FMO DATABASE

FMODB ID: 98832

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

Total energy (hartree)

FMO2-HF: Electronic energy	-733491.296172
FMO2-HF: Nuclear repulsion	695491.658022
FMO2-HF: Total energy	-37999.63815
FMO2-MP2: Total energy	-38111.523487

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.
-0.657	1.842	0.714	-1.071	-2.144	-0.002

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 : -0.006 / q_NPA : -0.021

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	0.000	-0.008	3.870	-0.836	0.567	-0.014	-0.620	-0.770	0.001
4	A	4	ASP	-1	-0.778	-0.871	6.266	-0.500	-0.500	0.000	0.000	0.000	0.000
5	A	5	TRP	0	0.012	-0.034	8.600	0.039	0.039	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-0.913	-0.940	11.659	-0.292	-0.292	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.948	-0.961	10.008	-1.108	-1.108	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.032	-0.026	10.715	0.074	0.074	0.000	0.000	0.000	0.000
9	A	9	LEU	0	-0.025	-0.029	13.449	0.096	0.096	0.000	0.000	0.000	0.000
10	A	10	GLY	0	-0.010	0.000	16.142	0.067	0.067	0.000	0.000	0.000	0.000
11	A	11	LEU	0	-0.017	-0.007	14.164	0.067	0.067	0.000	0.000	0.000	0.000
12	A	12	TRP	0	-0.050	-0.051	17.514	0.033	0.033	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.931	0.967	19.097	0.383	0.383	0.000	0.000	0.000	0.000
14	A	14	ALA	0	-0.041	-0.002	21.293	0.032	0.032	0.000	0.000	0.000	0.000
15	A	15	GLY	0	-0.004	0.012	22.335	0.020	0.020	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.928	0.981	19.470	0.423	0.423	0.000	0.000	0.000	0.000
17	A	17	TYR	0	0.016	-0.022	18.938	-0.034	-0.034	0.000	0.000	0.000	0.000
18	A	18	TYR	0	-0.034	-0.010	17.849	-0.013	-0.013	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.810	-0.927	16.335	-0.562	-0.562	0.000	0.000	0.000	0.000
20	A	20	VAL	0	-0.044	-0.004	14.514	-0.089	-0.089	0.000	0.000	0.000	0.000
21	A	21	HIS	0	-0.057	-0.032	13.552	-0.097	-0.097	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.840	-0.928	13.199	-0.848	-0.848	0.000	0.000	0.000	0.000
23	A	23	VAL	0	-0.012	0.007	8.899	-0.161	-0.161	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.007	-0.022	8.735	-0.347	-0.347	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.924	-0.956	9.321	-0.967	-0.967	0.000	0.000	0.000	0.000
26	A	26	PRO	0	0.030	0.003	6.286	0.026	0.026	0.000	0.000	0.000	0.000
27	A	27	TYR	0	0.032	0.015	2.500	-0.824	0.147	0.729	-0.448	-1.253	-0.003
28	A	28	TRP	0	-0.032	-0.027	6.356	0.333	0.333	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.046	-0.027	8.739	0.226	0.226	0.000	0.000	0.000	0.000
30	A	30	LYS	1	0.922	0.962	4.707	1.532	1.657	-0.001	-0.003	-0.121	0.000
31	A	31	ALA	0	0.038	0.063	7.172	0.311	0.311	0.000	0.000	0.000	0.000
32	A	32	THR	0	0.025	-0.008	8.006	0.134	0.134	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.031	0.012	10.812	-0.012	-0.012	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.898	-0.975	13.603	-0.096	-0.096	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.850	-0.921	6.921	-0.154	-0.154	0.000	0.000	0.000	0.000
36	A	36	ARG	1	0.853	0.939	10.711	0.357	0.357	0.000	0.000	0.000	0.000
37	A	37	ARG	1	0.788	0.893	11.626	0.115	0.115	0.000	0.000	0.000	0.000
38	A	38	LEU	0	0.041	0.024	11.632	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	39	LEU	0	0.016	0.011	7.808	0.028	0.028	0.000	0.000	0.000	0.000
40	A	40	GLN	0	-0.009	-0.004	12.485	-0.004	-0.004	0.000	0.000	0.000	0.000
41	A	41	GLY	0	-0.003	-0.006	15.361	0.043	0.043	0.000	0.000	0.000	0.000
42	A	42	VAL	0	0.024	0.009	14.735	0.050	0.050	0.000	0.000	0.000	0.000
43	A	43	ILE	0	0.046	0.036	12.392	0.049	0.049	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.055	-0.038	16.591	0.062	0.062	0.000	0.000	0.000	0.000
45	A	45	LEU	0	-0.015	-0.007	19.812	0.047	0.047	0.000	0.000	0.000	0.000
46	A	46	ALA	0	0.036	0.028	18.587	0.035	0.035	0.000	0.000	0.000	0.000
47	A	47	ALA	0	0.014	0.008	20.509	0.033	0.033	0.000	0.000	0.000	0.000
48	A	48	ALA	0	-0.068	-0.046	22.148	0.033	0.033	0.000	0.000	0.000	0.000
49	A	49	LEU	0	-0.009	-0.001	22.896	0.030	0.030	0.000	0.000	0.000	0.000
50	A	50	HIS	0	0.016	0.016	23.376	0.014	0.014	0.000	0.000	0.000	0.000
51	A	51	GLN	0	-0.026	-0.024	25.379	0.035	0.035	0.000	0.000	0.000	0.000
52	A	52	ARG	1	0.892	0.964	27.966	0.207	0.207	0.000	0.000	0.000	0.000
53	A	53	ARG	1	0.894	0.939	24.952	0.313	0.313	0.000	0.000	0.000	0.000
54	A	54	LEU	0	-0.048	-0.017	28.009	0.011	0.011	0.000	0.000	0.000	0.000
55	A	55	GLY	0	0.027	0.024	31.520	0.010	0.010	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.926	0.970	30.830	0.214	0.214	0.000	0.000	0.000	0.000
57	A	57	PRO	0	0.005	-0.016	31.695	-0.007	-0.007	0.000	0.000	0.000	0.000
58	A	58	GLY	0	0.071	0.030	28.464	-0.012	-0.012	0.000	0.000	0.000	0.000
59	A	59	LEU	0	0.018	-0.003	27.893	-0.013	-0.013	0.000	0.000	0.000	0.000
60	A	60	ARG	1	0.995	1.001	26.339	0.211	0.211	0.000	0.000	0.000	0.000
61	A	61	ASN	0	0.002	-0.005	23.933	0.006	0.006	0.000	0.000	0.000	0.000
62	A	62	LEU	0	0.004	0.020	24.121	-0.014	-0.014	0.000	0.000	0.000	0.000
63	A	63	ARG	1	0.986	1.001	25.483	0.153	0.153	0.000	0.000	0.000	0.000
64	A	64	LYS	1	0.932	0.981	22.275	0.278	0.278	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.012	-0.003	21.107	-0.005	-0.005	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.809	-0.908	21.495	-0.173	-0.173	0.000	0.000	0.000	0.000
67	A	67	ALA	0	0.011	0.014	23.677	0.011	0.011	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.844	0.931	17.819	0.292	0.292	0.000	0.000	0.000	0.000
69	A	69	LEU	0	0.047	0.005	17.736	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.933	-0.958	20.134	-0.100	-0.100	0.000	0.000	0.000	0.000
71	A	71	GLY	0	-0.019	-0.013	22.268	0.007	0.007	0.000	0.000	0.000	0.000
72	A	72	LEU	0	-0.045	0.007	16.062	0.016	0.016	0.000	0.000	0.000	0.000
73	A	73	PRO	0	0.045	0.037	16.856	-0.007	-0.007	0.000	0.000	0.000	0.000
74	A	74	CYS	0	-0.058	0.008	18.156	-0.057	-0.057	0.000	0.000	0.000	0.000
75	A	75	PRO	0	0.029	-0.003	16.214	0.021	0.021	0.000	0.000	0.000	0.000
76	A	76	LEU	0	0.016	0.008	12.230	0.043	0.043	0.000	0.000	0.000	0.000
77	A	77	MET	0	-0.020	-0.007	6.513	-0.078	-0.078	0.000	0.000	0.000	0.000
78	A	78	GLY	0	0.023	0.021	10.480	-0.092	-0.092	0.000	0.000	0.000	0.000
79	A	79	LEU	0	0.000	0.008	13.017	-0.011	-0.011	0.000	0.000	0.000	0.000
80	A	80	ASP	-1	-0.775	-0.865	14.892	-0.152	-0.152	0.000	0.000	0.000	0.000
81	A	81	TRP	0	0.001	-0.038	17.030	-0.029	-0.029	0.000	0.000	0.000	0.000
82	A	82	ARG	1	0.966	0.977	18.856	0.120	0.120	0.000	0.000	0.000	0.000
83	A	83	SER	0	-0.010	-0.044	22.042	0.013	0.013	0.000	0.000	0.000	0.000
84	A	84	LEU	0	0.025	0.016	17.318	0.007	0.007	0.000	0.000	0.000	0.000
85	A	85	LEU	0	-0.017	-0.005	21.817	0.006	0.006	0.000	0.000	0.000	0.000
86	A	86	GLN	0	-0.028	-0.027	23.847	0.009	0.009	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.814	-0.880	23.783	-0.269	-0.269	0.000	0.000	0.000	0.000
88	A	88	ALA	0	0.013	0.001	24.020	0.009	0.009	0.000	0.000	0.000	0.000
89	A	89	ARG	1	0.867	0.911	26.075	0.171	0.171	0.000	0.000	0.000	0.000
90	A	90	ARG	1	0.954	0.993	27.752	0.185	0.185	0.000	0.000	0.000	0.000
91	A	91	ARG	1	0.860	0.917	26.110	0.252	0.252	0.000	0.000	0.000	0.000
92	A	92	LEU	0	-0.081	-0.038	26.664	0.004	0.004	0.000	0.000	0.000	0.000
93	A	93	GLY	0	0.010	0.018	30.972	0.007	0.007	0.000	0.000	0.000	0.000
94	A	94	ALA	0	-0.043	-0.024	31.150	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)