FMO DATABASE

FMODB ID: 2JL4R

Calculation Name: 3PJV-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3PJV

Chain ID: D

ChEMBL ID:

UniProt ID: Q3KK31

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	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	128
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-854443.804262
FMO2-HF: Nuclear repulsion	805861.37166
FMO2-HF: Total energy	-48582.432602
FMO2-MP2: Total energy	-48724.845753

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(D:23:PHE)

Summations of interaction energy for fragment #1(D:23: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.
-11.842	-7.51	3.525	-3.198	-4.66	-0.009

Interaction energy analysis for fragmet #1(D:23:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / q_NPA : -0.002

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	D	25	VAL	0	0.008	0.001	3.337	-5.272	-2.319	0.085	-1.382	-1.656	0.008
4	D	26	SER	0	0.051	0.029	2.184	-6.188	-5.308	3.440	-1.746	-2.575	-0.017
5	D	27	LEU	0	0.020	0.039	3.876	-0.804	-0.305	0.000	-0.070	-0.429	0.000
6	D	28	GLU	-1	-0.911	-0.953	5.526	-0.094	-0.094	0.000	0.000	0.000	0.000
7	D	29	SER	0	0.046	0.010	7.292	-0.014	-0.014	0.000	0.000	0.000	0.000
8	D	30	SER	0	-0.022	-0.034	5.493	-0.080	-0.080	0.000	0.000	0.000	0.000
9	D	31	ARG	1	0.960	0.983	7.869	0.490	0.490	0.000	0.000	0.000	0.000
10	D	32	THR	0	-0.021	-0.017	9.892	0.092	0.092	0.000	0.000	0.000	0.000
11	D	33	GLN	0	-0.006	-0.003	9.857	-0.058	-0.058	0.000	0.000	0.000	0.000
12	D	34	TYR	0	0.044	0.026	7.574	0.125	0.125	0.000	0.000	0.000	0.000
13	D	35	VAL	0	-0.026	-0.005	12.893	0.073	0.073	0.000	0.000	0.000	0.000
14	D	36	ASN	0	0.005	-0.004	15.231	0.073	0.073	0.000	0.000	0.000	0.000
15	D	37	GLN	0	0.012	0.023	14.476	-0.012	-0.012	0.000	0.000	0.000	0.000
16	D	38	LEU	0	0.022	0.008	14.419	0.035	0.035	0.000	0.000	0.000	0.000
17	D	39	ARG	1	0.910	0.952	18.076	0.267	0.267	0.000	0.000	0.000	0.000
18	D	40	SER	0	-0.005	-0.021	20.598	0.031	0.031	0.000	0.000	0.000	0.000
19	D	41	HIS	0	0.017	0.028	20.467	0.014	0.014	0.000	0.000	0.000	0.000
20	D	42	ALA	0	-0.008	-0.009	22.294	0.018	0.018	0.000	0.000	0.000	0.000
21	D	43	GLN	0	-0.021	-0.018	24.210	0.020	0.020	0.000	0.000	0.000	0.000
22	D	44	ASP	-1	-0.884	-0.938	25.333	-0.180	-0.180	0.000	0.000	0.000	0.000
23	D	45	ALA	0	-0.021	-0.004	26.585	0.013	0.013	0.000	0.000	0.000	0.000
24	D	46	ALA	0	0.003	0.003	28.341	0.012	0.012	0.000	0.000	0.000	0.000
25	D	47	THR	0	-0.022	-0.014	30.183	0.013	0.013	0.000	0.000	0.000	0.000
26	D	48	ALA	0	0.004	0.000	31.214	0.009	0.009	0.000	0.000	0.000	0.000
27	D	49	LEU	0	-0.002	0.012	32.420	0.008	0.008	0.000	0.000	0.000	0.000
28	D	50	ALA	0	0.022	0.004	34.187	0.008	0.008	0.000	0.000	0.000	0.000
29	D	51	LEU	0	-0.012	-0.001	35.965	0.007	0.007	0.000	0.000	0.000	0.000
30	D	52	SER	0	-0.030	-0.030	35.956	0.005	0.005	0.000	0.000	0.000	0.000
31	D	53	LEU	0	-0.010	-0.012	37.023	0.005	0.005	0.000	0.000	0.000	0.000
32	D	54	THR	0	-0.030	-0.007	40.156	0.005	0.005	0.000	0.000	0.000	0.000
33	D	55	PRO	0	-0.072	-0.036	42.163	0.004	0.004	0.000	0.000	0.000	0.000
34	D	56	ASN	0	-0.031	-0.025	42.219	0.005	0.005	0.000	0.000	0.000	0.000
35	D	57	ILE	0	-0.010	0.010	41.691	0.000	0.000	0.000	0.000	0.000	0.000
36	D	58	ASP	-1	-0.934	-0.967	44.536	-0.058	-0.058	0.000	0.000	0.000	0.000
37	D	59	ASP	-1	-0.900	-0.948	46.503	-0.062	-0.062	0.000	0.000	0.000	0.000
38	D	60	PRO	0	0.015	-0.007	44.964	-0.003	-0.003	0.000	0.000	0.000	0.000
39	D	61	ALA	0	0.016	0.011	43.792	-0.004	-0.004	0.000	0.000	0.000	0.000
40	D	62	MET	0	0.007	0.010	42.967	-0.005	-0.005	0.000	0.000	0.000	0.000
41	D	63	VAL	0	-0.008	-0.001	39.984	-0.005	-0.005	0.000	0.000	0.000	0.000
42	D	64	GLU	-1	-0.815	-0.892	39.088	-0.090	-0.090	0.000	0.000	0.000	0.000
43	D	65	LEU	0	-0.024	-0.002	38.322	-0.006	-0.006	0.000	0.000	0.000	0.000
44	D	66	LEU	0	-0.018	-0.010	37.638	-0.006	-0.006	0.000	0.000	0.000	0.000
45	D	67	VAL	0	0.000	-0.003	33.765	-0.007	-0.007	0.000	0.000	0.000	0.000
46	D	68	SER	0	-0.038	-0.039	33.447	-0.008	-0.008	0.000	0.000	0.000	0.000
47	D	69	SER	0	-0.041	-0.001	33.353	-0.007	-0.007	0.000	0.000	0.000	0.000
48	D	70	ILE	0	0.029	0.014	29.303	-0.007	-0.007	0.000	0.000	0.000	0.000
49	D	71	PHE	0	-0.003	-0.013	28.093	-0.012	-0.012	0.000	0.000	0.000	0.000
50	D	72	ASP	-1	-0.872	-0.945	28.846	-0.132	-0.132	0.000	0.000	0.000	0.000
51	D	73	SER	0	-0.080	-0.029	26.275	-0.006	-0.006	0.000	0.000	0.000	0.000
52	D	74	GLY	0	-0.044	-0.032	25.268	-0.008	-0.008	0.000	0.000	0.000	0.000
53	D	75	TYR	0	-0.062	-0.028	22.267	-0.014	-0.014	0.000	0.000	0.000	0.000
54	D	76	TYR	0	0.013	0.005	22.193	-0.015	-0.015	0.000	0.000	0.000	0.000
55	D	77	SER	0	0.019	0.004	21.928	0.003	0.003	0.000	0.000	0.000	0.000
56	D	78	SER	0	-0.015	-0.010	24.382	0.009	0.009	0.000	0.000	0.000	0.000
57	D	79	ILE	0	-0.004	0.013	27.692	-0.006	-0.006	0.000	0.000	0.000	0.000
58	D	80	ARG	1	0.886	0.942	30.492	0.100	0.100	0.000	0.000	0.000	0.000
59	D	81	VAL	0	0.012	0.017	33.594	-0.002	-0.002	0.000	0.000	0.000	0.000
60	D	82	VAL	0	0.008	0.000	36.010	0.002	0.002	0.000	0.000	0.000	0.000
61	D	83	ASP	-1	-0.780	-0.863	38.729	-0.063	-0.063	0.000	0.000	0.000	0.000
62	D	84	LEU	0	0.002	-0.003	39.197	0.002	0.002	0.000	0.000	0.000	0.000
63	D	85	LYS	1	0.901	0.957	42.887	0.056	0.056	0.000	0.000	0.000	0.000
64	D	86	THR	0	-0.075	-0.076	45.777	0.002	0.002	0.000	0.000	0.000	0.000
65	D	87	ASP	-1	-0.949	-0.964	40.569	-0.069	-0.069	0.000	0.000	0.000	0.000
66	D	88	GLN	0	-0.044	-0.006	41.478	-0.001	-0.001	0.000	0.000	0.000	0.000
67	D	89	THR	0	-0.043	-0.039	37.465	-0.001	-0.001	0.000	0.000	0.000	0.000
68	D	90	ILE	0	-0.022	-0.003	39.708	0.003	0.003	0.000	0.000	0.000	0.000
69	D	91	VAL	0	0.017	-0.002	37.136	0.001	0.001	0.000	0.000	0.000	0.000
70	D	92	GLU	-1	-0.862	-0.939	33.869	-0.105	-0.105	0.000	0.000	0.000	0.000
71	D	93	ARG	1	0.790	0.890	31.717	0.105	0.105	0.000	0.000	0.000	0.000
72	D	94	ASN	0	0.000	-0.014	29.051	-0.012	-0.012	0.000	0.000	0.000	0.000
73	D	95	GLY	0	0.025	0.020	26.603	0.006	0.006	0.000	0.000	0.000	0.000
74	D	96	ILE	0	-0.036	-0.019	22.701	0.003	0.003	0.000	0.000	0.000	0.000
75	D	97	PRO	0	0.003	-0.003	21.774	-0.011	-0.011	0.000	0.000	0.000	0.000
76	D	98	ALA	0	-0.047	-0.012	19.054	-0.023	-0.023	0.000	0.000	0.000	0.000
77	D	99	VAL	0	0.016	0.004	14.087	0.000	0.000	0.000	0.000	0.000	0.000
78	D	100	THR	0	-0.016	-0.007	17.492	0.019	0.019	0.000	0.000	0.000	0.000
79	D	101	ASN	0	-0.033	-0.020	15.653	-0.041	-0.041	0.000	0.000	0.000	0.000
80	D	102	VAL	0	0.001	0.007	18.475	0.023	0.023	0.000	0.000	0.000	0.000
81	D	103	PRO	0	-0.002	0.011	20.248	-0.008	-0.008	0.000	0.000	0.000	0.000
82	D	104	ASP	-1	-0.827	-0.922	19.342	-0.178	-0.178	0.000	0.000	0.000	0.000
83	D	105	TRP	0	-0.072	-0.061	22.145	0.008	0.008	0.000	0.000	0.000	0.000
84	D	106	PHE	0	0.033	0.020	25.054	0.010	0.010	0.000	0.000	0.000	0.000
85	D	107	VAL	0	0.038	0.024	22.087	0.005	0.005	0.000	0.000	0.000	0.000
86	D	108	LYS	1	0.908	0.961	25.535	0.105	0.105	0.000	0.000	0.000	0.000
87	D	109	LEU	0	-0.043	-0.012	28.094	0.006	0.006	0.000	0.000	0.000	0.000
88	D	110	ILE	0	-0.014	-0.011	28.350	0.005	0.005	0.000	0.000	0.000	0.000
89	D	111	GLY	0	-0.022	0.002	29.149	0.004	0.004	0.000	0.000	0.000	0.000
90	D	112	LEU	0	-0.016	-0.019	26.730	0.003	0.003	0.000	0.000	0.000	0.000
91	D	113	GLU	-1	-0.955	-0.968	28.772	-0.104	-0.104	0.000	0.000	0.000	0.000
92	D	114	PRO	0	-0.034	-0.042	27.417	-0.006	-0.006	0.000	0.000	0.000	0.000
93	D	115	ALA	0	0.009	0.015	28.116	-0.009	-0.009	0.000	0.000	0.000	0.000
94	D	116	GLY	0	-0.027	-0.004	29.205	-0.005	-0.005	0.000	0.000	0.000	0.000
95	D	117	GLY	0	0.013	0.015	30.071	0.007	0.007	0.000	0.000	0.000	0.000
96	D	118	ASP	-1	-0.954	-0.986	30.938	-0.101	-0.101	0.000	0.000	0.000	0.000
97	D	119	ALA	0	0.025	0.013	33.163	0.004	0.004	0.000	0.000	0.000	0.000
98	D	120	LEU	0	-0.015	-0.008	34.523	-0.002	-0.002	0.000	0.000	0.000	0.000
99	D	121	VAL	0	0.015	0.014	33.442	-0.001	-0.001	0.000	0.000	0.000	0.000
100	D	122	SER	0	-0.010	-0.019	36.799	0.004	0.004	0.000	0.000	0.000	0.000
101	D	123	ARG	1	0.918	0.959	37.428	0.055	0.055	0.000	0.000	0.000	0.000
102	D	124	GLY	0	-0.001	-0.005	41.007	0.003	0.003	0.000	0.000	0.000	0.000
103	D	125	TRP	0	-0.020	-0.026	44.469	-0.001	-0.001	0.000	0.000	0.000	0.000
104	D	126	GLU	-1	-0.902	-0.927	42.903	-0.049	-0.049	0.000	0.000	0.000	0.000
105	D	127	GLN	0	-0.002	0.003	40.463	-0.006	-0.006	0.000	0.000	0.000	0.000
106	D	128	ALA	0	-0.023	-0.016	37.924	0.002	0.002	0.000	0.000	0.000	0.000
107	D	129	ALA	0	-0.011	-0.012	33.358	0.000	0.000	0.000	0.000	0.000	0.000
108	D	130	ARG	1	0.827	0.905	33.420	0.089	0.089	0.000	0.000	0.000	0.000
109	D	131	VAL	0	-0.035	-0.010	28.660	-0.004	-0.004	0.000	0.000	0.000	0.000
110	D	132	GLU	-1	-0.805	-0.883	28.929	-0.100	-0.100	0.000	0.000	0.000	0.000
111	D	133	VAL	0	-0.020	-0.015	25.334	-0.012	-0.012	0.000	0.000	0.000	0.000
112	D	134	VAL	0	0.028	0.008	24.719	0.010	0.010	0.000	0.000	0.000	0.000
113	D	135	SER	0	0.008	0.011	23.638	-0.020	-0.020	0.000	0.000	0.000	0.000
114	D	136	HIS	0	0.031	0.010	16.776	0.016	0.016	0.000	0.000	0.000	0.000
115	D	137	PRO	0	0.062	0.033	21.079	-0.001	-0.001	0.000	0.000	0.000	0.000
116	D	138	MET	0	-0.012	-0.005	14.329	0.004	0.004	0.000	0.000	0.000	0.000
117	D	139	PHE	0	0.040	0.013	18.452	0.006	0.006	0.000	0.000	0.000	0.000
118	D	140	ALA	0	0.047	0.026	22.168	0.013	0.013	0.000	0.000	0.000	0.000
119	D	141	LEU	0	0.013	-0.006	21.968	0.012	0.012	0.000	0.000	0.000	0.000
120	D	142	ALA	0	0.002	0.002	21.119	0.010	0.010	0.000	0.000	0.000	0.000
121	D	143	LYS	1	0.913	0.964	23.153	0.161	0.161	0.000	0.000	0.000	0.000
122	D	144	LEU	0	0.017	0.016	26.582	0.011	0.011	0.000	0.000	0.000	0.000
123	D	145	TRP	0	0.034	0.005	23.715	0.013	0.013	0.000	0.000	0.000	0.000
124	D	146	GLN	0	0.010	-0.009	24.000	-0.006	-0.006	0.000	0.000	0.000	0.000
125	D	147	SER	0	-0.030	-0.021	27.740	0.009	0.009	0.000	0.000	0.000	0.000
126	D	148	ALA	0	-0.056	-0.022	29.548	0.008	0.008	0.000	0.000	0.000	0.000
127	D	149	LEU	0	-0.067	-0.023	26.138	0.006	0.006	0.000	0.000	0.000	0.000
128	D	150	GLY	0	-0.041	-0.001	30.718	0.007	0.007	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:23:PHE)