FMO DATABASE

FMODB ID: 5228Z

Calculation Name: 4XS5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4XS5

Chain ID: A

ChEMBL ID:

UniProt ID: C6VVE1

Base Structure: X-ray

Registration Date: 2023-06-21

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	-1001637.912942
FMO2-HF: Nuclear repulsion	954540.743866
FMO2-HF: Total energy	-47097.169076
FMO2-MP2: Total energy	-47234.218687

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:2:ASP)

Summations of interaction energy for fragment #1(A:2:ASP)

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.
140.772	142.787	-0.027	-0.884	-1.104	0.005

Interaction energy analysis for fragmet #1(A:2:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.948 / q_NPA : -0.986

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	4	LYS	1	0.916	0.968	3.806	-46.226	-44.446	-0.025	-0.840	-0.915	0.005
4	A	5	LEU	0	0.005	-0.003	6.335	-2.822	-2.822	0.000	0.000	0.000	0.000
5	A	6	GLU	-1	-0.896	-0.935	9.354	19.346	19.346	0.000	0.000	0.000	0.000
6	A	7	LYS	1	0.860	0.923	12.339	-20.567	-20.567	0.000	0.000	0.000	0.000
7	A	8	LYS	1	0.891	0.953	15.248	-15.530	-15.530	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.933	-0.975	18.884	12.115	12.115	0.000	0.000	0.000	0.000
9	A	10	GLN	0	0.024	0.017	21.633	-0.018	-0.018	0.000	0.000	0.000	0.000
10	A	11	TYR	0	0.051	0.024	17.342	-0.228	-0.228	0.000	0.000	0.000	0.000
11	A	12	VAL	0	0.001	0.001	12.105	0.269	0.269	0.000	0.000	0.000	0.000
12	A	13	TYR	0	-0.019	-0.002	13.091	-0.642	-0.642	0.000	0.000	0.000	0.000
13	A	14	ILE	0	-0.002	-0.015	7.698	1.563	1.563	0.000	0.000	0.000	0.000
14	A	15	GLU	-1	-0.867	-0.941	8.421	26.119	26.119	0.000	0.000	0.000	0.000
15	A	16	THR	0	-0.003	-0.022	4.208	3.520	3.492	-0.001	-0.015	0.044	0.000
16	A	17	ASP	-1	-0.865	-0.938	4.389	55.942	56.205	-0.001	-0.029	-0.233	0.000
17	A	18	ALA	0	-0.023	-0.008	5.470	-2.889	-2.889	0.000	0.000	0.000	0.000
18	A	19	PRO	0	0.024	0.016	6.958	-2.789	-2.789	0.000	0.000	0.000	0.000
19	A	20	ALA	0	-0.013	-0.016	9.837	-2.491	-2.491	0.000	0.000	0.000	0.000
20	A	21	PHE	0	0.006	0.020	8.644	2.320	2.320	0.000	0.000	0.000	0.000
21	A	22	ALA	0	0.056	-0.001	10.308	-2.196	-2.196	0.000	0.000	0.000	0.000
22	A	23	GLY	0	-0.014	-0.004	10.368	2.273	2.273	0.000	0.000	0.000	0.000
23	A	24	ASP	-1	-0.887	-0.952	8.782	24.620	24.620	0.000	0.000	0.000	0.000
24	A	25	VAL	0	-0.028	-0.005	6.005	1.998	1.998	0.000	0.000	0.000	0.000
25	A	26	PRO	0	-0.027	-0.004	7.663	0.833	0.833	0.000	0.000	0.000	0.000
26	A	27	ALA	0	0.062	0.027	10.554	-0.814	-0.814	0.000	0.000	0.000	0.000
27	A	28	ALA	0	-0.002	0.011	5.340	-0.618	-0.618	0.000	0.000	0.000	0.000
28	A	29	PHE	0	0.010	-0.004	7.290	-0.329	-0.329	0.000	0.000	0.000	0.000
29	A	30	GLU	-1	-0.880	-0.951	8.208	16.549	16.549	0.000	0.000	0.000	0.000
30	A	31	GLU	-1	-0.977	-0.979	8.598	19.701	19.701	0.000	0.000	0.000	0.000
31	A	32	THR	0	0.001	-0.015	6.345	0.016	0.016	0.000	0.000	0.000	0.000
32	A	33	ALA	0	0.002	0.007	8.769	-1.497	-1.497	0.000	0.000	0.000	0.000
33	A	34	ARG	1	0.911	0.955	11.930	-17.921	-17.921	0.000	0.000	0.000	0.000
34	A	35	SER	0	-0.122	-0.055	10.959	-1.136	-1.136	0.000	0.000	0.000	0.000
35	A	36	LEU	0	0.034	0.014	10.751	-0.826	-0.826	0.000	0.000	0.000	0.000
36	A	37	PHE	0	0.041	0.015	14.195	-0.712	-0.712	0.000	0.000	0.000	0.000
37	A	38	ARG	1	0.901	0.952	15.361	-17.187	-17.187	0.000	0.000	0.000	0.000
38	A	39	GLU	-1	-0.917	-0.950	14.582	18.047	18.047	0.000	0.000	0.000	0.000
39	A	40	GLY	0	-0.034	-0.015	18.465	-0.369	-0.369	0.000	0.000	0.000	0.000
40	A	41	TYR	0	-0.072	-0.021	16.068	0.041	0.041	0.000	0.000	0.000	0.000
41	A	42	HIS	0	0.096	0.055	18.913	0.807	0.807	0.000	0.000	0.000	0.000
42	A	43	SER	0	-0.001	0.001	19.252	-0.220	-0.220	0.000	0.000	0.000	0.000
43	A	44	LEU	0	-0.072	-0.034	13.126	0.808	0.808	0.000	0.000	0.000	0.000
44	A	45	ILE	0	0.020	0.022	15.051	-0.535	-0.535	0.000	0.000	0.000	0.000
45	A	46	VAL	0	0.001	0.014	10.015	1.364	1.364	0.000	0.000	0.000	0.000
46	A	47	ASN	0	-0.017	-0.027	11.198	-1.411	-1.411	0.000	0.000	0.000	0.000
47	A	48	MET	0	0.009	-0.004	10.421	1.783	1.783	0.000	0.000	0.000	0.000
48	A	49	GLN	0	0.087	0.061	12.118	-0.937	-0.937	0.000	0.000	0.000	0.000
49	A	50	THR	0	-0.120	-0.053	8.890	-1.948	-1.948	0.000	0.000	0.000	0.000
50	A	51	VAL	0	-0.040	-0.001	9.872	0.180	0.180	0.000	0.000	0.000	0.000
51	A	52	LYS	1	0.912	0.963	12.292	-18.822	-18.822	0.000	0.000	0.000	0.000
52	A	53	SER	0	-0.040	-0.022	14.392	-0.982	-0.982	0.000	0.000	0.000	0.000
53	A	54	LEU	0	0.023	0.012	14.142	1.355	1.355	0.000	0.000	0.000	0.000
54	A	55	ASP	-1	-0.770	-0.888	14.839	18.236	18.236	0.000	0.000	0.000	0.000
55	A	56	ALA	0	-0.004	-0.010	17.069	-0.143	-0.143	0.000	0.000	0.000	0.000
56	A	57	THR	0	-0.001	-0.008	14.710	-0.745	-0.745	0.000	0.000	0.000	0.000
57	A	58	GLY	0	0.048	0.012	13.890	0.222	0.222	0.000	0.000	0.000	0.000
58	A	59	ILE	0	0.024	0.024	14.722	-0.036	-0.036	0.000	0.000	0.000	0.000
59	A	60	THR	0	-0.050	-0.027	18.023	-0.266	-0.266	0.000	0.000	0.000	0.000
60	A	61	THR	0	0.005	0.007	12.725	-0.203	-0.203	0.000	0.000	0.000	0.000
61	A	62	LEU	0	0.003	0.002	14.141	-0.068	-0.068	0.000	0.000	0.000	0.000
62	A	63	LYS	1	0.922	0.958	16.506	-13.041	-13.041	0.000	0.000	0.000	0.000
63	A	64	LYS	1	0.883	0.949	17.816	-14.830	-14.830	0.000	0.000	0.000	0.000
64	A	65	VAL	0	0.023	0.002	13.710	-0.431	-0.431	0.000	0.000	0.000	0.000
65	A	66	ASN	0	0.063	0.026	17.048	-0.153	-0.153	0.000	0.000	0.000	0.000
66	A	67	TYR	0	-0.039	-0.009	19.750	-0.600	-0.600	0.000	0.000	0.000	0.000
67	A	68	LEU	0	-0.066	-0.057	17.877	-0.475	-0.475	0.000	0.000	0.000	0.000
68	A	69	CYS	0	-0.013	0.021	17.902	0.099	0.099	0.000	0.000	0.000	0.000
69	A	70	ALA	0	0.060	0.042	20.722	-0.363	-0.363	0.000	0.000	0.000	0.000
70	A	71	ASN	0	-0.092	-0.050	24.028	-0.759	-0.759	0.000	0.000	0.000	0.000
71	A	72	ASP	-1	-0.939	-0.955	22.465	12.212	12.212	0.000	0.000	0.000	0.000
72	A	73	LEU	0	-0.074	-0.042	24.766	-0.158	-0.158	0.000	0.000	0.000	0.000
73	A	74	GLY	0	0.016	0.008	22.653	-0.126	-0.126	0.000	0.000	0.000	0.000
74	A	75	MET	0	-0.001	0.004	21.572	-0.338	-0.338	0.000	0.000	0.000	0.000
75	A	76	LEU	0	-0.031	-0.027	15.051	0.765	0.765	0.000	0.000	0.000	0.000
76	A	77	ALA	0	0.000	0.005	18.031	-0.430	-0.430	0.000	0.000	0.000	0.000
77	A	78	ILE	0	-0.002	-0.013	14.821	1.301	1.301	0.000	0.000	0.000	0.000
78	A	79	VAL	0	-0.022	-0.013	15.278	-0.808	-0.808	0.000	0.000	0.000	0.000
79	A	80	THR	0	-0.012	-0.018	15.264	1.349	1.349	0.000	0.000	0.000	0.000
80	A	81	ARG	1	0.945	0.946	17.434	-14.610	-14.610	0.000	0.000	0.000	0.000
81	A	82	ASP	-1	-0.922	-0.954	18.783	14.383	14.383	0.000	0.000	0.000	0.000
82	A	83	ASP	-1	-0.867	-0.934	20.530	12.190	12.190	0.000	0.000	0.000	0.000
83	A	84	ASP	-1	-0.891	-0.941	21.527	13.501	13.501	0.000	0.000	0.000	0.000
84	A	85	PHE	0	0.002	-0.008	14.733	0.270	0.270	0.000	0.000	0.000	0.000
85	A	86	ILE	0	-0.028	-0.020	20.127	0.255	0.255	0.000	0.000	0.000	0.000
86	A	87	ASP	-1	-0.899	-0.945	21.902	11.184	11.184	0.000	0.000	0.000	0.000
87	A	88	LEU	0	-0.054	-0.021	19.278	-0.161	-0.161	0.000	0.000	0.000	0.000
88	A	89	LEU	0	-0.027	-0.037	16.888	-0.052	-0.052	0.000	0.000	0.000	0.000
89	A	90	GLU	-1	-0.818	-0.872	20.967	10.492	10.492	0.000	0.000	0.000	0.000
90	A	91	ASP	-1	-0.904	-0.948	24.335	10.463	10.463	0.000	0.000	0.000	0.000
91	A	92	LEU	0	-0.117	-0.050	19.362	-0.150	-0.150	0.000	0.000	0.000	0.000
92	A	93	ARG	1	0.676	0.808	24.018	-10.795	-10.795	0.000	0.000	0.000	0.000
93	A	94	ILE	0	-0.056	-0.029	20.651	-0.213	-0.213	0.000	0.000	0.000	0.000
94	A	95	PRO	0	-0.040	-0.009	24.680	0.100	0.100	0.000	0.000	0.000	0.000
95	A	96	ASP	-1	-0.840	-0.929	24.775	10.990	10.990	0.000	0.000	0.000	0.000
96	A	97	LEU	0	-0.070	-0.022	18.308	0.456	0.456	0.000	0.000	0.000	0.000
97	A	98	THR	0	0.019	0.015	21.206	-0.562	-0.562	0.000	0.000	0.000	0.000
98	A	99	VAL	0	-0.020	-0.010	19.040	0.844	0.844	0.000	0.000	0.000	0.000
99	A	100	LEU	0	0.009	0.006	20.020	-0.655	-0.655	0.000	0.000	0.000	0.000
100	A	101	PRO	0	0.027	0.026	19.863	0.875	0.875	0.000	0.000	0.000	0.000
101	A	102	THR	0	-0.029	-0.027	19.979	0.690	0.690	0.000	0.000	0.000	0.000
102	A	103	LYS	1	0.898	0.950	15.671	-18.534	-18.534	0.000	0.000	0.000	0.000
103	A	104	GLU	-1	-0.936	-0.990	19.179	14.245	14.245	0.000	0.000	0.000	0.000
104	A	105	GLU	-1	-0.863	-0.921	22.715	11.596	11.596	0.000	0.000	0.000	0.000
105	A	106	ALA	0	0.002	-0.010	19.399	-0.246	-0.246	0.000	0.000	0.000	0.000
106	A	107	ILE	0	-0.057	-0.043	19.532	0.035	0.035	0.000	0.000	0.000	0.000
107	A	108	ASP	-1	-0.894	-0.941	22.182	11.334	11.334	0.000	0.000	0.000	0.000
108	A	109	ALA	0	-0.014	-0.008	23.521	-0.403	-0.403	0.000	0.000	0.000	0.000
109	A	110	VAL	0	0.009	-0.005	20.302	-0.201	-0.201	0.000	0.000	0.000	0.000
110	A	111	PHE	0	-0.059	-0.039	23.199	-0.224	-0.224	0.000	0.000	0.000	0.000
111	A	112	MET	0	-0.013	-0.003	26.584	-0.477	-0.477	0.000	0.000	0.000	0.000
112	A	113	HIS	0	0.039	0.024	25.554	-0.446	-0.446	0.000	0.000	0.000	0.000
113	A	114	SER	0	-0.039	-0.014	26.845	-0.360	-0.360	0.000	0.000	0.000	0.000
114	A	115	LEU	0	-0.032	-0.030	28.542	-0.342	-0.342	0.000	0.000	0.000	0.000
115	A	116	GLU	-1	-0.938	-0.973	30.818	8.751	8.751	0.000	0.000	0.000	0.000
116	A	117	ASN	0	-0.064	-0.017	28.321	-0.346	-0.346	0.000	0.000	0.000	0.000
117	A	118	GLU	-1	-1.012	-0.993	32.612	8.399	8.399	0.000	0.000	0.000	0.000
118	A	119	PHE	0	-0.111	-0.064	35.278	-0.350	-0.350	0.000	0.000	0.000	0.000
119	A	121	GLY	0	-0.037	0.006	35.937	-0.272	-0.272	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:ASP)