FMO DATABASE

FMODB ID: 76KRK

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:

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

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	167
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1594891.844893
FMO2-HF: Nuclear repulsion	1533634.44531
FMO2-HF: Total energy	-61257.399582
FMO2-MP2: Total energy	-61439.314121

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.
-10.96	-2.66	2.85	-5.27	-5.88	-0.033

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 : -0.047 / q_NPA : -0.016

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	-0.051	-0.042	3.530	-0.979	1.588	0.001	-1.425	-1.143	0.005
4	A	5	VAL	0	0.026	0.035	6.303	0.034	0.034	0.000	0.000	0.000	0.000
5	A	6	HIS	0	-0.015	-0.004	9.420	0.031	0.031	0.000	0.000	0.000	0.000
6	A	7	PHE	0	-0.032	-0.025	12.419	0.023	0.023	0.000	0.000	0.000	0.000
7	A	8	GLN	0	-0.050	-0.043	15.106	0.021	0.021	0.000	0.000	0.000	0.000
8	A	9	GLY	0	0.015	0.016	16.226	0.024	0.024	0.000	0.000	0.000	0.000
9	A	10	ASN	0	-0.055	-0.028	14.508	-0.001	-0.001	0.000	0.000	0.000	0.000
10	A	11	PRO	0	0.032	0.037	8.937	-0.028	-0.028	0.000	0.000	0.000	0.000
11	A	12	VAL	0	-0.002	-0.005	8.138	0.022	0.022	0.000	0.000	0.000	0.000
12	A	13	THR	0	0.017	0.011	2.618	-0.918	-0.195	0.483	-0.433	-0.774	0.000
13	A	14	VAL	0	0.010	0.014	3.511	0.031	0.389	0.005	-0.102	-0.260	0.000
14	A	15	ALA	0	-0.011	-0.012	2.560	-4.784	-2.406	1.460	-1.888	-1.950	-0.023
15	A	16	ASN	0	-0.049	-0.028	2.996	-0.696	0.162	0.319	-0.437	-0.740	-0.004
16	A	17	SER	0	0.026	-0.005	2.750	-3.113	-1.697	0.582	-0.985	-1.013	-0.011
17	A	18	ILE	0	-0.002	0.021	5.440	0.328	0.328	0.000	0.000	0.000	0.000
18	A	19	PRO	0	0.015	0.013	8.604	0.061	0.061	0.000	0.000	0.000	0.000
19	A	20	GLN	0	-0.015	0.006	9.789	-0.058	-0.058	0.000	0.000	0.000	0.000
20	A	21	ALA	0	0.044	0.027	13.480	0.051	0.051	0.000	0.000	0.000	0.000
21	A	22	GLY	0	-0.020	-0.010	17.028	0.011	0.011	0.000	0.000	0.000	0.000
22	A	23	SER	0	-0.076	-0.034	15.080	0.040	0.040	0.000	0.000	0.000	0.000
23	A	24	LYS	1	0.996	0.990	17.169	-0.171	-0.171	0.000	0.000	0.000	0.000
24	A	25	ALA	0	0.008	0.006	16.563	0.019	0.019	0.000	0.000	0.000	0.000
25	A	26	GLN	0	-0.040	-0.017	12.398	0.046	0.046	0.000	0.000	0.000	0.000
26	A	27	THR	0	0.007	0.009	16.917	-0.035	-0.035	0.000	0.000	0.000	0.000
27	A	28	PHE	0	0.028	0.001	17.658	0.015	0.015	0.000	0.000	0.000	0.000
28	A	29	THR	0	0.022	0.004	19.502	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	30	LEU	0	-0.030	-0.005	18.221	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	31	VAL	0	-0.004	0.025	22.207	0.006	0.006	0.000	0.000	0.000	0.000
31	A	32	ALA	0	0.034	0.033	25.261	-0.013	-0.013	0.000	0.000	0.000	0.000
32	A	33	LYS	1	0.977	0.964	27.777	0.044	0.044	0.000	0.000	0.000	0.000
33	A	34	ASP	-1	-0.869	-0.929	30.335	-0.024	-0.024	0.000	0.000	0.000	0.000
34	A	35	LEU	0	-0.076	-0.047	29.020	0.004	0.004	0.000	0.000	0.000	0.000
35	A	36	SER	0	-0.028	0.004	30.295	0.007	0.007	0.000	0.000	0.000	0.000
36	A	37	ASP	-1	-0.825	-0.925	26.450	0.003	0.003	0.000	0.000	0.000	0.000
37	A	38	VAL	0	-0.021	-0.024	25.061	0.001	0.001	0.000	0.000	0.000	0.000
38	A	39	THR	0	-0.016	-0.026	23.615	0.004	0.004	0.000	0.000	0.000	0.000
39	A	40	LEU	0	-0.005	0.010	19.927	-0.006	-0.006	0.000	0.000	0.000	0.000
40	A	41	GLY	0	0.051	0.018	23.387	-0.005	-0.005	0.000	0.000	0.000	0.000
41	A	42	GLN	0	-0.007	0.006	26.506	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	43	PHE	0	-0.018	-0.009	24.897	-0.006	-0.006	0.000	0.000	0.000	0.000
43	A	44	ALA	0	0.023	0.014	28.138	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	45	GLY	0	-0.008	-0.004	29.052	-0.003	-0.003	0.000	0.000	0.000	0.000
45	A	46	LYS	1	0.929	0.982	28.613	0.019	0.019	0.000	0.000	0.000	0.000
46	A	47	ARG	1	0.879	0.935	26.005	0.047	0.047	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.791	0.885	22.324	0.007	0.007	0.000	0.000	0.000	0.000
48	A	49	VAL	0	0.041	0.028	21.738	-0.007	-0.007	0.000	0.000	0.000	0.000
49	A	50	LEU	0	-0.025	-0.015	16.872	0.009	0.009	0.000	0.000	0.000	0.000
50	A	51	ASN	0	0.028	0.005	18.401	-0.044	-0.044	0.000	0.000	0.000	0.000
51	A	52	ILE	0	-0.019	-0.015	13.766	0.023	0.023	0.000	0.000	0.000	0.000
52	A	53	PHE	0	0.005	-0.012	16.069	-0.034	-0.034	0.000	0.000	0.000	0.000
53	A	54	PRO	0	-0.007	0.003	14.529	0.025	0.025	0.000	0.000	0.000	0.000
54	A	55	SER	0	-0.009	-0.034	16.348	0.024	0.024	0.000	0.000	0.000	0.000
55	A	56	ILE	0	-0.053	-0.029	20.082	-0.007	-0.007	0.000	0.000	0.000	0.000
56	A	57	ASP	-1	-0.942	-0.969	23.365	-0.118	-0.118	0.000	0.000	0.000	0.000
57	A	58	THR	0	-0.068	-0.036	20.632	-0.009	-0.009	0.000	0.000	0.000	0.000
58	A	59	GLY	0	0.013	0.010	21.183	-0.009	-0.009	0.000	0.000	0.000	0.000
59	A	60	VAL	0	0.019	0.001	20.263	0.016	0.016	0.000	0.000	0.000	0.000
60	A	61	SER	0	0.037	0.033	20.093	-0.004	-0.004	0.000	0.000	0.000	0.000
61	A	62	ALA	0	0.079	0.067	22.111	0.009	0.009	0.000	0.000	0.000	0.000
62	A	63	ALA	0	-0.021	-0.007	25.416	0.012	0.012	0.000	0.000	0.000	0.000
63	A	64	SER	0	-0.001	-0.018	22.373	0.005	0.005	0.000	0.000	0.000	0.000
64	A	65	VAL	0	0.013	-0.003	23.992	0.008	0.008	0.000	0.000	0.000	0.000
65	A	66	ARG	1	0.787	0.846	26.136	0.122	0.122	0.000	0.000	0.000	0.000
66	A	67	LYS	1	0.844	0.928	26.637	0.158	0.158	0.000	0.000	0.000	0.000
67	A	68	PHE	0	0.055	0.013	21.611	0.007	0.007	0.000	0.000	0.000	0.000
68	A	69	ASN	0	0.027	0.016	27.096	0.011	0.011	0.000	0.000	0.000	0.000
69	A	70	GLN	0	-0.020	0.014	30.121	0.008	0.008	0.000	0.000	0.000	0.000
70	A	71	LEU	0	0.026	0.019	27.017	0.004	0.004	0.000	0.000	0.000	0.000
71	A	72	ALA	0	-0.023	-0.010	29.418	0.005	0.005	0.000	0.000	0.000	0.000
72	A	73	THR	0	-0.106	-0.069	30.620	0.007	0.007	0.000	0.000	0.000	0.000
73	A	74	GLU	-1	-0.939	-0.970	32.656	-0.075	-0.075	0.000	0.000	0.000	0.000
74	A	75	ILE	0	-0.063	-0.022	28.272	0.000	0.000	0.000	0.000	0.000	0.000
75	A	76	ASP	-1	-0.855	-0.922	32.481	-0.037	-0.037	0.000	0.000	0.000	0.000
76	A	77	ASN	0	-0.092	-0.055	31.785	0.000	0.000	0.000	0.000	0.000	0.000
77	A	78	THR	0	0.007	-0.010	26.650	0.001	0.001	0.000	0.000	0.000	0.000
78	A	79	VAL	0	-0.053	-0.008	25.544	0.001	0.001	0.000	0.000	0.000	0.000
79	A	80	VAL	0	0.031	0.007	24.518	-0.005	-0.005	0.000	0.000	0.000	0.000
80	A	81	LEU	0	-0.009	-0.001	21.823	0.005	0.005	0.000	0.000	0.000	0.000
81	A	82	CYS	0	-0.041	-0.003	21.814	-0.019	-0.019	0.000	0.000	0.000	0.000
82	A	83	ILE	0	0.012	0.000	17.649	0.013	0.013	0.000	0.000	0.000	0.000
83	A	84	SER	0	-0.017	-0.038	17.597	-0.023	-0.023	0.000	0.000	0.000	0.000
84	A	85	ALA	0	0.074	0.039	16.446	0.023	0.023	0.000	0.000	0.000	0.000
85	A	86	ASP	-1	-0.755	-0.805	18.504	-0.150	-0.150	0.000	0.000	0.000	0.000
86	A	87	LEU	0	0.023	0.019	21.977	0.012	0.012	0.000	0.000	0.000	0.000
87	A	88	PRO	0	0.045	0.011	24.798	-0.007	-0.007	0.000	0.000	0.000	0.000
88	A	89	PHE	0	0.008	-0.001	26.899	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	90	ALA	0	0.024	0.026	25.737	0.002	0.002	0.000	0.000	0.000	0.000
90	A	91	GLN	0	-0.003	-0.028	22.154	0.011	0.011	0.000	0.000	0.000	0.000
91	A	92	SER	0	-0.022	-0.018	26.884	0.002	0.002	0.000	0.000	0.000	0.000
92	A	93	ARG	1	0.961	0.992	30.435	0.082	0.082	0.000	0.000	0.000	0.000
93	A	94	PHE	0	-0.002	-0.004	28.307	0.001	0.001	0.000	0.000	0.000	0.000
94	A	95	CYS	0	-0.003	-0.001	28.750	0.001	0.001	0.000	0.000	0.000	0.000
95	A	96	GLY	0	0.005	0.002	31.555	0.004	0.004	0.000	0.000	0.000	0.000
96	A	97	ALA	0	-0.066	-0.029	33.995	0.004	0.004	0.000	0.000	0.000	0.000
97	A	98	GLU	-1	-0.771	-0.850	32.682	-0.096	-0.096	0.000	0.000	0.000	0.000
98	A	99	GLY	0	-0.025	0.013	35.270	0.001	0.001	0.000	0.000	0.000	0.000
99	A	100	LEU	0	-0.086	-0.042	30.310	0.000	0.000	0.000	0.000	0.000	0.000
100	A	101	ASN	0	-0.020	-0.030	32.533	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	102	ASN	0	-0.051	-0.023	31.833	0.008	0.008	0.000	0.000	0.000	0.000
102	A	103	VAL	0	-0.008	0.008	26.842	0.001	0.001	0.000	0.000	0.000	0.000
103	A	104	ILE	0	-0.030	-0.015	26.456	0.007	0.007	0.000	0.000	0.000	0.000
104	A	105	THR	0	-0.049	-0.017	25.112	-0.006	-0.006	0.000	0.000	0.000	0.000
105	A	106	LEU	0	0.000	-0.015	22.191	0.012	0.012	0.000	0.000	0.000	0.000
106	A	107	SER	0	0.009	-0.001	21.518	-0.014	-0.014	0.000	0.000	0.000	0.000
107	A	108	THR	0	0.065	0.009	16.365	0.009	0.009	0.000	0.000	0.000	0.000
108	A	109	PHE	0	-0.047	-0.027	18.858	0.012	0.012	0.000	0.000	0.000	0.000
109	A	110	ARG	1	0.819	0.916	20.996	0.011	0.011	0.000	0.000	0.000	0.000
110	A	111	ASN	0	-0.020	-0.017	18.993	0.003	0.003	0.000	0.000	0.000	0.000
111	A	112	ALA	0	0.030	0.016	14.665	-0.008	-0.008	0.000	0.000	0.000	0.000
112	A	113	GLU	-1	-0.851	-0.936	13.689	0.069	0.069	0.000	0.000	0.000	0.000
113	A	114	PHE	0	0.051	0.020	13.211	0.046	0.046	0.000	0.000	0.000	0.000
114	A	115	LEU	0	-0.009	-0.010	11.194	-0.007	-0.007	0.000	0.000	0.000	0.000
115	A	116	GLN	0	-0.040	-0.018	8.413	0.153	0.153	0.000	0.000	0.000	0.000
116	A	117	ALA	0	-0.011	-0.003	8.468	0.110	0.110	0.000	0.000	0.000	0.000
117	A	118	TYR	0	-0.006	-0.026	10.498	0.023	0.023	0.000	0.000	0.000	0.000
118	A	119	GLY	0	0.008	0.017	6.494	-0.097	-0.097	0.000	0.000	0.000	0.000
119	A	120	VAL	0	0.026	0.011	7.142	-0.355	-0.355	0.000	0.000	0.000	0.000
120	A	121	ALA	0	-0.014	0.003	7.763	-0.005	-0.005	0.000	0.000	0.000	0.000
121	A	122	ILE	0	0.040	0.027	6.593	-0.256	-0.256	0.000	0.000	0.000	0.000
122	A	123	ALA	0	-0.065	-0.049	5.034	0.222	0.222	0.000	0.000	0.000	0.000
123	A	124	ASP	-1	-0.918	-0.976	7.006	-0.602	-0.602	0.000	0.000	0.000	0.000
124	A	125	GLY	0	0.010	0.015	9.185	0.003	0.003	0.000	0.000	0.000	0.000
125	A	126	PRO	0	-0.007	-0.026	12.336	0.029	0.029	0.000	0.000	0.000	0.000
126	A	127	LEU	0	0.015	0.015	12.053	0.036	0.036	0.000	0.000	0.000	0.000
127	A	128	LYS	1	0.932	0.985	10.039	0.378	0.378	0.000	0.000	0.000	0.000
128	A	129	GLY	0	-0.045	-0.019	11.363	0.070	0.070	0.000	0.000	0.000	0.000
129	A	130	LEU	0	-0.010	0.002	12.880	0.052	0.052	0.000	0.000	0.000	0.000
130	A	131	ALA	0	0.005	0.002	11.498	-0.060	-0.060	0.000	0.000	0.000	0.000
131	A	132	ALA	0	-0.001	-0.006	9.254	0.004	0.004	0.000	0.000	0.000	0.000
132	A	133	ARG	1	0.834	0.900	11.383	0.390	0.390	0.000	0.000	0.000	0.000
133	A	134	ALA	0	0.003	0.005	12.043	-0.073	-0.073	0.000	0.000	0.000	0.000
134	A	135	VAL	0	-0.008	0.003	14.208	0.056	0.056	0.000	0.000	0.000	0.000
135	A	136	VAL	0	0.008	0.011	13.845	-0.027	-0.027	0.000	0.000	0.000	0.000
136	A	137	VAL	0	-0.023	-0.003	16.697	0.018	0.018	0.000	0.000	0.000	0.000
137	A	138	ILE	0	-0.034	-0.010	18.391	0.005	0.005	0.000	0.000	0.000	0.000
138	A	139	ASP	-1	-0.758	-0.876	21.279	-0.004	-0.004	0.000	0.000	0.000	0.000
139	A	140	GLU	-1	-0.862	-0.957	24.542	-0.016	-0.016	0.000	0.000	0.000	0.000
140	A	141	ASN	0	-0.107	-0.051	26.009	0.008	0.008	0.000	0.000	0.000	0.000
141	A	142	ASP	-1	-0.876	-0.928	21.926	0.031	0.031	0.000	0.000	0.000	0.000
142	A	143	ASN	0	-0.040	-0.011	20.544	0.031	0.031	0.000	0.000	0.000	0.000
143	A	144	VAL	0	0.003	-0.001	15.353	-0.018	-0.018	0.000	0.000	0.000	0.000
144	A	145	ILE	0	-0.012	-0.012	18.605	0.005	0.005	0.000	0.000	0.000	0.000
145	A	146	PHE	0	0.021	-0.002	18.236	-0.011	-0.011	0.000	0.000	0.000	0.000
146	A	147	SER	0	-0.048	-0.034	12.870	-0.003	-0.003	0.000	0.000	0.000	0.000
147	A	148	GLN	0	0.059	0.040	14.078	0.018	0.018	0.000	0.000	0.000	0.000
148	A	149	LEU	0	0.012	0.015	7.387	0.033	0.033	0.000	0.000	0.000	0.000
149	A	150	VAL	0	-0.067	-0.044	11.606	-0.019	-0.019	0.000	0.000	0.000	0.000
150	A	151	ASP	-1	-0.882	-0.937	12.070	-0.647	-0.647	0.000	0.000	0.000	0.000
151	A	152	GLU	-1	-0.698	-0.826	12.794	-0.409	-0.409	0.000	0.000	0.000	0.000
152	A	153	ILE	0	0.014	0.009	11.971	0.046	0.046	0.000	0.000	0.000	0.000
153	A	154	THR	0	-0.093	-0.070	15.083	0.047	0.047	0.000	0.000	0.000	0.000
154	A	155	THR	0	-0.035	-0.016	17.961	0.038	0.038	0.000	0.000	0.000	0.000
155	A	156	GLU	-1	-0.835	-0.898	18.699	-0.194	-0.194	0.000	0.000	0.000	0.000
156	A	157	PRO	0	-0.003	0.005	18.343	-0.016	-0.016	0.000	0.000	0.000	0.000
157	A	158	ASP	-1	-0.877	-0.951	19.534	-0.176	-0.176	0.000	0.000	0.000	0.000
158	A	159	TYR	0	-0.040	-0.081	21.548	0.003	0.003	0.000	0.000	0.000	0.000
159	A	160	GLU	-1	-0.906	-0.946	24.008	-0.102	-0.102	0.000	0.000	0.000	0.000
160	A	161	ALA	0	-0.026	-0.010	21.208	0.013	0.013	0.000	0.000	0.000	0.000
161	A	162	ALA	0	-0.046	-0.009	21.001	0.008	0.008	0.000	0.000	0.000	0.000
162	A	163	LEU	0	0.042	-0.006	22.273	0.015	0.015	0.000	0.000	0.000	0.000
163	A	164	ALA	0	-0.028	-0.004	25.258	0.014	0.014	0.000	0.000	0.000	0.000
164	A	165	VAL	0	-0.021	-0.008	21.992	0.011	0.011	0.000	0.000	0.000	0.000
165	A	166	LEU	0	-0.033	-0.005	25.201	0.012	0.012	0.000	0.000	0.000	0.000
166	A	167	LYS	1	0.954	0.996	27.704	0.091	0.091	0.000	0.000	0.000	0.000
167	A	168	ALA	0	0.001	0.005	30.334	0.001	0.001	0.000	0.000	0.000	0.000

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