FMO DATABASE

FMODB ID: VR7M1

Calculation Name: 4JOI-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4JOI

Chain ID: D

ChEMBL ID:

UniProt ID: Q9H668

Base Structure: X-ray

Registration Date: 2023-06-20

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	118
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-968167.49072
FMO2-HF: Nuclear repulsion	920423.8747
FMO2-HF: Total energy	-47743.616021
FMO2-MP2: Total energy	-47879.908399

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(D:2:MET)

Summations of interaction energy for fragment #1(D:2:MET)

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.
-1.671	0.386	-0.035	-0.967	-1.054	0.002

Interaction energy analysis for fragmet #1(D:2:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.012 / 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	D	4	PRO	0	-0.004	0.014	3.798	-1.887	0.170	-0.035	-0.967	-1.054	0.002
4	D	5	LYS	1	1.005	0.991	6.886	0.406	0.406	0.000	0.000	0.000	0.000
5	D	6	PRO	0	0.020	0.007	9.651	-0.099	-0.099	0.000	0.000	0.000	0.000
6	D	7	GLY	0	0.031	0.011	12.492	-0.074	-0.074	0.000	0.000	0.000	0.000
7	D	8	THR	0	-0.015	0.010	15.371	0.048	0.048	0.000	0.000	0.000	0.000
8	D	9	TYR	0	0.032	0.011	18.027	-0.036	-0.036	0.000	0.000	0.000	0.000
9	D	10	TYR	0	0.027	0.018	19.275	0.015	0.015	0.000	0.000	0.000	0.000
10	D	11	LEU	0	0.001	0.015	23.842	-0.010	-0.010	0.000	0.000	0.000	0.000
11	D	12	PRO	0	0.029	0.032	26.878	-0.006	-0.006	0.000	0.000	0.000	0.000
12	D	13	TRP	0	0.067	0.013	27.894	-0.012	-0.012	0.000	0.000	0.000	0.000
13	D	14	GLU	-1	-0.732	-0.829	26.498	0.019	0.019	0.000	0.000	0.000	0.000
14	D	15	VAL	0	-0.039	-0.030	23.664	-0.007	-0.007	0.000	0.000	0.000	0.000
15	D	16	SER	0	-0.043	-0.032	25.969	-0.007	-0.007	0.000	0.000	0.000	0.000
16	D	17	ALA	0	-0.042	-0.002	29.212	-0.005	-0.005	0.000	0.000	0.000	0.000
17	D	18	GLY	0	0.002	0.010	26.896	0.002	0.002	0.000	0.000	0.000	0.000
18	D	19	GLN	0	-0.018	-0.019	26.811	0.006	0.006	0.000	0.000	0.000	0.000
19	D	20	VAL	0	-0.053	-0.019	20.424	0.014	0.014	0.000	0.000	0.000	0.000
20	D	21	PRO	0	0.015	0.011	19.732	-0.018	-0.018	0.000	0.000	0.000	0.000
21	D	22	ASP	-1	-0.810	-0.901	19.545	-0.265	-0.265	0.000	0.000	0.000	0.000
22	D	23	GLY	0	0.001	0.011	15.772	0.006	0.006	0.000	0.000	0.000	0.000
23	D	24	SER	0	-0.106	-0.073	14.539	-0.004	-0.004	0.000	0.000	0.000	0.000
24	D	25	THR	0	-0.062	-0.058	12.087	-0.032	-0.032	0.000	0.000	0.000	0.000
25	D	26	LEU	0	-0.050	-0.024	14.762	0.075	0.075	0.000	0.000	0.000	0.000
26	D	27	ARG	1	0.892	0.927	15.625	-0.124	-0.124	0.000	0.000	0.000	0.000
27	D	28	THR	0	-0.004	-0.017	19.624	0.014	0.014	0.000	0.000	0.000	0.000
28	D	29	PHE	0	-0.005	-0.010	23.219	-0.008	-0.008	0.000	0.000	0.000	0.000
29	D	30	GLY	0	0.043	0.021	26.110	0.000	0.000	0.000	0.000	0.000	0.000
30	D	31	ARG	1	0.876	0.934	29.089	0.038	0.038	0.000	0.000	0.000	0.000
31	D	32	LEU	0	0.004	0.015	27.897	-0.005	-0.005	0.000	0.000	0.000	0.000
32	D	33	CYS	0	-0.034	-0.015	30.639	0.008	0.008	0.000	0.000	0.000	0.000
33	D	34	LEU	0	0.012	0.014	31.039	0.003	0.003	0.000	0.000	0.000	0.000
34	D	35	TYR	0	-0.017	-0.037	25.666	-0.001	-0.001	0.000	0.000	0.000	0.000
35	D	36	ASP	-1	-0.868	-0.920	29.282	-0.147	-0.147	0.000	0.000	0.000	0.000
36	D	37	MET	0	0.052	0.010	27.108	-0.009	-0.009	0.000	0.000	0.000	0.000
37	D	38	ILE	0	0.006	0.021	27.377	-0.018	-0.018	0.000	0.000	0.000	0.000
38	D	39	GLN	0	-0.077	-0.042	27.931	-0.006	-0.006	0.000	0.000	0.000	0.000
39	D	40	SER	0	-0.045	-0.023	23.094	-0.020	-0.020	0.000	0.000	0.000	0.000
40	D	41	ARG	1	0.915	0.969	24.092	0.166	0.166	0.000	0.000	0.000	0.000
41	D	42	VAL	0	0.054	0.027	24.958	0.011	0.011	0.000	0.000	0.000	0.000
42	D	43	THR	0	-0.070	-0.020	26.667	-0.002	-0.002	0.000	0.000	0.000	0.000
43	D	44	LEU	0	-0.009	-0.002	24.630	0.005	0.005	0.000	0.000	0.000	0.000
44	D	45	MET	0	-0.005	-0.008	28.807	-0.001	-0.001	0.000	0.000	0.000	0.000
45	D	46	ALA	0	-0.004	-0.005	31.242	0.005	0.005	0.000	0.000	0.000	0.000
46	D	47	GLN	0	-0.002	0.006	33.123	-0.002	-0.002	0.000	0.000	0.000	0.000
47	D	48	HIS	0	0.001	-0.004	34.781	0.005	0.005	0.000	0.000	0.000	0.000
48	D	49	GLY	0	-0.017	0.009	36.885	-0.003	-0.003	0.000	0.000	0.000	0.000
49	D	50	SER	0	0.016	-0.007	40.160	0.003	0.003	0.000	0.000	0.000	0.000
50	D	51	ASP	-1	-0.898	-0.924	38.212	-0.035	-0.035	0.000	0.000	0.000	0.000
51	D	52	GLN	0	-0.052	-0.051	36.307	0.005	0.005	0.000	0.000	0.000	0.000
52	D	53	HIS	0	0.020	0.010	31.931	-0.006	-0.006	0.000	0.000	0.000	0.000
53	D	54	GLN	0	0.043	0.000	30.618	-0.006	-0.006	0.000	0.000	0.000	0.000
54	D	55	VAL	0	0.004	0.013	24.364	-0.001	-0.001	0.000	0.000	0.000	0.000
55	D	56	LEU	0	-0.009	0.006	25.706	-0.005	-0.005	0.000	0.000	0.000	0.000
56	D	57	VAL	0	0.030	0.019	21.081	-0.010	-0.010	0.000	0.000	0.000	0.000
57	D	58	CYS	0	-0.049	-0.020	20.110	-0.005	-0.005	0.000	0.000	0.000	0.000
58	D	59	THR	0	0.020	-0.024	19.886	-0.023	-0.023	0.000	0.000	0.000	0.000
59	D	60	LYS	1	0.976	0.974	18.722	0.344	0.344	0.000	0.000	0.000	0.000
60	D	61	LEU	0	-0.059	-0.027	12.814	-0.020	-0.020	0.000	0.000	0.000	0.000
61	D	62	VAL	0	-0.031	-0.003	16.275	-0.017	-0.017	0.000	0.000	0.000	0.000
62	D	63	GLU	-1	-0.798	-0.865	18.719	-0.208	-0.208	0.000	0.000	0.000	0.000
63	D	64	PRO	0	-0.054	-0.028	19.971	-0.028	-0.028	0.000	0.000	0.000	0.000
64	D	65	PHE	0	0.026	0.000	23.265	0.010	0.010	0.000	0.000	0.000	0.000
65	D	66	HIS	0	-0.020	-0.014	24.435	0.019	0.019	0.000	0.000	0.000	0.000
66	D	67	ALA	0	-0.039	-0.014	27.440	0.008	0.008	0.000	0.000	0.000	0.000
67	D	68	GLN	0	0.030	0.017	29.144	0.012	0.012	0.000	0.000	0.000	0.000
68	D	69	VAL	0	0.016	-0.015	31.432	0.004	0.004	0.000	0.000	0.000	0.000
69	D	70	GLY	0	0.021	0.014	33.067	0.006	0.006	0.000	0.000	0.000	0.000
70	D	71	SER	0	-0.016	0.002	31.405	0.011	0.011	0.000	0.000	0.000	0.000
71	D	72	LEU	0	-0.053	-0.032	29.952	-0.008	-0.008	0.000	0.000	0.000	0.000
72	D	73	TYR	0	0.033	0.024	24.667	-0.001	-0.001	0.000	0.000	0.000	0.000
73	D	74	ILE	0	-0.015	-0.009	21.160	0.011	0.011	0.000	0.000	0.000	0.000
74	D	75	VAL	0	-0.017	0.002	19.402	-0.017	-0.017	0.000	0.000	0.000	0.000
75	D	76	LEU	0	-0.026	-0.025	13.683	0.042	0.042	0.000	0.000	0.000	0.000
76	D	77	GLY	0	0.037	0.011	14.521	-0.057	-0.057	0.000	0.000	0.000	0.000
77	D	78	GLU	-1	-0.730	-0.795	11.607	-0.471	-0.471	0.000	0.000	0.000	0.000
78	D	79	LEU	0	-0.016	0.008	15.218	-0.011	-0.011	0.000	0.000	0.000	0.000
79	D	80	GLN	0	-0.017	-0.010	15.437	-0.062	-0.062	0.000	0.000	0.000	0.000
80	D	81	HIS	0	0.056	0.031	19.491	0.030	0.030	0.000	0.000	0.000	0.000
81	D	82	GLN	0	-0.054	-0.023	22.239	-0.049	-0.049	0.000	0.000	0.000	0.000
82	D	83	GLN	0	0.024	0.049	24.033	0.013	0.013	0.000	0.000	0.000	0.000
83	D	84	ASP	-1	-0.910	-0.994	27.578	-0.144	-0.144	0.000	0.000	0.000	0.000
84	D	85	ARG	1	0.856	0.939	28.767	0.155	0.155	0.000	0.000	0.000	0.000
85	D	86	GLY	0	0.050	0.024	28.094	0.003	0.003	0.000	0.000	0.000	0.000
86	D	87	SER	0	0.048	0.006	23.428	-0.019	-0.019	0.000	0.000	0.000	0.000
87	D	88	VAL	0	-0.061	-0.024	21.480	0.013	0.013	0.000	0.000	0.000	0.000
88	D	89	VAL	0	0.013	0.009	18.404	-0.019	-0.019	0.000	0.000	0.000	0.000
89	D	90	LYS	1	0.954	0.968	14.345	0.609	0.609	0.000	0.000	0.000	0.000
90	D	91	ALA	0	-0.011	-0.001	15.783	-0.024	-0.024	0.000	0.000	0.000	0.000
91	D	92	ARG	1	0.796	0.847	10.302	0.464	0.464	0.000	0.000	0.000	0.000
92	D	93	VAL	0	-0.012	-0.008	14.557	-0.004	-0.004	0.000	0.000	0.000	0.000
93	D	94	LEU	0	0.006	0.007	17.093	0.021	0.021	0.000	0.000	0.000	0.000
94	D	95	THR	0	0.010	0.009	20.591	-0.002	-0.002	0.000	0.000	0.000	0.000
95	D	96	CYS	0	-0.031	-0.002	22.948	0.011	0.011	0.000	0.000	0.000	0.000
96	D	97	VAL	0	-0.006	-0.028	25.598	0.008	0.008	0.000	0.000	0.000	0.000
97	D	98	GLU	-1	-0.768	-0.879	28.367	-0.028	-0.028	0.000	0.000	0.000	0.000
98	D	99	GLY	0	-0.002	0.007	32.139	-0.001	-0.001	0.000	0.000	0.000	0.000
99	D	100	MET	0	-0.038	-0.015	27.644	0.010	0.010	0.000	0.000	0.000	0.000
100	D	101	ASN	0	0.011	0.001	31.780	-0.005	-0.005	0.000	0.000	0.000	0.000
101	D	102	LEU	0	0.012	0.001	30.347	0.006	0.006	0.000	0.000	0.000	0.000
102	D	103	PRO	0	0.071	0.026	32.079	0.005	0.005	0.000	0.000	0.000	0.000
103	D	104	LEU	0	0.014	0.016	32.243	0.006	0.006	0.000	0.000	0.000	0.000
104	D	105	LEU	0	-0.009	-0.001	25.496	0.010	0.010	0.000	0.000	0.000	0.000
105	D	106	GLU	-1	-0.900	-0.973	28.735	0.017	0.017	0.000	0.000	0.000	0.000
106	D	107	GLN	0	-0.055	-0.049	30.426	-0.002	-0.002	0.000	0.000	0.000	0.000
107	D	108	ALA	0	0.019	0.014	27.756	0.010	0.010	0.000	0.000	0.000	0.000
108	D	109	ILE	0	-0.039	-0.020	24.920	0.015	0.015	0.000	0.000	0.000	0.000
109	D	110	ARG	1	0.929	0.956	26.907	-0.029	-0.029	0.000	0.000	0.000	0.000
110	D	111	GLU	-1	-0.809	-0.879	29.502	0.096	0.096	0.000	0.000	0.000	0.000
111	D	112	GLN	0	-0.077	-0.024	21.728	0.018	0.018	0.000	0.000	0.000	0.000
112	D	113	ARG	1	0.703	0.798	24.221	-0.039	-0.039	0.000	0.000	0.000	0.000
113	D	114	LEU	0	0.035	0.026	26.346	0.007	0.007	0.000	0.000	0.000	0.000
114	D	115	TYR	0	0.092	0.061	25.050	0.024	0.024	0.000	0.000	0.000	0.000
115	D	116	LYS	1	0.878	0.927	19.958	-0.216	-0.216	0.000	0.000	0.000	0.000
116	D	117	GLN	0	-0.054	-0.036	25.578	0.008	0.008	0.000	0.000	0.000	0.000
117	D	118	GLU	-1	-0.919	-0.956	28.162	0.120	0.120	0.000	0.000	0.000	0.000
118	D	119	ARG	1	0.855	0.950	21.930	-0.291	-0.291	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:2:MET)