FMO DATABASE

FMODB ID: LNR99

Calculation Name: 4ZM8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ZM8

Chain ID: A

ChEMBL ID:

UniProt ID: Q8MVB6

Base Structure: X-ray

Registration Date: 2023-09-23

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	109
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-635799.106706
FMO2-HF: Nuclear repulsion	592691.392574
FMO2-HF: Total energy	-43107.714132
FMO2-MP2: Total energy	-43231.830037

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:4:PHE)

Summations of interaction energy for fragment #1(A:4:PHE)

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.
-3.767	-0.779	0.01	-1.281	-1.717	0.003

Interaction energy analysis for fragmet #1(A:4:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.039 / 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	6	GLY	0	0.033	0.016	3.446	-4.182	-1.528	0.011	-1.240	-1.425	0.003
4	A	7	TYR	0	-0.032	-0.014	4.455	2.578	2.800	0.000	-0.024	-0.198	0.000
5	A	8	SER	0	-0.016	0.010	4.423	-0.517	-0.405	-0.001	-0.017	-0.094	0.000
6	A	9	GLU	-1	-0.911	-0.972	6.139	0.055	0.055	0.000	0.000	0.000	0.000
7	A	10	ARG	1	0.922	0.955	8.178	-1.254	-1.254	0.000	0.000	0.000	0.000
8	A	11	ALA	0	-0.002	-0.003	12.450	-0.045	-0.045	0.000	0.000	0.000	0.000
9	A	12	ASN	0	-0.048	0.002	15.115	-0.054	-0.054	0.000	0.000	0.000	0.000
10	A	13	HIS	0	0.009	-0.008	16.169	0.058	0.058	0.000	0.000	0.000	0.000
11	A	14	GLN	0	0.051	0.008	17.802	0.000	0.000	0.000	0.000	0.000	0.000
12	A	15	ALA	0	-0.029	0.000	21.086	-0.011	-0.011	0.000	0.000	0.000	0.000
13	A	16	ASN	0	-0.015	-0.002	18.303	-0.008	-0.008	0.000	0.000	0.000	0.000
14	A	17	PRO	0	0.060	0.016	20.917	0.004	0.004	0.000	0.000	0.000	0.000
15	A	18	GLU	-1	-0.890	-0.945	19.427	0.323	0.323	0.000	0.000	0.000	0.000
16	A	19	PHE	0	-0.021	-0.013	14.467	0.024	0.024	0.000	0.000	0.000	0.000
17	A	20	LEU	0	0.008	0.020	19.613	-0.017	-0.017	0.000	0.000	0.000	0.000
18	A	21	ASN	0	0.017	-0.010	23.121	-0.030	-0.030	0.000	0.000	0.000	0.000
19	A	22	LEU	0	0.014	0.006	18.006	-0.014	-0.014	0.000	0.000	0.000	0.000
20	A	23	ALA	0	0.006	0.019	21.623	-0.014	-0.014	0.000	0.000	0.000	0.000
21	A	24	HIS	0	0.027	0.023	22.852	-0.026	-0.026	0.000	0.000	0.000	0.000
22	A	25	TYR	0	0.002	0.022	23.495	-0.013	-0.013	0.000	0.000	0.000	0.000
23	A	26	ALA	0	0.007	0.017	22.286	-0.015	-0.015	0.000	0.000	0.000	0.000
24	A	27	THR	0	-0.019	-0.022	24.430	-0.018	-0.018	0.000	0.000	0.000	0.000
25	A	28	SER	0	-0.051	-0.028	26.925	-0.016	-0.016	0.000	0.000	0.000	0.000
26	A	29	THR	0	-0.029	-0.045	27.139	-0.014	-0.014	0.000	0.000	0.000	0.000
27	A	30	TRP	0	-0.024	-0.004	26.312	-0.009	-0.009	0.000	0.000	0.000	0.000
28	A	31	SER	0	0.006	-0.027	28.434	-0.013	-0.013	0.000	0.000	0.000	0.000
29	A	32	ALA	0	0.006	0.013	31.310	-0.009	-0.009	0.000	0.000	0.000	0.000
30	A	33	GLN	0	-0.045	-0.022	29.347	-0.008	-0.008	0.000	0.000	0.000	0.000
31	A	34	GLN	0	-0.064	-0.007	30.709	-0.012	-0.012	0.000	0.000	0.000	0.000
32	A	35	PRO	0	0.030	0.024	33.968	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	36	GLY	0	-0.022	-0.013	37.113	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	37	LYS	1	0.917	0.946	33.586	-0.062	-0.062	0.000	0.000	0.000	0.000
35	A	38	THR	0	0.011	0.002	37.893	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	39	HIS	0	-0.041	-0.007	37.911	0.001	0.001	0.000	0.000	0.000	0.000
37	A	40	PHE	0	-0.019	-0.003	33.461	0.000	0.000	0.000	0.000	0.000	0.000
38	A	41	ASP	-1	-0.882	-0.930	30.337	0.075	0.075	0.000	0.000	0.000	0.000
39	A	42	THR	0	-0.012	-0.038	30.041	0.009	0.009	0.000	0.000	0.000	0.000
40	A	43	VAL	0	-0.031	-0.012	25.124	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	44	ALA	0	-0.039	-0.002	27.931	-0.004	-0.004	0.000	0.000	0.000	0.000
42	A	45	GLU	-1	-0.922	-0.984	23.973	0.116	0.116	0.000	0.000	0.000	0.000
43	A	46	VAL	0	-0.018	0.000	19.608	0.002	0.002	0.000	0.000	0.000	0.000
44	A	47	VAL	0	0.030	0.020	19.532	0.006	0.006	0.000	0.000	0.000	0.000
45	A	48	LYS	1	0.949	0.967	13.321	-0.121	-0.121	0.000	0.000	0.000	0.000
46	A	49	VAL	0	0.013	0.004	13.632	0.008	0.008	0.000	0.000	0.000	0.000
47	A	50	GLU	-1	-0.914	-0.955	9.488	0.344	0.344	0.000	0.000	0.000	0.000
48	A	51	THR	0	-0.057	-0.021	9.282	0.026	0.026	0.000	0.000	0.000	0.000
49	A	52	GLN	0	0.060	-0.004	7.069	0.316	0.316	0.000	0.000	0.000	0.000
50	A	53	VAL	0	-0.032	-0.001	6.932	-0.469	-0.469	0.000	0.000	0.000	0.000
51	A	54	VAL	0	0.020	0.013	8.125	0.038	0.038	0.000	0.000	0.000	0.000
52	A	55	ALA	0	-0.007	-0.008	10.130	-0.059	-0.059	0.000	0.000	0.000	0.000
53	A	56	GLY	0	0.036	0.000	11.635	-0.024	-0.024	0.000	0.000	0.000	0.000
54	A	57	THR	0	-0.046	0.004	14.384	0.012	0.012	0.000	0.000	0.000	0.000
55	A	58	ASN	0	0.021	-0.001	18.092	-0.033	-0.033	0.000	0.000	0.000	0.000
56	A	59	TYR	0	-0.004	0.004	17.851	0.000	0.000	0.000	0.000	0.000	0.000
57	A	60	ARG	1	0.945	0.975	23.067	-0.085	-0.085	0.000	0.000	0.000	0.000
58	A	61	LEU	0	-0.015	-0.012	24.634	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	62	THR	0	0.014	0.003	28.389	0.000	0.000	0.000	0.000	0.000	0.000
60	A	63	LEU	0	-0.029	-0.012	28.413	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	64	LYS	1	0.955	0.984	32.882	0.003	0.003	0.000	0.000	0.000	0.000
62	A	65	VAL	0	-0.003	-0.003	32.312	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	66	ALA	0	0.026	0.000	34.870	0.003	0.003	0.000	0.000	0.000	0.000
64	A	67	GLU	-1	-0.929	-0.953	35.247	-0.047	-0.047	0.000	0.000	0.000	0.000
65	A	68	SER	0	0.018	0.006	33.660	0.000	0.000	0.000	0.000	0.000	0.000
66	A	69	THR	0	-0.012	-0.023	35.688	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	70	CYS	0	-0.139	-0.043	31.032	0.001	0.001	0.000	0.000	0.000	0.000
68	A	71	GLU	-1	-0.836	-0.904	34.146	-0.066	-0.066	0.000	0.000	0.000	0.000
69	A	72	LEU	0	0.022	0.011	29.949	-0.006	-0.006	0.000	0.000	0.000	0.000
70	A	73	THR	0	-0.077	-0.026	29.835	-0.009	-0.009	0.000	0.000	0.000	0.000
71	A	74	SER	0	-0.041	-0.035	30.254	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	75	THR	0	-0.001	-0.003	25.126	-0.009	-0.009	0.000	0.000	0.000	0.000
73	A	76	TYR	0	0.034	0.012	25.754	0.007	0.007	0.000	0.000	0.000	0.000
74	A	77	ASN	0	0.069	0.004	26.203	-0.009	-0.009	0.000	0.000	0.000	0.000
75	A	78	LYS	1	0.951	0.996	23.833	0.094	0.094	0.000	0.000	0.000	0.000
76	A	79	ASP	-1	-0.911	-0.957	28.672	-0.066	-0.066	0.000	0.000	0.000	0.000
77	A	80	THR	0	-0.059	-0.030	31.137	0.002	0.002	0.000	0.000	0.000	0.000
78	A	82	LEU	0	0.026	0.014	32.920	0.003	0.003	0.000	0.000	0.000	0.000
79	A	83	PRO	0	-0.011	-0.014	35.185	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	84	LYS	1	0.953	0.970	37.307	0.040	0.040	0.000	0.000	0.000	0.000
81	A	85	ALA	0	-0.004	0.000	40.447	0.002	0.002	0.000	0.000	0.000	0.000
82	A	86	ASP	-1	-0.961	-0.965	43.494	-0.027	-0.027	0.000	0.000	0.000	0.000
83	A	87	ALA	0	-0.011	-0.003	40.286	0.001	0.001	0.000	0.000	0.000	0.000
84	A	88	ALA	0	0.011	0.002	42.143	0.002	0.002	0.000	0.000	0.000	0.000
85	A	89	HIS	0	-0.068	-0.039	39.251	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	90	ARG	1	0.972	0.979	34.648	0.032	0.032	0.000	0.000	0.000	0.000
87	A	91	THR	0	0.018	0.009	36.580	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	92	CYS	0	-0.157	-0.071	32.295	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	93	THR	0	0.034	0.005	30.192	0.003	0.003	0.000	0.000	0.000	0.000
90	A	94	THR	0	-0.001	0.009	25.947	-0.003	-0.003	0.000	0.000	0.000	0.000
91	A	95	VAL	0	-0.020	-0.018	22.550	0.008	0.008	0.000	0.000	0.000	0.000
92	A	96	VAL	0	0.010	0.007	19.432	-0.013	-0.013	0.000	0.000	0.000	0.000
93	A	97	PHE	0	0.000	0.018	13.256	0.023	0.023	0.000	0.000	0.000	0.000
94	A	98	GLU	-1	-0.916	-0.960	13.888	-0.072	-0.072	0.000	0.000	0.000	0.000
95	A	99	ASN	0	0.016	0.009	8.682	0.038	0.038	0.000	0.000	0.000	0.000
96	A	100	LEU	0	-0.002	-0.024	8.599	-0.048	-0.048	0.000	0.000	0.000	0.000
97	A	101	GLN	0	-0.062	-0.020	4.874	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	102	GLY	0	0.040	0.036	7.894	-0.146	-0.146	0.000	0.000	0.000	0.000
99	A	103	ASP	-1	-0.921	-0.963	8.480	-0.565	-0.565	0.000	0.000	0.000	0.000
100	A	104	LYS	1	0.918	0.952	11.826	0.245	0.245	0.000	0.000	0.000	0.000
101	A	105	SER	0	-0.044	-0.014	15.490	-0.033	-0.033	0.000	0.000	0.000	0.000
102	A	106	VAL	0	0.020	-0.002	18.040	0.019	0.019	0.000	0.000	0.000	0.000
103	A	107	SER	0	-0.036	0.011	21.809	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	108	PRO	0	0.043	-0.015	24.522	-0.007	-0.007	0.000	0.000	0.000	0.000
105	A	109	PHE	0	-0.027	-0.023	26.307	0.008	0.008	0.000	0.000	0.000	0.000
106	A	110	GLU	-1	-0.870	-0.911	29.898	0.004	0.004	0.000	0.000	0.000	0.000
107	A	112	GLU	-1	-0.893	-0.948	35.583	0.014	0.014	0.000	0.000	0.000	0.000
108	A	113	ALA	0	-0.034	-0.018	39.096	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	114	ALA	0	-0.012	0.007	42.119	-0.002	-0.002	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:4:PHE)