FMO DATABASE

FMODB ID: 669JZ

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	OptH
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	-859344.154329
FMO2-HF: Nuclear repulsion	817054.578514
FMO2-HF: Total energy	-42289.575814
FMO2-MP2: Total energy	-42413.854212

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.
-11.531	-3.807	3.79	-5.752	-5.761	-0.036

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 : -0.065

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	0.009	0.017	3.071	-0.763	2.171	0.013	-1.499	-1.448	0.006
4	A	5	PRO	0	0.033	0.027	3.265	-0.318	0.377	0.064	-0.309	-0.449	-0.003
5	A	6	ASN	0	0.046	0.006	5.319	-0.085	-0.085	0.000	0.000	0.000	0.000
6	A	7	ARG	1	0.951	0.991	6.522	-0.365	-0.365	0.000	0.000	0.000	0.000
7	A	8	MET	0	-0.013	0.007	7.116	-0.025	-0.025	0.000	0.000	0.000	0.000
8	A	9	ALA	0	0.053	0.035	11.617	0.016	0.016	0.000	0.000	0.000	0.000
9	A	10	LEU	0	0.021	0.025	15.154	-0.020	-0.020	0.000	0.000	0.000	0.000
10	A	11	SER	0	0.033	0.012	17.392	0.009	0.009	0.000	0.000	0.000	0.000
11	A	12	ARG	1	1.019	1.011	20.769	0.017	0.017	0.000	0.000	0.000	0.000
12	A	13	GLN	0	-0.016	-0.014	23.922	-0.002	-0.002	0.000	0.000	0.000	0.000
13	A	14	THR	0	0.025	0.001	19.396	0.004	0.004	0.000	0.000	0.000	0.000
14	A	15	GLU	-1	-0.805	-0.909	20.405	-0.015	-0.015	0.000	0.000	0.000	0.000
15	A	16	ASP	-1	-0.956	-0.985	22.733	-0.014	-0.014	0.000	0.000	0.000	0.000
16	A	17	GLN	0	0.042	0.017	24.845	0.004	0.004	0.000	0.000	0.000	0.000
17	A	18	LEU	0	0.004	0.009	19.521	0.001	0.001	0.000	0.000	0.000	0.000
18	A	19	LYS	1	0.939	0.971	24.012	0.012	0.012	0.000	0.000	0.000	0.000
19	A	20	LYS	1	0.915	0.960	26.673	0.018	0.018	0.000	0.000	0.000	0.000
20	A	21	LEU	0	0.057	0.040	24.245	0.001	0.001	0.000	0.000	0.000	0.000
21	A	22	LYS	1	0.945	0.995	25.604	0.011	0.011	0.000	0.000	0.000	0.000
22	A	23	GLY	0	-0.060	-0.018	27.875	0.002	0.002	0.000	0.000	0.000	0.000
23	A	24	TYR	0	0.002	0.004	31.222	0.001	0.001	0.000	0.000	0.000	0.000
24	A	25	THR	0	-0.035	-0.029	28.122	0.000	0.000	0.000	0.000	0.000	0.000
25	A	26	GLY	0	0.041	0.015	29.170	0.001	0.001	0.000	0.000	0.000	0.000
26	A	27	ILE	0	-0.047	-0.026	23.120	0.000	0.000	0.000	0.000	0.000	0.000
27	A	28	THR	0	0.024	0.005	21.137	0.000	0.000	0.000	0.000	0.000	0.000
28	A	29	PRO	0	0.052	0.009	20.647	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	30	ASN	0	-0.006	-0.022	16.283	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	31	ILE	0	0.020	0.026	16.900	-0.011	-0.011	0.000	0.000	0.000	0.000
31	A	32	ALA	0	0.014	0.001	19.064	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	33	ALA	0	0.017	0.009	15.994	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	34	ARG	1	0.856	0.936	13.996	0.062	0.062	0.000	0.000	0.000	0.000
34	A	35	LEU	0	0.002	-0.008	15.923	0.001	0.001	0.000	0.000	0.000	0.000
35	A	36	ALA	0	-0.038	-0.003	18.855	0.003	0.003	0.000	0.000	0.000	0.000
36	A	37	PHE	0	0.034	0.007	11.559	-0.008	-0.008	0.000	0.000	0.000	0.000
37	A	38	PHE	0	0.006	-0.019	12.456	0.002	0.002	0.000	0.000	0.000	0.000
38	A	39	ARG	1	0.940	0.977	17.290	0.037	0.037	0.000	0.000	0.000	0.000
39	A	40	SER	0	-0.029	-0.031	18.204	0.000	0.000	0.000	0.000	0.000	0.000
40	A	41	VAL	0	-0.052	-0.020	14.349	0.004	0.004	0.000	0.000	0.000	0.000
41	A	42	GLU	-1	-1.009	-0.982	17.760	-0.012	-0.012	0.000	0.000	0.000	0.000
42	A	43	SER	0	-0.024	-0.025	20.555	0.002	0.002	0.000	0.000	0.000	0.000
43	A	44	GLU	-1	-0.940	-0.983	22.068	-0.022	-0.022	0.000	0.000	0.000	0.000
44	A	45	PHE	0	-0.014	0.015	18.486	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	46	ARG	1	0.881	0.923	17.960	0.030	0.030	0.000	0.000	0.000	0.000
46	A	47	TYR	0	-0.078	-0.046	16.106	-0.008	-0.008	0.000	0.000	0.000	0.000
47	A	48	SER	0	-0.027	-0.083	18.274	0.002	0.002	0.000	0.000	0.000	0.000
48	A	49	PRO	0	-0.011	0.005	17.717	0.001	0.001	0.000	0.000	0.000	0.000
49	A	50	GLU	-1	-0.817	-0.850	19.497	-0.063	-0.063	0.000	0.000	0.000	0.000
50	A	51	ARG	1	0.864	0.921	22.450	0.061	0.061	0.000	0.000	0.000	0.000
51	A	52	ASP	-1	-0.750	-0.873	18.889	-0.099	-0.099	0.000	0.000	0.000	0.000
52	A	53	SER	0	-0.071	-0.061	22.425	0.000	0.000	0.000	0.000	0.000	0.000
53	A	54	LYS	1	0.908	0.990	20.829	0.058	0.058	0.000	0.000	0.000	0.000
54	A	55	LYS	1	0.927	0.955	20.692	0.045	0.045	0.000	0.000	0.000	0.000
55	A	56	LEU	0	-0.036	-0.017	15.357	0.002	0.002	0.000	0.000	0.000	0.000
56	A	57	ASP	-1	-0.850	-0.927	19.127	-0.025	-0.025	0.000	0.000	0.000	0.000
57	A	58	GLY	0	-0.042	-0.009	20.053	0.004	0.004	0.000	0.000	0.000	0.000
58	A	59	THR	0	-0.042	-0.031	20.837	0.005	0.005	0.000	0.000	0.000	0.000
59	A	60	LEU	0	-0.014	-0.007	18.334	0.008	0.008	0.000	0.000	0.000	0.000
60	A	61	VAL	0	-0.035	-0.009	13.549	-0.009	-0.009	0.000	0.000	0.000	0.000
61	A	62	LEU	0	-0.007	-0.005	14.209	0.022	0.022	0.000	0.000	0.000	0.000
62	A	63	ASP	-1	-0.875	-0.948	10.576	0.142	0.142	0.000	0.000	0.000	0.000
63	A	64	LYS	1	0.846	0.907	2.489	-0.061	0.325	0.591	-0.328	-0.649	0.002
64	A	65	ILE	0	0.040	0.020	8.403	-0.058	-0.058	0.000	0.000	0.000	0.000
65	A	66	THR	0	0.040	0.026	10.253	-0.011	-0.011	0.000	0.000	0.000	0.000
66	A	67	TRP	0	-0.017	-0.013	11.288	-0.010	-0.010	0.000	0.000	0.000	0.000
67	A	68	LEU	0	0.002	0.013	7.394	0.000	0.000	0.000	0.000	0.000	0.000
68	A	69	GLY	0	0.005	0.017	11.525	0.015	0.015	0.000	0.000	0.000	0.000
69	A	70	GLU	-1	-0.871	-0.949	11.405	-0.114	-0.114	0.000	0.000	0.000	0.000
70	A	71	THR	0	-0.087	-0.045	12.203	-0.005	-0.005	0.000	0.000	0.000	0.000
71	A	72	LEU	0	-0.010	0.015	5.251	0.018	0.018	0.000	0.000	0.000	0.000
72	A	73	GLN	0	0.087	0.033	6.575	-0.026	-0.026	0.000	0.000	0.000	0.000
73	A	74	ALA	0	0.033	0.020	7.663	0.181	0.181	0.000	0.000	0.000	0.000
74	A	75	THR	0	-0.003	-0.017	8.321	0.066	0.066	0.000	0.000	0.000	0.000
75	A	76	GLU	-1	-0.825	-0.956	2.429	-9.176	-5.490	3.123	-3.614	-3.195	-0.041
76	A	77	LEU	0	-0.040	-0.003	5.827	0.362	0.362	0.000	0.000	0.000	0.000
77	A	78	VAL	0	0.043	0.012	8.368	-0.034	-0.034	0.000	0.000	0.000	0.000
78	A	79	LEU	0	0.000	-0.011	7.493	-0.021	-0.021	0.000	0.000	0.000	0.000
79	A	80	LYS	1	0.922	0.971	5.379	-1.296	-1.273	-0.001	-0.002	-0.020	0.000
80	A	81	MET	0	-0.037	-0.029	8.792	-0.073	-0.073	0.000	0.000	0.000	0.000
81	A	82	LEU	0	-0.031	-0.001	12.222	-0.034	-0.034	0.000	0.000	0.000	0.000
82	A	83	TYR	0	-0.056	-0.054	11.208	-0.025	-0.025	0.000	0.000	0.000	0.000
83	A	84	PRO	0	0.028	0.025	11.460	-0.058	-0.058	0.000	0.000	0.000	0.000
84	A	85	GLN	0	-0.018	-0.023	11.980	-0.033	-0.033	0.000	0.000	0.000	0.000
85	A	86	LEU	0	-0.055	-0.002	11.586	-0.014	-0.014	0.000	0.000	0.000	0.000
86	A	87	GLU	-1	-0.834	-0.916	10.032	-0.485	-0.485	0.000	0.000	0.000	0.000
87	A	88	GLN	0	0.031	0.006	5.556	0.056	0.056	0.000	0.000	0.000	0.000
88	A	89	LYS	1	0.924	0.944	8.662	0.208	0.208	0.000	0.000	0.000	0.000
89	A	90	ALA	0	0.012	0.000	12.195	0.045	0.045	0.000	0.000	0.000	0.000
90	A	91	LEU	0	0.065	0.039	6.487	0.040	0.040	0.000	0.000	0.000	0.000
91	A	92	ILE	0	-0.031	-0.014	9.478	0.051	0.051	0.000	0.000	0.000	0.000
92	A	93	LYS	1	0.900	0.964	11.126	0.163	0.163	0.000	0.000	0.000	0.000
93	A	94	ALA	0	0.043	0.038	12.074	0.026	0.026	0.000	0.000	0.000	0.000
94	A	95	TRP	0	0.011	-0.005	10.135	0.023	0.023	0.000	0.000	0.000	0.000
95	A	96	ALA	0	-0.004	-0.021	12.277	0.030	0.030	0.000	0.000	0.000	0.000
96	A	97	ALA	0	-0.003	0.004	15.287	0.018	0.018	0.000	0.000	0.000	0.000
97	A	98	HIS	0	0.057	0.050	14.368	0.010	0.010	0.000	0.000	0.000	0.000
98	A	99	VAL	0	-0.055	-0.012	14.884	0.012	0.012	0.000	0.000	0.000	0.000
99	A	100	GLU	-1	-0.954	-0.997	17.547	-0.045	-0.045	0.000	0.000	0.000	0.000
100	A	101	ASP	-1	-0.832	-0.884	20.282	-0.036	-0.036	0.000	0.000	0.000	0.000
101	A	102	GLY	0	0.061	0.028	20.273	0.006	0.006	0.000	0.000	0.000	0.000
102	A	103	ILE	0	-0.103	-0.059	21.478	0.006	0.006	0.000	0.000	0.000	0.000
103	A	104	ALA	0	-0.001	0.003	23.364	0.004	0.004	0.000	0.000	0.000	0.000
104	A	105	ALA	0	-0.028	0.004	25.215	0.003	0.003	0.000	0.000	0.000	0.000
105	A	106	LEU	0	-0.070	-0.036	25.464	0.002	0.002	0.000	0.000	0.000	0.000
106	A	107	ARG	1	0.867	0.933	27.342	0.028	0.028	0.000	0.000	0.000	0.000
107	A	108	ASN	0	0.029	0.025	31.883	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)