FMO DATABASE

FMODB ID: VQMY1

Calculation Name: 2P04-A-Xray372

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: 2023-09-24

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	107
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-869604.657221
FMO2-HF: Nuclear repulsion	826427.837438
FMO2-HF: Total energy	-43176.819784
FMO2-MP2: Total energy	-43303.4083

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.
-1.331	0.919	2.444	-0.851	-3.842	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 : -0.012 / 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	-0.007	0.011	2.102	-0.045	2.696	2.375	-1.521	-3.594
4	A	4	PRO	0	0.003	0.005	4.034	-1.208	-1.699	0.069	0.670	-0.248
5	A	5	HIS	0	0.034	0.004	7.405	0.059	0.059	0.000	0.000	0.000
6	A	6	LEU	0	-0.028	-0.007	9.610	-0.137	-0.137	0.000	0.000	0.000
7	A	7	THR	0	0.024	0.003	12.976	0.090	0.090	0.000	0.000	0.000
8	A	8	LEU	0	-0.027	-0.006	15.487	-0.045	-0.045	0.000	0.000	0.000
9	A	9	SER	0	0.048	0.027	19.203	0.005	0.005	0.000	0.000	0.000
10	A	10	PRO	0	0.086	0.020	21.257	0.005	0.005	0.000	0.000	0.000
11	A	11	GLU	-1	-0.910	-0.946	23.507	0.045	0.045	0.000	0.000	0.000
12	A	12	LEU	0	0.009	-0.001	21.736	0.000	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.009	-0.004	20.648	0.005	0.005	0.000	0.000	0.000
14	A	14	ALA	0	0.007	0.000	23.665	0.001	0.001	0.000	0.000	0.000
15	A	15	LYS	1	0.880	0.950	27.114	-0.058	-0.058	0.000	0.000	0.000
16	A	16	ALA	0	-0.022	-0.005	24.322	-0.002	-0.002	0.000	0.000	0.000
17	A	17	PHE	0	-0.017	-0.016	21.982	0.005	0.005	0.000	0.000	0.000
18	A	18	PRO	0	0.030	0.024	26.941	-0.002	-0.002	0.000	0.000	0.000
19	A	19	PHE	0	-0.020	-0.035	29.830	-0.007	-0.007	0.000	0.000	0.000
20	A	20	HIS	0	-0.005	0.013	25.468	0.003	0.003	0.000	0.000	0.000
21	A	21	PHE	0	0.020	0.009	27.273	-0.010	-0.010	0.000	0.000	0.000
22	A	22	ALA	0	0.018	0.027	24.545	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	0.079	0.008	25.915	0.010	0.010	0.000	0.000	0.000
25	A	25	ARG	1	0.885	0.928	23.106	-0.081	-0.081	0.000	0.000	0.000
26	A	26	ASN	0	-0.032	0.020	27.801	0.004	0.004	0.000	0.000	0.000
27	A	27	ARG	1	0.902	0.944	30.306	-0.053	-0.053	0.000	0.000	0.000
28	A	28	GLU	-1	-0.860	-0.912	31.392	0.039	0.039	0.000	0.000	0.000
29	A	29	ILE	0	-0.025	-0.011	30.246	0.008	0.008	0.000	0.000	0.000
30	A	30	VAL	0	0.032	0.021	26.450	-0.006	-0.006	0.000	0.000	0.000
31	A	31	GLN	0	-0.035	-0.033	24.335	-0.008	-0.008	0.000	0.000	0.000
32	A	32	THR	0	0.009	-0.005	28.891	0.004	0.004	0.000	0.000	0.000
33	A	33	GLY	0	-0.032	-0.001	29.433	-0.001	-0.001	0.000	0.000	0.000
34	A	34	GLU	-1	-0.841	-0.940	30.085	0.053	0.053	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	-0.012	-0.012	32.023	-0.004	-0.004	0.000	0.000	0.000
37	A	37	GLU	-1	-0.941	-0.964	33.776	0.044	0.044	0.000	0.000	0.000
38	A	38	ARG	1	0.937	0.983	36.301	-0.048	-0.048	0.000	0.000	0.000
39	A	39	ILE	0	-0.080	-0.053	37.940	-0.003	-0.003	0.000	0.000	0.000
40	A	40	SER	0	-0.048	-0.045	38.449	-0.001	-0.001	0.000	0.000	0.000
41	A	41	PRO	0	-0.015	0.001	40.452	-0.002	-0.002	0.000	0.000	0.000
42	A	42	GLU	-1	-0.928	-0.958	41.243	0.030	0.030	0.000	0.000	0.000
43	A	43	PRO	0	0.036	0.033	39.054	0.003	0.003	0.000	0.000	0.000
44	A	44	LEU	0	0.019	0.002	34.816	0.000	0.000	0.000	0.000	0.000
45	A	45	VAL	0	0.014	0.011	32.205	0.002	0.002	0.000	0.000	0.000
46	A	46	GLY	0	0.008	0.003	33.796	-0.005	-0.005	0.000	0.000	0.000
47	A	47	LYS	1	0.822	0.927	35.534	-0.035	-0.035	0.000	0.000	0.000
48	A	48	LEU	0	0.011	0.015	34.860	0.004	0.004	0.000	0.000	0.000
49	A	49	ILE	0	0.049	0.008	30.974	-0.001	-0.001	0.000	0.000	0.000
50	A	50	GLU	-1	-0.890	-0.950	34.358	0.051	0.051	0.000	0.000	0.000
51	A	51	GLN	0	-0.029	-0.006	37.069	-0.002	-0.002	0.000	0.000	0.000
52	A	52	HIS	1	0.845	0.916	36.623	-0.047	-0.047	0.000	0.000	0.000
53	A	53	PHE	0	0.004	0.014	33.915	0.001	0.001	0.000	0.000	0.000
54	A	54	GLN	0	0.041	0.033	36.395	-0.002	-0.002	0.000	0.000	0.000
55	A	55	ILE	0	0.023	0.006	30.635	0.004	0.004	0.000	0.000	0.000
56	A	56	ASN	0	-0.040	-0.013	34.245	-0.002	-0.002	0.000	0.000	0.000
57	A	57	ARG	1	0.854	0.925	31.911	-0.076	-0.076	0.000	0.000	0.000
58	A	58	PRO	0	0.126	0.063	28.402	0.002	0.002	0.000	0.000	0.000
59	A	59	LYS	1	0.896	0.946	31.494	-0.065	-0.065	0.000	0.000	0.000
60	A	60	ILE	0	0.003	0.007	29.191	-0.003	-0.003	0.000	0.000	0.000
61	A	61	LEU	0	0.050	0.016	33.521	-0.001	-0.001	0.000	0.000	0.000
62	A	62	ILE	0	-0.014	0.001	32.006	0.006	0.006	0.000	0.000	0.000
63	A	63	ASP	-1	-0.862	-0.942	30.710	0.065	0.065	0.000	0.000	0.000
64	A	64	PHE	0	0.045	0.027	23.284	0.007	0.007	0.000	0.000	0.000
65	A	65	ASP	-1	-0.786	-0.908	25.446	0.095	0.095	0.000	0.000	0.000
66	A	66	ALA	0	-0.087	-0.035	25.889	0.011	0.011	0.000	0.000	0.000
67	A	67	ILE	0	-0.028	-0.020	24.902	0.007	0.007	0.000	0.000	0.000
68	A	68	SER	0	-0.021	0.001	21.946	0.012	0.012	0.000	0.000	0.000
69	A	69	LYS	1	0.872	0.947	21.437	-0.078	-0.078	0.000	0.000	0.000
70	A	70	GLN	0	-0.003	-0.023	22.905	-0.003	-0.003	0.000	0.000	0.000
71	A	71	PRO	0	0.036	0.012	18.055	0.001	0.001	0.000	0.000	0.000
72	A	72	ARG	1	0.945	0.971	14.337	-0.286	-0.286	0.000	0.000	0.000
73	A	73	ALA	0	-0.023	0.020	20.582	-0.008	-0.008	0.000	0.000	0.000
74	A	74	LEU	0	-0.015	-0.007	23.860	0.007	0.007	0.000	0.000	0.000
75	A	75	PHE	0	0.008	-0.005	24.542	-0.012	-0.012	0.000	0.000	0.000
76	A	76	ILE	0	-0.050	-0.026	28.172	0.001	0.001	0.000	0.000	0.000
77	A	77	LEU	0	0.007	-0.001	30.019	-0.003	-0.003	0.000	0.000	0.000
78	A	78	GLU	-1	-0.879	-0.930	33.291	0.055	0.055	0.000	0.000	0.000
79	A	79	PHE	0	0.000	-0.009	36.505	0.000	0.000	0.000	0.000	0.000
80	A	80	LEU	0	0.022	-0.013	37.738	-0.003	-0.003	0.000	0.000	0.000
81	A	81	HIS	0	-0.026	0.003	40.867	-0.003	-0.003	0.000	0.000	0.000
82	A	82	ASN	0	0.023	-0.002	40.105	0.000	0.000	0.000	0.000	0.000
83	A	83	GLY	0	0.053	0.039	41.410	-0.001	-0.001	0.000	0.000	0.000
84	A	84	MET	0	-0.072	-0.014	36.909	0.002	0.002	0.000	0.000	0.000
85	A	85	GLN	0	0.021	0.006	35.488	0.002	0.002	0.000	0.000	0.000
86	A	86	LEU	0	-0.043	-0.030	31.245	0.001	0.001	0.000	0.000	0.000
87	A	87	LYS	1	0.948	0.971	28.222	-0.111	-0.111	0.000	0.000	0.000
88	A	88	GLY	0	-0.003	-0.013	25.651	0.002	0.002	0.000	0.000	0.000
89	A	89	GLN	0	0.002	0.008	18.935	0.007	0.007	0.000	0.000	0.000
90	A	90	MET	0	0.011	0.029	22.690	-0.005	-0.005	0.000	0.000	0.000
91	A	91	MET	0	-0.045	-0.019	17.471	0.009	0.009	0.000	0.000	0.000
92	A	92	TYR	0	0.021	-0.005	17.927	-0.016	-0.016	0.000	0.000	0.000
93	A	93	GLN	0	0.016	0.014	15.035	0.083	0.083	0.000	0.000	0.000
94	A	94	PRO	0	-0.034	-0.035	14.328	-0.034	-0.034	0.000	0.000	0.000
95	A	95	GLU	-1	-0.980	-0.966	13.728	0.169	0.169	0.000	0.000	0.000
96	A	96	GLU	-1	-0.884	-0.962	16.668	0.121	0.121	0.000	0.000	0.000
97	A	97	GLU	-1	-0.937	-0.957	19.574	0.047	0.047	0.000	0.000	0.000
98	A	98	VAL	0	-0.038	-0.017	21.047	-0.013	-0.013	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	0.010	19.522	-0.016	-0.016	0.000	0.000	0.000
101	A	101	PHE	0	0.020	0.006	22.874	0.012	0.012	0.000	0.000	0.000
102	A	102	LEU	0	-0.011	-0.005	20.175	-0.008	-0.008	0.000	0.000	0.000
103	A	103	GLY	0	0.019	-0.013	24.323	0.004	0.004	0.000	0.000	0.000
104	A	104	SER	0	-0.040	-0.023	27.535	-0.004	-0.004	0.000	0.000	0.000
105	A	105	PRO	0	0.027	0.015	30.074	0.002	0.002	0.000	0.000	0.000
106	A	106	TRP	0	-0.074	-0.032	32.227	0.006	0.006	0.000	0.000	0.000
107	A	107	ILE	0	0.012	0.010	33.741	-0.005	-0.005	0.000	0.000	0.000

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