FMO DATABASE

FMODB ID: R5R38

Calculation Name: 4LRV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4LRV

Chain ID: A

ChEMBL ID:

UniProt ID:

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:

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	107
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-861381.75023
FMO2-HF: Nuclear repulsion	819091.202495
FMO2-HF: Total energy	-42290.547735
FMO2-MP2: Total energy	-42414.821286

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.
-11.321	-3.774	4.901	-6.283	-6.163	-0.037

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 : -0.044 / q_NPA : -0.024

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	LEU	0	0.012	0.026	3.260	-0.317	2.623	-0.005	-1.621	-1.314	0.000
4	A	5	PRO	0	0.052	0.034	3.137	-1.551	-0.569	0.103	-0.516	-0.569	-0.005
5	A	6	ASN	0	0.017	-0.004	5.493	0.129	0.129	0.000	0.000	0.000	0.000
6	A	7	ARG	1	0.826	0.898	6.993	0.052	0.052	0.000	0.000	0.000	0.000
7	A	8	MET	0	-0.026	0.003	7.052	-0.127	-0.127	0.000	0.000	0.000	0.000
8	A	9	ALA	0	0.039	0.028	11.725	0.075	0.075	0.000	0.000	0.000	0.000
9	A	10	LEU	0	0.025	0.018	14.714	-0.046	-0.046	0.000	0.000	0.000	0.000
10	A	11	SER	0	0.013	-0.009	17.315	0.011	0.011	0.000	0.000	0.000	0.000
11	A	12	ARG	1	0.887	0.931	20.731	0.113	0.113	0.000	0.000	0.000	0.000
12	A	13	GLN	0	0.039	0.014	23.708	0.003	0.003	0.000	0.000	0.000	0.000
13	A	14	THR	0	0.001	0.007	19.281	0.013	0.013	0.000	0.000	0.000	0.000
14	A	15	GLU	-1	-0.763	-0.862	20.730	-0.115	-0.115	0.000	0.000	0.000	0.000
15	A	16	ASP	-1	-0.810	-0.886	22.722	-0.058	-0.058	0.000	0.000	0.000	0.000
16	A	17	GLN	0	0.020	0.023	24.875	0.018	0.018	0.000	0.000	0.000	0.000
17	A	18	LEU	0	0.028	0.013	19.463	0.010	0.010	0.000	0.000	0.000	0.000
18	A	19	LYS	1	0.857	0.917	23.984	0.073	0.073	0.000	0.000	0.000	0.000
19	A	20	LYS	1	0.845	0.903	26.584	0.074	0.074	0.000	0.000	0.000	0.000
20	A	21	LEU	0	0.035	0.029	24.385	0.005	0.005	0.000	0.000	0.000	0.000
21	A	22	LYS	1	0.927	0.981	25.800	0.022	0.022	0.000	0.000	0.000	0.000
22	A	23	GLY	0	-0.026	-0.006	28.141	0.005	0.005	0.000	0.000	0.000	0.000
23	A	24	TYR	0	-0.011	0.000	31.065	0.002	0.002	0.000	0.000	0.000	0.000
24	A	25	THR	0	-0.028	-0.022	28.339	0.004	0.004	0.000	0.000	0.000	0.000
25	A	26	GLY	0	0.037	0.010	28.874	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	27	ILE	0	-0.023	-0.005	22.996	0.003	0.003	0.000	0.000	0.000	0.000
27	A	28	THR	0	0.007	-0.010	20.576	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	29	PRO	0	0.046	0.000	20.568	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	30	ASN	0	0.025	0.022	16.076	-0.015	-0.015	0.000	0.000	0.000	0.000
30	A	31	ILE	0	0.022	0.019	16.841	-0.011	-0.011	0.000	0.000	0.000	0.000
31	A	32	ALA	0	-0.004	-0.008	18.990	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	33	ALA	0	0.027	0.005	16.154	-0.005	-0.005	0.000	0.000	0.000	0.000
33	A	34	ARG	1	0.857	0.940	13.941	-0.006	-0.006	0.000	0.000	0.000	0.000
34	A	35	LEU	0	0.009	-0.004	16.054	0.002	0.002	0.000	0.000	0.000	0.000
35	A	36	ALA	0	-0.062	-0.003	18.975	0.007	0.007	0.000	0.000	0.000	0.000
36	A	37	PHE	0	0.033	0.002	11.246	-0.018	-0.018	0.000	0.000	0.000	0.000
37	A	38	PHE	0	-0.009	-0.022	11.924	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	39	ARG	1	0.925	0.970	16.883	0.065	0.065	0.000	0.000	0.000	0.000
39	A	40	SER	0	-0.017	-0.023	18.125	-0.005	-0.005	0.000	0.000	0.000	0.000
40	A	41	VAL	0	-0.053	-0.018	14.051	0.001	0.001	0.000	0.000	0.000	0.000
41	A	42	GLU	-1	-0.965	-0.980	17.378	0.001	0.001	0.000	0.000	0.000	0.000
42	A	43	SER	0	-0.032	-0.007	20.304	0.004	0.004	0.000	0.000	0.000	0.000
43	A	44	GLU	-1	-0.878	-0.951	21.482	-0.057	-0.057	0.000	0.000	0.000	0.000
44	A	45	PHE	0	-0.056	-0.005	18.750	-0.016	-0.016	0.000	0.000	0.000	0.000
45	A	46	ARG	1	0.835	0.893	17.434	0.089	0.089	0.000	0.000	0.000	0.000
46	A	47	TYR	0	-0.056	-0.041	16.170	-0.017	-0.017	0.000	0.000	0.000	0.000
47	A	48	SER	0	0.002	-0.056	18.366	0.004	0.004	0.000	0.000	0.000	0.000
48	A	49	PRO	0	-0.018	0.003	17.948	0.007	0.007	0.000	0.000	0.000	0.000
49	A	50	GLU	-1	-0.775	-0.844	19.902	-0.200	-0.200	0.000	0.000	0.000	0.000
50	A	51	ARG	1	0.862	0.912	22.846	0.184	0.184	0.000	0.000	0.000	0.000
51	A	52	ASP	-1	-0.775	-0.847	18.740	-0.327	-0.327	0.000	0.000	0.000	0.000
52	A	53	SER	0	-0.019	-0.012	22.080	-0.017	-0.017	0.000	0.000	0.000	0.000
53	A	54	LYS	1	0.807	0.892	20.611	0.188	0.188	0.000	0.000	0.000	0.000
54	A	55	LYS	1	0.896	0.934	20.683	0.175	0.175	0.000	0.000	0.000	0.000
55	A	56	LEU	0	-0.024	-0.019	15.049	0.009	0.009	0.000	0.000	0.000	0.000
56	A	57	ASP	-1	-0.826	-0.909	19.034	-0.173	-0.173	0.000	0.000	0.000	0.000
57	A	58	GLY	0	-0.047	-0.008	20.070	0.021	0.021	0.000	0.000	0.000	0.000
58	A	59	THR	0	-0.044	-0.057	20.812	0.000	0.000	0.000	0.000	0.000	0.000
59	A	60	LEU	0	-0.010	-0.012	18.648	0.010	0.010	0.000	0.000	0.000	0.000
60	A	61	VAL	0	-0.022	-0.006	13.889	-0.024	-0.024	0.000	0.000	0.000	0.000
61	A	62	LEU	0	0.021	0.016	14.503	0.031	0.031	0.000	0.000	0.000	0.000
62	A	63	ASP	-1	-0.774	-0.879	10.718	0.011	0.011	0.000	0.000	0.000	0.000
63	A	64	LYS	1	0.792	0.867	2.348	1.055	1.020	1.726	-0.764	-0.927	0.005
64	A	65	ILE	0	0.055	0.026	8.367	-0.028	-0.028	0.000	0.000	0.000	0.000
65	A	66	THR	0	0.027	0.018	10.106	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	67	TRP	0	-0.026	-0.026	11.095	0.016	0.016	0.000	0.000	0.000	0.000
67	A	68	LEU	0	-0.017	-0.001	7.969	-0.006	-0.006	0.000	0.000	0.000	0.000
68	A	69	GLY	0	-0.007	0.005	11.733	0.024	0.024	0.000	0.000	0.000	0.000
69	A	70	GLU	-1	-0.868	-0.950	10.743	0.157	0.157	0.000	0.000	0.000	0.000
70	A	71	THR	0	-0.009	0.006	11.498	0.028	0.028	0.000	0.000	0.000	0.000
71	A	72	LEU	0	-0.023	0.019	4.271	-0.105	-0.017	-0.001	-0.011	-0.076	0.000
72	A	73	GLN	0	0.063	0.015	6.035	-0.205	-0.205	0.000	0.000	0.000	0.000
73	A	74	ALA	0	0.038	0.019	6.940	0.181	0.181	0.000	0.000	0.000	0.000
74	A	75	THR	0	-0.022	-0.033	7.931	-0.010	-0.010	0.000	0.000	0.000	0.000
75	A	76	GLU	-1	-0.729	-0.872	2.556	-10.298	-6.713	3.079	-3.369	-3.294	-0.037
76	A	77	LEU	0	-0.019	0.010	5.284	0.196	0.183	-0.001	-0.002	0.017	0.000
77	A	78	VAL	0	0.045	0.012	7.410	-0.096	-0.096	0.000	0.000	0.000	0.000
78	A	79	LEU	0	-0.015	-0.009	7.218	-0.047	-0.047	0.000	0.000	0.000	0.000
79	A	80	LYS	1	0.906	0.949	5.703	-0.361	-0.361	0.000	0.000	0.000	0.000
80	A	81	MET	0	-0.020	-0.018	8.328	0.018	0.018	0.000	0.000	0.000	0.000
81	A	82	LEU	0	-0.020	0.005	11.723	-0.024	-0.024	0.000	0.000	0.000	0.000
82	A	83	TYR	0	-0.041	-0.045	11.362	-0.010	-0.010	0.000	0.000	0.000	0.000
83	A	84	PRO	0	0.017	0.014	10.838	-0.137	-0.137	0.000	0.000	0.000	0.000
84	A	85	GLN	0	-0.027	-0.016	11.906	-0.029	-0.029	0.000	0.000	0.000	0.000
85	A	86	LEU	0	-0.058	-0.014	11.799	-0.004	-0.004	0.000	0.000	0.000	0.000
86	A	87	GLU	-1	-0.799	-0.913	10.793	-1.348	-1.348	0.000	0.000	0.000	0.000
87	A	88	GLN	0	0.019	0.017	6.146	-0.226	-0.226	0.000	0.000	0.000	0.000
88	A	89	LYS	1	0.902	0.938	9.105	0.691	0.691	0.000	0.000	0.000	0.000
89	A	90	ALA	0	0.025	0.009	12.324	0.108	0.108	0.000	0.000	0.000	0.000
90	A	91	LEU	0	0.049	0.023	7.075	0.067	0.067	0.000	0.000	0.000	0.000
91	A	92	ILE	0	-0.002	-0.008	9.078	0.092	0.092	0.000	0.000	0.000	0.000
92	A	93	LYS	1	0.803	0.905	10.866	0.467	0.467	0.000	0.000	0.000	0.000
93	A	94	ALA	0	0.028	0.018	12.188	0.074	0.074	0.000	0.000	0.000	0.000
94	A	95	TRP	0	0.006	-0.005	10.306	0.053	0.053	0.000	0.000	0.000	0.000
95	A	96	ALA	0	0.015	-0.008	12.437	0.084	0.084	0.000	0.000	0.000	0.000
96	A	97	ALA	0	-0.016	-0.005	15.289	0.053	0.053	0.000	0.000	0.000	0.000
97	A	98	HIS	0	0.056	0.046	14.004	0.019	0.019	0.000	0.000	0.000	0.000
98	A	99	VAL	0	-0.047	-0.013	15.093	0.038	0.038	0.000	0.000	0.000	0.000
99	A	100	GLU	-1	-0.792	-0.866	17.794	-0.158	-0.158	0.000	0.000	0.000	0.000
100	A	101	ASP	-1	-0.821	-0.883	20.607	-0.096	-0.096	0.000	0.000	0.000	0.000
101	A	102	GLY	0	0.056	0.036	20.390	0.018	0.018	0.000	0.000	0.000	0.000
102	A	103	ILE	0	-0.093	-0.067	21.385	0.019	0.019	0.000	0.000	0.000	0.000
103	A	104	ALA	0	-0.038	-0.018	23.473	0.011	0.011	0.000	0.000	0.000	0.000
104	A	105	ALA	0	-0.015	0.005	25.105	0.009	0.009	0.000	0.000	0.000	0.000
105	A	106	LEU	0	-0.048	-0.022	26.049	0.009	0.009	0.000	0.000	0.000	0.000
106	A	107	ARG	1	0.858	0.926	27.750	0.082	0.082	0.000	0.000	0.000	0.000
107	A	108	ASN	0	0.034	0.031	31.897	0.000	0.000	0.000	0.000	0.000	0.000

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