FMO DATABASE

FMODB ID: VR4N1

Calculation Name: 1VQ3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VQ3

Chain ID: A

ChEMBL ID:

UniProt ID: Q9X0X1

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	OptHSide
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	86
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-556626.25005
FMO2-HF: Nuclear repulsion	521644.800479
FMO2-HF: Total energy	-34981.449571
FMO2-MP2: Total energy	-35085.706129

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:-3:HIS)

Summations of interaction energy for fragment #1(A:-3: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.
-3.227	-0.595	0.1	-1.013	-1.718	-0.002

Interaction energy analysis for fragmet #1(A:-3:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / q_NPA : -0.021

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	A	-1	HIS	0	-0.041	-0.018	2.891	-3.949	-1.429	0.101	-0.998	-1.622	-0.002
4	A	0	HIS	0	0.006	0.002	4.479	0.875	0.987	-0.001	-0.015	-0.096	0.000
5	A	1	LEU	0	-0.006	0.009	8.290	-0.321	-0.321	0.000	0.000	0.000	0.000
6	A	2	PRO	0	-0.053	-0.022	10.003	0.150	0.150	0.000	0.000	0.000	0.000
7	A	3	LEU	0	0.038	0.029	13.753	0.026	0.026	0.000	0.000	0.000	0.000
8	A	4	PHE	0	-0.031	-0.018	15.523	-0.048	-0.048	0.000	0.000	0.000	0.000
9	A	5	LYS	1	0.834	0.899	19.572	-0.151	-0.151	0.000	0.000	0.000	0.000
10	A	6	PHE	0	0.017	0.001	20.800	-0.033	-0.033	0.000	0.000	0.000	0.000
11	A	7	ALA	0	-0.013	-0.004	25.488	0.024	0.024	0.000	0.000	0.000	0.000
12	A	8	ILE	0	-0.013	-0.012	26.571	-0.018	-0.018	0.000	0.000	0.000	0.000
13	A	9	ASP	-1	-0.791	-0.881	30.441	0.041	0.041	0.000	0.000	0.000	0.000
14	A	10	VAL	0	-0.014	-0.002	33.059	-0.009	-0.009	0.000	0.000	0.000	0.000
15	A	11	GLN	0	0.010	0.002	35.659	0.006	0.006	0.000	0.000	0.000	0.000
16	A	12	TYR	0	0.020	0.010	39.415	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	13	ARG	1	0.875	0.937	38.223	0.005	0.005	0.000	0.000	0.000	0.000
18	A	14	SER	0	0.023	-0.001	43.321	0.003	0.003	0.000	0.000	0.000	0.000
19	A	15	ASN	0	-0.042	-0.018	46.309	0.001	0.001	0.000	0.000	0.000	0.000
20	A	16	VAL	0	-0.047	-0.012	44.327	0.001	0.001	0.000	0.000	0.000	0.000
21	A	17	ARG	1	0.831	0.906	47.393	-0.019	-0.019	0.000	0.000	0.000	0.000
22	A	18	ASP	-1	-0.746	-0.880	45.832	0.037	0.037	0.000	0.000	0.000	0.000
23	A	19	PRO	0	0.022	0.001	47.934	0.000	0.000	0.000	0.000	0.000	0.000
24	A	20	ARG	1	0.962	0.991	41.793	-0.062	-0.062	0.000	0.000	0.000	0.000
25	A	21	GLY	0	0.068	0.032	47.335	0.001	0.001	0.000	0.000	0.000	0.000
26	A	22	GLU	-1	-0.828	-0.913	47.931	0.021	0.021	0.000	0.000	0.000	0.000
27	A	23	THR	0	-0.068	-0.041	50.918	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	24	ILE	0	0.008	-0.005	46.246	0.000	0.000	0.000	0.000	0.000	0.000
29	A	25	GLU	-1	-0.816	-0.904	50.404	0.017	0.017	0.000	0.000	0.000	0.000
30	A	26	ARG	1	0.869	0.938	52.071	-0.035	-0.035	0.000	0.000	0.000	0.000
31	A	27	VAL	0	-0.006	-0.008	52.782	0.000	0.000	0.000	0.000	0.000	0.000
32	A	28	LEU	0	-0.010	-0.010	49.028	0.000	0.000	0.000	0.000	0.000	0.000
33	A	29	ARG	1	0.791	0.888	53.713	-0.021	-0.021	0.000	0.000	0.000	0.000
34	A	30	GLU	-1	-0.854	-0.943	56.735	0.023	0.023	0.000	0.000	0.000	0.000
35	A	31	GLU	-1	-0.878	-0.917	56.682	0.036	0.036	0.000	0.000	0.000	0.000
36	A	32	LYS	1	0.841	0.925	53.604	-0.042	-0.042	0.000	0.000	0.000	0.000
37	A	33	GLY	0	0.033	0.045	56.892	0.000	0.000	0.000	0.000	0.000	0.000
38	A	34	LEU	0	-0.011	-0.011	52.275	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	35	PRO	0	0.019	0.011	55.425	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	36	VAL	0	0.000	-0.003	50.358	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	37	LYS	1	0.842	0.901	51.759	-0.010	-0.010	0.000	0.000	0.000	0.000
42	A	38	LYS	1	0.939	0.978	49.570	0.004	0.004	0.000	0.000	0.000	0.000
43	A	39	LEU	0	0.004	0.018	46.440	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	40	ARG	1	0.816	0.898	41.657	-0.006	-0.006	0.000	0.000	0.000	0.000
45	A	41	LEU	0	-0.015	0.004	42.170	0.002	0.002	0.000	0.000	0.000	0.000
46	A	42	GLY	0	0.052	0.015	39.346	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	43	LYS	1	0.738	0.872	34.107	-0.052	-0.052	0.000	0.000	0.000	0.000
48	A	44	SER	0	0.038	0.016	32.618	-0.011	-0.011	0.000	0.000	0.000	0.000
49	A	45	ILE	0	-0.061	-0.019	27.645	0.012	0.012	0.000	0.000	0.000	0.000
50	A	46	HIS	0	0.027	0.010	27.356	-0.016	-0.016	0.000	0.000	0.000	0.000
51	A	47	LEU	0	-0.015	-0.008	22.835	0.020	0.020	0.000	0.000	0.000	0.000
52	A	48	GLU	-1	-0.812	-0.891	19.354	0.194	0.194	0.000	0.000	0.000	0.000
53	A	49	VAL	0	-0.025	-0.012	17.168	0.030	0.030	0.000	0.000	0.000	0.000
54	A	50	GLU	-1	-0.898	-0.947	10.962	0.756	0.756	0.000	0.000	0.000	0.000
55	A	51	ALA	0	-0.033	-0.028	12.896	-0.018	-0.018	0.000	0.000	0.000	0.000
56	A	52	GLU	-1	-0.859	-0.929	9.236	-1.159	-1.159	0.000	0.000	0.000	0.000
57	A	53	ASN	0	-0.001	-0.005	12.308	0.015	0.015	0.000	0.000	0.000	0.000
58	A	54	LYS	1	0.913	0.940	15.858	0.194	0.194	0.000	0.000	0.000	0.000
59	A	55	GLU	-1	-0.870	-0.942	19.315	-0.260	-0.260	0.000	0.000	0.000	0.000
60	A	56	LYS	1	0.970	0.986	12.151	0.457	0.457	0.000	0.000	0.000	0.000
61	A	57	ALA	0	0.003	-0.008	17.814	0.047	0.047	0.000	0.000	0.000	0.000
62	A	58	TYR	0	0.014	0.010	18.893	0.039	0.039	0.000	0.000	0.000	0.000
63	A	59	GLU	-1	-0.837	-0.907	20.726	-0.142	-0.142	0.000	0.000	0.000	0.000
64	A	60	ILE	0	-0.030	-0.011	16.257	0.020	0.020	0.000	0.000	0.000	0.000
65	A	61	VAL	0	0.012	0.018	20.823	0.030	0.030	0.000	0.000	0.000	0.000
66	A	62	LYS	1	0.866	0.920	23.672	0.142	0.142	0.000	0.000	0.000	0.000
67	A	63	LYS	1	0.818	0.905	22.718	0.041	0.041	0.000	0.000	0.000	0.000
68	A	64	ALA	0	0.031	0.011	23.353	0.015	0.015	0.000	0.000	0.000	0.000
69	A	65	CYS	0	-0.079	-0.047	25.130	0.012	0.012	0.000	0.000	0.000	0.000
70	A	66	GLU	-1	-0.915	-0.947	27.871	-0.051	-0.051	0.000	0.000	0.000	0.000
71	A	67	GLU	-1	-0.914	-0.951	25.181	0.020	0.020	0.000	0.000	0.000	0.000
72	A	68	LEU	0	-0.056	-0.021	27.217	0.015	0.015	0.000	0.000	0.000	0.000
73	A	69	LEU	0	-0.061	-0.030	26.337	0.002	0.002	0.000	0.000	0.000	0.000
74	A	70	VAL	0	-0.033	-0.016	30.469	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	71	ASN	0	0.046	0.027	33.305	-0.009	-0.009	0.000	0.000	0.000	0.000
76	A	72	PRO	0	0.059	0.030	34.961	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	73	VAL	0	-0.005	-0.004	36.969	-0.008	-0.008	0.000	0.000	0.000	0.000
78	A	74	VAL	0	-0.022	-0.026	40.229	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	75	GLU	-1	-0.810	-0.883	36.607	0.046	0.046	0.000	0.000	0.000	0.000
80	A	76	GLU	-1	-0.853	-0.914	37.027	-0.014	-0.014	0.000	0.000	0.000	0.000
81	A	77	TYR	0	0.016	-0.026	29.438	0.008	0.008	0.000	0.000	0.000	0.000
82	A	78	GLU	-1	-0.922	-0.934	33.440	-0.026	-0.026	0.000	0.000	0.000	0.000
83	A	79	VAL	0	-0.018	-0.015	26.771	0.013	0.013	0.000	0.000	0.000	0.000
84	A	80	ARG	1	0.827	0.905	29.555	-0.034	-0.034	0.000	0.000	0.000	0.000
85	A	81	GLU	-1	-0.810	-0.885	24.778	-0.085	-0.085	0.000	0.000	0.000	0.000
86	A	82	LEU	0	-0.040	-0.024	25.717	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:-3:HIS)