FMO DATABASE

FMODB ID: GN211

Calculation Name: 1RP3-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1RP3

Chain ID: B

ChEMBL ID:

UniProt ID: O67268

Base Structure: X-ray

Registration Date: 2023-06-20

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	77
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-392620.998099
FMO2-HF: Nuclear repulsion	362251.101707
FMO2-HF: Total energy	-30369.896392
FMO2-MP2: Total energy	-30460.754174

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(B:2:VAL)

Summations of interaction energy for fragment #1(B:2:VAL)

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.
-17.631	-18.644	27.237	-13.075	-13.149	-0.015

Interaction energy analysis for fragmet #1(B:2:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.027 / q_NPA : -0.005

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	B	4	ARG	1	0.937	0.936	3.487	-5.241	-0.838	0.003	-2.375	-2.030	0.007
4	B	5	ILE	0	-0.002	0.003	2.498	-4.603	-3.060	2.183	-1.379	-2.347	0.014
5	B	6	GLU	-1	-0.760	-0.854	1.862	-3.654	-8.034	15.613	-7.272	-3.961	-0.010
6	B	7	LEU	0	0.016	0.014	3.230	-0.739	-0.824	0.065	0.354	-0.335	-0.001
7	B	8	SER	0	-0.024	-0.015	6.039	-0.311	-0.311	0.000	0.000	0.000	0.000
8	B	9	ARG	1	0.840	0.919	6.357	-0.291	-0.291	0.000	0.000	0.000	0.000
9	B	10	LEU	0	-0.027	-0.020	6.377	-0.238	-0.238	0.000	0.000	0.000	0.000
10	B	11	ILE	0	0.022	0.004	9.065	-0.080	-0.080	0.000	0.000	0.000	0.000
11	B	12	GLY	0	0.004	0.006	11.042	-0.061	-0.061	0.000	0.000	0.000	0.000
12	B	13	LEU	0	-0.030	-0.018	11.363	-0.065	-0.065	0.000	0.000	0.000	0.000
13	B	14	LEU	0	-0.017	-0.017	13.506	-0.040	-0.040	0.000	0.000	0.000	0.000
14	B	15	LEU	0	-0.071	-0.047	15.249	-0.015	-0.015	0.000	0.000	0.000	0.000
15	B	16	GLU	-1	-0.936	-0.929	16.927	0.192	0.192	0.000	0.000	0.000	0.000
16	B	17	THR	0	-0.087	-0.023	18.635	-0.019	-0.019	0.000	0.000	0.000	0.000
17	B	28	SER	0	0.002	-0.017	23.802	-0.008	-0.008	0.000	0.000	0.000	0.000
18	B	29	GLY	0	0.094	0.060	21.477	0.007	0.007	0.000	0.000	0.000	0.000
19	B	30	THR	0	-0.096	-0.048	22.135	-0.021	-0.021	0.000	0.000	0.000	0.000
20	B	31	ASN	0	0.083	0.009	21.467	-0.014	-0.014	0.000	0.000	0.000	0.000
21	B	32	LYS	1	0.952	0.990	20.887	0.048	0.048	0.000	0.000	0.000	0.000
22	B	33	ILE	0	-0.017	-0.010	20.898	-0.015	-0.015	0.000	0.000	0.000	0.000
23	B	34	GLU	-1	-0.866	-0.931	17.899	-0.066	-0.066	0.000	0.000	0.000	0.000
24	B	35	ASP	-1	-0.819	-0.925	16.382	-0.040	-0.040	0.000	0.000	0.000	0.000
25	B	36	LYS	1	0.868	0.955	16.050	0.197	0.197	0.000	0.000	0.000	0.000
26	B	37	VAL	0	0.013	-0.007	13.209	-0.044	-0.044	0.000	0.000	0.000	0.000
27	B	38	THR	0	0.034	0.017	11.623	-0.102	-0.102	0.000	0.000	0.000	0.000
28	B	39	LEU	0	0.010	-0.005	11.299	-0.059	-0.059	0.000	0.000	0.000	0.000
29	B	40	SER	0	-0.066	-0.028	12.322	-0.010	-0.010	0.000	0.000	0.000	0.000
30	B	41	LYS	1	0.946	0.978	7.806	0.497	0.497	0.000	0.000	0.000	0.000
31	B	42	ILE	0	0.018	0.010	7.481	-0.253	-0.253	0.000	0.000	0.000	0.000
32	B	43	ALA	0	0.016	0.004	8.637	-0.079	-0.079	0.000	0.000	0.000	0.000
33	B	44	GLN	0	-0.007	-0.009	7.878	0.110	0.110	0.000	0.000	0.000	0.000
34	B	45	GLU	-1	-0.890	-0.948	2.319	-4.693	-7.708	8.211	-1.976	-3.220	-0.030
35	B	46	LEU	0	-0.047	-0.028	5.455	0.026	0.026	0.000	0.000	0.000	0.000
36	B	47	SER	0	-0.014	0.016	8.146	0.094	0.094	0.000	0.000	0.000	0.000
37	B	48	LYS	1	0.802	0.908	2.365	2.302	2.823	1.162	-0.427	-1.256	0.005
38	B	49	ASN	0	-0.071	-0.048	6.042	-0.024	-0.024	0.000	0.000	0.000	0.000
39	B	50	ASP	-1	-0.839	-0.921	9.399	-0.281	-0.281	0.000	0.000	0.000	0.000
40	B	51	VAL	0	-0.024	-0.023	12.572	0.003	0.003	0.000	0.000	0.000	0.000
41	B	52	GLU	-1	-0.937	-0.975	15.842	-0.102	-0.102	0.000	0.000	0.000	0.000
42	B	53	GLU	-1	-0.875	-0.932	17.729	-0.140	-0.140	0.000	0.000	0.000	0.000
43	B	54	LYS	1	0.804	0.924	16.209	0.146	0.146	0.000	0.000	0.000	0.000
44	B	55	ASP	-1	-0.864	-0.962	21.282	-0.053	-0.053	0.000	0.000	0.000	0.000
45	B	56	LEU	0	-0.010	0.012	24.166	0.009	0.009	0.000	0.000	0.000	0.000
46	B	57	GLU	-1	-0.738	-0.888	26.012	-0.078	-0.078	0.000	0.000	0.000	0.000
47	B	58	LYS	1	0.809	0.911	24.718	0.082	0.082	0.000	0.000	0.000	0.000
48	B	59	LYS	1	0.978	0.995	27.442	0.046	0.046	0.000	0.000	0.000	0.000
49	B	60	VAL	0	0.017	0.015	29.855	0.005	0.005	0.000	0.000	0.000	0.000
50	B	61	LYS	1	0.847	0.922	32.120	0.046	0.046	0.000	0.000	0.000	0.000
51	B	62	GLU	-1	-0.891	-0.960	33.244	-0.022	-0.022	0.000	0.000	0.000	0.000
52	B	63	LEU	0	-0.006	-0.018	32.542	0.004	0.004	0.000	0.000	0.000	0.000
53	B	64	LYS	1	0.836	0.926	35.827	0.041	0.041	0.000	0.000	0.000	0.000
54	B	65	GLU	-1	-0.823	-0.899	37.955	-0.033	-0.033	0.000	0.000	0.000	0.000
55	B	66	LYS	1	0.930	0.974	37.761	0.018	0.018	0.000	0.000	0.000	0.000
56	B	67	ILE	0	-0.031	-0.008	38.019	0.002	0.002	0.000	0.000	0.000	0.000
57	B	68	GLU	-1	-0.908	-0.953	41.711	-0.033	-0.033	0.000	0.000	0.000	0.000
58	B	69	LYS	1	0.789	0.899	42.124	0.027	0.027	0.000	0.000	0.000	0.000
59	B	70	GLY	0	0.018	0.015	45.002	0.002	0.002	0.000	0.000	0.000	0.000
60	B	71	GLU	-1	-0.980	-0.989	42.722	-0.013	-0.013	0.000	0.000	0.000	0.000
61	B	72	TYR	0	-0.019	-0.032	35.662	-0.001	-0.001	0.000	0.000	0.000	0.000
62	B	73	GLU	-1	-0.926	-0.951	41.071	-0.006	-0.006	0.000	0.000	0.000	0.000
63	B	74	VAL	0	-0.020	-0.007	40.442	-0.001	-0.001	0.000	0.000	0.000	0.000
64	B	75	SER	0	0.010	0.002	40.429	0.002	0.002	0.000	0.000	0.000	0.000
65	B	76	ASP	-1	-0.835	-0.941	40.811	-0.005	-0.005	0.000	0.000	0.000	0.000
66	B	77	GLU	-1	-0.943	-0.978	37.814	0.008	0.008	0.000	0.000	0.000	0.000
67	B	78	LYS	1	0.957	0.985	36.637	0.005	0.005	0.000	0.000	0.000	0.000
68	B	79	VAL	0	-0.004	0.012	35.755	-0.001	-0.001	0.000	0.000	0.000	0.000
69	B	80	VAL	0	0.004	0.006	36.413	-0.001	-0.001	0.000	0.000	0.000	0.000
70	B	81	LYS	1	0.831	0.902	30.481	-0.014	-0.014	0.000	0.000	0.000	0.000
71	B	82	GLY	0	-0.002	-0.008	31.960	0.001	0.001	0.000	0.000	0.000	0.000
72	B	83	LEU	0	-0.015	-0.014	31.528	-0.002	-0.002	0.000	0.000	0.000	0.000
73	B	84	ILE	0	0.013	0.005	32.506	0.000	0.000	0.000	0.000	0.000	0.000
74	B	85	GLU	-1	-0.858	-0.899	27.872	0.017	0.017	0.000	0.000	0.000	0.000
75	B	86	PHE	0	-0.075	-0.023	26.350	-0.001	-0.001	0.000	0.000	0.000	0.000
76	B	87	PHE	0	-0.049	-0.032	27.969	-0.003	-0.003	0.000	0.000	0.000	0.000
77	B	88	THR	0	-0.076	-0.033	27.627	0.007	0.007	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:2:VAL)