FMO DATABASE

FMODB ID: QVMRY

Calculation Name: 1XSV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1XSV

Chain ID: A

ChEMBL ID:

UniProt ID: P67248

Base Structure: X-ray

Registration Date: 2023-09-23

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	106
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-865036.055909
FMO2-HF: Nuclear repulsion	819252.486049
FMO2-HF: Total energy	-45783.569859
FMO2-MP2: Total energy	-45918.799714

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:5:ASP)

Summations of interaction energy for fragment #1(A:5: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.
-36.125	-33.942	19.903	-10.197	-11.887	0.11

Interaction energy analysis for fragmet #1(A:5:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.828 / q_NPA : -0.915

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	7	VAL	0	0.030	0.018	2.341	-16.430	-12.477	3.532	-3.193	-4.292	0.035
4	A	8	LYS	1	0.836	0.907	1.765	-77.225	-80.941	16.329	-6.184	-6.429	0.071
5	A	9	THR	0	0.019	-0.008	2.952	-16.277	-14.750	0.043	-0.763	-0.807	0.004
6	A	10	LEU	0	-0.028	-0.006	5.362	-6.395	-6.281	-0.001	-0.008	-0.104	0.000
7	A	11	ARG	1	0.841	0.894	6.548	-35.754	-35.754	0.000	0.000	0.000	0.000
8	A	12	MET	0	-0.045	-0.014	7.769	-2.562	-2.562	0.000	0.000	0.000	0.000
9	A	13	ASN	0	-0.035	-0.032	8.914	-4.993	-4.993	0.000	0.000	0.000	0.000
10	A	14	TYR	0	-0.013	0.003	10.053	-0.710	-0.710	0.000	0.000	0.000	0.000
11	A	15	LEU	0	-0.030	-0.025	11.073	-1.906	-1.906	0.000	0.000	0.000	0.000
12	A	16	PHE	0	-0.013	0.008	13.540	-1.266	-1.266	0.000	0.000	0.000	0.000
13	A	17	ASP	-1	-0.870	-0.951	15.182	15.786	15.786	0.000	0.000	0.000	0.000
14	A	18	PHE	0	-0.065	-0.019	17.095	-1.026	-1.026	0.000	0.000	0.000	0.000
15	A	19	TYR	0	-0.009	-0.048	15.584	-1.096	-1.096	0.000	0.000	0.000	0.000
16	A	20	GLN	0	0.001	0.012	17.413	-0.411	-0.411	0.000	0.000	0.000	0.000
17	A	21	SER	0	-0.026	-0.015	18.633	-0.085	-0.085	0.000	0.000	0.000	0.000
18	A	22	LEU	0	-0.033	-0.013	19.508	-0.597	-0.597	0.000	0.000	0.000	0.000
19	A	23	LEU	0	-0.061	-0.008	15.325	0.095	0.095	0.000	0.000	0.000	0.000
20	A	24	THR	0	0.012	-0.014	19.537	-0.809	-0.809	0.000	0.000	0.000	0.000
21	A	25	ASN	0	0.048	0.012	19.765	0.720	0.720	0.000	0.000	0.000	0.000
22	A	26	LYS	1	0.931	0.985	18.047	-13.903	-13.903	0.000	0.000	0.000	0.000
23	A	27	GLN	0	0.001	0.011	15.771	-0.523	-0.523	0.000	0.000	0.000	0.000
24	A	28	ARG	1	0.889	0.940	14.879	-13.616	-13.616	0.000	0.000	0.000	0.000
25	A	29	ASN	0	0.010	0.005	15.537	0.297	0.297	0.000	0.000	0.000	0.000
26	A	30	TYR	0	-0.036	-0.032	13.098	0.105	0.105	0.000	0.000	0.000	0.000
27	A	31	LEU	0	0.002	0.004	9.904	1.353	1.353	0.000	0.000	0.000	0.000
28	A	32	GLU	-1	-0.776	-0.894	10.965	17.536	17.536	0.000	0.000	0.000	0.000
29	A	33	LEU	0	0.038	0.015	12.571	0.580	0.580	0.000	0.000	0.000	0.000
30	A	34	PHE	0	-0.066	-0.027	4.609	0.613	0.680	-0.001	-0.001	-0.064	0.000
31	A	35	TYR	0	-0.015	-0.035	3.602	-0.226	0.012	0.001	-0.048	-0.191	0.000
32	A	36	LEU	0	-0.024	0.008	8.207	0.778	0.778	0.000	0.000	0.000	0.000
33	A	37	GLU	-1	-0.917	-0.954	11.505	15.674	15.674	0.000	0.000	0.000	0.000
34	A	38	ASP	-1	-0.957	-0.954	8.868	24.193	24.193	0.000	0.000	0.000	0.000
35	A	39	TYR	0	-0.061	-0.033	10.208	-1.007	-1.007	0.000	0.000	0.000	0.000
36	A	40	SER	0	-0.058	-0.077	9.972	1.889	1.889	0.000	0.000	0.000	0.000
37	A	41	LEU	0	0.010	-0.025	9.000	-1.155	-1.155	0.000	0.000	0.000	0.000
38	A	42	SER	0	-0.043	-0.045	11.976	-0.764	-0.764	0.000	0.000	0.000	0.000
39	A	43	GLU	-1	-0.744	-0.807	14.026	17.168	17.168	0.000	0.000	0.000	0.000
40	A	44	ILE	0	0.005	0.023	11.499	-0.841	-0.841	0.000	0.000	0.000	0.000
41	A	45	ALA	0	-0.072	-0.052	15.565	-0.695	-0.695	0.000	0.000	0.000	0.000
42	A	46	ASP	-1	-0.931	-0.958	17.649	12.180	12.180	0.000	0.000	0.000	0.000
43	A	47	THR	0	-0.002	-0.001	18.295	-0.643	-0.643	0.000	0.000	0.000	0.000
44	A	48	PHE	0	-0.053	-0.040	17.321	-0.558	-0.558	0.000	0.000	0.000	0.000
45	A	49	ASN	0	-0.050	-0.004	21.330	-0.628	-0.628	0.000	0.000	0.000	0.000
46	A	50	VAL	0	-0.067	-0.027	18.552	-0.243	-0.243	0.000	0.000	0.000	0.000
47	A	51	SER	0	0.013	0.000	19.715	0.485	0.485	0.000	0.000	0.000	0.000
48	A	52	ARG	1	1.059	1.015	12.949	-19.794	-19.794	0.000	0.000	0.000	0.000
49	A	53	GLN	0	-0.084	-0.037	14.432	1.242	1.242	0.000	0.000	0.000	0.000
50	A	54	ALA	0	0.015	0.002	15.216	0.812	0.812	0.000	0.000	0.000	0.000
51	A	55	VAL	0	0.022	0.014	12.430	0.584	0.584	0.000	0.000	0.000	0.000
52	A	56	TYR	0	0.037	0.023	8.130	2.775	2.775	0.000	0.000	0.000	0.000
53	A	57	ASP	-1	-0.857	-0.933	10.952	21.782	21.782	0.000	0.000	0.000	0.000
54	A	58	ASN	0	-0.093	-0.049	13.121	1.007	1.007	0.000	0.000	0.000	0.000
55	A	59	ILE	0	0.079	0.041	7.905	-0.092	-0.092	0.000	0.000	0.000	0.000
56	A	60	ARG	1	0.931	0.977	7.055	-34.068	-34.068	0.000	0.000	0.000	0.000
57	A	61	ARG	1	0.932	0.958	9.447	-18.353	-18.353	0.000	0.000	0.000	0.000
58	A	62	THR	0	0.000	-0.001	11.977	-1.018	-1.018	0.000	0.000	0.000	0.000
59	A	63	GLY	0	0.087	0.037	8.087	-0.412	-0.412	0.000	0.000	0.000	0.000
60	A	64	ASP	-1	-0.941	-0.965	7.903	37.491	37.491	0.000	0.000	0.000	0.000
61	A	65	LEU	0	-0.040	-0.010	10.108	-1.177	-1.177	0.000	0.000	0.000	0.000
62	A	66	VAL	0	0.038	0.012	11.397	-1.248	-1.248	0.000	0.000	0.000	0.000
63	A	67	GLU	-1	-0.789	-0.871	8.099	34.505	34.505	0.000	0.000	0.000	0.000
64	A	68	ASP	-1	-0.859	-0.902	11.452	17.127	17.127	0.000	0.000	0.000	0.000
65	A	69	TYR	0	0.016	-0.006	14.397	-1.621	-1.621	0.000	0.000	0.000	0.000
66	A	70	GLU	-1	-0.745	-0.830	13.770	18.107	18.107	0.000	0.000	0.000	0.000
67	A	71	LYS	1	0.893	0.952	14.774	-19.733	-19.733	0.000	0.000	0.000	0.000
68	A	72	LYS	1	0.758	0.845	16.475	-18.025	-18.025	0.000	0.000	0.000	0.000
69	A	73	LEU	0	-0.015	-0.006	19.238	-0.938	-0.938	0.000	0.000	0.000	0.000
70	A	74	GLU	-1	-0.862	-0.905	18.133	14.242	14.242	0.000	0.000	0.000	0.000
71	A	75	LEU	0	0.014	0.000	19.212	-0.521	-0.521	0.000	0.000	0.000	0.000
72	A	76	TYR	0	-0.065	-0.030	14.021	0.169	0.169	0.000	0.000	0.000	0.000
73	A	77	GLN	0	-0.058	-0.043	17.051	0.245	0.245	0.000	0.000	0.000	0.000
74	A	78	LYS	1	0.885	0.930	18.411	-14.663	-14.663	0.000	0.000	0.000	0.000
75	A	79	PHE	0	-0.053	-0.020	20.791	-0.827	-0.827	0.000	0.000	0.000	0.000
76	A	80	GLU	-1	-0.769	-0.882	17.964	15.603	15.603	0.000	0.000	0.000	0.000
77	A	81	GLN	0	-0.016	-0.007	21.324	-0.237	-0.237	0.000	0.000	0.000	0.000
78	A	82	ARG	1	0.885	0.929	23.576	-12.840	-12.840	0.000	0.000	0.000	0.000
79	A	83	ARG	1	0.749	0.864	21.088	-14.369	-14.369	0.000	0.000	0.000	0.000
80	A	84	GLU	-1	-0.835	-0.912	23.368	12.751	12.751	0.000	0.000	0.000	0.000
81	A	85	ILE	0	0.052	0.036	26.205	-0.493	-0.493	0.000	0.000	0.000	0.000
82	A	86	TYR	0	-0.032	-0.024	28.484	-0.379	-0.379	0.000	0.000	0.000	0.000
83	A	87	ASP	-1	-0.837	-0.913	27.411	10.783	10.783	0.000	0.000	0.000	0.000
84	A	88	GLU	-1	-0.836	-0.890	29.539	10.060	10.060	0.000	0.000	0.000	0.000
85	A	89	MET	0	-0.046	-0.017	31.953	-0.347	-0.347	0.000	0.000	0.000	0.000
86	A	90	LYS	1	0.796	0.885	30.665	-10.568	-10.568	0.000	0.000	0.000	0.000
87	A	91	GLN	0	-0.069	-0.025	32.969	-0.402	-0.402	0.000	0.000	0.000	0.000
88	A	92	HIS	0	-0.058	-0.038	34.900	-0.362	-0.362	0.000	0.000	0.000	0.000
89	A	93	LEU	0	0.018	0.014	38.044	-0.148	-0.148	0.000	0.000	0.000	0.000
90	A	94	SER	0	-0.039	-0.014	40.834	-0.136	-0.136	0.000	0.000	0.000	0.000
91	A	95	ASN	0	-0.030	-0.013	41.373	-0.233	-0.233	0.000	0.000	0.000	0.000
92	A	96	PRO	0	0.048	0.017	42.037	0.184	0.184	0.000	0.000	0.000	0.000
93	A	97	GLU	-1	-0.876	-0.944	42.843	7.141	7.141	0.000	0.000	0.000	0.000
94	A	98	GLN	0	-0.035	0.004	36.003	-0.094	-0.094	0.000	0.000	0.000	0.000
95	A	99	ILE	0	-0.006	-0.007	37.861	0.247	0.247	0.000	0.000	0.000	0.000
96	A	100	GLN	0	0.017	0.006	38.283	0.209	0.209	0.000	0.000	0.000	0.000
97	A	101	ARG	1	0.889	0.928	37.165	-7.950	-7.950	0.000	0.000	0.000	0.000
98	A	102	TYR	0	-0.033	-0.047	32.368	-0.029	-0.029	0.000	0.000	0.000	0.000
99	A	103	ILE	0	0.008	0.004	33.811	0.274	0.274	0.000	0.000	0.000	0.000
100	A	104	GLN	0	-0.051	-0.010	35.138	-0.113	-0.113	0.000	0.000	0.000	0.000
101	A	105	GLN	0	0.005	-0.006	30.961	0.320	0.320	0.000	0.000	0.000	0.000
102	A	106	LEU	0	-0.038	-0.026	29.571	0.365	0.365	0.000	0.000	0.000	0.000
103	A	107	GLU	-1	-0.929	-0.965	31.076	8.779	8.779	0.000	0.000	0.000	0.000
104	A	108	ASP	-1	-0.950	-0.974	31.492	9.574	9.574	0.000	0.000	0.000	0.000
105	A	109	LEU	0	-0.082	-0.026	25.359	0.391	0.391	0.000	0.000	0.000	0.000
106	A	110	GLU	-1	-0.983	-0.968	27.539	11.188	11.188	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:5:ASP)