FMO DATABASE

FMODB ID: YZ6N2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1508218.500264
FMO2-HF: Nuclear repulsion	1445802.210657
FMO2-HF: Total energy	-62416.289608
FMO2-MP2: Total energy	-62602.745773

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.
-0.339	2.853	0.436	-1.619	-2.009	0.004

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 : 0.023 / 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	4	PRO	0	0.059	0.011	3.635	-0.691	1.795	-0.004	-1.306	-1.176	0.006
4	A	5	ASP	-1	-0.840	-0.936	6.072	0.042	0.042	0.000	0.000	0.000	0.000
5	A	6	LEU	0	-0.047	-0.013	2.703	-0.645	0.019	0.441	-0.311	-0.795	-0.002
6	A	7	ASN	0	-0.021	-0.032	5.384	0.340	0.382	-0.001	-0.002	-0.038	0.000
7	A	8	LYS	1	0.935	0.978	7.988	0.079	0.079	0.000	0.000	0.000	0.000
8	A	9	LEU	0	-0.026	-0.004	8.200	-0.014	-0.014	0.000	0.000	0.000	0.000
9	A	10	LEU	0	0.008	-0.005	8.108	-0.004	-0.004	0.000	0.000	0.000	0.000
10	A	11	GLU	-1	-0.910	-0.953	10.885	0.362	0.362	0.000	0.000	0.000	0.000
11	A	12	LEU	0	-0.049	-0.028	13.455	-0.042	-0.042	0.000	0.000	0.000	0.000
12	A	13	TRP	0	0.004	0.006	12.976	-0.022	-0.022	0.000	0.000	0.000	0.000
13	A	14	PRO	0	0.021	0.008	15.172	-0.019	-0.019	0.000	0.000	0.000	0.000
14	A	15	HIS	0	0.050	0.034	18.196	-0.029	-0.029	0.000	0.000	0.000	0.000
15	A	16	ILE	0	-0.051	-0.024	15.082	-0.021	-0.021	0.000	0.000	0.000	0.000
16	A	17	GLN	0	-0.082	-0.050	18.918	0.007	0.007	0.000	0.000	0.000	0.000
17	A	18	GLU	-1	-0.862	-0.928	20.383	0.109	0.109	0.000	0.000	0.000	0.000
18	A	19	TYR	0	-0.091	-0.047	22.436	-0.016	-0.016	0.000	0.000	0.000	0.000
19	A	20	GLN	0	0.020	0.003	21.621	-0.012	-0.012	0.000	0.000	0.000	0.000
20	A	21	ASP	-1	-0.829	-0.904	23.623	0.138	0.138	0.000	0.000	0.000	0.000
21	A	22	LEU	0	-0.032	-0.013	26.179	-0.009	-0.009	0.000	0.000	0.000	0.000
22	A	23	ALA	0	-0.009	-0.010	26.242	-0.008	-0.008	0.000	0.000	0.000	0.000
23	A	24	LEU	0	0.020	0.012	25.749	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	25	LYS	1	0.843	0.942	29.060	-0.065	-0.065	0.000	0.000	0.000	0.000
25	A	26	HIS	0	-0.062	-0.044	31.468	-0.007	-0.007	0.000	0.000	0.000	0.000
26	A	27	GLY	0	0.039	0.032	32.399	-0.005	-0.005	0.000	0.000	0.000	0.000
27	A	28	ILE	0	-0.043	-0.025	27.021	-0.003	-0.003	0.000	0.000	0.000	0.000
28	A	29	ASN	0	0.014	-0.015	26.813	0.002	0.002	0.000	0.000	0.000	0.000
29	A	30	ASP	-1	-0.795	-0.881	21.509	0.108	0.108	0.000	0.000	0.000	0.000
30	A	31	ILE	0	-0.039	-0.025	20.271	-0.015	-0.015	0.000	0.000	0.000	0.000
31	A	32	PHE	0	-0.040	-0.022	17.299	-0.018	-0.018	0.000	0.000	0.000	0.000
32	A	33	GLN	0	-0.032	-0.013	21.028	-0.021	-0.021	0.000	0.000	0.000	0.000
33	A	34	GLY	0	0.033	0.015	23.807	0.000	0.000	0.000	0.000	0.000	0.000
34	A	35	ASN	0	-0.050	-0.037	25.754	-0.005	-0.005	0.000	0.000	0.000	0.000
35	A	36	GLY	0	0.104	0.061	25.995	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	37	GLY	0	0.021	0.002	24.556	0.002	0.002	0.000	0.000	0.000	0.000
37	A	38	LYS	1	0.830	0.931	25.435	0.020	0.020	0.000	0.000	0.000	0.000
38	A	39	LEU	0	0.018	0.009	28.187	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	40	LEU	0	0.044	0.024	28.083	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	41	GLN	0	0.033	0.026	28.931	-0.004	-0.004	0.000	0.000	0.000	0.000
41	A	42	VAL	0	0.029	0.011	31.750	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	43	LEU	0	-0.021	0.017	33.222	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	44	LEU	0	0.004	-0.001	32.101	0.000	0.000	0.000	0.000	0.000	0.000
44	A	45	ILE	0	-0.075	-0.025	34.462	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	46	THR	0	-0.064	-0.063	37.687	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	47	GLY	0	0.006	0.019	39.216	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	48	LEU	0	-0.045	-0.006	39.014	0.001	0.001	0.000	0.000	0.000	0.000
48	A	49	THR	0	-0.007	-0.013	37.940	0.004	0.004	0.000	0.000	0.000	0.000
49	A	50	VAL	0	0.004	0.006	33.372	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	51	LEU	0	0.045	0.021	36.800	0.004	0.004	0.000	0.000	0.000	0.000
51	A	52	PRO	0	-0.018	-0.010	36.189	0.001	0.001	0.000	0.000	0.000	0.000
52	A	53	GLY	0	-0.010	-0.015	36.269	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	54	ARG	1	0.843	0.952	31.833	-0.047	-0.047	0.000	0.000	0.000	0.000
54	A	55	GLU	-1	-0.843	-0.906	36.496	0.023	0.023	0.000	0.000	0.000	0.000
55	A	56	GLY	0	-0.038	-0.022	34.246	0.000	0.000	0.000	0.000	0.000	0.000
56	A	57	ASN	0	-0.096	-0.058	30.650	0.007	0.007	0.000	0.000	0.000	0.000
57	A	58	ASP	-1	-0.828	-0.906	34.648	0.023	0.023	0.000	0.000	0.000	0.000
58	A	59	ALA	0	-0.010	-0.016	37.749	0.004	0.004	0.000	0.000	0.000	0.000
59	A	60	VAL	0	0.035	0.026	39.568	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	61	ASP	-1	-0.786	-0.888	42.303	0.018	0.018	0.000	0.000	0.000	0.000
61	A	62	ASN	0	-0.023	-0.030	44.852	0.002	0.002	0.000	0.000	0.000	0.000
62	A	63	ALA	0	-0.061	-0.024	47.097	0.001	0.001	0.000	0.000	0.000	0.000
63	A	64	GLY	0	-0.007	0.009	46.873	0.000	0.000	0.000	0.000	0.000	0.000
64	A	65	GLN	0	-0.100	-0.041	47.296	0.000	0.000	0.000	0.000	0.000	0.000
65	A	66	GLU	-1	-0.843	-0.941	42.655	0.023	0.023	0.000	0.000	0.000	0.000
66	A	67	TYR	0	-0.071	-0.055	41.609	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	68	GLU	-1	-0.808	-0.885	38.187	0.009	0.009	0.000	0.000	0.000	0.000
68	A	69	LEU	0	0.002	0.000	35.709	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	70	LYS	1	0.789	0.906	34.887	0.000	0.000	0.000	0.000	0.000	0.000
70	A	71	SER	0	-0.008	-0.021	30.988	0.002	0.002	0.000	0.000	0.000	0.000
71	A	72	ILE	0	-0.057	-0.017	31.415	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	73	ASN	0	0.062	0.039	25.772	0.003	0.003	0.000	0.000	0.000	0.000
73	A	74	ILE	0	0.047	0.009	29.681	-0.006	-0.006	0.000	0.000	0.000	0.000
74	A	75	ASP	-1	-0.841	-0.888	27.903	-0.067	-0.067	0.000	0.000	0.000	0.000
75	A	76	LEU	0	-0.064	-0.029	24.575	-0.007	-0.007	0.000	0.000	0.000	0.000
76	A	77	THR	0	-0.003	-0.009	29.063	0.000	0.000	0.000	0.000	0.000	0.000
77	A	78	LYS	1	0.920	0.940	32.236	0.058	0.058	0.000	0.000	0.000	0.000
78	A	79	GLY	0	-0.002	0.005	35.077	0.003	0.003	0.000	0.000	0.000	0.000
79	A	80	PHE	0	0.044	0.019	34.833	-0.003	-0.003	0.000	0.000	0.000	0.000
80	A	81	SER	0	0.008	-0.013	31.848	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	82	THR	0	-0.006	-0.017	34.869	0.003	0.003	0.000	0.000	0.000	0.000
82	A	83	HIS	0	0.093	0.047	36.133	0.000	0.000	0.000	0.000	0.000	0.000
83	A	84	HIS	0	-0.057	-0.032	31.606	-0.004	-0.004	0.000	0.000	0.000	0.000
84	A	85	HIS	0	-0.003	-0.007	34.604	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	86	MET	0	0.004	0.023	38.875	0.003	0.003	0.000	0.000	0.000	0.000
86	A	87	ASN	0	0.030	-0.009	41.644	0.000	0.000	0.000	0.000	0.000	0.000
87	A	88	PRO	0	0.078	0.014	45.181	0.001	0.001	0.000	0.000	0.000	0.000
88	A	89	VAL	0	-0.006	0.020	45.516	0.001	0.001	0.000	0.000	0.000	0.000
89	A	90	ILE	0	-0.032	-0.011	40.738	0.001	0.001	0.000	0.000	0.000	0.000
90	A	91	ILE	0	0.012	-0.009	43.755	0.000	0.000	0.000	0.000	0.000	0.000
91	A	92	ALA	0	-0.036	-0.007	46.008	0.000	0.000	0.000	0.000	0.000	0.000
92	A	93	LYS	1	0.828	0.898	40.859	-0.015	-0.015	0.000	0.000	0.000	0.000
93	A	94	TYR	0	-0.037	-0.021	38.790	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	95	ARG	1	0.817	0.884	45.211	0.001	0.001	0.000	0.000	0.000	0.000
95	A	96	GLN	0	0.019	0.004	48.922	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	97	VAL	0	0.012	0.044	44.232	0.001	0.001	0.000	0.000	0.000	0.000
97	A	98	PRO	0	-0.008	0.009	46.064	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	99	TRP	0	-0.045	-0.031	39.711	0.000	0.000	0.000	0.000	0.000	0.000
99	A	100	ILE	0	0.014	0.009	38.598	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	101	PHE	0	-0.012	-0.016	37.861	0.000	0.000	0.000	0.000	0.000	0.000
101	A	102	ALA	0	0.024	0.015	34.072	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	103	ILE	0	-0.012	-0.023	34.334	-0.003	-0.003	0.000	0.000	0.000	0.000
103	A	104	TYR	0	0.015	-0.017	28.886	0.001	0.001	0.000	0.000	0.000	0.000
104	A	105	ARG	1	0.874	0.936	29.445	0.053	0.053	0.000	0.000	0.000	0.000
105	A	106	GLY	0	0.049	0.010	25.718	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	107	ILE	0	-0.020	-0.028	22.019	0.005	0.005	0.000	0.000	0.000	0.000
107	A	108	ALA	0	0.012	0.016	25.795	0.009	0.009	0.000	0.000	0.000	0.000
108	A	109	ILE	0	-0.009	-0.001	28.851	-0.005	-0.005	0.000	0.000	0.000	0.000
109	A	110	GLU	-1	-0.894	-0.957	31.953	-0.020	-0.020	0.000	0.000	0.000	0.000
110	A	111	ALA	0	-0.047	-0.024	35.095	0.002	0.002	0.000	0.000	0.000	0.000
111	A	112	ILE	0	0.021	0.002	36.485	0.000	0.000	0.000	0.000	0.000	0.000
112	A	113	TYR	0	0.014	0.009	39.180	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	114	ARG	1	0.869	0.925	41.822	-0.006	-0.006	0.000	0.000	0.000	0.000
114	A	115	LEU	0	-0.023	-0.014	43.748	-0.002	-0.002	0.000	0.000	0.000	0.000
115	A	116	GLU	-1	-0.738	-0.845	46.426	0.006	0.006	0.000	0.000	0.000	0.000
116	A	117	PRO	0	0.056	0.023	49.318	-0.002	-0.002	0.000	0.000	0.000	0.000
117	A	118	LYS	1	0.911	0.949	50.339	0.004	0.004	0.000	0.000	0.000	0.000
118	A	119	ASP	-1	-0.861	-0.928	49.371	-0.006	-0.006	0.000	0.000	0.000	0.000
119	A	120	LEU	0	0.001	0.013	44.751	-0.002	-0.002	0.000	0.000	0.000	0.000
120	A	121	GLU	-1	-0.829	-0.927	48.377	-0.004	-0.004	0.000	0.000	0.000	0.000
121	A	122	PHE	0	0.008	0.021	48.763	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	123	TYR	0	-0.030	-0.037	44.573	-0.002	-0.002	0.000	0.000	0.000	0.000
123	A	124	TYR	0	0.044	0.027	45.126	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	125	ASP	-1	-0.774	-0.858	48.641	-0.008	-0.008	0.000	0.000	0.000	0.000
125	A	126	LYS	1	0.819	0.925	46.497	0.016	0.016	0.000	0.000	0.000	0.000
126	A	127	TRP	0	0.008	-0.025	42.440	-0.001	-0.001	0.000	0.000	0.000	0.000
127	A	128	GLU	-1	-0.790	-0.883	47.345	-0.003	-0.003	0.000	0.000	0.000	0.000
128	A	129	ARG	1	0.827	0.900	50.136	0.010	0.010	0.000	0.000	0.000	0.000
129	A	130	LYS	1	0.897	0.965	44.133	0.021	0.021	0.000	0.000	0.000	0.000
130	A	131	TRP	0	0.017	0.000	45.767	0.000	0.000	0.000	0.000	0.000	0.000
131	A	132	TYR	0	-0.088	-0.054	48.643	0.000	0.000	0.000	0.000	0.000	0.000
132	A	133	SER	0	-0.028	-0.027	51.220	0.000	0.000	0.000	0.000	0.000	0.000
133	A	134	ASP	-1	-0.875	-0.943	46.550	-0.019	-0.019	0.000	0.000	0.000	0.000
134	A	135	GLY	0	-0.017	-0.008	49.167	0.000	0.000	0.000	0.000	0.000	0.000
135	A	136	HIS	1	0.845	0.928	49.218	0.007	0.007	0.000	0.000	0.000	0.000
136	A	137	LYS	1	0.912	0.975	43.549	0.018	0.018	0.000	0.000	0.000	0.000
137	A	138	ASP	-1	-0.767	-0.877	41.412	-0.005	-0.005	0.000	0.000	0.000	0.000
138	A	139	ILE	0	-0.064	-0.033	41.202	-0.003	-0.003	0.000	0.000	0.000	0.000
139	A	140	ASN	0	-0.009	-0.006	34.399	0.003	0.003	0.000	0.000	0.000	0.000
140	A	141	ASN	0	0.000	0.006	32.954	-0.002	-0.002	0.000	0.000	0.000	0.000
141	A	142	PRO	0	0.040	0.041	36.925	-0.004	-0.004	0.000	0.000	0.000	0.000
142	A	143	LYS	1	0.823	0.913	34.039	0.034	0.034	0.000	0.000	0.000	0.000
143	A	144	ILE	0	0.050	0.044	38.977	0.000	0.000	0.000	0.000	0.000	0.000
144	A	145	PRO	0	-0.035	-0.021	39.392	-0.001	-0.001	0.000	0.000	0.000	0.000
145	A	146	VAL	0	0.054	0.020	36.632	0.002	0.002	0.000	0.000	0.000	0.000
146	A	147	LYS	1	0.803	0.885	39.939	0.026	0.026	0.000	0.000	0.000	0.000
147	A	148	TYR	0	-0.008	-0.019	43.253	0.001	0.001	0.000	0.000	0.000	0.000
148	A	149	VAL	0	0.026	0.009	40.716	0.002	0.002	0.000	0.000	0.000	0.000
149	A	150	MET	0	-0.064	-0.037	41.295	0.001	0.001	0.000	0.000	0.000	0.000
150	A	151	GLU	-1	-0.843	-0.903	44.239	-0.020	-0.020	0.000	0.000	0.000	0.000
151	A	152	HIS	0	-0.006	-0.002	47.454	0.002	0.002	0.000	0.000	0.000	0.000
152	A	153	GLY	0	0.000	0.015	46.015	0.002	0.002	0.000	0.000	0.000	0.000
153	A	154	THR	0	-0.004	0.008	46.912	-0.001	-0.001	0.000	0.000	0.000	0.000
154	A	155	LYS	1	0.828	0.915	40.510	0.014	0.014	0.000	0.000	0.000	0.000
155	A	156	ILE	0	0.014	-0.002	41.527	0.001	0.001	0.000	0.000	0.000	0.000
156	A	157	TYR	0	-0.004	0.017	35.471	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)