FMO DATABASE

FMODB ID: 3JZML

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1080647.063279
FMO2-HF: Nuclear repulsion	1030001.909814
FMO2-HF: Total energy	-50645.153465
FMO2-MP2: Total energy	-50793.076844

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.
-16.943	-8.773	2.913	-4.073	-7.008	-0.014

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 : 0.052 / q_NPA : 0.012

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	3	ALA	0	0.047	0.017	3.168	-4.338	-1.901	0.053	-1.123	-1.367	0.004
4	A	4	HIS	0	0.007	0.006	2.416	-3.080	-0.908	1.570	-1.426	-2.316	-0.006
5	A	5	GLN	0	0.029	0.007	2.843	-0.769	0.600	0.185	-0.436	-1.117	0.000
6	A	6	ASP	-1	-0.883	-0.947	5.523	1.016	1.016	0.000	0.000	0.000	0.000
7	A	7	ILE	0	-0.006	0.013	6.657	0.001	0.001	0.000	0.000	0.000	0.000
8	A	8	ILE	0	-0.014	-0.015	7.411	0.108	0.108	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.035	0.034	9.500	0.074	0.074	0.000	0.000	0.000	0.000
10	A	10	ASN	0	-0.057	-0.033	11.292	0.082	0.082	0.000	0.000	0.000	0.000
11	A	11	ILE	0	-0.019	-0.014	12.493	0.040	0.040	0.000	0.000	0.000	0.000
12	A	12	GLY	0	0.038	0.007	13.349	0.027	0.027	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.981	-0.991	15.022	-0.004	-0.004	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.824	0.917	17.517	0.080	0.080	0.000	0.000	0.000	0.000
15	A	15	LEU	0	-0.008	0.000	16.657	0.011	0.011	0.000	0.000	0.000	0.000
16	A	16	GLY	0	-0.035	0.009	19.429	0.004	0.004	0.000	0.000	0.000	0.000
17	A	17	LEU	0	-0.028	-0.029	16.094	0.003	0.003	0.000	0.000	0.000	0.000
18	A	18	PRO	0	-0.038	-0.014	14.186	-0.012	-0.012	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.003	0.007	11.523	-0.039	-0.039	0.000	0.000	0.000	0.000
20	A	20	THR	0	0.002	-0.010	6.989	0.076	0.076	0.000	0.000	0.000	0.000
21	A	21	PHE	0	-0.038	-0.006	4.218	-0.308	-0.048	0.000	-0.023	-0.236	0.000
22	A	22	ASP	-1	-0.812	-0.911	5.792	-1.588	-1.588	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.948	-0.988	4.647	-2.116	-2.013	-0.001	-0.004	-0.099	0.000
24	A	24	ASN	0	-0.126	-0.058	5.391	-0.225	-0.225	0.000	0.000	0.000	0.000
25	A	25	ASN	0	-0.031	-0.017	2.545	-4.539	-2.833	1.108	-1.045	-1.769	-0.012
26	A	26	GLN	0	0.024	0.003	4.598	0.546	0.581	-0.001	-0.006	-0.027	0.000
27	A	27	CYS	0	-0.003	0.012	7.993	0.032	0.032	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.048	-0.019	10.322	0.087	0.087	0.000	0.000	0.000	0.000
29	A	29	LEU	0	0.012	-0.005	13.937	0.029	0.029	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.024	0.002	16.967	0.011	0.011	0.000	0.000	0.000	0.000
31	A	31	LEU	0	0.003	-0.006	19.155	0.008	0.008	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.847	-0.925	22.625	-0.177	-0.177	0.000	0.000	0.000	0.000
33	A	33	SER	0	-0.165	-0.084	25.041	0.017	0.017	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.936	-0.990	26.155	-0.195	-0.195	0.000	0.000	0.000	0.000
35	A	35	ILE	0	0.014	0.034	21.981	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	36	PHE	0	-0.001	-0.004	20.200	-0.018	-0.018	0.000	0.000	0.000	0.000
37	A	37	THR	0	0.005	-0.005	16.263	0.016	0.016	0.000	0.000	0.000	0.000
38	A	38	SER	0	-0.049	-0.019	13.076	-0.054	-0.054	0.000	0.000	0.000	0.000
39	A	39	ILE	0	0.035	0.022	9.470	0.068	0.068	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.915	-0.967	8.364	-1.200	-1.200	0.000	0.000	0.000	0.000
41	A	41	ALA	0	-0.035	0.005	4.257	0.134	0.222	-0.001	-0.010	-0.077	0.000
42	A	42	LYS	1	0.953	0.962	6.298	0.444	0.444	0.000	0.000	0.000	0.000
43	A	43	ASP	-1	-0.932	-0.967	6.652	-0.403	-0.403	0.000	0.000	0.000	0.000
44	A	44	ASP	-1	-0.976	-1.001	6.177	-0.236	-0.236	0.000	0.000	0.000	0.000
45	A	45	ILE	0	-0.013	0.010	8.148	0.133	0.133	0.000	0.000	0.000	0.000
46	A	46	TRP	0	-0.029	-0.019	6.660	-0.131	-0.131	0.000	0.000	0.000	0.000
47	A	47	LEU	0	-0.028	-0.021	10.503	0.177	0.177	0.000	0.000	0.000	0.000
48	A	48	LEU	0	-0.002	0.011	12.378	-0.083	-0.083	0.000	0.000	0.000	0.000
49	A	49	ASN	0	0.038	0.008	14.938	0.059	0.059	0.000	0.000	0.000	0.000
50	A	50	GLY	0	0.043	0.008	17.127	-0.016	-0.016	0.000	0.000	0.000	0.000
51	A	51	MET	0	-0.041	-0.007	20.205	0.021	0.021	0.000	0.000	0.000	0.000
52	A	52	ILE	0	0.003	0.005	22.563	0.011	0.011	0.000	0.000	0.000	0.000
53	A	53	ILE	0	0.004	-0.010	26.178	0.010	0.010	0.000	0.000	0.000	0.000
54	A	54	PRO	0	-0.017	0.023	28.049	-0.007	-0.007	0.000	0.000	0.000	0.000
55	A	55	LEU	0	0.065	-0.015	29.072	0.013	0.013	0.000	0.000	0.000	0.000
56	A	56	SER	0	0.020	0.017	31.306	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	57	PRO	0	0.085	0.045	32.213	0.003	0.003	0.000	0.000	0.000	0.000
58	A	58	VAL	0	-0.054	-0.038	33.633	0.006	0.006	0.000	0.000	0.000	0.000
59	A	59	CYS	0	-0.015	0.008	35.396	0.005	0.005	0.000	0.000	0.000	0.000
60	A	60	GLY	0	0.036	0.024	37.495	0.006	0.006	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.919	-0.977	38.654	-0.100	-0.100	0.000	0.000	0.000	0.000
62	A	62	SER	0	-0.104	-0.052	39.417	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	63	ILE	0	0.091	0.053	35.018	0.000	0.000	0.000	0.000	0.000	0.000
64	A	64	TRP	0	0.031	0.019	30.785	-0.006	-0.006	0.000	0.000	0.000	0.000
65	A	65	ARG	1	0.922	0.954	34.811	0.089	0.089	0.000	0.000	0.000	0.000
66	A	66	GLN	0	0.060	0.042	35.971	0.001	0.001	0.000	0.000	0.000	0.000
67	A	67	ILE	0	0.049	0.022	30.418	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	68	MET	0	-0.021	-0.016	31.401	-0.008	-0.008	0.000	0.000	0.000	0.000
69	A	69	VAL	0	-0.066	-0.027	33.054	0.003	0.003	0.000	0.000	0.000	0.000
70	A	70	ILE	0	0.058	0.038	30.192	0.001	0.001	0.000	0.000	0.000	0.000
71	A	71	ASN	0	0.006	-0.001	27.714	-0.011	-0.011	0.000	0.000	0.000	0.000
72	A	72	GLY	0	-0.048	-0.010	29.655	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	73	GLU	-1	-0.952	-0.988	31.805	-0.111	-0.111	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.003	0.000	26.304	0.002	0.002	0.000	0.000	0.000	0.000
75	A	75	ALA	0	0.004	0.003	27.050	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	76	ALA	0	-0.072	-0.024	27.971	0.005	0.005	0.000	0.000	0.000	0.000
77	A	77	ASN	0	-0.054	-0.032	28.270	0.015	0.015	0.000	0.000	0.000	0.000
78	A	78	ASN	0	-0.054	-0.020	20.961	-0.012	-0.012	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.877	-0.951	23.193	-0.189	-0.189	0.000	0.000	0.000	0.000
80	A	80	GLY	0	-0.001	0.007	21.967	-0.025	-0.025	0.000	0.000	0.000	0.000
81	A	81	THR	0	-0.094	-0.041	22.339	0.028	0.028	0.000	0.000	0.000	0.000
82	A	82	LEU	0	0.006	0.001	23.231	-0.024	-0.024	0.000	0.000	0.000	0.000
83	A	83	ALA	0	-0.008	-0.012	22.935	0.013	0.013	0.000	0.000	0.000	0.000
84	A	84	TYR	0	-0.012	-0.031	25.080	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	85	ILE	0	-0.025	-0.002	20.653	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	86	ASP	-1	-0.875	-0.966	24.079	-0.187	-0.187	0.000	0.000	0.000	0.000
87	A	87	ALA	0	-0.017	-0.008	23.655	0.007	0.007	0.000	0.000	0.000	0.000
88	A	88	ALA	0	-0.014	-0.005	23.099	0.001	0.001	0.000	0.000	0.000	0.000
89	A	89	GLU	-1	-0.892	-0.914	25.243	-0.164	-0.164	0.000	0.000	0.000	0.000
90	A	90	THR	0	-0.047	-0.025	24.054	0.007	0.007	0.000	0.000	0.000	0.000
91	A	91	LEU	0	-0.018	0.011	25.524	-0.008	-0.008	0.000	0.000	0.000	0.000
92	A	92	LEU	0	-0.021	-0.023	19.297	-0.006	-0.006	0.000	0.000	0.000	0.000
93	A	93	LEU	0	0.023	0.021	21.734	0.015	0.015	0.000	0.000	0.000	0.000
94	A	94	ILE	0	-0.013	-0.012	17.274	-0.034	-0.034	0.000	0.000	0.000	0.000
95	A	95	HIS	0	0.046	0.012	17.631	0.035	0.035	0.000	0.000	0.000	0.000
96	A	96	ALA	0	0.000	0.019	15.186	-0.058	-0.058	0.000	0.000	0.000	0.000
97	A	97	ILE	0	-0.014	0.003	13.280	0.064	0.064	0.000	0.000	0.000	0.000
98	A	98	THR	0	-0.003	-0.030	12.819	-0.054	-0.054	0.000	0.000	0.000	0.000
99	A	99	ASP	-1	-0.866	-0.899	13.209	-0.020	-0.020	0.000	0.000	0.000	0.000
100	A	100	LEU	0	0.007	-0.009	8.178	-0.020	-0.020	0.000	0.000	0.000	0.000
101	A	101	THR	0	-0.072	-0.050	11.147	0.056	0.056	0.000	0.000	0.000	0.000
102	A	102	ASN	0	-0.008	-0.009	13.384	0.020	0.020	0.000	0.000	0.000	0.000
103	A	103	THR	0	0.066	0.023	14.896	-0.025	-0.025	0.000	0.000	0.000	0.000
104	A	104	TYR	0	0.024	-0.005	15.800	-0.026	-0.026	0.000	0.000	0.000	0.000
105	A	105	HIS	0	-0.022	0.009	17.366	0.000	0.000	0.000	0.000	0.000	0.000
106	A	106	ILE	0	0.045	0.029	12.084	-0.013	-0.013	0.000	0.000	0.000	0.000
107	A	107	ILE	0	-0.019	-0.010	16.307	-0.026	-0.026	0.000	0.000	0.000	0.000
108	A	108	SER	0	-0.002	0.006	18.376	-0.007	-0.007	0.000	0.000	0.000	0.000
109	A	109	GLN	0	0.030	0.001	17.028	0.010	0.010	0.000	0.000	0.000	0.000
110	A	110	LEU	0	-0.031	-0.017	14.190	-0.016	-0.016	0.000	0.000	0.000	0.000
111	A	111	GLU	-1	-0.961	-0.972	18.243	-0.158	-0.158	0.000	0.000	0.000	0.000
112	A	112	SER	0	0.004	-0.004	21.801	0.010	0.010	0.000	0.000	0.000	0.000
113	A	113	PHE	0	0.008	0.010	19.046	0.001	0.001	0.000	0.000	0.000	0.000
114	A	114	VAL	0	0.019	0.002	19.829	0.001	0.001	0.000	0.000	0.000	0.000
115	A	115	ASN	0	0.036	0.018	22.300	0.008	0.008	0.000	0.000	0.000	0.000
116	A	116	GLN	0	-0.020	-0.001	24.405	0.018	0.018	0.000	0.000	0.000	0.000
117	A	117	GLN	0	-0.030	-0.029	21.300	-0.003	-0.003	0.000	0.000	0.000	0.000
118	A	118	GLU	-1	-0.955	-0.975	24.932	-0.163	-0.163	0.000	0.000	0.000	0.000
119	A	119	ALA	0	-0.008	-0.006	27.532	0.012	0.012	0.000	0.000	0.000	0.000
120	A	120	LEU	0	-0.001	-0.011	26.206	0.010	0.010	0.000	0.000	0.000	0.000
121	A	121	LYS	1	0.893	0.958	26.037	0.215	0.215	0.000	0.000	0.000	0.000
122	A	122	ASN	0	-0.015	-0.007	29.846	0.005	0.005	0.000	0.000	0.000	0.000
123	A	123	ILE	0	-0.072	-0.025	32.635	0.009	0.009	0.000	0.000	0.000	0.000
124	A	124	LEU	0	-0.008	-0.010	30.244	0.006	0.006	0.000	0.000	0.000	0.000
125	A	125	GLN	0	0.021	0.027	32.092	-0.007	-0.007	0.000	0.000	0.000	0.000
126	A	126	GLU	-1	-0.980	-0.998	34.116	-0.109	-0.109	0.000	0.000	0.000	0.000
127	A	127	TYR	0	-0.085	-0.051	34.663	0.005	0.005	0.000	0.000	0.000	0.000
128	A	128	ALA	0	-0.050	-0.007	32.623	-0.005	-0.005	0.000	0.000	0.000	0.000
129	A	129	LYS	1	0.809	0.894	30.715	0.187	0.187	0.000	0.000	0.000	0.000
130	A	130	VAL	0	-0.017	0.002	34.732	-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)