FMO DATABASE

FMODB ID: ZVZKN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-719366.920779
FMO2-HF: Nuclear repulsion	681842.125365
FMO2-HF: Total energy	-37524.795413
FMO2-MP2: Total energy	-37635.01183

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.
-12.368	-8.085	0.364	-1.623	-3.025	0.006

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 : -0.017 / 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	0.052	0.026	3.198	0.898	2.599	0.012	-0.654	-1.060	0.001
4	A	10	ASN	0	0.021	0.008	3.310	-3.412	-1.851	0.332	-0.639	-1.255	0.004
5	A	11	LYS	1	0.951	0.979	3.473	-4.033	-3.110	0.022	-0.326	-0.619	0.001
6	A	12	ALA	0	0.076	0.057	6.055	-0.051	-0.051	0.000	0.000	0.000	0.000
7	A	13	ILE	0	-0.011	0.006	7.683	-0.080	-0.080	0.000	0.000	0.000	0.000
8	A	14	ARG	1	0.850	0.930	8.801	-1.338	-1.338	0.000	0.000	0.000	0.000
9	A	15	THR	0	0.035	0.009	10.030	-0.202	-0.202	0.000	0.000	0.000	0.000
10	A	16	ALA	0	0.029	0.039	12.245	-0.099	-0.099	0.000	0.000	0.000	0.000
11	A	17	VAL	0	-0.119	-0.058	13.606	-0.053	-0.053	0.000	0.000	0.000	0.000
12	A	18	ASP	-1	-0.888	-0.945	14.152	0.621	0.621	0.000	0.000	0.000	0.000
13	A	19	THR	0	-0.069	-0.039	15.789	-0.087	-0.087	0.000	0.000	0.000	0.000
14	A	20	GLY	0	0.071	0.049	17.501	-0.057	-0.057	0.000	0.000	0.000	0.000
15	A	21	LYS	1	0.870	0.944	19.130	-0.265	-0.265	0.000	0.000	0.000	0.000
16	A	22	VAL	0	0.040	0.019	15.298	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	23	ILE	0	-0.078	-0.024	18.559	0.002	0.002	0.000	0.000	0.000	0.000
18	A	24	LEU	0	0.034	0.008	16.253	0.049	0.049	0.000	0.000	0.000	0.000
19	A	25	GLY	0	0.017	0.000	18.808	-0.060	-0.060	0.000	0.000	0.000	0.000
20	A	26	SER	0	0.029	0.022	20.688	-0.031	-0.031	0.000	0.000	0.000	0.000
21	A	27	LYS	1	1.004	0.992	21.620	-0.372	-0.372	0.000	0.000	0.000	0.000
22	A	28	ARG	1	0.958	0.980	23.240	-0.415	-0.415	0.000	0.000	0.000	0.000
23	A	29	THR	0	0.046	0.023	19.463	-0.021	-0.021	0.000	0.000	0.000	0.000
24	A	30	ILE	0	0.043	0.024	22.356	-0.031	-0.031	0.000	0.000	0.000	0.000
25	A	31	LYS	1	0.900	0.959	24.898	-0.249	-0.249	0.000	0.000	0.000	0.000
26	A	32	PHE	0	0.005	-0.010	24.257	-0.012	-0.012	0.000	0.000	0.000	0.000
27	A	33	VAL	0	0.071	0.055	22.081	-0.019	-0.019	0.000	0.000	0.000	0.000
28	A	34	LYS	1	0.860	0.947	25.253	-0.239	-0.239	0.000	0.000	0.000	0.000
29	A	35	HIS	0	-0.124	-0.078	28.525	-0.025	-0.025	0.000	0.000	0.000	0.000
30	A	36	GLY	0	0.038	0.031	27.814	-0.012	-0.012	0.000	0.000	0.000	0.000
31	A	37	GLU	-1	-0.950	-0.967	26.058	0.186	0.186	0.000	0.000	0.000	0.000
32	A	38	GLY	0	-0.034	-0.042	22.116	0.027	0.027	0.000	0.000	0.000	0.000
33	A	39	LYS	1	0.868	0.937	19.037	-0.137	-0.137	0.000	0.000	0.000	0.000
34	A	40	LEU	0	0.039	0.011	12.479	-0.018	-0.018	0.000	0.000	0.000	0.000
35	A	41	VAL	0	-0.011	0.015	16.607	0.060	0.060	0.000	0.000	0.000	0.000
36	A	42	VAL	0	-0.014	0.008	10.495	0.021	0.021	0.000	0.000	0.000	0.000
37	A	43	LEU	0	-0.023	-0.018	13.370	-0.005	-0.005	0.000	0.000	0.000	0.000
38	A	44	ALA	0	0.010	0.001	12.420	0.151	0.151	0.000	0.000	0.000	0.000
39	A	45	GLY	0	0.010	-0.007	12.566	-0.152	-0.152	0.000	0.000	0.000	0.000
40	A	46	ASN	0	0.003	0.023	13.918	-0.031	-0.031	0.000	0.000	0.000	0.000
41	A	47	ILE	0	-0.018	0.002	17.110	-0.036	-0.036	0.000	0.000	0.000	0.000
42	A	48	PRO	0	-0.012	-0.005	18.872	-0.032	-0.032	0.000	0.000	0.000	0.000
43	A	49	LYS	1	1.019	0.997	22.397	-0.242	-0.242	0.000	0.000	0.000	0.000
44	A	50	ASP	-1	-0.819	-0.895	23.534	0.309	0.309	0.000	0.000	0.000	0.000
45	A	51	LEU	0	-0.029	-0.024	22.796	0.004	0.004	0.000	0.000	0.000	0.000
46	A	52	GLU	-1	-0.891	-0.942	18.925	0.370	0.370	0.000	0.000	0.000	0.000
47	A	53	GLU	-1	-0.912	-0.974	21.453	0.217	0.217	0.000	0.000	0.000	0.000
48	A	54	ASP	-1	-0.901	-0.944	24.374	0.236	0.236	0.000	0.000	0.000	0.000
49	A	55	VAL	0	-0.082	-0.053	19.801	-0.012	-0.012	0.000	0.000	0.000	0.000
50	A	56	LYS	1	0.879	0.928	18.324	-0.348	-0.348	0.000	0.000	0.000	0.000
51	A	57	TYR	0	-0.014	0.014	22.491	-0.033	-0.033	0.000	0.000	0.000	0.000
52	A	58	TYR	0	0.042	-0.009	25.764	-0.017	-0.017	0.000	0.000	0.000	0.000
53	A	59	ALA	0	0.019	0.003	21.493	-0.013	-0.013	0.000	0.000	0.000	0.000
54	A	60	LYS	1	0.936	0.975	23.571	-0.124	-0.124	0.000	0.000	0.000	0.000
55	A	61	LEU	0	-0.054	-0.022	25.140	-0.019	-0.019	0.000	0.000	0.000	0.000
56	A	62	SER	0	0.010	0.016	26.047	-0.016	-0.016	0.000	0.000	0.000	0.000
57	A	63	ASN	0	-0.064	-0.025	24.692	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	64	ILE	0	-0.010	0.009	19.860	-0.005	-0.005	0.000	0.000	0.000	0.000
59	A	65	PRO	0	0.008	0.013	16.762	0.020	0.020	0.000	0.000	0.000	0.000
60	A	66	VAL	0	0.038	-0.005	16.344	0.053	0.053	0.000	0.000	0.000	0.000
61	A	67	TYR	0	-0.024	-0.015	6.597	-0.269	-0.269	0.000	0.000	0.000	0.000
62	A	68	GLN	0	-0.031	-0.021	12.821	0.032	0.032	0.000	0.000	0.000	0.000
63	A	69	HIS	0	0.016	0.006	5.388	-1.014	-0.984	-0.001	0.000	-0.029	0.000
64	A	70	LYS	1	0.977	0.970	4.169	-2.962	-2.894	-0.001	-0.004	-0.062	0.000
65	A	71	ILE	0	-0.048	-0.008	6.555	-0.049	-0.049	0.000	0.000	0.000	0.000
66	A	72	THR	0	0.028	0.018	9.510	-0.295	-0.295	0.000	0.000	0.000	0.000
67	A	73	SER	0	0.047	-0.020	12.433	0.157	0.157	0.000	0.000	0.000	0.000
68	A	74	LEU	0	-0.008	0.004	14.809	0.022	0.022	0.000	0.000	0.000	0.000
69	A	75	GLU	-1	-0.845	-0.919	9.287	2.288	2.288	0.000	0.000	0.000	0.000
70	A	76	LEU	0	0.001	-0.009	9.875	0.327	0.327	0.000	0.000	0.000	0.000
71	A	77	GLY	0	0.018	0.003	11.282	-0.013	-0.013	0.000	0.000	0.000	0.000
72	A	78	ALA	0	0.042	0.026	11.393	-0.074	-0.074	0.000	0.000	0.000	0.000
73	A	79	VAL	0	-0.051	-0.008	6.998	0.093	0.093	0.000	0.000	0.000	0.000
74	A	80	CYS	0	-0.046	-0.029	9.536	-0.233	-0.233	0.000	0.000	0.000	0.000
75	A	81	GLY	0	-0.013	-0.003	12.444	-0.211	-0.211	0.000	0.000	0.000	0.000
76	A	82	LYS	1	0.852	0.927	14.089	-0.855	-0.855	0.000	0.000	0.000	0.000
77	A	83	PRO	0	0.022	0.014	15.889	0.103	0.103	0.000	0.000	0.000	0.000
78	A	84	PHE	0	-0.008	0.003	18.425	-0.034	-0.034	0.000	0.000	0.000	0.000
79	A	85	PRO	0	0.008	-0.015	17.071	0.102	0.102	0.000	0.000	0.000	0.000
80	A	86	VAL	0	-0.010	-0.004	15.020	-0.113	-0.113	0.000	0.000	0.000	0.000
81	A	87	ALA	0	0.017	0.001	15.236	0.105	0.105	0.000	0.000	0.000	0.000
82	A	88	ALA	0	0.018	0.005	16.125	0.004	0.004	0.000	0.000	0.000	0.000
83	A	89	LEU	0	-0.032	-0.002	12.286	-0.010	-0.010	0.000	0.000	0.000	0.000
84	A	90	LEU	0	0.001	-0.003	16.716	-0.013	-0.013	0.000	0.000	0.000	0.000
85	A	91	VAL	0	0.019	0.019	14.521	0.014	0.014	0.000	0.000	0.000	0.000
86	A	92	LEU	0	-0.029	-0.028	17.691	-0.045	-0.045	0.000	0.000	0.000	0.000
87	A	93	ASP	-1	-0.887	-0.945	20.001	0.109	0.109	0.000	0.000	0.000	0.000
88	A	94	GLU	-1	-0.790	-0.899	15.847	0.169	0.169	0.000	0.000	0.000	0.000
89	A	95	GLY	0	0.029	0.013	16.188	0.017	0.017	0.000	0.000	0.000	0.000
90	A	96	LEU	0	-0.055	-0.039	16.374	-0.044	-0.044	0.000	0.000	0.000	0.000
91	A	97	SER	0	-0.078	-0.057	11.486	-0.120	-0.120	0.000	0.000	0.000	0.000
92	A	98	ASN	0	0.055	0.036	9.487	0.109	0.109	0.000	0.000	0.000	0.000
93	A	99	ILE	0	-0.018	-0.031	8.953	-0.037	-0.037	0.000	0.000	0.000	0.000
94	A	100	MET	0	-0.011	-0.004	11.263	0.043	0.043	0.000	0.000	0.000	0.000
95	A	101	GLU	-1	-0.809	-0.913	13.368	-0.188	-0.188	0.000	0.000	0.000	0.000
96	A	102	LEU	0	-0.069	-0.025	6.562	-0.066	-0.066	0.000	0.000	0.000	0.000
97	A	103	VAL	0	-0.071	-0.042	10.121	0.000	0.000	0.000	0.000	0.000	0.000
98	A	104	GLU	-1	-0.974	-0.966	11.375	-0.196	-0.196	0.000	0.000	0.000	0.000
99	A	105	LYS	1	0.842	0.930	10.333	-0.038	-0.038	0.000	0.000	0.000	0.000

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