FMO DATABASE

FMODB ID: VRYZ1

Calculation Name: 3GW2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GW2

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-03-14

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	93
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-588599.162044
FMO2-HF: Nuclear repulsion	554258.809083
FMO2-HF: Total energy	-34340.352961
FMO2-MP2: Total energy	-34442.279746

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:7:ARG)

Summations of interaction energy for fragment #1(A:7:ARG)

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.
5.025	11.724	2.551	-4.137	-5.114	-0.025

Interaction energy analysis for fragmet #1(A:7:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.997 / q_NPA : 1.002

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

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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	9	ALA	0	-0.024	0.013	2.440	0.110	4.148	0.883	-2.096	-2.826	0.001
4	A	10	ALA	0	0.020	-0.001	2.511	-18.796	-16.135	1.668	-2.041	-2.288	-0.026
5	A	11	LEU	0	0.079	0.029	5.312	4.609	4.609	0.000	0.000	0.000	0.000
6	A	12	LEU	0	0.020	-0.012	6.352	3.070	3.070	0.000	0.000	0.000	0.000
7	A	13	ASP	-1	-0.847	-0.924	7.397	-29.697	-29.697	0.000	0.000	0.000	0.000
8	A	14	GLN	0	0.005	0.013	9.859	1.577	1.577	0.000	0.000	0.000	0.000
9	A	15	VAL	0	0.038	0.021	11.047	1.701	1.701	0.000	0.000	0.000	0.000
10	A	16	ALA	0	0.026	0.018	12.288	1.626	1.626	0.000	0.000	0.000	0.000
11	A	17	ARG	1	0.860	0.927	10.656	24.661	24.661	0.000	0.000	0.000	0.000
12	A	18	VAL	0	0.020	0.019	15.554	1.041	1.041	0.000	0.000	0.000	0.000
13	A	19	GLY	0	0.051	0.018	16.773	0.943	0.943	0.000	0.000	0.000	0.000
14	A	20	LYS	1	0.948	0.964	18.193	14.958	14.958	0.000	0.000	0.000	0.000
15	A	21	ALA	0	-0.036	-0.016	19.982	0.801	0.801	0.000	0.000	0.000	0.000
16	A	22	LEU	0	0.061	0.030	20.591	0.675	0.675	0.000	0.000	0.000	0.000
17	A	23	ALA	0	-0.027	0.015	22.435	0.502	0.502	0.000	0.000	0.000	0.000
18	A	24	ASN	0	-0.053	-0.043	24.329	0.509	0.509	0.000	0.000	0.000	0.000
19	A	25	GLY	0	0.095	0.049	27.886	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	26	ARG	1	0.867	0.922	30.596	8.419	8.419	0.000	0.000	0.000	0.000
21	A	27	ARG	1	0.788	0.876	24.441	11.827	11.827	0.000	0.000	0.000	0.000
22	A	28	LEU	0	0.034	0.016	25.860	-0.111	-0.111	0.000	0.000	0.000	0.000
23	A	29	GLN	0	0.045	0.030	29.570	0.091	0.091	0.000	0.000	0.000	0.000
24	A	30	ILE	0	-0.034	-0.022	30.377	0.130	0.130	0.000	0.000	0.000	0.000
25	A	31	LEU	0	-0.030	-0.010	25.597	0.011	0.011	0.000	0.000	0.000	0.000
26	A	32	ASP	-1	-0.799	-0.918	29.940	-9.362	-9.362	0.000	0.000	0.000	0.000
27	A	33	LEU	0	-0.099	-0.033	32.946	0.219	0.219	0.000	0.000	0.000	0.000
28	A	34	LEU	0	-0.085	-0.052	30.063	0.113	0.113	0.000	0.000	0.000	0.000
29	A	35	ALA	0	-0.043	0.039	30.793	-0.114	-0.114	0.000	0.000	0.000	0.000
30	A	36	GLN	0	0.053	-0.002	30.055	0.131	0.131	0.000	0.000	0.000	0.000
31	A	37	GLY	0	0.015	-0.002	33.686	0.320	0.320	0.000	0.000	0.000	0.000
32	A	38	GLU	-1	-0.857	-0.915	32.971	-9.459	-9.459	0.000	0.000	0.000	0.000
33	A	39	ARG	1	0.958	0.988	34.375	8.288	8.288	0.000	0.000	0.000	0.000
34	A	40	ALA	0	0.028	0.014	35.073	-0.253	-0.253	0.000	0.000	0.000	0.000
35	A	41	VAL	0	0.020	-0.003	33.684	0.055	0.055	0.000	0.000	0.000	0.000
36	A	42	GLU	-1	-0.808	-0.862	36.247	-7.356	-7.356	0.000	0.000	0.000	0.000
37	A	43	ALA	0	0.020	0.013	39.271	0.124	0.124	0.000	0.000	0.000	0.000
38	A	44	ILE	0	0.033	0.020	33.146	0.077	0.077	0.000	0.000	0.000	0.000
39	A	45	ALA	0	-0.030	-0.008	37.098	-0.018	-0.018	0.000	0.000	0.000	0.000
40	A	46	THR	0	-0.012	-0.017	38.372	0.126	0.126	0.000	0.000	0.000	0.000
41	A	47	ALA	0	-0.030	-0.008	38.897	0.120	0.120	0.000	0.000	0.000	0.000
42	A	48	THR	0	-0.007	-0.012	35.167	0.012	0.012	0.000	0.000	0.000	0.000
43	A	49	GLY	0	0.066	0.052	38.518	-0.019	-0.019	0.000	0.000	0.000	0.000
44	A	50	MET	0	-0.090	-0.024	32.876	-0.087	-0.087	0.000	0.000	0.000	0.000
45	A	51	ASN	0	0.067	0.035	38.054	0.011	0.011	0.000	0.000	0.000	0.000
46	A	52	LEU	0	0.108	0.018	37.545	-0.253	-0.253	0.000	0.000	0.000	0.000
47	A	53	THR	0	0.021	0.018	34.722	-0.227	-0.227	0.000	0.000	0.000	0.000
48	A	54	THR	0	-0.025	-0.018	33.740	-0.251	-0.251	0.000	0.000	0.000	0.000
49	A	55	ALA	0	0.064	0.033	32.733	-0.321	-0.321	0.000	0.000	0.000	0.000
50	A	56	SER	0	0.008	0.011	32.002	-0.452	-0.452	0.000	0.000	0.000	0.000
51	A	57	ALA	0	0.000	-0.001	29.444	-0.408	-0.408	0.000	0.000	0.000	0.000
52	A	58	ASN	0	-0.004	-0.010	27.996	-0.737	-0.737	0.000	0.000	0.000	0.000
53	A	59	LEU	0	0.051	0.024	27.493	-0.379	-0.379	0.000	0.000	0.000	0.000
54	A	60	GLN	0	0.019	0.018	25.912	-0.712	-0.712	0.000	0.000	0.000	0.000
55	A	61	ALA	0	-0.052	-0.011	23.640	-0.673	-0.673	0.000	0.000	0.000	0.000
56	A	62	LEU	0	0.040	0.011	22.595	-0.627	-0.627	0.000	0.000	0.000	0.000
57	A	63	LYS	1	0.938	0.978	22.476	12.667	12.667	0.000	0.000	0.000	0.000
58	A	64	SER	0	-0.066	-0.040	19.533	-0.641	-0.641	0.000	0.000	0.000	0.000
59	A	65	GLY	0	-0.003	-0.003	18.015	-1.026	-1.026	0.000	0.000	0.000	0.000
60	A	66	GLY	0	-0.044	-0.019	18.447	-0.442	-0.442	0.000	0.000	0.000	0.000
61	A	67	LEU	0	0.004	0.007	19.591	0.174	0.174	0.000	0.000	0.000	0.000
62	A	68	VAL	0	-0.003	-0.007	22.426	0.567	0.567	0.000	0.000	0.000	0.000
63	A	69	GLU	-1	-0.893	-0.935	23.610	-13.213	-13.213	0.000	0.000	0.000	0.000
64	A	70	ALA	0	-0.048	-0.037	26.188	0.447	0.447	0.000	0.000	0.000	0.000
65	A	71	ARG	1	0.807	0.883	28.711	8.723	8.723	0.000	0.000	0.000	0.000
66	A	72	ARG	1	0.917	0.952	31.464	9.666	9.666	0.000	0.000	0.000	0.000
67	A	73	GLU	-1	-0.803	-0.868	34.203	-8.146	-8.146	0.000	0.000	0.000	0.000
68	A	74	GLY	0	0.052	0.030	37.739	0.179	0.179	0.000	0.000	0.000	0.000
69	A	75	THR	0	-0.006	-0.014	38.974	-0.147	-0.147	0.000	0.000	0.000	0.000
70	A	76	ARG	1	0.794	0.875	38.610	7.437	7.437	0.000	0.000	0.000	0.000
71	A	77	GLN	0	-0.009	-0.007	30.200	0.060	0.060	0.000	0.000	0.000	0.000
72	A	78	TYR	0	-0.035	-0.035	33.921	0.157	0.157	0.000	0.000	0.000	0.000
73	A	79	TYR	0	0.012	-0.024	27.845	-0.206	-0.206	0.000	0.000	0.000	0.000
74	A	80	ARG	1	0.900	0.930	27.348	11.393	11.393	0.000	0.000	0.000	0.000
75	A	81	ILE	0	0.048	0.029	25.998	-0.446	-0.446	0.000	0.000	0.000	0.000
76	A	82	ALA	0	-0.023	-0.010	22.793	0.171	0.171	0.000	0.000	0.000	0.000
77	A	83	GLY	0	0.036	0.020	24.145	-0.137	-0.137	0.000	0.000	0.000	0.000
78	A	84	GLU	-1	-0.846	-0.931	24.964	-10.993	-10.993	0.000	0.000	0.000	0.000
79	A	85	ASP	-1	-0.870	-0.914	20.033	-14.316	-14.316	0.000	0.000	0.000	0.000
80	A	86	VAL	0	-0.042	-0.017	20.971	-0.142	-0.142	0.000	0.000	0.000	0.000
81	A	87	ALA	0	0.017	0.012	22.966	0.201	0.201	0.000	0.000	0.000	0.000
82	A	88	ARG	1	0.887	0.920	21.414	13.295	13.295	0.000	0.000	0.000	0.000
83	A	89	LEU	0	-0.052	-0.015	19.145	0.031	0.031	0.000	0.000	0.000	0.000
84	A	90	PHE	0	-0.031	-0.029	22.801	-0.035	-0.035	0.000	0.000	0.000	0.000
85	A	91	ALA	0	0.055	0.031	25.598	0.273	0.273	0.000	0.000	0.000	0.000
86	A	92	LEU	0	0.000	-0.006	21.980	0.170	0.170	0.000	0.000	0.000	0.000
87	A	93	VAL	0	-0.037	-0.024	23.032	0.012	0.012	0.000	0.000	0.000	0.000
88	A	94	GLN	0	-0.009	-0.003	24.913	0.355	0.355	0.000	0.000	0.000	0.000
89	A	95	VAL	0	0.014	0.020	27.801	0.249	0.249	0.000	0.000	0.000	0.000
90	A	96	VAL	0	-0.062	-0.042	23.377	0.079	0.079	0.000	0.000	0.000	0.000
91	A	97	ALA	0	-0.069	-0.037	26.655	0.095	0.095	0.000	0.000	0.000	0.000
92	A	98	ASP	-1	-0.975	-0.976	28.486	-8.614	-8.614	0.000	0.000	0.000	0.000
93	A	99	GLU	-1	-1.056	-1.005	28.718	-9.411	-9.411	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:ARG)