FMO DATABASE

FMODB ID: VR941

Calculation Name: 3MGJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MGJ

Chain ID: A

ChEMBL ID:

UniProt ID: Q58875

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	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	97
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-721882.037961
FMO2-HF: Nuclear repulsion	682238.478501
FMO2-HF: Total energy	-39643.559459
FMO2-MP2: Total energy	-39758.463228

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:MET)

Summations of interaction energy for fragment #1(A:1: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.
-23.394	-15.209	20.418	-11.642	-16.963	-0.086

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.038 / 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	A	3	MET	0	0.015	0.005	3.659	-2.339	0.088	-0.003	-1.149	-1.276	0.002
4	A	4	ARG	1	0.745	0.846	5.830	0.311	0.311	0.000	0.000	0.000	0.000
5	A	5	GLU	-1	-0.901	-0.951	9.511	-0.212	-0.212	0.000	0.000	0.000	0.000
6	A	6	ILE	0	0.015	0.012	12.134	0.025	0.025	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.888	-0.963	14.995	-0.068	-0.068	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.032	0.000	17.785	0.014	0.014	0.000	0.000	0.000	0.000
9	A	9	ARG	1	0.911	0.924	20.865	-0.001	-0.001	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.031	0.019	24.445	0.006	0.006	0.000	0.000	0.000	0.000
11	A	11	HIS	0	-0.026	-0.014	27.714	-0.003	-0.003	0.000	0.000	0.000	0.000
12	A	12	ILE	0	-0.001	0.001	22.792	0.008	0.008	0.000	0.000	0.000	0.000
13	A	13	ILE	0	-0.017	-0.020	25.593	0.010	0.010	0.000	0.000	0.000	0.000
14	A	14	ASP	-1	-0.953	-0.971	27.903	0.045	0.045	0.000	0.000	0.000	0.000
15	A	15	SER	0	0.021	0.031	26.403	0.004	0.004	0.000	0.000	0.000	0.000
16	A	16	LEU	0	-0.032	-0.029	25.628	0.004	0.004	0.000	0.000	0.000	0.000
17	A	17	ILE	0	0.018	0.005	21.621	0.014	0.014	0.000	0.000	0.000	0.000
18	A	18	LEU	0	0.024	0.017	18.832	0.010	0.010	0.000	0.000	0.000	0.000
19	A	19	PRO	0	0.005	-0.006	19.093	0.018	0.018	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.977	1.008	19.645	-0.093	-0.093	0.000	0.000	0.000	0.000
21	A	21	VAL	0	0.032	0.012	15.573	0.018	0.018	0.000	0.000	0.000	0.000
22	A	22	PHE	0	-0.032	-0.026	14.803	0.017	0.017	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.893	-0.941	14.616	0.295	0.295	0.000	0.000	0.000	0.000
24	A	24	LYS	1	0.796	0.894	15.864	-0.176	-0.176	0.000	0.000	0.000	0.000
25	A	25	ILE	0	0.010	-0.004	9.804	0.019	0.019	0.000	0.000	0.000	0.000
26	A	26	LEU	0	-0.025	-0.006	11.157	0.061	0.061	0.000	0.000	0.000	0.000
27	A	27	ASP	-1	-0.919	-0.943	12.330	0.322	0.322	0.000	0.000	0.000	0.000
28	A	28	MET	0	-0.120	-0.041	11.747	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	29	GLY	0	-0.062	-0.028	9.513	-0.010	-0.010	0.000	0.000	0.000	0.000
30	A	30	GLY	0	-0.040	-0.018	6.462	0.136	0.136	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.890	-0.947	6.589	1.281	1.281	0.000	0.000	0.000	0.000
32	A	32	TYR	0	-0.023	-0.025	7.898	-0.234	-0.234	0.000	0.000	0.000	0.000
33	A	33	LYS	1	0.936	0.975	9.594	0.000	0.000	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.008	-0.010	11.394	-0.082	-0.082	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.080	-0.034	11.093	0.001	0.001	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.845	-0.917	14.917	-0.124	-0.124	0.000	0.000	0.000	0.000
37	A	37	PHE	0	-0.018	-0.037	18.607	0.021	0.021	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.887	-0.890	21.693	-0.051	-0.051	0.000	0.000	0.000	0.000
39	A	39	ILE	0	-0.029	-0.019	25.067	0.007	0.007	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.052	0.041	28.389	-0.006	-0.006	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.842	0.911	31.364	0.009	0.009	0.000	0.000	0.000	0.000
42	A	42	ARG	1	0.876	0.909	34.688	0.003	0.003	0.000	0.000	0.000	0.000
43	A	43	LYS	1	1.049	1.032	34.032	-0.023	-0.023	0.000	0.000	0.000	0.000
44	A	44	THR	0	0.010	0.003	34.432	0.003	0.003	0.000	0.000	0.000	0.000
45	A	45	ASP	-1	-0.896	-0.934	33.282	-0.004	-0.004	0.000	0.000	0.000	0.000
46	A	46	PRO	0	-0.004	0.011	28.572	0.003	0.003	0.000	0.000	0.000	0.000
47	A	47	SER	0	-0.037	-0.030	26.416	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	48	TYR	0	-0.058	-0.059	21.644	0.003	0.003	0.000	0.000	0.000	0.000
49	A	49	ALA	0	-0.013	-0.003	19.265	0.001	0.001	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.866	0.959	16.028	0.103	0.103	0.000	0.000	0.000	0.000
51	A	51	ILE	0	-0.030	-0.024	12.320	0.022	0.022	0.000	0.000	0.000	0.000
52	A	52	LEU	0	0.016	0.020	6.878	-0.022	-0.022	0.000	0.000	0.000	0.000
53	A	53	VAL	0	0.016	0.004	8.442	0.199	0.199	0.000	0.000	0.000	0.000
54	A	54	ILE	0	0.010	0.001	2.667	-1.038	-0.822	2.118	-0.473	-1.861	0.000
55	A	55	GLY	0	0.051	0.009	4.036	0.483	0.864	0.000	-0.094	-0.287	0.000
56	A	56	ARG	1	0.883	0.935	2.441	-4.358	-3.463	4.239	-2.353	-2.781	-0.027
57	A	57	ASP	-1	-0.816	-0.914	2.618	2.133	3.574	1.965	-1.326	-2.081	-0.012
58	A	58	GLU	-1	-0.819	-0.904	4.179	-0.900	-0.801	0.000	-0.016	-0.083	0.000
59	A	59	ARG	1	0.951	0.977	7.134	-0.756	-0.756	0.000	0.000	0.000	0.000
60	A	60	HIS	1	0.769	0.843	6.946	-0.642	-0.642	0.000	0.000	0.000	0.000
61	A	61	VAL	0	0.027	0.028	5.550	-0.070	-0.070	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.784	-0.878	8.285	0.131	0.131	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.939	-0.940	11.266	0.341	0.341	0.000	0.000	0.000	0.000
64	A	64	ILE	0	-0.024	-0.018	8.542	-0.023	-0.023	0.000	0.000	0.000	0.000
65	A	65	LEU	0	0.027	0.002	10.969	-0.017	-0.017	0.000	0.000	0.000	0.000
66	A	66	ASN	0	-0.045	-0.037	13.954	-0.030	-0.030	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.790	-0.876	15.868	0.177	0.177	0.000	0.000	0.000	0.000
68	A	68	LEU	0	-0.066	-0.032	13.582	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	69	ARG	1	0.851	0.917	17.508	-0.102	-0.102	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.889	-0.925	19.680	0.091	0.091	0.000	0.000	0.000	0.000
71	A	71	LEU	0	-0.044	-0.020	19.345	-0.005	-0.005	0.000	0.000	0.000	0.000
72	A	72	GLY	0	-0.004	-0.017	21.751	-0.005	-0.005	0.000	0.000	0.000	0.000
73	A	73	ALA	0	-0.028	0.002	23.331	-0.007	-0.007	0.000	0.000	0.000	0.000
74	A	74	GLU	-1	-0.998	-0.982	25.584	0.072	0.072	0.000	0.000	0.000	0.000
75	A	75	ILE	0	-0.094	-0.056	25.574	-0.004	-0.004	0.000	0.000	0.000	0.000
76	A	76	PRO	0	0.035	0.018	27.672	-0.004	-0.004	0.000	0.000	0.000	0.000
77	A	77	GLU	-1	-0.975	-0.984	29.511	0.030	0.030	0.000	0.000	0.000	0.000
78	A	78	ILE	0	-0.118	-0.068	22.912	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.830	-0.882	24.866	0.008	0.008	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.904	-0.977	16.904	0.034	0.034	0.000	0.000	0.000	0.000
81	A	81	VAL	0	-0.017	-0.006	19.555	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	82	GLU	-1	-0.810	-0.904	14.824	-0.029	-0.029	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.031	-0.016	15.321	0.006	0.006	0.000	0.000	0.000	0.000
84	A	84	GLN	0	-0.057	-0.032	14.610	-0.034	-0.034	0.000	0.000	0.000	0.000
85	A	85	PRO	0	0.061	0.042	11.872	0.016	0.016	0.000	0.000	0.000	0.000
86	A	86	ALA	0	-0.075	-0.037	14.689	0.033	0.033	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.957	-0.990	12.560	-0.706	-0.706	0.000	0.000	0.000	0.000
88	A	88	LYS	1	0.900	0.940	13.645	0.201	0.201	0.000	0.000	0.000	0.000
89	A	89	ASP	-1	-0.883	-0.942	8.034	-0.705	-0.705	0.000	0.000	0.000	0.000
90	A	90	MET	0	0.021	0.018	8.075	-0.102	-0.102	0.000	0.000	0.000	0.000
91	A	91	VAL	0	-0.032	-0.017	2.809	-1.468	-0.564	0.196	-0.440	-0.660	0.003
92	A	92	LEU	0	-0.010	-0.003	2.522	-0.854	0.792	2.135	-0.908	-2.873	0.000
93	A	93	PRO	0	-0.028	-0.005	1.898	-6.533	-9.270	9.342	-3.497	-3.108	-0.037
94	A	94	GLU	-1	-0.899	-0.963	2.657	-9.475	-6.750	0.427	-1.381	-1.771	-0.015
95	A	95	GLY	0	-0.024	-0.014	5.494	0.370	0.370	0.000	0.000	0.000	0.000
96	A	96	PHE	0	-0.010	-0.003	4.416	0.034	0.222	-0.001	-0.005	-0.182	0.000
97	A	97	TYR	0	-0.043	-0.011	6.008	0.780	0.780	0.000	0.000	0.000	0.000

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