FMO DATABASE

FMODB ID: 53Y9Z

Calculation Name: 1TX9-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1TX9

Chain ID: B

ChEMBL ID:

UniProt ID: P69486

Base Structure: X-ray

Registration Date: 2023-03-13

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	130
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1130417.410986
FMO2-HF: Nuclear repulsion	1079878.899362
FMO2-HF: Total energy	-50538.511624
FMO2-MP2: Total energy	-50686.778755

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(B:6:GLU)

Summations of interaction energy for fragment #1(B:6:GLU)

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.
-47.676	-38.537	0.903	-4.765	-5.275	0.05

Interaction energy analysis for fragmet #1(B:6:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.893 / q_NPA : -0.963

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	B	8	SER	0	0.003	0.009	3.163	-11.157	-8.086	0.196	-1.565	-1.701	0.010
4	B	9	VAL	0	0.061	0.015	2.960	-6.185	-5.123	0.083	-0.306	-0.839	0.001
5	B	10	ARG	1	0.947	0.974	2.473	-82.954	-78.257	0.612	-2.833	-2.475	0.039
6	B	11	PHE	0	0.000	0.030	6.500	-4.532	-4.532	0.000	0.000	0.000	0.000
7	B	12	GLN	0	0.038	0.012	7.383	1.002	1.002	0.000	0.000	0.000	0.000
8	B	13	THR	0	0.017	0.035	8.332	-2.642	-2.642	0.000	0.000	0.000	0.000
9	B	14	ALA	0	-0.034	-0.012	10.775	-1.835	-1.835	0.000	0.000	0.000	0.000
10	B	15	LEU	0	-0.014	-0.011	11.215	-1.796	-1.796	0.000	0.000	0.000	0.000
11	B	16	ALA	0	-0.055	-0.037	13.245	-1.438	-1.438	0.000	0.000	0.000	0.000
12	B	17	SER	0	0.027	0.008	14.671	-1.149	-1.149	0.000	0.000	0.000	0.000
13	B	18	ILE	0	0.003	-0.005	16.661	-0.964	-0.964	0.000	0.000	0.000	0.000
14	B	19	LYS	1	0.928	0.942	16.018	-16.837	-16.837	0.000	0.000	0.000	0.000
15	B	20	LEU	0	-0.022	0.003	19.311	-0.751	-0.751	0.000	0.000	0.000	0.000
16	B	21	ILE	0	0.016	0.021	20.764	-0.567	-0.567	0.000	0.000	0.000	0.000
17	B	22	GLN	0	-0.111	-0.024	23.054	-0.711	-0.711	0.000	0.000	0.000	0.000
18	B	23	ALA	0	0.012	-0.024	25.456	-0.243	-0.243	0.000	0.000	0.000	0.000
19	B	24	SER	0	-0.030	-0.007	24.914	-0.288	-0.288	0.000	0.000	0.000	0.000
20	B	25	ALA	0	-0.009	0.018	25.053	-0.205	-0.205	0.000	0.000	0.000	0.000
21	B	26	VAL	0	0.018	0.001	27.090	-0.130	-0.130	0.000	0.000	0.000	0.000
22	B	27	LEU	0	-0.020	-0.009	23.675	0.241	0.241	0.000	0.000	0.000	0.000
23	B	28	ASP	-1	-0.937	-0.951	27.564	9.954	9.954	0.000	0.000	0.000	0.000
24	B	29	LEU	0	-0.047	-0.053	27.267	0.045	0.045	0.000	0.000	0.000	0.000
25	B	30	THR	0	0.036	0.042	31.365	-0.092	-0.092	0.000	0.000	0.000	0.000
26	B	31	GLH	0	-0.015	-0.066	34.486	0.060	0.060	0.000	0.000	0.000	0.000
27	B	32	ASP	-1	-0.858	-0.886	35.842	8.212	8.212	0.000	0.000	0.000	0.000
28	B	33	ASP	-1	-0.874	-0.953	31.981	9.590	9.590	0.000	0.000	0.000	0.000
29	B	34	PHE	0	-0.002	0.010	28.090	0.294	0.294	0.000	0.000	0.000	0.000
30	B	35	ASP	-1	-0.878	-0.920	31.676	8.940	8.940	0.000	0.000	0.000	0.000
31	B	36	PHE	0	-0.053	-0.015	31.117	0.064	0.064	0.000	0.000	0.000	0.000
32	B	37	LEU	0	-0.035	-0.023	26.095	0.110	0.110	0.000	0.000	0.000	0.000
33	B	38	THR	0	-0.015	-0.031	27.863	0.323	0.323	0.000	0.000	0.000	0.000
34	B	39	SER	0	-0.076	-0.046	30.014	-0.061	-0.061	0.000	0.000	0.000	0.000
35	B	40	ASN	0	-0.071	-0.052	32.092	0.122	0.122	0.000	0.000	0.000	0.000
36	B	41	LYS	1	0.990	0.981	33.811	-8.077	-8.077	0.000	0.000	0.000	0.000
37	B	42	VAL	0	0.010	-0.003	33.989	0.151	0.151	0.000	0.000	0.000	0.000
38	B	43	TRP	0	-0.039	-0.002	26.753	0.007	0.007	0.000	0.000	0.000	0.000
39	B	44	ILE	0	-0.013	0.010	33.702	0.046	0.046	0.000	0.000	0.000	0.000
40	B	45	ALA	0	0.032	0.001	34.832	0.143	0.143	0.000	0.000	0.000	0.000
41	B	46	THR	0	0.044	-0.005	34.576	0.189	0.189	0.000	0.000	0.000	0.000
42	B	47	ASP	-1	-0.899	-0.943	34.005	8.972	8.972	0.000	0.000	0.000	0.000
43	B	48	ARG	1	0.954	0.988	28.182	-10.711	-10.711	0.000	0.000	0.000	0.000
44	B	49	SER	0	-0.028	-0.033	30.387	0.396	0.396	0.000	0.000	0.000	0.000
45	B	50	ARG	1	0.939	0.980	30.574	-8.888	-8.888	0.000	0.000	0.000	0.000
46	B	51	ALA	0	0.066	0.046	28.348	0.201	0.201	0.000	0.000	0.000	0.000
47	B	52	ARG	1	0.977	0.998	25.352	-11.122	-11.122	0.000	0.000	0.000	0.000
48	B	53	ARG	1	0.957	0.963	25.829	-10.443	-10.443	0.000	0.000	0.000	0.000
49	B	54	CYS	0	-0.011	0.024	27.397	-0.043	-0.043	0.000	0.000	0.000	0.000
50	B	55	VAL	0	0.044	0.003	21.677	0.351	0.351	0.000	0.000	0.000	0.000
51	B	56	GLU	-1	-0.923	-0.978	22.155	13.707	13.707	0.000	0.000	0.000	0.000
52	B	57	ALA	0	0.038	0.020	22.514	0.482	0.482	0.000	0.000	0.000	0.000
53	B	58	CYS	0	-0.066	-0.006	22.258	0.030	0.030	0.000	0.000	0.000	0.000
54	B	59	VAL	0	0.018	0.005	17.139	0.537	0.537	0.000	0.000	0.000	0.000
55	B	60	TYR	0	-0.012	-0.017	18.427	0.603	0.603	0.000	0.000	0.000	0.000
56	B	61	GLY	0	0.067	0.057	20.042	0.280	0.280	0.000	0.000	0.000	0.000
57	B	62	THR	0	-0.042	-0.066	17.318	0.089	0.089	0.000	0.000	0.000	0.000
58	B	63	LEU	0	-0.090	-0.026	13.969	0.496	0.496	0.000	0.000	0.000	0.000
59	B	64	ASP	-1	-0.771	-0.891	17.451	14.755	14.755	0.000	0.000	0.000	0.000
60	B	65	PHE	0	-0.113	-0.051	20.311	-0.349	-0.349	0.000	0.000	0.000	0.000
61	B	66	VAL	0	-0.013	-0.003	14.489	0.313	0.313	0.000	0.000	0.000	0.000
62	B	67	GLY	0	-0.050	-0.010	17.081	0.261	0.261	0.000	0.000	0.000	0.000
63	B	68	TYR	0	-0.072	-0.025	10.964	1.594	1.594	0.000	0.000	0.000	0.000
64	B	69	PRO	0	0.013	-0.003	13.657	-1.019	-1.019	0.000	0.000	0.000	0.000
65	B	70	ARG	1	0.890	0.918	15.404	-13.212	-13.212	0.000	0.000	0.000	0.000
66	B	71	PHE	0	-0.025	0.011	16.438	-0.716	-0.716	0.000	0.000	0.000	0.000
67	B	72	PRO	0	0.022	-0.001	13.285	-0.634	-0.634	0.000	0.000	0.000	0.000
68	B	73	ALA	0	0.007	0.006	14.009	0.992	0.992	0.000	0.000	0.000	0.000
69	B	74	PRO	0	-0.007	0.002	10.201	0.688	0.688	0.000	0.000	0.000	0.000
70	B	75	VAL	0	0.084	0.038	10.429	-1.660	-1.660	0.000	0.000	0.000	0.000
71	B	76	GLU	-1	-0.869	-0.955	7.337	35.059	35.059	0.000	0.000	0.000	0.000
72	B	77	PHE	0	0.055	0.006	11.188	-1.645	-1.645	0.000	0.000	0.000	0.000
73	B	78	ILE	0	0.008	0.024	14.418	-1.626	-1.626	0.000	0.000	0.000	0.000
74	B	79	ALA	0	0.001	-0.001	13.755	-1.109	-1.109	0.000	0.000	0.000	0.000
75	B	80	ALA	0	-0.004	-0.005	14.437	-1.147	-1.147	0.000	0.000	0.000	0.000
76	B	81	VAL	0	-0.024	-0.009	16.259	-1.095	-1.095	0.000	0.000	0.000	0.000
77	B	82	ILE	0	-0.038	-0.013	18.892	-1.019	-1.019	0.000	0.000	0.000	0.000
78	B	83	ALA	0	-0.051	-0.041	18.150	-0.705	-0.705	0.000	0.000	0.000	0.000
79	B	84	TYR	0	-0.108	-0.055	19.421	-0.455	-0.455	0.000	0.000	0.000	0.000
80	B	85	TYR	0	0.043	0.018	21.199	-0.678	-0.678	0.000	0.000	0.000	0.000
81	B	86	VAL	0	0.001	0.018	23.787	-0.568	-0.568	0.000	0.000	0.000	0.000
82	B	87	HIS	0	0.083	0.060	25.425	0.305	0.305	0.000	0.000	0.000	0.000
83	B	88	PRO	0	-0.043	-0.046	26.419	0.072	0.072	0.000	0.000	0.000	0.000
84	B	89	VAL	0	-0.049	-0.012	27.877	0.047	0.047	0.000	0.000	0.000	0.000
85	B	90	ASN	0	0.064	0.001	28.611	-0.239	-0.239	0.000	0.000	0.000	0.000
86	B	91	ILE	0	0.039	0.022	22.455	0.280	0.280	0.000	0.000	0.000	0.000
87	B	92	GLN	0	0.030	0.012	24.004	0.358	0.358	0.000	0.000	0.000	0.000
88	B	93	THR	0	-0.016	0.016	24.752	0.398	0.398	0.000	0.000	0.000	0.000
89	B	94	ALA	0	0.059	0.015	23.862	0.023	0.023	0.000	0.000	0.000	0.000
90	B	95	CYS	0	-0.080	-0.009	20.824	0.565	0.565	0.000	0.000	0.000	0.000
91	B	96	LEU	0	0.028	-0.008	22.152	0.262	0.262	0.000	0.000	0.000	0.000
92	B	97	ILE	0	-0.093	-0.036	24.455	-0.266	-0.266	0.000	0.000	0.000	0.000
93	B	98	MET	0	0.012	-0.003	20.387	-0.310	-0.310	0.000	0.000	0.000	0.000
94	B	99	GLU	-1	-0.872	-0.886	20.665	14.267	14.267	0.000	0.000	0.000	0.000
95	B	100	GLY	0	-0.038	-0.033	21.699	0.010	0.010	0.000	0.000	0.000	0.000
96	B	101	ALA	0	-0.089	-0.033	21.970	-0.500	-0.500	0.000	0.000	0.000	0.000
97	B	102	GLU	-1	-0.964	-0.977	20.210	14.461	14.461	0.000	0.000	0.000	0.000
98	B	103	PHE	0	-0.022	-0.023	17.422	-0.014	-0.014	0.000	0.000	0.000	0.000
99	B	104	THR	0	-0.014	-0.001	13.403	0.842	0.842	0.000	0.000	0.000	0.000
100	B	105	GLU	-1	-0.864	-0.933	15.740	19.157	19.157	0.000	0.000	0.000	0.000
101	B	106	ASN	0	-0.010	-0.018	11.042	0.847	0.847	0.000	0.000	0.000	0.000
102	B	107	ILE	0	0.034	0.013	8.190	-0.193	-0.193	0.000	0.000	0.000	0.000
103	B	108	ILE	0	-0.104	-0.037	9.570	2.107	2.107	0.000	0.000	0.000	0.000
104	B	109	ASN	0	-0.003	-0.006	10.379	-0.704	-0.704	0.000	0.000	0.000	0.000
105	B	110	GLY	0	0.002	0.014	10.228	-1.722	-1.722	0.000	0.000	0.000	0.000
106	B	111	VAL	0	-0.049	-0.037	11.417	-0.761	-0.761	0.000	0.000	0.000	0.000
107	B	112	GLU	-1	-0.894	-0.954	13.984	20.350	20.350	0.000	0.000	0.000	0.000
108	B	113	ARG	1	0.897	0.950	15.051	-21.217	-21.217	0.000	0.000	0.000	0.000
109	B	114	PRO	0	0.031	0.012	15.605	0.897	0.897	0.000	0.000	0.000	0.000
110	B	115	VAL	0	-0.012	0.005	14.312	0.765	0.765	0.000	0.000	0.000	0.000
111	B	116	LYS	1	0.922	0.958	16.556	-16.765	-16.765	0.000	0.000	0.000	0.000
112	B	117	ALA	0	0.037	0.006	17.945	0.632	0.632	0.000	0.000	0.000	0.000
113	B	118	ALA	0	-0.051	-0.030	19.543	0.189	0.189	0.000	0.000	0.000	0.000
114	B	119	GLU	-1	-0.868	-0.943	14.179	20.242	20.242	0.000	0.000	0.000	0.000
115	B	120	LEU	0	0.053	0.026	15.365	0.722	0.722	0.000	0.000	0.000	0.000
116	B	121	PHE	0	0.033	-0.005	16.747	-0.004	-0.004	0.000	0.000	0.000	0.000
117	B	122	ALA	0	-0.001	0.005	15.388	-0.059	-0.059	0.000	0.000	0.000	0.000
118	B	123	PHE	0	0.012	0.001	9.158	0.168	0.168	0.000	0.000	0.000	0.000
119	B	124	THR	0	-0.009	0.023	14.395	-0.228	-0.228	0.000	0.000	0.000	0.000
120	B	125	LEU	0	0.005	-0.023	17.301	-0.489	-0.489	0.000	0.000	0.000	0.000
121	B	126	ARG	1	0.911	0.956	11.479	-20.881	-20.881	0.000	0.000	0.000	0.000
122	B	127	VAL	0	0.010	0.009	13.618	-0.289	-0.289	0.000	0.000	0.000	0.000
123	B	128	ARG	1	0.911	0.957	15.300	-13.565	-13.565	0.000	0.000	0.000	0.000
124	B	129	ALA	0	-0.043	-0.008	16.948	-0.613	-0.613	0.000	0.000	0.000	0.000
125	B	130	GLY	0	-0.026	-0.005	16.017	-0.599	-0.599	0.000	0.000	0.000	0.000
126	B	131	ASN	0	-0.064	-0.043	13.011	0.492	0.492	0.000	0.000	0.000	0.000
127	B	132	THR	0	0.028	0.001	8.687	0.213	0.213	0.000	0.000	0.000	0.000
128	B	133	ASP	-1	-0.903	-0.926	7.715	25.740	25.740	0.000	0.000	0.000	0.000
129	B	134	VAL	0	-0.097	-0.047	6.794	-1.985	-1.985	0.000	0.000	0.000	0.000
130	B	135	LEU	0	0.013	0.015	3.506	1.475	1.784	0.012	-0.061	-0.260	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(B:6:GLU)