FMO DATABASE

FMODB ID: G6V61

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

Total energy (hartree)

FMO2-HF: Electronic energy	-526529.976091
FMO2-HF: Nuclear repulsion	487305.553455
FMO2-HF: Total energy	-39224.422636
FMO2-MP2: Total energy	-39336.36805

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.
-2.78	1.05	0.39	-1.729	-2.491	0.007

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 : 0.016 / q_NPA : 0.011

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	0.905	0.960	3.543	-0.211	2.785	-0.010	-1.528	-1.458	0.006
4	C	4	PHE	0	0.083	0.032	5.771	0.040	0.040	0.000	0.000	0.000	0.000
5	C	5	SER	0	0.002	-0.015	7.820	-0.032	-0.032	0.000	0.000	0.000	0.000
6	C	6	GLN	0	-0.024	-0.025	8.768	0.002	0.002	0.000	0.000	0.000	0.000
7	C	7	THR	0	0.017	0.017	6.501	-0.143	-0.143	0.000	0.000	0.000	0.000
8	C	8	CYS	0	-0.059	-0.013	8.201	0.021	0.021	0.000	0.000	0.000	0.000
9	C	9	TYR	0	0.036	0.010	11.290	0.026	0.026	0.000	0.000	0.000	0.000
10	C	10	ASN	0	-0.002	-0.017	15.032	0.038	0.038	0.000	0.000	0.000	0.000
11	C	11	SER	0	-0.024	-0.022	13.977	0.012	0.012	0.000	0.000	0.000	0.000
12	C	12	ALA	0	-0.019	-0.002	16.353	0.004	0.004	0.000	0.000	0.000	0.000
13	C	13	ILE	0	0.000	-0.002	17.703	0.008	0.008	0.000	0.000	0.000	0.000
14	C	14	GLN	0	0.005	0.012	19.762	-0.009	-0.009	0.000	0.000	0.000	0.000
15	C	15	GLY	0	0.002	-0.003	21.925	0.014	0.014	0.000	0.000	0.000	0.000
16	C	16	SER	0	-0.020	-0.029	19.914	-0.015	-0.015	0.000	0.000	0.000	0.000
17	C	17	VAL	0	-0.001	0.003	17.655	0.009	0.009	0.000	0.000	0.000	0.000
18	C	18	LEU	0	-0.010	0.004	12.104	-0.025	-0.025	0.000	0.000	0.000	0.000
19	C	19	THR	0	0.016	0.008	14.761	0.049	0.049	0.000	0.000	0.000	0.000
20	C	20	SER	0	0.022	0.022	11.911	-0.060	-0.060	0.000	0.000	0.000	0.000
21	C	21	THR	0	-0.046	-0.016	13.452	0.058	0.058	0.000	0.000	0.000	0.000
22	C	23	GLU	-1	-0.815	-0.901	7.591	-0.965	-0.965	0.000	0.000	0.000	0.000
23	C	24	ARG	1	0.905	0.944	6.803	-0.354	-0.354	0.000	0.000	0.000	0.000
24	C	25	THR	0	-0.002	-0.007	3.852	-0.553	-0.404	0.000	-0.023	-0.126	0.000
25	C	26	ASN	0	-0.017	-0.015	5.585	-0.232	-0.232	0.000	0.000	0.000	0.000
26	C	27	GLY	0	0.047	0.041	8.970	0.049	0.049	0.000	0.000	0.000	0.000
27	C	28	GLY	0	-0.013	-0.004	11.044	0.111	0.111	0.000	0.000	0.000	0.000
28	C	29	TYR	0	-0.042	-0.042	10.912	-0.031	-0.031	0.000	0.000	0.000	0.000
29	C	30	ASN	0	-0.022	-0.014	11.052	0.064	0.064	0.000	0.000	0.000	0.000
30	C	31	THR	0	0.010	0.026	12.452	-0.074	-0.074	0.000	0.000	0.000	0.000
31	C	32	SER	0	-0.058	-0.015	11.532	0.082	0.082	0.000	0.000	0.000	0.000
32	C	33	SER	0	0.035	-0.017	13.958	-0.053	-0.053	0.000	0.000	0.000	0.000
33	C	34	ILE	0	-0.013	0.001	10.287	0.063	0.063	0.000	0.000	0.000	0.000
34	C	35	ASP	-1	-0.797	-0.879	13.863	0.044	0.044	0.000	0.000	0.000	0.000
35	C	36	LEU	0	-0.008	-0.020	13.045	0.016	0.016	0.000	0.000	0.000	0.000
36	C	37	ASN	0	-0.028	-0.018	16.105	-0.018	-0.018	0.000	0.000	0.000	0.000
37	C	38	SER	0	0.013	0.015	16.524	-0.001	-0.001	0.000	0.000	0.000	0.000
38	C	39	VAL	0	-0.045	-0.021	12.681	0.009	0.009	0.000	0.000	0.000	0.000
39	C	40	ILE	0	-0.051	-0.014	14.316	-0.022	-0.022	0.000	0.000	0.000	0.000
40	C	41	GLU	-1	-0.840	-0.921	17.329	0.038	0.038	0.000	0.000	0.000	0.000
41	C	42	ASN	0	-0.023	-0.025	20.965	-0.018	-0.018	0.000	0.000	0.000	0.000
42	C	43	VAL	0	0.024	0.020	22.453	0.006	0.006	0.000	0.000	0.000	0.000
43	C	44	ASP	-1	-0.905	-0.957	25.064	-0.018	-0.018	0.000	0.000	0.000	0.000
44	C	45	GLY	0	-0.006	-0.001	27.481	-0.005	-0.005	0.000	0.000	0.000	0.000
45	C	46	SER	0	-0.070	-0.036	22.911	-0.012	-0.012	0.000	0.000	0.000	0.000
46	C	47	LEU	0	-0.003	0.002	19.253	0.008	0.008	0.000	0.000	0.000	0.000
47	C	48	LYS	1	0.904	0.953	18.273	0.045	0.045	0.000	0.000	0.000	0.000
48	C	49	TRP	0	-0.008	-0.004	11.346	0.010	0.010	0.000	0.000	0.000	0.000
49	C	50	GLN	0	0.034	0.035	15.924	-0.006	-0.006	0.000	0.000	0.000	0.000
50	C	51	GLY	0	-0.009	0.004	16.430	0.009	0.009	0.000	0.000	0.000	0.000
51	C	52	SER	0	-0.006	-0.016	17.803	0.010	0.010	0.000	0.000	0.000	0.000
52	C	53	ASN	0	0.063	0.027	19.495	-0.018	-0.018	0.000	0.000	0.000	0.000
53	C	54	PHE	0	0.069	0.010	22.889	0.008	0.008	0.000	0.000	0.000	0.000
54	C	55	ILE	0	-0.001	0.000	24.908	0.000	0.000	0.000	0.000	0.000	0.000
55	C	56	GLU	-1	-0.949	-0.951	19.622	0.193	0.193	0.000	0.000	0.000	0.000
56	C	57	THR	0	-0.025	-0.019	18.708	0.013	0.013	0.000	0.000	0.000	0.000
57	C	58	CYS	0	-0.091	-0.033	21.762	0.002	0.002	0.000	0.000	0.000	0.000
58	C	59	ARG	1	0.840	0.894	24.768	-0.067	-0.067	0.000	0.000	0.000	0.000
59	C	60	ASN	0	-0.033	-0.041	27.615	-0.003	-0.003	0.000	0.000	0.000	0.000
60	C	61	THR	0	0.005	0.012	29.820	-0.003	-0.003	0.000	0.000	0.000	0.000
61	C	62	GLN	0	-0.055	-0.028	31.993	0.002	0.002	0.000	0.000	0.000	0.000
62	C	63	LEU	0	0.018	0.019	34.880	-0.001	-0.001	0.000	0.000	0.000	0.000
63	C	64	ALA	0	-0.007	-0.006	35.795	0.000	0.000	0.000	0.000	0.000	0.000
64	C	65	GLY	0	0.038	0.020	37.677	-0.002	-0.002	0.000	0.000	0.000	0.000
65	C	66	SER	0	-0.003	-0.016	40.909	0.001	0.001	0.000	0.000	0.000	0.000
66	C	67	SER	0	-0.029	-0.027	39.343	0.000	0.000	0.000	0.000	0.000	0.000
67	C	68	GLU	-1	-0.952	-0.950	34.882	0.010	0.010	0.000	0.000	0.000	0.000
68	C	69	LEU	0	-0.008	0.006	30.745	0.002	0.002	0.000	0.000	0.000	0.000
69	C	70	ALA	0	0.003	-0.003	31.396	-0.002	-0.002	0.000	0.000	0.000	0.000
70	C	71	ALA	0	0.021	-0.004	27.857	0.005	0.005	0.000	0.000	0.000	0.000
71	C	72	GLU	-1	-0.781	-0.833	26.055	0.051	0.051	0.000	0.000	0.000	0.000
72	C	74	LYS	1	0.887	0.943	18.083	-0.158	-0.158	0.000	0.000	0.000	0.000
73	C	75	THR	0	0.007	0.005	16.417	0.001	0.001	0.000	0.000	0.000	0.000
74	C	76	ARG	1	0.879	0.909	12.536	-0.043	-0.043	0.000	0.000	0.000	0.000
75	C	77	ALA	0	-0.019	-0.001	11.337	-0.011	-0.011	0.000	0.000	0.000	0.000
76	C	78	GLN	0	0.007	0.002	5.427	-0.044	-0.044	0.000	0.000	0.000	0.000
77	C	79	GLN	0	-0.004	0.006	8.461	-0.061	-0.061	0.000	0.000	0.000	0.000
78	C	80	PHE	0	0.001	0.001	2.637	-0.737	-0.052	0.400	-0.178	-0.907	0.001
79	C	81	VAL	0	0.008	0.004	8.072	-0.031	-0.031	0.000	0.000	0.000	0.000
80	C	82	SER	0	-0.013	-0.009	9.590	-0.025	-0.025	0.000	0.000	0.000	0.000
81	C	83	THR	0	-0.003	-0.002	9.862	0.047	0.047	0.000	0.000	0.000	0.000
82	C	84	LYS	1	0.945	0.959	12.377	0.049	0.049	0.000	0.000	0.000	0.000
83	C	85	ILE	0	0.040	0.023	13.672	0.029	0.029	0.000	0.000	0.000	0.000
84	C	86	ASN	0	-0.017	-0.018	16.320	-0.038	-0.038	0.000	0.000	0.000	0.000
85	C	87	LEU	0	0.021	0.005	14.318	0.024	0.024	0.000	0.000	0.000	0.000
86	C	88	ASP	-1	-0.857	-0.936	18.399	0.038	0.038	0.000	0.000	0.000	0.000
87	C	89	ASP	-1	-0.952	-0.952	20.825	0.105	0.105	0.000	0.000	0.000	0.000
88	C	90	HIS	1	0.824	0.892	20.294	-0.158	-0.158	0.000	0.000	0.000	0.000
89	C	91	ILE	0	-0.054	0.000	17.642	0.017	0.017	0.000	0.000	0.000	0.000
90	C	92	ALA	0	0.072	0.048	21.262	-0.019	-0.019	0.000	0.000	0.000	0.000
91	C	93	ASN	0	-0.015	-0.021	24.031	0.007	0.007	0.000	0.000	0.000	0.000
92	C	94	ILE	0	-0.010	-0.014	26.305	-0.002	-0.002	0.000	0.000	0.000	0.000
93	C	95	ASP	-1	-0.927	-0.965	28.455	0.038	0.038	0.000	0.000	0.000	0.000
94	C	96	GLY	0	0.017	0.016	28.152	-0.002	-0.002	0.000	0.000	0.000	0.000
95	C	97	THR	0	-0.072	-0.038	24.193	-0.001	-0.001	0.000	0.000	0.000	0.000
96	C	98	LEU	0	-0.003	-0.003	19.303	0.005	0.005	0.000	0.000	0.000	0.000
97	C	99	LYS	1	0.901	0.957	21.917	-0.088	-0.088	0.000	0.000	0.000	0.000
98	C	100	TYR	0	0.011	0.021	18.956	-0.003	-0.003	0.000	0.000	0.000	0.000
99	C	101	GLU	-1	-0.912	-0.961	21.728	0.102	0.102	0.000	0.000	0.000	0.000

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