FMO DATABASE

FMODB ID: 39NRL

Calculation Name: 1R8O-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1R8O

Chain ID: B

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	71
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-381843.775138
FMO2-HF: Nuclear repulsion	354957.300978
FMO2-HF: Total energy	-26886.47416
FMO2-MP2: Total energy	-26967.251937

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:97:TRP)

Summations of interaction energy for fragment #1(B:97:TRP)

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.
-6.344	-1.472	5.462	-1.828	-8.506	0.019

Interaction energy analysis for fragmet #1(B:97:TRP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.054 / q_NPA : 0.013

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	99	LEU	0	0.046	0.040	2.085	-2.623	1.280	4.736	-1.775	-6.864	0.012
4	B	100	PRO	0	0.012	0.013	2.425	-1.614	-0.645	0.726	-0.053	-1.642	0.007
5	B	101	SER	0	-0.018	-0.019	5.471	0.303	0.303	0.000	0.000	0.000	0.000
6	B	102	VAL	0	0.050	0.034	9.066	-0.157	-0.157	0.000	0.000	0.000	0.000
7	B	103	THR	0	-0.067	-0.033	12.472	0.122	0.122	0.000	0.000	0.000	0.000
8	B	104	VAL	0	0.070	0.024	14.620	-0.067	-0.067	0.000	0.000	0.000	0.000
9	B	105	GLY	0	-0.016	-0.008	16.170	-0.011	-0.011	0.000	0.000	0.000	0.000
10	B	106	ASN	0	0.017	0.021	14.171	0.028	0.028	0.000	0.000	0.000	0.000
11	B	107	PRO	0	0.029	0.008	16.837	-0.021	-0.021	0.000	0.000	0.000	0.000
12	B	108	LYS	1	0.900	0.939	15.761	0.114	0.114	0.000	0.000	0.000	0.000
13	B	109	VAL	0	-0.017	0.005	16.563	-0.037	-0.037	0.000	0.000	0.000	0.000
14	B	110	SER	0	0.004	0.010	19.724	0.015	0.015	0.000	0.000	0.000	0.000
15	B	111	VAL	0	0.010	-0.005	22.478	0.004	0.004	0.000	0.000	0.000	0.000
16	B	112	PHE	0	0.011	-0.002	25.130	0.012	0.012	0.000	0.000	0.000	0.000
17	B	113	GLY	0	0.007	0.016	24.315	-0.012	-0.012	0.000	0.000	0.000	0.000
18	B	114	GLY	0	0.001	-0.010	20.226	0.012	0.012	0.000	0.000	0.000	0.000
19	B	115	PRO	0	-0.026	-0.002	15.446	0.002	0.002	0.000	0.000	0.000	0.000
20	B	116	PHE	0	-0.001	-0.001	13.790	-0.036	-0.036	0.000	0.000	0.000	0.000
21	B	117	LYS	1	0.877	0.934	17.859	0.267	0.267	0.000	0.000	0.000	0.000
22	B	118	ILE	0	0.004	0.002	19.292	0.002	0.002	0.000	0.000	0.000	0.000
23	B	119	GLU	-1	-0.935	-0.969	19.903	-0.181	-0.181	0.000	0.000	0.000	0.000
24	B	120	GLU	-1	-0.891	-0.951	22.316	-0.059	-0.059	0.000	0.000	0.000	0.000
25	B	121	GLY	0	-0.011	-0.021	21.388	-0.017	-0.017	0.000	0.000	0.000	0.000
26	B	122	LYS	1	0.920	0.962	19.406	0.065	0.065	0.000	0.000	0.000	0.000
27	B	123	SER	0	-0.053	-0.035	23.929	0.012	0.012	0.000	0.000	0.000	0.000
28	B	124	GLY	0	0.015	0.011	24.825	0.012	0.012	0.000	0.000	0.000	0.000
29	B	125	TYR	0	0.023	0.032	23.030	-0.004	-0.004	0.000	0.000	0.000	0.000
30	B	126	LYS	1	0.824	0.898	16.467	0.220	0.220	0.000	0.000	0.000	0.000
31	B	127	ASP	-1	-0.859	-0.916	16.604	-0.050	-0.050	0.000	0.000	0.000	0.000
32	B	128	VAL	0	-0.027	-0.025	14.810	-0.014	-0.014	0.000	0.000	0.000	0.000
33	B	129	TYR	0	0.001	-0.008	9.863	-0.068	-0.068	0.000	0.000	0.000	0.000
34	B	130	SER	0	-0.006	-0.016	13.172	-0.053	-0.053	0.000	0.000	0.000	0.000
35	B	131	SER	0	-0.069	-0.038	10.473	-0.051	-0.051	0.000	0.000	0.000	0.000
36	B	132	SER	0	0.020	-0.010	11.969	0.028	0.028	0.000	0.000	0.000	0.000
37	B	133	LYS	1	0.909	0.944	10.182	1.090	1.090	0.000	0.000	0.000	0.000
38	B	134	GLY	0	0.024	0.031	13.995	0.043	0.043	0.000	0.000	0.000	0.000
39	B	135	ARG	1	0.832	0.910	10.487	0.645	0.645	0.000	0.000	0.000	0.000
40	B	136	ASP	-1	-0.731	-0.836	13.334	-0.409	-0.409	0.000	0.000	0.000	0.000
41	B	137	LEU	0	-0.061	-0.038	8.273	-0.031	-0.031	0.000	0.000	0.000	0.000
42	B	138	ASP	-1	-0.761	-0.863	11.961	-0.216	-0.216	0.000	0.000	0.000	0.000
43	B	139	ASP	-1	-0.856	-0.921	10.774	-0.257	-0.257	0.000	0.000	0.000	0.000
44	B	140	GLY	0	0.025	-0.008	11.081	0.008	0.008	0.000	0.000	0.000	0.000
45	B	141	ILE	0	-0.074	-0.031	11.915	0.073	0.073	0.000	0.000	0.000	0.000
46	B	142	GLU	-1	-0.896	-0.948	7.001	0.378	0.378	0.000	0.000	0.000	0.000
47	B	143	VAL	0	-0.047	-0.028	10.831	0.050	0.050	0.000	0.000	0.000	0.000
48	B	144	ASN	0	-0.030	-0.039	11.112	0.018	0.018	0.000	0.000	0.000	0.000
49	B	145	LYS	1	0.984	0.970	9.558	-1.620	-1.620	0.000	0.000	0.000	0.000
50	B	146	LYS	1	0.892	0.940	12.512	-0.750	-0.750	0.000	0.000	0.000	0.000
51	B	147	LYS	1	0.967	1.003	15.539	-0.376	-0.376	0.000	0.000	0.000	0.000
52	B	148	GLU	-1	-0.776	-0.867	15.191	0.656	0.656	0.000	0.000	0.000	0.000
53	B	149	LYS	1	0.937	0.966	14.755	-0.173	-0.173	0.000	0.000	0.000	0.000
54	B	150	ARG	1	0.911	0.968	9.115	-1.156	-1.156	0.000	0.000	0.000	0.000
55	B	151	LEU	0	0.079	0.052	12.329	0.002	0.002	0.000	0.000	0.000	0.000
56	B	152	VAL	0	-0.057	-0.044	7.435	0.126	0.126	0.000	0.000	0.000	0.000
57	B	153	VAL	0	0.082	0.049	6.286	-0.115	-0.115	0.000	0.000	0.000	0.000
58	B	154	LYS	1	0.819	0.904	6.142	-0.032	-0.032	0.000	0.000	0.000	0.000
59	B	155	ASP	-1	-0.790	-0.883	7.503	-0.557	-0.557	0.000	0.000	0.000	0.000
60	B	156	GLY	0	0.048	0.037	9.341	0.011	0.011	0.000	0.000	0.000	0.000
61	B	157	ASN	0	-0.114	-0.056	10.214	0.082	0.082	0.000	0.000	0.000	0.000
62	B	158	PRO	0	0.019	0.015	12.735	0.041	0.041	0.000	0.000	0.000	0.000
63	B	159	PHE	0	-0.062	-0.034	14.766	0.038	0.038	0.000	0.000	0.000	0.000
64	B	160	ILE	0	-0.018	-0.005	16.559	-0.014	-0.014	0.000	0.000	0.000	0.000
65	B	161	ILE	0	-0.028	0.006	19.705	0.024	0.024	0.000	0.000	0.000	0.000
66	B	162	ARG	1	0.988	0.981	22.494	-0.044	-0.044	0.000	0.000	0.000	0.000
67	B	163	PHE	0	0.045	0.016	22.784	0.015	0.015	0.000	0.000	0.000	0.000
68	B	164	LYS	1	0.935	0.969	27.584	-0.040	-0.040	0.000	0.000	0.000	0.000
69	B	165	LYS	1	0.981	0.995	30.551	0.002	0.002	0.000	0.000	0.000	0.000
70	B	166	SER	0	0.030	0.001	32.378	0.006	0.006	0.000	0.000	0.000	0.000
71	B	167	GLY	0	0.006	0.015	33.737	-0.005	-0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:97:TRP)