FMO DATABASE

FMODB ID: R5GL8

Calculation Name: 4EXW-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4EXW

Chain ID: D

ChEMBL ID:

UniProt ID: Q1J1N6

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	119
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-964886.515915
FMO2-HF: Nuclear repulsion	917561.09705
FMO2-HF: Total energy	-47325.418865
FMO2-MP2: Total energy	-47465.446866

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:-1:PHE)

Summations of interaction energy for fragment #1(D:-1:PHE)

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.
-1.626	1.233	-0.017	-1.407	-1.434	0.006

Interaction energy analysis for fragmet #1(D:-1:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.059 / q_NPA : 0.022

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	D	1	MET	0	0.011	0.006	3.762	-1.760	1.099	-0.017	-1.407	-1.434	0.006
4	D	2	LEU	0	-0.027	-0.006	6.035	0.217	0.217	0.000	0.000	0.000	0.000
5	D	3	HIS	1	0.864	0.907	8.388	1.541	1.541	0.000	0.000	0.000	0.000
6	D	4	ILE	0	0.006	0.022	12.620	0.078	0.078	0.000	0.000	0.000	0.000
7	D	5	GLU	-1	-0.924	-0.956	16.181	-0.371	-0.371	0.000	0.000	0.000	0.000
8	D	6	PHE	0	0.005	-0.011	18.306	0.036	0.036	0.000	0.000	0.000	0.000
9	D	7	ILE	0	-0.029	-0.008	22.056	0.004	0.004	0.000	0.000	0.000	0.000
10	D	8	THR	0	-0.008	-0.013	23.961	0.010	0.010	0.000	0.000	0.000	0.000
11	D	9	ASP	-1	-0.853	-0.934	26.474	-0.171	-0.171	0.000	0.000	0.000	0.000
12	D	10	LEU	0	-0.050	-0.027	28.907	0.013	0.013	0.000	0.000	0.000	0.000
13	D	11	GLY	0	-0.036	-0.014	29.455	0.006	0.006	0.000	0.000	0.000	0.000
14	D	12	ALA	0	-0.025	0.000	25.216	-0.004	-0.004	0.000	0.000	0.000	0.000
15	D	13	LYS	1	0.985	0.985	22.158	0.261	0.261	0.000	0.000	0.000	0.000
16	D	14	VAL	0	0.009	0.008	19.038	-0.013	-0.013	0.000	0.000	0.000	0.000
17	D	15	THR	0	-0.003	-0.003	14.345	0.004	0.004	0.000	0.000	0.000	0.000
18	D	16	VAL	0	-0.021	-0.008	14.518	-0.014	-0.014	0.000	0.000	0.000	0.000
19	D	17	ASP	-1	-0.855	-0.916	9.586	-1.288	-1.288	0.000	0.000	0.000	0.000
20	D	18	VAL	0	-0.030	-0.026	10.094	0.136	0.136	0.000	0.000	0.000	0.000
21	D	19	GLU	-1	-0.896	-0.935	6.835	-0.974	-0.974	0.000	0.000	0.000	0.000
22	D	20	SER	0	0.016	-0.034	6.419	-0.103	-0.103	0.000	0.000	0.000	0.000
23	D	21	ALA	0	0.009	-0.010	8.930	0.006	0.006	0.000	0.000	0.000	0.000
24	D	22	ASP	-1	-0.907	-0.922	11.693	-0.358	-0.358	0.000	0.000	0.000	0.000
25	D	23	LYS	1	0.949	0.972	10.243	0.587	0.587	0.000	0.000	0.000	0.000
26	D	24	LEU	0	-0.018	-0.002	14.286	-0.012	-0.012	0.000	0.000	0.000	0.000
27	D	25	LEU	0	0.012	-0.017	15.429	0.019	0.019	0.000	0.000	0.000	0.000
28	D	26	ASP	-1	-0.888	-0.931	16.857	-0.270	-0.270	0.000	0.000	0.000	0.000
29	D	27	VAL	0	0.001	-0.004	14.261	0.021	0.021	0.000	0.000	0.000	0.000
30	D	28	GLN	0	-0.008	-0.017	17.669	0.012	0.012	0.000	0.000	0.000	0.000
31	D	29	ARG	1	0.875	0.930	20.389	0.222	0.222	0.000	0.000	0.000	0.000
32	D	30	GLN	0	-0.057	-0.019	18.622	0.004	0.004	0.000	0.000	0.000	0.000
33	D	31	TYR	0	0.012	0.001	17.717	0.025	0.025	0.000	0.000	0.000	0.000
34	D	32	GLY	0	0.051	0.040	22.692	0.015	0.015	0.000	0.000	0.000	0.000
35	D	33	ARG	1	0.901	0.931	23.090	0.226	0.226	0.000	0.000	0.000	0.000
36	D	34	LEU	0	-0.061	-0.013	24.172	0.015	0.015	0.000	0.000	0.000	0.000
37	D	35	GLY	0	-0.029	-0.001	27.626	0.008	0.008	0.000	0.000	0.000	0.000
38	D	36	TRP	0	-0.031	-0.009	20.747	-0.006	-0.006	0.000	0.000	0.000	0.000
39	D	37	THR	0	-0.046	-0.033	25.706	0.000	0.000	0.000	0.000	0.000	0.000
40	D	38	SER	0	-0.004	-0.018	21.205	-0.017	-0.017	0.000	0.000	0.000	0.000
41	D	39	GLY	0	0.014	0.020	23.630	0.007	0.007	0.000	0.000	0.000	0.000
42	D	40	GLU	-1	-0.943	-0.972	25.372	-0.174	-0.174	0.000	0.000	0.000	0.000
43	D	41	VAL	0	-0.048	-0.021	29.099	-0.001	-0.001	0.000	0.000	0.000	0.000
44	D	42	PRO	0	-0.010	0.012	30.193	0.005	0.005	0.000	0.000	0.000	0.000
45	D	43	VAL	0	0.045	0.002	32.638	0.006	0.006	0.000	0.000	0.000	0.000
46	D	44	GLY	0	-0.018	-0.005	36.312	0.003	0.003	0.000	0.000	0.000	0.000
47	D	45	GLY	0	-0.012	0.002	35.169	0.004	0.004	0.000	0.000	0.000	0.000
48	D	46	TYR	0	0.034	-0.001	28.109	0.003	0.003	0.000	0.000	0.000	0.000
49	D	47	GLN	0	-0.003	-0.003	32.332	0.014	0.014	0.000	0.000	0.000	0.000
50	D	48	PHE	0	-0.014	0.001	28.937	-0.006	-0.006	0.000	0.000	0.000	0.000
51	D	49	PRO	0	0.014	-0.006	32.096	0.005	0.005	0.000	0.000	0.000	0.000
52	D	50	LEU	0	-0.001	0.002	35.139	-0.002	-0.002	0.000	0.000	0.000	0.000
53	D	51	GLU	-1	-0.878	-0.945	36.848	-0.080	-0.080	0.000	0.000	0.000	0.000
54	D	52	ASN	0	-0.038	-0.037	31.364	0.002	0.002	0.000	0.000	0.000	0.000
55	D	53	GLU	-1	-0.867	-0.924	34.615	-0.092	-0.092	0.000	0.000	0.000	0.000
56	D	54	PRO	0	-0.013	0.000	37.210	-0.002	-0.002	0.000	0.000	0.000	0.000
57	D	55	ASP	-1	-0.839	-0.918	34.279	-0.102	-0.102	0.000	0.000	0.000	0.000
58	D	56	PHE	0	0.013	0.008	29.518	-0.008	-0.008	0.000	0.000	0.000	0.000
59	D	57	ASP	-1	-0.793	-0.883	27.199	-0.169	-0.169	0.000	0.000	0.000	0.000
60	D	58	TRP	0	0.018	-0.011	29.038	-0.010	-0.010	0.000	0.000	0.000	0.000
61	D	59	SER	0	-0.035	-0.017	26.812	-0.009	-0.009	0.000	0.000	0.000	0.000
62	D	60	LEU	0	-0.014	-0.006	23.594	-0.018	-0.018	0.000	0.000	0.000	0.000
63	D	61	ILE	0	-0.051	-0.023	25.176	-0.012	-0.012	0.000	0.000	0.000	0.000
64	D	62	GLY	0	0.017	0.013	27.283	0.004	0.004	0.000	0.000	0.000	0.000
65	D	63	ALA	0	-0.097	-0.039	28.365	0.009	0.009	0.000	0.000	0.000	0.000
66	D	64	ARG	1	0.978	0.981	31.398	0.113	0.113	0.000	0.000	0.000	0.000
67	D	65	LYS	1	0.902	0.947	34.046	0.101	0.101	0.000	0.000	0.000	0.000
68	D	66	TRP	0	-0.031	-0.028	37.376	-0.002	-0.002	0.000	0.000	0.000	0.000
69	D	67	THR	0	0.032	0.026	40.318	0.000	0.000	0.000	0.000	0.000	0.000
70	D	68	ASN	0	-0.073	-0.009	44.028	0.002	0.002	0.000	0.000	0.000	0.000
71	D	69	PRO	0	0.054	0.018	46.773	0.001	0.001	0.000	0.000	0.000	0.000
72	D	70	GLU	-1	-0.925	-0.973	46.305	-0.061	-0.061	0.000	0.000	0.000	0.000
73	D	71	GLY	0	0.007	0.017	47.815	0.002	0.002	0.000	0.000	0.000	0.000
74	D	72	GLU	-1	-0.838	-0.906	46.936	-0.069	-0.069	0.000	0.000	0.000	0.000
75	D	73	GLU	-1	-0.869	-0.958	40.687	-0.092	-0.092	0.000	0.000	0.000	0.000
76	D	74	MET	0	-0.078	-0.026	41.997	0.001	0.001	0.000	0.000	0.000	0.000
77	D	75	ILE	0	0.014	0.013	35.808	-0.003	-0.003	0.000	0.000	0.000	0.000
78	D	76	LEU	0	-0.048	-0.029	36.411	0.001	0.001	0.000	0.000	0.000	0.000
79	D	77	HIS	0	0.011	-0.007	30.333	-0.004	-0.004	0.000	0.000	0.000	0.000
80	D	78	ARG	1	0.990	1.000	28.636	0.183	0.183	0.000	0.000	0.000	0.000
81	D	79	GLY	0	0.048	0.040	34.705	0.004	0.004	0.000	0.000	0.000	0.000
82	D	80	HIS	0	-0.110	-0.050	37.675	0.006	0.006	0.000	0.000	0.000	0.000
83	D	81	ALA	0	0.053	0.020	38.693	-0.003	-0.003	0.000	0.000	0.000	0.000
84	D	82	TYR	0	-0.045	-0.010	37.086	0.005	0.005	0.000	0.000	0.000	0.000
85	D	83	ARG	1	0.891	0.937	41.244	0.071	0.071	0.000	0.000	0.000	0.000
86	D	84	ARG	1	0.905	0.954	42.043	0.076	0.076	0.000	0.000	0.000	0.000
87	D	85	ARG	1	0.905	0.948	43.822	0.077	0.077	0.000	0.000	0.000	0.000
88	D	86	GLU	-1	-0.807	-0.903	44.746	-0.074	-0.074	0.000	0.000	0.000	0.000
89	D	98	PRO	0	0.037	0.019	44.542	0.001	0.001	0.000	0.000	0.000	0.000
90	D	99	ALA	0	-0.029	-0.015	45.909	-0.001	-0.001	0.000	0.000	0.000	0.000
91	D	100	ALA	0	0.036	0.002	42.583	-0.003	-0.003	0.000	0.000	0.000	0.000
92	D	101	VAL	0	0.019	0.045	40.927	0.003	0.003	0.000	0.000	0.000	0.000
93	D	102	LYS	1	0.770	0.877	40.725	0.072	0.072	0.000	0.000	0.000	0.000
94	D	103	TYR	0	0.040	0.021	38.550	0.002	0.002	0.000	0.000	0.000	0.000
95	D	104	SER	0	-0.032	-0.020	39.948	-0.003	-0.003	0.000	0.000	0.000	0.000
96	D	105	ARG	1	0.970	0.986	39.295	0.103	0.103	0.000	0.000	0.000	0.000
97	D	106	GLY	0	0.035	-0.002	44.266	0.001	0.001	0.000	0.000	0.000	0.000
98	D	107	ALA	0	-0.035	0.005	43.886	0.002	0.002	0.000	0.000	0.000	0.000
99	D	108	LYS	1	0.984	0.988	45.421	0.079	0.079	0.000	0.000	0.000	0.000
100	D	109	ASN	0	0.037	0.037	40.789	0.004	0.004	0.000	0.000	0.000	0.000
101	D	125	TYR	0	0.009	-0.016	44.419	-0.001	-0.001	0.000	0.000	0.000	0.000
102	D	126	VAL	0	0.006	0.011	39.434	-0.001	-0.001	0.000	0.000	0.000	0.000
103	D	127	THR	0	-0.073	-0.055	39.228	-0.001	-0.001	0.000	0.000	0.000	0.000
104	D	128	LEU	0	0.043	0.044	33.298	-0.003	-0.003	0.000	0.000	0.000	0.000
105	D	129	ALA	0	0.021	-0.004	34.471	-0.007	-0.007	0.000	0.000	0.000	0.000
106	D	130	ILE	0	-0.046	-0.023	36.142	0.008	0.008	0.000	0.000	0.000	0.000
107	D	131	PHE	0	0.014	0.020	34.016	-0.004	-0.004	0.000	0.000	0.000	0.000
108	D	132	ARG	1	0.918	0.932	37.710	0.096	0.096	0.000	0.000	0.000	0.000
109	D	133	GLY	0	0.033	0.030	38.068	-0.003	-0.003	0.000	0.000	0.000	0.000
110	D	134	GLY	0	0.016	0.012	35.609	-0.004	-0.004	0.000	0.000	0.000	0.000
111	D	135	LYS	1	1.003	1.013	30.317	0.095	0.095	0.000	0.000	0.000	0.000
112	D	136	ARG	1	0.846	0.877	33.173	0.093	0.093	0.000	0.000	0.000	0.000
113	D	137	GLN	0	-0.059	-0.032	27.676	-0.010	-0.010	0.000	0.000	0.000	0.000
114	D	138	GLU	-1	-0.773	-0.880	27.817	-0.109	-0.109	0.000	0.000	0.000	0.000
115	D	139	ARG	1	0.900	0.966	23.313	0.166	0.166	0.000	0.000	0.000	0.000
116	D	140	TYR	0	-0.047	-0.039	25.485	-0.016	-0.016	0.000	0.000	0.000	0.000
117	D	141	ALA	0	0.048	0.045	27.987	0.001	0.001	0.000	0.000	0.000	0.000
118	D	142	VAL	0	-0.021	-0.008	28.134	-0.012	-0.012	0.000	0.000	0.000	0.000
119	D	143	PRO	0	-0.005	0.011	25.911	0.009	0.009	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:-1:PHE)