FMO DATABASE

FMODB ID: 1N6VZ

Calculation Name: 3TV0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

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:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	142
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1254784.489263
FMO2-HF: Nuclear repulsion	1199569.387961
FMO2-HF: Total energy	-55215.101303
FMO2-MP2: Total energy	-55371.54476

3D Structure Molmil

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.
-4.038	0.638	0.692	-2.478	-2.89	-0.015

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 : 0.028 / q_NPA : -0.014

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	0.784	0.878	3.475	1.830	4.136	-0.002	-1.022	-1.283	0.000
4	A	11	ILE	0	0.053	0.023	5.673	0.083	0.083	0.000	0.000	0.000	0.000
5	A	12	ALA	0	-0.025	0.005	9.123	0.177	0.177	0.000	0.000	0.000	0.000
6	A	13	PRO	0	0.023	0.002	12.148	0.016	0.016	0.000	0.000	0.000	0.000
7	A	14	GLY	0	-0.026	-0.022	14.425	-0.014	-0.014	0.000	0.000	0.000	0.000
8	A	15	ALA	0	-0.043	0.003	13.385	-0.005	-0.005	0.000	0.000	0.000	0.000
9	A	16	VAL	0	-0.032	-0.020	15.167	0.036	0.036	0.000	0.000	0.000	0.000
10	A	17	VAL	0	0.028	0.014	11.072	-0.039	-0.039	0.000	0.000	0.000	0.000
11	A	18	CYS	0	-0.029	-0.005	14.353	0.067	0.067	0.000	0.000	0.000	0.000
12	A	19	VAL	0	0.046	0.025	13.683	-0.051	-0.051	0.000	0.000	0.000	0.000
13	A	20	GLU	-1	-0.929	-0.962	14.068	-0.087	-0.087	0.000	0.000	0.000	0.000
14	A	21	SER	0	-0.084	-0.030	13.190	-0.047	-0.047	0.000	0.000	0.000	0.000
15	A	22	GLU	-1	-0.897	-0.940	11.390	-0.440	-0.440	0.000	0.000	0.000	0.000
16	A	23	ILE	0	0.025	0.008	6.958	-0.114	-0.114	0.000	0.000	0.000	0.000
17	A	24	ARG	1	0.879	0.930	6.178	0.648	0.648	0.000	0.000	0.000	0.000
18	A	25	GLY	0	0.058	0.035	4.004	0.353	0.521	0.000	-0.051	-0.117	0.000
19	A	26	ASP	-1	-0.909	-0.945	2.491	-7.143	-5.124	0.678	-1.459	-1.238	-0.014
20	A	27	VAL	0	0.049	0.022	3.324	1.748	1.931	0.016	0.054	-0.252	-0.001
21	A	28	THR	0	-0.016	-0.011	6.020	-0.382	-0.382	0.000	0.000	0.000	0.000
22	A	29	ILE	0	0.001	0.008	8.593	0.165	0.165	0.000	0.000	0.000	0.000
23	A	30	GLY	0	0.028	0.010	11.353	0.090	0.090	0.000	0.000	0.000	0.000
24	A	31	PRO	0	0.031	-0.002	14.315	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	32	ARG	1	0.935	0.961	16.395	0.103	0.103	0.000	0.000	0.000	0.000
26	A	33	THR	0	0.014	0.034	15.409	0.021	0.021	0.000	0.000	0.000	0.000
27	A	34	VAL	0	-0.016	-0.002	16.885	0.009	0.009	0.000	0.000	0.000	0.000
28	A	35	ILE	0	-0.011	-0.010	12.595	-0.030	-0.030	0.000	0.000	0.000	0.000
29	A	36	HIS	0	0.010	-0.004	16.609	0.029	0.029	0.000	0.000	0.000	0.000
30	A	37	PRO	0	0.032	-0.003	17.320	-0.040	-0.040	0.000	0.000	0.000	0.000
31	A	38	LYS	1	0.930	0.933	17.256	0.151	0.151	0.000	0.000	0.000	0.000
32	A	39	ALA	0	-0.024	0.033	15.834	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	40	ARG	1	0.929	0.957	13.702	0.329	0.329	0.000	0.000	0.000	0.000
34	A	41	ILE	0	0.009	-0.001	9.794	0.017	0.017	0.000	0.000	0.000	0.000
35	A	42	ILE	0	0.006	-0.006	9.114	-0.241	-0.241	0.000	0.000	0.000	0.000
36	A	43	ALA	0	0.001	-0.013	6.119	0.187	0.187	0.000	0.000	0.000	0.000
37	A	44	GLU	-1	-0.974	-0.982	7.511	-0.926	-0.926	0.000	0.000	0.000	0.000
38	A	45	ALA	0	-0.014	-0.004	10.163	0.018	0.018	0.000	0.000	0.000	0.000
39	A	46	GLY	0	-0.075	-0.051	9.857	0.132	0.132	0.000	0.000	0.000	0.000
40	A	47	PRO	0	-0.017	-0.001	7.076	-0.158	-0.158	0.000	0.000	0.000	0.000
41	A	48	ILE	0	0.016	0.018	7.525	0.216	0.216	0.000	0.000	0.000	0.000
42	A	49	VAL	0	-0.046	-0.005	8.705	-0.220	-0.220	0.000	0.000	0.000	0.000
43	A	50	ILE	0	0.044	0.016	11.363	0.086	0.086	0.000	0.000	0.000	0.000
44	A	51	GLY	0	0.029	0.024	13.704	-0.011	-0.011	0.000	0.000	0.000	0.000
45	A	52	GLU	-1	-0.954	-1.002	16.562	-0.202	-0.202	0.000	0.000	0.000	0.000
46	A	53	GLY	0	0.064	0.021	18.775	0.003	0.003	0.000	0.000	0.000	0.000
47	A	54	ASN	0	-0.032	-0.010	17.605	0.037	0.037	0.000	0.000	0.000	0.000
48	A	55	LEU	0	0.030	0.016	19.382	-0.007	-0.007	0.000	0.000	0.000	0.000
49	A	56	ILE	0	-0.037	-0.015	15.947	-0.010	-0.010	0.000	0.000	0.000	0.000
50	A	57	GLU	-1	-0.846	-0.932	18.912	-0.185	-0.185	0.000	0.000	0.000	0.000
51	A	58	GLU	-1	-0.817	-0.918	20.152	-0.203	-0.203	0.000	0.000	0.000	0.000
52	A	59	GLN	0	-0.080	-0.061	19.967	0.014	0.014	0.000	0.000	0.000	0.000
53	A	60	ALA	0	-0.003	0.044	18.743	0.001	0.001	0.000	0.000	0.000	0.000
54	A	61	LEU	0	-0.069	-0.040	15.445	-0.035	-0.035	0.000	0.000	0.000	0.000
55	A	62	ILE	0	0.041	0.022	13.543	0.031	0.031	0.000	0.000	0.000	0.000
56	A	63	ILE	0	-0.018	-0.016	12.723	-0.103	-0.103	0.000	0.000	0.000	0.000
57	A	64	ASN	0	-0.049	-0.013	10.899	0.161	0.161	0.000	0.000	0.000	0.000
58	A	65	ALA	0	0.060	0.032	12.472	-0.057	-0.057	0.000	0.000	0.000	0.000
59	A	66	TYR	0	0.016	0.001	12.953	0.031	0.031	0.000	0.000	0.000	0.000
60	A	67	PRO	0	-0.033	-0.008	17.135	0.003	0.003	0.000	0.000	0.000	0.000
61	A	68	ASP	-1	-0.872	-0.920	20.612	-0.221	-0.221	0.000	0.000	0.000	0.000
62	A	69	ASN	0	-0.084	-0.065	23.075	0.016	0.016	0.000	0.000	0.000	0.000
63	A	70	ILE	0	0.009	0.018	22.521	-0.016	-0.016	0.000	0.000	0.000	0.000
64	A	80	LYS	1	0.970	0.967	11.140	0.377	0.377	0.000	0.000	0.000	0.000
65	A	81	PRO	0	0.020	0.018	11.656	-0.058	-0.058	0.000	0.000	0.000	0.000
66	A	82	MET	0	-0.007	0.019	11.901	0.037	0.037	0.000	0.000	0.000	0.000
67	A	83	ILE	0	-0.067	-0.052	12.897	-0.070	-0.070	0.000	0.000	0.000	0.000
68	A	84	ILE	0	-0.007	-0.008	14.374	0.037	0.037	0.000	0.000	0.000	0.000
69	A	85	GLY	0	0.013	0.018	16.842	-0.018	-0.018	0.000	0.000	0.000	0.000
70	A	86	THR	0	-0.067	-0.034	18.773	-0.030	-0.030	0.000	0.000	0.000	0.000
71	A	87	ASN	0	-0.017	-0.023	21.274	0.011	0.011	0.000	0.000	0.000	0.000
72	A	88	ASN	0	-0.007	0.006	20.237	0.040	0.040	0.000	0.000	0.000	0.000
73	A	89	VAL	0	0.017	0.008	21.678	-0.019	-0.019	0.000	0.000	0.000	0.000
74	A	90	PHE	0	-0.025	-0.033	18.454	-0.007	-0.007	0.000	0.000	0.000	0.000
75	A	91	GLU	-1	-0.788	-0.904	21.907	-0.164	-0.164	0.000	0.000	0.000	0.000
76	A	92	VAL	0	0.049	0.013	23.403	-0.018	-0.018	0.000	0.000	0.000	0.000
77	A	93	GLY	0	-0.066	-0.043	23.041	0.012	0.012	0.000	0.000	0.000	0.000
78	A	94	CYS	0	-0.091	-0.003	22.076	-0.005	-0.005	0.000	0.000	0.000	0.000
79	A	95	TYR	0	-0.010	-0.017	18.175	-0.042	-0.042	0.000	0.000	0.000	0.000
80	A	96	SER	0	0.018	0.008	18.373	0.038	0.038	0.000	0.000	0.000	0.000
81	A	97	GLN	0	0.012	-0.021	17.252	-0.041	-0.041	0.000	0.000	0.000	0.000
82	A	98	ALA	0	0.016	0.032	18.104	-0.008	-0.008	0.000	0.000	0.000	0.000
83	A	99	MET	0	-0.032	-0.020	14.475	-0.046	-0.046	0.000	0.000	0.000	0.000
84	A	100	LYS	1	0.936	0.965	17.170	0.189	0.189	0.000	0.000	0.000	0.000
85	A	101	MET	0	-0.016	0.006	19.440	0.016	0.016	0.000	0.000	0.000	0.000
86	A	102	GLY	0	-0.001	0.003	20.418	-0.015	-0.015	0.000	0.000	0.000	0.000
87	A	103	ASP	-1	-0.825	-0.909	21.944	-0.225	-0.225	0.000	0.000	0.000	0.000
88	A	104	ASN	0	-0.028	-0.025	24.382	0.009	0.009	0.000	0.000	0.000	0.000
89	A	105	ASN	0	-0.048	-0.018	23.732	0.029	0.029	0.000	0.000	0.000	0.000
90	A	106	VAL	0	0.040	0.019	25.190	-0.010	-0.010	0.000	0.000	0.000	0.000
91	A	107	ILE	0	-0.037	-0.016	21.693	0.007	0.007	0.000	0.000	0.000	0.000
92	A	108	GLU	-1	-0.813	-0.905	25.354	-0.140	-0.140	0.000	0.000	0.000	0.000
93	A	109	SER	0	0.010	-0.007	26.773	-0.010	-0.010	0.000	0.000	0.000	0.000
94	A	110	LYS	1	0.866	0.918	26.054	0.160	0.160	0.000	0.000	0.000	0.000
95	A	111	ALA	0	-0.003	0.036	26.314	0.006	0.006	0.000	0.000	0.000	0.000
96	A	112	TYR	0	-0.049	-0.029	21.409	-0.016	-0.016	0.000	0.000	0.000	0.000
97	A	113	VAL	0	0.018	0.008	22.119	0.018	0.018	0.000	0.000	0.000	0.000
98	A	114	GLY	0	0.068	0.017	21.857	-0.029	-0.029	0.000	0.000	0.000	0.000
99	A	115	ARG	1	0.920	0.947	16.973	0.340	0.340	0.000	0.000	0.000	0.000
100	A	116	ASN	0	-0.112	-0.037	21.242	-0.012	-0.012	0.000	0.000	0.000	0.000
101	A	117	VAL	0	0.025	0.032	23.478	0.020	0.020	0.000	0.000	0.000	0.000
102	A	118	ILE	0	-0.052	-0.029	22.495	-0.022	-0.022	0.000	0.000	0.000	0.000
103	A	119	LEU	0	0.032	0.012	23.278	0.020	0.020	0.000	0.000	0.000	0.000
104	A	120	THR	0	-0.039	-0.057	24.117	-0.010	-0.010	0.000	0.000	0.000	0.000
105	A	121	SER	0	0.072	0.040	25.303	-0.022	-0.022	0.000	0.000	0.000	0.000
106	A	122	GLY	0	0.011	0.017	27.628	0.012	0.012	0.000	0.000	0.000	0.000
107	A	123	CYS	0	-0.088	-0.015	27.800	0.012	0.012	0.000	0.000	0.000	0.000
108	A	124	ILE	0	0.007	-0.001	28.601	-0.007	-0.007	0.000	0.000	0.000	0.000
109	A	125	ILE	0	-0.032	-0.017	26.418	0.007	0.007	0.000	0.000	0.000	0.000
110	A	126	GLY	0	0.039	0.000	29.062	-0.004	-0.004	0.000	0.000	0.000	0.000
111	A	127	ALA	0	0.055	0.012	30.027	-0.008	-0.008	0.000	0.000	0.000	0.000
112	A	128	CYS	0	-0.151	-0.082	29.878	0.010	0.010	0.000	0.000	0.000	0.000
113	A	129	CYS	0	-0.099	-0.003	30.347	-0.003	-0.003	0.000	0.000	0.000	0.000
114	A	130	ASN	0	0.027	0.013	27.865	-0.026	-0.026	0.000	0.000	0.000	0.000
115	A	131	LEU	0	0.042	0.008	27.192	0.010	0.010	0.000	0.000	0.000	0.000
116	A	132	ASN	0	-0.023	-0.016	25.885	-0.027	-0.027	0.000	0.000	0.000	0.000
117	A	133	THR	0	-0.006	-0.010	27.665	0.006	0.006	0.000	0.000	0.000	0.000
118	A	134	PHE	0	-0.007	-0.026	27.161	-0.015	-0.015	0.000	0.000	0.000	0.000
119	A	135	GLU	-1	-0.813	-0.885	27.698	-0.125	-0.125	0.000	0.000	0.000	0.000
120	A	136	VAL	0	-0.001	0.008	27.015	-0.015	-0.015	0.000	0.000	0.000	0.000
121	A	137	ILE	0	0.002	0.004	27.689	0.011	0.011	0.000	0.000	0.000	0.000
122	A	138	PRO	0	-0.002	0.020	29.583	-0.004	-0.004	0.000	0.000	0.000	0.000
123	A	139	GLU	-1	-0.872	-0.941	30.190	-0.128	-0.128	0.000	0.000	0.000	0.000
124	A	140	ASN	0	-0.088	-0.042	31.430	0.002	0.002	0.000	0.000	0.000	0.000
125	A	141	THR	0	0.024	0.011	32.128	0.010	0.010	0.000	0.000	0.000	0.000
126	A	142	VAL	0	-0.012	0.004	32.046	-0.008	-0.008	0.000	0.000	0.000	0.000
127	A	143	ILE	0	0.004	0.002	30.588	0.008	0.008	0.000	0.000	0.000	0.000
128	A	144	TYR	0	0.034	0.010	32.536	-0.004	-0.004	0.000	0.000	0.000	0.000
129	A	145	GLY	0	0.019	0.016	34.750	0.006	0.006	0.000	0.000	0.000	0.000
130	A	146	ALA	0	0.025	0.013	33.907	-0.006	-0.006	0.000	0.000	0.000	0.000
131	A	147	ASP	-1	-0.881	-0.953	33.557	-0.108	-0.108	0.000	0.000	0.000	0.000
132	A	149	LEU	0	-0.041	-0.024	34.519	0.001	0.001	0.000	0.000	0.000	0.000
133	A	150	ARG	1	0.900	0.963	37.392	0.088	0.088	0.000	0.000	0.000	0.000
134	A	151	ARG	1	0.866	0.893	32.711	0.118	0.118	0.000	0.000	0.000	0.000
135	A	152	VAL	0	-0.029	-0.002	37.125	0.006	0.006	0.000	0.000	0.000	0.000
136	A	153	GLN	0	0.040	0.012	36.128	-0.010	-0.010	0.000	0.000	0.000	0.000
137	A	154	THR	0	0.020	0.016	34.059	0.007	0.007	0.000	0.000	0.000	0.000
138	A	155	GLU	-1	-0.974	-0.986	37.442	-0.067	-0.067	0.000	0.000	0.000	0.000
139	A	156	ARG	1	0.902	0.953	35.790	0.083	0.083	0.000	0.000	0.000	0.000
140	A	157	PRO	0	-0.017	-0.013	36.372	-0.002	-0.002	0.000	0.000	0.000	0.000
141	A	158	GLN	0	0.103	0.042	29.792	-0.010	-0.010	0.000	0.000	0.000	0.000
142	A	159	PRO	0	-0.034	0.007	30.853	-0.005	-0.005	0.000	0.000	0.000	0.000

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