FMO DATABASE

FMODB ID: V58K1

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	OptAll
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	-1519769.055051
FMO2-HF: Nuclear repulsion	1457352.38699
FMO2-HF: Total energy	-62416.668062
FMO2-MP2: Total energy	-62603.156197

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.
0.892	3.54	0.895	-1.464	-2.079	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 : 0.045 / q_NPA : 0.024

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	0.054	0.014	3.641	-1.272	0.886	0.004	-1.062	-1.100	0.005
4	A	5	ASP	-1	-0.853	-0.943	5.503	-0.716	-0.716	0.000	0.000	0.000	0.000
5	A	6	LEU	0	-0.030	-0.010	2.458	-0.011	0.435	0.892	-0.400	-0.937	-0.003
6	A	7	ASN	0	-0.025	-0.028	5.363	0.996	1.040	-0.001	-0.002	-0.042	0.000
7	A	8	LYS	1	0.924	0.969	7.626	1.264	1.264	0.000	0.000	0.000	0.000
8	A	9	LEU	0	-0.017	-0.001	8.222	0.137	0.137	0.000	0.000	0.000	0.000
9	A	10	LEU	0	0.004	0.001	8.222	0.144	0.144	0.000	0.000	0.000	0.000
10	A	11	GLU	-1	-0.915	-0.962	10.564	-0.116	-0.116	0.000	0.000	0.000	0.000
11	A	12	LEU	0	-0.040	-0.025	13.162	0.032	0.032	0.000	0.000	0.000	0.000
12	A	13	TRP	0	-0.001	0.007	12.979	0.030	0.030	0.000	0.000	0.000	0.000
13	A	14	PRO	0	0.004	0.003	14.987	0.026	0.026	0.000	0.000	0.000	0.000
14	A	15	HIS	0	0.058	0.031	17.719	0.014	0.014	0.000	0.000	0.000	0.000
15	A	16	ILE	0	-0.062	-0.026	14.952	-0.001	-0.001	0.000	0.000	0.000	0.000
16	A	17	GLN	0	-0.083	-0.044	18.743	0.029	0.029	0.000	0.000	0.000	0.000
17	A	18	GLU	-1	-0.866	-0.936	20.237	-0.007	-0.007	0.000	0.000	0.000	0.000
18	A	19	TYR	0	-0.075	-0.045	22.416	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	20	GLN	0	0.021	0.009	21.511	0.002	0.002	0.000	0.000	0.000	0.000
20	A	21	ASP	-1	-0.824	-0.903	23.522	0.086	0.086	0.000	0.000	0.000	0.000
21	A	22	LEU	0	-0.030	-0.016	25.942	0.000	0.000	0.000	0.000	0.000	0.000
22	A	23	ALA	0	0.000	0.001	26.107	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	24	LEU	0	0.016	0.008	25.613	0.003	0.003	0.000	0.000	0.000	0.000
24	A	25	LYS	1	0.792	0.899	28.971	-0.020	-0.020	0.000	0.000	0.000	0.000
25	A	26	HIS	0	-0.035	-0.024	31.451	-0.007	-0.007	0.000	0.000	0.000	0.000
26	A	27	GLY	0	0.053	0.048	32.421	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	28	ILE	0	-0.041	-0.025	27.185	0.001	0.001	0.000	0.000	0.000	0.000
28	A	29	ASN	0	0.006	-0.017	27.144	-0.008	-0.008	0.000	0.000	0.000	0.000
29	A	30	ASP	-1	-0.794	-0.885	21.845	0.103	0.103	0.000	0.000	0.000	0.000
30	A	31	ILE	0	-0.020	-0.011	20.221	-0.014	-0.014	0.000	0.000	0.000	0.000
31	A	32	PHE	0	-0.022	-0.013	17.361	-0.026	-0.026	0.000	0.000	0.000	0.000
32	A	33	GLN	0	-0.038	-0.018	21.013	-0.009	-0.009	0.000	0.000	0.000	0.000
33	A	34	GLY	0	0.039	0.014	23.604	-0.006	-0.006	0.000	0.000	0.000	0.000
34	A	35	ASN	0	-0.062	-0.033	25.500	-0.017	-0.017	0.000	0.000	0.000	0.000
35	A	36	GLY	0	0.097	0.054	26.203	-0.008	-0.008	0.000	0.000	0.000	0.000
36	A	37	GLY	0	0.032	0.006	24.622	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	38	LYS	1	0.803	0.920	25.356	0.083	0.083	0.000	0.000	0.000	0.000
38	A	39	LEU	0	0.011	0.009	28.283	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	40	LEU	0	0.046	0.024	27.844	0.001	0.001	0.000	0.000	0.000	0.000
40	A	41	GLN	0	0.038	0.029	28.482	0.000	0.000	0.000	0.000	0.000	0.000
41	A	42	VAL	0	0.011	0.001	31.881	0.000	0.000	0.000	0.000	0.000	0.000
42	A	43	LEU	0	0.002	0.025	33.578	0.001	0.001	0.000	0.000	0.000	0.000
43	A	44	LEU	0	-0.007	-0.004	32.053	0.000	0.000	0.000	0.000	0.000	0.000
44	A	45	ILE	0	-0.073	-0.030	34.231	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	46	THR	0	-0.059	-0.060	37.627	0.001	0.001	0.000	0.000	0.000	0.000
46	A	47	GLY	0	-0.017	0.004	39.443	0.001	0.001	0.000	0.000	0.000	0.000
47	A	48	LEU	0	-0.032	-0.003	39.010	0.004	0.004	0.000	0.000	0.000	0.000
48	A	49	THR	0	-0.009	-0.013	38.188	0.001	0.001	0.000	0.000	0.000	0.000
49	A	50	VAL	0	-0.022	-0.007	33.456	0.001	0.001	0.000	0.000	0.000	0.000
50	A	51	LEU	0	0.038	0.028	36.785	0.004	0.004	0.000	0.000	0.000	0.000
51	A	52	PRO	0	-0.019	-0.011	36.317	0.003	0.003	0.000	0.000	0.000	0.000
52	A	53	GLY	0	-0.022	-0.026	36.519	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	54	ARG	1	0.795	0.922	31.646	-0.037	-0.037	0.000	0.000	0.000	0.000
54	A	55	GLU	-1	-0.840	-0.899	36.429	0.037	0.037	0.000	0.000	0.000	0.000
55	A	56	GLY	0	-0.045	-0.036	33.323	0.004	0.004	0.000	0.000	0.000	0.000
56	A	57	ASN	0	-0.073	-0.042	30.569	0.008	0.008	0.000	0.000	0.000	0.000
57	A	58	ASP	-1	-0.797	-0.882	34.294	0.021	0.021	0.000	0.000	0.000	0.000
58	A	59	ALA	0	0.012	-0.010	37.615	0.004	0.004	0.000	0.000	0.000	0.000
59	A	60	VAL	0	0.042	0.035	39.527	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	61	ASP	-1	-0.759	-0.872	42.258	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	62	ASN	0	-0.025	-0.033	44.893	0.003	0.003	0.000	0.000	0.000	0.000
62	A	63	ALA	0	-0.056	-0.018	47.211	0.001	0.001	0.000	0.000	0.000	0.000
63	A	64	GLY	0	-0.017	0.001	46.953	0.001	0.001	0.000	0.000	0.000	0.000
64	A	65	GLN	0	-0.100	-0.046	46.953	0.001	0.001	0.000	0.000	0.000	0.000
65	A	66	GLU	-1	-0.841	-0.939	42.405	0.016	0.016	0.000	0.000	0.000	0.000
66	A	67	TYR	0	-0.068	-0.048	41.379	-0.005	-0.005	0.000	0.000	0.000	0.000
67	A	68	GLU	-1	-0.784	-0.875	37.514	0.003	0.003	0.000	0.000	0.000	0.000
68	A	69	LEU	0	0.010	0.000	35.486	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	70	LYS	1	0.780	0.910	34.671	0.007	0.007	0.000	0.000	0.000	0.000
70	A	71	SER	0	0.010	-0.016	30.994	-0.004	-0.004	0.000	0.000	0.000	0.000
71	A	72	ILE	0	-0.064	-0.019	31.066	0.001	0.001	0.000	0.000	0.000	0.000
72	A	73	ASN	0	0.063	0.033	25.788	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	74	ILE	0	0.046	0.014	29.497	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	75	ASP	-1	-0.847	-0.901	27.791	-0.149	-0.149	0.000	0.000	0.000	0.000
75	A	76	LEU	0	-0.047	-0.018	24.256	-0.007	-0.007	0.000	0.000	0.000	0.000
76	A	77	THR	0	-0.010	-0.001	28.880	0.007	0.007	0.000	0.000	0.000	0.000
77	A	78	LYS	1	0.913	0.932	32.131	0.098	0.098	0.000	0.000	0.000	0.000
78	A	79	GLY	0	0.010	0.010	35.098	0.004	0.004	0.000	0.000	0.000	0.000
79	A	80	PHE	0	0.037	0.025	34.781	-0.003	-0.003	0.000	0.000	0.000	0.000
80	A	81	SER	0	0.014	-0.012	31.599	0.002	0.002	0.000	0.000	0.000	0.000
81	A	82	THR	0	-0.019	-0.021	34.631	0.003	0.003	0.000	0.000	0.000	0.000
82	A	83	HIS	0	0.111	0.044	35.791	0.001	0.001	0.000	0.000	0.000	0.000
83	A	84	HIS	0	-0.045	-0.025	31.570	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	85	HIS	0	0.009	0.000	34.719	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	86	MET	0	0.002	0.027	38.898	0.003	0.003	0.000	0.000	0.000	0.000
86	A	87	ASN	0	0.036	-0.002	41.438	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	88	PRO	0	0.085	0.017	44.903	0.000	0.000	0.000	0.000	0.000	0.000
88	A	89	VAL	0	-0.004	0.015	45.259	0.000	0.000	0.000	0.000	0.000	0.000
89	A	90	ILE	0	-0.020	-0.006	40.426	0.001	0.001	0.000	0.000	0.000	0.000
90	A	91	ILE	0	-0.014	-0.016	43.429	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	92	ALA	0	-0.036	-0.018	45.953	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	93	LYS	1	0.806	0.881	40.868	-0.028	-0.028	0.000	0.000	0.000	0.000
93	A	94	TYR	0	-0.029	-0.018	38.434	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	95	ARG	1	0.771	0.853	45.108	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	96	GLN	0	-0.004	0.003	48.280	-0.003	-0.003	0.000	0.000	0.000	0.000
96	A	97	VAL	0	0.015	0.029	43.729	0.001	0.001	0.000	0.000	0.000	0.000
97	A	98	PRO	0	-0.006	0.004	45.876	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	99	TRP	0	-0.059	-0.033	39.374	0.000	0.000	0.000	0.000	0.000	0.000
99	A	100	ILE	0	0.019	0.008	38.406	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	101	PHE	0	-0.018	-0.018	37.420	0.001	0.001	0.000	0.000	0.000	0.000
101	A	102	ALA	0	0.025	0.024	33.780	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	103	ILE	0	-0.020	-0.026	33.880	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	104	TYR	0	0.016	-0.022	28.832	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	105	ARG	1	0.880	0.925	29.268	0.147	0.147	0.000	0.000	0.000	0.000
105	A	106	GLY	0	0.064	0.028	25.401	-0.011	-0.011	0.000	0.000	0.000	0.000
106	A	107	ILE	0	-0.042	-0.032	22.415	0.013	0.013	0.000	0.000	0.000	0.000
107	A	108	ALA	0	0.032	0.034	25.993	0.011	0.011	0.000	0.000	0.000	0.000
108	A	109	ILE	0	0.003	0.002	29.056	0.000	0.000	0.000	0.000	0.000	0.000
109	A	110	GLU	-1	-0.870	-0.921	32.308	-0.072	-0.072	0.000	0.000	0.000	0.000
110	A	111	ALA	0	-0.018	-0.030	35.577	0.005	0.005	0.000	0.000	0.000	0.000
111	A	112	ILE	0	0.043	0.030	36.444	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	113	TYR	0	-0.024	-0.002	38.880	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	114	ARG	1	0.854	0.903	41.380	0.014	0.014	0.000	0.000	0.000	0.000
114	A	115	LEU	0	-0.033	-0.002	43.545	-0.002	-0.002	0.000	0.000	0.000	0.000
115	A	116	GLU	-1	-0.727	-0.833	46.228	-0.010	-0.010	0.000	0.000	0.000	0.000
116	A	117	PRO	0	0.062	0.026	48.674	-0.002	-0.002	0.000	0.000	0.000	0.000
117	A	118	LYS	1	0.881	0.922	49.640	0.016	0.016	0.000	0.000	0.000	0.000
118	A	119	ASP	-1	-0.852	-0.907	49.354	-0.019	-0.019	0.000	0.000	0.000	0.000
119	A	120	LEU	0	0.007	0.017	44.317	-0.003	-0.003	0.000	0.000	0.000	0.000
120	A	121	GLU	-1	-0.759	-0.881	47.786	-0.005	-0.005	0.000	0.000	0.000	0.000
121	A	122	PHE	0	0.007	0.011	48.628	0.000	0.000	0.000	0.000	0.000	0.000
122	A	123	TYR	0	-0.062	-0.047	44.375	-0.002	-0.002	0.000	0.000	0.000	0.000
123	A	124	TYR	0	0.038	0.027	44.714	0.000	0.000	0.000	0.000	0.000	0.000
124	A	125	ASP	-1	-0.750	-0.836	48.143	-0.009	-0.009	0.000	0.000	0.000	0.000
125	A	126	LYS	1	0.798	0.915	46.587	0.022	0.022	0.000	0.000	0.000	0.000
126	A	127	TRP	0	0.016	-0.010	42.184	0.000	0.000	0.000	0.000	0.000	0.000
127	A	128	GLU	-1	-0.756	-0.848	46.888	0.003	0.003	0.000	0.000	0.000	0.000
128	A	129	ARG	1	0.817	0.879	49.707	0.011	0.011	0.000	0.000	0.000	0.000
129	A	130	LYS	1	0.843	0.921	44.218	0.012	0.012	0.000	0.000	0.000	0.000
130	A	131	TRP	0	0.030	0.000	45.518	0.000	0.000	0.000	0.000	0.000	0.000
131	A	132	TYR	0	-0.091	-0.079	48.383	0.003	0.003	0.000	0.000	0.000	0.000
132	A	133	SER	0	-0.020	-0.018	51.317	0.001	0.001	0.000	0.000	0.000	0.000
133	A	134	ASP	-1	-0.839	-0.901	46.562	-0.008	-0.008	0.000	0.000	0.000	0.000
134	A	135	GLY	0	0.020	0.016	48.768	0.001	0.001	0.000	0.000	0.000	0.000
135	A	136	HIS	1	0.846	0.921	49.161	-0.006	-0.006	0.000	0.000	0.000	0.000
136	A	137	LYS	1	0.852	0.938	43.591	0.003	0.003	0.000	0.000	0.000	0.000
137	A	138	ASP	-1	-0.798	-0.887	41.392	0.013	0.013	0.000	0.000	0.000	0.000
138	A	139	ILE	0	-0.057	-0.028	41.022	-0.002	-0.002	0.000	0.000	0.000	0.000
139	A	140	ASN	0	0.006	-0.004	34.024	0.001	0.001	0.000	0.000	0.000	0.000
140	A	141	ASN	0	0.001	0.012	32.758	-0.005	-0.005	0.000	0.000	0.000	0.000
141	A	142	PRO	0	0.027	0.032	36.654	-0.007	-0.007	0.000	0.000	0.000	0.000
142	A	143	LYS	1	0.829	0.924	33.902	0.035	0.035	0.000	0.000	0.000	0.000
143	A	144	ILE	0	0.056	0.044	38.886	0.001	0.001	0.000	0.000	0.000	0.000
144	A	145	PRO	0	-0.041	-0.024	39.247	-0.004	-0.004	0.000	0.000	0.000	0.000
145	A	146	VAL	0	0.033	0.006	36.249	0.002	0.002	0.000	0.000	0.000	0.000
146	A	147	LYS	1	0.813	0.885	39.568	0.049	0.049	0.000	0.000	0.000	0.000
147	A	148	TYR	0	0.000	-0.024	42.876	0.001	0.001	0.000	0.000	0.000	0.000
148	A	149	VAL	0	0.018	0.002	40.219	0.002	0.002	0.000	0.000	0.000	0.000
149	A	150	MET	0	-0.034	-0.032	40.604	0.000	0.000	0.000	0.000	0.000	0.000
150	A	151	GLU	-1	-0.826	-0.884	43.680	-0.045	-0.045	0.000	0.000	0.000	0.000
151	A	152	HIS	0	-0.014	-0.006	46.902	0.003	0.003	0.000	0.000	0.000	0.000
152	A	153	GLY	0	0.007	0.011	45.564	0.003	0.003	0.000	0.000	0.000	0.000
153	A	154	THR	0	-0.016	-0.006	46.641	-0.002	-0.002	0.000	0.000	0.000	0.000
154	A	155	LYS	1	0.792	0.885	40.342	0.061	0.061	0.000	0.000	0.000	0.000
155	A	156	ILE	0	-0.001	-0.016	41.765	0.001	0.001	0.000	0.000	0.000	0.000
156	A	157	TYR	0	-0.012	0.014	35.264	0.001	0.001	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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