FMO DATABASE

FMODB ID: 9GVK2

Calculation Name: 4RWX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4RWX

Chain ID: A

ChEMBL ID:

UniProt ID: Q8Y3Y7

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	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	76
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-453558.629903
FMO2-HF: Nuclear repulsion	423862.234791
FMO2-HF: Total energy	-29696.395112
FMO2-MP2: Total energy	-29782.201546

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.
-16.523	-33.216	54.345	-20.842	-16.81	-0.113

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 : -0.043 / q_NPA : -0.025

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	LEU	0	0.000	0.002	3.388	-1.478	2.215	0.003	-1.974	-1.723	0.006
4	A	4	ILE	0	-0.003	-0.004	5.500	-0.111	-0.111	0.000	0.000	0.000	0.000
5	A	5	PHE	0	-0.003	-0.003	8.614	0.291	0.291	0.000	0.000	0.000	0.000
6	A	6	ALA	0	0.028	0.011	11.950	-0.054	-0.054	0.000	0.000	0.000	0.000
7	A	7	ILE	0	-0.021	-0.004	14.553	0.060	0.060	0.000	0.000	0.000	0.000
8	A	8	VAL	0	0.015	-0.003	17.793	-0.015	-0.015	0.000	0.000	0.000	0.000
9	A	9	GLN	0	0.025	0.013	20.484	0.001	0.001	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.822	-0.920	23.183	0.033	0.033	0.000	0.000	0.000	0.000
11	A	11	GLN	0	-0.088	-0.061	24.836	0.010	0.010	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.777	-0.906	22.221	0.005	0.005	0.000	0.000	0.000	0.000
13	A	13	SER	0	-0.015	0.004	20.682	0.027	0.027	0.000	0.000	0.000	0.000
14	A	14	ASN	0	0.043	0.004	20.560	0.026	0.026	0.000	0.000	0.000	0.000
15	A	15	ARG	1	0.895	0.965	21.873	-0.028	-0.028	0.000	0.000	0.000	0.000
16	A	16	LEU	0	0.024	0.032	16.076	0.013	0.013	0.000	0.000	0.000	0.000
17	A	17	SER	0	-0.005	-0.016	16.930	0.027	0.027	0.000	0.000	0.000	0.000
18	A	18	ASP	-1	-0.924	-0.941	17.500	0.255	0.255	0.000	0.000	0.000	0.000
19	A	19	ALA	0	-0.029	-0.031	18.687	0.033	0.033	0.000	0.000	0.000	0.000
20	A	20	LEU	0	0.001	0.001	12.412	0.018	0.018	0.000	0.000	0.000	0.000
21	A	21	THR	0	0.040	0.032	13.758	0.114	0.114	0.000	0.000	0.000	0.000
22	A	22	LYS	1	0.922	0.970	15.377	-0.163	-0.163	0.000	0.000	0.000	0.000
23	A	23	GLY	0	-0.009	0.000	14.951	-0.009	-0.009	0.000	0.000	0.000	0.000
24	A	24	ASN	0	-0.034	-0.015	11.597	0.056	0.056	0.000	0.000	0.000	0.000
25	A	25	PHE	0	0.007	0.017	8.549	0.228	0.228	0.000	0.000	0.000	0.000
26	A	26	GLY	0	0.013	0.018	8.621	-0.178	-0.178	0.000	0.000	0.000	0.000
27	A	27	ALA	0	-0.018	-0.020	9.195	0.061	0.061	0.000	0.000	0.000	0.000
28	A	28	THR	0	-0.007	-0.001	11.556	0.002	0.002	0.000	0.000	0.000	0.000
29	A	29	LYS	1	0.904	0.953	13.779	-0.281	-0.281	0.000	0.000	0.000	0.000
30	A	30	LEU	0	0.019	0.003	15.317	0.011	0.011	0.000	0.000	0.000	0.000
31	A	31	ALA	0	0.003	0.017	18.920	-0.032	-0.032	0.000	0.000	0.000	0.000
32	A	41	ASN	0	-0.019	-0.011	22.440	0.003	0.003	0.000	0.000	0.000	0.000
33	A	42	THR	0	-0.076	-0.055	19.103	0.017	0.017	0.000	0.000	0.000	0.000
34	A	43	THR	0	-0.003	0.005	15.169	-0.036	-0.036	0.000	0.000	0.000	0.000
35	A	44	PHE	0	-0.024	-0.025	13.355	0.052	0.052	0.000	0.000	0.000	0.000
36	A	45	ILE	0	0.009	0.007	9.006	-0.090	-0.090	0.000	0.000	0.000	0.000
37	A	46	ILE	0	0.010	-0.013	7.756	0.189	0.189	0.000	0.000	0.000	0.000
38	A	47	GLY	0	0.005	0.023	4.329	-0.719	-0.653	-0.001	-0.022	-0.043	0.000
39	A	48	THR	0	-0.051	-0.030	3.329	-0.344	0.392	0.018	-0.188	-0.566	0.000
40	A	49	GLU	-1	-0.785	-0.897	2.251	-2.949	0.438	4.163	-3.324	-4.226	-0.029
41	A	50	ASP	-1	-0.844	-0.926	1.520	-6.468	-35.395	47.868	-13.759	-5.182	-0.086
42	A	51	GLU	-1	-0.893	-0.960	4.223	0.514	0.935	0.001	-0.203	-0.219	-0.001
43	A	52	ARG	1	0.832	0.903	6.705	-1.157	-1.157	0.000	0.000	0.000	0.000
44	A	53	VAL	0	0.006	0.011	5.940	-0.012	-0.012	0.000	0.000	0.000	0.000
45	A	54	GLU	-1	-0.899	-0.964	8.378	-0.436	-0.436	0.000	0.000	0.000	0.000
46	A	55	ASP	-1	-0.913	-0.945	11.493	0.210	0.210	0.000	0.000	0.000	0.000
47	A	56	ALA	0	-0.005	-0.005	10.067	0.030	0.030	0.000	0.000	0.000	0.000
48	A	57	LEU	0	-0.022	-0.017	12.016	0.015	0.015	0.000	0.000	0.000	0.000
49	A	58	ALA	0	-0.009	0.007	14.059	0.023	0.023	0.000	0.000	0.000	0.000
50	A	59	ILE	0	0.011	0.007	14.461	0.011	0.011	0.000	0.000	0.000	0.000
51	A	60	ILE	0	-0.020	-0.016	12.901	0.001	0.001	0.000	0.000	0.000	0.000
52	A	61	LYS	1	0.921	0.953	17.216	0.112	0.112	0.000	0.000	0.000	0.000
53	A	62	GLU	-1	-0.980	-0.974	19.897	0.069	0.069	0.000	0.000	0.000	0.000
54	A	63	ASN	0	-0.073	-0.046	19.172	0.007	0.007	0.000	0.000	0.000	0.000
55	A	64	CYS	0	0.004	0.014	21.396	0.004	0.004	0.000	0.000	0.000	0.000
56	A	65	LYS	1	0.894	0.949	23.045	-0.038	-0.038	0.000	0.000	0.000	0.000
57	A	66	ALA	0	0.018	0.014	26.842	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	67	ARG	1	0.936	0.987	27.860	0.022	0.022	0.000	0.000	0.000	0.000
59	A	92	GLN	0	-0.021	-0.018	33.961	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	93	VAL	0	0.035	0.006	29.381	-0.005	-0.005	0.000	0.000	0.000	0.000
61	A	94	GLY	0	0.012	-0.002	27.449	0.009	0.009	0.000	0.000	0.000	0.000
62	A	95	GLY	0	-0.015	0.000	24.287	-0.010	-0.010	0.000	0.000	0.000	0.000
63	A	96	ALA	0	-0.006	-0.003	18.908	0.019	0.019	0.000	0.000	0.000	0.000
64	A	97	THR	0	-0.024	0.003	18.180	-0.019	-0.019	0.000	0.000	0.000	0.000
65	A	98	VAL	0	-0.004	-0.006	12.797	0.031	0.031	0.000	0.000	0.000	0.000
66	A	99	PHE	0	-0.014	0.005	12.968	-0.027	-0.027	0.000	0.000	0.000	0.000
67	A	100	VAL	0	0.034	0.013	7.893	0.031	0.031	0.000	0.000	0.000	0.000
68	A	101	MET	0	-0.023	-0.007	7.934	0.037	0.037	0.000	0.000	0.000	0.000
69	A	102	PRO	0	0.001	0.000	5.723	-0.864	-0.864	0.000	0.000	0.000	0.000
70	A	103	VAL	0	-0.008	-0.003	2.275	-0.372	1.031	1.028	-0.617	-1.813	-0.001
71	A	104	GLU	-1	-0.944	-0.963	4.062	-1.873	-1.654	0.000	-0.073	-0.146	0.000
72	A	105	SER	0	-0.030	-0.023	5.089	0.222	0.222	0.000	0.000	0.000	0.000
73	A	106	PHE	0	0.026	0.012	2.312	-1.354	0.838	1.266	-0.657	-2.801	-0.002
74	A	107	HIS	0	-0.018	-0.011	4.437	-0.345	-0.228	-0.001	-0.025	-0.091	0.000
75	A	108	HIS	0	0.013	0.006	7.679	0.221	0.221	0.000	0.000	0.000	0.000
76	A	109	PHE	0	-0.023	0.000	9.470	-0.168	-0.168	0.000	0.000	0.000	0.000

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