FMO DATABASE

FMODB ID: 6NGZZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-858036.381995
FMO2-HF: Nuclear repulsion	809453.760779
FMO2-HF: Total energy	-48582.621216
FMO2-MP2: Total energy	-48725.054853

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.
-10.013	-5.749	2.611	-2.686	-4.188	-0.013

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 : 0.053 / q_NPA : 0.011

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	0.007	-0.002	3.737	-4.286	-1.982	0.041	-1.017	-1.328	0.006
4	D	26	SER	0	0.034	0.026	2.246	-5.298	-3.921	2.568	-1.572	-2.373	-0.019
5	D	27	LEU	0	0.009	0.026	4.068	-0.798	-0.215	0.002	-0.097	-0.487	0.000
6	D	28	GLU	-1	-0.909	-0.954	5.781	-0.184	-0.184	0.000	0.000	0.000	0.000
7	D	29	SER	0	0.046	0.023	7.226	0.005	0.005	0.000	0.000	0.000	0.000
8	D	30	SER	0	0.001	-0.013	5.476	-0.053	-0.053	0.000	0.000	0.000	0.000
9	D	31	ARG	1	0.944	0.974	7.963	0.465	0.465	0.000	0.000	0.000	0.000
10	D	32	THR	0	-0.018	-0.021	9.765	0.093	0.093	0.000	0.000	0.000	0.000
11	D	33	GLN	0	-0.015	-0.009	9.649	-0.069	-0.069	0.000	0.000	0.000	0.000
12	D	34	TYR	0	0.043	0.019	7.189	0.137	0.137	0.000	0.000	0.000	0.000
13	D	35	VAL	0	-0.010	-0.002	12.543	0.072	0.072	0.000	0.000	0.000	0.000
14	D	36	ASN	0	-0.003	0.000	14.954	0.084	0.084	0.000	0.000	0.000	0.000
15	D	37	GLN	0	0.016	0.028	14.194	-0.014	-0.014	0.000	0.000	0.000	0.000
16	D	38	LEU	0	0.005	-0.005	13.980	0.036	0.036	0.000	0.000	0.000	0.000
17	D	39	ARG	1	0.893	0.935	17.797	0.271	0.271	0.000	0.000	0.000	0.000
18	D	40	SER	0	-0.026	-0.019	20.250	0.030	0.030	0.000	0.000	0.000	0.000
19	D	41	HIS	0	0.008	0.005	20.243	0.019	0.019	0.000	0.000	0.000	0.000
20	D	42	ALA	0	0.000	0.000	22.087	0.018	0.018	0.000	0.000	0.000	0.000
21	D	43	GLN	0	0.014	0.010	23.956	0.018	0.018	0.000	0.000	0.000	0.000
22	D	44	ASP	-1	-0.898	-0.945	24.749	-0.187	-0.187	0.000	0.000	0.000	0.000
23	D	45	ALA	0	-0.015	0.000	26.318	0.013	0.013	0.000	0.000	0.000	0.000
24	D	46	ALA	0	0.005	0.002	28.044	0.012	0.012	0.000	0.000	0.000	0.000
25	D	47	THR	0	-0.026	-0.023	29.941	0.013	0.013	0.000	0.000	0.000	0.000
26	D	48	ALA	0	0.001	-0.002	31.023	0.009	0.009	0.000	0.000	0.000	0.000
27	D	49	LEU	0	0.000	0.018	32.105	0.008	0.008	0.000	0.000	0.000	0.000
28	D	50	ALA	0	0.034	0.011	33.857	0.007	0.007	0.000	0.000	0.000	0.000
29	D	51	LEU	0	-0.021	0.002	35.690	0.007	0.007	0.000	0.000	0.000	0.000
30	D	52	SER	0	-0.013	-0.029	35.767	0.006	0.006	0.000	0.000	0.000	0.000
31	D	53	LEU	0	-0.021	-0.008	36.571	0.005	0.005	0.000	0.000	0.000	0.000
32	D	54	THR	0	-0.029	-0.015	39.768	0.005	0.005	0.000	0.000	0.000	0.000
33	D	55	PRO	0	-0.084	-0.042	41.713	0.004	0.004	0.000	0.000	0.000	0.000
34	D	56	ASN	0	-0.033	-0.033	41.861	0.005	0.005	0.000	0.000	0.000	0.000
35	D	57	ILE	0	-0.008	0.008	41.301	0.000	0.000	0.000	0.000	0.000	0.000
36	D	58	ASP	-1	-0.925	-0.965	44.188	-0.060	-0.060	0.000	0.000	0.000	0.000
37	D	59	ASP	-1	-0.878	-0.932	46.293	-0.062	-0.062	0.000	0.000	0.000	0.000
38	D	60	PRO	0	0.006	-0.011	44.396	-0.003	-0.003	0.000	0.000	0.000	0.000
39	D	61	ALA	0	0.006	0.008	43.371	-0.003	-0.003	0.000	0.000	0.000	0.000
40	D	62	MET	0	-0.010	-0.002	42.527	-0.005	-0.005	0.000	0.000	0.000	0.000
41	D	63	VAL	0	-0.011	-0.006	39.708	-0.005	-0.005	0.000	0.000	0.000	0.000
42	D	64	GLU	-1	-0.809	-0.891	38.779	-0.089	-0.089	0.000	0.000	0.000	0.000
43	D	65	LEU	0	-0.021	0.005	37.970	-0.006	-0.006	0.000	0.000	0.000	0.000
44	D	66	LEU	0	-0.010	-0.004	37.151	-0.006	-0.006	0.000	0.000	0.000	0.000
45	D	67	VAL	0	0.012	-0.002	33.585	-0.008	-0.008	0.000	0.000	0.000	0.000
46	D	68	SER	0	-0.038	-0.042	33.093	-0.008	-0.008	0.000	0.000	0.000	0.000
47	D	69	SER	0	-0.026	-0.009	32.919	-0.005	-0.005	0.000	0.000	0.000	0.000
48	D	70	ILE	0	-0.015	0.013	28.827	-0.006	-0.006	0.000	0.000	0.000	0.000
49	D	71	PHE	0	0.009	0.004	27.852	-0.011	-0.011	0.000	0.000	0.000	0.000
50	D	72	ASP	-1	-0.866	-0.942	28.336	-0.132	-0.132	0.000	0.000	0.000	0.000
51	D	73	SER	0	-0.046	-0.017	26.115	-0.006	-0.006	0.000	0.000	0.000	0.000
52	D	74	GLY	0	-0.013	-0.013	24.906	-0.008	-0.008	0.000	0.000	0.000	0.000
53	D	75	TYR	0	-0.071	-0.032	21.944	-0.014	-0.014	0.000	0.000	0.000	0.000
54	D	76	TYR	0	0.031	0.008	22.056	-0.014	-0.014	0.000	0.000	0.000	0.000
55	D	77	SER	0	0.010	0.002	21.917	0.005	0.005	0.000	0.000	0.000	0.000
56	D	78	SER	0	-0.027	-0.015	24.223	0.008	0.008	0.000	0.000	0.000	0.000
57	D	79	ILE	0	0.000	0.009	27.380	-0.007	-0.007	0.000	0.000	0.000	0.000
58	D	80	ARG	1	0.875	0.936	30.258	0.098	0.098	0.000	0.000	0.000	0.000
59	D	81	VAL	0	0.015	0.017	33.396	-0.002	-0.002	0.000	0.000	0.000	0.000
60	D	82	VAL	0	0.005	0.007	36.235	0.002	0.002	0.000	0.000	0.000	0.000
61	D	83	ASP	-1	-0.737	-0.842	39.015	-0.062	-0.062	0.000	0.000	0.000	0.000
62	D	84	LEU	0	0.000	-0.012	38.905	0.002	0.002	0.000	0.000	0.000	0.000
63	D	85	LYS	1	0.834	0.916	42.824	0.062	0.062	0.000	0.000	0.000	0.000
64	D	86	THR	0	-0.067	-0.055	45.053	0.002	0.002	0.000	0.000	0.000	0.000
65	D	87	ASP	-1	-0.942	-0.958	39.896	-0.072	-0.072	0.000	0.000	0.000	0.000
66	D	88	GLN	0	-0.036	-0.017	40.656	-0.003	-0.003	0.000	0.000	0.000	0.000
67	D	89	THR	0	-0.050	-0.049	37.367	-0.001	-0.001	0.000	0.000	0.000	0.000
68	D	90	ILE	0	-0.028	-0.002	39.767	0.003	0.003	0.000	0.000	0.000	0.000
69	D	91	VAL	0	0.024	0.004	37.144	0.001	0.001	0.000	0.000	0.000	0.000
70	D	92	GLU	-1	-0.834	-0.908	33.660	-0.104	-0.104	0.000	0.000	0.000	0.000
71	D	93	ARG	1	0.784	0.885	31.497	0.104	0.104	0.000	0.000	0.000	0.000
72	D	94	ASN	0	-0.002	-0.017	29.049	-0.012	-0.012	0.000	0.000	0.000	0.000
73	D	95	GLY	0	0.039	0.021	26.899	0.006	0.006	0.000	0.000	0.000	0.000
74	D	96	ILE	0	-0.033	-0.005	22.475	0.002	0.002	0.000	0.000	0.000	0.000
75	D	97	PRO	0	-0.010	-0.003	21.750	-0.012	-0.012	0.000	0.000	0.000	0.000
76	D	98	ALA	0	-0.024	-0.014	18.558	-0.020	-0.020	0.000	0.000	0.000	0.000
77	D	99	VAL	0	0.004	-0.007	13.862	0.005	0.005	0.000	0.000	0.000	0.000
78	D	100	THR	0	-0.015	-0.012	17.278	0.011	0.011	0.000	0.000	0.000	0.000
79	D	101	ASN	0	-0.020	-0.011	15.904	-0.031	-0.031	0.000	0.000	0.000	0.000
80	D	102	VAL	0	0.011	0.013	18.743	0.024	0.024	0.000	0.000	0.000	0.000
81	D	103	PRO	0	-0.013	0.005	20.253	-0.008	-0.008	0.000	0.000	0.000	0.000
82	D	104	ASP	-1	-0.837	-0.926	19.827	-0.154	-0.154	0.000	0.000	0.000	0.000
83	D	105	TRP	0	-0.054	-0.051	22.557	0.008	0.008	0.000	0.000	0.000	0.000
84	D	106	PHE	0	0.036	0.027	25.189	0.008	0.008	0.000	0.000	0.000	0.000
85	D	107	VAL	0	0.030	0.011	21.984	0.004	0.004	0.000	0.000	0.000	0.000
86	D	108	LYS	1	0.897	0.947	25.443	0.096	0.096	0.000	0.000	0.000	0.000
87	D	109	LEU	0	-0.049	-0.012	28.021	0.005	0.005	0.000	0.000	0.000	0.000
88	D	110	ILE	0	-0.006	-0.008	28.339	0.005	0.005	0.000	0.000	0.000	0.000
89	D	111	GLY	0	-0.026	0.003	29.553	0.002	0.002	0.000	0.000	0.000	0.000
90	D	112	LEU	0	-0.030	-0.023	26.847	0.002	0.002	0.000	0.000	0.000	0.000
91	D	113	GLU	-1	-0.897	-0.935	28.494	-0.106	-0.106	0.000	0.000	0.000	0.000
92	D	114	PRO	0	-0.034	-0.043	27.550	-0.007	-0.007	0.000	0.000	0.000	0.000
93	D	115	ALA	0	-0.006	0.009	28.040	-0.010	-0.010	0.000	0.000	0.000	0.000
94	D	116	GLY	0	-0.032	-0.009	29.185	-0.006	-0.006	0.000	0.000	0.000	0.000
95	D	117	GLY	0	-0.006	0.001	29.998	0.008	0.008	0.000	0.000	0.000	0.000
96	D	118	ASP	-1	-0.959	-0.986	30.831	-0.100	-0.100	0.000	0.000	0.000	0.000
97	D	119	ALA	0	0.031	0.019	33.024	0.003	0.003	0.000	0.000	0.000	0.000
98	D	120	LEU	0	-0.003	-0.003	34.230	-0.002	-0.002	0.000	0.000	0.000	0.000
99	D	121	VAL	0	0.012	0.009	33.304	-0.002	-0.002	0.000	0.000	0.000	0.000
100	D	122	SER	0	-0.004	-0.024	36.734	0.003	0.003	0.000	0.000	0.000	0.000
101	D	123	ARG	1	0.851	0.909	37.297	0.056	0.056	0.000	0.000	0.000	0.000
102	D	124	GLY	0	0.007	0.000	41.198	0.004	0.004	0.000	0.000	0.000	0.000
103	D	125	TRP	0	-0.020	-0.020	44.377	0.000	0.000	0.000	0.000	0.000	0.000
104	D	126	GLU	-1	-0.853	-0.894	42.655	-0.051	-0.051	0.000	0.000	0.000	0.000
105	D	127	GLN	0	-0.006	0.008	40.670	-0.006	-0.006	0.000	0.000	0.000	0.000
106	D	128	ALA	0	-0.014	-0.010	38.280	0.002	0.002	0.000	0.000	0.000	0.000
107	D	129	ALA	0	-0.019	-0.009	33.297	0.000	0.000	0.000	0.000	0.000	0.000
108	D	130	ARG	1	0.807	0.889	33.124	0.090	0.090	0.000	0.000	0.000	0.000
109	D	131	VAL	0	-0.026	0.003	28.208	-0.004	-0.004	0.000	0.000	0.000	0.000
110	D	132	GLU	-1	-0.803	-0.888	28.683	-0.097	-0.097	0.000	0.000	0.000	0.000
111	D	133	VAL	0	-0.023	-0.016	25.419	-0.013	-0.013	0.000	0.000	0.000	0.000
112	D	134	VAL	0	0.028	0.009	24.534	0.011	0.011	0.000	0.000	0.000	0.000
113	D	135	SER	0	0.014	0.013	23.566	-0.020	-0.020	0.000	0.000	0.000	0.000
114	D	136	HIS	0	0.042	0.016	16.557	0.020	0.020	0.000	0.000	0.000	0.000
115	D	137	PRO	0	0.060	0.032	21.358	-0.002	-0.002	0.000	0.000	0.000	0.000
116	D	138	MET	0	-0.021	-0.008	14.590	0.003	0.003	0.000	0.000	0.000	0.000
117	D	139	PHE	0	0.047	0.017	18.389	0.005	0.005	0.000	0.000	0.000	0.000
118	D	140	ALA	0	0.036	0.028	22.383	0.012	0.012	0.000	0.000	0.000	0.000
119	D	141	LEU	0	0.011	-0.004	22.118	0.011	0.011	0.000	0.000	0.000	0.000
120	D	142	ALA	0	0.009	0.005	21.292	0.009	0.009	0.000	0.000	0.000	0.000
121	D	143	LYS	1	0.855	0.923	23.328	0.154	0.154	0.000	0.000	0.000	0.000
122	D	144	LEU	0	0.027	0.022	26.814	0.011	0.011	0.000	0.000	0.000	0.000
123	D	145	TRP	0	-0.002	-0.008	23.116	0.014	0.014	0.000	0.000	0.000	0.000
124	D	146	GLN	0	0.020	-0.006	24.020	-0.007	-0.007	0.000	0.000	0.000	0.000
125	D	147	SER	0	-0.033	-0.014	27.588	0.008	0.008	0.000	0.000	0.000	0.000
126	D	148	ALA	0	-0.041	-0.022	29.645	0.007	0.007	0.000	0.000	0.000	0.000
127	D	149	LEU	0	-0.075	-0.024	25.867	0.005	0.005	0.000	0.000	0.000	0.000
128	D	150	GLY	0	-0.038	-0.004	30.539	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)