FMO DATABASE

FMODB ID: YYRV2

Calculation Name: 3CXJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CXJ

Chain ID: A

ChEMBL ID:

UniProt ID: O27461

Base Structure: X-ray

Registration Date: 2023-03-14

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
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	144
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1394489.429904
FMO2-HF: Nuclear repulsion	1334769.050815
FMO2-HF: Total energy	-59720.37909
FMO2-MP2: Total energy	-59893.136126

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:3:LEU)

Summations of interaction energy for fragment #1(A:3: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.
-3.739	0.967	0.524	-1.777	-3.453	-0.002

Interaction energy analysis for fragmet #1(A:3:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.029 / q_NPA : 0.007

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	5	GLN	0	0.098	0.048	3.007	-4.130	-1.672	0.123	-1.006	-1.575	0.002
4	A	6	GLU	-1	-0.849	-0.912	2.794	-3.411	-1.813	0.388	-0.638	-1.347	-0.004
5	A	7	MET	0	-0.065	-0.030	3.384	0.322	0.972	0.013	-0.133	-0.531	0.000
6	A	8	ILE	0	-0.006	0.002	5.979	0.371	0.371	0.000	0.000	0.000	0.000
7	A	9	LYS	1	0.845	0.934	6.704	1.032	1.032	0.000	0.000	0.000	0.000
8	A	10	LYS	1	0.924	0.952	8.097	1.067	1.067	0.000	0.000	0.000	0.000
9	A	11	TRP	0	-0.026	-0.034	8.223	0.100	0.100	0.000	0.000	0.000	0.000
10	A	12	LEU	0	0.014	0.008	11.537	0.110	0.110	0.000	0.000	0.000	0.000
11	A	13	ASP	-1	-0.842	-0.928	12.420	-0.396	-0.396	0.000	0.000	0.000	0.000
12	A	14	GLU	-1	-0.896	-0.932	11.909	-0.516	-0.516	0.000	0.000	0.000	0.000
13	A	15	GLU	-1	-0.893	-0.929	15.804	-0.195	-0.195	0.000	0.000	0.000	0.000
14	A	16	GLY	0	-0.017	-0.007	17.919	0.033	0.033	0.000	0.000	0.000	0.000
15	A	17	PHE	0	-0.022	-0.013	16.856	0.027	0.027	0.000	0.000	0.000	0.000
16	A	18	LEU	0	-0.048	-0.010	11.620	0.040	0.040	0.000	0.000	0.000	0.000
17	A	19	ARG	1	0.819	0.911	15.720	0.149	0.149	0.000	0.000	0.000	0.000
18	A	20	MET	0	-0.020	-0.015	15.499	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	21	GLU	-1	-0.861	-0.936	9.259	-0.288	-0.288	0.000	0.000	0.000	0.000
20	A	22	VAL	0	-0.038	-0.027	13.176	-0.004	-0.004	0.000	0.000	0.000	0.000
21	A	23	PRO	0	-0.007	-0.009	14.146	0.035	0.035	0.000	0.000	0.000	0.000
22	A	24	ASP	-1	-0.732	-0.860	14.850	0.204	0.204	0.000	0.000	0.000	0.000
23	A	25	GLU	-1	-0.930	-0.964	15.798	0.181	0.181	0.000	0.000	0.000	0.000
24	A	26	ASN	0	-0.140	-0.068	17.628	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	27	ALA	0	-0.016	-0.003	13.189	0.025	0.025	0.000	0.000	0.000	0.000
26	A	28	ARG	1	0.728	0.857	8.840	-1.048	-1.048	0.000	0.000	0.000	0.000
27	A	29	PHE	0	0.000	-0.010	6.875	0.026	0.026	0.000	0.000	0.000	0.000
28	A	30	HIS	0	-0.019	-0.027	10.020	-0.010	-0.010	0.000	0.000	0.000	0.000
29	A	31	TYR	0	-0.035	-0.018	6.505	-0.173	-0.173	0.000	0.000	0.000	0.000
30	A	32	VAL	0	0.034	0.027	13.322	0.024	0.024	0.000	0.000	0.000	0.000
31	A	33	VAL	0	-0.004	-0.014	15.395	-0.040	-0.040	0.000	0.000	0.000	0.000
32	A	34	ASN	0	-0.014	-0.005	17.841	0.012	0.012	0.000	0.000	0.000	0.000
33	A	35	TYR	0	0.030	0.019	21.219	-0.017	-0.017	0.000	0.000	0.000	0.000
34	A	36	PRO	0	-0.052	-0.023	23.016	0.012	0.012	0.000	0.000	0.000	0.000
35	A	37	GLU	-1	-0.862	-0.962	25.907	-0.065	-0.065	0.000	0.000	0.000	0.000
36	A	38	ASP	-1	-0.924	-0.960	25.117	-0.069	-0.069	0.000	0.000	0.000	0.000
37	A	39	HIS	0	-0.042	-0.015	24.613	0.016	0.016	0.000	0.000	0.000	0.000
38	A	40	VAL	0	0.019	0.005	21.298	-0.012	-0.012	0.000	0.000	0.000	0.000
39	A	41	ILE	0	-0.062	-0.032	19.081	0.009	0.009	0.000	0.000	0.000	0.000
40	A	42	ASP	-1	-0.864	-0.924	17.607	0.018	0.018	0.000	0.000	0.000	0.000
41	A	43	ILE	0	-0.050	-0.035	12.246	0.011	0.011	0.000	0.000	0.000	0.000
42	A	44	ILE	0	0.031	0.015	12.941	0.004	0.004	0.000	0.000	0.000	0.000
43	A	45	GLN	0	-0.014	-0.006	8.347	0.263	0.263	0.000	0.000	0.000	0.000
44	A	46	PRO	0	0.054	0.027	11.873	0.022	0.022	0.000	0.000	0.000	0.000
45	A	47	ALA	0	0.030	0.008	13.892	0.085	0.085	0.000	0.000	0.000	0.000
46	A	48	GLY	0	-0.043	-0.024	14.455	0.069	0.069	0.000	0.000	0.000	0.000
47	A	49	LYS	1	0.769	0.871	14.122	-0.474	-0.474	0.000	0.000	0.000	0.000
48	A	50	ASP	-1	-0.784	-0.883	8.871	1.132	1.132	0.000	0.000	0.000	0.000
49	A	51	ASP	-1	-0.829	-0.898	8.960	0.920	0.920	0.000	0.000	0.000	0.000
50	A	52	MET	0	-0.029	0.000	11.174	-0.155	-0.155	0.000	0.000	0.000	0.000
51	A	53	ILE	0	-0.003	0.005	9.959	0.129	0.129	0.000	0.000	0.000	0.000
52	A	54	LEU	0	0.003	0.003	12.704	-0.047	-0.047	0.000	0.000	0.000	0.000
53	A	55	ILE	0	-0.018	-0.004	15.439	-0.016	-0.016	0.000	0.000	0.000	0.000
54	A	56	ALA	0	0.033	0.008	17.660	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	57	CYS	0	0.036	0.020	20.657	-0.022	-0.022	0.000	0.000	0.000	0.000
56	A	58	ALA	0	0.042	0.038	23.550	0.003	0.003	0.000	0.000	0.000	0.000
57	A	59	THR	0	-0.034	-0.038	26.081	-0.012	-0.012	0.000	0.000	0.000	0.000
58	A	60	SER	0	0.035	0.011	29.496	0.005	0.005	0.000	0.000	0.000	0.000
59	A	61	VAL	0	-0.070	-0.031	32.563	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	62	SER	0	0.042	0.012	35.925	0.001	0.001	0.000	0.000	0.000	0.000
61	A	63	PRO	0	0.037	0.003	37.588	0.001	0.001	0.000	0.000	0.000	0.000
62	A	64	GLU	-1	-0.899	-0.945	40.800	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	65	HIS	0	-0.005	-0.001	38.387	0.002	0.002	0.000	0.000	0.000	0.000
64	A	66	GLN	0	-0.041	-0.050	38.091	0.002	0.002	0.000	0.000	0.000	0.000
65	A	67	ALA	0	-0.009	0.004	41.918	0.002	0.002	0.000	0.000	0.000	0.000
66	A	68	GLY	0	0.023	0.013	44.971	0.000	0.000	0.000	0.000	0.000	0.000
67	A	69	ILE	0	-0.015	-0.022	40.750	0.001	0.001	0.000	0.000	0.000	0.000
68	A	70	ARG	1	0.924	0.961	41.972	-0.018	-0.018	0.000	0.000	0.000	0.000
69	A	71	ALA	0	-0.010	0.010	47.072	0.001	0.001	0.000	0.000	0.000	0.000
70	A	72	LEU	0	-0.059	-0.010	46.027	0.000	0.000	0.000	0.000	0.000	0.000
71	A	73	SER	0	0.014	-0.014	49.747	0.001	0.001	0.000	0.000	0.000	0.000
72	A	74	MET	0	0.059	0.037	46.474	0.000	0.000	0.000	0.000	0.000	0.000
73	A	75	GLU	-1	-0.828	-0.886	48.382	0.018	0.018	0.000	0.000	0.000	0.000
74	A	76	LYS	1	0.915	0.930	48.623	-0.011	-0.011	0.000	0.000	0.000	0.000
75	A	77	ARG	1	0.811	0.913	44.988	-0.019	-0.019	0.000	0.000	0.000	0.000
76	A	78	THR	0	0.002	-0.020	44.098	0.002	0.002	0.000	0.000	0.000	0.000
77	A	79	GLU	-1	-0.864	-0.900	44.142	0.014	0.014	0.000	0.000	0.000	0.000
78	A	80	PHE	0	-0.024	-0.008	39.723	0.000	0.000	0.000	0.000	0.000	0.000
79	A	81	ILE	0	-0.002	-0.004	38.969	0.001	0.001	0.000	0.000	0.000	0.000
80	A	82	TRP	0	0.026	0.008	39.363	0.003	0.003	0.000	0.000	0.000	0.000
81	A	83	LYS	1	0.863	0.924	40.100	-0.013	-0.013	0.000	0.000	0.000	0.000
82	A	84	VAL	0	0.028	0.032	35.070	0.000	0.000	0.000	0.000	0.000	0.000
83	A	85	ARG	1	0.867	0.948	35.529	-0.038	-0.038	0.000	0.000	0.000	0.000
84	A	86	PHE	0	-0.019	-0.031	35.545	0.003	0.003	0.000	0.000	0.000	0.000
85	A	87	THR	0	-0.014	-0.018	34.676	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	88	LEU	0	0.029	0.017	30.045	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	89	ASN	0	-0.016	0.004	31.282	0.006	0.006	0.000	0.000	0.000	0.000
88	A	90	ARG	1	0.883	0.939	32.947	-0.025	-0.025	0.000	0.000	0.000	0.000
89	A	91	PHE	0	-0.025	-0.009	28.905	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	92	GLY	0	-0.056	-0.010	27.644	-0.003	-0.003	0.000	0.000	0.000	0.000
91	A	93	VAL	0	-0.024	-0.013	24.595	0.001	0.001	0.000	0.000	0.000	0.000
92	A	94	ASP	-1	-0.833	-0.898	24.562	0.104	0.104	0.000	0.000	0.000	0.000
93	A	95	PHE	0	-0.072	-0.064	26.321	-0.009	-0.009	0.000	0.000	0.000	0.000
94	A	96	GLN	0	-0.025	-0.004	28.258	0.003	0.003	0.000	0.000	0.000	0.000
95	A	97	LEU	0	-0.030	-0.024	30.077	-0.007	-0.007	0.000	0.000	0.000	0.000
96	A	98	ASP	-1	-0.755	-0.831	33.304	0.043	0.043	0.000	0.000	0.000	0.000
97	A	99	HIS	0	0.040	-0.003	35.006	-0.003	-0.003	0.000	0.000	0.000	0.000
98	A	100	PRO	0	-0.001	0.007	38.171	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	101	GLU	-1	-0.848	-0.914	40.769	0.024	0.024	0.000	0.000	0.000	0.000
100	A	102	ASN	0	-0.046	-0.033	42.031	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	103	VAL	0	-0.011	-0.013	41.325	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	104	LEU	0	-0.038	-0.016	35.139	0.002	0.002	0.000	0.000	0.000	0.000
103	A	105	ASN	0	-0.026	-0.010	35.360	-0.007	-0.007	0.000	0.000	0.000	0.000
104	A	106	SER	0	-0.042	-0.040	31.476	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	107	TYR	0	-0.031	-0.026	30.594	0.001	0.001	0.000	0.000	0.000	0.000
106	A	108	LEU	0	0.007	0.023	23.689	-0.005	-0.005	0.000	0.000	0.000	0.000
107	A	109	VAL	0	0.005	-0.004	25.562	0.002	0.002	0.000	0.000	0.000	0.000
108	A	110	THR	0	-0.018	-0.033	20.550	0.005	0.005	0.000	0.000	0.000	0.000
109	A	111	ASP	-1	-0.759	-0.832	20.556	0.057	0.057	0.000	0.000	0.000	0.000
110	A	112	GLU	-1	-0.887	-0.952	17.335	0.229	0.229	0.000	0.000	0.000	0.000
111	A	113	ILE	0	-0.027	-0.011	13.574	-0.038	-0.038	0.000	0.000	0.000	0.000
112	A	114	PHE	0	0.036	0.026	13.828	0.077	0.077	0.000	0.000	0.000	0.000
113	A	115	PHE	0	0.011	-0.029	6.875	-0.062	-0.062	0.000	0.000	0.000	0.000
114	A	116	ASP	-1	-0.911	-0.947	10.641	0.247	0.247	0.000	0.000	0.000	0.000
115	A	117	GLY	0	-0.026	-0.010	13.018	-0.050	-0.050	0.000	0.000	0.000	0.000
116	A	118	LEU	0	-0.053	-0.008	7.830	-0.043	-0.043	0.000	0.000	0.000	0.000
117	A	119	SER	0	-0.002	-0.007	10.663	-0.055	-0.055	0.000	0.000	0.000	0.000
118	A	120	LYS	1	0.824	0.895	11.641	0.360	0.360	0.000	0.000	0.000	0.000
119	A	121	ASP	-1	-0.921	-0.955	12.979	-0.072	-0.072	0.000	0.000	0.000	0.000
120	A	122	ARG	1	0.851	0.919	14.823	-0.040	-0.040	0.000	0.000	0.000	0.000
121	A	123	LEU	0	0.035	0.015	11.692	0.021	0.021	0.000	0.000	0.000	0.000
122	A	124	ILE	0	0.018	-0.001	15.231	0.025	0.025	0.000	0.000	0.000	0.000
123	A	125	SER	0	-0.048	-0.030	17.712	0.017	0.017	0.000	0.000	0.000	0.000
124	A	126	SER	0	-0.044	-0.048	18.080	0.009	0.009	0.000	0.000	0.000	0.000
125	A	127	ILE	0	0.002	0.012	15.700	0.010	0.010	0.000	0.000	0.000	0.000
126	A	128	LYS	1	0.899	0.956	20.108	0.107	0.107	0.000	0.000	0.000	0.000
127	A	129	ASN	0	-0.022	-0.010	23.078	-0.002	-0.002	0.000	0.000	0.000	0.000
128	A	130	VAL	0	0.058	0.027	21.435	0.003	0.003	0.000	0.000	0.000	0.000
129	A	131	PHE	0	-0.003	0.007	24.141	0.002	0.002	0.000	0.000	0.000	0.000
130	A	132	ARG	1	0.901	0.939	25.329	0.031	0.031	0.000	0.000	0.000	0.000
131	A	133	ALA	0	0.016	0.016	27.639	0.001	0.001	0.000	0.000	0.000	0.000
132	A	134	LYS	1	0.851	0.910	27.240	0.009	0.009	0.000	0.000	0.000	0.000
133	A	135	LEU	0	-0.001	0.011	29.721	0.000	0.000	0.000	0.000	0.000	0.000
134	A	136	GLN	0	0.028	-0.001	31.633	0.002	0.002	0.000	0.000	0.000	0.000
135	A	137	VAL	0	-0.014	0.002	32.874	0.001	0.001	0.000	0.000	0.000	0.000
136	A	138	MET	0	0.014	0.029	31.988	-0.001	-0.001	0.000	0.000	0.000	0.000
137	A	139	TRP	0	0.019	0.002	34.817	0.000	0.000	0.000	0.000	0.000	0.000
138	A	140	MET	0	-0.011	0.008	36.717	0.001	0.001	0.000	0.000	0.000	0.000
139	A	141	ILE	0	0.011	0.014	36.210	0.001	0.001	0.000	0.000	0.000	0.000
140	A	142	GLN	0	0.004	-0.012	36.804	0.000	0.000	0.000	0.000	0.000	0.000
141	A	143	GLU	-1	-0.840	-0.901	40.895	0.000	0.000	0.000	0.000	0.000	0.000
142	A	144	ARG	1	0.697	0.834	42.502	-0.005	-0.005	0.000	0.000	0.000	0.000
143	A	145	PHE	0	-0.003	-0.002	42.507	0.001	0.001	0.000	0.000	0.000	0.000
144	A	146	GLY	0	-0.016	0.007	41.829	-0.002	-0.002	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:3:LEU)