FMO DATABASE

FMODB ID: ZY3MN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-860166.225246
FMO2-HF: Nuclear repulsion	817875.928555
FMO2-HF: Total energy	-42290.296691
FMO2-MP2: Total energy	-42414.564362

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.
-10.268	-4.08	6.056	-6.245	-6	-0.031

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 : -0.065 / q_NPA : -0.034

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	-0.002	0.018	3.114	-0.571	2.128	0.014	-1.448	-1.265	0.006
4	A	5	PRO	0	0.033	0.034	3.039	-1.899	-0.849	0.150	-0.483	-0.718	-0.005
5	A	6	ASN	0	0.042	-0.002	5.268	0.056	0.056	0.000	0.000	0.000	0.000
6	A	7	ARG	1	0.851	0.921	6.496	0.119	0.119	0.000	0.000	0.000	0.000
7	A	8	MET	0	-0.014	0.006	7.322	-0.104	-0.104	0.000	0.000	0.000	0.000
8	A	9	ALA	0	0.056	0.035	11.563	0.068	0.068	0.000	0.000	0.000	0.000
9	A	10	LEU	0	0.007	0.018	15.061	-0.033	-0.033	0.000	0.000	0.000	0.000
10	A	11	SER	0	0.015	0.002	17.341	0.007	0.007	0.000	0.000	0.000	0.000
11	A	12	ARG	1	0.940	0.959	20.678	0.096	0.096	0.000	0.000	0.000	0.000
12	A	13	GLN	0	0.007	-0.001	23.854	0.002	0.002	0.000	0.000	0.000	0.000
13	A	14	THR	0	0.003	-0.005	19.362	0.016	0.016	0.000	0.000	0.000	0.000
14	A	15	GLU	-1	-0.777	-0.865	20.643	-0.100	-0.100	0.000	0.000	0.000	0.000
15	A	16	ASP	-1	-0.827	-0.906	22.763	-0.047	-0.047	0.000	0.000	0.000	0.000
16	A	17	GLN	0	0.027	0.014	24.871	0.015	0.015	0.000	0.000	0.000	0.000
17	A	18	LEU	0	0.020	0.015	19.499	0.008	0.008	0.000	0.000	0.000	0.000
18	A	19	LYS	1	0.865	0.926	24.046	0.060	0.060	0.000	0.000	0.000	0.000
19	A	20	LYS	1	0.878	0.939	26.791	0.059	0.059	0.000	0.000	0.000	0.000
20	A	21	LEU	0	0.051	0.037	24.371	0.004	0.004	0.000	0.000	0.000	0.000
21	A	22	LYS	1	0.928	0.988	26.070	0.021	0.021	0.000	0.000	0.000	0.000
22	A	23	GLY	0	-0.046	-0.010	27.910	0.004	0.004	0.000	0.000	0.000	0.000
23	A	24	TYR	0	-0.006	0.000	31.252	0.002	0.002	0.000	0.000	0.000	0.000
24	A	25	THR	0	-0.030	-0.021	28.179	0.004	0.004	0.000	0.000	0.000	0.000
25	A	26	GLY	0	0.042	0.016	29.201	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	27	ILE	0	-0.046	-0.026	23.108	0.001	0.001	0.000	0.000	0.000	0.000
27	A	28	THR	0	0.026	0.002	21.272	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	29	PRO	0	0.059	0.007	20.920	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	30	ASN	0	0.006	-0.006	16.578	-0.006	-0.006	0.000	0.000	0.000	0.000
30	A	31	ILE	0	0.020	0.020	16.932	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	32	ALA	0	0.010	0.005	19.084	0.002	0.002	0.000	0.000	0.000	0.000
32	A	33	ALA	0	0.022	0.011	16.034	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	34	ARG	1	0.853	0.929	13.976	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	35	LEU	0	0.004	-0.006	15.938	0.005	0.005	0.000	0.000	0.000	0.000
35	A	36	ALA	0	-0.045	-0.008	18.863	0.004	0.004	0.000	0.000	0.000	0.000
36	A	37	PHE	0	0.038	0.006	11.568	-0.014	-0.014	0.000	0.000	0.000	0.000
37	A	38	PHE	0	-0.009	-0.025	12.368	0.003	0.003	0.000	0.000	0.000	0.000
38	A	39	ARG	1	0.934	0.976	17.280	0.036	0.036	0.000	0.000	0.000	0.000
39	A	40	SER	0	-0.043	-0.039	18.192	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	41	VAL	0	-0.049	-0.026	14.313	0.003	0.003	0.000	0.000	0.000	0.000
41	A	42	GLU	-1	-1.005	-0.989	17.739	0.032	0.032	0.000	0.000	0.000	0.000
42	A	43	SER	0	-0.014	-0.012	20.528	0.000	0.000	0.000	0.000	0.000	0.000
43	A	44	GLU	-1	-0.902	-0.957	22.040	-0.025	-0.025	0.000	0.000	0.000	0.000
44	A	45	PHE	0	-0.040	0.002	18.598	-0.013	-0.013	0.000	0.000	0.000	0.000
45	A	46	ARG	1	0.868	0.910	17.774	0.038	0.038	0.000	0.000	0.000	0.000
46	A	47	TYR	0	-0.066	-0.044	15.866	-0.023	-0.023	0.000	0.000	0.000	0.000
47	A	48	SER	0	0.007	-0.052	18.263	0.010	0.010	0.000	0.000	0.000	0.000
48	A	49	PRO	0	-0.027	0.000	17.682	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	50	GLU	-1	-0.802	-0.855	19.492	-0.158	-0.158	0.000	0.000	0.000	0.000
50	A	51	ARG	1	0.847	0.908	22.446	0.137	0.137	0.000	0.000	0.000	0.000
51	A	52	ASP	-1	-0.741	-0.845	18.894	-0.268	-0.268	0.000	0.000	0.000	0.000
52	A	53	SER	0	-0.036	-0.020	22.434	-0.013	-0.013	0.000	0.000	0.000	0.000
53	A	54	LYS	1	0.783	0.868	20.894	0.157	0.157	0.000	0.000	0.000	0.000
54	A	55	LYS	1	0.911	0.956	20.571	0.152	0.152	0.000	0.000	0.000	0.000
55	A	56	LEU	0	-0.023	-0.011	15.285	0.012	0.012	0.000	0.000	0.000	0.000
56	A	57	ASP	-1	-0.840	-0.917	18.957	-0.152	-0.152	0.000	0.000	0.000	0.000
57	A	58	GLY	0	-0.041	-0.006	19.954	0.020	0.020	0.000	0.000	0.000	0.000
58	A	59	THR	0	-0.054	-0.062	20.746	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	60	LEU	0	-0.019	-0.011	18.446	0.005	0.005	0.000	0.000	0.000	0.000
60	A	61	VAL	0	-0.022	-0.004	13.408	-0.024	-0.024	0.000	0.000	0.000	0.000
61	A	62	LEU	0	-0.006	0.002	14.295	0.033	0.033	0.000	0.000	0.000	0.000
62	A	63	ASP	-1	-0.804	-0.899	10.711	-0.040	-0.040	0.000	0.000	0.000	0.000
63	A	64	LYS	1	0.792	0.856	2.337	0.995	1.471	1.016	-0.610	-0.881	0.005
64	A	65	ILE	0	0.041	0.021	8.360	-0.010	-0.010	0.000	0.000	0.000	0.000
65	A	66	THR	0	0.031	0.022	10.305	0.017	0.017	0.000	0.000	0.000	0.000
66	A	67	TRP	0	-0.021	-0.021	11.413	0.031	0.031	0.000	0.000	0.000	0.000
67	A	68	LEU	0	-0.020	0.000	7.446	0.007	0.007	0.000	0.000	0.000	0.000
68	A	69	GLY	0	-0.011	0.006	11.556	0.029	0.029	0.000	0.000	0.000	0.000
69	A	70	GLU	-1	-0.859	-0.942	11.249	0.132	0.132	0.000	0.000	0.000	0.000
70	A	71	THR	0	-0.031	-0.010	11.946	0.021	0.021	0.000	0.000	0.000	0.000
71	A	72	LEU	0	-0.019	0.023	4.821	0.001	0.001	0.000	0.000	0.000	0.000
72	A	73	GLN	0	0.080	0.028	6.616	-0.075	-0.075	0.000	0.000	0.000	0.000
73	A	74	ALA	0	0.036	0.021	7.701	0.181	0.181	0.000	0.000	0.000	0.000
74	A	75	THR	0	-0.014	-0.036	8.244	0.024	0.024	0.000	0.000	0.000	0.000
75	A	76	GLU	-1	-0.737	-0.885	2.299	-7.839	-5.908	4.877	-3.701	-3.107	-0.037
76	A	77	LEU	0	-0.034	0.001	5.797	0.333	0.333	0.000	0.000	0.000	0.000
77	A	78	VAL	0	0.048	0.014	8.314	-0.089	-0.089	0.000	0.000	0.000	0.000
78	A	79	LEU	0	-0.007	-0.012	7.306	-0.066	-0.066	0.000	0.000	0.000	0.000
79	A	80	LYS	1	0.907	0.960	5.328	-1.305	-1.273	-0.001	-0.003	-0.029	0.000
80	A	81	MET	0	-0.030	-0.025	8.739	-0.095	-0.095	0.000	0.000	0.000	0.000
81	A	82	LEU	0	-0.031	0.002	12.178	-0.051	-0.051	0.000	0.000	0.000	0.000
82	A	83	TYR	0	-0.047	-0.056	11.216	-0.048	-0.048	0.000	0.000	0.000	0.000
83	A	84	PRO	0	0.032	0.025	11.432	-0.103	-0.103	0.000	0.000	0.000	0.000
84	A	85	GLN	0	-0.025	-0.022	11.980	-0.036	-0.036	0.000	0.000	0.000	0.000
85	A	86	LEU	0	-0.053	-0.004	11.597	-0.037	-0.037	0.000	0.000	0.000	0.000
86	A	87	GLU	-1	-0.831	-0.914	10.623	-1.053	-1.053	0.000	0.000	0.000	0.000
87	A	88	GLN	0	0.036	0.006	5.503	-0.422	-0.422	0.000	0.000	0.000	0.000
88	A	89	LYS	1	0.927	0.947	8.971	0.648	0.648	0.000	0.000	0.000	0.000
89	A	90	ALA	0	0.019	0.004	12.168	0.092	0.092	0.000	0.000	0.000	0.000
90	A	91	LEU	0	0.059	0.034	6.800	0.083	0.083	0.000	0.000	0.000	0.000
91	A	92	ILE	0	-0.022	-0.010	9.323	0.100	0.100	0.000	0.000	0.000	0.000
92	A	93	LYS	1	0.834	0.919	11.154	0.409	0.409	0.000	0.000	0.000	0.000
93	A	94	ALA	0	0.034	0.033	12.045	0.062	0.062	0.000	0.000	0.000	0.000
94	A	95	TRP	0	0.014	-0.007	10.148	0.040	0.040	0.000	0.000	0.000	0.000
95	A	96	ALA	0	0.010	-0.012	12.289	0.062	0.062	0.000	0.000	0.000	0.000
96	A	97	ALA	0	-0.025	-0.008	15.310	0.041	0.041	0.000	0.000	0.000	0.000
97	A	98	HIS	0	0.058	0.041	14.219	0.023	0.023	0.000	0.000	0.000	0.000
98	A	99	VAL	0	-0.043	-0.005	14.878	0.027	0.027	0.000	0.000	0.000	0.000
99	A	100	GLU	-1	-0.781	-0.882	17.563	-0.123	-0.123	0.000	0.000	0.000	0.000
100	A	101	ASP	-1	-0.826	-0.878	20.270	-0.059	-0.059	0.000	0.000	0.000	0.000
101	A	102	GLY	0	0.075	0.036	20.278	0.013	0.013	0.000	0.000	0.000	0.000
102	A	103	ILE	0	-0.100	-0.054	21.483	0.014	0.014	0.000	0.000	0.000	0.000
103	A	104	ALA	0	-0.017	-0.009	23.379	0.006	0.006	0.000	0.000	0.000	0.000
104	A	105	ALA	0	-0.033	0.004	25.220	0.006	0.006	0.000	0.000	0.000	0.000
105	A	106	LEU	0	-0.057	-0.030	25.869	0.007	0.007	0.000	0.000	0.000	0.000
106	A	107	ARG	1	0.859	0.926	27.419	0.061	0.061	0.000	0.000	0.000	0.000
107	A	108	ASN	0	0.037	0.029	31.896	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)