FMO DATABASE

FMODB ID: 3JQLL

Calculation Name: 1VR4-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VR4

Chain ID: B

ChEMBL ID:

UniProt ID: Q81H14

Base Structure: X-ray

Registration Date: 2023-09-21

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	82
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-479170.584158
FMO2-HF: Nuclear repulsion	447165.644991
FMO2-HF: Total energy	-32004.939167
FMO2-MP2: Total energy	-32094.259859

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(B:1:MET)

Summations of interaction energy for fragment #1(B:1:MET)

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.
-32.468	-33.189	40.531	-16.028	-23.782	-0.023

Interaction energy analysis for fragmet #1(B:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : 0.064

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

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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	B	3	VAL	0	0.036	0.010	2.410	-3.758	-0.491	1.092	-1.753	-2.606	-0.002
4	B	4	THR	0	-0.043	-0.007	4.566	0.592	0.676	-0.001	-0.018	-0.065	0.000
5	B	5	THR	0	0.086	0.048	8.344	0.019	0.019	0.000	0.000	0.000	0.000
6	B	6	THR	0	-0.052	-0.020	11.298	0.097	0.097	0.000	0.000	0.000	0.000
7	B	7	SER	0	0.041	0.004	11.387	-0.139	-0.139	0.000	0.000	0.000	0.000
8	B	8	GLY	0	0.012	0.005	11.984	0.105	0.105	0.000	0.000	0.000	0.000
9	B	9	ILE	0	0.003	0.007	7.398	-0.182	-0.182	0.000	0.000	0.000	0.000
10	B	10	GLN	0	0.027	0.015	11.205	0.221	0.221	0.000	0.000	0.000	0.000
11	B	11	GLY	0	0.008	0.001	12.640	-0.071	-0.071	0.000	0.000	0.000	0.000
12	B	12	LYS	1	0.840	0.910	9.168	1.355	1.355	0.000	0.000	0.000	0.000
13	B	13	GLU	-1	-0.905	-0.936	12.135	-0.746	-0.746	0.000	0.000	0.000	0.000
14	B	14	ILE	0	-0.026	-0.019	9.555	-0.180	-0.180	0.000	0.000	0.000	0.000
15	B	15	ILE	0	-0.020	-0.001	11.262	0.144	0.144	0.000	0.000	0.000	0.000
16	B	16	GLU	-1	-0.858	-0.922	9.819	-0.561	-0.561	0.000	0.000	0.000	0.000
17	B	17	TYR	0	0.005	-0.014	9.250	-0.339	-0.339	0.000	0.000	0.000	0.000
18	B	18	ILE	0	-0.049	-0.002	6.040	0.116	0.116	0.000	0.000	0.000	0.000
19	B	19	ASP	-1	-0.778	-0.885	8.903	-0.055	-0.055	0.000	0.000	0.000	0.000
20	B	20	ILE	0	-0.045	-0.013	8.954	-0.246	-0.246	0.000	0.000	0.000	0.000
21	B	21	VAL	0	-0.034	-0.012	5.839	0.123	0.123	0.000	0.000	0.000	0.000
22	B	22	ASN	0	0.025	-0.022	8.981	-0.109	-0.109	0.000	0.000	0.000	0.000
23	B	23	GLY	0	0.026	0.025	10.529	0.228	0.228	0.000	0.000	0.000	0.000
24	B	24	GLU	-1	-0.918	-0.965	12.425	0.212	0.212	0.000	0.000	0.000	0.000
25	B	25	ALA	0	-0.006	0.010	15.590	0.075	0.075	0.000	0.000	0.000	0.000
26	B	26	ILE	0	0.016	-0.002	17.921	-0.060	-0.060	0.000	0.000	0.000	0.000
27	B	27	MET	0	-0.076	-0.027	21.751	0.016	0.016	0.000	0.000	0.000	0.000
28	B	28	GLY	0	0.083	0.024	24.197	-0.022	-0.022	0.000	0.000	0.000	0.000
29	B	29	ALA	0	-0.063	-0.014	28.023	0.001	0.001	0.000	0.000	0.000	0.000
30	B	51	GLU	-1	-0.923	-0.964	23.818	-0.011	-0.011	0.000	0.000	0.000	0.000
31	B	52	SER	0	-0.035	-0.042	22.615	-0.001	-0.001	0.000	0.000	0.000	0.000
32	B	53	LYS	1	0.860	0.904	21.407	-0.184	-0.184	0.000	0.000	0.000	0.000
33	B	54	LEU	0	0.023	0.030	19.670	0.028	0.028	0.000	0.000	0.000	0.000
34	B	55	LYS	1	0.779	0.857	15.276	-0.135	-0.135	0.000	0.000	0.000	0.000
35	B	56	GLU	-1	-0.759	-0.860	16.828	0.240	0.240	0.000	0.000	0.000	0.000
36	B	57	ALA	0	0.016	0.013	16.784	0.074	0.074	0.000	0.000	0.000	0.000
37	B	58	ARG	1	0.962	0.969	14.049	0.074	0.074	0.000	0.000	0.000	0.000
38	B	59	ASP	-1	-0.810	-0.880	12.557	0.267	0.267	0.000	0.000	0.000	0.000
39	B	60	ILE	0	0.022	0.011	11.770	0.194	0.194	0.000	0.000	0.000	0.000
40	B	61	ALA	0	0.030	0.035	11.946	0.200	0.200	0.000	0.000	0.000	0.000
41	B	62	MET	0	0.014	0.000	8.753	0.125	0.125	0.000	0.000	0.000	0.000
42	B	63	ASP	-1	-0.901	-0.927	7.444	2.285	2.285	0.000	0.000	0.000	0.000
43	B	64	GLU	-1	-0.895	-0.946	7.653	1.716	1.716	0.000	0.000	0.000	0.000
44	B	65	MET	0	-0.011	0.025	6.770	0.097	0.097	0.000	0.000	0.000	0.000
45	B	66	LYS	1	0.775	0.848	3.423	-2.915	-1.715	0.534	-0.363	-1.372	0.000
46	B	67	GLU	-1	-0.923	-0.947	3.905	3.733	5.284	0.172	-0.754	-0.969	-0.008
47	B	68	LEU	0	0.020	0.009	5.806	-0.430	-0.430	0.000	0.000	0.000	0.000
48	B	69	ALA	0	-0.001	-0.005	2.434	-1.398	-1.364	1.970	-0.604	-1.399	-0.002
49	B	70	LYS	1	0.822	0.867	2.135	-23.869	-35.436	25.752	-7.677	-6.509	0.054
50	B	71	GLN	0	-0.066	-0.039	3.766	-0.730	-0.692	0.005	0.005	-0.049	0.000
51	B	72	LYS	1	0.834	0.918	5.654	-0.043	-0.043	0.000	0.000	0.000	0.000
52	B	73	GLY	0	0.003	0.008	5.906	-0.206	-0.206	0.000	0.000	0.000	0.000
53	B	74	ALA	0	-0.012	0.000	2.350	-0.233	-0.184	1.387	-0.419	-1.016	-0.001
54	B	75	ASN	0	-0.055	-0.042	2.382	-2.012	-0.940	2.891	-1.430	-2.533	-0.017
55	B	76	ALA	0	-0.038	-0.024	2.207	-4.762	-2.547	4.658	-2.777	-4.095	-0.034
56	B	77	ILE	0	0.039	0.016	2.790	-1.376	-0.307	2.075	-0.215	-2.930	-0.013
57	B	78	VAL	0	-0.024	-0.011	4.786	-0.050	-0.004	-0.001	-0.008	-0.037	0.000
58	B	79	GLY	0	0.000	-0.007	8.597	0.214	0.214	0.000	0.000	0.000	0.000
59	B	80	VAL	0	-0.064	-0.034	7.288	0.109	0.109	0.000	0.000	0.000	0.000
60	B	81	ASP	-1	-0.844	-0.921	10.626	-0.359	-0.359	0.000	0.000	0.000	0.000
61	B	82	VAL	0	-0.124	-0.082	13.231	0.091	0.091	0.000	0.000	0.000	0.000
62	B	83	ASP	-1	-0.849	-0.898	15.451	-0.115	-0.115	0.000	0.000	0.000	0.000
63	B	84	TYR	0	-0.054	-0.050	17.539	0.061	0.061	0.000	0.000	0.000	0.000
64	B	85	GLU	-1	-0.854	-0.916	21.452	-0.016	-0.016	0.000	0.000	0.000	0.000
65	B	86	VAL	0	-0.045	-0.020	24.470	0.025	0.025	0.000	0.000	0.000	0.000
66	B	87	VAL	0	0.010	0.003	24.261	-0.005	-0.005	0.000	0.000	0.000	0.000
67	B	88	ARG	1	0.915	0.950	27.511	-0.091	-0.091	0.000	0.000	0.000	0.000
68	B	89	ASP	-1	-0.865	-0.926	30.149	0.041	0.041	0.000	0.000	0.000	0.000
69	B	90	GLY	0	-0.063	-0.031	31.395	0.007	0.007	0.000	0.000	0.000	0.000
70	B	91	MET	0	-0.088	-0.029	25.240	0.013	0.013	0.000	0.000	0.000	0.000
71	B	92	LEU	0	0.008	0.007	23.035	-0.013	-0.013	0.000	0.000	0.000	0.000
72	B	93	MET	0	0.006	-0.002	19.995	0.038	0.038	0.000	0.000	0.000	0.000
73	B	94	VAL	0	-0.050	-0.026	16.460	-0.039	-0.039	0.000	0.000	0.000	0.000
74	B	95	ALA	0	0.024	0.005	15.759	0.071	0.071	0.000	0.000	0.000	0.000
75	B	96	VAL	0	-0.020	-0.021	10.553	-0.066	-0.066	0.000	0.000	0.000	0.000
76	B	97	SER	0	0.034	0.021	11.371	0.055	0.055	0.000	0.000	0.000	0.000
77	B	98	GLY	0	0.058	0.014	8.807	-0.062	-0.062	0.000	0.000	0.000	0.000
78	B	99	THR	0	-0.037	-0.009	8.619	0.140	0.140	0.000	0.000	0.000	0.000
79	B	100	ALA	0	0.001	0.003	4.586	-0.591	-0.538	-0.001	-0.006	-0.046	0.000
80	B	101	VAL	0	-0.018	-0.016	4.326	0.524	0.625	-0.001	-0.005	-0.094	0.000
81	B	102	ARG	1	0.874	0.924	4.743	-0.459	-0.392	-0.001	-0.004	-0.062	0.000
82	B	103	ILE	0	0.006	0.003	5.423	0.445	0.445	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:1:MET)