FMO DATABASE

FMODB ID: K34K3

Calculation Name: 3R84-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3R84

Chain ID: A

ChEMBL ID:

UniProt ID: Q99278

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	81
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-496663.244589
FMO2-HF: Nuclear repulsion	463556.267839
FMO2-HF: Total energy	-33106.97675
FMO2-MP2: Total energy	-33204.121235

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:4:GLY)

Summations of interaction energy for fragment #1(A:4:GLY)

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.
-4.287	1.007	4.022	-4.368	-4.948	-0.022

Interaction energy analysis for fragmet #1(A:4:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.077 / q_NPA : 0.040

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	6	ILE	0	0.066	0.024	3.848	-0.465	1.176	-0.002	-0.880	-0.759	0.003
4	A	7	GLN	0	0.054	0.021	1.983	-2.643	-1.578	3.511	-2.078	-2.498	-0.009
5	A	8	GLU	-1	-0.802	-0.892	2.622	-9.070	-6.617	0.514	-1.382	-1.585	-0.016
6	A	9	ARG	1	0.810	0.899	5.539	3.402	3.402	0.000	0.000	0.000	0.000
7	A	10	LEU	0	-0.001	0.001	6.935	0.434	0.434	0.000	0.000	0.000	0.000
8	A	11	LYS	1	0.877	0.916	3.595	4.080	4.215	-0.001	-0.028	-0.106	0.000
9	A	12	SER	0	-0.039	-0.029	9.172	0.388	0.388	0.000	0.000	0.000	0.000
10	A	13	LEU	0	0.008	0.002	11.384	0.220	0.220	0.000	0.000	0.000	0.000
11	A	14	ASN	0	-0.003	-0.009	11.038	0.021	0.021	0.000	0.000	0.000	0.000
12	A	15	ASP	-1	-0.816	-0.884	13.253	-0.513	-0.513	0.000	0.000	0.000	0.000
13	A	16	ILE	0	0.004	-0.004	15.039	0.108	0.108	0.000	0.000	0.000	0.000
14	A	17	GLU	-1	-0.862	-0.932	15.403	-0.527	-0.527	0.000	0.000	0.000	0.000
15	A	18	THR	0	0.001	-0.003	16.834	0.083	0.083	0.000	0.000	0.000	0.000
16	A	19	GLN	0	-0.063	-0.042	17.425	0.093	0.093	0.000	0.000	0.000	0.000
17	A	20	LEU	0	0.023	0.011	20.844	0.044	0.044	0.000	0.000	0.000	0.000
18	A	21	CYS	0	-0.032	-0.023	21.600	0.040	0.040	0.000	0.000	0.000	0.000
19	A	22	SER	0	-0.053	-0.043	22.779	0.034	0.034	0.000	0.000	0.000	0.000
20	A	23	MET	0	-0.026	-0.005	25.270	0.015	0.015	0.000	0.000	0.000	0.000
21	A	24	LEU	0	0.031	0.021	26.553	0.021	0.021	0.000	0.000	0.000	0.000
22	A	25	GLN	0	0.044	0.034	27.658	0.024	0.024	0.000	0.000	0.000	0.000
23	A	26	GLU	-1	-0.799	-0.850	28.784	-0.166	-0.166	0.000	0.000	0.000	0.000
24	A	27	ALA	0	0.037	0.017	31.411	0.014	0.014	0.000	0.000	0.000	0.000
25	A	28	SER	0	-0.014	-0.008	32.462	0.014	0.014	0.000	0.000	0.000	0.000
26	A	29	GLN	0	-0.052	-0.040	31.662	0.018	0.018	0.000	0.000	0.000	0.000
27	A	30	VAL	0	0.000	0.002	35.190	0.009	0.009	0.000	0.000	0.000	0.000
28	A	31	THR	0	-0.019	-0.020	37.116	0.008	0.008	0.000	0.000	0.000	0.000
29	A	32	PHE	0	-0.011	-0.010	38.809	0.007	0.007	0.000	0.000	0.000	0.000
30	A	33	ILE	0	0.009	-0.004	38.332	0.006	0.006	0.000	0.000	0.000	0.000
31	A	34	PHE	0	-0.005	0.006	41.590	0.006	0.006	0.000	0.000	0.000	0.000
32	A	35	GLY	0	0.017	0.010	43.580	0.005	0.005	0.000	0.000	0.000	0.000
33	A	36	GLU	-1	-0.804	-0.866	44.136	-0.064	-0.064	0.000	0.000	0.000	0.000
34	A	37	LEU	0	-0.011	-0.002	43.790	0.004	0.004	0.000	0.000	0.000	0.000
35	A	38	LYS	1	0.883	0.954	47.365	0.076	0.076	0.000	0.000	0.000	0.000
36	A	39	ARG	1	0.814	0.876	48.106	0.066	0.066	0.000	0.000	0.000	0.000
37	A	40	GLY	0	0.023	0.020	50.739	0.003	0.003	0.000	0.000	0.000	0.000
38	A	41	ASN	0	-0.044	-0.011	46.847	0.003	0.003	0.000	0.000	0.000	0.000
39	A	42	GLU	-1	-0.763	-0.895	47.268	-0.077	-0.077	0.000	0.000	0.000	0.000
40	A	43	SER	0	-0.071	-0.043	46.930	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	44	VAL	0	0.008	-0.001	42.189	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	45	LYS	1	0.844	0.927	42.058	0.073	0.073	0.000	0.000	0.000	0.000
43	A	46	PRO	0	0.053	0.010	41.173	-0.005	-0.005	0.000	0.000	0.000	0.000
44	A	47	GLN	0	0.005	0.003	38.049	-0.008	-0.008	0.000	0.000	0.000	0.000
45	A	48	PHE	0	-0.019	-0.004	37.418	-0.009	-0.009	0.000	0.000	0.000	0.000
46	A	49	GLU	-1	-0.874	-0.946	37.845	-0.102	-0.102	0.000	0.000	0.000	0.000
47	A	50	ASN	0	0.009	-0.004	33.011	-0.011	-0.011	0.000	0.000	0.000	0.000
48	A	51	HIS	1	0.835	0.909	32.515	0.128	0.128	0.000	0.000	0.000	0.000
49	A	52	VAL	0	0.016	0.009	33.216	-0.012	-0.012	0.000	0.000	0.000	0.000
50	A	53	LYS	1	0.790	0.892	31.801	0.149	0.149	0.000	0.000	0.000	0.000
51	A	54	GLN	0	0.034	0.019	28.377	0.000	0.000	0.000	0.000	0.000	0.000
52	A	55	PHE	0	-0.046	-0.023	28.733	-0.020	-0.020	0.000	0.000	0.000	0.000
53	A	56	TYR	0	-0.031	-0.028	29.121	-0.010	-0.010	0.000	0.000	0.000	0.000
54	A	57	GLU	-1	-0.807	-0.907	27.509	-0.197	-0.197	0.000	0.000	0.000	0.000
55	A	58	ARG	1	0.826	0.895	24.135	0.215	0.215	0.000	0.000	0.000	0.000
56	A	59	LEU	0	0.047	0.042	24.258	-0.033	-0.033	0.000	0.000	0.000	0.000
57	A	60	ASP	-1	-0.884	-0.893	25.379	-0.282	-0.282	0.000	0.000	0.000	0.000
58	A	61	LYS	1	0.845	0.930	16.887	0.520	0.520	0.000	0.000	0.000	0.000
59	A	62	SER	0	0.017	-0.016	20.340	-0.042	-0.042	0.000	0.000	0.000	0.000
60	A	63	THR	0	-0.055	-0.047	20.715	-0.042	-0.042	0.000	0.000	0.000	0.000
61	A	64	THR	0	0.008	0.005	20.986	-0.019	-0.019	0.000	0.000	0.000	0.000
62	A	65	GLN	0	-0.026	-0.012	13.953	0.067	0.067	0.000	0.000	0.000	0.000
63	A	66	LEU	0	0.026	0.000	17.318	-0.077	-0.077	0.000	0.000	0.000	0.000
64	A	67	ARG	1	0.904	0.951	18.866	0.390	0.390	0.000	0.000	0.000	0.000
65	A	68	LYS	1	0.844	0.912	13.437	0.972	0.972	0.000	0.000	0.000	0.000
66	A	69	GLU	-1	-0.755	-0.832	12.373	-1.434	-1.434	0.000	0.000	0.000	0.000
67	A	70	ILE	0	0.009	0.002	15.413	-0.034	-0.034	0.000	0.000	0.000	0.000
68	A	71	GLN	0	-0.011	0.003	17.674	0.035	0.035	0.000	0.000	0.000	0.000
69	A	72	LEU	0	-0.035	-0.013	11.292	-0.026	-0.026	0.000	0.000	0.000	0.000
70	A	73	LEU	0	-0.027	-0.005	13.615	-0.062	-0.062	0.000	0.000	0.000	0.000
71	A	74	ASP	-1	-0.894	-0.944	15.311	-0.356	-0.356	0.000	0.000	0.000	0.000
72	A	75	GLU	-1	-0.875	-0.937	15.158	-0.583	-0.583	0.000	0.000	0.000	0.000
73	A	76	ASN	0	-0.048	-0.044	11.268	-0.042	-0.042	0.000	0.000	0.000	0.000
74	A	77	VAL	0	0.037	0.028	14.095	0.017	0.017	0.000	0.000	0.000	0.000
75	A	78	GLY	0	-0.017	-0.004	16.578	0.035	0.035	0.000	0.000	0.000	0.000
76	A	79	THR	0	-0.054	-0.026	13.423	0.012	0.012	0.000	0.000	0.000	0.000
77	A	80	ARG	1	0.825	0.897	8.047	0.772	0.772	0.000	0.000	0.000	0.000
78	A	81	LEU	0	-0.031	0.007	11.261	-0.038	-0.038	0.000	0.000	0.000	0.000
79	A	82	LEU	0	0.022	0.009	13.959	0.057	0.057	0.000	0.000	0.000	0.000
80	A	83	PRO	0	0.029	0.008	17.252	-0.020	-0.020	0.000	0.000	0.000	0.000
81	A	84	ILE	0	-0.025	0.006	20.231	0.019	0.019	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:GLY)