FMO DATABASE

FMODB ID: NNNJQ

Calculation Name: 5J4G-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5J4G

Chain ID: A

ChEMBL ID:

UniProt ID: O25562

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	99
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-720935.721572
FMO2-HF: Nuclear repulsion	681651.033578
FMO2-HF: Total energy	-39284.687994
FMO2-MP2: Total energy	-39396.7056

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.
-0.667	1.252	-0.009	-0.758	-1.152	0.001

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 : -0.068 / q_NPA : -0.047

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	3	VAL	0	-0.062	-0.029	3.836	0.851	2.770	-0.009	-0.758	-1.152	0.001
4	A	4	VAL	0	0.004	0.019	6.630	-0.309	-0.309	0.000	0.000	0.000	0.000
5	A	5	HIS	0	0.066	0.026	9.624	0.221	0.221	0.000	0.000	0.000	0.000
6	A	6	PHE	0	-0.006	-0.018	11.449	-0.065	-0.065	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.011	-0.018	15.233	-0.036	-0.036	0.000	0.000	0.000	0.000
8	A	8	GLU	-1	-0.936	-0.952	14.977	-0.170	-0.170	0.000	0.000	0.000	0.000
9	A	9	GLY	0	0.006	0.000	18.037	0.002	0.002	0.000	0.000	0.000	0.000
10	A	10	VAL	0	-0.022	-0.004	20.438	0.015	0.015	0.000	0.000	0.000	0.000
11	A	11	CYS	0	-0.029	-0.008	22.426	-0.022	-0.022	0.000	0.000	0.000	0.000
12	A	12	PHE	0	-0.009	-0.013	24.999	0.014	0.014	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.914	-0.957	28.331	0.042	0.042	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.923	0.942	28.682	-0.046	-0.046	0.000	0.000	0.000	0.000
15	A	15	LEU	0	-0.006	0.001	25.936	0.006	0.006	0.000	0.000	0.000	0.000
16	A	16	HIS	0	-0.035	0.000	21.937	0.003	0.003	0.000	0.000	0.000	0.000
17	A	17	ILE	0	0.018	0.001	20.311	0.032	0.032	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.845	-0.916	17.449	0.112	0.112	0.000	0.000	0.000	0.000
19	A	19	VAL	0	-0.041	-0.027	13.047	0.072	0.072	0.000	0.000	0.000	0.000
20	A	20	LEU	0	0.019	0.012	11.797	-0.059	-0.059	0.000	0.000	0.000	0.000
21	A	21	ASN	0	0.040	0.014	6.327	-0.155	-0.155	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.890	-0.945	8.644	0.433	0.433	0.000	0.000	0.000	0.000
23	A	23	ASN	0	0.074	0.039	7.271	-0.071	-0.071	0.000	0.000	0.000	0.000
24	A	24	SER	0	-0.039	-0.028	8.976	-0.223	-0.223	0.000	0.000	0.000	0.000
25	A	25	SER	0	-0.009	-0.002	11.284	-0.061	-0.061	0.000	0.000	0.000	0.000
26	A	26	HIS	0	0.013	0.013	10.556	-0.240	-0.240	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.948	0.979	12.002	-0.473	-0.473	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.788	-0.866	9.692	1.369	1.369	0.000	0.000	0.000	0.000
29	A	29	ILE	0	-0.011	-0.013	12.514	-0.102	-0.102	0.000	0.000	0.000	0.000
30	A	30	ARG	1	0.858	0.931	15.795	-0.179	-0.179	0.000	0.000	0.000	0.000
31	A	31	ILE	0	-0.024	-0.016	17.573	-0.043	-0.043	0.000	0.000	0.000	0.000
32	A	32	CYS	0	-0.024	0.017	21.342	0.007	0.007	0.000	0.000	0.000	0.000
33	A	33	MET	0	0.020	-0.016	23.588	-0.009	-0.009	0.000	0.000	0.000	0.000
34	A	34	PRO	0	0.031	0.019	26.914	0.000	0.000	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.928	0.969	30.086	-0.094	-0.094	0.000	0.000	0.000	0.000
36	A	36	GLY	0	-0.017	-0.008	32.690	-0.010	-0.010	0.000	0.000	0.000	0.000
37	A	37	ALA	0	-0.050	-0.012	30.252	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	38	VAL	0	0.002	-0.010	31.860	0.009	0.009	0.000	0.000	0.000	0.000
39	A	39	MET	0	-0.050	-0.015	24.645	0.002	0.002	0.000	0.000	0.000	0.000
40	A	40	ASP	-1	-0.808	-0.916	30.147	0.155	0.155	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.885	0.929	31.290	-0.134	-0.134	0.000	0.000	0.000	0.000
42	A	42	HIS	0	0.017	0.036	26.067	0.004	0.004	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.873	0.950	28.220	-0.200	-0.200	0.000	0.000	0.000	0.000
44	A	44	ALA	0	0.022	0.027	22.837	0.001	0.001	0.000	0.000	0.000	0.000
45	A	45	PRO	0	-0.039	-0.022	21.681	-0.008	-0.008	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.054	0.014	20.847	-0.015	-0.015	0.000	0.000	0.000	0.000
47	A	47	ALA	0	0.033	0.022	20.359	-0.017	-0.017	0.000	0.000	0.000	0.000
48	A	48	ILE	0	-0.010	-0.016	19.519	0.055	0.055	0.000	0.000	0.000	0.000
49	A	49	SER	0	-0.042	-0.014	17.575	0.001	0.001	0.000	0.000	0.000	0.000
50	A	50	VAL	0	0.027	0.019	18.979	0.034	0.034	0.000	0.000	0.000	0.000
51	A	51	GLN	0	0.047	0.011	17.797	0.034	0.034	0.000	0.000	0.000	0.000
52	A	52	VAL	0	-0.030	0.008	20.312	0.012	0.012	0.000	0.000	0.000	0.000
53	A	53	LEU	0	-0.011	0.001	16.192	0.000	0.000	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.935	-0.988	20.525	0.155	0.155	0.000	0.000	0.000	0.000
55	A	55	GLY	0	0.030	0.027	23.724	0.004	0.004	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.878	0.929	27.253	-0.146	-0.146	0.000	0.000	0.000	0.000
57	A	57	ILE	0	0.013	0.016	25.942	-0.011	-0.011	0.000	0.000	0.000	0.000
58	A	58	VAL	0	-0.003	0.006	29.330	0.002	0.002	0.000	0.000	0.000	0.000
59	A	59	PHE	0	0.013	0.000	25.648	0.007	0.007	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.893	-0.948	29.947	0.147	0.147	0.000	0.000	0.000	0.000
61	A	61	VAL	0	0.022	-0.005	30.802	0.009	0.009	0.000	0.000	0.000	0.000
62	A	62	GLY	0	-0.023	-0.001	32.941	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	63	ASP	-1	-0.947	-0.972	36.295	0.145	0.145	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.948	-0.950	34.184	0.191	0.191	0.000	0.000	0.000	0.000
65	A	65	LYS	1	0.865	0.902	34.563	-0.144	-0.144	0.000	0.000	0.000	0.000
66	A	66	ILE	0	0.014	0.010	30.210	-0.005	-0.005	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.911	-0.964	31.445	0.173	0.173	0.000	0.000	0.000	0.000
68	A	68	MET	0	-0.052	-0.024	24.268	0.005	0.005	0.000	0.000	0.000	0.000
69	A	69	PRO	0	0.031	0.007	27.847	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	70	LYS	1	0.986	0.981	22.320	-0.249	-0.249	0.000	0.000	0.000	0.000
71	A	71	GLY	0	-0.037	-0.020	22.064	-0.010	-0.010	0.000	0.000	0.000	0.000
72	A	72	ALA	0	-0.020	0.007	22.870	0.027	0.027	0.000	0.000	0.000	0.000
73	A	73	LEU	0	0.000	-0.020	19.028	0.022	0.022	0.000	0.000	0.000	0.000
74	A	74	ILE	0	-0.013	0.003	22.460	-0.024	-0.024	0.000	0.000	0.000	0.000
75	A	75	SER	0	-0.009	-0.008	21.958	0.055	0.055	0.000	0.000	0.000	0.000
76	A	76	LEU	0	0.004	-0.001	23.154	-0.040	-0.040	0.000	0.000	0.000	0.000
77	A	77	GLU	-1	-0.882	-0.940	23.542	0.418	0.418	0.000	0.000	0.000	0.000
78	A	78	ALA	0	-0.046	-0.021	23.843	-0.008	-0.008	0.000	0.000	0.000	0.000
79	A	79	GLN	0	-0.031	-0.027	25.324	-0.033	-0.033	0.000	0.000	0.000	0.000
80	A	80	VAL	0	0.052	0.032	27.629	-0.022	-0.022	0.000	0.000	0.000	0.000
81	A	81	LEU	0	-0.071	-0.055	28.460	0.009	0.009	0.000	0.000	0.000	0.000
82	A	82	HIS	0	-0.030	-0.009	25.819	0.012	0.012	0.000	0.000	0.000	0.000
83	A	83	ARG	1	0.879	0.941	30.155	-0.152	-0.152	0.000	0.000	0.000	0.000
84	A	84	LEU	0	-0.008	0.007	24.893	0.010	0.010	0.000	0.000	0.000	0.000
85	A	85	ASP	-1	-0.797	-0.892	29.523	0.145	0.145	0.000	0.000	0.000	0.000
86	A	86	ALA	0	0.016	0.011	29.084	0.011	0.011	0.000	0.000	0.000	0.000
87	A	87	LEU	0	-0.024	-0.012	30.787	-0.015	-0.015	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.902	-0.966	30.479	0.106	0.106	0.000	0.000	0.000	0.000
89	A	89	ASN	0	0.006	0.034	28.266	0.013	0.013	0.000	0.000	0.000	0.000
90	A	90	SER	0	0.010	-0.027	25.551	0.007	0.007	0.000	0.000	0.000	0.000
91	A	91	VAL	0	-0.006	0.016	19.451	-0.005	-0.005	0.000	0.000	0.000	0.000
92	A	92	ILE	0	-0.030	-0.024	20.553	0.022	0.022	0.000	0.000	0.000	0.000
93	A	93	ARG	1	0.873	0.918	11.340	-1.199	-1.199	0.000	0.000	0.000	0.000
94	A	94	LEU	0	0.001	-0.009	17.175	-0.009	-0.009	0.000	0.000	0.000	0.000
95	A	95	SER	0	-0.044	-0.018	13.922	0.057	0.057	0.000	0.000	0.000	0.000
96	A	96	LEU	0	-0.023	-0.013	15.499	-0.087	-0.087	0.000	0.000	0.000	0.000
97	A	97	SER	0	-0.013	0.001	15.178	0.086	0.086	0.000	0.000	0.000	0.000
98	A	98	LYS	1	0.821	0.908	12.532	-0.739	-0.739	0.000	0.000	0.000	0.000
99	A	99	LYS	1	0.978	0.987	17.203	-0.345	-0.345	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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