FMO DATABASE

FMODB ID: K34L3

Calculation Name: 3VJZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3VJZ

Chain ID: A

ChEMBL ID:

UniProt ID: Q9K0P4

Base Structure: X-ray

Registration Date: 2023-06-20

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	OptHSide
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	164
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1667653.70704
FMO2-HF: Nuclear repulsion	1603355.727191
FMO2-HF: Total energy	-64297.979849
FMO2-MP2: Total energy	-64487.884399

3D Structure Molmil

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:0:HIS)

Summations of interaction energy for fragment #1(A:0:HIS)

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.
-53.067	-50.069	14.496	-8.774	-8.72	-0.094

Interaction energy analysis for fragmet #1(A:0:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.119 / q_NPA : -0.081

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	2	THR	0	0.016	0.016	3.857	-1.627	-0.409	-0.011	-0.491	-0.717	0.002
4	A	3	ALA	0	-0.015	-0.012	6.171	1.181	1.181	0.000	0.000	0.000	0.000
5	A	4	LEU	0	0.010	0.032	8.839	-0.552	-0.552	0.000	0.000	0.000	0.000
6	A	5	THR	0	-0.026	-0.019	11.360	0.426	0.426	0.000	0.000	0.000	0.000
7	A	6	LEU	0	-0.015	-0.009	14.104	-0.032	-0.032	0.000	0.000	0.000	0.000
8	A	7	PRO	0	0.042	0.024	15.922	0.148	0.148	0.000	0.000	0.000	0.000
9	A	8	GLU	-1	-0.865	-0.931	18.468	-0.528	-0.528	0.000	0.000	0.000	0.000
10	A	9	ASP	-1	-0.882	-0.947	21.738	-0.675	-0.675	0.000	0.000	0.000	0.000
11	A	10	ILE	0	0.043	0.027	18.747	0.039	0.039	0.000	0.000	0.000	0.000
12	A	11	ARG	1	0.758	0.867	23.117	0.556	0.556	0.000	0.000	0.000	0.000
13	A	12	GLN	0	-0.068	-0.044	26.040	0.077	0.077	0.000	0.000	0.000	0.000
14	A	13	GLN	0	0.032	0.046	22.498	0.035	0.035	0.000	0.000	0.000	0.000
15	A	14	GLU	-1	-0.897	-0.949	27.898	-0.385	-0.385	0.000	0.000	0.000	0.000
16	A	15	PRO	0	-0.010	-0.019	29.145	-0.034	-0.034	0.000	0.000	0.000	0.000
17	A	16	SER	0	-0.024	-0.024	29.040	-0.020	-0.020	0.000	0.000	0.000	0.000
18	A	17	ALA	0	0.069	0.049	26.446	-0.024	-0.024	0.000	0.000	0.000	0.000
19	A	18	LEU	0	0.029	0.031	24.051	-0.061	-0.061	0.000	0.000	0.000	0.000
20	A	19	LEU	0	-0.054	-0.037	24.102	-0.052	-0.052	0.000	0.000	0.000	0.000
21	A	20	TYR	0	-0.044	-0.031	22.732	-0.052	-0.052	0.000	0.000	0.000	0.000
22	A	21	THR	0	0.065	0.022	19.663	-0.101	-0.101	0.000	0.000	0.000	0.000
23	A	22	LEU	0	-0.048	-0.014	19.470	-0.120	-0.120	0.000	0.000	0.000	0.000
24	A	23	VAL	0	-0.038	-0.027	19.607	-0.076	-0.076	0.000	0.000	0.000	0.000
25	A	24	SER	0	0.002	-0.006	18.582	-0.035	-0.035	0.000	0.000	0.000	0.000
26	A	25	ALA	0	0.014	0.014	15.418	-0.158	-0.158	0.000	0.000	0.000	0.000
27	A	26	TYR	0	-0.036	-0.024	14.924	-0.128	-0.128	0.000	0.000	0.000	0.000
28	A	27	LEU	0	-0.007	0.015	15.607	-0.058	-0.058	0.000	0.000	0.000	0.000
29	A	28	GLU	-1	-0.780	-0.895	10.575	-2.804	-2.804	0.000	0.000	0.000	0.000
30	A	29	HIS	0	-0.079	-0.043	9.782	0.126	0.126	0.000	0.000	0.000	0.000
31	A	30	THR	0	-0.041	-0.046	11.111	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	31	ALA	0	-0.033	-0.019	13.153	0.106	0.106	0.000	0.000	0.000	0.000
33	A	32	GLN	0	-0.038	-0.030	7.366	0.113	0.113	0.000	0.000	0.000	0.000
34	A	33	THR	0	-0.018	0.002	6.628	-0.334	-0.334	0.000	0.000	0.000	0.000
35	A	34	GLY	0	-0.023	0.000	8.724	0.363	0.363	0.000	0.000	0.000	0.000
36	A	35	ASP	-1	-0.777	-0.883	12.232	-0.331	-0.331	0.000	0.000	0.000	0.000
37	A	36	GLU	-1	-0.884	-0.929	7.930	0.380	0.380	0.000	0.000	0.000	0.000
38	A	37	SER	0	-0.097	-0.063	11.294	0.204	0.204	0.000	0.000	0.000	0.000
39	A	38	LEU	0	-0.063	-0.017	13.504	0.116	0.116	0.000	0.000	0.000	0.000
40	A	39	SER	0	-0.079	-0.027	16.481	0.095	0.095	0.000	0.000	0.000	0.000
41	A	40	CYS	0	-0.120	-0.065	18.081	0.031	0.031	0.000	0.000	0.000	0.000
42	A	41	LEU	0	-0.030	-0.015	17.387	0.023	0.023	0.000	0.000	0.000	0.000
43	A	42	SER	0	0.020	0.009	18.322	-0.012	-0.012	0.000	0.000	0.000	0.000
44	A	43	ASP	-1	-0.848	-0.938	15.260	-0.628	-0.628	0.000	0.000	0.000	0.000
45	A	44	ASP	-1	-0.849	-0.946	17.250	-0.556	-0.556	0.000	0.000	0.000	0.000
46	A	45	GLN	0	-0.034	-0.030	19.862	-0.078	-0.078	0.000	0.000	0.000	0.000
47	A	46	HIS	0	-0.033	-0.002	13.327	-0.227	-0.227	0.000	0.000	0.000	0.000
48	A	47	THR	0	-0.032	-0.016	15.336	-0.187	-0.187	0.000	0.000	0.000	0.000
49	A	48	LEU	0	-0.040	-0.024	16.666	-0.069	-0.069	0.000	0.000	0.000	0.000
50	A	49	THR	0	-0.015	-0.015	15.256	0.015	0.015	0.000	0.000	0.000	0.000
51	A	50	ALA	0	0.034	0.030	13.031	-0.082	-0.082	0.000	0.000	0.000	0.000
52	A	51	PHE	0	-0.039	-0.030	14.525	-0.059	-0.059	0.000	0.000	0.000	0.000
53	A	52	CYS	0	0.010	0.007	17.563	0.056	0.056	0.000	0.000	0.000	0.000
54	A	53	TYR	0	-0.006	0.006	11.700	0.201	0.201	0.000	0.000	0.000	0.000
55	A	54	LEU	0	-0.015	-0.026	15.285	-0.008	-0.008	0.000	0.000	0.000	0.000
56	A	55	ASP	-1	-0.804	-0.879	16.465	-0.748	-0.748	0.000	0.000	0.000	0.000
57	A	56	SER	0	-0.006	-0.017	19.263	0.027	0.027	0.000	0.000	0.000	0.000
58	A	57	GLN	0	-0.011	0.016	15.379	0.025	0.025	0.000	0.000	0.000	0.000
59	A	58	VAL	0	-0.070	-0.045	17.669	0.063	0.063	0.000	0.000	0.000	0.000
60	A	59	GLU	-1	-0.867	-0.937	20.197	-0.604	-0.604	0.000	0.000	0.000	0.000
61	A	60	GLU	-1	-0.973	-0.987	22.621	-0.589	-0.589	0.000	0.000	0.000	0.000
62	A	61	GLY	0	0.031	0.020	21.319	0.054	0.054	0.000	0.000	0.000	0.000
63	A	62	GLY	0	-0.051	-0.016	20.664	0.007	0.007	0.000	0.000	0.000	0.000
64	A	63	PHE	0	0.001	-0.038	15.756	-0.138	-0.138	0.000	0.000	0.000	0.000
65	A	64	VAL	0	-0.014	0.004	15.609	-0.200	-0.200	0.000	0.000	0.000	0.000
66	A	65	GLN	0	0.019	0.011	15.600	-0.048	-0.048	0.000	0.000	0.000	0.000
67	A	66	LEU	0	0.002	0.027	11.995	-0.155	-0.155	0.000	0.000	0.000	0.000
68	A	67	ILE	0	-0.059	-0.050	10.670	-0.353	-0.353	0.000	0.000	0.000	0.000
69	A	68	ALA	0	-0.052	-0.026	10.941	-0.313	-0.313	0.000	0.000	0.000	0.000
70	A	69	SER	0	-0.043	-0.030	12.348	0.029	0.029	0.000	0.000	0.000	0.000
71	A	70	GLY	0	0.053	0.018	8.999	-0.106	-0.106	0.000	0.000	0.000	0.000
72	A	71	TYR	0	-0.009	-0.037	6.648	0.153	0.153	0.000	0.000	0.000	0.000
73	A	72	GLY	0	0.081	0.047	7.707	0.238	0.238	0.000	0.000	0.000	0.000
74	A	73	GLU	-1	-0.872	-0.921	1.786	-41.555	-41.857	14.327	-7.543	-6.482	-0.092
75	A	74	TYR	0	-0.007	-0.017	3.131	-2.726	-0.742	0.181	-0.737	-1.428	-0.004
76	A	75	ILE	0	-0.011	0.014	6.962	1.058	1.058	0.000	0.000	0.000	0.000
77	A	76	PHE	0	-0.008	-0.017	9.358	0.646	0.646	0.000	0.000	0.000	0.000
78	A	77	ARG	1	0.784	0.869	4.694	3.736	3.834	-0.001	-0.003	-0.093	0.000
79	A	78	ASN	0	0.076	0.063	6.052	0.117	0.117	0.000	0.000	0.000	0.000
80	A	79	PRO	0	-0.010	-0.009	8.432	0.089	0.089	0.000	0.000	0.000	0.000
81	A	80	LEU	0	0.069	0.046	12.091	0.175	0.175	0.000	0.000	0.000	0.000
82	A	81	ALA	0	0.039	0.010	13.933	0.162	0.162	0.000	0.000	0.000	0.000
83	A	82	ASP	-1	-0.878	-0.946	15.411	-0.386	-0.386	0.000	0.000	0.000	0.000
84	A	83	SER	0	-0.007	-0.010	15.700	0.128	0.128	0.000	0.000	0.000	0.000
85	A	84	LEU	0	0.064	0.045	17.655	0.076	0.076	0.000	0.000	0.000	0.000
86	A	85	ARG	1	0.778	0.857	17.784	0.608	0.608	0.000	0.000	0.000	0.000
87	A	86	ARG	1	0.898	0.947	19.205	0.299	0.299	0.000	0.000	0.000	0.000
88	A	87	TRP	0	0.004	0.002	20.439	0.029	0.029	0.000	0.000	0.000	0.000
89	A	88	LYS	1	0.835	0.909	24.454	0.272	0.272	0.000	0.000	0.000	0.000
90	A	89	ILE	0	0.095	0.084	23.063	0.020	0.020	0.000	0.000	0.000	0.000
91	A	90	LYS	1	0.792	0.880	23.209	0.356	0.356	0.000	0.000	0.000	0.000
92	A	91	ALA	0	-0.004	0.011	23.803	-0.005	-0.005	0.000	0.000	0.000	0.000
93	A	92	VAL	0	0.122	0.056	19.667	-0.015	-0.015	0.000	0.000	0.000	0.000
94	A	93	PRO	0	-0.018	-0.010	18.880	-0.054	-0.054	0.000	0.000	0.000	0.000
95	A	94	LYS	1	0.891	0.958	19.188	0.391	0.391	0.000	0.000	0.000	0.000
96	A	95	VAL	0	0.013	0.016	20.057	0.009	0.009	0.000	0.000	0.000	0.000
97	A	96	LEU	0	0.018	0.016	14.836	-0.029	-0.029	0.000	0.000	0.000	0.000
98	A	97	ASP	-1	-0.834	-0.906	16.067	-0.668	-0.668	0.000	0.000	0.000	0.000
99	A	98	LYS	1	0.745	0.889	17.235	0.476	0.476	0.000	0.000	0.000	0.000
100	A	99	ALA	0	0.050	0.021	16.529	0.015	0.015	0.000	0.000	0.000	0.000
101	A	100	LYS	1	0.861	0.922	9.500	1.279	1.279	0.000	0.000	0.000	0.000
102	A	101	ALA	0	-0.036	-0.015	13.505	-0.043	-0.043	0.000	0.000	0.000	0.000
103	A	102	LEU	0	0.016	0.015	15.687	0.038	0.038	0.000	0.000	0.000	0.000
104	A	103	TYR	0	-0.058	-0.040	7.119	-0.052	-0.052	0.000	0.000	0.000	0.000
105	A	104	GLU	-1	-0.834	-0.903	9.622	-1.653	-1.653	0.000	0.000	0.000	0.000
106	A	105	GLN	0	-0.105	-0.034	12.441	0.141	0.141	0.000	0.000	0.000	0.000
107	A	106	HIS	0	-0.049	-0.055	14.282	0.095	0.095	0.000	0.000	0.000	0.000
108	A	107	GLY	0	0.053	0.029	10.553	0.004	0.004	0.000	0.000	0.000	0.000
109	A	108	LYS	1	0.973	0.991	5.549	0.088	0.088	0.000	0.000	0.000	0.000
110	A	109	THR	0	-0.019	-0.001	9.082	0.097	0.097	0.000	0.000	0.000	0.000
111	A	110	ILE	0	0.034	0.017	12.375	0.073	0.073	0.000	0.000	0.000	0.000
112	A	111	GLU	-1	-0.820	-0.886	6.380	-4.451	-4.451	0.000	0.000	0.000	0.000
113	A	112	THR	0	-0.063	-0.048	9.672	0.226	0.226	0.000	0.000	0.000	0.000
114	A	113	LEU	0	-0.049	-0.028	10.804	0.140	0.140	0.000	0.000	0.000	0.000
115	A	114	ALA	0	0.009	0.008	12.288	0.103	0.103	0.000	0.000	0.000	0.000
116	A	115	ASP	-1	-0.970	-0.973	10.375	-0.898	-0.898	0.000	0.000	0.000	0.000
117	A	116	GLY	0	-0.053	-0.022	12.514	0.141	0.141	0.000	0.000	0.000	0.000
118	A	117	GLY	0	-0.039	-0.022	15.536	0.097	0.097	0.000	0.000	0.000	0.000
119	A	118	ALA	0	-0.082	-0.031	17.022	0.052	0.052	0.000	0.000	0.000	0.000
120	A	119	ASP	-1	-0.828	-0.891	18.107	-0.638	-0.638	0.000	0.000	0.000	0.000
121	A	120	ILE	0	0.075	0.015	17.309	-0.009	-0.009	0.000	0.000	0.000	0.000
122	A	121	PRO	0	0.025	0.016	20.463	0.014	0.014	0.000	0.000	0.000	0.000
123	A	122	SER	0	-0.068	-0.059	21.829	0.050	0.050	0.000	0.000	0.000	0.000
124	A	123	LEU	0	-0.021	-0.012	16.033	0.026	0.026	0.000	0.000	0.000	0.000
125	A	124	ARG	1	0.779	0.865	19.720	0.723	0.723	0.000	0.000	0.000	0.000
126	A	125	LYS	1	0.896	0.951	21.860	0.406	0.406	0.000	0.000	0.000	0.000
127	A	126	GLN	0	-0.078	-0.037	19.520	0.034	0.034	0.000	0.000	0.000	0.000
128	A	127	PHE	0	-0.013	0.002	16.953	0.016	0.016	0.000	0.000	0.000	0.000
129	A	128	PRO	0	0.038	0.017	20.643	-0.057	-0.057	0.000	0.000	0.000	0.000
130	A	129	GLU	-1	-0.837	-0.921	21.194	-0.546	-0.546	0.000	0.000	0.000	0.000
131	A	130	PHE	0	-0.019	-0.030	15.513	-0.013	-0.013	0.000	0.000	0.000	0.000
132	A	131	GLU	-1	-0.868	-0.909	21.222	-0.552	-0.552	0.000	0.000	0.000	0.000
133	A	132	GLU	-1	-0.917	-0.955	24.502	-0.426	-0.426	0.000	0.000	0.000	0.000
134	A	133	TRP	0	0.016	-0.024	20.919	0.030	0.030	0.000	0.000	0.000	0.000
135	A	134	ASP	-1	-0.706	-0.838	21.217	-0.886	-0.886	0.000	0.000	0.000	0.000
136	A	135	GLY	0	0.017	0.013	23.141	0.011	0.011	0.000	0.000	0.000	0.000
137	A	136	ALA	0	0.005	0.000	24.463	0.018	0.018	0.000	0.000	0.000	0.000
138	A	137	TYR	0	-0.096	-0.074	20.192	-0.025	-0.025	0.000	0.000	0.000	0.000
139	A	138	TYR	0	-0.028	-0.013	23.590	0.017	0.017	0.000	0.000	0.000	0.000
140	A	139	GLU	-1	-0.950	-0.979	26.383	-0.371	-0.371	0.000	0.000	0.000	0.000
141	A	140	ALA	0	-0.079	-0.047	24.557	0.025	0.025	0.000	0.000	0.000	0.000
142	A	141	ALA	0	0.038	0.008	24.240	0.021	0.021	0.000	0.000	0.000	0.000
143	A	142	GLU	-1	-0.860	-0.897	25.976	-0.382	-0.382	0.000	0.000	0.000	0.000
144	A	143	GLN	0	-0.136	-0.064	28.622	0.054	0.054	0.000	0.000	0.000	0.000
145	A	144	ASP	-1	-0.806	-0.939	25.040	-0.483	-0.483	0.000	0.000	0.000	0.000
146	A	145	LEU	0	0.028	0.036	24.234	-0.003	-0.003	0.000	0.000	0.000	0.000
147	A	146	PRO	0	-0.037	-0.025	27.123	0.013	0.013	0.000	0.000	0.000	0.000
148	A	147	LEU	0	-0.010	0.011	28.139	0.018	0.018	0.000	0.000	0.000	0.000
149	A	148	LEU	0	-0.004	0.001	22.817	0.016	0.016	0.000	0.000	0.000	0.000
150	A	149	ALA	0	0.010	0.004	26.514	0.009	0.009	0.000	0.000	0.000	0.000
151	A	150	GLU	-1	-0.958	-0.975	29.078	-0.264	-0.264	0.000	0.000	0.000	0.000
152	A	151	HIS	0	-0.002	-0.002	24.300	0.049	0.049	0.000	0.000	0.000	0.000
153	A	152	ILE	0	0.013	0.000	24.764	0.023	0.023	0.000	0.000	0.000	0.000
154	A	153	GLN	0	-0.063	-0.043	28.374	0.010	0.010	0.000	0.000	0.000	0.000
155	A	154	SER	0	-0.082	-0.037	31.202	0.030	0.030	0.000	0.000	0.000	0.000
156	A	155	ASN	0	-0.104	-0.047	28.075	0.042	0.042	0.000	0.000	0.000	0.000
157	A	156	TRP	0	0.022	0.025	28.898	-0.023	-0.023	0.000	0.000	0.000	0.000
158	A	157	GLU	-1	-0.897	-0.961	29.762	-0.250	-0.250	0.000	0.000	0.000	0.000
159	A	158	THR	0	-0.040	-0.021	24.239	0.008	0.008	0.000	0.000	0.000	0.000
160	A	159	PHE	0	-0.015	-0.015	22.366	-0.032	-0.032	0.000	0.000	0.000	0.000
161	A	160	ALA	0	-0.023	0.007	26.398	-0.023	-0.023	0.000	0.000	0.000	0.000
162	A	161	HIS	0	-0.065	-0.020	27.148	0.011	0.011	0.000	0.000	0.000	0.000
163	A	162	ILE	0	0.042	0.024	23.702	-0.021	-0.021	0.000	0.000	0.000	0.000
164	A	163	GLY	0	-0.030	-0.007	24.652	0.025	0.025	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:HIS)