FMO DATABASE

FMODB ID: 7MJ1K

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

Total energy (hartree)

FMO2-HF: Electronic energy	-977970.085713
FMO2-HF: Nuclear repulsion	929809.767905
FMO2-HF: Total energy	-48160.317808
FMO2-MP2: Total energy	-48297.065141

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.
-13.012	-4.479	3.194	-4.595	-7.129	-0.023

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 : -0.002 / 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

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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	0.053	0.006	2.962	-2.213	0.818	0.254	-1.624	-1.661	0.001
4	A	5	ARG	1	0.938	0.946	5.226	1.424	1.503	-0.001	-0.001	-0.076	0.000
5	A	6	ASP	-1	-0.895	-0.944	2.381	-4.693	-1.741	1.464	-2.125	-2.290	-0.021
6	A	7	ILE	0	-0.041	-0.022	2.658	-0.058	0.452	1.015	-0.312	-1.213	-0.002
7	A	8	MET	0	-0.080	-0.010	5.295	0.224	0.230	-0.001	-0.002	-0.002	0.000
8	A	9	ASN	0	-0.081	-0.029	8.404	0.245	0.245	0.000	0.000	0.000	0.000
9	A	10	ALA	0	0.013	-0.017	11.750	-0.007	-0.007	0.000	0.000	0.000	0.000
10	A	11	GLY	0	-0.019	-0.007	13.320	0.063	0.063	0.000	0.000	0.000	0.000
11	A	12	VAL	0	-0.037	-0.003	15.629	0.037	0.037	0.000	0.000	0.000	0.000
12	A	13	THR	0	0.020	0.001	18.103	-0.004	-0.004	0.000	0.000	0.000	0.000
13	A	14	CYS	0	-0.046	-0.005	20.963	-0.055	-0.055	0.000	0.000	0.000	0.000
14	A	15	VAL	0	-0.004	0.011	22.118	0.026	0.026	0.000	0.000	0.000	0.000
15	A	16	GLY	0	0.036	0.014	25.384	-0.013	-0.013	0.000	0.000	0.000	0.000
16	A	17	GLU	-1	-0.838	-0.946	28.065	-0.217	-0.217	0.000	0.000	0.000	0.000
17	A	18	HIS	0	-0.019	-0.013	29.139	0.010	0.010	0.000	0.000	0.000	0.000
18	A	19	GLU	-1	-0.840	-0.875	28.950	-0.192	-0.192	0.000	0.000	0.000	0.000
19	A	20	THR	0	0.018	0.008	32.214	-0.008	-0.008	0.000	0.000	0.000	0.000
20	A	21	LEU	0	0.038	0.023	31.207	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	22	THR	0	-0.042	-0.037	32.227	-0.006	-0.006	0.000	0.000	0.000	0.000
22	A	23	ALA	0	-0.009	0.001	32.256	0.001	0.001	0.000	0.000	0.000	0.000
23	A	24	ALA	0	0.055	0.021	28.051	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	25	ALA	0	0.000	-0.006	28.248	-0.009	-0.009	0.000	0.000	0.000	0.000
25	A	26	GLN	0	-0.082	-0.047	29.859	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	27	TYR	0	-0.016	-0.018	25.849	0.002	0.002	0.000	0.000	0.000	0.000
27	A	28	MET	0	-0.038	-0.006	24.870	-0.003	-0.003	0.000	0.000	0.000	0.000
28	A	29	ARG	1	0.921	0.969	25.977	0.139	0.139	0.000	0.000	0.000	0.000
29	A	30	GLU	-1	-1.007	-1.005	26.625	-0.182	-0.182	0.000	0.000	0.000	0.000
30	A	31	HIS	0	-0.030	-0.020	21.946	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	32	ASP	-1	-0.976	-0.972	22.527	-0.230	-0.230	0.000	0.000	0.000	0.000
32	A	33	ILE	0	-0.066	-0.021	19.454	-0.031	-0.031	0.000	0.000	0.000	0.000
33	A	34	GLY	0	0.056	0.017	21.516	0.020	0.020	0.000	0.000	0.000	0.000
34	A	35	ALA	0	-0.068	-0.043	19.425	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	36	LEU	0	-0.024	-0.004	20.401	-0.019	-0.019	0.000	0.000	0.000	0.000
36	A	37	PRO	0	0.039	0.013	18.348	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	38	ILE	0	0.004	0.002	20.471	0.030	0.030	0.000	0.000	0.000	0.000
38	A	40	GLY	0	0.034	0.034	24.491	0.024	0.024	0.000	0.000	0.000	0.000
39	A	41	ASP	-1	-0.965	-0.990	26.738	-0.225	-0.225	0.000	0.000	0.000	0.000
40	A	42	DAS	-1	-0.825	-0.908	24.850	-0.274	-0.274	0.000	0.000	0.000	0.000
41	A	43	ASP	-1	-0.868	-0.938	20.948	-0.379	-0.379	0.000	0.000	0.000	0.000
42	A	44	ARG	1	0.880	0.951	20.803	0.365	0.365	0.000	0.000	0.000	0.000
43	A	45	LEU	0	0.001	-0.006	17.646	0.015	0.015	0.000	0.000	0.000	0.000
44	A	46	HIS	0	-0.043	-0.038	21.487	0.009	0.009	0.000	0.000	0.000	0.000
45	A	47	GLY	0	0.016	0.016	21.897	0.007	0.007	0.000	0.000	0.000	0.000
46	A	48	MET	0	-0.059	0.010	18.515	-0.023	-0.023	0.000	0.000	0.000	0.000
47	A	49	LEU	0	0.035	0.024	21.697	0.023	0.023	0.000	0.000	0.000	0.000
48	A	50	THR	0	-0.002	-0.008	22.258	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	51	ASP	-1	-0.805	-0.917	24.708	-0.240	-0.240	0.000	0.000	0.000	0.000
50	A	52	ARG	1	0.921	0.942	26.917	0.222	0.222	0.000	0.000	0.000	0.000
51	A	53	ASP	-1	-0.846	-0.920	26.049	-0.271	-0.271	0.000	0.000	0.000	0.000
52	A	54	ILE	0	0.038	0.019	28.983	0.016	0.016	0.000	0.000	0.000	0.000
53	A	55	VAL	0	-0.038	-0.011	31.337	0.015	0.015	0.000	0.000	0.000	0.000
54	A	56	ILE	0	-0.076	-0.055	31.671	0.011	0.011	0.000	0.000	0.000	0.000
55	A	57	LYS	1	0.926	0.960	27.748	0.266	0.266	0.000	0.000	0.000	0.000
56	A	58	GLY	0	0.060	0.042	33.433	0.004	0.004	0.000	0.000	0.000	0.000
57	A	59	LEU	0	-0.046	-0.027	35.059	0.010	0.010	0.000	0.000	0.000	0.000
58	A	60	ALA	0	-0.075	-0.036	36.738	0.009	0.009	0.000	0.000	0.000	0.000
59	A	61	ALA	0	-0.042	-0.011	36.948	0.005	0.005	0.000	0.000	0.000	0.000
60	A	62	GLY	0	-0.049	-0.020	38.876	0.003	0.003	0.000	0.000	0.000	0.000
61	A	63	LEU	0	-0.017	0.009	35.738	0.004	0.004	0.000	0.000	0.000	0.000
62	A	64	ASP	-1	-0.860	-0.922	39.596	-0.117	-0.117	0.000	0.000	0.000	0.000
63	A	65	PRO	0	0.018	0.003	36.536	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	66	ASN	0	-0.026	-0.027	36.538	-0.009	-0.009	0.000	0.000	0.000	0.000
65	A	67	THR	0	-0.077	-0.046	39.084	0.001	0.001	0.000	0.000	0.000	0.000
66	A	68	ALA	0	0.031	0.041	35.654	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	69	THR	0	-0.008	-0.019	32.838	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	70	ALA	0	0.038	0.003	27.852	-0.004	-0.004	0.000	0.000	0.000	0.000
69	A	71	GLY	0	0.040	0.008	28.400	-0.015	-0.015	0.000	0.000	0.000	0.000
70	A	72	GLU	-1	-0.992	-0.991	29.471	-0.176	-0.176	0.000	0.000	0.000	0.000
71	A	73	LEU	0	-0.004	-0.007	29.504	0.001	0.001	0.000	0.000	0.000	0.000
72	A	74	ALA	0	0.012	0.006	24.847	-0.010	-0.010	0.000	0.000	0.000	0.000
73	A	75	ARG	1	0.827	0.912	25.301	0.202	0.202	0.000	0.000	0.000	0.000
74	A	76	ASP	-1	-0.906	-0.934	27.354	-0.239	-0.239	0.000	0.000	0.000	0.000
75	A	77	SER	0	-0.086	-0.045	22.619	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	78	ILE	0	0.005	0.003	20.878	-0.027	-0.027	0.000	0.000	0.000	0.000
77	A	79	TYR	0	0.035	0.017	16.226	0.006	0.006	0.000	0.000	0.000	0.000
78	A	80	TYR	0	-0.016	-0.035	14.557	0.034	0.034	0.000	0.000	0.000	0.000
79	A	81	VAL	0	-0.009	0.010	9.119	-0.019	-0.019	0.000	0.000	0.000	0.000
80	A	82	ASP	-1	-0.822	-0.924	11.702	-1.119	-1.119	0.000	0.000	0.000	0.000
81	A	83	ALA	0	0.010	-0.006	9.253	-0.311	-0.311	0.000	0.000	0.000	0.000
82	A	84	ASN	0	-0.038	-0.021	7.614	-0.564	-0.564	0.000	0.000	0.000	0.000
83	A	85	ALA	0	-0.050	-0.010	7.270	-0.306	-0.306	0.000	0.000	0.000	0.000
84	A	86	SER	0	0.027	-0.020	4.743	-1.163	-1.107	-0.001	-0.017	-0.038	0.000
85	A	87	ILE	0	0.058	0.007	2.734	-0.367	0.622	0.454	-0.250	-1.192	0.000
86	A	88	GLN	0	0.011	-0.002	5.513	0.124	0.124	0.000	0.000	0.000	0.000
87	A	89	GLU	-1	-0.852	-0.892	8.532	-1.255	-1.255	0.000	0.000	0.000	0.000
88	A	90	MET	0	-0.038	-0.006	3.789	0.333	0.450	0.000	-0.014	-0.103	0.000
89	A	91	LEU	0	0.006	0.000	9.185	0.233	0.233	0.000	0.000	0.000	0.000
90	A	92	ASN	0	-0.006	0.002	11.317	0.224	0.224	0.000	0.000	0.000	0.000
91	A	93	VAL	0	-0.004	0.009	12.871	0.113	0.113	0.000	0.000	0.000	0.000
92	A	94	MET	0	-0.056	-0.035	10.232	0.091	0.091	0.000	0.000	0.000	0.000
93	A	95	GLU	-1	-0.950	-0.966	14.753	-0.359	-0.359	0.000	0.000	0.000	0.000
94	A	96	GLU	-1	-0.946	-0.974	17.124	-0.443	-0.443	0.000	0.000	0.000	0.000
95	A	97	HIS	0	-0.035	-0.030	17.612	0.069	0.069	0.000	0.000	0.000	0.000
96	A	98	GLN	0	-0.097	-0.025	19.200	0.055	0.055	0.000	0.000	0.000	0.000
97	A	99	VAL	0	-0.044	-0.005	15.971	0.027	0.027	0.000	0.000	0.000	0.000
98	A	100	ARG	1	0.854	0.881	15.343	0.493	0.493	0.000	0.000	0.000	0.000
99	A	101	ARG	1	0.944	0.966	13.199	0.444	0.444	0.000	0.000	0.000	0.000
100	A	102	VAL	0	-0.005	0.017	11.666	0.083	0.083	0.000	0.000	0.000	0.000
101	A	103	PRO	0	0.034	0.009	12.365	-0.082	-0.082	0.000	0.000	0.000	0.000
102	A	104	VAL	0	-0.004	0.004	9.151	-0.092	-0.092	0.000	0.000	0.000	0.000
103	A	105	ILE	0	-0.004	0.000	12.096	0.134	0.134	0.000	0.000	0.000	0.000
104	A	106	SER	0	0.005	-0.021	13.410	-0.142	-0.142	0.000	0.000	0.000	0.000
105	A	107	GLU	-1	-0.962	-0.965	15.318	-0.314	-0.314	0.000	0.000	0.000	0.000
106	A	108	HIS	0	-0.042	-0.036	18.456	0.025	0.025	0.000	0.000	0.000	0.000
107	A	109	ARG	1	0.834	0.896	18.709	0.334	0.334	0.000	0.000	0.000	0.000
108	A	110	LEU	0	0.006	-0.001	15.625	-0.089	-0.089	0.000	0.000	0.000	0.000
109	A	111	VAL	0	-0.046	-0.025	12.258	0.036	0.036	0.000	0.000	0.000	0.000
110	A	112	GLY	0	0.033	-0.006	12.287	0.022	0.022	0.000	0.000	0.000	0.000
111	A	113	ILE	0	-0.015	0.013	12.562	-0.014	-0.014	0.000	0.000	0.000	0.000
112	A	114	VAL	0	0.015	0.024	6.877	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	115	THR	0	-0.048	-0.035	9.910	0.120	0.120	0.000	0.000	0.000	0.000
114	A	116	GLU	-1	-0.753	-0.873	9.780	-0.775	-0.775	0.000	0.000	0.000	0.000
115	A	117	ALA	0	-0.032	-0.021	10.268	-0.045	-0.045	0.000	0.000	0.000	0.000
116	A	118	ASP	-1	-0.792	-0.902	7.562	-0.798	-0.798	0.000	0.000	0.000	0.000
117	A	119	ILE	0	0.018	0.009	5.611	-0.167	-0.167	0.000	0.000	0.000	0.000
118	A	120	ALA	0	-0.042	-0.021	6.421	-0.084	-0.084	0.000	0.000	0.000	0.000
119	A	121	ARG	1	0.840	0.924	8.412	0.688	0.688	0.000	0.000	0.000	0.000
120	A	122	HIS	0	-0.007	0.005	3.913	0.405	0.570	0.001	-0.020	-0.146	0.000
121	A	123	LEU	0	-0.009	0.015	3.663	-2.202	-1.703	0.010	-0.208	-0.301	-0.001
122	A	124	PRO	0	-0.032	-0.009	4.256	0.163	0.292	-0.001	-0.022	-0.107	0.000

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