FMO DATABASE

FMODB ID: 72MYK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-854617.52205
FMO2-HF: Nuclear repulsion	806035.60588
FMO2-HF: Total energy	-48581.916169
FMO2-MP2: Total energy	-48724.364916

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.
-17.599	-12.102	2.058	-3.115	-4.44	0.021

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 : 0.033 / q_NPA : 0.012

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	0.005	0.002	3.008	-3.141	-0.261	0.098	-1.300	-1.678	0.007
4	D	26	SER	0	0.003	0.002	2.407	-10.706	-8.566	1.960	-1.742	-2.358	0.014
5	D	27	LEU	0	0.038	0.028	4.389	-2.376	-1.899	0.000	-0.073	-0.404	0.000
6	D	28	GLU	-1	-0.918	-0.959	5.535	0.191	0.191	0.000	0.000	0.000	0.000
7	D	29	SER	0	0.039	0.000	8.076	-0.096	-0.096	0.000	0.000	0.000	0.000
8	D	30	SER	0	0.002	0.002	5.247	-0.469	-0.469	0.000	0.000	0.000	0.000
9	D	31	ARG	1	0.964	0.986	7.888	-0.240	-0.240	0.000	0.000	0.000	0.000
10	D	32	THR	0	-0.014	-0.011	9.910	-0.112	-0.112	0.000	0.000	0.000	0.000
11	D	33	GLN	0	-0.001	0.002	10.130	-0.167	-0.167	0.000	0.000	0.000	0.000
12	D	34	TYR	0	0.048	0.027	7.954	-0.086	-0.086	0.000	0.000	0.000	0.000
13	D	35	VAL	0	-0.042	-0.010	13.030	-0.013	-0.013	0.000	0.000	0.000	0.000
14	D	36	ASN	0	-0.025	-0.029	15.313	-0.024	-0.024	0.000	0.000	0.000	0.000
15	D	37	GLN	0	0.010	0.010	14.831	-0.040	-0.040	0.000	0.000	0.000	0.000
16	D	38	LEU	0	0.031	0.011	15.123	-0.002	-0.002	0.000	0.000	0.000	0.000
17	D	39	ARG	1	0.931	0.973	18.251	-0.044	-0.044	0.000	0.000	0.000	0.000
18	D	40	SER	0	-0.002	-0.011	20.746	0.007	0.007	0.000	0.000	0.000	0.000
19	D	41	HIS	0	0.021	0.035	20.606	0.002	0.002	0.000	0.000	0.000	0.000
20	D	42	ALA	0	-0.009	-0.012	22.490	0.000	0.000	0.000	0.000	0.000	0.000
21	D	43	GLN	0	-0.034	-0.021	24.383	0.001	0.001	0.000	0.000	0.000	0.000
22	D	44	ASP	-1	-0.870	-0.938	25.507	-0.004	-0.004	0.000	0.000	0.000	0.000
23	D	45	ALA	0	-0.021	-0.004	26.841	0.001	0.001	0.000	0.000	0.000	0.000
24	D	46	ALA	0	-0.005	-0.001	28.559	0.001	0.001	0.000	0.000	0.000	0.000
25	D	47	THR	0	-0.017	-0.005	30.408	0.004	0.004	0.000	0.000	0.000	0.000
26	D	48	ALA	0	0.003	-0.003	31.431	0.002	0.002	0.000	0.000	0.000	0.000
27	D	49	LEU	0	-0.006	0.007	32.630	0.001	0.001	0.000	0.000	0.000	0.000
28	D	50	ALA	0	0.029	0.007	34.401	0.001	0.001	0.000	0.000	0.000	0.000
29	D	51	LEU	0	-0.011	-0.004	36.174	0.002	0.002	0.000	0.000	0.000	0.000
30	D	52	SER	0	-0.034	-0.028	36.249	0.000	0.000	0.000	0.000	0.000	0.000
31	D	53	LEU	0	-0.014	-0.016	37.376	0.000	0.000	0.000	0.000	0.000	0.000
32	D	54	THR	0	-0.032	-0.007	40.364	0.002	0.002	0.000	0.000	0.000	0.000
33	D	55	PRO	0	-0.073	-0.038	42.345	0.001	0.001	0.000	0.000	0.000	0.000
34	D	56	ASN	0	-0.018	-0.016	42.486	0.000	0.000	0.000	0.000	0.000	0.000
35	D	57	ILE	0	-0.018	0.004	41.802	-0.002	-0.002	0.000	0.000	0.000	0.000
36	D	58	ASP	-1	-0.920	-0.958	44.720	-0.013	-0.013	0.000	0.000	0.000	0.000
37	D	59	ASP	-1	-0.925	-0.962	46.693	-0.024	-0.024	0.000	0.000	0.000	0.000
38	D	60	PRO	0	0.022	-0.005	45.166	-0.002	-0.002	0.000	0.000	0.000	0.000
39	D	61	ALA	0	0.022	0.014	43.985	-0.002	-0.002	0.000	0.000	0.000	0.000
40	D	62	MET	0	0.001	0.010	43.238	-0.004	-0.004	0.000	0.000	0.000	0.000
41	D	63	VAL	0	-0.006	-0.001	40.065	-0.002	-0.002	0.000	0.000	0.000	0.000
42	D	64	GLU	-1	-0.860	-0.926	39.374	-0.048	-0.048	0.000	0.000	0.000	0.000
43	D	65	LEU	0	-0.008	-0.013	38.536	-0.004	-0.004	0.000	0.000	0.000	0.000
44	D	66	LEU	0	-0.036	-0.015	37.874	-0.004	-0.004	0.000	0.000	0.000	0.000
45	D	67	VAL	0	-0.011	-0.010	33.846	-0.003	-0.003	0.000	0.000	0.000	0.000
46	D	68	SER	0	-0.029	-0.021	33.666	-0.006	-0.006	0.000	0.000	0.000	0.000
47	D	69	SER	0	-0.026	0.008	33.596	-0.007	-0.007	0.000	0.000	0.000	0.000
48	D	70	ILE	0	0.016	0.011	29.532	-0.005	-0.005	0.000	0.000	0.000	0.000
49	D	71	PHE	0	-0.018	-0.026	28.150	-0.009	-0.009	0.000	0.000	0.000	0.000
50	D	72	ASP	-1	-0.883	-0.941	29.076	-0.084	-0.084	0.000	0.000	0.000	0.000
51	D	73	SER	0	-0.076	-0.037	26.609	-0.009	-0.009	0.000	0.000	0.000	0.000
52	D	74	GLY	0	-0.061	-0.042	25.510	-0.011	-0.011	0.000	0.000	0.000	0.000
53	D	75	TYR	0	-0.057	-0.023	22.510	-0.010	-0.010	0.000	0.000	0.000	0.000
54	D	76	TYR	0	0.012	0.006	22.408	-0.006	-0.006	0.000	0.000	0.000	0.000
55	D	77	SER	0	0.014	0.000	22.118	-0.002	-0.002	0.000	0.000	0.000	0.000
56	D	78	SER	0	-0.036	-0.019	24.520	0.006	0.006	0.000	0.000	0.000	0.000
57	D	79	ILE	0	0.020	0.022	27.834	0.002	0.002	0.000	0.000	0.000	0.000
58	D	80	ARG	1	0.913	0.951	30.639	0.035	0.035	0.000	0.000	0.000	0.000
59	D	81	VAL	0	0.014	0.019	33.716	0.003	0.003	0.000	0.000	0.000	0.000
60	D	82	VAL	0	-0.001	-0.008	36.183	-0.002	-0.002	0.000	0.000	0.000	0.000
61	D	83	ASP	-1	-0.816	-0.905	38.826	-0.012	-0.012	0.000	0.000	0.000	0.000
62	D	84	LEU	0	0.021	-0.003	39.460	0.001	0.001	0.000	0.000	0.000	0.000
63	D	85	LYS	1	0.886	0.949	42.965	0.007	0.007	0.000	0.000	0.000	0.000
64	D	86	THR	0	-0.054	-0.034	45.609	0.000	0.000	0.000	0.000	0.000	0.000
65	D	87	ASP	-1	-0.940	-0.964	40.841	-0.016	-0.016	0.000	0.000	0.000	0.000
66	D	88	GLN	0	-0.013	0.017	41.523	-0.002	-0.002	0.000	0.000	0.000	0.000
67	D	89	THR	0	-0.017	-0.025	37.429	0.002	0.002	0.000	0.000	0.000	0.000
68	D	90	ILE	0	-0.009	0.012	39.823	0.000	0.000	0.000	0.000	0.000	0.000
69	D	91	VAL	0	0.017	0.000	36.979	-0.001	-0.001	0.000	0.000	0.000	0.000
70	D	92	GLU	-1	-0.942	-0.980	34.080	-0.053	-0.053	0.000	0.000	0.000	0.000
71	D	93	ARG	1	0.823	0.917	31.882	0.058	0.058	0.000	0.000	0.000	0.000
72	D	94	ASN	0	0.013	-0.003	29.176	-0.003	-0.003	0.000	0.000	0.000	0.000
73	D	95	GLY	0	0.014	0.015	26.752	0.001	0.001	0.000	0.000	0.000	0.000
74	D	96	ILE	0	-0.029	-0.013	22.060	0.007	0.007	0.000	0.000	0.000	0.000
75	D	97	PRO	0	-0.017	-0.010	21.869	-0.009	-0.009	0.000	0.000	0.000	0.000
76	D	98	ALA	0	-0.044	-0.009	19.102	-0.017	-0.017	0.000	0.000	0.000	0.000
77	D	99	VAL	0	0.030	0.008	14.172	0.005	0.005	0.000	0.000	0.000	0.000
78	D	100	THR	0	-0.005	0.000	17.601	0.009	0.009	0.000	0.000	0.000	0.000
79	D	101	ASN	0	-0.042	-0.025	15.713	-0.045	-0.045	0.000	0.000	0.000	0.000
80	D	102	VAL	0	0.001	0.008	18.618	0.020	0.020	0.000	0.000	0.000	0.000
81	D	103	PRO	0	0.000	0.014	20.451	-0.014	-0.014	0.000	0.000	0.000	0.000
82	D	104	ASP	-1	-0.824	-0.920	19.643	-0.257	-0.257	0.000	0.000	0.000	0.000
83	D	105	TRP	0	-0.051	-0.065	22.374	0.017	0.017	0.000	0.000	0.000	0.000
84	D	106	PHE	0	0.045	0.017	25.265	0.014	0.014	0.000	0.000	0.000	0.000
85	D	107	VAL	0	0.039	0.028	22.424	0.011	0.011	0.000	0.000	0.000	0.000
86	D	108	LYS	1	0.882	0.961	25.808	0.161	0.161	0.000	0.000	0.000	0.000
87	D	109	LEU	0	-0.048	-0.013	28.373	0.008	0.008	0.000	0.000	0.000	0.000
88	D	110	ILE	0	-0.021	-0.009	28.560	0.008	0.008	0.000	0.000	0.000	0.000
89	D	111	GLY	0	-0.017	0.001	29.444	0.007	0.007	0.000	0.000	0.000	0.000
90	D	112	LEU	0	-0.013	-0.018	26.796	0.006	0.006	0.000	0.000	0.000	0.000
91	D	113	GLU	-1	-0.972	-0.974	29.114	-0.085	-0.085	0.000	0.000	0.000	0.000
92	D	114	PRO	0	-0.041	-0.041	27.808	-0.003	-0.003	0.000	0.000	0.000	0.000
93	D	115	ALA	0	0.027	0.018	28.490	-0.003	-0.003	0.000	0.000	0.000	0.000
94	D	116	GLY	0	-0.026	-0.003	29.596	0.000	0.000	0.000	0.000	0.000	0.000
95	D	117	GLY	0	0.011	0.015	30.395	0.005	0.005	0.000	0.000	0.000	0.000
96	D	118	ASP	-1	-0.965	-0.990	31.201	-0.054	-0.054	0.000	0.000	0.000	0.000
97	D	119	ALA	0	0.023	0.012	33.431	0.003	0.003	0.000	0.000	0.000	0.000
98	D	120	LEU	0	-0.019	-0.007	34.799	-0.001	-0.001	0.000	0.000	0.000	0.000
99	D	121	VAL	0	0.014	0.015	33.584	0.002	0.002	0.000	0.000	0.000	0.000
100	D	122	SER	0	0.000	0.000	36.972	0.000	0.000	0.000	0.000	0.000	0.000
101	D	123	ARG	1	0.958	0.977	36.794	0.006	0.006	0.000	0.000	0.000	0.000
102	D	124	GLY	0	-0.004	-0.003	40.799	0.000	0.000	0.000	0.000	0.000	0.000
103	D	125	TRP	0	-0.003	-0.017	44.271	-0.001	-0.001	0.000	0.000	0.000	0.000
104	D	126	GLU	-1	-0.943	-0.954	42.924	-0.011	-0.011	0.000	0.000	0.000	0.000
105	D	127	GLN	0	-0.029	-0.020	40.729	-0.001	-0.001	0.000	0.000	0.000	0.000
106	D	128	ALA	0	-0.028	-0.019	37.658	0.000	0.000	0.000	0.000	0.000	0.000
107	D	129	ALA	0	-0.009	-0.012	33.475	-0.001	-0.001	0.000	0.000	0.000	0.000
108	D	130	ARG	1	0.861	0.925	33.644	0.049	0.049	0.000	0.000	0.000	0.000
109	D	131	VAL	0	-0.030	-0.008	28.928	-0.002	-0.002	0.000	0.000	0.000	0.000
110	D	132	GLU	-1	-0.811	-0.894	29.068	-0.063	-0.063	0.000	0.000	0.000	0.000
111	D	133	VAL	0	-0.014	-0.009	25.603	-0.005	-0.005	0.000	0.000	0.000	0.000
112	D	134	VAL	0	0.023	0.005	24.925	0.002	0.002	0.000	0.000	0.000	0.000
113	D	135	SER	0	0.002	0.007	24.029	-0.009	-0.009	0.000	0.000	0.000	0.000
114	D	136	HIS	0	0.029	0.012	17.249	0.007	0.007	0.000	0.000	0.000	0.000
115	D	137	PRO	0	0.071	0.038	21.297	0.003	0.003	0.000	0.000	0.000	0.000
116	D	138	MET	0	-0.014	-0.008	14.650	0.002	0.002	0.000	0.000	0.000	0.000
117	D	139	PHE	0	0.048	0.017	18.592	-0.001	-0.001	0.000	0.000	0.000	0.000
118	D	140	ALA	0	0.033	0.020	22.435	0.009	0.009	0.000	0.000	0.000	0.000
119	D	141	LEU	0	0.016	-0.006	22.336	0.006	0.006	0.000	0.000	0.000	0.000
120	D	142	ALA	0	0.005	0.004	21.356	0.003	0.003	0.000	0.000	0.000	0.000
121	D	143	LYS	1	0.932	0.969	23.372	0.120	0.120	0.000	0.000	0.000	0.000
122	D	144	LEU	0	0.015	0.008	26.798	0.007	0.007	0.000	0.000	0.000	0.000
123	D	145	TRP	0	0.040	0.012	24.257	0.007	0.007	0.000	0.000	0.000	0.000
124	D	146	GLN	0	0.004	-0.019	24.426	-0.009	-0.009	0.000	0.000	0.000	0.000
125	D	147	SER	0	-0.021	-0.008	27.899	0.009	0.009	0.000	0.000	0.000	0.000
126	D	148	ALA	0	-0.053	-0.019	29.722	0.006	0.006	0.000	0.000	0.000	0.000
127	D	149	LEU	0	-0.069	-0.026	26.246	0.003	0.003	0.000	0.000	0.000	0.000
128	D	150	GLY	0	-0.042	0.001	30.847	0.005	0.005	0.000	0.000	0.000	0.000

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