FMO DATABASE

FMODB ID: LNY29

Calculation Name: 1TP6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1TP6

Chain ID: A

ChEMBL ID:

UniProt ID: Q9I430

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	126
LigandResidueName
LigandFragmentNumber	0
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1059854.353676
FMO2-HF: Nuclear repulsion	1010629.056594
FMO2-HF: Total energy	-49225.297082
FMO2-MP2: Total energy	-49368.793894

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:3:CYM)

Summations of interaction energy for fragment #1(A:3:CYM)

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.
-71.368	-86.675	38.04	-9.187	-13.545	0.092

Interaction energy analysis for fragmet #1(A:3:CYM)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.870 / q_NPA : -0.884

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	5	TYR	0	0.104	0.026	2.480	-18.209	-23.100	14.881	-3.905	-6.085	0.029
4	A	6	ARG	1	0.886	0.914	2.098	-64.817	-75.705	23.157	-5.998	-6.271	0.052
5	A	7	ARG	1	0.908	0.950	3.605	-58.386	-58.289	0.003	0.758	-0.858	0.011
6	A	8	GLU	-1	-0.699	-0.793	5.397	21.271	21.383	-0.001	-0.007	-0.104	0.000
7	A	9	ILE	0	0.006	0.005	6.652	-5.679	-5.679	0.000	0.000	0.000	0.000
8	A	10	HIS	0	-0.045	-0.034	7.254	-5.703	-5.703	0.000	0.000	0.000	0.000
9	A	11	HIS	0	-0.033	-0.037	9.259	-3.574	-3.574	0.000	0.000	0.000	0.000
10	A	12	ALA	0	0.004	0.023	11.293	-2.582	-2.582	0.000	0.000	0.000	0.000
11	A	13	HIS	1	0.860	0.915	12.759	-24.335	-24.335	0.000	0.000	0.000	0.000
12	A	14	VAL	0	-0.013	0.014	13.152	-1.514	-1.514	0.000	0.000	0.000	0.000
13	A	15	ALA	0	0.020	0.012	15.389	-1.351	-1.351	0.000	0.000	0.000	0.000
14	A	16	ILE	0	-0.011	-0.005	16.360	-1.252	-1.252	0.000	0.000	0.000	0.000
15	A	17	ARG	1	0.821	0.888	16.859	-17.985	-17.985	0.000	0.000	0.000	0.000
16	A	18	ASP	-1	-0.810	-0.887	19.231	15.469	15.469	0.000	0.000	0.000	0.000
17	A	19	TRP	0	-0.053	-0.036	21.411	-0.885	-0.885	0.000	0.000	0.000	0.000
18	A	20	LEU	0	-0.023	-0.020	22.005	-0.704	-0.704	0.000	0.000	0.000	0.000
19	A	21	ALA	0	-0.027	-0.006	23.907	-0.601	-0.601	0.000	0.000	0.000	0.000
20	A	22	GLY	0	-0.004	0.003	25.608	-0.488	-0.488	0.000	0.000	0.000	0.000
21	A	23	ASP	-1	-0.970	-0.959	23.873	11.814	11.814	0.000	0.000	0.000	0.000
22	A	24	SER	0	-0.036	-0.018	23.176	0.602	0.602	0.000	0.000	0.000	0.000
23	A	25	ARG	1	0.950	0.970	21.217	-14.502	-14.502	0.000	0.000	0.000	0.000
24	A	26	ALA	0	0.013	-0.010	24.597	-0.171	-0.171	0.000	0.000	0.000	0.000
25	A	27	ASP	-1	-0.911	-0.966	25.957	12.317	12.317	0.000	0.000	0.000	0.000
26	A	28	ALA	0	-0.028	-0.011	23.141	0.453	0.453	0.000	0.000	0.000	0.000
27	A	29	LEU	0	-0.004	0.004	22.690	0.611	0.611	0.000	0.000	0.000	0.000
28	A	30	ASP	-1	-0.836	-0.915	23.225	12.631	12.631	0.000	0.000	0.000	0.000
29	A	31	ALA	0	-0.007	-0.003	20.574	0.553	0.553	0.000	0.000	0.000	0.000
30	A	32	LEU	0	-0.048	-0.019	17.655	1.055	1.055	0.000	0.000	0.000	0.000
31	A	33	MET	0	0.022	0.002	18.696	0.759	0.759	0.000	0.000	0.000	0.000
32	A	34	ALA	0	-0.026	-0.004	19.916	0.097	0.097	0.000	0.000	0.000	0.000
33	A	35	ARG	1	0.808	0.876	11.750	-24.412	-24.412	0.000	0.000	0.000	0.000
34	A	36	PHE	0	-0.046	-0.016	15.513	1.451	1.451	0.000	0.000	0.000	0.000
35	A	37	ALA	0	0.063	0.040	17.419	-0.860	-0.860	0.000	0.000	0.000	0.000
36	A	38	GLU	-1	-0.942	-0.978	19.050	12.210	12.210	0.000	0.000	0.000	0.000
37	A	39	ASP	-1	-0.839	-0.919	20.860	15.003	15.003	0.000	0.000	0.000	0.000
38	A	40	PHE	0	-0.046	-0.019	16.854	0.244	0.244	0.000	0.000	0.000	0.000
39	A	41	SER	0	-0.016	-0.009	19.993	-0.993	-0.993	0.000	0.000	0.000	0.000
40	A	42	MET	0	-0.027	-0.010	19.752	0.949	0.949	0.000	0.000	0.000	0.000
41	A	43	VAL	0	0.003	-0.001	20.939	-0.887	-0.887	0.000	0.000	0.000	0.000
42	A	44	THR	0	0.017	-0.003	21.652	0.497	0.497	0.000	0.000	0.000	0.000
43	A	45	PRO	0	0.006	-0.005	22.338	-0.311	-0.311	0.000	0.000	0.000	0.000
44	A	46	HIS	0	-0.029	-0.009	24.574	-0.497	-0.497	0.000	0.000	0.000	0.000
45	A	47	GLY	0	-0.003	0.005	26.333	-0.428	-0.428	0.000	0.000	0.000	0.000
46	A	48	VAL	0	-0.048	-0.018	27.098	-0.319	-0.319	0.000	0.000	0.000	0.000
47	A	49	VAL	0	0.008	-0.001	25.300	0.580	0.580	0.000	0.000	0.000	0.000
48	A	50	LEU	0	-0.038	-0.016	24.270	-0.477	-0.477	0.000	0.000	0.000	0.000
49	A	51	ASP	-1	-0.798	-0.896	23.910	12.366	12.366	0.000	0.000	0.000	0.000
50	A	52	LYS	1	0.899	0.929	21.150	-15.012	-15.012	0.000	0.000	0.000	0.000
51	A	53	THR	0	0.002	0.004	23.928	0.076	0.076	0.000	0.000	0.000	0.000
52	A	54	ALA	0	0.020	0.017	27.181	-0.139	-0.139	0.000	0.000	0.000	0.000
53	A	55	LEU	0	-0.049	-0.014	20.176	-0.096	-0.096	0.000	0.000	0.000	0.000
54	A	56	GLY	0	0.061	0.011	24.776	0.085	0.085	0.000	0.000	0.000	0.000
55	A	57	GLU	-1	-0.943	-0.969	25.887	10.125	10.125	0.000	0.000	0.000	0.000
56	A	58	LEU	0	-0.034	-0.011	25.274	-0.306	-0.306	0.000	0.000	0.000	0.000
57	A	59	PHE	0	0.047	-0.006	20.257	-0.157	-0.157	0.000	0.000	0.000	0.000
58	A	60	ARG	1	0.951	0.997	25.982	-11.226	-11.226	0.000	0.000	0.000	0.000
59	A	61	SER	0	-0.060	-0.026	29.022	-0.297	-0.297	0.000	0.000	0.000	0.000
60	A	62	LYS	1	0.885	0.930	27.147	-10.959	-10.959	0.000	0.000	0.000	0.000
61	A	63	GLY	0	0.030	0.047	27.258	0.258	0.258	0.000	0.000	0.000	0.000
62	A	64	GLY	0	0.025	-0.005	27.341	-0.468	-0.468	0.000	0.000	0.000	0.000
63	A	65	THR	0	-0.114	-0.064	28.764	-0.301	-0.301	0.000	0.000	0.000	0.000
64	A	66	ARG	1	0.784	0.872	23.718	-13.138	-13.138	0.000	0.000	0.000	0.000
65	A	67	PRO	0	0.067	0.032	26.553	0.467	0.467	0.000	0.000	0.000	0.000
66	A	68	GLY	0	-0.005	-0.008	26.160	-0.102	-0.102	0.000	0.000	0.000	0.000
67	A	69	LEU	0	-0.063	-0.013	21.659	0.286	0.286	0.000	0.000	0.000	0.000
68	A	70	ARG	1	0.900	0.953	20.206	-12.790	-12.790	0.000	0.000	0.000	0.000
69	A	71	ILE	0	-0.019	-0.023	15.703	-0.415	-0.415	0.000	0.000	0.000	0.000
70	A	72	GLU	-1	-0.929	-0.950	13.898	21.769	21.769	0.000	0.000	0.000	0.000
71	A	73	ILE	0	-0.041	-0.021	9.953	-0.307	-0.307	0.000	0.000	0.000	0.000
72	A	74	ASP	-1	-0.793	-0.858	10.567	21.996	21.996	0.000	0.000	0.000	0.000
73	A	75	GLY	0	0.044	0.012	11.558	-0.291	-0.291	0.000	0.000	0.000	0.000
74	A	76	GLU	-1	-0.828	-0.912	6.900	36.293	36.293	0.000	0.000	0.000	0.000
75	A	77	SER	0	-0.030	-0.009	8.586	0.687	0.687	0.000	0.000	0.000	0.000
76	A	78	LEU	0	-0.012	-0.004	5.336	0.166	0.277	-0.001	-0.008	-0.102	0.000
77	A	79	LEU	0	-0.012	-0.011	7.702	-3.166	-3.166	0.000	0.000	0.000	0.000
78	A	80	ALA	0	0.014	0.003	10.210	-2.516	-2.516	0.000	0.000	0.000	0.000
79	A	81	SER	0	-0.005	-0.011	8.164	3.921	3.921	0.000	0.000	0.000	0.000
80	A	82	GLY	0	-0.016	-0.009	10.190	-2.229	-2.229	0.000	0.000	0.000	0.000
81	A	83	VAL	0	0.006	-0.002	11.210	2.055	2.055	0.000	0.000	0.000	0.000
82	A	84	ASP	-1	-0.807	-0.889	13.439	18.991	18.991	0.000	0.000	0.000	0.000
83	A	85	GLY	0	0.002	0.016	10.277	-0.207	-0.207	0.000	0.000	0.000	0.000
84	A	86	ALA	0	-0.030	-0.018	7.397	0.781	0.781	0.000	0.000	0.000	0.000
85	A	87	THR	0	-0.033	-0.003	9.433	-2.196	-2.196	0.000	0.000	0.000	0.000
86	A	88	LEU	0	-0.027	-0.015	4.703	2.442	2.594	0.001	-0.027	-0.125	0.000
87	A	89	ALA	0	0.018	0.017	9.358	-3.047	-3.047	0.000	0.000	0.000	0.000
88	A	90	TYR	0	-0.003	-0.003	9.935	3.503	3.503	0.000	0.000	0.000	0.000
89	A	91	ARG	1	0.773	0.849	11.879	-20.564	-20.564	0.000	0.000	0.000	0.000
90	A	92	GLU	-1	-0.754	-0.878	14.036	20.418	20.418	0.000	0.000	0.000	0.000
91	A	93	ILE	0	-0.058	-0.029	16.312	-1.506	-1.506	0.000	0.000	0.000	0.000
92	A	94	GLN	0	-0.035	-0.018	18.602	-0.578	-0.578	0.000	0.000	0.000	0.000
93	A	95	SER	0	-0.025	-0.024	21.172	-0.467	-0.467	0.000	0.000	0.000	0.000
94	A	96	ASP	-1	-0.745	-0.872	23.928	12.105	12.105	0.000	0.000	0.000	0.000
95	A	97	ALA	0	0.019	0.012	26.798	-0.159	-0.159	0.000	0.000	0.000	0.000
96	A	98	ALA	0	-0.034	-0.009	30.031	-0.307	-0.307	0.000	0.000	0.000	0.000
97	A	99	GLY	0	0.008	0.013	29.120	-0.207	-0.207	0.000	0.000	0.000	0.000
98	A	100	ARG	1	0.843	0.898	21.322	-13.635	-13.635	0.000	0.000	0.000	0.000
99	A	101	SER	0	-0.049	-0.018	23.682	-0.265	-0.265	0.000	0.000	0.000	0.000
100	A	102	GLU	-1	-0.758	-0.866	20.093	15.650	15.650	0.000	0.000	0.000	0.000
101	A	103	ARG	1	0.839	0.922	18.334	-16.468	-16.468	0.000	0.000	0.000	0.000
102	A	104	LEU	0	0.014	0.006	16.683	1.004	1.004	0.000	0.000	0.000	0.000
103	A	105	SER	0	0.013	-0.008	14.431	-1.325	-1.325	0.000	0.000	0.000	0.000
104	A	106	THR	0	-0.034	-0.011	13.463	1.146	1.146	0.000	0.000	0.000	0.000
105	A	107	VAL	0	-0.001	-0.004	9.869	-1.433	-1.433	0.000	0.000	0.000	0.000
106	A	108	VAL	0	-0.002	0.007	11.493	1.833	1.833	0.000	0.000	0.000	0.000
107	A	109	LEU	0	-0.026	-0.020	7.294	-0.698	-0.698	0.000	0.000	0.000	0.000
108	A	110	HIS	0	-0.007	-0.016	11.148	1.071	1.071	0.000	0.000	0.000	0.000
109	A	111	ARG	1	0.822	0.901	9.279	-23.801	-23.801	0.000	0.000	0.000	0.000
110	A	112	ASP	-1	-0.726	-0.832	12.274	19.279	19.279	0.000	0.000	0.000	0.000
111	A	113	ASP	-1	-0.827	-0.934	13.111	21.276	21.276	0.000	0.000	0.000	0.000
112	A	114	GLU	-1	-0.967	-0.962	14.309	17.952	17.952	0.000	0.000	0.000	0.000
113	A	115	GLY	0	-0.088	-0.043	10.367	0.900	0.900	0.000	0.000	0.000	0.000
114	A	116	ARG	1	0.780	0.874	10.034	-15.578	-15.578	0.000	0.000	0.000	0.000
115	A	117	LEU	0	-0.011	-0.009	6.731	1.013	1.013	0.000	0.000	0.000	0.000
116	A	118	TYR	0	-0.048	-0.031	11.406	-1.513	-1.513	0.000	0.000	0.000	0.000
117	A	119	TRP	0	-0.086	-0.052	11.142	0.898	0.898	0.000	0.000	0.000	0.000
118	A	120	ARG	1	0.855	0.914	14.378	-17.364	-17.364	0.000	0.000	0.000	0.000
119	A	121	HIS	0	0.008	0.003	15.386	-1.550	-1.550	0.000	0.000	0.000	0.000
120	A	122	LEU	0	0.012	0.011	14.482	1.863	1.863	0.000	0.000	0.000	0.000
121	A	123	GLN	0	-0.009	0.019	16.824	-1.261	-1.261	0.000	0.000	0.000	0.000
122	A	124	GLU	-1	-0.793	-0.898	17.593	18.244	18.244	0.000	0.000	0.000	0.000
123	A	125	THR	0	-0.056	-0.032	19.713	-1.021	-1.021	0.000	0.000	0.000	0.000
124	A	126	PHE	0	0.022	0.010	21.587	0.582	0.582	0.000	0.000	0.000	0.000
125	A	127	CYS	0	-0.023	0.000	21.114	-0.045	-0.045	0.000	0.000	0.000	0.000
126	A	128	GLY	0	0.011	0.012	24.515	-0.403	-0.403	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:CYM)