FMO DATABASE

FMODB ID: 1JGZZ

Calculation Name: 2P04-A-Xray311

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2P04

Chain ID: A

ChEMBL ID:

UniProt ID: D0VWX5

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	108
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-871015.635476
FMO2-HF: Nuclear repulsion	827819.689676
FMO2-HF: Total energy	-43195.945799
FMO2-MP2: Total energy	-43322.636776

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:1:MET )

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

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.
-1.306	0.91	2.497	-0.9	-3.814	0

Interaction energy analysis for fragmet #1(A:1:MET )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / 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

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].
3	A	3	PRO	0	-0.008	0.010	2.102	0.078	2.785	2.422	-1.562	-3.568
4	A	4	PRO	0	0.003	0.006	4.034	-1.281	-1.772	0.075	0.662	-0.246
5	A	5	HIS	0	0.035	0.005	7.405	0.043	0.043	0.000	0.000	0.000
6	A	6	LEU	0	-0.029	-0.008	9.610	-0.140	-0.140	0.000	0.000	0.000
7	A	7	THR	0	0.025	0.003	12.976	0.089	0.089	0.000	0.000	0.000
8	A	8	LEU	0	-0.029	-0.007	15.487	-0.046	-0.046	0.000	0.000	0.000
9	A	9	SER	0	0.048	0.027	19.203	0.004	0.004	0.000	0.000	0.000
10	A	10	PRO	0	0.086	0.021	21.257	0.005	0.005	0.000	0.000	0.000
11	A	11	GLU	-1	-0.909	-0.945	23.507	0.044	0.044	0.000	0.000	0.000
12	A	12	LEU	0	0.010	-0.001	21.735	0.000	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.010	-0.004	20.648	0.005	0.005	0.000	0.000	0.000
14	A	14	ALA	0	0.008	0.000	23.665	0.001	0.001	0.000	0.000	0.000
15	A	15	LYS	1	0.882	0.951	27.114	-0.057	-0.057	0.000	0.000	0.000
16	A	16	ALA	0	-0.022	-0.005	24.322	-0.001	-0.001	0.000	0.000	0.000
17	A	17	PHE	0	-0.019	-0.017	21.981	0.005	0.005	0.000	0.000	0.000
18	A	18	PRO	0	0.032	0.024	26.941	-0.003	-0.003	0.000	0.000	0.000
19	A	19	PHE	0	-0.018	-0.034	29.830	-0.007	-0.007	0.000	0.000	0.000
20	A	20	HIS	0	-0.010	0.012	25.468	0.003	0.003	0.000	0.000	0.000
21	A	21	PHE	0	0.027	0.010	27.271	-0.010	-0.010	0.000	0.000	0.000
22	A	22	ALA	0	0.015	0.026	24.546	0.014	0.014	0.000	0.000	0.000
23	A	23	PHE	0	-0.006	-0.013	25.930	-0.011	-0.011	0.000	0.000	0.000
24	A	24	SER	0	0.080	0.007	25.915	0.010	0.010	0.000	0.000	0.000
25	A	25	ARG	1	0.883	0.928	23.105	-0.077	-0.077	0.000	0.000	0.000
26	A	26	ASN	0	-0.033	0.021	27.801	0.004	0.004	0.000	0.000	0.000
27	A	27	ARG	1	0.897	0.942	30.306	-0.051	-0.051	0.000	0.000	0.000
28	A	28	GLU	-1	-0.854	-0.910	31.392	0.037	0.037	0.000	0.000	0.000
29	A	29	ILE	0	-0.023	-0.010	30.246	0.008	0.008	0.000	0.000	0.000
30	A	30	VAL	0	0.031	0.021	26.450	-0.006	-0.006	0.000	0.000	0.000
31	A	31	GLN	0	-0.036	-0.033	24.335	-0.008	-0.008	0.000	0.000	0.000
32	A	32	THR	0	0.012	-0.005	28.891	0.004	0.004	0.000	0.000	0.000
33	A	33	GLY	0	-0.035	-0.002	29.433	-0.001	-0.001	0.000	0.000	0.000
34	A	34	GLU	-1	-0.842	-0.940	30.085	0.052	0.052	0.000	0.000	0.000
35	A	35	VAL	0	-0.062	-0.027	33.110	-0.005	-0.005	0.000	0.000	0.000
36	A	36	LEU	0	-0.010	-0.010	32.024	-0.004	-0.004	0.000	0.000	0.000
37	A	37	GLU	-1	-0.945	-0.966	33.776	0.042	0.042	0.000	0.000	0.000
38	A	38	ARG	1	0.938	0.984	36.301	-0.047	-0.047	0.000	0.000	0.000
39	A	39	ILE	0	-0.081	-0.054	37.939	-0.003	-0.003	0.000	0.000	0.000
40	A	40	SER	0	-0.050	-0.047	38.448	-0.001	-0.001	0.000	0.000	0.000
41	A	41	PRO	0	-0.018	0.000	40.452	-0.002	-0.002	0.000	0.000	0.000
42	A	42	GLU	-1	-0.924	-0.956	41.243	0.029	0.029	0.000	0.000	0.000
43	A	43	PRO	0	0.036	0.033	39.055	0.003	0.003	0.000	0.000	0.000
44	A	44	LEU	0	0.021	0.003	34.814	0.000	0.000	0.000	0.000	0.000
45	A	45	VAL	0	0.012	0.010	32.203	0.002	0.002	0.000	0.000	0.000
46	A	46	GLY	0	0.010	0.003	33.796	-0.005	-0.005	0.000	0.000	0.000
47	A	47	LYS	1	0.819	0.926	35.534	-0.034	-0.034	0.000	0.000	0.000
48	A	48	LEU	0	0.014	0.015	34.860	0.004	0.004	0.000	0.000	0.000
49	A	49	ILE	0	0.043	0.006	30.972	0.000	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.884	-0.947	34.358	0.049	0.049	0.000	0.000	0.000
51	A	51	GLN	0	-0.030	-0.006	37.069	-0.002	-0.002	0.000	0.000	0.000
52	A	52	HIS	1	0.843	0.916	36.623	-0.045	-0.045	0.000	0.000	0.000
53	A	53	PHE	0	0.002	0.013	33.915	0.002	0.002	0.000	0.000	0.000
54	A	54	GLN	0	0.041	0.032	36.395	-0.002	-0.002	0.000	0.000	0.000
55	A	55	ILE	0	0.025	0.007	30.632	0.004	0.004	0.000	0.000	0.000
56	A	56	ASN	0	-0.042	-0.013	34.245	-0.002	-0.002	0.000	0.000	0.000
57	A	57	ARG	1	0.853	0.925	31.911	-0.073	-0.073	0.000	0.000	0.000
58	A	58	PRO	0	0.128	0.063	28.401	0.002	0.002	0.000	0.000	0.000
59	A	59	LYS	1	0.897	0.948	31.493	-0.063	-0.063	0.000	0.000	0.000
60	A	60	ILE	0	0.000	0.005	29.185	-0.003	-0.003	0.000	0.000	0.000
61	A	61	LEU	0	0.053	0.016	33.520	-0.002	-0.002	0.000	0.000	0.000
62	A	62	ILE	0	-0.014	0.002	32.006	0.006	0.006	0.000	0.000	0.000
63	A	63	ASP	-1	-0.859	-0.941	30.710	0.063	0.063	0.000	0.000	0.000
64	A	64	PHE	0	0.041	0.025	23.284	0.007	0.007	0.000	0.000	0.000
65	A	65	ASP	-1	-0.785	-0.908	25.446	0.091	0.091	0.000	0.000	0.000
66	A	66	ALA	0	-0.086	-0.034	25.889	0.011	0.011	0.000	0.000	0.000
67	A	67	ILE	0	-0.029	-0.020	24.901	0.007	0.007	0.000	0.000	0.000
68	A	68	SER	0	-0.024	0.001	21.946	0.012	0.012	0.000	0.000	0.000
69	A	69	LYS	1	0.876	0.948	21.437	-0.074	-0.074	0.000	0.000	0.000
70	A	70	GLN	0	-0.003	-0.023	22.904	-0.002	-0.002	0.000	0.000	0.000
71	A	71	PRO	0	0.034	0.011	18.055	0.002	0.002	0.000	0.000	0.000
72	A	72	ARG	1	0.947	0.972	14.336	-0.278	-0.278	0.000	0.000	0.000
73	A	73	ALA	0	-0.024	0.019	20.581	-0.008	-0.008	0.000	0.000	0.000
74	A	74	LEU	0	-0.014	-0.007	23.860	0.007	0.007	0.000	0.000	0.000
75	A	75	PHE	0	0.007	-0.005	24.541	-0.012	-0.012	0.000	0.000	0.000
76	A	76	ILE	0	-0.051	-0.026	28.172	0.000	0.000	0.000	0.000	0.000
77	A	77	LEU	0	0.009	0.000	30.017	-0.003	-0.003	0.000	0.000	0.000
78	A	78	GLU	-1	-0.879	-0.930	33.291	0.053	0.053	0.000	0.000	0.000
79	A	79	PHE	0	-0.001	-0.010	36.505	0.000	0.000	0.000	0.000	0.000
80	A	80	LEU	0	0.023	-0.012	37.738	-0.003	-0.003	0.000	0.000	0.000
81	A	81	HIS	0	-0.028	0.002	40.867	-0.003	-0.003	0.000	0.000	0.000
82	A	82	ASN	0	0.025	-0.001	40.106	0.000	0.000	0.000	0.000	0.000
83	A	83	GLY	0	0.051	0.038	41.409	0.000	0.000	0.000	0.000	0.000
84	A	84	MET	0	-0.072	-0.015	36.909	0.003	0.003	0.000	0.000	0.000
85	A	85	GLN	0	0.025	0.008	35.487	0.002	0.002	0.000	0.000	0.000
86	A	86	LEU	0	-0.042	-0.030	31.244	0.002	0.002	0.000	0.000	0.000
87	A	87	LYS	1	0.947	0.971	28.221	-0.108	-0.108	0.000	0.000	0.000
88	A	88	GLY	0	-0.004	-0.013	25.651	0.002	0.002	0.000	0.000	0.000
89	A	89	GLN	0	0.004	0.008	18.935	0.007	0.007	0.000	0.000	0.000
90	A	90	MET	0	0.007	0.028	22.690	-0.005	-0.005	0.000	0.000	0.000
91	A	91	MET	0	-0.039	-0.018	17.471	0.009	0.009	0.000	0.000	0.000
92	A	92	TYR	0	0.018	-0.006	17.927	-0.016	-0.016	0.000	0.000	0.000
93	A	93	GLN	0	0.018	0.014	15.035	0.081	0.081	0.000	0.000	0.000
94	A	94	PRO	0	-0.036	-0.036	14.328	-0.034	-0.034	0.000	0.000	0.000
95	A	95	GLU	-1	-0.981	-0.966	13.728	0.159	0.159	0.000	0.000	0.000
96	A	96	GLU	-1	-0.882	-0.961	16.668	0.115	0.115	0.000	0.000	0.000
97	A	97	GLU	-1	-0.939	-0.957	19.574	0.044	0.044	0.000	0.000	0.000
98	A	98	VAL	0	-0.036	-0.018	21.046	-0.012	-0.012	0.000	0.000	0.000
99	A	99	ILE	0	-0.046	-0.016	21.040	0.029	0.029	0.000	0.000	0.000
100	A	100	PHE	0	0.022	0.009	19.522	-0.016	-0.016	0.000	0.000	0.000
101	A	101	PHE	0	0.021	0.006	22.874	0.012	0.012	0.000	0.000	0.000
102	A	102	LEU	0	-0.011	-0.005	20.174	-0.008	-0.008	0.000	0.000	0.000
103	A	103	GLY	0	0.018	-0.013	24.322	0.004	0.004	0.000	0.000	0.000
104	A	104	SER	0	-0.039	-0.024	27.534	-0.004	-0.004	0.000	0.000	0.000
105	A	105	PRO	0	0.025	0.015	30.074	0.001	0.001	0.000	0.000	0.000
106	A	106	TRP	0	-0.082	-0.037	32.226	0.006	0.006	0.000	0.000	0.000
107	A	107	ILE	0	0.007	0.000	33.741	-0.004	-0.004	0.000	0.000	0.000
108	A	108	NME	0	0.011	0.013	35.428	-0.002	-0.002	0.000	0.000	0.000

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