FMO DATABASE

FMODB ID: R8L68

Calculation Name: 3CPQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CPQ

Chain ID: A

ChEMBL ID:

UniProt ID: P54061

Base Structure: X-ray

Registration Date: 2023-09-23

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	OptHSide
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	99
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-719563.293061
FMO2-HF: Nuclear repulsion	682038.003222
FMO2-HF: Total energy	-37525.289839
FMO2-MP2: Total energy	-37635.495314

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:7:MET)

Summations of interaction energy for fragment #1(A:7:MET)

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.
-13.073	-8.741	0.237	-1.554	-3.014	0.008

Interaction energy analysis for fragmet #1(A:7:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.012 / q_NPA : -0.025

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

Sort

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	9	VAL	0	0.058	0.025	3.220	0.958	2.634	0.006	-0.628	-1.054	0.001
4	A	10	ASN	0	0.009	0.000	3.255	-2.608	-1.194	0.081	-0.504	-0.991	0.003
5	A	11	LYS	1	0.956	0.980	3.502	-6.432	-5.229	0.151	-0.422	-0.932	0.004
6	A	12	ALA	0	0.072	0.054	6.024	-0.080	-0.080	0.000	0.000	0.000	0.000
7	A	13	ILE	0	-0.002	0.014	7.509	-0.094	-0.094	0.000	0.000	0.000	0.000
8	A	14	ARG	1	0.808	0.889	8.747	-1.324	-1.324	0.000	0.000	0.000	0.000
9	A	15	THR	0	0.021	-0.002	9.967	-0.208	-0.208	0.000	0.000	0.000	0.000
10	A	16	ALA	0	0.029	0.044	12.210	-0.110	-0.110	0.000	0.000	0.000	0.000
11	A	17	VAL	0	-0.113	-0.057	13.570	-0.061	-0.061	0.000	0.000	0.000	0.000
12	A	18	ASP	-1	-0.852	-0.909	14.550	0.707	0.707	0.000	0.000	0.000	0.000
13	A	19	THR	0	-0.043	-0.033	15.792	-0.091	-0.091	0.000	0.000	0.000	0.000
14	A	20	GLY	0	0.061	0.046	17.447	-0.062	-0.062	0.000	0.000	0.000	0.000
15	A	21	LYS	1	0.856	0.928	19.086	-0.276	-0.276	0.000	0.000	0.000	0.000
16	A	22	VAL	0	0.045	0.024	15.291	-0.005	-0.005	0.000	0.000	0.000	0.000
17	A	23	ILE	0	-0.060	-0.014	18.559	0.008	0.008	0.000	0.000	0.000	0.000
18	A	24	LEU	0	0.033	0.011	16.134	0.044	0.044	0.000	0.000	0.000	0.000
19	A	25	GLY	0	0.031	0.003	18.803	-0.058	-0.058	0.000	0.000	0.000	0.000
20	A	26	SER	0	0.032	0.020	20.688	-0.028	-0.028	0.000	0.000	0.000	0.000
21	A	27	LYS	1	0.993	0.989	21.620	-0.341	-0.341	0.000	0.000	0.000	0.000
22	A	28	ARG	1	0.951	0.977	22.833	-0.423	-0.423	0.000	0.000	0.000	0.000
23	A	29	THR	0	0.034	0.019	19.449	-0.019	-0.019	0.000	0.000	0.000	0.000
24	A	30	ILE	0	0.019	0.013	22.362	-0.027	-0.027	0.000	0.000	0.000	0.000
25	A	31	LYS	1	0.862	0.939	24.929	-0.228	-0.228	0.000	0.000	0.000	0.000
26	A	32	PHE	0	-0.005	-0.024	24.348	-0.010	-0.010	0.000	0.000	0.000	0.000
27	A	33	VAL	0	0.055	0.042	22.043	-0.018	-0.018	0.000	0.000	0.000	0.000
28	A	34	LYS	1	0.762	0.903	25.287	-0.226	-0.226	0.000	0.000	0.000	0.000
29	A	35	HIS	0	-0.061	-0.036	28.564	-0.017	-0.017	0.000	0.000	0.000	0.000
30	A	36	GLY	0	0.049	0.036	27.866	-0.011	-0.011	0.000	0.000	0.000	0.000
31	A	37	GLU	-1	-0.947	-0.965	25.934	0.183	0.183	0.000	0.000	0.000	0.000
32	A	38	GLY	0	-0.031	-0.041	22.165	0.024	0.024	0.000	0.000	0.000	0.000
33	A	39	LYS	1	0.792	0.878	19.134	-0.148	-0.148	0.000	0.000	0.000	0.000
34	A	40	LEU	0	0.026	0.008	12.533	-0.019	-0.019	0.000	0.000	0.000	0.000
35	A	41	VAL	0	-0.017	0.012	16.640	0.064	0.064	0.000	0.000	0.000	0.000
36	A	42	VAL	0	-0.009	0.010	10.563	0.016	0.016	0.000	0.000	0.000	0.000
37	A	43	LEU	0	-0.026	-0.019	13.387	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	44	ALA	0	0.015	0.003	12.419	0.129	0.129	0.000	0.000	0.000	0.000
39	A	45	GLY	0	0.007	-0.009	12.533	-0.144	-0.144	0.000	0.000	0.000	0.000
40	A	46	ASN	0	0.001	0.013	13.881	-0.017	-0.017	0.000	0.000	0.000	0.000
41	A	47	ILE	0	-0.028	0.002	17.068	-0.030	-0.030	0.000	0.000	0.000	0.000
42	A	48	PRO	0	-0.003	-0.001	18.830	-0.032	-0.032	0.000	0.000	0.000	0.000
43	A	49	LYS	1	0.934	0.943	22.410	-0.197	-0.197	0.000	0.000	0.000	0.000
44	A	50	ASP	-1	-0.825	-0.908	23.543	0.274	0.274	0.000	0.000	0.000	0.000
45	A	51	LEU	0	-0.041	-0.032	22.773	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	52	GLU	-1	-0.860	-0.905	18.974	0.292	0.292	0.000	0.000	0.000	0.000
47	A	53	GLU	-1	-0.822	-0.908	21.470	0.177	0.177	0.000	0.000	0.000	0.000
48	A	54	ASP	-1	-0.816	-0.910	24.390	0.199	0.199	0.000	0.000	0.000	0.000
49	A	55	VAL	0	-0.034	-0.033	19.905	-0.010	-0.010	0.000	0.000	0.000	0.000
50	A	56	LYS	1	0.813	0.883	17.595	-0.325	-0.325	0.000	0.000	0.000	0.000
51	A	57	TYR	0	-0.016	0.011	22.513	-0.030	-0.030	0.000	0.000	0.000	0.000
52	A	58	TYR	0	0.028	-0.013	26.001	-0.020	-0.020	0.000	0.000	0.000	0.000
53	A	59	ALA	0	0.020	0.002	21.505	-0.011	-0.011	0.000	0.000	0.000	0.000
54	A	60	LYS	1	0.939	0.977	23.600	-0.088	-0.088	0.000	0.000	0.000	0.000
55	A	61	LEU	0	-0.049	-0.018	25.165	-0.018	-0.018	0.000	0.000	0.000	0.000
56	A	62	SER	0	0.010	0.015	26.038	-0.015	-0.015	0.000	0.000	0.000	0.000
57	A	63	ASN	0	-0.084	-0.037	24.698	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	64	ILE	0	0.004	0.016	19.903	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	65	PRO	0	0.010	0.012	16.741	0.016	0.016	0.000	0.000	0.000	0.000
60	A	66	VAL	0	0.027	-0.011	16.399	0.055	0.055	0.000	0.000	0.000	0.000
61	A	67	TYR	0	-0.013	-0.003	6.769	-0.198	-0.198	0.000	0.000	0.000	0.000
62	A	68	GLN	0	0.000	-0.003	12.839	0.041	0.041	0.000	0.000	0.000	0.000
63	A	69	HIS	0	0.038	0.009	5.173	-1.030	-0.991	-0.001	0.000	-0.037	0.000
64	A	70	LYS	1	0.969	0.974	4.815	-1.950	-1.950	0.000	0.000	0.000	0.000
65	A	71	ILE	0	-0.059	-0.012	6.507	-0.056	-0.056	0.000	0.000	0.000	0.000
66	A	72	THR	0	0.012	-0.017	9.464	-0.234	-0.234	0.000	0.000	0.000	0.000
67	A	73	SER	0	0.035	-0.019	12.379	0.161	0.161	0.000	0.000	0.000	0.000
68	A	74	LEU	0	-0.010	0.003	14.781	0.034	0.034	0.000	0.000	0.000	0.000
69	A	75	GLU	-1	-0.792	-0.868	9.146	1.919	1.919	0.000	0.000	0.000	0.000
70	A	76	LEU	0	0.006	-0.006	9.756	0.339	0.339	0.000	0.000	0.000	0.000
71	A	77	GLY	0	0.027	0.015	11.282	0.011	0.011	0.000	0.000	0.000	0.000
72	A	78	ALA	0	0.043	0.025	11.415	-0.053	-0.053	0.000	0.000	0.000	0.000
73	A	79	VAL	0	-0.047	-0.007	6.919	0.136	0.136	0.000	0.000	0.000	0.000
74	A	80	CYS	0	-0.043	-0.022	9.477	-0.191	-0.191	0.000	0.000	0.000	0.000
75	A	81	GLY	0	0.002	0.005	12.384	-0.228	-0.228	0.000	0.000	0.000	0.000
76	A	82	LYS	1	0.798	0.893	14.040	-0.973	-0.973	0.000	0.000	0.000	0.000
77	A	83	PRO	0	0.028	0.020	15.835	0.100	0.100	0.000	0.000	0.000	0.000
78	A	84	PHE	0	-0.001	0.005	18.373	-0.035	-0.035	0.000	0.000	0.000	0.000
79	A	85	PRO	0	0.016	-0.012	17.042	0.099	0.099	0.000	0.000	0.000	0.000
80	A	86	VAL	0	-0.021	-0.011	15.073	-0.102	-0.102	0.000	0.000	0.000	0.000
81	A	87	ALA	0	0.013	-0.001	15.236	0.095	0.095	0.000	0.000	0.000	0.000
82	A	88	ALA	0	0.021	0.006	16.108	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	89	LEU	0	-0.042	-0.008	12.366	0.000	0.000	0.000	0.000	0.000	0.000
84	A	90	LEU	0	-0.003	0.000	16.750	-0.015	-0.015	0.000	0.000	0.000	0.000
85	A	91	VAL	0	0.019	0.017	14.520	0.020	0.020	0.000	0.000	0.000	0.000
86	A	92	LEU	0	-0.011	-0.015	17.732	-0.046	-0.046	0.000	0.000	0.000	0.000
87	A	93	ASP	-1	-0.827	-0.921	20.041	0.109	0.109	0.000	0.000	0.000	0.000
88	A	94	GLU	-1	-0.790	-0.881	15.891	0.186	0.186	0.000	0.000	0.000	0.000
89	A	95	GLY	0	0.027	0.018	16.188	0.024	0.024	0.000	0.000	0.000	0.000
90	A	96	LEU	0	-0.047	-0.032	16.445	-0.045	-0.045	0.000	0.000	0.000	0.000
91	A	97	SER	0	-0.080	-0.058	11.509	-0.114	-0.114	0.000	0.000	0.000	0.000
92	A	98	ASN	0	0.048	0.033	9.615	0.089	0.089	0.000	0.000	0.000	0.000
93	A	99	ILE	0	-0.019	-0.025	8.953	-0.051	-0.051	0.000	0.000	0.000	0.000
94	A	100	MET	0	-0.006	-0.001	11.303	0.027	0.027	0.000	0.000	0.000	0.000
95	A	101	GLU	-1	-0.806	-0.915	13.354	-0.203	-0.203	0.000	0.000	0.000	0.000
96	A	102	LEU	0	-0.060	-0.022	6.591	-0.087	-0.087	0.000	0.000	0.000	0.000
97	A	103	VAL	0	-0.041	-0.029	10.149	-0.021	-0.021	0.000	0.000	0.000	0.000
98	A	104	GLU	-1	-0.968	-0.950	11.402	-0.221	-0.221	0.000	0.000	0.000	0.000
99	A	105	LYS	1	0.811	0.899	10.003	0.120	0.120	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:MET)