FMO DATABASE

FMODB ID: LNGV9

Calculation Name: 1JYO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1JYO

Chain ID: A

ChEMBL ID:

UniProt ID: P0CL16

Base Structure: X-ray

Registration Date: 2023-09-23

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	130
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1080612.255875
FMO2-HF: Nuclear repulsion	1029966.394278
FMO2-HF: Total energy	-50645.861597
FMO2-MP2: Total energy	-50793.722676

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:LEU)

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

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.
-15.826	-7.232	2.494	-3.826	-7.26	-0.012

Interaction energy analysis for fragmet #1(A:1:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.046 / q_NPA : 0.010

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	ALA	0	0.047	0.021	2.966	-4.044	-1.613	0.062	-1.092	-1.400	0.002
4	A	4	HIS	0	0.007	0.005	2.429	-2.219	-0.337	1.121	-1.027	-1.976	-0.002
5	A	5	GLN	0	0.014	0.001	2.607	-0.911	0.516	0.672	-0.560	-1.540	0.000
6	A	6	ASP	-1	-0.865	-0.929	4.979	0.760	0.872	-0.001	-0.008	-0.102	0.000
7	A	7	ILE	0	-0.014	0.004	6.748	0.081	0.081	0.000	0.000	0.000	0.000
8	A	8	ILE	0	-0.012	-0.011	6.917	0.152	0.152	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.034	0.031	9.001	0.106	0.106	0.000	0.000	0.000	0.000
10	A	10	ASN	0	-0.080	-0.053	10.769	0.087	0.087	0.000	0.000	0.000	0.000
11	A	11	ILE	0	-0.031	-0.019	12.319	0.051	0.051	0.000	0.000	0.000	0.000
12	A	12	GLY	0	0.047	0.014	12.938	0.037	0.037	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.877	-0.918	14.594	-0.060	-0.060	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.754	0.869	17.004	0.147	0.147	0.000	0.000	0.000	0.000
15	A	15	LEU	0	0.003	0.008	16.107	0.015	0.015	0.000	0.000	0.000	0.000
16	A	16	GLY	0	-0.037	0.007	18.993	0.009	0.009	0.000	0.000	0.000	0.000
17	A	17	LEU	0	-0.030	-0.033	15.878	0.009	0.009	0.000	0.000	0.000	0.000
18	A	18	PRO	0	-0.038	-0.013	13.991	-0.018	-0.018	0.000	0.000	0.000	0.000
19	A	19	LEU	0	0.000	0.015	11.074	-0.028	-0.028	0.000	0.000	0.000	0.000
20	A	20	THR	0	-0.012	-0.018	6.978	0.061	0.061	0.000	0.000	0.000	0.000
21	A	21	PHE	0	-0.020	-0.005	3.859	-0.329	-0.043	0.002	-0.032	-0.256	0.000
22	A	22	ASP	-1	-0.787	-0.893	5.348	-1.461	-1.461	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.931	-0.971	4.583	-2.021	-1.910	-0.001	-0.005	-0.104	0.000
24	A	24	ASN	0	-0.146	-0.076	5.233	-0.098	-0.098	0.000	0.000	0.000	0.000
25	A	25	ASN	0	-0.046	-0.027	2.753	-4.607	-2.359	0.641	-1.093	-1.796	-0.012
26	A	26	GLN	0	0.029	0.004	4.901	0.502	0.530	-0.001	-0.003	-0.024	0.000
27	A	27	CYS	0	-0.023	0.000	8.070	0.033	0.033	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.041	-0.012	10.209	0.081	0.081	0.000	0.000	0.000	0.000
29	A	29	LEU	0	0.012	-0.003	13.859	0.028	0.028	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.029	-0.005	16.818	0.013	0.013	0.000	0.000	0.000	0.000
31	A	31	LEU	0	0.007	-0.002	19.035	0.007	0.007	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.867	-0.940	22.567	-0.191	-0.191	0.000	0.000	0.000	0.000
33	A	33	SER	0	-0.140	-0.067	24.870	0.018	0.018	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.865	-0.942	26.015	-0.194	-0.194	0.000	0.000	0.000	0.000
35	A	35	ILE	0	0.020	0.034	22.329	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	36	PHE	0	0.000	0.000	20.306	-0.018	-0.018	0.000	0.000	0.000	0.000
37	A	37	THR	0	0.004	-0.004	16.527	0.014	0.014	0.000	0.000	0.000	0.000
38	A	38	SER	0	-0.046	-0.020	13.169	-0.055	-0.055	0.000	0.000	0.000	0.000
39	A	39	ILE	0	0.033	0.024	9.807	0.059	0.059	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.834	-0.927	8.648	-1.137	-1.137	0.000	0.000	0.000	0.000
41	A	41	ALA	0	-0.024	0.009	4.795	0.135	0.204	-0.001	-0.006	-0.062	0.000
42	A	42	LYS	1	0.834	0.901	6.321	0.681	0.681	0.000	0.000	0.000	0.000
43	A	43	ASP	-1	-0.908	-0.961	6.455	-0.496	-0.496	0.000	0.000	0.000	0.000
44	A	44	ASP	-1	-0.981	-0.990	6.332	-0.372	-0.372	0.000	0.000	0.000	0.000
45	A	45	ILE	0	-0.011	0.009	8.269	0.133	0.133	0.000	0.000	0.000	0.000
46	A	46	TRP	0	-0.019	-0.020	6.695	-0.122	-0.122	0.000	0.000	0.000	0.000
47	A	47	LEU	0	-0.027	-0.014	10.537	0.175	0.175	0.000	0.000	0.000	0.000
48	A	48	LEU	0	-0.004	0.012	12.818	-0.086	-0.086	0.000	0.000	0.000	0.000
49	A	49	ASN	0	0.004	-0.012	14.610	0.098	0.098	0.000	0.000	0.000	0.000
50	A	50	GLY	0	0.061	0.017	17.529	-0.018	-0.018	0.000	0.000	0.000	0.000
51	A	51	MET	0	-0.044	-0.010	20.500	0.024	0.024	0.000	0.000	0.000	0.000
52	A	52	ILE	0	-0.001	0.004	22.748	0.010	0.010	0.000	0.000	0.000	0.000
53	A	53	ILE	0	0.007	-0.004	26.369	0.010	0.010	0.000	0.000	0.000	0.000
54	A	54	PRO	0	-0.014	0.017	28.303	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	55	LEU	0	0.037	-0.020	29.311	0.012	0.012	0.000	0.000	0.000	0.000
56	A	56	SER	0	0.043	0.021	31.642	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	57	PRO	0	0.070	0.039	32.617	0.002	0.002	0.000	0.000	0.000	0.000
58	A	58	VAL	0	-0.064	-0.043	34.034	0.005	0.005	0.000	0.000	0.000	0.000
59	A	59	CYS	0	-0.026	0.002	34.965	0.007	0.007	0.000	0.000	0.000	0.000
60	A	60	GLY	0	0.049	0.033	37.854	0.005	0.005	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.911	-0.971	38.991	-0.100	-0.100	0.000	0.000	0.000	0.000
62	A	62	SER	0	-0.077	-0.050	39.636	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	63	ILE	0	0.047	0.039	35.400	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	64	TRP	0	0.038	0.022	31.035	-0.007	-0.007	0.000	0.000	0.000	0.000
65	A	65	ARG	1	0.919	0.958	35.056	0.091	0.091	0.000	0.000	0.000	0.000
66	A	66	GLN	0	0.037	0.039	36.457	0.002	0.002	0.000	0.000	0.000	0.000
67	A	67	ILE	0	0.054	0.024	30.784	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	68	MET	0	-0.015	-0.006	30.891	-0.008	-0.008	0.000	0.000	0.000	0.000
69	A	69	VAL	0	-0.069	-0.032	33.307	0.002	0.002	0.000	0.000	0.000	0.000
70	A	70	ILE	0	0.058	0.035	30.738	0.000	0.000	0.000	0.000	0.000	0.000
71	A	71	ASN	0	-0.006	-0.005	27.922	-0.013	-0.013	0.000	0.000	0.000	0.000
72	A	72	GLY	0	-0.044	-0.008	29.875	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	73	GLU	-1	-0.942	-0.982	31.865	-0.119	-0.119	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.001	0.000	26.835	0.001	0.001	0.000	0.000	0.000	0.000
75	A	75	ALA	0	0.003	0.002	27.034	-0.005	-0.005	0.000	0.000	0.000	0.000
76	A	76	ALA	0	-0.073	-0.025	28.044	0.003	0.003	0.000	0.000	0.000	0.000
77	A	77	ASN	0	-0.063	-0.035	28.345	0.014	0.014	0.000	0.000	0.000	0.000
78	A	78	ASN	0	-0.057	-0.025	21.021	-0.012	-0.012	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.828	-0.902	23.175	-0.212	-0.212	0.000	0.000	0.000	0.000
80	A	80	GLY	0	0.000	0.007	22.210	-0.025	-0.025	0.000	0.000	0.000	0.000
81	A	81	THR	0	-0.093	-0.044	22.774	0.029	0.029	0.000	0.000	0.000	0.000
82	A	82	LEU	0	0.002	0.002	23.638	-0.023	-0.023	0.000	0.000	0.000	0.000
83	A	83	ALA	0	-0.005	-0.010	23.090	0.014	0.014	0.000	0.000	0.000	0.000
84	A	84	TYR	0	-0.013	-0.031	25.254	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	85	ILE	0	-0.018	0.001	20.877	-0.004	-0.004	0.000	0.000	0.000	0.000
86	A	86	ASP	-1	-0.897	-0.970	24.506	-0.178	-0.178	0.000	0.000	0.000	0.000
87	A	87	ALA	0	-0.003	-0.003	23.908	0.007	0.007	0.000	0.000	0.000	0.000
88	A	88	ALA	0	-0.015	-0.006	23.428	0.002	0.002	0.000	0.000	0.000	0.000
89	A	89	GLU	-1	-0.882	-0.908	25.586	-0.158	-0.158	0.000	0.000	0.000	0.000
90	A	90	THR	0	-0.048	-0.028	24.263	0.008	0.008	0.000	0.000	0.000	0.000
91	A	91	LEU	0	-0.015	0.012	25.878	-0.007	-0.007	0.000	0.000	0.000	0.000
92	A	92	LEU	0	-0.016	-0.015	19.678	-0.005	-0.005	0.000	0.000	0.000	0.000
93	A	93	LEU	0	0.029	0.022	22.320	0.015	0.015	0.000	0.000	0.000	0.000
94	A	94	ILE	0	-0.008	-0.010	17.627	-0.033	-0.033	0.000	0.000	0.000	0.000
95	A	95	HIS	0	0.055	0.014	18.111	0.030	0.030	0.000	0.000	0.000	0.000
96	A	96	ALA	0	-0.007	0.016	15.235	-0.061	-0.061	0.000	0.000	0.000	0.000
97	A	97	ILE	0	0.009	0.015	13.362	0.057	0.057	0.000	0.000	0.000	0.000
98	A	98	THR	0	-0.006	-0.031	12.914	-0.061	-0.061	0.000	0.000	0.000	0.000
99	A	99	ASP	-1	-0.822	-0.879	13.269	-0.113	-0.113	0.000	0.000	0.000	0.000
100	A	100	LEU	0	-0.004	-0.007	8.354	-0.017	-0.017	0.000	0.000	0.000	0.000
101	A	101	THR	0	-0.075	-0.058	11.104	0.036	0.036	0.000	0.000	0.000	0.000
102	A	102	ASN	0	-0.013	-0.010	13.333	0.029	0.029	0.000	0.000	0.000	0.000
103	A	103	THR	0	0.068	0.025	14.185	-0.011	-0.011	0.000	0.000	0.000	0.000
104	A	104	TYR	0	0.042	0.003	15.734	-0.025	-0.025	0.000	0.000	0.000	0.000
105	A	105	HIS	0	-0.076	-0.023	17.651	-0.006	-0.006	0.000	0.000	0.000	0.000
106	A	106	ILE	0	0.056	0.034	12.075	-0.007	-0.007	0.000	0.000	0.000	0.000
107	A	107	ILE	0	-0.021	-0.010	16.290	-0.021	-0.021	0.000	0.000	0.000	0.000
108	A	108	SER	0	-0.018	0.003	18.309	0.003	0.003	0.000	0.000	0.000	0.000
109	A	109	GLN	0	0.048	0.009	16.873	-0.021	-0.021	0.000	0.000	0.000	0.000
110	A	110	LEU	0	-0.033	-0.020	14.130	-0.012	-0.012	0.000	0.000	0.000	0.000
111	A	111	GLU	-1	-0.968	-0.977	18.345	-0.179	-0.179	0.000	0.000	0.000	0.000
112	A	112	SER	0	0.002	-0.008	21.853	0.015	0.015	0.000	0.000	0.000	0.000
113	A	113	PHE	0	0.007	0.010	19.199	0.004	0.004	0.000	0.000	0.000	0.000
114	A	114	VAL	0	0.019	0.003	19.884	0.004	0.004	0.000	0.000	0.000	0.000
115	A	115	ASN	0	0.021	0.011	22.452	0.011	0.011	0.000	0.000	0.000	0.000
116	A	116	GLN	0	-0.055	-0.035	24.663	0.021	0.021	0.000	0.000	0.000	0.000
117	A	117	GLN	0	-0.043	-0.037	21.459	-0.007	-0.007	0.000	0.000	0.000	0.000
118	A	118	GLU	-1	-0.943	-0.970	25.200	-0.170	-0.170	0.000	0.000	0.000	0.000
119	A	119	ALA	0	-0.017	-0.010	27.722	0.014	0.014	0.000	0.000	0.000	0.000
120	A	120	LEU	0	0.003	-0.011	26.799	0.011	0.011	0.000	0.000	0.000	0.000
121	A	121	LYS	1	0.841	0.922	26.767	0.212	0.212	0.000	0.000	0.000	0.000
122	A	122	ASN	0	-0.044	-0.023	30.124	0.011	0.011	0.000	0.000	0.000	0.000
123	A	123	ILE	0	-0.062	-0.019	32.971	0.010	0.010	0.000	0.000	0.000	0.000
124	A	124	LEU	0	-0.001	-0.005	30.740	0.007	0.007	0.000	0.000	0.000	0.000
125	A	125	GLN	0	0.023	0.025	31.938	-0.006	-0.006	0.000	0.000	0.000	0.000
126	A	126	GLU	-1	-0.985	-1.002	34.267	-0.109	-0.109	0.000	0.000	0.000	0.000
127	A	127	TYR	0	-0.062	-0.051	34.967	0.006	0.006	0.000	0.000	0.000	0.000
128	A	128	ALA	0	-0.049	-0.006	32.797	-0.004	-0.004	0.000	0.000	0.000	0.000
129	A	129	LYS	1	0.810	0.891	30.628	0.184	0.184	0.000	0.000	0.000	0.000
130	A	130	VAL	0	-0.015	0.003	34.953	-0.002	-0.002	0.000	0.000	0.000	0.000

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