FMO DATABASE

FMODB ID: LZVZ9

Calculation Name: 4J4E-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4J4E

Chain ID: C

ChEMBL ID:

UniProt ID: P81180

Base Structure: X-ray

Registration Date: 2023-06-22

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	99
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-554754.352097
FMO2-HF: Nuclear repulsion	515530.963133
FMO2-HF: Total energy	-39223.388964
FMO2-MP2: Total energy	-39335.46308

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(C:1:LEU)

Summations of interaction energy for fragment #1(C:1:LEU)

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.
-1.57	1.296	0.919	-1.259	-2.526	0.003

Interaction energy analysis for fragmet #1(C:1:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.027 / q_NPA : -0.013

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	C	3	LYS	1	0.947	0.968	2.238	-1.572	1.294	0.919	-1.259	-2.526	0.003
4	C	4	PHE	0	0.081	0.033	6.284	0.321	0.321	0.000	0.000	0.000	0.000
5	C	5	SER	0	0.049	0.032	9.106	0.084	0.084	0.000	0.000	0.000	0.000
6	C	6	GLN	0	-0.021	0.001	8.132	-0.171	-0.171	0.000	0.000	0.000	0.000
7	C	7	THR	0	-0.063	-0.028	10.913	0.185	0.185	0.000	0.000	0.000	0.000
8	C	8	CYS	0	-0.115	-0.017	12.908	-0.021	-0.021	0.000	0.000	0.000	0.000
9	C	9	TYR	0	0.019	0.012	14.829	-0.052	-0.052	0.000	0.000	0.000	0.000
10	C	10	ASN	0	-0.038	-0.031	18.327	-0.015	-0.015	0.000	0.000	0.000	0.000
11	C	11	SER	0	0.004	-0.026	16.206	0.001	0.001	0.000	0.000	0.000	0.000
12	C	12	ALA	0	0.004	0.004	18.207	-0.012	-0.012	0.000	0.000	0.000	0.000
13	C	13	ILE	0	0.014	0.005	15.576	-0.003	-0.003	0.000	0.000	0.000	0.000
14	C	14	GLN	0	0.007	0.014	19.665	0.007	0.007	0.000	0.000	0.000	0.000
15	C	15	GLY	0	0.021	0.013	22.199	0.001	0.001	0.000	0.000	0.000	0.000
16	C	16	SER	0	0.008	-0.009	18.930	-0.010	-0.010	0.000	0.000	0.000	0.000
17	C	17	VAL	0	0.001	0.013	17.917	-0.018	-0.018	0.000	0.000	0.000	0.000
18	C	18	LEU	0	0.006	0.016	12.717	0.002	0.002	0.000	0.000	0.000	0.000
19	C	19	THR	0	0.007	-0.011	16.923	0.027	0.027	0.000	0.000	0.000	0.000
20	C	20	SER	0	0.032	0.015	15.516	-0.023	-0.023	0.000	0.000	0.000	0.000
21	C	21	THR	0	-0.006	0.009	17.655	0.009	0.009	0.000	0.000	0.000	0.000
22	C	23	GLU	-1	-0.807	-0.913	15.106	0.394	0.394	0.000	0.000	0.000	0.000
23	C	24	ARG	1	0.888	0.941	14.972	-0.225	-0.225	0.000	0.000	0.000	0.000
24	C	25	THR	0	0.032	0.016	13.372	-0.007	-0.007	0.000	0.000	0.000	0.000
25	C	26	ASN	0	0.005	-0.003	16.049	0.002	0.002	0.000	0.000	0.000	0.000
26	C	27	GLY	0	-0.027	-0.018	19.821	-0.031	-0.031	0.000	0.000	0.000	0.000
27	C	28	GLY	0	0.009	0.018	21.361	0.006	0.006	0.000	0.000	0.000	0.000
28	C	29	TYR	0	0.003	-0.006	19.138	0.017	0.017	0.000	0.000	0.000	0.000
29	C	30	ASN	0	-0.036	-0.022	17.788	-0.037	-0.037	0.000	0.000	0.000	0.000
30	C	31	THR	0	-0.004	0.003	18.346	0.022	0.022	0.000	0.000	0.000	0.000
31	C	32	SER	0	-0.063	-0.017	15.883	-0.001	-0.001	0.000	0.000	0.000	0.000
32	C	33	SER	0	0.027	-0.008	17.242	-0.008	-0.008	0.000	0.000	0.000	0.000
33	C	34	ILE	0	0.001	0.006	11.779	0.016	0.016	0.000	0.000	0.000	0.000
34	C	35	ASP	-1	-0.829	-0.905	15.906	-0.129	-0.129	0.000	0.000	0.000	0.000
35	C	36	LEU	0	0.008	-0.002	12.507	-0.024	-0.024	0.000	0.000	0.000	0.000
36	C	37	ASN	0	0.054	0.025	15.700	-0.047	-0.047	0.000	0.000	0.000	0.000
37	C	38	SER	0	-0.055	-0.021	17.183	-0.020	-0.020	0.000	0.000	0.000	0.000
38	C	39	VAL	0	-0.010	-0.006	11.360	-0.011	-0.011	0.000	0.000	0.000	0.000
39	C	40	ILE	0	-0.003	0.007	12.067	-0.076	-0.076	0.000	0.000	0.000	0.000
40	C	41	GLU	-1	-0.929	-0.953	14.735	-0.210	-0.210	0.000	0.000	0.000	0.000
41	C	42	ASN	0	0.003	-0.027	16.841	-0.034	-0.034	0.000	0.000	0.000	0.000
42	C	43	VAL	0	-0.037	-0.029	17.264	0.017	0.017	0.000	0.000	0.000	0.000
43	C	44	ASP	-1	-0.896	-0.972	20.091	-0.170	-0.170	0.000	0.000	0.000	0.000
44	C	45	GLY	0	0.063	0.045	22.197	0.006	0.006	0.000	0.000	0.000	0.000
45	C	46	SER	0	-0.079	-0.037	17.175	-0.010	-0.010	0.000	0.000	0.000	0.000
46	C	47	LEU	0	0.042	0.020	14.703	-0.004	-0.004	0.000	0.000	0.000	0.000
47	C	48	LYS	1	0.902	0.956	12.849	0.319	0.319	0.000	0.000	0.000	0.000
48	C	49	TRP	0	0.031	0.031	7.571	0.006	0.006	0.000	0.000	0.000	0.000
49	C	50	GLN	0	-0.027	-0.026	10.880	0.012	0.012	0.000	0.000	0.000	0.000
50	C	51	GLY	0	0.054	0.023	13.144	0.041	0.041	0.000	0.000	0.000	0.000
51	C	52	SER	0	-0.078	-0.030	15.657	-0.004	-0.004	0.000	0.000	0.000	0.000
52	C	53	ASN	0	0.041	-0.006	18.303	0.009	0.009	0.000	0.000	0.000	0.000
53	C	54	PHE	0	-0.010	-0.002	17.008	0.016	0.016	0.000	0.000	0.000	0.000
54	C	55	ILE	0	-0.004	-0.008	20.242	0.008	0.008	0.000	0.000	0.000	0.000
55	C	56	GLU	-1	-0.919	-0.941	22.448	-0.085	-0.085	0.000	0.000	0.000	0.000
56	C	57	THR	0	-0.119	-0.053	23.598	0.004	0.004	0.000	0.000	0.000	0.000
57	C	58	CYS	0	-0.078	-0.023	20.814	-0.008	-0.008	0.000	0.000	0.000	0.000
58	C	59	ARG	1	0.922	0.962	23.679	0.103	0.103	0.000	0.000	0.000	0.000
59	C	60	ASN	0	-0.056	-0.050	23.960	-0.003	-0.003	0.000	0.000	0.000	0.000
60	C	61	THR	0	-0.027	-0.017	20.005	-0.002	-0.002	0.000	0.000	0.000	0.000
61	C	62	GLN	0	0.001	-0.004	20.052	0.025	0.025	0.000	0.000	0.000	0.000
62	C	63	LEU	0	-0.015	-0.005	14.931	-0.026	-0.026	0.000	0.000	0.000	0.000
63	C	64	ALA	0	-0.007	0.008	16.672	0.022	0.022	0.000	0.000	0.000	0.000
64	C	65	GLY	0	0.022	0.002	15.803	-0.021	-0.021	0.000	0.000	0.000	0.000
65	C	66	SER	0	-0.011	-0.020	13.964	0.014	0.014	0.000	0.000	0.000	0.000
66	C	67	SER	0	-0.004	-0.021	10.013	0.039	0.039	0.000	0.000	0.000	0.000
67	C	68	GLU	-1	-0.976	-0.963	11.249	-0.364	-0.364	0.000	0.000	0.000	0.000
68	C	69	LEU	0	-0.017	0.008	13.066	0.048	0.048	0.000	0.000	0.000	0.000
69	C	70	ALA	0	0.000	-0.003	14.968	-0.023	-0.023	0.000	0.000	0.000	0.000
70	C	71	ALA	0	0.018	-0.008	18.069	0.016	0.016	0.000	0.000	0.000	0.000
71	C	72	GLU	-1	-0.859	-0.903	20.744	-0.105	-0.105	0.000	0.000	0.000	0.000
72	C	74	LYS	1	0.950	0.970	23.476	0.106	0.106	0.000	0.000	0.000	0.000
73	C	75	THR	0	0.030	0.026	24.904	-0.009	-0.009	0.000	0.000	0.000	0.000
74	C	76	ARG	1	0.916	0.946	22.515	0.186	0.186	0.000	0.000	0.000	0.000
75	C	77	ALA	0	-0.017	0.001	27.894	0.006	0.006	0.000	0.000	0.000	0.000
76	C	78	GLN	0	0.006	0.011	31.311	0.000	0.000	0.000	0.000	0.000	0.000
77	C	79	GLN	0	0.011	-0.015	34.325	0.000	0.000	0.000	0.000	0.000	0.000
78	C	80	PHE	0	-0.012	0.002	36.616	-0.001	-0.001	0.000	0.000	0.000	0.000
79	C	81	VAL	0	0.007	0.006	35.918	0.001	0.001	0.000	0.000	0.000	0.000
80	C	82	SER	0	-0.028	-0.019	39.315	0.001	0.001	0.000	0.000	0.000	0.000
81	C	83	THR	0	0.011	0.008	40.535	-0.003	-0.003	0.000	0.000	0.000	0.000
82	C	84	LYS	1	0.931	0.957	42.412	0.059	0.059	0.000	0.000	0.000	0.000
83	C	85	ILE	0	0.048	0.022	43.692	-0.003	-0.003	0.000	0.000	0.000	0.000
84	C	86	ASN	0	0.010	0.006	45.959	0.003	0.003	0.000	0.000	0.000	0.000
85	C	87	LEU	0	0.015	0.005	48.849	0.000	0.000	0.000	0.000	0.000	0.000
86	C	88	ASP	-1	-0.869	-0.945	51.398	-0.043	-0.043	0.000	0.000	0.000	0.000
87	C	89	ASP	-1	-0.998	-0.977	46.884	-0.057	-0.057	0.000	0.000	0.000	0.000
88	C	90	HIS	0	-0.070	-0.043	47.489	-0.002	-0.002	0.000	0.000	0.000	0.000
89	C	91	ILE	0	-0.070	-0.016	51.662	0.001	0.001	0.000	0.000	0.000	0.000
90	C	92	ALA	0	0.076	0.050	54.718	0.000	0.000	0.000	0.000	0.000	0.000
91	C	93	ASN	0	-0.022	-0.022	57.998	0.001	0.001	0.000	0.000	0.000	0.000
92	C	94	ILE	0	-0.005	-0.011	59.939	0.001	0.001	0.000	0.000	0.000	0.000
93	C	95	ASP	-1	-0.944	-0.976	63.285	-0.028	-0.028	0.000	0.000	0.000	0.000
94	C	96	GLY	0	0.009	0.004	66.015	0.001	0.001	0.000	0.000	0.000	0.000
95	C	97	THR	0	-0.071	-0.031	62.547	0.000	0.000	0.000	0.000	0.000	0.000
96	C	98	LEU	0	-0.029	-0.011	58.695	-0.001	-0.001	0.000	0.000	0.000	0.000
97	C	99	LYS	1	0.928	0.957	58.078	0.035	0.035	0.000	0.000	0.000	0.000
98	C	100	TYR	0	-0.001	0.016	48.114	0.000	0.000	0.000	0.000	0.000	0.000
99	C	101	GLU	-1	-0.934	-0.969	51.584	-0.041	-0.041	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:1:LEU)