FMO DATABASE

FMODB ID: 3JJVL

Calculation Name: 5X5J-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5X5J

Chain ID: A

ChEMBL ID:

UniProt ID: Q6TA00

Base Structure: X-ray

Registration Date: 2023-09-21

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	120
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1046883.78118
FMO2-HF: Nuclear repulsion	999055.040138
FMO2-HF: Total energy	-47828.741042
FMO2-MP2: Total energy	-47967.561912

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:10:CYS)

Summations of interaction energy for fragment #1(A:10:CYS)

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.
-4.923	-0.639	5.268	-2.719	-6.833	-0.006

Interaction energy analysis for fragmet #1(A:10:CYS)

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 : -0.029

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

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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	12	ASP	-1	-0.928	-0.963	3.791	-0.799	0.424	0.000	-0.398	-0.825	0.002
4	A	13	LYS	1	0.812	0.926	2.676	0.742	1.654	0.686	-0.458	-1.140	-0.002
5	A	14	VAL	0	0.011	0.000	5.177	0.237	0.251	-0.001	-0.004	-0.008	0.000
6	A	15	ILE	0	-0.025	-0.015	4.919	0.042	0.042	0.000	0.000	0.000	0.000
7	A	16	LEU	0	-0.006	0.004	8.889	0.115	0.115	0.000	0.000	0.000	0.000
8	A	17	VAL	0	0.007	-0.004	11.827	0.008	0.008	0.000	0.000	0.000	0.000
9	A	18	VAL	0	-0.027	-0.019	14.166	0.022	0.022	0.000	0.000	0.000	0.000
10	A	19	GLH	0	-0.059	-0.077	17.686	0.009	0.009	0.000	0.000	0.000	0.000
11	A	20	ASP	-1	-0.842	-0.919	19.787	-0.055	-0.055	0.000	0.000	0.000	0.000
12	A	21	ASP	-1	-0.871	-0.909	22.590	-0.035	-0.035	0.000	0.000	0.000	0.000
13	A	22	TYR	0	0.024	-0.024	21.547	-0.004	-0.004	0.000	0.000	0.000	0.000
14	A	23	ASP	-1	-0.851	-0.908	21.050	-0.026	-0.026	0.000	0.000	0.000	0.000
15	A	24	ILE	0	-0.029	-0.027	18.640	0.004	0.004	0.000	0.000	0.000	0.000
16	A	25	GLY	0	-0.006	-0.012	17.111	0.000	0.000	0.000	0.000	0.000	0.000
17	A	26	ASP	-1	-0.791	-0.868	16.179	-0.052	-0.052	0.000	0.000	0.000	0.000
18	A	27	ILE	0	-0.070	-0.034	16.026	0.014	0.014	0.000	0.000	0.000	0.000
19	A	28	ILE	0	-0.007	-0.011	12.152	0.024	0.024	0.000	0.000	0.000	0.000
20	A	29	GLU	-1	-0.801	-0.883	11.819	-0.091	-0.091	0.000	0.000	0.000	0.000
21	A	30	ASN	0	-0.007	-0.004	11.711	0.030	0.030	0.000	0.000	0.000	0.000
22	A	31	TYR	0	0.004	-0.009	10.627	0.028	0.028	0.000	0.000	0.000	0.000
23	A	32	LEU	0	0.009	-0.004	6.881	0.128	0.128	0.000	0.000	0.000	0.000
24	A	33	LYS	1	0.878	0.929	6.970	0.201	0.201	0.000	0.000	0.000	0.000
25	A	34	ARG	1	0.806	0.916	8.888	-0.082	-0.082	0.000	0.000	0.000	0.000
26	A	35	GLU	-1	-0.911	-0.948	4.357	0.291	0.523	0.006	-0.040	-0.198	0.000
27	A	36	GLY	0	-0.011	-0.002	4.260	0.362	0.857	0.043	-0.197	-0.341	-0.001
28	A	37	MET	0	-0.059	-0.017	3.318	-2.513	-1.245	0.617	-0.400	-1.485	-0.003
29	A	38	SER	0	0.014	0.004	5.886	0.506	0.506	0.000	0.000	0.000	0.000
30	A	39	VAL	0	-0.029	-0.019	8.522	-0.113	-0.113	0.000	0.000	0.000	0.000
31	A	40	ILE	0	-0.008	0.005	11.094	0.061	0.061	0.000	0.000	0.000	0.000
32	A	41	ARG	1	0.813	0.882	14.208	0.074	0.074	0.000	0.000	0.000	0.000
33	A	42	ALA	0	-0.003	0.003	16.835	0.009	0.009	0.000	0.000	0.000	0.000
34	A	43	MET	0	0.021	0.007	19.317	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	44	ASN	0	0.013	0.001	22.291	0.005	0.005	0.000	0.000	0.000	0.000
36	A	45	GLY	0	0.070	0.023	22.361	-0.010	-0.010	0.000	0.000	0.000	0.000
37	A	46	LYS	1	0.829	0.897	23.188	0.059	0.059	0.000	0.000	0.000	0.000
38	A	47	GLN	0	0.031	0.020	21.806	-0.008	-0.008	0.000	0.000	0.000	0.000
39	A	48	ALA	0	0.028	0.016	18.898	-0.010	-0.010	0.000	0.000	0.000	0.000
40	A	49	ILE	0	-0.020	-0.014	19.206	-0.014	-0.014	0.000	0.000	0.000	0.000
41	A	50	GLU	-1	-0.927	-0.961	21.343	-0.100	-0.100	0.000	0.000	0.000	0.000
42	A	51	LEU	0	0.008	-0.002	17.501	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	52	HIS	0	0.014	-0.002	15.272	0.006	0.006	0.000	0.000	0.000	0.000
44	A	53	ALA	0	-0.101	-0.065	17.503	-0.006	-0.006	0.000	0.000	0.000	0.000
45	A	54	SER	0	-0.006	0.005	19.703	0.004	0.004	0.000	0.000	0.000	0.000
46	A	55	GLN	0	-0.042	-0.010	14.970	0.002	0.002	0.000	0.000	0.000	0.000
47	A	56	PRO	0	-0.005	-0.001	12.370	0.000	0.000	0.000	0.000	0.000	0.000
48	A	57	ILE	0	-0.035	-0.009	11.153	-0.071	-0.071	0.000	0.000	0.000	0.000
49	A	58	ASP	-1	-0.803	-0.892	6.965	-0.991	-0.991	0.000	0.000	0.000	0.000
50	A	59	LEU	0	-0.050	-0.029	7.366	0.039	0.039	0.000	0.000	0.000	0.000
51	A	60	ILE	0	-0.017	-0.005	9.484	0.009	0.009	0.000	0.000	0.000	0.000
52	A	61	LEU	0	-0.002	0.008	10.110	0.020	0.020	0.000	0.000	0.000	0.000
53	A	62	LEU	0	0.007	-0.012	13.260	0.012	0.012	0.000	0.000	0.000	0.000
54	A	63	ASP	-1	-0.739	-0.813	17.006	-0.064	-0.064	0.000	0.000	0.000	0.000
55	A	64	ILE	0	-0.005	-0.009	19.806	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	65	LYS	1	0.806	0.908	22.859	0.057	0.057	0.000	0.000	0.000	0.000
57	A	66	LEU	0	-0.021	-0.020	21.435	0.000	0.000	0.000	0.000	0.000	0.000
58	A	67	PRO	0	0.003	-0.002	25.465	0.003	0.003	0.000	0.000	0.000	0.000
59	A	68	GLU	-1	-0.817	-0.888	27.972	-0.063	-0.063	0.000	0.000	0.000	0.000
60	A	69	LEU	0	-0.043	-0.011	26.348	0.001	0.001	0.000	0.000	0.000	0.000
61	A	70	ASN	0	0.105	0.043	27.478	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	71	GLY	0	0.072	0.015	23.762	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	72	TRP	0	0.053	0.015	22.673	-0.015	-0.015	0.000	0.000	0.000	0.000
64	A	73	GLU	-1	-0.825	-0.907	24.650	-0.081	-0.081	0.000	0.000	0.000	0.000
65	A	74	VAL	0	-0.058	-0.008	20.974	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	75	LEU	0	0.000	0.011	18.362	-0.007	-0.007	0.000	0.000	0.000	0.000
67	A	76	ASN	0	-0.050	-0.039	21.330	-0.010	-0.010	0.000	0.000	0.000	0.000
68	A	77	LYS	1	0.941	0.961	24.338	0.080	0.080	0.000	0.000	0.000	0.000
69	A	78	ILE	0	-0.001	0.001	17.744	0.000	0.000	0.000	0.000	0.000	0.000
70	A	79	ARG	1	0.782	0.872	15.881	0.196	0.196	0.000	0.000	0.000	0.000
71	A	80	GLN	0	-0.041	-0.001	21.526	0.004	0.004	0.000	0.000	0.000	0.000
72	A	81	LYS	1	0.832	0.930	19.585	0.161	0.161	0.000	0.000	0.000	0.000
73	A	82	ALA	0	-0.009	-0.012	17.681	0.001	0.001	0.000	0.000	0.000	0.000
74	A	83	GLN	0	0.013	-0.007	17.566	0.002	0.002	0.000	0.000	0.000	0.000
75	A	84	THR	0	0.013	0.027	12.279	0.006	0.006	0.000	0.000	0.000	0.000
76	A	85	PRO	0	0.052	0.044	10.200	0.048	0.048	0.000	0.000	0.000	0.000
77	A	86	VAL	0	-0.032	-0.025	12.352	-0.024	-0.024	0.000	0.000	0.000	0.000
78	A	87	ILE	0	0.003	0.012	10.005	0.016	0.016	0.000	0.000	0.000	0.000
79	A	88	MET	0	-0.039	-0.006	13.880	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	89	LEU	0	0.008	0.002	14.832	0.010	0.010	0.000	0.000	0.000	0.000
81	A	90	THR	0	0.016	-0.028	18.510	0.004	0.004	0.000	0.000	0.000	0.000
82	A	91	ALA	0	0.044	0.017	22.033	0.003	0.003	0.000	0.000	0.000	0.000
83	A	92	LEU	0	-0.039	-0.024	24.038	0.003	0.003	0.000	0.000	0.000	0.000
84	A	93	ASP	-1	-0.853	-0.879	26.309	-0.036	-0.036	0.000	0.000	0.000	0.000
85	A	94	GLN	0	-0.076	-0.077	29.512	0.000	0.000	0.000	0.000	0.000	0.000
86	A	95	ASP	-1	-0.903	-0.945	29.033	-0.056	-0.056	0.000	0.000	0.000	0.000
87	A	96	ILE	0	-0.073	-0.047	26.226	-0.004	-0.004	0.000	0.000	0.000	0.000
88	A	97	ASP	-1	-0.861	-0.922	26.904	-0.066	-0.066	0.000	0.000	0.000	0.000
89	A	98	LYS	1	0.998	0.997	26.588	0.060	0.060	0.000	0.000	0.000	0.000
90	A	99	VAL	0	-0.022	-0.018	24.789	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	100	MET	0	-0.001	0.010	21.766	-0.010	-0.010	0.000	0.000	0.000	0.000
92	A	101	ALA	0	0.048	0.025	21.972	-0.008	-0.008	0.000	0.000	0.000	0.000
93	A	102	LEU	0	-0.091	-0.051	22.957	-0.005	-0.005	0.000	0.000	0.000	0.000
94	A	103	ARG	1	0.847	0.941	17.529	0.140	0.140	0.000	0.000	0.000	0.000
95	A	104	ILE	0	-0.026	0.022	17.684	-0.017	-0.017	0.000	0.000	0.000	0.000
96	A	105	GLY	0	0.009	0.000	19.155	0.012	0.012	0.000	0.000	0.000	0.000
97	A	106	ALA	0	-0.064	-0.054	14.331	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	107	ASP	-1	-0.817	-0.883	13.577	-0.259	-0.259	0.000	0.000	0.000	0.000
99	A	108	ASP	-1	-0.787	-0.886	13.518	-0.129	-0.129	0.000	0.000	0.000	0.000
100	A	109	PHE	0	-0.066	-0.052	15.408	-0.004	-0.004	0.000	0.000	0.000	0.000
101	A	110	VAL	0	0.016	0.013	14.136	0.006	0.006	0.000	0.000	0.000	0.000
102	A	111	VAL	0	0.014	0.002	17.255	-0.004	-0.004	0.000	0.000	0.000	0.000
103	A	112	LYS	1	0.806	0.909	20.509	0.071	0.071	0.000	0.000	0.000	0.000
104	A	113	PRO	0	0.004	-0.007	22.203	0.000	0.000	0.000	0.000	0.000	0.000
105	A	114	PHE	0	0.091	0.025	16.285	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	115	ASN	0	0.037	0.026	16.341	0.016	0.016	0.000	0.000	0.000	0.000
107	A	116	PRO	0	0.040	0.008	14.259	0.001	0.001	0.000	0.000	0.000	0.000
108	A	117	ASN	0	-0.020	-0.030	11.715	0.048	0.048	0.000	0.000	0.000	0.000
109	A	118	GLU	-1	-0.851	-0.901	11.333	-0.011	-0.011	0.000	0.000	0.000	0.000
110	A	119	VAL	0	0.009	0.004	10.384	-0.008	-0.008	0.000	0.000	0.000	0.000
111	A	120	ILE	0	0.004	0.017	5.988	-0.051	-0.051	0.000	0.000	0.000	0.000
112	A	121	ALA	0	0.014	0.013	6.911	0.225	0.225	0.000	0.000	0.000	0.000
113	A	122	ARG	1	0.797	0.861	8.537	0.018	0.018	0.000	0.000	0.000	0.000
114	A	123	VAL	0	0.011	0.004	4.753	-0.192	-0.139	-0.001	-0.004	-0.048	0.000
115	A	124	GLN	0	-0.019	-0.020	2.874	-2.656	-3.168	3.784	-1.072	-2.201	-0.001
116	A	125	ALA	0	-0.074	-0.038	4.705	-0.813	-0.727	-0.001	-0.011	-0.074	0.000
117	A	126	VAL	0	-0.024	-0.021	7.672	-0.069	-0.069	0.000	0.000	0.000	0.000
118	A	127	LEU	0	-0.016	-0.004	2.920	-0.685	-0.172	0.135	-0.135	-0.513	-0.001
119	A	128	ARG	1	0.903	0.969	5.670	0.725	0.725	0.000	0.000	0.000	0.000
120	A	129	ARG	1	0.921	0.976	6.549	0.447	0.447	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:10:CYS)