FMO DATABASE

FMODB ID: MNN5Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-734229.038841
FMO2-HF: Nuclear repulsion	696228.990319
FMO2-HF: Total energy	-38000.048522
FMO2-MP2: Total energy	-38111.923862

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.
-0.669	1.672	0.864	-1.046	-2.159	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 : -0.014 / 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	0.005	0.000	3.872	-1.042	0.391	-0.015	-0.633	-0.785	0.002
4	A	4	ASP	-1	-0.803	-0.882	6.226	-0.381	-0.381	0.000	0.000	0.000	0.000
5	A	5	TRP	0	0.007	-0.041	8.649	-0.008	-0.008	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-0.794	-0.875	11.668	-0.263	-0.263	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.940	-0.951	9.976	-1.083	-1.083	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.027	-0.029	10.639	0.065	0.065	0.000	0.000	0.000	0.000
9	A	9	LEU	0	-0.010	-0.016	13.408	0.079	0.079	0.000	0.000	0.000	0.000
10	A	10	GLY	0	-0.039	-0.012	16.140	0.062	0.062	0.000	0.000	0.000	0.000
11	A	11	LEU	0	-0.016	0.002	14.058	0.057	0.057	0.000	0.000	0.000	0.000
12	A	12	TRP	0	-0.050	-0.051	17.462	0.030	0.030	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.819	0.888	18.191	0.363	0.363	0.000	0.000	0.000	0.000
14	A	14	ALA	0	-0.029	0.005	21.254	0.030	0.030	0.000	0.000	0.000	0.000
15	A	15	GLY	0	-0.013	0.006	22.252	0.018	0.018	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.937	0.980	19.517	0.398	0.398	0.000	0.000	0.000	0.000
17	A	17	TYR	0	-0.003	-0.030	18.833	-0.035	-0.035	0.000	0.000	0.000	0.000
18	A	18	TYR	0	-0.055	-0.041	18.415	-0.008	-0.008	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.786	-0.919	16.249	-0.523	-0.523	0.000	0.000	0.000	0.000
20	A	20	VAL	0	-0.049	-0.007	14.394	-0.088	-0.088	0.000	0.000	0.000	0.000
21	A	21	HIS	0	-0.063	-0.046	13.405	-0.086	-0.086	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.842	-0.904	13.309	-0.805	-0.805	0.000	0.000	0.000	0.000
23	A	23	VAL	0	-0.017	0.004	8.846	-0.161	-0.161	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.001	-0.014	8.690	-0.332	-0.332	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.902	-0.940	9.379	-0.937	-0.937	0.000	0.000	0.000	0.000
26	A	26	PRO	0	0.037	0.009	6.599	0.020	0.020	0.000	0.000	0.000	0.000
27	A	27	TYR	0	0.033	0.014	2.318	-1.185	-0.395	0.880	-0.410	-1.260	-0.002
28	A	28	TRP	0	-0.033	-0.025	6.357	0.315	0.315	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.031	-0.019	8.893	0.202	0.202	0.000	0.000	0.000	0.000
30	A	30	LYS	1	0.933	0.973	4.680	1.743	1.861	-0.001	-0.003	-0.114	0.000
31	A	31	ALA	0	0.039	0.064	7.390	0.279	0.279	0.000	0.000	0.000	0.000
32	A	32	THR	0	0.024	-0.005	8.235	0.115	0.115	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.041	0.020	11.011	0.013	0.013	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.870	-0.966	13.803	-0.077	-0.077	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.850	-0.920	7.243	0.107	0.107	0.000	0.000	0.000	0.000
36	A	36	ARG	1	0.821	0.906	10.945	0.409	0.409	0.000	0.000	0.000	0.000
37	A	37	ARG	1	0.780	0.885	11.879	0.084	0.084	0.000	0.000	0.000	0.000
38	A	38	LEU	0	0.036	0.021	11.812	-0.010	-0.010	0.000	0.000	0.000	0.000
39	A	39	LEU	0	0.023	0.011	8.108	0.011	0.011	0.000	0.000	0.000	0.000
40	A	40	GLN	0	0.005	0.004	12.651	0.080	0.080	0.000	0.000	0.000	0.000
41	A	41	GLY	0	0.016	-0.001	15.423	0.035	0.035	0.000	0.000	0.000	0.000
42	A	42	VAL	0	0.026	0.009	14.790	0.042	0.042	0.000	0.000	0.000	0.000
43	A	43	ILE	0	0.032	0.028	12.347	0.046	0.046	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.067	-0.041	16.654	0.054	0.054	0.000	0.000	0.000	0.000
45	A	45	LEU	0	0.000	0.001	19.866	0.042	0.042	0.000	0.000	0.000	0.000
46	A	46	ALA	0	0.032	0.025	18.494	0.032	0.032	0.000	0.000	0.000	0.000
47	A	47	ALA	0	0.012	0.004	20.495	0.030	0.030	0.000	0.000	0.000	0.000
48	A	48	ALA	0	-0.060	-0.037	22.230	0.030	0.030	0.000	0.000	0.000	0.000
49	A	49	LEU	0	-0.012	0.000	22.753	0.028	0.028	0.000	0.000	0.000	0.000
50	A	50	HIS	0	0.024	0.015	23.276	0.017	0.017	0.000	0.000	0.000	0.000
51	A	51	GLN	0	0.002	-0.001	25.337	0.032	0.032	0.000	0.000	0.000	0.000
52	A	52	ARG	1	0.896	0.954	28.063	0.189	0.189	0.000	0.000	0.000	0.000
53	A	53	ARG	1	0.870	0.937	24.435	0.297	0.297	0.000	0.000	0.000	0.000
54	A	54	LEU	0	-0.041	-0.014	27.944	0.010	0.010	0.000	0.000	0.000	0.000
55	A	55	GLY	0	0.024	0.022	31.513	0.010	0.010	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.890	0.946	29.878	0.213	0.213	0.000	0.000	0.000	0.000
57	A	57	PRO	0	0.000	-0.018	31.778	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	58	GLY	0	0.070	0.031	28.522	-0.012	-0.012	0.000	0.000	0.000	0.000
59	A	59	LEU	0	0.003	-0.010	27.943	-0.012	-0.012	0.000	0.000	0.000	0.000
60	A	60	ARG	1	0.990	1.002	26.175	0.214	0.214	0.000	0.000	0.000	0.000
61	A	61	ASN	0	-0.009	-0.015	23.885	0.011	0.011	0.000	0.000	0.000	0.000
62	A	62	LEU	0	0.024	0.030	24.144	-0.016	-0.016	0.000	0.000	0.000	0.000
63	A	63	ARG	1	0.929	0.950	25.607	0.141	0.141	0.000	0.000	0.000	0.000
64	A	64	LYS	1	0.879	0.962	20.551	0.325	0.325	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.016	-0.004	21.313	-0.005	-0.005	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.741	-0.854	21.759	-0.158	-0.158	0.000	0.000	0.000	0.000
67	A	67	ALA	0	0.007	0.010	23.934	0.012	0.012	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.852	0.937	18.316	0.261	0.261	0.000	0.000	0.000	0.000
69	A	69	LEU	0	0.043	0.006	17.874	0.002	0.002	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.908	-0.949	20.387	-0.078	-0.078	0.000	0.000	0.000	0.000
71	A	71	GLY	0	-0.014	-0.003	22.504	0.005	0.005	0.000	0.000	0.000	0.000
72	A	72	LEU	0	-0.070	0.002	16.347	0.016	0.016	0.000	0.000	0.000	0.000
73	A	73	PRO	0	0.038	0.023	17.023	-0.008	-0.008	0.000	0.000	0.000	0.000
74	A	74	CYS	0	-0.079	-0.003	18.356	-0.052	-0.052	0.000	0.000	0.000	0.000
75	A	75	PRO	0	0.043	0.002	16.209	0.016	0.016	0.000	0.000	0.000	0.000
76	A	76	LEU	0	0.009	-0.001	12.611	0.043	0.043	0.000	0.000	0.000	0.000
77	A	77	MET	0	-0.008	0.005	6.761	-0.126	-0.126	0.000	0.000	0.000	0.000
78	A	78	GLY	0	0.026	0.026	10.415	-0.075	-0.075	0.000	0.000	0.000	0.000
79	A	79	LEU	0	-0.010	0.005	13.026	-0.024	-0.024	0.000	0.000	0.000	0.000
80	A	80	ASP	-1	-0.779	-0.888	14.896	-0.113	-0.113	0.000	0.000	0.000	0.000
81	A	81	TRP	0	0.018	-0.025	17.067	-0.034	-0.034	0.000	0.000	0.000	0.000
82	A	82	ARG	1	0.955	0.974	18.874	0.084	0.084	0.000	0.000	0.000	0.000
83	A	83	SER	0	-0.003	-0.020	22.045	0.009	0.009	0.000	0.000	0.000	0.000
84	A	84	LEU	0	0.017	0.013	17.468	0.004	0.004	0.000	0.000	0.000	0.000
85	A	85	LEU	0	-0.012	-0.007	21.737	0.003	0.003	0.000	0.000	0.000	0.000
86	A	86	GLN	0	-0.029	-0.023	23.761	0.011	0.011	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.823	-0.883	23.727	-0.240	-0.240	0.000	0.000	0.000	0.000
88	A	88	ALA	0	0.018	0.002	23.872	0.007	0.007	0.000	0.000	0.000	0.000
89	A	89	ARG	1	0.882	0.916	25.962	0.151	0.151	0.000	0.000	0.000	0.000
90	A	90	ARG	1	0.966	0.997	27.613	0.160	0.160	0.000	0.000	0.000	0.000
91	A	91	ARG	1	0.860	0.918	25.862	0.235	0.235	0.000	0.000	0.000	0.000
92	A	92	LEU	0	-0.074	-0.034	26.663	0.003	0.003	0.000	0.000	0.000	0.000
93	A	93	GLY	0	0.036	0.036	30.865	0.006	0.006	0.000	0.000	0.000	0.000
94	A	94	ALA	0	-0.065	-0.032	31.179	0.007	0.007	0.000	0.000	0.000	0.000

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