FMO DATABASE

FMODB ID: N1G4Q

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

Total energy (hartree)

FMO2-HF: Electronic energy	-393493.272447
FMO2-HF: Nuclear repulsion	363122.727895
FMO2-HF: Total energy	-30370.544553
FMO2-MP2: Total energy	-30461.334682

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.
-29.232	-23.425	14.175	-8.442	-11.537	0.006

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 : 0.029 / q_NPA : 0.014

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	0.911	0.935	3.258	-5.226	-1.933	0.027	-1.569	-1.750	0.004
4	B	5	ILE	0	0.009	0.008	2.512	-5.549	-4.327	3.314	-1.769	-2.767	0.016
5	B	6	GLU	-1	-0.725	-0.824	2.197	-8.168	-9.038	7.320	-3.065	-3.385	0.008
6	B	7	LEU	0	0.037	0.018	3.632	-1.897	-1.547	0.016	-0.068	-0.297	0.000
7	B	8	SER	0	-0.001	0.005	6.041	-0.722	-0.722	0.000	0.000	0.000	0.000
8	B	9	ARG	1	0.833	0.893	6.438	-1.443	-1.443	0.000	0.000	0.000	0.000
9	B	10	LEU	0	-0.053	-0.017	6.485	-0.427	-0.427	0.000	0.000	0.000	0.000
10	B	11	ILE	0	0.031	0.010	9.411	-0.191	-0.191	0.000	0.000	0.000	0.000
11	B	12	GLY	0	0.009	0.004	11.302	-0.117	-0.117	0.000	0.000	0.000	0.000
12	B	13	LEU	0	-0.015	-0.019	10.808	-0.105	-0.105	0.000	0.000	0.000	0.000
13	B	14	LEU	0	-0.020	-0.017	13.525	-0.074	-0.074	0.000	0.000	0.000	0.000
14	B	15	LEU	0	-0.036	-0.013	15.435	-0.041	-0.041	0.000	0.000	0.000	0.000
15	B	16	GLU	-1	-0.956	-0.956	16.779	0.310	0.310	0.000	0.000	0.000	0.000
16	B	17	THR	0	-0.125	-0.061	18.065	-0.061	-0.061	0.000	0.000	0.000	0.000
17	B	28	SER	0	0.014	0.003	23.788	-0.007	-0.007	0.000	0.000	0.000	0.000
18	B	29	GLY	0	0.034	0.012	21.406	0.017	0.017	0.000	0.000	0.000	0.000
19	B	30	THR	0	-0.061	-0.037	22.453	-0.026	-0.026	0.000	0.000	0.000	0.000
20	B	31	ASN	0	-0.013	-0.014	21.030	-0.016	-0.016	0.000	0.000	0.000	0.000
21	B	32	LYS	1	0.957	0.987	20.591	-0.045	-0.045	0.000	0.000	0.000	0.000
22	B	33	ILE	0	-0.012	-0.003	20.980	-0.014	-0.014	0.000	0.000	0.000	0.000
23	B	34	GLU	-1	-0.802	-0.914	17.363	0.098	0.098	0.000	0.000	0.000	0.000
24	B	35	ASP	-1	-0.775	-0.874	16.103	0.149	0.149	0.000	0.000	0.000	0.000
25	B	36	LYS	1	0.888	0.952	16.110	0.090	0.090	0.000	0.000	0.000	0.000
26	B	37	VAL	0	0.009	-0.002	13.482	-0.040	-0.040	0.000	0.000	0.000	0.000
27	B	38	THR	0	-0.014	-0.012	11.492	-0.055	-0.055	0.000	0.000	0.000	0.000
28	B	39	LEU	0	0.021	-0.001	11.259	-0.003	-0.003	0.000	0.000	0.000	0.000
29	B	40	SER	0	-0.070	-0.029	12.740	-0.016	-0.016	0.000	0.000	0.000	0.000
30	B	41	LYS	1	0.889	0.941	7.524	0.213	0.213	0.000	0.000	0.000	0.000
31	B	42	ILE	0	0.019	0.008	7.861	-0.193	-0.193	0.000	0.000	0.000	0.000
32	B	43	ALA	0	0.044	0.022	8.959	-0.082	-0.082	0.000	0.000	0.000	0.000
33	B	44	GLN	0	0.012	0.015	8.249	0.048	0.048	0.000	0.000	0.000	0.000
34	B	45	GLU	-1	-0.895	-0.937	2.590	-7.210	-5.646	2.431	-1.674	-2.321	-0.021
35	B	46	LEU	0	-0.032	-0.032	5.557	-0.008	-0.008	0.000	0.000	0.000	0.000
36	B	47	SER	0	-0.005	0.006	8.250	0.059	0.059	0.000	0.000	0.000	0.000
37	B	48	LYS	1	0.721	0.854	2.430	1.957	2.205	1.067	-0.297	-1.017	-0.001
38	B	49	ASN	0	-0.046	-0.033	5.818	-0.125	-0.125	0.000	0.000	0.000	0.000
39	B	50	ASP	-1	-0.851	-0.921	9.341	-0.280	-0.280	0.000	0.000	0.000	0.000
40	B	51	VAL	0	-0.022	-0.016	12.621	0.003	0.003	0.000	0.000	0.000	0.000
41	B	52	GLU	-1	-0.824	-0.898	15.834	-0.106	-0.106	0.000	0.000	0.000	0.000
42	B	53	GLU	-1	-0.913	-0.944	17.952	-0.145	-0.145	0.000	0.000	0.000	0.000
43	B	54	LYS	1	0.758	0.860	16.483	0.134	0.134	0.000	0.000	0.000	0.000
44	B	55	ASP	-1	-0.855	-0.943	21.070	-0.080	-0.080	0.000	0.000	0.000	0.000
45	B	56	LEU	0	-0.023	0.012	23.995	0.011	0.011	0.000	0.000	0.000	0.000
46	B	57	GLU	-1	-0.742	-0.874	25.798	-0.094	-0.094	0.000	0.000	0.000	0.000
47	B	58	LYS	1	0.799	0.883	24.644	0.108	0.108	0.000	0.000	0.000	0.000
48	B	59	LYS	1	0.970	0.992	27.668	0.049	0.049	0.000	0.000	0.000	0.000
49	B	60	VAL	0	0.009	0.002	29.721	0.006	0.006	0.000	0.000	0.000	0.000
50	B	61	LYS	1	0.836	0.909	31.899	0.056	0.056	0.000	0.000	0.000	0.000
51	B	62	GLU	-1	-0.866	-0.947	33.311	-0.032	-0.032	0.000	0.000	0.000	0.000
52	B	63	LEU	0	-0.025	-0.021	32.490	0.004	0.004	0.000	0.000	0.000	0.000
53	B	64	LYS	1	0.790	0.896	35.763	0.047	0.047	0.000	0.000	0.000	0.000
54	B	65	GLU	-1	-0.801	-0.871	37.713	-0.040	-0.040	0.000	0.000	0.000	0.000
55	B	66	LYS	1	0.905	0.953	37.751	0.028	0.028	0.000	0.000	0.000	0.000
56	B	67	ILE	0	-0.013	-0.007	38.149	0.003	0.003	0.000	0.000	0.000	0.000
57	B	68	GLU	-1	-0.875	-0.936	41.595	-0.038	-0.038	0.000	0.000	0.000	0.000
58	B	69	LYS	1	0.783	0.887	42.244	0.034	0.034	0.000	0.000	0.000	0.000
59	B	70	GLY	0	0.011	0.017	44.939	0.002	0.002	0.000	0.000	0.000	0.000
60	B	71	GLU	-1	-0.924	-0.949	42.276	-0.022	-0.022	0.000	0.000	0.000	0.000
61	B	72	TYR	0	-0.049	-0.044	35.985	-0.001	-0.001	0.000	0.000	0.000	0.000
62	B	73	GLU	-1	-0.859	-0.923	41.308	-0.005	-0.005	0.000	0.000	0.000	0.000
63	B	74	VAL	0	-0.062	-0.030	40.275	-0.001	-0.001	0.000	0.000	0.000	0.000
64	B	75	SER	0	0.038	-0.005	40.598	0.000	0.000	0.000	0.000	0.000	0.000
65	B	76	ASP	-1	-0.872	-0.944	40.643	0.001	0.001	0.000	0.000	0.000	0.000
66	B	77	GLU	-1	-0.876	-0.923	38.441	0.006	0.006	0.000	0.000	0.000	0.000
67	B	78	LYS	1	0.882	0.947	36.379	0.009	0.009	0.000	0.000	0.000	0.000
68	B	79	VAL	0	-0.011	0.003	35.611	-0.001	-0.001	0.000	0.000	0.000	0.000
69	B	80	VAL	0	0.000	-0.005	36.453	0.001	0.001	0.000	0.000	0.000	0.000
70	B	81	LYS	1	0.839	0.909	30.224	-0.014	-0.014	0.000	0.000	0.000	0.000
71	B	82	GLY	0	0.008	0.002	31.827	0.002	0.002	0.000	0.000	0.000	0.000
72	B	83	LEU	0	-0.016	-0.014	31.619	0.000	0.000	0.000	0.000	0.000	0.000
73	B	84	ILE	0	0.020	0.006	32.757	0.002	0.002	0.000	0.000	0.000	0.000
74	B	85	GLU	-1	-0.848	-0.890	27.999	0.024	0.024	0.000	0.000	0.000	0.000
75	B	86	PHE	0	-0.054	-0.015	26.645	0.003	0.003	0.000	0.000	0.000	0.000
76	B	87	PHE	0	-0.030	-0.018	28.086	-0.001	-0.001	0.000	0.000	0.000	0.000
77	B	88	THR	0	-0.130	-0.070	28.057	0.015	0.015	0.000	0.000	0.000	0.000

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