FMO DATABASE

FMODB ID: G5Y71

Calculation Name: 3TV0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3TV0

Chain ID: A

ChEMBL ID:

UniProt ID: O00399

Base Structure: X-ray

Registration Date: 2023-09-22

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	142
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1255414.33246
FMO2-HF: Nuclear repulsion	1200198.600413
FMO2-HF: Total energy	-55215.732047
FMO2-MP2: Total energy	-55372.076526

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:8:SER)

Summations of interaction energy for fragment #1(A:8:SER)

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.
-4.277	0.143	0.633	-2.313	-2.74	-0.016

Interaction energy analysis for fragmet #1(A:8:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : -0.019

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	10	LYS	1	0.808	0.893	3.668	1.674	3.667	-0.009	-0.835	-1.149	-0.001
4	A	11	ILE	0	0.038	0.021	5.984	0.178	0.178	0.000	0.000	0.000	0.000
5	A	12	ALA	0	-0.009	0.012	9.356	0.173	0.173	0.000	0.000	0.000	0.000
6	A	13	PRO	0	0.024	0.003	12.428	0.011	0.011	0.000	0.000	0.000	0.000
7	A	14	GLY	0	-0.021	-0.024	14.638	0.002	0.002	0.000	0.000	0.000	0.000
8	A	15	ALA	0	-0.048	-0.001	13.559	0.009	0.009	0.000	0.000	0.000	0.000
9	A	16	VAL	0	-0.032	-0.022	15.288	0.024	0.024	0.000	0.000	0.000	0.000
10	A	17	VAL	0	0.023	0.012	11.066	-0.029	-0.029	0.000	0.000	0.000	0.000
11	A	18	CYS	0	-0.029	0.000	14.346	0.057	0.057	0.000	0.000	0.000	0.000
12	A	19	VAL	0	0.036	0.016	13.692	-0.064	-0.064	0.000	0.000	0.000	0.000
13	A	20	GLU	-1	-0.891	-0.947	14.083	-0.206	-0.206	0.000	0.000	0.000	0.000
14	A	21	SER	0	-0.091	-0.029	13.139	-0.036	-0.036	0.000	0.000	0.000	0.000
15	A	22	GLU	-1	-0.856	-0.906	11.524	-0.532	-0.532	0.000	0.000	0.000	0.000
16	A	23	ILE	0	0.027	0.006	6.931	-0.097	-0.097	0.000	0.000	0.000	0.000
17	A	24	ARG	1	0.843	0.901	6.176	0.619	0.619	0.000	0.000	0.000	0.000
18	A	25	GLY	0	0.047	0.030	3.933	0.391	0.568	0.000	-0.053	-0.124	0.000
19	A	26	ASP	-1	-0.898	-0.941	2.573	-6.909	-4.860	0.629	-1.460	-1.218	-0.015
20	A	27	VAL	0	0.043	0.019	3.388	1.543	1.744	0.013	0.035	-0.249	0.000
21	A	28	THR	0	-0.025	-0.015	6.084	-0.479	-0.479	0.000	0.000	0.000	0.000
22	A	29	ILE	0	0.017	0.009	8.682	0.182	0.182	0.000	0.000	0.000	0.000
23	A	30	GLY	0	0.027	0.016	11.433	0.078	0.078	0.000	0.000	0.000	0.000
24	A	31	PRO	0	0.027	-0.005	14.605	-0.010	-0.010	0.000	0.000	0.000	0.000
25	A	32	ARG	1	0.944	0.966	16.685	0.171	0.171	0.000	0.000	0.000	0.000
26	A	33	THR	0	0.012	0.038	15.331	0.028	0.028	0.000	0.000	0.000	0.000
27	A	34	VAL	0	-0.026	-0.010	17.061	-0.003	-0.003	0.000	0.000	0.000	0.000
28	A	35	ILE	0	-0.007	-0.011	12.596	-0.025	-0.025	0.000	0.000	0.000	0.000
29	A	36	HIS	0	0.015	0.000	16.623	0.019	0.019	0.000	0.000	0.000	0.000
30	A	37	PRO	0	0.025	0.001	17.330	-0.045	-0.045	0.000	0.000	0.000	0.000
31	A	38	LYS	1	0.898	0.924	17.249	0.225	0.225	0.000	0.000	0.000	0.000
32	A	39	ALA	0	-0.026	0.028	15.867	0.007	0.007	0.000	0.000	0.000	0.000
33	A	40	ARG	1	0.918	0.955	13.703	0.355	0.355	0.000	0.000	0.000	0.000
34	A	41	ILE	0	0.016	-0.001	9.816	0.030	0.030	0.000	0.000	0.000	0.000
35	A	42	ILE	0	0.010	-0.002	9.077	-0.268	-0.268	0.000	0.000	0.000	0.000
36	A	43	ALA	0	0.005	-0.010	6.100	0.208	0.208	0.000	0.000	0.000	0.000
37	A	44	GLU	-1	-0.959	-0.975	7.488	-0.868	-0.868	0.000	0.000	0.000	0.000
38	A	45	ALA	0	0.002	0.001	10.136	0.035	0.035	0.000	0.000	0.000	0.000
39	A	46	GLY	0	-0.060	-0.047	9.887	0.144	0.144	0.000	0.000	0.000	0.000
40	A	47	PRO	0	-0.008	0.013	7.136	-0.160	-0.160	0.000	0.000	0.000	0.000
41	A	48	ILE	0	0.007	0.017	7.585	0.200	0.200	0.000	0.000	0.000	0.000
42	A	49	VAL	0	-0.051	-0.019	8.784	-0.222	-0.222	0.000	0.000	0.000	0.000
43	A	50	ILE	0	0.035	0.016	11.448	0.087	0.087	0.000	0.000	0.000	0.000
44	A	51	GLY	0	0.042	0.033	13.778	-0.022	-0.022	0.000	0.000	0.000	0.000
45	A	52	GLU	-1	-0.958	-1.006	16.647	-0.263	-0.263	0.000	0.000	0.000	0.000
46	A	53	GLY	0	0.061	0.023	18.993	0.009	0.009	0.000	0.000	0.000	0.000
47	A	54	ASN	0	-0.050	-0.024	17.682	0.042	0.042	0.000	0.000	0.000	0.000
48	A	55	LEU	0	0.028	0.017	19.382	-0.016	-0.016	0.000	0.000	0.000	0.000
49	A	56	ILE	0	-0.035	-0.016	15.914	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	57	GLU	-1	-0.815	-0.914	18.921	-0.236	-0.236	0.000	0.000	0.000	0.000
51	A	58	GLU	-1	-0.809	-0.922	20.156	-0.258	-0.258	0.000	0.000	0.000	0.000
52	A	59	GLN	0	-0.070	-0.055	19.971	0.024	0.024	0.000	0.000	0.000	0.000
53	A	60	ALA	0	0.007	0.045	18.826	0.006	0.006	0.000	0.000	0.000	0.000
54	A	61	LEU	0	-0.078	-0.041	15.326	-0.041	-0.041	0.000	0.000	0.000	0.000
55	A	62	ILE	0	0.029	0.019	13.604	0.037	0.037	0.000	0.000	0.000	0.000
56	A	63	ILE	0	-0.005	-0.011	12.626	-0.109	-0.109	0.000	0.000	0.000	0.000
57	A	64	ASN	0	-0.041	-0.015	10.904	0.156	0.156	0.000	0.000	0.000	0.000
58	A	65	ALA	0	0.060	0.037	12.466	-0.051	-0.051	0.000	0.000	0.000	0.000
59	A	66	TYR	0	0.028	0.006	12.320	0.045	0.045	0.000	0.000	0.000	0.000
60	A	67	PRO	0	-0.024	-0.005	17.123	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	68	ASP	-1	-0.894	-0.934	20.609	-0.213	-0.213	0.000	0.000	0.000	0.000
62	A	69	ASN	0	-0.070	-0.056	23.067	0.016	0.016	0.000	0.000	0.000	0.000
63	A	70	ILE	0	0.009	0.019	22.545	-0.015	-0.015	0.000	0.000	0.000	0.000
64	A	80	LYS	1	0.939	0.966	10.682	0.422	0.422	0.000	0.000	0.000	0.000
65	A	81	PRO	0	-0.012	-0.011	11.721	-0.058	-0.058	0.000	0.000	0.000	0.000
66	A	82	MET	0	-0.023	0.011	11.962	0.021	0.021	0.000	0.000	0.000	0.000
67	A	83	ILE	0	-0.070	-0.048	12.969	-0.073	-0.073	0.000	0.000	0.000	0.000
68	A	84	ILE	0	0.003	-0.008	14.548	0.038	0.038	0.000	0.000	0.000	0.000
69	A	85	GLY	0	0.010	0.017	16.923	-0.021	-0.021	0.000	0.000	0.000	0.000
70	A	86	THR	0	-0.076	-0.058	18.851	-0.036	-0.036	0.000	0.000	0.000	0.000
71	A	87	ASN	0	-0.021	-0.025	21.353	0.012	0.012	0.000	0.000	0.000	0.000
72	A	88	ASN	0	-0.023	-0.001	20.388	0.041	0.041	0.000	0.000	0.000	0.000
73	A	89	VAL	0	0.022	0.009	21.726	-0.024	-0.024	0.000	0.000	0.000	0.000
74	A	90	PHE	0	-0.007	-0.031	18.367	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	91	GLU	-1	-0.756	-0.875	21.929	-0.195	-0.195	0.000	0.000	0.000	0.000
76	A	92	VAL	0	0.039	0.017	23.404	-0.019	-0.019	0.000	0.000	0.000	0.000
77	A	93	GLY	0	-0.071	-0.044	23.011	0.016	0.016	0.000	0.000	0.000	0.000
78	A	94	CYS	0	-0.102	-0.013	22.147	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	95	TYR	0	-0.007	-0.015	18.367	-0.042	-0.042	0.000	0.000	0.000	0.000
80	A	96	SER	0	0.024	0.012	18.454	0.042	0.042	0.000	0.000	0.000	0.000
81	A	97	GLN	0	0.009	-0.024	17.266	-0.049	-0.049	0.000	0.000	0.000	0.000
82	A	98	ALA	0	0.009	0.031	18.127	-0.005	-0.005	0.000	0.000	0.000	0.000
83	A	99	MET	0	-0.026	-0.019	14.602	-0.046	-0.046	0.000	0.000	0.000	0.000
84	A	100	LYS	1	0.937	0.964	17.231	0.200	0.200	0.000	0.000	0.000	0.000
85	A	101	MET	0	-0.019	0.003	19.346	0.018	0.018	0.000	0.000	0.000	0.000
86	A	102	GLY	0	0.013	0.010	20.492	-0.016	-0.016	0.000	0.000	0.000	0.000
87	A	103	ASP	-1	-0.827	-0.892	22.018	-0.254	-0.254	0.000	0.000	0.000	0.000
88	A	104	ASN	0	-0.001	-0.006	24.457	0.010	0.010	0.000	0.000	0.000	0.000
89	A	105	ASN	0	-0.052	-0.025	23.760	0.029	0.029	0.000	0.000	0.000	0.000
90	A	106	VAL	0	0.035	0.014	25.239	-0.013	-0.013	0.000	0.000	0.000	0.000
91	A	107	ILE	0	-0.027	-0.013	21.765	0.011	0.011	0.000	0.000	0.000	0.000
92	A	108	GLU	-1	-0.816	-0.907	25.374	-0.164	-0.164	0.000	0.000	0.000	0.000
93	A	109	SER	0	0.000	-0.025	26.762	-0.010	-0.010	0.000	0.000	0.000	0.000
94	A	110	LYS	1	0.857	0.915	26.017	0.186	0.186	0.000	0.000	0.000	0.000
95	A	111	ALA	0	-0.003	0.036	26.321	0.008	0.008	0.000	0.000	0.000	0.000
96	A	112	TYR	0	-0.059	-0.034	21.339	-0.017	-0.017	0.000	0.000	0.000	0.000
97	A	113	VAL	0	0.013	0.004	22.253	0.019	0.019	0.000	0.000	0.000	0.000
98	A	114	GLY	0	0.083	0.024	21.870	-0.029	-0.029	0.000	0.000	0.000	0.000
99	A	115	ARG	1	0.886	0.932	16.482	0.336	0.336	0.000	0.000	0.000	0.000
100	A	116	ASN	0	-0.094	-0.036	21.260	-0.012	-0.012	0.000	0.000	0.000	0.000
101	A	117	VAL	0	0.020	0.033	23.515	0.020	0.020	0.000	0.000	0.000	0.000
102	A	118	ILE	0	-0.059	-0.033	22.498	-0.023	-0.023	0.000	0.000	0.000	0.000
103	A	119	LEU	0	0.040	0.020	23.220	0.021	0.021	0.000	0.000	0.000	0.000
104	A	120	THR	0	-0.022	-0.045	24.181	-0.010	-0.010	0.000	0.000	0.000	0.000
105	A	121	SER	0	0.074	0.047	25.373	-0.024	-0.024	0.000	0.000	0.000	0.000
106	A	122	GLY	0	0.007	0.015	27.699	0.014	0.014	0.000	0.000	0.000	0.000
107	A	123	CYS	0	-0.092	-0.020	27.837	0.013	0.013	0.000	0.000	0.000	0.000
108	A	124	ILE	0	0.010	-0.001	28.650	-0.009	-0.009	0.000	0.000	0.000	0.000
109	A	125	ILE	0	-0.035	-0.019	26.650	0.009	0.009	0.000	0.000	0.000	0.000
110	A	126	GLY	0	0.044	0.007	29.084	-0.006	-0.006	0.000	0.000	0.000	0.000
111	A	127	ALA	0	0.063	0.011	30.036	-0.007	-0.007	0.000	0.000	0.000	0.000
112	A	128	CYS	0	-0.160	-0.081	29.876	0.011	0.011	0.000	0.000	0.000	0.000
113	A	129	CYS	0	-0.095	0.002	30.363	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	130	ASN	0	0.013	0.006	28.085	-0.027	-0.027	0.000	0.000	0.000	0.000
115	A	131	LEU	0	0.036	0.006	27.288	0.011	0.011	0.000	0.000	0.000	0.000
116	A	132	ASN	0	-0.020	-0.017	25.763	-0.028	-0.028	0.000	0.000	0.000	0.000
117	A	133	THR	0	-0.022	-0.037	27.673	0.008	0.008	0.000	0.000	0.000	0.000
118	A	134	PHE	0	-0.006	-0.019	27.185	-0.014	-0.014	0.000	0.000	0.000	0.000
119	A	135	GLU	-1	-0.776	-0.832	27.732	-0.133	-0.133	0.000	0.000	0.000	0.000
120	A	136	VAL	0	-0.006	0.002	27.115	-0.015	-0.015	0.000	0.000	0.000	0.000
121	A	137	ILE	0	-0.001	0.004	27.710	0.012	0.012	0.000	0.000	0.000	0.000
122	A	138	PRO	0	0.014	0.024	29.644	-0.005	-0.005	0.000	0.000	0.000	0.000
123	A	139	GLU	-1	-0.869	-0.926	29.988	-0.142	-0.142	0.000	0.000	0.000	0.000
124	A	140	ASN	0	-0.069	-0.031	31.477	0.003	0.003	0.000	0.000	0.000	0.000
125	A	141	THR	0	0.010	-0.005	32.116	0.011	0.011	0.000	0.000	0.000	0.000
126	A	142	VAL	0	-0.010	0.003	32.094	-0.010	-0.010	0.000	0.000	0.000	0.000
127	A	143	ILE	0	0.001	-0.001	30.411	0.009	0.009	0.000	0.000	0.000	0.000
128	A	144	TYR	0	0.037	0.013	32.562	-0.005	-0.005	0.000	0.000	0.000	0.000
129	A	145	GLY	0	0.027	0.018	34.770	0.007	0.007	0.000	0.000	0.000	0.000
130	A	146	ALA	0	0.025	0.012	33.903	-0.006	-0.006	0.000	0.000	0.000	0.000
131	A	147	ASP	-1	-0.875	-0.957	33.556	-0.117	-0.117	0.000	0.000	0.000	0.000
132	A	149	LEU	0	-0.035	-0.019	34.533	0.001	0.001	0.000	0.000	0.000	0.000
133	A	150	ARG	1	0.886	0.962	37.410	0.098	0.098	0.000	0.000	0.000	0.000
134	A	151	ARG	1	0.853	0.870	32.543	0.127	0.127	0.000	0.000	0.000	0.000
135	A	152	VAL	0	-0.036	-0.004	37.171	0.007	0.007	0.000	0.000	0.000	0.000
136	A	153	GLN	0	0.032	0.008	35.750	-0.009	-0.009	0.000	0.000	0.000	0.000
137	A	154	THR	0	0.012	0.003	34.159	0.007	0.007	0.000	0.000	0.000	0.000
138	A	155	GLU	-1	-0.952	-0.971	37.498	-0.078	-0.078	0.000	0.000	0.000	0.000
139	A	156	ARG	1	0.874	0.939	35.870	0.098	0.098	0.000	0.000	0.000	0.000
140	A	157	PRO	0	-0.024	-0.009	36.443	-0.002	-0.002	0.000	0.000	0.000	0.000
141	A	158	GLN	0	0.078	0.034	29.945	-0.011	-0.011	0.000	0.000	0.000	0.000
142	A	159	PRO	0	-0.013	0.008	30.936	-0.007	-0.007	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:8:SER)