.921	-0.810	-0.001	-0.029	-0.081	0.000
85	A	87	ILE	0	0.050	0.007	2.495	-0.550	0.085	1.399	-0.475	-1.559	-0.001
86	A	88	GLN	0	-0.004	0.003	5.316	-0.040	0.045	-0.001	-0.002	-0.082	0.000
87	A	89	GLU	-1	-0.828	-0.886	8.372	-0.355	-0.355	0.000	0.000	0.000	0.000
88	A	90	MET	0	-0.021	0.016	4.244	0.219	0.298	-0.001	-0.005	-0.074	0.000
89	A	91	LEU	0	0.024	0.010	8.947	0.171	0.171	0.000	0.000	0.000	0.000
90	A	92	ASN	0	-0.022	-0.008	11.260	0.153	0.153	0.000	0.000	0.000	0.000
91	A	93	VAL	0	0.014	0.014	13.302	0.085	0.085	0.000	0.000	0.000	0.000
92	A	94	MET	0	-0.045	-0.022	10.268	0.024	0.024	0.000	0.000	0.000	0.000
93	A	95	GLU	-1	-0.899	-0.934	14.988	-0.436	-0.436	0.000	0.000	0.000	0.000
94	A	96	GLU	-1	-0.966	-0.974	17.371	-0.276	-0.276	0.000	0.000	0.000	0.000
95	A	97	HIS	0	-0.057	-0.043	18.148	0.054	0.054	0.000	0.000	0.000	0.000
96	A	98	GLN	0	-0.109	-0.054	19.599	0.012	0.012	0.000	0.000	0.000	0.000
97	A	99	VAL	0	-0.038	0.006	15.955	0.013	0.013	0.000	0.000	0.000	0.000
98	A	100	ARG	1	0.865	0.896	15.679	0.570	0.570	0.000	0.000	0.000	0.000
99	A	101	ARG	1	0.847	0.917	13.228	0.519	0.519	0.000	0.000	0.000	0.000
100	A	102	VAL	0	0.020	0.028	11.675	0.104	0.104	0.000	0.000	0.000	0.000
101	A	103	PRO	0	0.010	0.012	12.277	-0.114	-0.114	0.000	0.000	0.000	0.000
102	A	104	VAL	0	-0.012	-0.005	9.185	-0.025	-0.025	0.000	0.000	0.000	0.000
103	A	105	ILE	0	0.033	0.016	12.233	0.083	0.083	0.000	0.000	0.000	0.000
104	A	106	SER	0	0.018	-0.012	13.367	0.009	0.009	0.000	0.000	0.000	0.000
105	A	107	GLU	-1	-0.901	-0.935	15.257	-0.020	-0.020	0.000	0.000	0.000	0.000
106	A	108	HIS	0	-0.006	-0.015	18.902	-0.032	-0.032	0.000	0.000	0.000	0.000
107	A	109	ARG	1	0.774	0.883	18.874	0.070	0.070	0.000	0.000	0.000	0.000
108	A	110	LEU	0	0.006	0.003	15.617	-0.037	-0.037	0.000	0.000	0.000	0.000
109	A	111	VAL	0	-0.043	-0.025	12.181	0.042	0.042	0.000	0.000	0.000	0.000
110	A	112	GLY	0	0.042	0.003	11.990	-0.015	-0.015	0.000	0.000	0.000	0.000
111	A	113	ILE	0	-0.001	0.014	12.458	0.025	0.025	0.000	0.000	0.000	0.000
112	A	114	VAL	0	0.015	0.028	7.182	-0.064	-0.064	0.000	0.000	0.000	0.000
113	A	115	THR	0	-0.036	-0.057	9.811	0.180	0.180	0.000	0.000	0.000	0.000
114	A	116	GLU	-1	-0.781	-0.889	9.896	-1.072	-1.072	0.000	0.000	0.000	0.000
115	A	117	ALA	0	-0.009	-0.013	10.339	-0.137	-0.137	0.000	0.000	0.000	0.000
116	A	118	ASP	-1	-0.795	-0.851	7.590	-1.369	-1.369	0.000	0.000	0.000	0.000
117	A	119	ILE	0	0.037	0.014	5.537	-0.550	-0.550	0.000	0.000	0.000	0.000
118	A	120	ALA	0	-0.033	-0.018	6.160	-0.381	-0.381	0.000	0.000	0.000	0.000
119	A	121	ARG	1	0.821	0.895	7.917	1.229	1.229	0.000	0.000	0.000	0.000
120	A	122	HIS	0	0.014	0.013	3.210	0.124	0.438	0.028	-0.063	-0.279	0.000
121	A	123	LEU	0	0.011	0.027	3.313	-4.313	-3.323	0.046	-0.502	-0.534	-0.004
122	A	124	PRO	0	-0.086	-0.038	4.091	1.166	1.317	-0.001	-0.018	-0.133	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:THR)