FMO DATABASE

FMODB ID: MVMYZ

Calculation Name: 1R8O-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1R8O

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-21

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	95
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-585327.941085
FMO2-HF: Nuclear repulsion	549557.821589
FMO2-HF: Total energy	-35770.119495
FMO2-MP2: Total energy	-35873.137705

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:ARG)

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

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.
-9.431	-5.939	1.096	-1.4	-3.188	-0.006

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.956 / q_NPA : 0.962

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	A	3	VAL	0	-0.059	-0.014	2.235	-1.843	1.289	1.093	-1.331	-2.893	-0.006
4	A	4	ASP	-1	-0.773	-0.896	4.650	-30.485	-30.355	-0.001	-0.018	-0.112	0.000
5	A	5	THR	0	-0.012	-0.022	6.768	-3.731	-3.731	0.000	0.000	0.000	0.000
6	A	6	ASP	-1	-0.946	-0.949	8.577	-23.560	-23.560	0.000	0.000	0.000	0.000
7	A	7	GLY	0	-0.061	-0.036	5.444	0.122	0.122	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.922	0.957	6.209	23.486	23.486	0.000	0.000	0.000	0.000
9	A	9	PRO	0	-0.028	-0.010	5.904	-2.014	-2.014	0.000	0.000	0.000	0.000
10	A	10	ILE	0	0.018	0.011	6.827	2.619	2.619	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.873	-0.937	9.336	-18.581	-18.581	0.000	0.000	0.000	0.000
12	A	12	ASN	0	-0.085	-0.050	12.585	0.077	0.077	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.954	-0.994	14.271	-13.352	-13.352	0.000	0.000	0.000	0.000
14	A	14	GLY	0	0.012	0.013	16.971	0.657	0.657	0.000	0.000	0.000	0.000
15	A	15	ALA	0	-0.009	-0.007	15.052	0.741	0.741	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.934	-0.967	16.502	-14.448	-14.448	0.000	0.000	0.000	0.000
17	A	17	TYR	0	0.005	0.004	11.509	-0.977	-0.977	0.000	0.000	0.000	0.000
18	A	18	TYR	0	0.063	0.031	15.567	0.850	0.850	0.000	0.000	0.000	0.000
19	A	19	ILE	0	-0.040	-0.012	13.557	-1.611	-1.611	0.000	0.000	0.000	0.000
20	A	20	LEU	0	0.007	-0.003	13.236	1.475	1.475	0.000	0.000	0.000	0.000
21	A	21	PRO	0	-0.023	0.012	12.883	-1.692	-1.692	0.000	0.000	0.000	0.000
22	A	22	SER	0	0.020	-0.007	9.997	-1.051	-1.051	0.000	0.000	0.000	0.000
23	A	23	VAL	0	-0.057	-0.025	12.210	0.514	0.514	0.000	0.000	0.000	0.000
24	A	24	ARG	1	1.003	0.999	15.428	16.731	16.731	0.000	0.000	0.000	0.000
25	A	25	GLY	0	-0.003	-0.009	18.402	0.200	0.200	0.000	0.000	0.000	0.000
26	A	26	LYS	1	0.926	0.957	19.577	14.478	14.478	0.000	0.000	0.000	0.000
27	A	27	GLY	0	0.062	0.037	20.500	-0.431	-0.431	0.000	0.000	0.000	0.000
28	A	28	GLY	0	-0.008	-0.008	19.960	-0.659	-0.659	0.000	0.000	0.000	0.000
29	A	29	GLY	0	0.020	-0.011	17.922	-0.486	-0.486	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.053	-0.017	17.373	1.001	1.001	0.000	0.000	0.000	0.000
31	A	31	VAL	0	0.039	0.021	20.155	0.038	0.038	0.000	0.000	0.000	0.000
32	A	32	LEU	0	-0.033	-0.015	23.689	-0.070	-0.070	0.000	0.000	0.000	0.000
33	A	33	ALA	0	0.009	0.003	26.944	0.243	0.243	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.890	0.956	29.862	8.654	8.654	0.000	0.000	0.000	0.000
35	A	35	SER	0	0.021	0.007	30.587	-0.074	-0.074	0.000	0.000	0.000	0.000
36	A	36	GLY	0	-0.018	-0.016	33.217	0.148	0.148	0.000	0.000	0.000	0.000
37	A	37	GLY	0	0.016	0.009	36.445	0.136	0.136	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.841	-0.901	32.678	-9.740	-9.740	0.000	0.000	0.000	0.000
39	A	39	LYS	1	0.960	0.961	37.015	7.405	7.405	0.000	0.000	0.000	0.000
40	A	40	CYS	0	-0.046	-0.007	34.987	0.047	0.047	0.000	0.000	0.000	0.000
41	A	41	PRO	0	-0.023	-0.033	31.198	-0.015	-0.015	0.000	0.000	0.000	0.000
42	A	42	LEU	0	0.035	0.017	30.321	-0.199	-0.199	0.000	0.000	0.000	0.000
43	A	43	SER	0	-0.015	0.002	28.211	-0.294	-0.294	0.000	0.000	0.000	0.000
44	A	44	VAL	0	0.016	0.002	21.411	0.035	0.035	0.000	0.000	0.000	0.000
45	A	45	VAL	0	-0.019	-0.002	23.801	0.108	0.108	0.000	0.000	0.000	0.000
46	A	46	GLN	0	-0.051	-0.011	19.030	-0.217	-0.217	0.000	0.000	0.000	0.000
47	A	47	SER	0	-0.016	-0.012	22.109	0.914	0.914	0.000	0.000	0.000	0.000
48	A	48	PRO	0	0.013	-0.002	23.717	-0.299	-0.299	0.000	0.000	0.000	0.000
49	A	49	SER	0	0.003	0.017	25.622	-0.113	-0.113	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.806	-0.924	21.709	-13.015	-13.015	0.000	0.000	0.000	0.000
51	A	51	LEU	0	-0.043	-0.018	20.915	-0.621	-0.621	0.000	0.000	0.000	0.000
52	A	52	SER	0	-0.049	0.000	21.923	-0.439	-0.439	0.000	0.000	0.000	0.000
53	A	53	ASN	0	0.068	0.016	18.198	-1.132	-1.132	0.000	0.000	0.000	0.000
54	A	54	GLY	0	-0.030	-0.004	19.490	-0.573	-0.573	0.000	0.000	0.000	0.000
55	A	55	LEU	0	-0.033	-0.031	21.925	0.352	0.352	0.000	0.000	0.000	0.000
56	A	56	PRO	0	0.016	0.035	19.826	-0.804	-0.804	0.000	0.000	0.000	0.000
57	A	57	VAL	0	-0.036	-0.030	16.645	0.641	0.641	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.919	0.969	17.713	13.583	13.583	0.000	0.000	0.000	0.000
59	A	59	PHE	0	-0.002	-0.004	13.007	0.234	0.234	0.000	0.000	0.000	0.000
60	A	60	LYS	1	0.952	0.982	16.076	13.700	13.700	0.000	0.000	0.000	0.000
61	A	61	ALA	0	0.036	0.016	14.062	0.140	0.140	0.000	0.000	0.000	0.000
62	A	62	SER	0	0.018	0.004	16.126	0.287	0.287	0.000	0.000	0.000	0.000
63	A	63	PRO	0	-0.007	0.004	14.685	0.573	0.573	0.000	0.000	0.000	0.000
64	A	64	ARG	1	0.978	0.997	16.738	14.887	14.887	0.000	0.000	0.000	0.000
65	A	65	SER	0	-0.005	0.004	12.056	0.424	0.424	0.000	0.000	0.000	0.000
66	A	66	LYS	1	0.939	0.953	13.246	16.866	16.866	0.000	0.000	0.000	0.000
67	A	67	TYR	0	0.032	0.019	8.653	0.692	0.692	0.000	0.000	0.000	0.000
68	A	68	ILE	0	-0.001	0.010	8.790	0.585	0.585	0.000	0.000	0.000	0.000
69	A	69	SER	0	0.007	-0.005	5.738	-2.095	-2.095	0.000	0.000	0.000	0.000
70	A	70	VAL	0	-0.003	-0.013	3.761	1.205	1.435	0.004	-0.051	-0.183	0.000
71	A	71	GLY	0	0.000	-0.009	6.230	1.147	1.147	0.000	0.000	0.000	0.000
72	A	72	MET	0	-0.035	0.017	9.509	1.720	1.720	0.000	0.000	0.000	0.000
73	A	73	LEU	0	0.002	-0.003	11.279	-0.177	-0.177	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.022	-0.023	11.805	0.044	0.044	0.000	0.000	0.000	0.000
75	A	75	GLY	0	0.003	0.012	15.801	0.401	0.401	0.000	0.000	0.000	0.000
76	A	76	ILE	0	0.002	-0.010	15.529	-0.880	-0.880	0.000	0.000	0.000	0.000
77	A	77	GLU	-1	-0.884	-0.964	18.772	-12.028	-12.028	0.000	0.000	0.000	0.000
78	A	78	VAL	0	-0.042	-0.031	21.256	-0.564	-0.564	0.000	0.000	0.000	0.000
79	A	79	ILE	0	-0.017	-0.004	21.467	0.586	0.586	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.892	-0.930	24.287	-11.797	-11.797	0.000	0.000	0.000	0.000
81	A	81	SER	0	-0.012	-0.048	26.663	-0.118	-0.118	0.000	0.000	0.000	0.000
82	A	82	PRO	0	-0.033	-0.032	29.082	0.330	0.330	0.000	0.000	0.000	0.000
83	A	83	GLU	-1	-0.937	-0.968	32.716	-8.432	-8.432	0.000	0.000	0.000	0.000
84	A	85	ALA	0	-0.013	0.000	30.790	0.053	0.053	0.000	0.000	0.000	0.000
85	A	86	PRO	0	0.011	0.003	30.805	0.120	0.120	0.000	0.000	0.000	0.000
86	A	87	LYS	1	0.922	0.994	29.909	9.797	9.797	0.000	0.000	0.000	0.000
87	A	88	PRO	0	0.029	-0.004	26.103	0.315	0.315	0.000	0.000	0.000	0.000
88	A	89	SER	0	-0.015	0.012	26.561	0.150	0.150	0.000	0.000	0.000	0.000
89	A	90	MET	0	-0.022	0.007	21.500	-0.544	-0.544	0.000	0.000	0.000	0.000
90	A	91	TRP	0	0.012	0.005	17.458	0.166	0.166	0.000	0.000	0.000	0.000
91	A	92	SER	0	-0.031	-0.014	22.839	0.088	0.088	0.000	0.000	0.000	0.000
92	A	93	VAL	0	0.011	-0.001	22.812	-0.117	-0.117	0.000	0.000	0.000	0.000
93	A	94	LYS	1	0.958	0.990	25.526	10.319	10.319	0.000	0.000	0.000	0.000
94	A	95	SER	0	0.041	0.015	29.114	-0.272	-0.272	0.000	0.000	0.000	0.000
95	A	96	GLY	0	-0.011	0.001	30.653	0.035	0.035	0.000	0.000	0.000	0.000

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