FMO DATABASE

FMODB ID: 6Y4QZ

Calculation Name: 3HVV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3HVV

Chain ID: A

ChEMBL ID:

UniProt ID: P0A862

Base Structure: X-ray

Registration Date: 2023-09-23

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	167
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1600209.803154
FMO2-HF: Nuclear repulsion	1538951.348475
FMO2-HF: Total energy	-61258.454679
FMO2-MP2: Total energy	-61440.224862

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.
-12.737	-5.036	2.713	-4.961	-5.452	-0.035

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 : -0.048 / 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	THR	0	-0.070	-0.051	3.457	0.943	3.325	0.016	-1.332	-1.066	0.003
4	A	5	VAL	0	0.011	0.032	6.227	-0.328	-0.328	0.000	0.000	0.000	0.000
5	A	6	HIS	0	-0.054	-0.034	9.662	0.314	0.314	0.000	0.000	0.000	0.000
6	A	7	PHE	0	0.000	-0.002	12.746	-0.057	-0.057	0.000	0.000	0.000	0.000
7	A	8	GLN	0	-0.051	-0.037	15.566	0.062	0.062	0.000	0.000	0.000	0.000
8	A	9	GLY	0	0.024	0.014	16.338	0.015	0.015	0.000	0.000	0.000	0.000
9	A	10	ASN	0	-0.073	-0.041	15.020	0.049	0.049	0.000	0.000	0.000	0.000
10	A	11	PRO	0	0.018	0.012	9.755	-0.054	-0.054	0.000	0.000	0.000	0.000
11	A	12	VAL	0	-0.011	-0.006	8.718	0.116	0.116	0.000	0.000	0.000	0.000
12	A	13	THR	0	0.029	0.017	2.999	-1.026	-0.605	0.119	-0.144	-0.395	0.000
13	A	14	VAL	0	-0.016	-0.003	3.630	-0.257	0.008	0.001	-0.063	-0.203	0.000
14	A	15	ALA	0	0.015	0.002	2.603	-4.827	-2.561	0.919	-1.520	-1.666	-0.018
15	A	16	ASN	0	-0.060	-0.044	3.019	-1.609	-0.622	0.412	-0.524	-0.875	-0.005
16	A	17	SER	0	0.015	-0.014	2.629	-5.391	-4.011	1.246	-1.378	-1.247	-0.015
17	A	18	ILE	0	-0.002	0.025	5.401	0.710	0.710	0.000	0.000	0.000	0.000
18	A	19	PRO	0	0.014	0.018	8.685	-0.045	-0.045	0.000	0.000	0.000	0.000
19	A	20	GLN	0	-0.017	0.011	10.210	0.111	0.111	0.000	0.000	0.000	0.000
20	A	21	ALA	0	0.036	0.029	13.503	0.097	0.097	0.000	0.000	0.000	0.000
21	A	22	GLY	0	-0.002	0.001	17.154	-0.015	-0.015	0.000	0.000	0.000	0.000
22	A	23	SER	0	-0.085	-0.046	14.696	0.017	0.017	0.000	0.000	0.000	0.000
23	A	24	LYS	1	0.977	0.979	16.684	0.234	0.234	0.000	0.000	0.000	0.000
24	A	25	ALA	0	0.027	0.021	16.464	-0.045	-0.045	0.000	0.000	0.000	0.000
25	A	26	GLN	0	-0.029	-0.015	12.196	-0.007	-0.007	0.000	0.000	0.000	0.000
26	A	27	THR	0	0.020	0.006	16.483	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	28	PHE	0	0.022	0.005	17.394	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	29	THR	0	-0.041	-0.029	19.145	0.013	0.013	0.000	0.000	0.000	0.000
29	A	30	LEU	0	0.008	0.017	18.034	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	31	VAL	0	-0.015	0.008	22.013	0.004	0.004	0.000	0.000	0.000	0.000
31	A	32	ALA	0	0.048	0.029	25.068	-0.008	-0.008	0.000	0.000	0.000	0.000
32	A	33	LYS	1	0.965	0.962	27.590	0.073	0.073	0.000	0.000	0.000	0.000
33	A	34	ASP	-1	-0.848	-0.894	30.215	-0.038	-0.038	0.000	0.000	0.000	0.000
34	A	35	LEU	0	-0.060	-0.031	29.208	0.007	0.007	0.000	0.000	0.000	0.000
35	A	36	SER	0	-0.014	-0.018	29.914	0.004	0.004	0.000	0.000	0.000	0.000
36	A	37	ASP	-1	-0.846	-0.913	26.102	-0.024	-0.024	0.000	0.000	0.000	0.000
37	A	38	VAL	0	-0.033	-0.021	25.466	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	39	THR	0	-0.022	-0.030	23.185	-0.008	-0.008	0.000	0.000	0.000	0.000
39	A	40	LEU	0	-0.009	0.004	19.615	0.002	0.002	0.000	0.000	0.000	0.000
40	A	41	GLY	0	0.056	0.024	23.099	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	42	GLN	0	-0.012	0.004	26.298	0.003	0.003	0.000	0.000	0.000	0.000
42	A	43	PHE	0	-0.021	-0.014	24.467	0.006	0.006	0.000	0.000	0.000	0.000
43	A	44	ALA	0	0.033	0.016	27.826	-0.011	-0.011	0.000	0.000	0.000	0.000
44	A	45	GLY	0	-0.008	0.003	28.710	0.009	0.009	0.000	0.000	0.000	0.000
45	A	46	LYS	1	0.927	0.977	28.693	0.120	0.120	0.000	0.000	0.000	0.000
46	A	47	ARG	1	0.844	0.923	25.886	0.177	0.177	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.757	0.858	22.265	0.225	0.225	0.000	0.000	0.000	0.000
48	A	49	VAL	0	0.022	0.023	21.786	-0.032	-0.032	0.000	0.000	0.000	0.000
49	A	50	LEU	0	-0.027	-0.012	17.091	0.030	0.030	0.000	0.000	0.000	0.000
50	A	51	ASN	0	0.033	-0.004	18.236	-0.067	-0.067	0.000	0.000	0.000	0.000
51	A	52	ILE	0	-0.005	-0.003	13.946	0.034	0.034	0.000	0.000	0.000	0.000
52	A	53	PHE	0	0.011	-0.007	16.625	-0.021	-0.021	0.000	0.000	0.000	0.000
53	A	54	PRO	0	0.011	0.009	14.956	0.018	0.018	0.000	0.000	0.000	0.000
54	A	55	SER	0	-0.006	-0.041	16.695	0.025	0.025	0.000	0.000	0.000	0.000
55	A	56	ILE	0	-0.019	-0.011	20.452	-0.008	-0.008	0.000	0.000	0.000	0.000
56	A	57	ASP	-1	-0.889	-0.934	23.653	-0.022	-0.022	0.000	0.000	0.000	0.000
57	A	58	THR	0	-0.047	-0.026	20.767	0.012	0.012	0.000	0.000	0.000	0.000
58	A	59	GLY	0	0.038	0.014	22.024	-0.017	-0.017	0.000	0.000	0.000	0.000
59	A	60	VAL	0	0.013	-0.001	20.918	0.003	0.003	0.000	0.000	0.000	0.000
60	A	61	SER	0	0.011	0.022	20.665	-0.027	-0.027	0.000	0.000	0.000	0.000
61	A	62	ALA	0	0.064	0.054	22.371	-0.010	-0.010	0.000	0.000	0.000	0.000
62	A	63	ALA	0	-0.034	-0.021	25.499	0.000	0.000	0.000	0.000	0.000	0.000
63	A	64	SER	0	0.014	0.004	22.436	-0.008	-0.008	0.000	0.000	0.000	0.000
64	A	65	VAL	0	0.012	-0.001	24.186	-0.006	-0.006	0.000	0.000	0.000	0.000
65	A	66	ARG	1	0.787	0.852	26.177	0.073	0.073	0.000	0.000	0.000	0.000
66	A	67	LYS	1	0.837	0.907	26.708	0.147	0.147	0.000	0.000	0.000	0.000
67	A	68	PHE	0	0.041	0.005	21.702	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	69	ASN	0	0.019	0.012	27.073	0.003	0.003	0.000	0.000	0.000	0.000
69	A	70	GLN	0	-0.053	-0.021	30.196	0.011	0.011	0.000	0.000	0.000	0.000
70	A	71	LEU	0	0.045	0.019	27.060	0.000	0.000	0.000	0.000	0.000	0.000
71	A	72	ALA	0	-0.017	-0.014	29.469	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	73	THR	0	-0.108	-0.055	30.741	0.006	0.006	0.000	0.000	0.000	0.000
73	A	74	GLU	-1	-0.902	-0.936	32.541	-0.124	-0.124	0.000	0.000	0.000	0.000
74	A	75	ILE	0	-0.051	-0.025	28.286	-0.008	-0.008	0.000	0.000	0.000	0.000
75	A	76	ASP	-1	-0.864	-0.921	32.487	-0.112	-0.112	0.000	0.000	0.000	0.000
76	A	77	ASN	0	-0.090	-0.057	31.786	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	78	THR	0	0.012	-0.001	26.837	-0.015	-0.015	0.000	0.000	0.000	0.000
78	A	79	VAL	0	-0.053	-0.009	25.578	0.014	0.014	0.000	0.000	0.000	0.000
79	A	80	VAL	0	0.034	0.008	25.031	-0.020	-0.020	0.000	0.000	0.000	0.000
80	A	81	LEU	0	-0.007	0.008	21.833	0.018	0.018	0.000	0.000	0.000	0.000
81	A	82	CYS	0	-0.055	-0.015	21.896	-0.023	-0.023	0.000	0.000	0.000	0.000
82	A	83	ILE	0	0.003	0.003	17.856	0.022	0.022	0.000	0.000	0.000	0.000
83	A	84	SER	0	-0.008	-0.028	17.787	-0.020	-0.020	0.000	0.000	0.000	0.000
84	A	85	ALA	0	0.051	0.022	16.638	0.008	0.008	0.000	0.000	0.000	0.000
85	A	86	ASP	-1	-0.779	-0.807	18.682	-0.024	-0.024	0.000	0.000	0.000	0.000
86	A	87	LEU	0	0.027	0.026	22.323	-0.006	-0.006	0.000	0.000	0.000	0.000
87	A	88	PRO	0	0.064	0.026	25.291	-0.005	-0.005	0.000	0.000	0.000	0.000
88	A	89	PHE	0	0.003	0.018	27.270	-0.005	-0.005	0.000	0.000	0.000	0.000
89	A	90	ALA	0	0.001	0.015	26.253	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	91	GLN	0	0.000	-0.026	22.388	0.000	0.000	0.000	0.000	0.000	0.000
91	A	92	SER	0	-0.007	-0.023	27.263	-0.004	-0.004	0.000	0.000	0.000	0.000
92	A	93	ARG	1	0.878	0.938	30.021	0.013	0.013	0.000	0.000	0.000	0.000
93	A	94	PHE	0	-0.009	-0.010	28.504	0.000	0.000	0.000	0.000	0.000	0.000
94	A	95	CYS	0	-0.021	-0.018	28.848	-0.005	-0.005	0.000	0.000	0.000	0.000
95	A	96	GLY	0	-0.016	-0.003	31.683	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	97	ALA	0	-0.047	-0.027	34.199	0.001	0.001	0.000	0.000	0.000	0.000
97	A	98	GLU	-1	-0.766	-0.847	32.131	-0.063	-0.063	0.000	0.000	0.000	0.000
98	A	99	GLY	0	-0.007	0.008	35.312	-0.004	-0.004	0.000	0.000	0.000	0.000
99	A	100	LEU	0	-0.062	-0.020	30.120	-0.005	-0.005	0.000	0.000	0.000	0.000
100	A	101	ASN	0	-0.061	-0.055	32.034	0.000	0.000	0.000	0.000	0.000	0.000
101	A	102	ASN	0	-0.034	-0.011	31.955	0.006	0.006	0.000	0.000	0.000	0.000
102	A	103	VAL	0	-0.015	0.008	27.035	-0.009	-0.009	0.000	0.000	0.000	0.000
103	A	104	ILE	0	-0.046	-0.027	26.521	0.013	0.013	0.000	0.000	0.000	0.000
104	A	105	THR	0	-0.052	-0.026	25.214	-0.011	-0.011	0.000	0.000	0.000	0.000
105	A	106	LEU	0	0.032	0.012	22.336	0.010	0.010	0.000	0.000	0.000	0.000
106	A	107	SER	0	0.013	0.001	21.307	-0.007	-0.007	0.000	0.000	0.000	0.000
107	A	108	THR	0	0.081	0.021	16.128	-0.005	-0.005	0.000	0.000	0.000	0.000
108	A	109	PHE	0	-0.057	-0.026	19.019	0.023	0.023	0.000	0.000	0.000	0.000
109	A	110	ARG	1	0.784	0.876	21.351	0.026	0.026	0.000	0.000	0.000	0.000
110	A	111	ASN	0	-0.018	-0.022	18.834	0.005	0.005	0.000	0.000	0.000	0.000
111	A	112	ALA	0	0.040	0.020	14.812	-0.030	-0.030	0.000	0.000	0.000	0.000
112	A	113	GLU	-1	-0.849	-0.926	13.486	-0.008	-0.008	0.000	0.000	0.000	0.000
113	A	114	PHE	0	0.049	0.023	13.121	-0.052	-0.052	0.000	0.000	0.000	0.000
114	A	115	LEU	0	0.021	0.004	11.312	-0.086	-0.086	0.000	0.000	0.000	0.000
115	A	116	GLN	0	-0.017	0.000	8.100	-0.124	-0.124	0.000	0.000	0.000	0.000
116	A	117	ALA	0	-0.010	0.000	8.509	-0.166	-0.166	0.000	0.000	0.000	0.000
117	A	118	TYR	0	-0.010	-0.029	10.729	-0.101	-0.101	0.000	0.000	0.000	0.000
118	A	119	GLY	0	-0.005	0.009	6.520	-0.126	-0.126	0.000	0.000	0.000	0.000
119	A	120	VAL	0	0.028	0.007	7.226	-0.290	-0.290	0.000	0.000	0.000	0.000
120	A	121	ALA	0	-0.007	0.007	8.142	0.159	0.159	0.000	0.000	0.000	0.000
121	A	122	ILE	0	0.023	0.014	6.967	-0.100	-0.100	0.000	0.000	0.000	0.000
122	A	123	ALA	0	-0.013	-0.008	4.842	0.102	0.102	0.000	0.000	0.000	0.000
123	A	124	ASP	-1	-0.853	-0.920	6.842	1.099	1.099	0.000	0.000	0.000	0.000
124	A	125	GLY	0	0.048	0.029	9.330	-0.129	-0.129	0.000	0.000	0.000	0.000
125	A	126	PRO	0	-0.031	-0.042	12.379	-0.032	-0.032	0.000	0.000	0.000	0.000
126	A	127	LEU	0	0.012	0.017	12.456	-0.043	-0.043	0.000	0.000	0.000	0.000
127	A	128	LYS	1	0.812	0.897	9.935	-0.918	-0.918	0.000	0.000	0.000	0.000
128	A	129	GLY	0	-0.029	-0.010	11.145	-0.024	-0.024	0.000	0.000	0.000	0.000
129	A	130	LEU	0	-0.020	-0.002	12.978	-0.058	-0.058	0.000	0.000	0.000	0.000
130	A	131	ALA	0	-0.002	-0.003	11.838	-0.011	-0.011	0.000	0.000	0.000	0.000
131	A	132	ALA	0	0.018	-0.004	9.412	0.051	0.051	0.000	0.000	0.000	0.000
132	A	133	ARG	1	0.801	0.892	11.550	0.169	0.169	0.000	0.000	0.000	0.000
133	A	134	ALA	0	0.010	0.004	12.320	-0.092	-0.092	0.000	0.000	0.000	0.000
134	A	135	VAL	0	-0.007	0.003	14.462	0.086	0.086	0.000	0.000	0.000	0.000
135	A	136	VAL	0	-0.005	-0.004	13.760	-0.087	-0.087	0.000	0.000	0.000	0.000
136	A	137	VAL	0	-0.015	-0.002	16.776	0.059	0.059	0.000	0.000	0.000	0.000
137	A	138	ILE	0	-0.002	0.006	18.113	-0.037	-0.037	0.000	0.000	0.000	0.000
138	A	139	ASP	-1	-0.688	-0.821	21.342	-0.222	-0.222	0.000	0.000	0.000	0.000
139	A	140	GLU	-1	-0.801	-0.901	24.780	-0.186	-0.186	0.000	0.000	0.000	0.000
140	A	141	ASN	0	-0.126	-0.077	26.052	0.031	0.031	0.000	0.000	0.000	0.000
141	A	142	ASP	-1	-0.850	-0.913	21.876	-0.212	-0.212	0.000	0.000	0.000	0.000
142	A	143	ASN	0	-0.057	-0.036	20.619	-0.030	-0.030	0.000	0.000	0.000	0.000
143	A	144	VAL	0	-0.011	-0.007	15.444	0.023	0.023	0.000	0.000	0.000	0.000
144	A	145	ILE	0	-0.023	-0.018	18.675	-0.010	-0.010	0.000	0.000	0.000	0.000
145	A	146	PHE	0	0.025	0.005	18.395	-0.008	-0.008	0.000	0.000	0.000	0.000
146	A	147	SER	0	-0.056	-0.044	13.115	0.002	0.002	0.000	0.000	0.000	0.000
147	A	148	GLN	0	0.057	0.041	14.076	0.018	0.018	0.000	0.000	0.000	0.000
148	A	149	LEU	0	0.027	0.021	7.678	0.085	0.085	0.000	0.000	0.000	0.000
149	A	150	VAL	0	-0.070	-0.041	11.835	0.010	0.010	0.000	0.000	0.000	0.000
150	A	151	ASP	-1	-0.861	-0.911	12.207	-0.418	-0.418	0.000	0.000	0.000	0.000
151	A	152	GLU	-1	-0.669	-0.801	12.866	0.002	0.002	0.000	0.000	0.000	0.000
152	A	153	ILE	0	0.027	0.031	12.358	-0.008	-0.008	0.000	0.000	0.000	0.000
153	A	154	THR	0	-0.092	-0.083	15.411	0.013	0.013	0.000	0.000	0.000	0.000
154	A	155	THR	0	-0.065	-0.042	18.077	0.004	0.004	0.000	0.000	0.000	0.000
155	A	156	GLU	-1	-0.809	-0.876	19.115	-0.163	-0.163	0.000	0.000	0.000	0.000
156	A	157	PRO	0	0.008	0.005	18.364	-0.017	-0.017	0.000	0.000	0.000	0.000
157	A	158	ASP	-1	-0.883	-0.942	19.702	-0.267	-0.267	0.000	0.000	0.000	0.000
158	A	159	TYR	0	-0.049	-0.075	21.718	-0.018	-0.018	0.000	0.000	0.000	0.000
159	A	160	GLU	-1	-0.779	-0.873	24.078	-0.192	-0.192	0.000	0.000	0.000	0.000
160	A	161	ALA	0	-0.030	-0.015	21.550	0.002	0.002	0.000	0.000	0.000	0.000
161	A	162	ALA	0	-0.032	-0.016	20.909	-0.008	-0.008	0.000	0.000	0.000	0.000
162	A	163	LEU	0	0.030	0.000	22.269	0.007	0.007	0.000	0.000	0.000	0.000
163	A	164	ALA	0	-0.036	-0.013	25.152	0.015	0.015	0.000	0.000	0.000	0.000
164	A	165	VAL	0	-0.037	-0.017	22.233	0.014	0.014	0.000	0.000	0.000	0.000
165	A	166	LEU	0	-0.025	-0.008	25.257	0.007	0.007	0.000	0.000	0.000	0.000
166	A	167	LYS	1	0.813	0.906	27.858	0.218	0.218	0.000	0.000	0.000	0.000
167	A	168	ALA	0	-0.008	0.001	30.570	-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:2:SER)