FMO DATABASE

FMODB ID: 2LKVR

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

Total energy (hartree)

FMO2-HF: Electronic energy	-978444.576382
FMO2-HF: Nuclear repulsion	930283.89207
FMO2-HF: Total energy	-48160.684311
FMO2-MP2: Total energy	-48297.427615

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.
-10.771	-4.22	3.027	-3.477	-6.102	-0.02

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 : -0.056 / q_NPA : -0.035

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	0.048	0.005	2.990	-2.579	-0.358	0.163	-1.113	-1.271	-0.005
4	A	5	ARG	1	0.920	0.934	5.401	0.496	0.496	0.000	0.000	0.000	0.000
5	A	6	ASP	-1	-0.871	-0.904	2.592	-2.049	-0.008	0.839	-1.389	-1.491	-0.011
6	A	7	ILE	0	-0.035	-0.016	2.567	-0.374	0.054	1.035	-0.297	-1.167	-0.002
7	A	8	MET	0	-0.083	-0.010	5.204	0.336	0.346	-0.001	-0.001	-0.008	0.000
8	A	9	ASN	0	-0.089	-0.044	8.298	0.216	0.216	0.000	0.000	0.000	0.000
9	A	10	ALA	0	0.013	-0.016	11.778	0.047	0.047	0.000	0.000	0.000	0.000
10	A	11	GLY	0	-0.015	-0.006	13.268	0.037	0.037	0.000	0.000	0.000	0.000
11	A	12	VAL	0	-0.035	-0.004	15.619	0.025	0.025	0.000	0.000	0.000	0.000
12	A	13	THR	0	0.011	-0.001	18.009	0.011	0.011	0.000	0.000	0.000	0.000
13	A	14	CYS	0	-0.040	0.006	20.930	-0.046	-0.046	0.000	0.000	0.000	0.000
14	A	15	VAL	0	-0.007	0.008	22.146	0.025	0.025	0.000	0.000	0.000	0.000
15	A	16	GLY	0	0.047	0.021	25.432	-0.003	-0.003	0.000	0.000	0.000	0.000
16	A	17	GLU	-1	-0.826	-0.931	28.137	-0.158	-0.158	0.000	0.000	0.000	0.000
17	A	18	HIS	0	-0.025	-0.018	29.273	0.005	0.005	0.000	0.000	0.000	0.000
18	A	19	GLU	-1	-0.839	-0.875	29.019	-0.178	-0.178	0.000	0.000	0.000	0.000
19	A	20	THR	0	0.015	0.005	32.326	-0.008	-0.008	0.000	0.000	0.000	0.000
20	A	21	LEU	0	0.037	0.025	31.346	-0.012	-0.012	0.000	0.000	0.000	0.000
21	A	22	THR	0	-0.042	-0.034	32.319	-0.011	-0.011	0.000	0.000	0.000	0.000
22	A	23	ALA	0	-0.016	-0.003	32.336	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	24	ALA	0	0.060	0.024	28.155	-0.009	-0.009	0.000	0.000	0.000	0.000
24	A	25	ALA	0	0.001	-0.004	28.297	-0.016	-0.016	0.000	0.000	0.000	0.000
25	A	26	GLN	0	-0.092	-0.052	29.882	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	27	TYR	0	-0.015	-0.021	25.891	-0.006	-0.006	0.000	0.000	0.000	0.000
27	A	28	MET	0	-0.027	-0.003	24.977	-0.011	-0.011	0.000	0.000	0.000	0.000
28	A	29	ARG	1	0.930	0.971	25.947	0.173	0.173	0.000	0.000	0.000	0.000
29	A	30	GLU	-1	-0.974	-0.978	26.612	-0.226	-0.226	0.000	0.000	0.000	0.000
30	A	31	HIS	0	-0.071	-0.051	21.883	-0.025	-0.025	0.000	0.000	0.000	0.000
31	A	32	ASP	-1	-0.974	-0.965	22.500	-0.346	-0.346	0.000	0.000	0.000	0.000
32	A	33	ILE	0	-0.071	-0.034	19.402	-0.050	-0.050	0.000	0.000	0.000	0.000
33	A	34	GLY	0	0.076	0.031	21.575	0.029	0.029	0.000	0.000	0.000	0.000
34	A	35	ALA	0	-0.075	-0.046	19.626	0.010	0.010	0.000	0.000	0.000	0.000
35	A	36	LEU	0	-0.015	0.005	20.488	-0.028	-0.028	0.000	0.000	0.000	0.000
36	A	37	PRO	0	0.036	0.006	18.334	0.006	0.006	0.000	0.000	0.000	0.000
37	A	38	ILE	0	-0.006	-0.007	20.598	0.025	0.025	0.000	0.000	0.000	0.000
38	A	40	GLY	0	0.030	0.030	24.617	0.013	0.013	0.000	0.000	0.000	0.000
39	A	41	ASP	-1	-0.966	-0.990	26.828	-0.126	-0.126	0.000	0.000	0.000	0.000
40	A	42	DAS	-1	-0.839	-0.924	24.868	-0.120	-0.120	0.000	0.000	0.000	0.000
41	A	43	ASP	-1	-0.872	-0.942	20.976	-0.263	-0.263	0.000	0.000	0.000	0.000
42	A	44	ARG	1	0.879	0.955	21.207	0.200	0.200	0.000	0.000	0.000	0.000
43	A	45	LEU	0	0.005	-0.010	17.831	0.000	0.000	0.000	0.000	0.000	0.000
44	A	46	HIS	0	-0.025	-0.020	21.669	0.012	0.012	0.000	0.000	0.000	0.000
45	A	47	GLY	0	0.012	0.011	22.154	0.009	0.009	0.000	0.000	0.000	0.000
46	A	48	MET	0	-0.056	0.010	18.374	-0.020	-0.020	0.000	0.000	0.000	0.000
47	A	49	LEU	0	0.015	0.017	21.905	0.021	0.021	0.000	0.000	0.000	0.000
48	A	50	THR	0	-0.026	-0.050	22.433	-0.018	-0.018	0.000	0.000	0.000	0.000
49	A	51	ASP	-1	-0.814	-0.924	24.889	-0.288	-0.288	0.000	0.000	0.000	0.000
50	A	52	ARG	1	0.936	0.950	27.106	0.257	0.257	0.000	0.000	0.000	0.000
51	A	53	ASP	-1	-0.791	-0.864	26.076	-0.265	-0.265	0.000	0.000	0.000	0.000
52	A	54	ILE	0	0.046	0.025	28.947	0.019	0.019	0.000	0.000	0.000	0.000
53	A	55	VAL	0	-0.035	-0.011	31.517	0.017	0.017	0.000	0.000	0.000	0.000
54	A	56	ILE	0	-0.075	-0.055	31.916	0.013	0.013	0.000	0.000	0.000	0.000
55	A	57	LYS	1	0.855	0.923	27.945	0.249	0.249	0.000	0.000	0.000	0.000
56	A	58	GLY	0	0.045	0.034	33.686	0.007	0.007	0.000	0.000	0.000	0.000
57	A	59	LEU	0	-0.045	-0.028	35.271	0.010	0.010	0.000	0.000	0.000	0.000
58	A	60	ALA	0	-0.071	-0.036	36.951	0.009	0.009	0.000	0.000	0.000	0.000
59	A	61	ALA	0	-0.038	-0.008	37.177	0.006	0.006	0.000	0.000	0.000	0.000
60	A	62	GLY	0	-0.048	-0.019	39.129	0.005	0.005	0.000	0.000	0.000	0.000
61	A	63	LEU	0	-0.018	0.008	36.079	0.006	0.006	0.000	0.000	0.000	0.000
62	A	64	ASP	-1	-0.770	-0.866	39.799	-0.119	-0.119	0.000	0.000	0.000	0.000
63	A	65	PRO	0	-0.009	0.000	36.592	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	66	ASN	0	-0.072	-0.051	36.651	-0.009	-0.009	0.000	0.000	0.000	0.000
65	A	67	THR	0	-0.070	-0.067	39.186	0.004	0.004	0.000	0.000	0.000	0.000
66	A	68	ALA	0	0.001	0.029	35.931	0.000	0.000	0.000	0.000	0.000	0.000
67	A	69	THR	0	-0.020	-0.029	32.958	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	70	ALA	0	0.034	-0.001	28.030	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	71	GLY	0	0.043	0.008	28.594	-0.013	-0.013	0.000	0.000	0.000	0.000
70	A	72	GLU	-1	-0.978	-0.992	29.662	-0.146	-0.146	0.000	0.000	0.000	0.000
71	A	73	LEU	0	0.016	0.005	29.690	0.001	0.001	0.000	0.000	0.000	0.000
72	A	74	ALA	0	0.003	0.001	25.095	-0.010	-0.010	0.000	0.000	0.000	0.000
73	A	75	ARG	1	0.810	0.902	25.567	0.152	0.152	0.000	0.000	0.000	0.000
74	A	76	ASP	-1	-0.874	-0.906	27.663	-0.197	-0.197	0.000	0.000	0.000	0.000
75	A	77	SER	0	-0.088	-0.050	22.908	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	78	ILE	0	-0.005	-0.004	21.351	-0.025	-0.025	0.000	0.000	0.000	0.000
77	A	79	TYR	0	0.042	0.023	16.582	-0.012	-0.012	0.000	0.000	0.000	0.000
78	A	80	TYR	0	-0.009	-0.029	14.868	0.009	0.009	0.000	0.000	0.000	0.000
79	A	81	VAL	0	-0.003	0.011	9.440	0.003	0.003	0.000	0.000	0.000	0.000
80	A	82	ASP	-1	-0.785	-0.892	11.913	-0.288	-0.288	0.000	0.000	0.000	0.000
81	A	83	ALA	0	0.015	-0.006	9.398	-0.254	-0.254	0.000	0.000	0.000	0.000
82	A	84	ASN	0	-0.109	-0.068	7.633	-0.118	-0.118	0.000	0.000	0.000	0.000
83	A	85	ALA	0	-0.039	-0.004	7.376	0.147	0.147	0.000	0.000	0.000	0.000
84	A	86	SER	0	0.021	-0.026	4.807	-1.033	-1.033	0.000	0.000	0.000	0.000
85	A	87	ILE	0	0.061	0.007	2.557	-0.622	0.182	0.970	-0.349	-1.424	0.000
86	A	88	GLN	0	0.009	0.001	5.434	0.054	0.054	0.000	0.000	0.000	0.000
87	A	89	GLU	-1	-0.841	-0.890	8.461	-0.633	-0.633	0.000	0.000	0.000	0.000
88	A	90	MET	0	-0.041	-0.002	4.131	0.273	0.356	-0.001	-0.006	-0.077	0.000
89	A	91	LEU	0	0.009	0.003	9.192	0.181	0.181	0.000	0.000	0.000	0.000
90	A	92	ASN	0	-0.011	-0.002	11.477	0.171	0.171	0.000	0.000	0.000	0.000
91	A	93	VAL	0	0.001	0.011	13.306	0.096	0.096	0.000	0.000	0.000	0.000
92	A	94	MET	0	-0.042	-0.025	10.495	0.054	0.054	0.000	0.000	0.000	0.000
93	A	95	GLU	-1	-0.925	-0.957	15.136	-0.443	-0.443	0.000	0.000	0.000	0.000
94	A	96	GLU	-1	-0.944	-0.956	17.392	-0.320	-0.320	0.000	0.000	0.000	0.000
95	A	97	HIS	0	-0.051	-0.042	18.299	0.054	0.054	0.000	0.000	0.000	0.000
96	A	98	GLN	0	-0.119	-0.049	19.566	0.035	0.035	0.000	0.000	0.000	0.000
97	A	99	VAL	0	-0.046	-0.007	16.173	0.020	0.020	0.000	0.000	0.000	0.000
98	A	100	ARG	1	0.869	0.897	15.597	0.600	0.600	0.000	0.000	0.000	0.000
99	A	101	ARG	1	0.925	0.958	13.395	0.498	0.498	0.000	0.000	0.000	0.000
100	A	102	VAL	0	0.005	0.021	11.969	0.101	0.101	0.000	0.000	0.000	0.000
101	A	103	PRO	0	0.028	0.018	12.554	-0.099	-0.099	0.000	0.000	0.000	0.000
102	A	104	VAL	0	-0.002	0.001	9.232	-0.054	-0.054	0.000	0.000	0.000	0.000
103	A	105	ILE	0	0.001	-0.001	12.267	0.104	0.104	0.000	0.000	0.000	0.000
104	A	106	SER	0	0.009	-0.012	13.585	-0.013	-0.013	0.000	0.000	0.000	0.000
105	A	107	GLU	-1	-0.927	-0.961	15.432	-0.056	-0.056	0.000	0.000	0.000	0.000
106	A	108	HIS	0	-0.026	-0.021	18.619	-0.014	-0.014	0.000	0.000	0.000	0.000
107	A	109	ARG	1	0.815	0.904	18.819	0.115	0.115	0.000	0.000	0.000	0.000
108	A	110	LEU	0	-0.001	0.001	15.829	-0.048	-0.048	0.000	0.000	0.000	0.000
109	A	111	VAL	0	-0.041	-0.028	12.342	0.039	0.039	0.000	0.000	0.000	0.000
110	A	112	GLY	0	0.036	-0.003	12.248	-0.005	-0.005	0.000	0.000	0.000	0.000
111	A	113	ILE	0	-0.011	0.011	12.547	0.016	0.016	0.000	0.000	0.000	0.000
112	A	114	VAL	0	0.021	0.028	7.181	-0.053	-0.053	0.000	0.000	0.000	0.000
113	A	115	THR	0	-0.045	-0.061	10.005	0.163	0.163	0.000	0.000	0.000	0.000
114	A	116	GLU	-1	-0.776	-0.881	9.919	-1.032	-1.032	0.000	0.000	0.000	0.000
115	A	117	ALA	0	-0.021	-0.016	10.384	-0.120	-0.120	0.000	0.000	0.000	0.000
116	A	118	ASP	-1	-0.784	-0.863	7.816	-1.256	-1.256	0.000	0.000	0.000	0.000
117	A	119	ILE	0	0.026	0.011	5.727	-0.409	-0.409	0.000	0.000	0.000	0.000
118	A	120	ALA	0	-0.042	-0.021	6.440	-0.278	-0.278	0.000	0.000	0.000	0.000
119	A	121	ARG	1	0.833	0.914	8.317	1.133	1.133	0.000	0.000	0.000	0.000
120	A	122	HIS	0	-0.005	0.007	3.830	0.251	0.431	0.002	-0.024	-0.158	0.000
121	A	123	LEU	0	0.019	0.032	3.493	-3.216	-2.594	0.020	-0.274	-0.368	-0.002
122	A	124	PRO	0	-0.071	-0.035	3.887	0.814	0.976	0.000	-0.024	-0.138	0.000

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