FMO DATABASE

FMODB ID: 85Q5Y

Calculation Name: 4J4F-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4J4F

Chain ID: C

ChEMBL ID:

UniProt ID: P81180

Base Structure: X-ray

Registration Date: 2023-06-22

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	99
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-526107.612176
FMO2-HF: Nuclear repulsion	486882.993848
FMO2-HF: Total energy	-39224.618327
FMO2-MP2: Total energy	-39336.58811

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(C:1:LEU)

Summations of interaction energy for fragment #1(C: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.
-2.714	1.115	0.317	-1.775	-2.37	0.004

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.028 / q_NPA : 0.016

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	C	3	LYS	1	0.891	0.955	3.484	-0.328	2.579	0.008	-1.546	-1.368	0.004
4	C	4	PHE	0	0.113	0.037	5.832	0.023	0.023	0.000	0.000	0.000	0.000
5	C	5	SER	0	0.002	-0.013	7.974	-0.049	-0.049	0.000	0.000	0.000	0.000
6	C	6	GLN	0	-0.031	-0.022	9.208	0.058	0.058	0.000	0.000	0.000	0.000
7	C	7	THR	0	0.014	0.018	6.738	-0.189	-0.189	0.000	0.000	0.000	0.000
8	C	8	CYS	0	-0.070	-0.005	8.604	0.027	0.027	0.000	0.000	0.000	0.000
9	C	9	TYR	0	0.053	0.019	11.528	0.033	0.033	0.000	0.000	0.000	0.000
10	C	10	ASN	0	-0.012	-0.008	15.297	0.031	0.031	0.000	0.000	0.000	0.000
11	C	11	SER	0	-0.022	-0.015	14.431	0.014	0.014	0.000	0.000	0.000	0.000
12	C	12	ALA	0	-0.012	-0.001	16.757	0.003	0.003	0.000	0.000	0.000	0.000
13	C	13	ILE	0	-0.002	-0.003	17.832	0.007	0.007	0.000	0.000	0.000	0.000
14	C	14	GLN	0	0.006	0.015	19.939	-0.010	-0.010	0.000	0.000	0.000	0.000
15	C	15	GLY	0	0.002	-0.005	22.473	0.014	0.014	0.000	0.000	0.000	0.000
16	C	16	SER	0	-0.025	-0.034	20.098	-0.012	-0.012	0.000	0.000	0.000	0.000
17	C	17	VAL	0	0.007	0.005	17.980	0.010	0.010	0.000	0.000	0.000	0.000
18	C	18	LEU	0	0.015	0.022	12.302	-0.023	-0.023	0.000	0.000	0.000	0.000
19	C	19	THR	0	-0.005	0.000	15.169	0.047	0.047	0.000	0.000	0.000	0.000
20	C	20	SER	0	0.008	0.007	12.451	-0.046	-0.046	0.000	0.000	0.000	0.000
21	C	21	THR	0	-0.013	0.011	13.929	0.063	0.063	0.000	0.000	0.000	0.000
22	C	23	GLU	-1	-0.794	-0.889	7.963	-0.937	-0.937	0.000	0.000	0.000	0.000
23	C	24	ARG	1	0.906	0.956	6.698	-0.109	-0.109	0.000	0.000	0.000	0.000
24	C	25	THR	0	-0.009	-0.010	3.788	-0.884	-0.631	0.002	-0.071	-0.184	0.000
25	C	26	ASN	0	0.002	0.002	5.498	-0.047	-0.047	0.000	0.000	0.000	0.000
26	C	27	GLY	0	0.035	0.030	9.067	0.085	0.085	0.000	0.000	0.000	0.000
27	C	28	GLY	0	-0.018	-0.009	11.120	0.098	0.098	0.000	0.000	0.000	0.000
28	C	29	TYR	0	-0.047	-0.062	10.836	-0.065	-0.065	0.000	0.000	0.000	0.000
29	C	30	ASN	0	-0.028	-0.024	11.095	0.082	0.082	0.000	0.000	0.000	0.000
30	C	31	THR	0	-0.023	-0.001	12.548	-0.048	-0.048	0.000	0.000	0.000	0.000
31	C	32	SER	0	-0.069	-0.028	11.530	0.075	0.075	0.000	0.000	0.000	0.000
32	C	33	SER	0	0.049	-0.012	13.909	-0.053	-0.053	0.000	0.000	0.000	0.000
33	C	34	ILE	0	-0.022	-0.009	10.751	0.062	0.062	0.000	0.000	0.000	0.000
34	C	35	ASP	-1	-0.795	-0.878	14.179	0.063	0.063	0.000	0.000	0.000	0.000
35	C	36	LEU	0	0.008	-0.012	13.511	0.018	0.018	0.000	0.000	0.000	0.000
36	C	37	ASN	0	-0.012	-0.011	16.481	-0.012	-0.012	0.000	0.000	0.000	0.000
37	C	38	SER	0	-0.040	-0.003	16.630	0.009	0.009	0.000	0.000	0.000	0.000
38	C	39	VAL	0	-0.028	-0.019	12.873	0.013	0.013	0.000	0.000	0.000	0.000
39	C	40	ILE	0	-0.064	-0.026	14.497	-0.018	-0.018	0.000	0.000	0.000	0.000
40	C	41	GLU	-1	-0.817	-0.897	17.494	0.061	0.061	0.000	0.000	0.000	0.000
41	C	42	ASN	0	-0.034	-0.042	21.070	-0.017	-0.017	0.000	0.000	0.000	0.000
42	C	43	VAL	0	0.018	0.018	22.953	0.005	0.005	0.000	0.000	0.000	0.000
43	C	44	ASP	-1	-0.886	-0.950	25.492	-0.003	-0.003	0.000	0.000	0.000	0.000
44	C	45	GLY	0	-0.013	0.002	27.602	-0.005	-0.005	0.000	0.000	0.000	0.000
45	C	46	SER	0	-0.082	-0.040	22.997	-0.011	-0.011	0.000	0.000	0.000	0.000
46	C	47	LEU	0	0.030	0.015	19.629	0.008	0.008	0.000	0.000	0.000	0.000
47	C	48	LYS	1	0.882	0.945	18.530	0.016	0.016	0.000	0.000	0.000	0.000
48	C	49	TRP	0	0.006	0.004	11.476	0.010	0.010	0.000	0.000	0.000	0.000
49	C	50	GLN	0	0.015	0.008	15.882	-0.006	-0.006	0.000	0.000	0.000	0.000
50	C	51	GLY	0	-0.003	0.014	16.754	0.016	0.016	0.000	0.000	0.000	0.000
51	C	52	SER	0	-0.008	-0.017	17.779	0.010	0.010	0.000	0.000	0.000	0.000
52	C	53	ASN	0	0.053	0.026	19.570	-0.023	-0.023	0.000	0.000	0.000	0.000
53	C	54	PHE	0	0.078	0.020	23.043	0.009	0.009	0.000	0.000	0.000	0.000
54	C	55	ILE	0	-0.009	-0.007	25.082	0.001	0.001	0.000	0.000	0.000	0.000
55	C	56	GLU	-1	-0.935	-0.944	19.563	0.216	0.216	0.000	0.000	0.000	0.000
56	C	57	THR	0	-0.024	-0.018	18.728	0.015	0.015	0.000	0.000	0.000	0.000
57	C	58	CYS	0	-0.093	-0.035	21.768	0.001	0.001	0.000	0.000	0.000	0.000
58	C	59	ARG	1	0.835	0.883	24.861	-0.082	-0.082	0.000	0.000	0.000	0.000
59	C	60	ASN	0	-0.028	-0.036	27.842	-0.004	-0.004	0.000	0.000	0.000	0.000
60	C	61	THR	0	-0.004	0.009	29.633	-0.003	-0.003	0.000	0.000	0.000	0.000
61	C	62	GLN	0	-0.063	-0.034	31.993	0.002	0.002	0.000	0.000	0.000	0.000
62	C	63	LEU	0	0.021	0.019	34.996	0.000	0.000	0.000	0.000	0.000	0.000
63	C	64	ALA	0	0.001	0.001	36.044	0.000	0.000	0.000	0.000	0.000	0.000
64	C	65	GLY	0	0.077	0.034	37.940	-0.001	-0.001	0.000	0.000	0.000	0.000
65	C	66	SER	0	-0.037	-0.028	40.813	0.000	0.000	0.000	0.000	0.000	0.000
66	C	67	SER	0	-0.079	-0.041	39.979	0.000	0.000	0.000	0.000	0.000	0.000
67	C	68	GLU	-1	-0.910	-0.933	35.170	0.023	0.023	0.000	0.000	0.000	0.000
68	C	69	LEU	0	-0.006	-0.003	30.786	0.002	0.002	0.000	0.000	0.000	0.000
69	C	70	ALA	0	0.012	0.007	31.479	-0.001	-0.001	0.000	0.000	0.000	0.000
70	C	71	ALA	0	0.018	-0.004	28.135	0.004	0.004	0.000	0.000	0.000	0.000
71	C	72	GLU	-1	-0.782	-0.830	26.193	0.067	0.067	0.000	0.000	0.000	0.000
72	C	74	LYS	1	0.891	0.934	18.101	-0.186	-0.186	0.000	0.000	0.000	0.000
73	C	75	THR	0	0.001	0.001	16.488	-0.005	-0.005	0.000	0.000	0.000	0.000
74	C	76	ARG	1	0.864	0.905	12.298	-0.085	-0.085	0.000	0.000	0.000	0.000
75	C	77	ALA	0	0.005	0.011	11.387	-0.015	-0.015	0.000	0.000	0.000	0.000
76	C	78	GLN	0	0.003	0.000	5.669	-0.059	-0.059	0.000	0.000	0.000	0.000
77	C	79	GLN	0	-0.007	0.007	8.231	-0.070	-0.070	0.000	0.000	0.000	0.000
78	C	80	PHE	0	0.002	0.000	2.799	-0.712	-0.043	0.307	-0.158	-0.818	0.000
79	C	81	VAL	0	-0.008	-0.014	8.156	-0.020	-0.020	0.000	0.000	0.000	0.000
80	C	82	SER	0	-0.004	0.000	9.583	-0.021	-0.021	0.000	0.000	0.000	0.000
81	C	83	THR	0	-0.001	0.000	9.783	0.046	0.046	0.000	0.000	0.000	0.000
82	C	84	LYS	1	0.942	0.959	12.183	0.046	0.046	0.000	0.000	0.000	0.000
83	C	85	ILE	0	0.033	0.021	13.658	0.037	0.037	0.000	0.000	0.000	0.000
84	C	86	ASN	0	-0.030	-0.023	16.210	-0.049	-0.049	0.000	0.000	0.000	0.000
85	C	87	LEU	0	0.022	0.006	14.291	0.024	0.024	0.000	0.000	0.000	0.000
86	C	88	ASP	-1	-0.861	-0.933	18.350	0.017	0.017	0.000	0.000	0.000	0.000
87	C	89	ASP	-1	-0.908	-0.930	20.828	0.085	0.085	0.000	0.000	0.000	0.000
88	C	90	HIS	1	0.799	0.880	19.969	-0.132	-0.132	0.000	0.000	0.000	0.000
89	C	91	ILE	0	-0.044	0.000	17.472	0.014	0.014	0.000	0.000	0.000	0.000
90	C	92	ALA	0	0.070	0.042	21.125	-0.017	-0.017	0.000	0.000	0.000	0.000
91	C	93	ASN	0	-0.021	-0.027	24.158	0.005	0.005	0.000	0.000	0.000	0.000
92	C	94	ILE	0	-0.033	-0.013	26.088	-0.001	-0.001	0.000	0.000	0.000	0.000
93	C	95	ASP	-1	-0.880	-0.953	28.063	0.019	0.019	0.000	0.000	0.000	0.000
94	C	96	GLY	0	0.018	0.018	28.371	0.001	0.001	0.000	0.000	0.000	0.000
95	C	97	THR	0	-0.073	-0.037	23.795	-0.005	-0.005	0.000	0.000	0.000	0.000
96	C	98	LEU	0	-0.005	0.001	19.267	0.006	0.006	0.000	0.000	0.000	0.000
97	C	99	LYS	1	0.882	0.947	21.728	-0.053	-0.053	0.000	0.000	0.000	0.000
98	C	100	TYR	0	0.008	0.008	18.506	0.000	0.000	0.000	0.000	0.000	0.000
99	C	101	GLU	-1	-0.914	-0.952	21.401	0.101	0.101	0.000	0.000	0.000	0.000

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