FMO DATABASE

FMODB ID: VRN81

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	OptAll
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
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1129140.329004
FMO2-HF: Nuclear repulsion	1078599.335234
FMO2-HF: Total energy	-50540.99377
FMO2-MP2: Total energy	-50688.910069

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.
-94.805	-102.217	33.742	-14.36	-11.97	0.142

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 : -0.807 / q_NPA : -0.877

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	B	8	SER	0	-0.028	-0.011	3.231	-12.379	-9.604	0.105	-1.354	-1.527	0.005
4	B	9	VAL	0	0.060	0.028	2.186	-5.804	-4.550	0.984	-0.697	-1.540	-0.001
5	B	10	ARG	1	0.792	0.861	1.713	-133.598	-145.468	32.631	-12.209	-8.552	0.138
6	B	11	PHE	0	0.035	0.007	6.073	-6.047	-6.047	0.000	0.000	0.000	0.000
7	B	12	GLN	0	-0.027	-0.005	7.031	-2.050	-2.050	0.000	0.000	0.000	0.000
8	B	13	THR	0	-0.018	-0.018	7.981	-3.158	-3.158	0.000	0.000	0.000	0.000
9	B	14	ALA	0	0.028	0.040	10.343	-2.531	-2.531	0.000	0.000	0.000	0.000
10	B	15	LEU	0	-0.010	-0.023	10.937	-2.369	-2.369	0.000	0.000	0.000	0.000
11	B	16	ALA	0	-0.047	-0.018	12.746	-1.711	-1.711	0.000	0.000	0.000	0.000
12	B	17	SER	0	0.004	-0.015	14.133	-1.434	-1.434	0.000	0.000	0.000	0.000
13	B	18	ILE	0	-0.003	-0.001	16.234	-1.117	-1.117	0.000	0.000	0.000	0.000
14	B	19	LYS	1	0.944	0.970	15.477	-17.820	-17.820	0.000	0.000	0.000	0.000
15	B	20	LEU	0	-0.008	0.009	18.807	-0.816	-0.816	0.000	0.000	0.000	0.000
16	B	21	ILE	0	0.036	0.020	19.783	-0.643	-0.643	0.000	0.000	0.000	0.000
17	B	22	GLN	0	-0.059	-0.022	21.925	-1.079	-1.079	0.000	0.000	0.000	0.000
18	B	23	ALA	0	-0.040	-0.032	24.896	-0.456	-0.456	0.000	0.000	0.000	0.000
19	B	24	SER	0	-0.051	-0.023	23.995	-0.434	-0.434	0.000	0.000	0.000	0.000
20	B	25	ALA	0	-0.022	0.002	24.548	-0.061	-0.061	0.000	0.000	0.000	0.000
21	B	26	VAL	0	-0.010	0.001	26.667	-0.187	-0.187	0.000	0.000	0.000	0.000
22	B	27	LEU	0	-0.009	0.000	22.574	0.313	0.313	0.000	0.000	0.000	0.000
23	B	28	ASP	-1	-0.887	-0.933	26.646	10.594	10.594	0.000	0.000	0.000	0.000
24	B	29	LEU	0	-0.018	-0.021	26.371	0.080	0.080	0.000	0.000	0.000	0.000
25	B	30	THR	0	-0.013	-0.010	30.339	-0.075	-0.075	0.000	0.000	0.000	0.000
26	B	31	GLH	0	-0.001	-0.042	32.930	0.187	0.187	0.000	0.000	0.000	0.000
27	B	32	ASP	-1	-0.801	-0.857	34.771	8.639	8.639	0.000	0.000	0.000	0.000
28	B	33	ASP	-1	-0.837	-0.921	30.925	9.939	9.939	0.000	0.000	0.000	0.000
29	B	34	PHE	0	0.000	0.005	27.248	0.314	0.314	0.000	0.000	0.000	0.000
30	B	35	ASP	-1	-0.885	-0.941	30.808	9.379	9.379	0.000	0.000	0.000	0.000
31	B	36	PHE	0	-0.060	-0.020	30.393	0.100	0.100	0.000	0.000	0.000	0.000
32	B	37	LEU	0	-0.025	-0.005	25.016	0.170	0.170	0.000	0.000	0.000	0.000
33	B	38	THR	0	0.004	-0.013	27.698	0.474	0.474	0.000	0.000	0.000	0.000
34	B	39	SER	0	-0.043	-0.019	29.529	-0.065	-0.065	0.000	0.000	0.000	0.000
35	B	40	ASN	0	-0.058	-0.044	31.877	0.220	0.220	0.000	0.000	0.000	0.000
36	B	41	LYS	1	0.979	0.992	33.544	-8.628	-8.628	0.000	0.000	0.000	0.000
37	B	42	VAL	0	0.014	0.007	33.668	0.255	0.255	0.000	0.000	0.000	0.000
38	B	43	TRP	0	-0.030	-0.024	26.100	-0.031	-0.031	0.000	0.000	0.000	0.000
39	B	44	ILE	0	0.002	0.011	33.452	0.067	0.067	0.000	0.000	0.000	0.000
40	B	45	ALA	0	0.019	-0.006	34.374	0.167	0.167	0.000	0.000	0.000	0.000
41	B	46	THR	0	-0.014	-0.019	34.332	0.166	0.166	0.000	0.000	0.000	0.000
42	B	47	ASP	-1	-0.854	-0.922	33.524	9.279	9.279	0.000	0.000	0.000	0.000
43	B	48	ARG	1	0.897	0.952	26.609	-11.632	-11.632	0.000	0.000	0.000	0.000
44	B	49	SER	0	0.001	-0.007	29.187	0.505	0.505	0.000	0.000	0.000	0.000
45	B	50	ARG	1	0.835	0.925	29.800	-9.332	-9.332	0.000	0.000	0.000	0.000
46	B	51	ALA	0	0.038	0.013	28.010	0.249	0.249	0.000	0.000	0.000	0.000
47	B	52	ARG	1	0.911	0.944	24.433	-11.927	-11.927	0.000	0.000	0.000	0.000
48	B	53	ARG	1	0.930	0.953	24.905	-10.823	-10.823	0.000	0.000	0.000	0.000
49	B	54	CYS	0	-0.028	0.002	26.262	0.045	0.045	0.000	0.000	0.000	0.000
50	B	55	VAL	0	0.033	0.010	20.820	0.370	0.370	0.000	0.000	0.000	0.000
51	B	56	GLU	-1	-0.826	-0.900	21.471	14.085	14.085	0.000	0.000	0.000	0.000
52	B	57	ALA	0	-0.001	0.010	21.837	0.496	0.496	0.000	0.000	0.000	0.000
53	B	58	CYS	0	-0.023	-0.003	21.262	0.019	0.019	0.000	0.000	0.000	0.000
54	B	59	VAL	0	-0.010	0.013	16.142	0.626	0.626	0.000	0.000	0.000	0.000
55	B	60	TYR	0	-0.050	-0.055	17.752	1.017	1.017	0.000	0.000	0.000	0.000
56	B	61	GLY	0	0.070	0.044	19.500	0.265	0.265	0.000	0.000	0.000	0.000
57	B	62	THR	0	-0.052	-0.059	16.316	-0.113	-0.113	0.000	0.000	0.000	0.000
58	B	63	LEU	0	-0.058	-0.020	13.049	0.680	0.680	0.000	0.000	0.000	0.000
59	B	64	ASP	-1	-0.814	-0.895	16.428	15.453	15.453	0.000	0.000	0.000	0.000
60	B	65	PHE	0	-0.065	-0.030	19.599	-0.332	-0.332	0.000	0.000	0.000	0.000
61	B	66	VAL	0	-0.022	-0.010	13.745	0.005	0.005	0.000	0.000	0.000	0.000
62	B	67	GLY	0	-0.019	0.001	16.222	0.448	0.448	0.000	0.000	0.000	0.000
63	B	68	TYR	0	-0.038	-0.024	8.790	0.560	0.560	0.000	0.000	0.000	0.000
64	B	69	PRO	0	0.011	-0.013	13.384	-0.911	-0.911	0.000	0.000	0.000	0.000
65	B	70	ARG	1	0.873	0.932	14.797	-13.435	-13.435	0.000	0.000	0.000	0.000
66	B	71	PHE	0	-0.038	-0.009	16.222	-0.703	-0.703	0.000	0.000	0.000	0.000
67	B	72	PRO	0	0.024	0.018	12.562	-0.729	-0.729	0.000	0.000	0.000	0.000
68	B	73	ALA	0	0.008	-0.003	12.993	1.601	1.601	0.000	0.000	0.000	0.000
69	B	74	PRO	0	0.017	0.013	9.104	0.591	0.591	0.000	0.000	0.000	0.000
70	B	75	VAL	0	0.041	0.017	9.882	-1.992	-1.992	0.000	0.000	0.000	0.000
71	B	76	GLU	-1	-0.805	-0.891	6.467	44.323	44.323	0.000	0.000	0.000	0.000
72	B	77	PHE	0	0.051	0.004	10.162	-2.158	-2.158	0.000	0.000	0.000	0.000
73	B	78	ILE	0	-0.002	0.015	13.261	-1.987	-1.987	0.000	0.000	0.000	0.000
74	B	79	ALA	0	0.001	-0.005	13.337	-1.466	-1.466	0.000	0.000	0.000	0.000
75	B	80	ALA	0	0.005	0.002	13.928	-1.294	-1.294	0.000	0.000	0.000	0.000
76	B	81	VAL	0	-0.019	0.000	15.809	-1.341	-1.341	0.000	0.000	0.000	0.000
77	B	82	ILE	0	-0.030	-0.027	18.474	-1.093	-1.093	0.000	0.000	0.000	0.000
78	B	83	ALA	0	-0.019	-0.015	17.477	-0.833	-0.833	0.000	0.000	0.000	0.000
79	B	84	TYR	0	-0.081	-0.039	19.122	-0.690	-0.690	0.000	0.000	0.000	0.000
80	B	85	TYR	0	0.053	0.022	20.805	-0.780	-0.780	0.000	0.000	0.000	0.000
81	B	86	VAL	0	-0.019	0.015	23.235	-0.633	-0.633	0.000	0.000	0.000	0.000
82	B	87	HIS	0	0.070	0.045	24.994	0.263	0.263	0.000	0.000	0.000	0.000
83	B	88	PRO	0	-0.021	-0.040	25.697	0.117	0.117	0.000	0.000	0.000	0.000
84	B	89	VAL	0	-0.044	-0.011	27.238	0.099	0.099	0.000	0.000	0.000	0.000
85	B	90	ASN	0	0.038	0.008	28.503	-0.250	-0.250	0.000	0.000	0.000	0.000
86	B	91	ILE	0	-0.017	0.008	22.418	0.287	0.287	0.000	0.000	0.000	0.000
87	B	92	GLN	0	0.027	0.011	23.847	0.514	0.514	0.000	0.000	0.000	0.000
88	B	93	THR	0	0.011	0.009	25.104	0.345	0.345	0.000	0.000	0.000	0.000
89	B	94	ALA	0	0.057	0.014	23.709	0.126	0.126	0.000	0.000	0.000	0.000
90	B	95	CYS	0	-0.073	-0.015	20.987	0.677	0.677	0.000	0.000	0.000	0.000
91	B	96	LEU	0	0.042	0.019	22.008	0.303	0.303	0.000	0.000	0.000	0.000
92	B	97	ILE	0	-0.080	-0.031	24.725	-0.394	-0.394	0.000	0.000	0.000	0.000
93	B	98	MET	0	-0.014	-0.007	19.692	-0.424	-0.424	0.000	0.000	0.000	0.000
94	B	99	GLU	-1	-0.802	-0.892	20.494	15.322	15.322	0.000	0.000	0.000	0.000
95	B	100	GLY	0	-0.085	-0.039	21.507	-0.126	-0.126	0.000	0.000	0.000	0.000
96	B	101	ALA	0	-0.032	-0.029	21.031	-0.703	-0.703	0.000	0.000	0.000	0.000
97	B	102	GLU	-1	-0.943	-0.942	19.334	15.410	15.410	0.000	0.000	0.000	0.000
98	B	103	PHE	0	-0.022	-0.034	16.483	0.070	0.070	0.000	0.000	0.000	0.000
99	B	104	THR	0	-0.019	-0.016	13.147	1.258	1.258	0.000	0.000	0.000	0.000
100	B	105	GLU	-1	-0.864	-0.930	14.479	20.469	20.469	0.000	0.000	0.000	0.000
101	B	106	ASN	0	-0.024	-0.024	10.965	0.775	0.775	0.000	0.000	0.000	0.000
102	B	107	ILE	0	0.060	0.048	8.118	0.173	0.173	0.000	0.000	0.000	0.000
103	B	108	ILE	0	-0.042	-0.014	8.490	3.688	3.688	0.000	0.000	0.000	0.000
104	B	109	ASN	0	-0.045	-0.035	9.971	-1.449	-1.449	0.000	0.000	0.000	0.000
105	B	110	GLY	0	-0.008	0.000	9.869	-1.833	-1.833	0.000	0.000	0.000	0.000
106	B	111	VAL	0	-0.015	-0.004	11.008	-0.355	-0.355	0.000	0.000	0.000	0.000
107	B	112	GLU	-1	-0.873	-0.939	13.187	21.471	21.471	0.000	0.000	0.000	0.000
108	B	113	ARG	1	0.731	0.813	14.323	-22.600	-22.600	0.000	0.000	0.000	0.000
109	B	114	PRO	0	0.013	0.007	15.013	1.239	1.239	0.000	0.000	0.000	0.000
110	B	115	VAL	0	-0.013	0.001	13.646	0.248	0.248	0.000	0.000	0.000	0.000
111	B	116	LYS	1	0.943	0.980	16.025	-18.228	-18.228	0.000	0.000	0.000	0.000
112	B	117	ALA	0	0.002	-0.003	17.887	0.829	0.829	0.000	0.000	0.000	0.000
113	B	118	ALA	0	-0.024	-0.019	19.696	0.170	0.170	0.000	0.000	0.000	0.000
114	B	119	GLU	-1	-0.760	-0.840	13.916	21.189	21.189	0.000	0.000	0.000	0.000
115	B	120	LEU	0	0.030	0.020	15.148	0.922	0.922	0.000	0.000	0.000	0.000
116	B	121	PHE	0	0.010	-0.008	16.883	0.039	0.039	0.000	0.000	0.000	0.000
117	B	122	ALA	0	-0.007	-0.004	15.889	-0.203	-0.203	0.000	0.000	0.000	0.000
118	B	123	PHE	0	0.000	-0.009	9.567	0.125	0.125	0.000	0.000	0.000	0.000
119	B	124	THR	0	0.033	0.017	14.491	-0.190	-0.190	0.000	0.000	0.000	0.000
120	B	125	LEU	0	-0.012	0.001	17.192	-0.459	-0.459	0.000	0.000	0.000	0.000
121	B	126	ARG	1	0.900	0.933	12.595	-21.293	-21.293	0.000	0.000	0.000	0.000
122	B	127	VAL	0	0.021	0.021	12.698	-0.004	-0.004	0.000	0.000	0.000	0.000
123	B	128	ARG	1	0.841	0.917	14.866	-14.684	-14.684	0.000	0.000	0.000	0.000
124	B	129	ALA	0	-0.049	-0.019	16.954	-0.724	-0.724	0.000	0.000	0.000	0.000
125	B	130	GLY	0	-0.008	-0.001	15.412	-0.304	-0.304	0.000	0.000	0.000	0.000
126	B	131	ASN	0	-0.050	-0.010	12.939	0.290	0.290	0.000	0.000	0.000	0.000
127	B	132	THR	0	0.045	0.013	8.897	0.049	0.049	0.000	0.000	0.000	0.000
128	B	133	ASP	-1	-0.869	-0.904	6.928	30.366	30.366	0.000	0.000	0.000	0.000
129	B	134	VAL	0	-0.073	-0.043	6.341	-2.211	-2.211	0.000	0.000	0.000	0.000
130	B	135	LEU	0	-0.030	-0.016	3.332	-0.188	0.241	0.022	-0.100	-0.351	0.000

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