FMO DATABASE

FMODB ID: 1NR9Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-870386.180491
FMO2-HF: Nuclear repulsion	827208.752429
FMO2-HF: Total energy	-43177.428062
FMO2-MP2: Total energy	-43304.010323

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.
-1.997	0.184	3.401	-0.458	-5.124	-0.001

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 : 0.006

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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	3	PRO	0	-0.003	0.008	2.179	-1.437	1.983	3.307	-2.024	-4.703	0.000
4	A	4	PRO	0	0.004	0.007	3.774	-0.748	-1.987	0.094	1.566	-0.421	-0.001
5	A	5	HIS	0	0.036	0.002	7.196	0.089	0.089	0.000	0.000	0.000	0.000
6	A	6	LEU	0	-0.035	-0.008	9.754	-0.165	-0.165	0.000	0.000	0.000	0.000
7	A	7	THR	0	0.025	0.003	12.854	0.064	0.064	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.023	-0.001	15.409	-0.037	-0.037	0.000	0.000	0.000	0.000
9	A	9	SER	0	0.050	0.024	19.132	0.005	0.005	0.000	0.000	0.000	0.000
10	A	10	PRO	0	0.082	0.018	21.285	-0.001	-0.001	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.913	-0.955	23.550	0.049	0.049	0.000	0.000	0.000	0.000
12	A	12	LEU	0	0.021	0.010	21.622	-0.003	-0.003	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.003	-0.004	20.453	-0.001	-0.001	0.000	0.000	0.000	0.000
14	A	14	ALA	0	0.013	0.001	23.601	-0.003	-0.003	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.850	0.927	27.041	-0.057	-0.057	0.000	0.000	0.000	0.000
16	A	16	ALA	0	-0.028	-0.012	23.918	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	17	PHE	0	-0.008	-0.010	21.231	0.000	0.000	0.000	0.000	0.000	0.000
18	A	18	PRO	0	0.019	0.021	26.467	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	19	PHE	0	-0.016	-0.038	29.341	-0.005	-0.005	0.000	0.000	0.000	0.000
20	A	20	HIS	0	-0.001	0.022	25.284	0.002	0.002	0.000	0.000	0.000	0.000
21	A	21	PHE	0	0.016	0.005	26.968	-0.006	-0.006	0.000	0.000	0.000	0.000
22	A	22	ALA	0	0.022	0.029	24.386	0.008	0.008	0.000	0.000	0.000	0.000
23	A	23	PHE	0	-0.006	-0.013	25.691	-0.008	-0.008	0.000	0.000	0.000	0.000
24	A	24	SER	0	0.096	0.033	25.637	0.007	0.007	0.000	0.000	0.000	0.000
25	A	25	ARG	1	0.860	0.891	22.357	-0.081	-0.081	0.000	0.000	0.000	0.000
26	A	26	ASN	0	-0.049	-0.023	27.611	0.001	0.001	0.000	0.000	0.000	0.000
27	A	27	ARG	1	0.822	0.893	29.991	-0.049	-0.049	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.865	-0.898	31.207	0.045	0.045	0.000	0.000	0.000	0.000
29	A	29	ILE	0	-0.016	-0.008	30.102	0.006	0.006	0.000	0.000	0.000	0.000
30	A	30	VAL	0	0.019	0.010	26.458	-0.004	-0.004	0.000	0.000	0.000	0.000
31	A	31	GLN	0	-0.038	-0.032	24.384	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	32	THR	0	-0.035	-0.039	29.102	0.002	0.002	0.000	0.000	0.000	0.000
33	A	33	GLY	0	-0.022	0.003	29.381	0.001	0.001	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.818	-0.915	29.976	0.046	0.046	0.000	0.000	0.000	0.000
35	A	35	VAL	0	-0.072	-0.034	32.977	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	36	LEU	0	-0.011	-0.004	31.503	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.883	-0.927	33.490	0.046	0.046	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.921	0.972	36.250	-0.039	-0.039	0.000	0.000	0.000	0.000
39	A	39	ILE	0	-0.064	-0.041	37.130	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	40	SER	0	-0.040	-0.025	38.225	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	41	PRO	0	-0.016	-0.001	40.257	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.893	-0.953	41.547	0.032	0.032	0.000	0.000	0.000	0.000
43	A	43	PRO	0	0.035	0.018	39.195	0.002	0.002	0.000	0.000	0.000	0.000
44	A	44	LEU	0	0.032	0.006	34.791	0.000	0.000	0.000	0.000	0.000	0.000
45	A	45	VAL	0	0.013	0.009	32.371	0.001	0.001	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.004	0.004	33.827	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	47	LYS	1	0.821	0.938	35.484	-0.036	-0.036	0.000	0.000	0.000	0.000
48	A	48	LEU	0	0.005	0.011	34.689	0.003	0.003	0.000	0.000	0.000	0.000
49	A	49	ILE	0	0.046	0.007	29.842	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.819	-0.898	33.941	0.043	0.043	0.000	0.000	0.000	0.000
51	A	51	GLN	0	-0.035	-0.005	36.500	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	52	HIS	1	0.827	0.907	36.334	-0.040	-0.040	0.000	0.000	0.000	0.000
53	A	53	PHE	0	0.013	0.013	33.466	0.000	0.000	0.000	0.000	0.000	0.000
54	A	54	GLN	0	0.038	0.030	35.843	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	55	ILE	0	0.024	0.010	29.898	0.002	0.002	0.000	0.000	0.000	0.000
56	A	56	ASN	0	-0.069	-0.041	33.640	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.854	0.929	31.421	-0.046	-0.046	0.000	0.000	0.000	0.000
58	A	58	PRO	0	0.124	0.062	27.777	0.002	0.002	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.918	0.957	30.935	-0.040	-0.040	0.000	0.000	0.000	0.000
60	A	60	ILE	0	0.004	0.001	28.316	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	61	LEU	0	0.040	0.014	32.674	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	62	ILE	0	-0.004	0.002	31.217	0.003	0.003	0.000	0.000	0.000	0.000
63	A	63	ASP	-1	-0.832	-0.928	29.496	0.055	0.055	0.000	0.000	0.000	0.000
64	A	64	PHE	0	0.030	0.027	22.976	0.002	0.002	0.000	0.000	0.000	0.000
65	A	65	ASP	-1	-0.747	-0.868	24.859	0.076	0.076	0.000	0.000	0.000	0.000
66	A	66	ALA	0	-0.056	-0.032	24.775	0.004	0.004	0.000	0.000	0.000	0.000
67	A	67	ILE	0	-0.033	-0.020	24.151	0.001	0.001	0.000	0.000	0.000	0.000
68	A	68	SER	0	-0.013	0.008	20.984	0.005	0.005	0.000	0.000	0.000	0.000
69	A	69	LYS	1	0.758	0.875	20.339	-0.064	-0.064	0.000	0.000	0.000	0.000
70	A	70	GLN	0	-0.012	-0.022	21.929	-0.006	-0.006	0.000	0.000	0.000	0.000
71	A	71	PRO	0	0.036	0.014	17.258	0.000	0.000	0.000	0.000	0.000	0.000
72	A	72	ARG	1	0.937	0.965	13.528	-0.108	-0.108	0.000	0.000	0.000	0.000
73	A	73	ALA	0	-0.015	0.022	20.077	-0.004	-0.004	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.019	-0.007	23.337	0.005	0.005	0.000	0.000	0.000	0.000
75	A	75	PHE	0	0.011	-0.003	23.948	-0.007	-0.007	0.000	0.000	0.000	0.000
76	A	76	ILE	0	-0.047	-0.026	27.640	0.001	0.001	0.000	0.000	0.000	0.000
77	A	77	LEU	0	0.008	0.002	29.399	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	78	GLU	-1	-0.875	-0.909	32.751	0.038	0.038	0.000	0.000	0.000	0.000
79	A	79	PHE	0	0.014	-0.007	35.896	0.001	0.001	0.000	0.000	0.000	0.000
80	A	80	LEU	0	0.008	-0.016	37.200	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	81	HIS	0	-0.036	-0.002	40.384	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	82	ASN	0	0.014	-0.021	39.548	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	83	GLY	0	0.051	0.041	40.871	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	84	MET	0	-0.062	0.003	35.767	0.001	0.001	0.000	0.000	0.000	0.000
85	A	85	GLN	0	0.024	0.008	35.016	0.001	0.001	0.000	0.000	0.000	0.000
86	A	86	LEU	0	-0.050	-0.029	30.694	0.001	0.001	0.000	0.000	0.000	0.000
87	A	87	LYS	1	0.967	0.978	27.766	-0.065	-0.065	0.000	0.000	0.000	0.000
88	A	88	GLY	0	-0.002	-0.013	25.134	0.002	0.002	0.000	0.000	0.000	0.000
89	A	89	GLN	0	-0.002	0.008	18.619	0.000	0.000	0.000	0.000	0.000	0.000
90	A	90	MET	0	0.010	0.027	22.170	0.001	0.001	0.000	0.000	0.000	0.000
91	A	91	MET	0	-0.049	-0.026	16.513	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	92	TYR	0	-0.043	-0.049	17.486	0.001	0.001	0.000	0.000	0.000	0.000
93	A	93	GLN	0	-0.047	-0.025	14.866	0.039	0.039	0.000	0.000	0.000	0.000
94	A	94	PRO	0	-0.021	-0.020	14.335	-0.018	-0.018	0.000	0.000	0.000	0.000
95	A	95	GLU	-1	-0.939	-0.954	13.801	0.226	0.226	0.000	0.000	0.000	0.000
96	A	96	GLU	-1	-0.868	-0.945	16.675	0.137	0.137	0.000	0.000	0.000	0.000
97	A	97	GLU	-1	-0.851	-0.880	19.538	0.073	0.073	0.000	0.000	0.000	0.000
98	A	98	VAL	0	-0.027	-0.012	20.963	-0.012	-0.012	0.000	0.000	0.000	0.000
99	A	99	ILE	0	-0.037	-0.012	20.739	0.016	0.016	0.000	0.000	0.000	0.000
100	A	100	PHE	0	0.030	0.015	19.924	-0.009	-0.009	0.000	0.000	0.000	0.000
101	A	101	PHE	0	0.007	-0.018	22.419	0.003	0.003	0.000	0.000	0.000	0.000
102	A	102	LEU	0	-0.005	-0.003	19.714	-0.003	-0.003	0.000	0.000	0.000	0.000
103	A	103	GLY	0	0.008	0.001	23.799	0.000	0.000	0.000	0.000	0.000	0.000
104	A	104	SER	0	-0.036	-0.021	27.014	-0.002	-0.002	0.000	0.000	0.000	0.000
105	A	105	PRO	0	0.030	0.011	29.572	0.000	0.000	0.000	0.000	0.000	0.000
106	A	106	TRP	0	-0.083	-0.036	31.739	0.003	0.003	0.000	0.000	0.000	0.000
107	A	107	ILE	0	0.020	0.011	33.247	-0.003	-0.003	0.000	0.000	0.000	0.000

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