FMO DATABASE

FMODB ID: 7669K

Calculation Name: 2CXD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2CXD

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SM75

Base Structure: X-ray

Registration Date: 2023-09-21

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	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	94
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-738367.91037
FMO2-HF: Nuclear repulsion	700367.701262
FMO2-HF: Total energy	-38000.209108
FMO2-MP2: Total energy	-38112.119922

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:MET)

Summations of interaction energy for fragment #1(A:1: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.
-0.055000000000001	2.193	0.719	-1.03	-1.936	0

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / q_NPA : -0.018

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	PRO	0	-0.002	-0.004	3.888	-0.967	0.527	-0.015	-0.699	-0.780	0.002
4	A	4	ASP	-1	-0.795	-0.874	6.378	-0.101	-0.101	0.000	0.000	0.000	0.000
5	A	5	TRP	0	0.025	-0.038	8.826	-0.088	-0.088	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-0.765	-0.850	11.767	-0.179	-0.179	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.926	-0.949	9.910	-0.976	-0.976	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.027	-0.017	10.537	0.050	0.050	0.000	0.000	0.000	0.000
9	A	9	LEU	0	0.008	-0.004	13.339	0.057	0.057	0.000	0.000	0.000	0.000
10	A	10	GLY	0	-0.048	-0.005	16.092	0.050	0.050	0.000	0.000	0.000	0.000
11	A	11	LEU	0	-0.004	-0.001	13.877	0.045	0.045	0.000	0.000	0.000	0.000
12	A	12	TRP	0	-0.058	-0.049	17.411	0.021	0.021	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.765	0.834	17.981	0.280	0.280	0.000	0.000	0.000	0.000
14	A	14	ALA	0	-0.029	0.003	21.122	0.026	0.026	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.010	0.007	22.417	0.008	0.008	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.863	0.930	19.392	0.356	0.356	0.000	0.000	0.000	0.000
17	A	17	TYR	0	-0.002	-0.027	18.785	-0.036	-0.036	0.000	0.000	0.000	0.000
18	A	18	TYR	0	-0.058	-0.036	18.568	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.744	-0.886	16.051	-0.469	-0.469	0.000	0.000	0.000	0.000
20	A	20	VAL	0	-0.056	-0.017	14.250	-0.083	-0.083	0.000	0.000	0.000	0.000
21	A	21	HIS	0	-0.045	-0.035	13.498	-0.063	-0.063	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.852	-0.905	13.182	-0.790	-0.790	0.000	0.000	0.000	0.000
23	A	23	VAL	0	-0.012	0.004	8.788	-0.160	-0.160	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.001	-0.010	8.610	-0.315	-0.315	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.887	-0.942	9.730	-0.954	-0.954	0.000	0.000	0.000	0.000
26	A	26	PRO	0	0.020	0.004	7.120	-0.037	-0.037	0.000	0.000	0.000	0.000
27	A	27	TYR	0	0.033	0.026	2.331	-1.239	-0.485	0.734	-0.331	-1.156	-0.002
28	A	28	TRP	0	-0.033	-0.018	6.591	0.265	0.265	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.019	-0.022	9.174	0.167	0.167	0.000	0.000	0.000	0.000
30	A	30	LYS	1	0.907	0.955	5.176	2.125	2.125	0.000	0.000	0.000	0.000
31	A	31	ALA	0	0.062	0.059	7.558	0.225	0.225	0.000	0.000	0.000	0.000
32	A	32	THR	0	0.037	0.002	8.380	0.132	0.132	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.037	0.016	11.351	0.015	0.015	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.820	-0.921	14.368	-0.089	-0.089	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.852	-0.924	7.763	0.023	0.023	0.000	0.000	0.000	0.000
36	A	36	ARG	1	0.808	0.906	11.168	0.606	0.606	0.000	0.000	0.000	0.000
37	A	37	ARG	1	0.784	0.869	12.459	0.106	0.106	0.000	0.000	0.000	0.000
38	A	38	LEU	0	0.028	0.019	11.851	-0.007	-0.007	0.000	0.000	0.000	0.000
39	A	39	LEU	0	0.019	0.010	8.563	0.013	0.013	0.000	0.000	0.000	0.000
40	A	40	GLN	0	0.013	0.011	12.904	0.077	0.077	0.000	0.000	0.000	0.000
41	A	41	GLY	0	0.026	0.005	15.780	0.035	0.035	0.000	0.000	0.000	0.000
42	A	42	VAL	0	0.023	0.005	14.767	0.036	0.036	0.000	0.000	0.000	0.000
43	A	43	ILE	0	0.038	0.031	12.539	0.042	0.042	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.046	-0.026	16.698	0.052	0.052	0.000	0.000	0.000	0.000
45	A	45	LEU	0	-0.016	-0.006	20.038	0.041	0.041	0.000	0.000	0.000	0.000
46	A	46	ALA	0	0.042	0.032	18.462	0.031	0.031	0.000	0.000	0.000	0.000
47	A	47	ALA	0	0.011	0.000	20.386	0.030	0.030	0.000	0.000	0.000	0.000
48	A	48	ALA	0	-0.061	-0.036	22.087	0.029	0.029	0.000	0.000	0.000	0.000
49	A	49	LEU	0	-0.006	0.003	22.692	0.028	0.028	0.000	0.000	0.000	0.000
50	A	50	HIS	0	0.059	0.031	23.225	0.020	0.020	0.000	0.000	0.000	0.000
51	A	51	GLN	0	-0.006	-0.004	25.306	0.031	0.031	0.000	0.000	0.000	0.000
52	A	52	ARG	1	0.877	0.939	27.981	0.175	0.175	0.000	0.000	0.000	0.000
53	A	53	ARG	1	0.836	0.915	24.047	0.275	0.275	0.000	0.000	0.000	0.000
54	A	54	LEU	0	-0.036	-0.010	27.674	0.010	0.010	0.000	0.000	0.000	0.000
55	A	55	GLY	0	0.030	0.028	31.255	0.008	0.008	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.901	0.948	30.080	0.208	0.208	0.000	0.000	0.000	0.000
57	A	57	PRO	0	0.025	-0.009	31.875	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	58	GLY	0	0.012	0.007	28.255	-0.007	-0.007	0.000	0.000	0.000	0.000
59	A	59	LEU	0	0.002	-0.009	27.841	-0.012	-0.012	0.000	0.000	0.000	0.000
60	A	60	ARG	1	0.977	0.997	26.122	0.227	0.227	0.000	0.000	0.000	0.000
61	A	61	ASN	0	-0.005	-0.010	23.790	0.010	0.010	0.000	0.000	0.000	0.000
62	A	62	LEU	0	0.026	0.032	24.192	-0.015	-0.015	0.000	0.000	0.000	0.000
63	A	63	ARG	1	0.914	0.936	25.541	0.136	0.136	0.000	0.000	0.000	0.000
64	A	64	LYS	1	0.859	0.945	20.560	0.349	0.349	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.021	0.009	21.343	-0.009	-0.009	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.706	-0.830	22.008	-0.149	-0.149	0.000	0.000	0.000	0.000
67	A	67	ALA	0	-0.008	0.004	24.041	0.011	0.011	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.817	0.911	18.747	0.246	0.246	0.000	0.000	0.000	0.000
69	A	69	LEU	0	0.050	0.016	18.095	0.006	0.006	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.862	-0.921	20.566	-0.070	-0.070	0.000	0.000	0.000	0.000
71	A	71	GLY	0	-0.040	-0.029	22.485	-0.004	-0.004	0.000	0.000	0.000	0.000
72	A	72	LEU	0	-0.070	0.001	16.728	0.017	0.017	0.000	0.000	0.000	0.000
73	A	73	PRO	0	0.081	0.043	17.380	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	74	CYS	0	-0.103	-0.024	18.701	-0.049	-0.049	0.000	0.000	0.000	0.000
75	A	75	PRO	0	0.063	0.025	16.119	0.012	0.012	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.022	-0.015	12.687	0.042	0.042	0.000	0.000	0.000	0.000
77	A	77	MET	0	-0.015	0.001	7.006	-0.158	-0.158	0.000	0.000	0.000	0.000
78	A	78	GLY	0	0.031	0.032	9.896	0.007	0.007	0.000	0.000	0.000	0.000
79	A	79	LEU	0	-0.015	0.010	12.558	-0.009	-0.009	0.000	0.000	0.000	0.000
80	A	80	ASP	-1	-0.750	-0.878	14.839	-0.077	-0.077	0.000	0.000	0.000	0.000
81	A	81	TRP	0	0.025	-0.018	17.167	-0.040	-0.040	0.000	0.000	0.000	0.000
82	A	82	ARG	1	0.865	0.938	18.963	0.061	0.061	0.000	0.000	0.000	0.000
83	A	83	SER	0	-0.015	-0.032	22.241	0.003	0.003	0.000	0.000	0.000	0.000
84	A	84	LEU	0	0.023	0.016	17.773	0.001	0.001	0.000	0.000	0.000	0.000
85	A	85	LEU	0	0.003	0.000	21.946	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	86	GLN	0	-0.008	-0.008	23.873	0.007	0.007	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.829	-0.883	23.503	-0.207	-0.207	0.000	0.000	0.000	0.000
88	A	88	ALA	0	0.023	0.009	23.750	0.003	0.003	0.000	0.000	0.000	0.000
89	A	89	ARG	1	0.868	0.911	25.822	0.135	0.135	0.000	0.000	0.000	0.000
90	A	90	ARG	1	0.937	0.976	27.376	0.130	0.130	0.000	0.000	0.000	0.000
91	A	91	ARG	1	0.874	0.919	25.267	0.208	0.208	0.000	0.000	0.000	0.000
92	A	92	LEU	0	-0.042	-0.023	26.472	0.000	0.000	0.000	0.000	0.000	0.000
93	A	93	GLY	0	0.018	0.030	30.548	0.004	0.004	0.000	0.000	0.000	0.000
94	A	94	ALA	0	-0.061	-0.033	31.357	0.006	0.006	0.000	0.000	0.000	0.000

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