FMO DATABASE

FMODB ID: 52ZRZ

Calculation Name: 3PVI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3PVI

Chain ID: A

ChEMBL ID:

UniProt ID: P23657

Base Structure: X-ray

Registration Date: 2023-06-21

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	156
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1506269.574907
FMO2-HF: Nuclear repulsion	1443854.183762
FMO2-HF: Total energy	-62415.391145
FMO2-MP2: Total energy	-62601.810884

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:2:SER)

Summations of interaction energy for fragment #1(A:2: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.
-2.365	0.5	0.364	-1.413	-1.816	0.002

Interaction energy analysis for fragmet #1(A:2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.039 / q_NPA : 0.012

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	4	PRO	0	0.043	0.001	3.634	-1.884	0.335	-0.002	-1.124	-1.093	0.004
4	A	5	ASP	-1	-0.874	-0.951	6.024	-0.833	-0.833	0.000	0.000	0.000	0.000
5	A	6	LEU	0	-0.055	-0.019	2.764	-0.489	0.157	0.366	-0.289	-0.723	-0.002
6	A	7	ASN	0	0.015	-0.010	5.430	0.136	0.136	0.000	0.000	0.000	0.000
7	A	8	LYS	1	0.951	0.985	7.972	0.921	0.921	0.000	0.000	0.000	0.000
8	A	9	LEU	0	-0.035	-0.005	8.109	0.147	0.147	0.000	0.000	0.000	0.000
9	A	10	LEU	0	0.012	-0.006	7.771	0.137	0.137	0.000	0.000	0.000	0.000
10	A	11	GLU	-1	-0.923	-0.961	10.917	-0.708	-0.708	0.000	0.000	0.000	0.000
11	A	12	LEU	0	-0.055	-0.029	13.547	0.095	0.095	0.000	0.000	0.000	0.000
12	A	13	TRP	0	0.010	0.006	12.943	0.055	0.055	0.000	0.000	0.000	0.000
13	A	14	PRO	0	0.021	0.009	15.241	0.056	0.056	0.000	0.000	0.000	0.000
14	A	15	HIS	0	0.059	0.037	18.524	0.055	0.055	0.000	0.000	0.000	0.000
15	A	16	ILE	0	-0.044	-0.019	15.214	0.034	0.034	0.000	0.000	0.000	0.000
16	A	17	GLN	0	-0.068	-0.046	19.000	0.020	0.020	0.000	0.000	0.000	0.000
17	A	18	GLU	-1	-0.881	-0.935	20.470	-0.173	-0.173	0.000	0.000	0.000	0.000
18	A	19	TYR	0	-0.090	-0.046	22.511	0.025	0.025	0.000	0.000	0.000	0.000
19	A	20	GLN	0	0.024	0.005	21.707	0.020	0.020	0.000	0.000	0.000	0.000
20	A	21	ASP	-1	-0.834	-0.909	23.731	-0.131	-0.131	0.000	0.000	0.000	0.000
21	A	22	LEU	0	-0.048	-0.023	26.276	0.016	0.016	0.000	0.000	0.000	0.000
22	A	23	ALA	0	-0.008	-0.016	26.451	0.012	0.012	0.000	0.000	0.000	0.000
23	A	24	LEU	0	0.015	0.012	25.888	0.011	0.011	0.000	0.000	0.000	0.000
24	A	25	LYS	1	0.897	0.969	29.173	0.085	0.085	0.000	0.000	0.000	0.000
25	A	26	HIS	0	-0.079	-0.044	31.579	0.008	0.008	0.000	0.000	0.000	0.000
26	A	27	GLY	0	0.032	0.026	32.527	0.004	0.004	0.000	0.000	0.000	0.000
27	A	28	ILE	0	-0.060	-0.036	27.043	0.008	0.008	0.000	0.000	0.000	0.000
28	A	29	ASN	0	0.018	-0.016	26.841	-0.013	-0.013	0.000	0.000	0.000	0.000
29	A	30	ASP	-1	-0.853	-0.920	21.636	-0.045	-0.045	0.000	0.000	0.000	0.000
30	A	31	ILE	0	-0.044	-0.025	20.308	0.010	0.010	0.000	0.000	0.000	0.000
31	A	32	PHE	0	-0.042	-0.023	17.315	-0.006	-0.006	0.000	0.000	0.000	0.000
32	A	33	GLN	0	0.016	0.019	21.169	0.018	0.018	0.000	0.000	0.000	0.000
33	A	34	GLY	0	0.035	0.018	23.825	-0.008	-0.008	0.000	0.000	0.000	0.000
34	A	35	ASN	0	-0.034	-0.029	25.764	-0.008	-0.008	0.000	0.000	0.000	0.000
35	A	36	GLY	0	0.100	0.058	26.135	-0.006	-0.006	0.000	0.000	0.000	0.000
36	A	37	GLY	0	0.022	0.002	24.683	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	38	LYS	1	0.862	0.948	25.528	0.064	0.064	0.000	0.000	0.000	0.000
38	A	39	LEU	0	0.024	0.008	28.315	0.000	0.000	0.000	0.000	0.000	0.000
39	A	40	LEU	0	0.049	0.029	28.142	0.003	0.003	0.000	0.000	0.000	0.000
40	A	41	GLN	0	0.026	0.010	29.305	0.002	0.002	0.000	0.000	0.000	0.000
41	A	42	VAL	0	0.020	0.008	31.866	0.003	0.003	0.000	0.000	0.000	0.000
42	A	43	LEU	0	-0.014	0.009	33.320	0.003	0.003	0.000	0.000	0.000	0.000
43	A	44	LEU	0	0.008	0.000	32.323	0.001	0.001	0.000	0.000	0.000	0.000
44	A	45	ILE	0	-0.073	-0.021	34.863	0.001	0.001	0.000	0.000	0.000	0.000
45	A	46	THR	0	-0.073	-0.060	37.799	0.004	0.004	0.000	0.000	0.000	0.000
46	A	47	GLY	0	0.008	0.018	39.331	0.003	0.003	0.000	0.000	0.000	0.000
47	A	48	LEU	0	-0.053	-0.010	39.172	0.003	0.003	0.000	0.000	0.000	0.000
48	A	49	THR	0	-0.001	-0.006	38.065	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	50	VAL	0	-0.005	0.004	33.541	0.004	0.004	0.000	0.000	0.000	0.000
50	A	51	LEU	0	0.038	0.010	36.929	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	52	PRO	0	-0.023	-0.015	36.318	0.002	0.002	0.000	0.000	0.000	0.000
52	A	53	GLY	0	-0.008	-0.015	36.363	0.002	0.002	0.000	0.000	0.000	0.000
53	A	54	ARG	1	0.871	0.978	31.850	0.026	0.026	0.000	0.000	0.000	0.000
54	A	55	GLU	-1	-0.917	-0.965	36.584	0.016	0.016	0.000	0.000	0.000	0.000
55	A	56	GLY	0	-0.028	-0.014	34.222	0.005	0.005	0.000	0.000	0.000	0.000
56	A	57	ASN	0	-0.105	-0.062	30.750	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	58	ASP	-1	-0.855	-0.916	34.772	-0.013	-0.013	0.000	0.000	0.000	0.000
58	A	59	ALA	0	-0.003	-0.013	37.932	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	60	VAL	0	0.029	0.017	39.705	0.003	0.003	0.000	0.000	0.000	0.000
60	A	61	ASP	-1	-0.795	-0.914	42.433	-0.028	-0.028	0.000	0.000	0.000	0.000
61	A	62	ASN	0	0.000	-0.021	44.981	0.000	0.000	0.000	0.000	0.000	0.000
62	A	63	ALA	0	-0.082	-0.033	47.220	0.001	0.001	0.000	0.000	0.000	0.000
63	A	64	GLY	0	-0.006	0.011	47.005	0.002	0.002	0.000	0.000	0.000	0.000
64	A	65	GLN	0	-0.097	-0.038	47.408	0.003	0.003	0.000	0.000	0.000	0.000
65	A	66	GLU	-1	-0.858	-0.949	42.415	-0.015	-0.015	0.000	0.000	0.000	0.000
66	A	67	TYR	0	-0.068	-0.037	41.771	0.000	0.000	0.000	0.000	0.000	0.000
67	A	68	GLU	-1	-0.861	-0.919	38.141	-0.006	-0.006	0.000	0.000	0.000	0.000
68	A	69	LEU	0	-0.004	-0.007	35.693	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	70	LYS	1	0.844	0.945	34.850	0.006	0.006	0.000	0.000	0.000	0.000
70	A	71	SER	0	0.005	-0.014	30.917	-0.005	-0.005	0.000	0.000	0.000	0.000
71	A	72	ILE	0	-0.064	-0.021	31.398	0.005	0.005	0.000	0.000	0.000	0.000
72	A	73	ASN	0	0.050	0.032	25.565	-0.011	-0.011	0.000	0.000	0.000	0.000
73	A	74	ILE	0	0.033	-0.002	29.659	0.006	0.006	0.000	0.000	0.000	0.000
74	A	75	ASP	-1	-0.864	-0.917	27.846	-0.080	-0.080	0.000	0.000	0.000	0.000
75	A	76	LEU	0	-0.076	-0.035	24.762	0.002	0.002	0.000	0.000	0.000	0.000
76	A	77	THR	0	-0.010	-0.010	29.047	0.008	0.008	0.000	0.000	0.000	0.000
77	A	78	LYS	1	0.967	0.973	32.220	0.030	0.030	0.000	0.000	0.000	0.000
78	A	79	GLY	0	-0.002	0.003	35.060	0.001	0.001	0.000	0.000	0.000	0.000
79	A	80	PHE	0	0.043	0.023	34.817	0.001	0.001	0.000	0.000	0.000	0.000
80	A	81	SER	0	0.000	-0.020	31.692	0.004	0.004	0.000	0.000	0.000	0.000
81	A	82	THR	0	-0.012	-0.014	34.852	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	83	HIS	0	0.090	0.044	36.125	0.001	0.001	0.000	0.000	0.000	0.000
83	A	84	HIS	0	-0.046	-0.026	31.556	0.003	0.003	0.000	0.000	0.000	0.000
84	A	85	HIS	0	-0.003	-0.008	34.855	0.001	0.001	0.000	0.000	0.000	0.000
85	A	86	MET	0	-0.003	0.019	38.867	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	87	ASN	0	0.043	0.005	41.633	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	88	PRO	0	0.068	0.011	45.170	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	89	VAL	0	0.005	0.027	45.042	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	90	ILE	0	-0.020	-0.005	40.721	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	91	ILE	0	0.009	-0.009	43.741	-0.003	-0.003	0.000	0.000	0.000	0.000
91	A	92	ALA	0	-0.046	-0.015	45.992	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	93	LYS	1	0.923	0.967	41.127	-0.017	-0.017	0.000	0.000	0.000	0.000
93	A	94	TYR	0	-0.032	-0.021	38.985	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	95	ARG	1	0.895	0.937	45.191	-0.007	-0.007	0.000	0.000	0.000	0.000
95	A	96	GLN	0	0.013	-0.002	48.901	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	97	VAL	0	0.015	0.050	44.187	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	98	PRO	0	-0.002	0.014	46.188	0.001	0.001	0.000	0.000	0.000	0.000
98	A	99	TRP	0	-0.051	-0.033	39.829	0.001	0.001	0.000	0.000	0.000	0.000
99	A	100	ILE	0	0.017	0.012	38.692	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	101	PHE	0	-0.015	-0.016	37.951	0.001	0.001	0.000	0.000	0.000	0.000
101	A	102	ALA	0	0.022	0.011	34.194	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	103	ILE	0	-0.023	-0.026	34.446	0.003	0.003	0.000	0.000	0.000	0.000
103	A	104	TYR	0	0.020	0.002	29.270	0.000	0.000	0.000	0.000	0.000	0.000
104	A	105	ARG	1	0.883	0.951	29.852	0.094	0.094	0.000	0.000	0.000	0.000
105	A	106	GLY	0	0.044	0.009	25.831	-0.011	-0.011	0.000	0.000	0.000	0.000
106	A	107	ILE	0	-0.030	-0.029	22.175	0.007	0.007	0.000	0.000	0.000	0.000
107	A	108	ALA	0	0.010	0.016	25.910	0.000	0.000	0.000	0.000	0.000	0.000
108	A	109	ILE	0	-0.031	-0.015	28.957	0.007	0.007	0.000	0.000	0.000	0.000
109	A	110	GLU	-1	-0.976	-0.989	32.065	-0.061	-0.061	0.000	0.000	0.000	0.000
110	A	111	ALA	0	-0.039	-0.021	35.205	0.002	0.002	0.000	0.000	0.000	0.000
111	A	112	ILE	0	0.033	0.010	36.602	0.000	0.000	0.000	0.000	0.000	0.000
112	A	113	TYR	0	0.014	0.005	39.303	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	114	ARG	1	0.895	0.953	41.954	0.025	0.025	0.000	0.000	0.000	0.000
114	A	115	LEU	0	-0.020	-0.015	43.815	0.000	0.000	0.000	0.000	0.000	0.000
115	A	116	GLU	-1	-0.752	-0.870	46.512	-0.019	-0.019	0.000	0.000	0.000	0.000
116	A	117	PRO	0	0.059	0.028	49.342	0.001	0.001	0.000	0.000	0.000	0.000
117	A	118	LYS	1	0.918	0.953	50.315	0.008	0.008	0.000	0.000	0.000	0.000
118	A	119	ASP	-1	-0.865	-0.927	49.526	-0.013	-0.013	0.000	0.000	0.000	0.000
119	A	120	LEU	0	-0.029	-0.016	44.498	0.000	0.000	0.000	0.000	0.000	0.000
120	A	121	GLU	-1	-0.875	-0.955	48.357	0.002	0.002	0.000	0.000	0.000	0.000
121	A	122	PHE	0	-0.022	0.010	48.340	0.002	0.002	0.000	0.000	0.000	0.000
122	A	123	TYR	0	-0.036	-0.043	44.846	0.002	0.002	0.000	0.000	0.000	0.000
123	A	124	TYR	0	0.031	0.018	45.085	0.002	0.002	0.000	0.000	0.000	0.000
124	A	125	ASP	-1	-0.824	-0.907	48.625	0.004	0.004	0.000	0.000	0.000	0.000
125	A	126	LYS	1	0.817	0.919	46.448	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	127	TRP	0	-0.002	-0.031	42.483	0.002	0.002	0.000	0.000	0.000	0.000
127	A	128	GLU	-1	-0.845	-0.919	47.334	0.012	0.012	0.000	0.000	0.000	0.000
128	A	129	ARG	1	0.958	0.984	50.125	-0.004	-0.004	0.000	0.000	0.000	0.000
129	A	130	LYS	1	0.931	0.974	43.469	-0.020	-0.020	0.000	0.000	0.000	0.000
130	A	131	TRP	0	0.024	0.021	45.983	0.001	0.001	0.000	0.000	0.000	0.000
131	A	132	TYR	0	-0.036	-0.026	48.637	0.003	0.003	0.000	0.000	0.000	0.000
132	A	133	SER	0	-0.040	-0.027	51.234	0.001	0.001	0.000	0.000	0.000	0.000
133	A	134	ASP	-1	-0.910	-0.955	47.003	0.025	0.025	0.000	0.000	0.000	0.000
134	A	135	GLY	0	-0.035	-0.017	49.166	0.002	0.002	0.000	0.000	0.000	0.000
135	A	136	HIS	1	0.843	0.923	49.260	-0.022	-0.022	0.000	0.000	0.000	0.000
136	A	137	LYS	1	0.969	1.002	43.376	-0.033	-0.033	0.000	0.000	0.000	0.000
137	A	138	ASP	-1	-0.809	-0.909	41.300	0.032	0.032	0.000	0.000	0.000	0.000
138	A	139	ILE	0	-0.066	-0.036	41.104	0.001	0.001	0.000	0.000	0.000	0.000
139	A	140	ASN	0	-0.022	-0.012	34.447	-0.003	-0.003	0.000	0.000	0.000	0.000
140	A	141	ASN	0	0.007	0.010	33.142	-0.005	-0.005	0.000	0.000	0.000	0.000
141	A	142	PRO	0	0.012	0.018	36.915	-0.002	-0.002	0.000	0.000	0.000	0.000
142	A	143	LYS	1	0.859	0.934	33.986	-0.014	-0.014	0.000	0.000	0.000	0.000
143	A	144	ILE	0	0.045	0.043	38.961	0.001	0.001	0.000	0.000	0.000	0.000
144	A	145	PRO	0	-0.035	-0.020	39.374	-0.003	-0.003	0.000	0.000	0.000	0.000
145	A	146	VAL	0	0.057	0.017	36.682	-0.001	-0.001	0.000	0.000	0.000	0.000
146	A	147	LYS	1	0.877	0.941	39.918	0.018	0.018	0.000	0.000	0.000	0.000
147	A	148	TYR	0	-0.007	-0.006	43.232	0.000	0.000	0.000	0.000	0.000	0.000
148	A	149	VAL	0	0.023	0.010	40.565	0.000	0.000	0.000	0.000	0.000	0.000
149	A	150	MET	0	-0.069	-0.043	41.394	-0.001	-0.001	0.000	0.000	0.000	0.000
150	A	151	GLU	-1	-0.920	-0.956	44.268	-0.021	-0.021	0.000	0.000	0.000	0.000
151	A	152	HIS	0	0.001	0.002	47.444	0.000	0.000	0.000	0.000	0.000	0.000
152	A	153	GLY	0	0.005	0.022	46.136	0.000	0.000	0.000	0.000	0.000	0.000
153	A	154	THR	0	-0.002	0.009	47.043	-0.001	-0.001	0.000	0.000	0.000	0.000
154	A	155	LYS	1	0.889	0.938	41.276	0.048	0.048	0.000	0.000	0.000	0.000
155	A	156	ILE	0	0.014	-0.001	41.669	0.000	0.000	0.000	0.000	0.000	0.000
156	A	157	TYR	0	-0.007	0.014	35.709	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:SER)