FMO DATABASE

FMODB ID: ZYK5N

Calculation Name: 3JRZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3JRZ

Chain ID: A

ChEMBL ID:

UniProt ID: Q84B82

Base Structure: X-ray

Registration Date: 2023-06-19

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	104
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-806579.737247
FMO2-HF: Nuclear repulsion	765650.683503
FMO2-HF: Total energy	-40929.053745
FMO2-MP2: Total energy	-41049.067391

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:SER)

Summations of interaction energy for fragment #1(A:2:SER)

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.
-22.15	-15.262	7.79	-6.523	-8.159	-0.049

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : 0.002

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	4	PHE	0	-0.027	-0.032	3.800	-1.111	0.125	0.002	-0.507	-0.732	0.001
4	A	5	THR	0	0.002	-0.001	2.076	-1.500	-0.099	2.875	-1.810	-2.466	-0.020
5	A	6	LEU	0	-0.021	-0.010	4.523	0.648	0.731	-0.001	-0.029	-0.054	0.000
6	A	7	TYR	0	0.028	0.007	2.919	-4.642	-3.168	0.279	-0.801	-0.952	0.009
7	A	8	LYS	1	0.843	0.922	8.702	-0.437	-0.437	0.000	0.000	0.000	0.000
8	A	9	ASN	0	-0.036	-0.016	12.496	0.130	0.130	0.000	0.000	0.000	0.000
9	A	10	LYS	1	0.853	0.897	13.817	-0.552	-0.552	0.000	0.000	0.000	0.000
10	A	11	ASP	-1	-0.802	-0.860	17.435	0.175	0.175	0.000	0.000	0.000	0.000
11	A	12	LYS	1	0.872	0.930	19.597	-0.265	-0.265	0.000	0.000	0.000	0.000
12	A	13	SER	0	-0.037	-0.032	22.825	-0.018	-0.018	0.000	0.000	0.000	0.000
13	A	14	SER	0	-0.014	-0.030	19.705	-0.011	-0.011	0.000	0.000	0.000	0.000
14	A	15	ALA	0	0.020	0.021	18.783	-0.020	-0.020	0.000	0.000	0.000	0.000
15	A	16	LYS	1	0.928	0.961	19.724	-0.074	-0.074	0.000	0.000	0.000	0.000
16	A	17	THR	0	-0.017	-0.009	21.652	-0.014	-0.014	0.000	0.000	0.000	0.000
17	A	18	TYR	0	-0.028	-0.018	17.371	-0.030	-0.030	0.000	0.000	0.000	0.000
18	A	19	PRO	0	0.040	0.027	17.035	0.043	0.043	0.000	0.000	0.000	0.000
19	A	20	TYR	0	0.027	0.009	12.112	0.069	0.069	0.000	0.000	0.000	0.000
20	A	21	PHE	0	-0.026	-0.013	10.500	-0.066	-0.066	0.000	0.000	0.000	0.000
21	A	22	VAL	0	0.024	0.023	8.080	0.146	0.146	0.000	0.000	0.000	0.000
22	A	23	ASP	-1	-0.830	-0.931	4.927	1.483	1.705	-0.001	-0.013	-0.209	0.000
23	A	24	VAL	0	0.010	-0.007	7.021	-0.821	-0.821	0.000	0.000	0.000	0.000
24	A	25	GLN	0	-0.023	0.007	6.616	0.004	0.004	0.000	0.000	0.000	0.000
25	A	26	SER	0	0.016	0.015	5.529	-0.642	-0.642	0.000	0.000	0.000	0.000
26	A	27	ASP	-1	-0.757	-0.899	2.442	-16.005	-13.733	4.638	-3.335	-3.576	-0.039
27	A	28	LEU	0	-0.029	-0.014	5.134	0.759	0.795	-0.001	0.000	-0.035	0.000
28	A	29	LEU	0	-0.048	-0.029	7.979	0.335	0.335	0.000	0.000	0.000	0.000
29	A	30	ASP	-1	-0.850	-0.922	4.268	1.564	1.728	-0.001	-0.028	-0.135	0.000
30	A	31	ASN	0	-0.051	-0.021	6.887	0.476	0.476	0.000	0.000	0.000	0.000
31	A	32	LEU	0	0.022	0.034	10.140	0.102	0.102	0.000	0.000	0.000	0.000
32	A	33	ASN	0	-0.007	-0.021	10.498	0.249	0.249	0.000	0.000	0.000	0.000
33	A	34	THR	0	-0.048	-0.016	11.875	0.087	0.087	0.000	0.000	0.000	0.000
34	A	35	ARG	1	0.827	0.911	4.987	-1.575	-1.575	0.000	0.000	0.000	0.000
35	A	36	LEU	0	0.003	0.007	9.354	0.014	0.014	0.000	0.000	0.000	0.000
36	A	37	VAL	0	0.019	0.006	8.776	-0.101	-0.101	0.000	0.000	0.000	0.000
37	A	38	ILE	0	0.024	0.000	11.152	-0.029	-0.029	0.000	0.000	0.000	0.000
38	A	39	PRO	0	-0.020	0.010	12.733	0.018	0.018	0.000	0.000	0.000	0.000
39	A	40	LEU	0	0.015	0.008	12.639	-0.065	-0.065	0.000	0.000	0.000	0.000
40	A	41	THR	0	-0.052	-0.049	16.221	0.050	0.050	0.000	0.000	0.000	0.000
41	A	42	PRO	0	0.039	0.017	19.777	-0.023	-0.023	0.000	0.000	0.000	0.000
42	A	43	ILE	0	0.021	0.011	21.788	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	44	GLU	-1	-0.887	-0.955	23.905	-0.030	-0.030	0.000	0.000	0.000	0.000
44	A	45	LEU	0	-0.078	-0.032	23.596	0.007	0.007	0.000	0.000	0.000	0.000
45	A	46	LEU	0	-0.062	-0.029	22.847	0.001	0.001	0.000	0.000	0.000	0.000
46	A	47	ASP	-1	-0.791	-0.880	27.144	-0.045	-0.045	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.790	0.882	29.954	0.042	0.042	0.000	0.000	0.000	0.000
48	A	49	LYS	1	0.870	0.924	24.729	0.082	0.082	0.000	0.000	0.000	0.000
49	A	50	ALA	0	0.037	0.032	27.896	0.002	0.002	0.000	0.000	0.000	0.000
50	A	51	PRO	0	0.030	0.009	24.299	-0.008	-0.008	0.000	0.000	0.000	0.000
51	A	52	SER	0	-0.067	-0.046	21.399	0.012	0.012	0.000	0.000	0.000	0.000
52	A	53	HIS	0	-0.014	0.009	23.003	-0.011	-0.011	0.000	0.000	0.000	0.000
53	A	54	LEU	0	0.036	0.022	21.622	-0.022	-0.022	0.000	0.000	0.000	0.000
54	A	55	CYS	0	-0.057	0.000	20.447	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	56	PRO	0	0.043	0.025	16.823	0.023	0.023	0.000	0.000	0.000	0.000
56	A	57	THR	0	-0.022	-0.019	19.067	0.032	0.032	0.000	0.000	0.000	0.000
57	A	58	ILE	0	-0.037	-0.011	14.281	-0.026	-0.026	0.000	0.000	0.000	0.000
58	A	59	HIS	1	0.838	0.894	17.169	0.235	0.235	0.000	0.000	0.000	0.000
59	A	60	ILE	0	-0.021	0.004	13.468	-0.044	-0.044	0.000	0.000	0.000	0.000
60	A	61	ASP	-1	-0.842	-0.914	15.830	-0.057	-0.057	0.000	0.000	0.000	0.000
61	A	62	GLU	-1	-0.881	-0.944	13.870	0.002	0.002	0.000	0.000	0.000	0.000
62	A	63	GLY	0	-0.018	-0.012	17.415	0.019	0.019	0.000	0.000	0.000	0.000
63	A	64	ASP	-1	-0.857	-0.907	18.882	-0.142	-0.142	0.000	0.000	0.000	0.000
64	A	65	PHE	0	-0.028	-0.031	17.320	0.028	0.028	0.000	0.000	0.000	0.000
65	A	66	ILE	0	-0.025	-0.008	19.588	-0.026	-0.026	0.000	0.000	0.000	0.000
66	A	67	MET	0	-0.001	0.007	12.852	0.012	0.012	0.000	0.000	0.000	0.000
67	A	68	LEU	0	-0.019	-0.014	17.415	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	69	THR	0	0.060	0.007	16.752	0.008	0.008	0.000	0.000	0.000	0.000
69	A	70	GLN	0	0.015	-0.005	18.304	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	71	GLN	0	-0.069	-0.034	19.122	0.047	0.047	0.000	0.000	0.000	0.000
71	A	72	MET	0	-0.010	0.015	14.220	0.007	0.007	0.000	0.000	0.000	0.000
72	A	73	THR	0	-0.028	-0.011	14.956	0.016	0.016	0.000	0.000	0.000	0.000
73	A	74	SER	0	0.032	0.021	13.390	0.012	0.012	0.000	0.000	0.000	0.000
74	A	75	VAL	0	-0.001	0.005	11.478	-0.010	-0.010	0.000	0.000	0.000	0.000
75	A	76	PRO	0	0.024	-0.009	12.392	0.079	0.079	0.000	0.000	0.000	0.000
76	A	77	VAL	0	0.031	0.006	7.653	-0.027	-0.027	0.000	0.000	0.000	0.000
77	A	78	LYS	1	0.876	0.938	10.006	-0.533	-0.533	0.000	0.000	0.000	0.000
78	A	79	ILE	0	-0.014	0.000	12.010	-0.056	-0.056	0.000	0.000	0.000	0.000
79	A	80	LEU	0	-0.025	0.021	6.852	-0.156	-0.156	0.000	0.000	0.000	0.000
80	A	81	SER	0	0.008	-0.004	9.785	0.032	0.032	0.000	0.000	0.000	0.000
81	A	82	GLU	-1	-0.802	-0.894	10.054	0.326	0.326	0.000	0.000	0.000	0.000
82	A	83	PRO	0	0.028	0.016	5.637	-0.066	-0.066	0.000	0.000	0.000	0.000
83	A	84	VAL	0	-0.050	-0.019	7.600	-0.083	-0.083	0.000	0.000	0.000	0.000
84	A	85	ASN	0	0.007	-0.002	9.082	-0.090	-0.090	0.000	0.000	0.000	0.000
85	A	86	GLU	-1	-0.871	-0.905	5.929	-1.421	-1.421	0.000	0.000	0.000	0.000
86	A	87	LEU	0	0.017	0.003	7.685	0.251	0.251	0.000	0.000	0.000	0.000
87	A	88	SER	0	-0.041	-0.049	6.542	0.110	0.110	0.000	0.000	0.000	0.000
88	A	89	THR	0	-0.024	-0.013	8.617	0.103	0.103	0.000	0.000	0.000	0.000
89	A	90	PHE	0	0.054	0.024	12.093	0.071	0.071	0.000	0.000	0.000	0.000
90	A	91	ARG	1	0.916	0.957	9.539	1.060	1.060	0.000	0.000	0.000	0.000
91	A	92	ASN	0	-0.016	-0.014	11.788	-0.034	-0.034	0.000	0.000	0.000	0.000
92	A	93	GLU	-1	-0.770	-0.867	15.237	-0.291	-0.291	0.000	0.000	0.000	0.000
93	A	94	ILE	0	-0.001	-0.003	11.326	0.041	0.041	0.000	0.000	0.000	0.000
94	A	95	ILE	0	-0.008	-0.011	11.253	0.040	0.040	0.000	0.000	0.000	0.000
95	A	96	ALA	0	0.020	0.017	14.863	0.060	0.060	0.000	0.000	0.000	0.000
96	A	97	ALA	0	0.002	0.013	17.598	0.048	0.048	0.000	0.000	0.000	0.000
97	A	98	ILE	0	-0.038	-0.035	13.084	0.042	0.042	0.000	0.000	0.000	0.000
98	A	99	ASP	-1	-0.876	-0.911	17.558	-0.306	-0.306	0.000	0.000	0.000	0.000
99	A	100	PHE	0	0.017	0.012	19.896	0.048	0.048	0.000	0.000	0.000	0.000
100	A	101	LEU	0	-0.075	-0.042	19.147	0.034	0.034	0.000	0.000	0.000	0.000
101	A	102	ILE	0	-0.085	-0.042	18.429	0.026	0.026	0.000	0.000	0.000	0.000
102	A	103	THR	0	-0.061	-0.054	22.754	0.026	0.026	0.000	0.000	0.000	0.000
103	A	104	GLY	0	-0.010	0.020	25.102	0.019	0.019	0.000	0.000	0.000	0.000
104	A	105	ILE	0	-0.033	-0.027	26.306	-0.010	-0.010	0.000	0.000	0.000	0.000

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