FMO DATABASE

FMODB ID: YY3Y2

Calculation Name: 4G7W-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4G7W

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-20

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
LigandResidueName
LigandFragmentNumber	0
LigandCharge	DGL=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-674834.3946
FMO2-HF: Nuclear repulsion	634647.3283
FMO2-HF: Total energy	-40187.0663
FMO2-MP2: Total energy	-40296.633654

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:SER)

Summations of interaction energy for fragment #1(A:1:SER)

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.
-3.029	0.131	0.037	-1.66	-1.537	0.005

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.030 / 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

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	ILE	0	0.013	0.001	3.334	-0.410	2.353	0.036	-1.589	-1.211	0.005
4	A	4	ASN	0	-0.028	-0.007	6.031	-0.195	-0.195	0.000	0.000	0.000	0.000
5	A	5	CYS	0	-0.062	-0.018	8.579	0.233	0.233	0.000	0.000	0.000	0.000
6	A	6	ASP	-1	-0.829	-0.920	12.080	0.043	0.043	0.000	0.000	0.000	0.000
7	A	7	PRO	0	-0.029	-0.012	14.026	0.060	0.060	0.000	0.000	0.000	0.000
8	A	8	ASN	0	-0.115	-0.057	17.166	0.025	0.025	0.000	0.000	0.000	0.000
9	A	9	THR	0	0.041	0.038	11.826	0.044	0.044	0.000	0.000	0.000	0.000
10	A	10	THR	0	-0.005	-0.021	14.756	-0.019	-0.019	0.000	0.000	0.000	0.000
11	A	11	THR	0	-0.056	-0.025	9.080	-0.012	-0.012	0.000	0.000	0.000	0.000
12	A	12	SER	0	-0.043	-0.038	11.628	-0.001	-0.001	0.000	0.000	0.000	0.000
13	A	13	HIS	1	0.849	0.931	8.064	-0.460	-0.460	0.000	0.000	0.000	0.000
14	A	14	GLN	0	0.040	0.019	10.543	-0.215	-0.215	0.000	0.000	0.000	0.000
15	A	15	LEU	0	-0.051	-0.018	11.320	0.070	0.070	0.000	0.000	0.000	0.000
16	A	16	LEU	0	0.025	0.017	13.564	-0.016	-0.016	0.000	0.000	0.000	0.000
17	A	17	PHE	0	0.051	0.017	15.747	-0.041	-0.041	0.000	0.000	0.000	0.000
18	A	18	GLY	0	0.089	0.061	18.832	0.020	0.020	0.000	0.000	0.000	0.000
19	A	19	PHE	0	0.013	-0.001	21.879	0.003	0.003	0.000	0.000	0.000	0.000
20	A	20	GLY	0	-0.024	-0.012	24.525	-0.014	-0.014	0.000	0.000	0.000	0.000
21	A	21	SER	0	-0.042	-0.031	23.338	-0.015	-0.015	0.000	0.000	0.000	0.000
22	A	22	PRO	0	-0.059	-0.015	25.565	0.009	0.009	0.000	0.000	0.000	0.000
23	A	23	ILE	0	0.008	-0.008	23.795	0.005	0.005	0.000	0.000	0.000	0.000
24	A	24	VAL	0	-0.024	0.012	19.674	-0.015	-0.015	0.000	0.000	0.000	0.000
25	A	25	GLN	0	-0.015	0.006	21.308	0.023	0.023	0.000	0.000	0.000	0.000
26	A	26	SER	0	-0.028	-0.053	19.806	0.012	0.012	0.000	0.000	0.000	0.000
27	A	27	VAL	0	-0.005	0.003	14.696	-0.008	-0.008	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.025	-0.003	14.770	0.010	0.010	0.000	0.000	0.000	0.000
29	A	29	PHE	0	0.000	-0.022	7.347	0.102	0.102	0.000	0.000	0.000	0.000
30	A	30	ASP	-1	-0.876	-0.939	8.414	-1.578	-1.578	0.000	0.000	0.000	0.000
31	A	31	GLY	0	0.025	0.015	11.121	-0.086	-0.086	0.000	0.000	0.000	0.000
32	A	33	MET	0	-0.024	-0.014	14.076	0.028	0.028	0.000	0.000	0.000	0.000
33	A	34	LEU	0	-0.008	-0.020	11.857	0.043	0.043	0.000	0.000	0.000	0.000
34	A	35	ASP	-1	-0.780	-0.848	16.367	-0.007	-0.007	0.000	0.000	0.000	0.000
35	A	36	ILE	0	-0.042	-0.007	18.475	0.037	0.037	0.000	0.000	0.000	0.000
36	A	37	GLU	-1	-0.802	-0.890	17.433	0.328	0.328	0.000	0.000	0.000	0.000
37	A	38	LYS	1	0.876	0.919	20.468	-0.109	-0.109	0.000	0.000	0.000	0.000
38	A	39	ASP	-1	-0.888	-0.945	24.057	0.203	0.203	0.000	0.000	0.000	0.000
39	A	40	ASP	-1	-0.974	-0.981	25.766	0.126	0.126	0.000	0.000	0.000	0.000
40	A	41	TYR	0	-0.016	-0.015	28.394	-0.015	-0.015	0.000	0.000	0.000	0.000
41	A	42	GLY	0	0.005	0.000	27.964	-0.010	-0.010	0.000	0.000	0.000	0.000
42	A	43	PHE	0	-0.020	0.003	23.796	0.002	0.002	0.000	0.000	0.000	0.000
43	A	44	VAL	0	0.026	0.016	19.914	0.004	0.004	0.000	0.000	0.000	0.000
44	A	45	TRP	0	0.005	-0.017	19.872	0.028	0.028	0.000	0.000	0.000	0.000
45	A	46	SER	0	-0.026	-0.020	21.422	-0.019	-0.019	0.000	0.000	0.000	0.000
46	A	47	CYS	0	-0.070	0.010	20.548	0.000	0.000	0.000	0.000	0.000	0.000
47	A	48	LEU	0	-0.014	-0.012	23.314	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	49	SER	0	0.042	0.008	24.826	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	50	ASN	0	-0.033	-0.015	25.672	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	51	GLU	-1	-0.885	-0.949	28.049	0.115	0.115	0.000	0.000	0.000	0.000
51	A	52	ASN	0	-0.099	-0.049	25.135	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	53	GLY	0	0.020	0.014	23.377	0.003	0.003	0.000	0.000	0.000	0.000
53	A	54	ASP	-1	-0.949	-0.968	23.485	0.106	0.106	0.000	0.000	0.000	0.000
54	A	55	TYR	0	-0.002	0.003	19.500	0.016	0.016	0.000	0.000	0.000	0.000
55	A	57	LYS	1	0.896	0.940	14.265	-0.505	-0.505	0.000	0.000	0.000	0.000
56	A	58	GLY	0	0.065	0.043	17.026	-0.026	-0.026	0.000	0.000	0.000	0.000
57	A	59	LEU	0	-0.045	-0.006	14.629	0.084	0.084	0.000	0.000	0.000	0.000
58	A	60	TYR	0	-0.002	-0.009	14.243	-0.061	-0.061	0.000	0.000	0.000	0.000
59	A	61	LYS	1	0.901	0.948	14.254	-0.237	-0.237	0.000	0.000	0.000	0.000
60	A	62	PRO	0	0.014	0.018	13.203	-0.040	-0.040	0.000	0.000	0.000	0.000
61	A	63	ARG	1	0.814	0.897	16.081	0.040	0.040	0.000	0.000	0.000	0.000
62	A	64	PHE	0	0.031	0.006	19.069	-0.024	-0.024	0.000	0.000	0.000	0.000
63	A	65	THR	0	-0.035	-0.017	20.711	-0.017	-0.017	0.000	0.000	0.000	0.000
64	A	66	GLN	0	0.035	0.006	16.910	-0.036	-0.036	0.000	0.000	0.000	0.000
65	A	67	GLY	0	0.021	0.012	19.230	0.007	0.007	0.000	0.000	0.000	0.000
66	A	68	VAL	0	-0.044	-0.027	20.631	-0.008	-0.008	0.000	0.000	0.000	0.000
67	A	69	SER	0	0.048	0.023	20.191	-0.012	-0.012	0.000	0.000	0.000	0.000
68	A	70	PRO	0	-0.053	-0.013	21.145	0.004	0.004	0.000	0.000	0.000	0.000
69	A	71	ASN	0	-0.029	-0.018	22.810	-0.017	-0.017	0.000	0.000	0.000	0.000
70	A	72	TRP	0	-0.009	-0.007	20.562	0.022	0.022	0.000	0.000	0.000	0.000
71	A	73	PRO	0	0.063	0.028	22.926	-0.019	-0.019	0.000	0.000	0.000	0.000
72	A	74	MET	0	0.009	0.007	18.387	-0.016	-0.016	0.000	0.000	0.000	0.000
73	A	75	CYS	0	-0.082	-0.020	17.300	0.024	0.024	0.000	0.000	0.000	0.000
74	A	76	ASP	-1	-0.791	-0.894	18.925	-0.030	-0.030	0.000	0.000	0.000	0.000
75	A	77	LEU	0	-0.016	-0.026	14.664	0.025	0.025	0.000	0.000	0.000	0.000
76	A	78	SER	0	-0.027	-0.017	18.887	0.024	0.024	0.000	0.000	0.000	0.000
77	A	79	GLY	0	-0.011	0.009	22.190	0.004	0.004	0.000	0.000	0.000	0.000
78	A	80	ALA	0	0.012	-0.007	24.014	0.009	0.009	0.000	0.000	0.000	0.000
79	A	81	SER	0	0.063	0.033	21.353	0.003	0.003	0.000	0.000	0.000	0.000
80	A	82	ALA	0	-0.049	-0.027	23.575	-0.017	-0.017	0.000	0.000	0.000	0.000
81	A	83	GLU	-1	-0.813	-0.902	23.511	0.020	0.020	0.000	0.000	0.000	0.000
82	A	84	ARG	1	0.815	0.884	22.276	0.018	0.018	0.000	0.000	0.000	0.000
83	A	86	ILE	0	0.023	0.015	16.105	0.004	0.004	0.000	0.000	0.000	0.000
84	A	87	TYR	0	0.001	-0.041	11.616	0.058	0.058	0.000	0.000	0.000	0.000
85	A	88	PRO	0	-0.006	0.011	13.588	-0.082	-0.082	0.000	0.000	0.000	0.000
86	A	89	TYR	0	-0.017	-0.022	3.378	-0.045	0.129	0.001	-0.052	-0.123	0.000
87	A	90	CYS	0	-0.051	-0.023	9.247	-0.180	-0.180	0.000	0.000	0.000	0.000
88	A	91	PRO	0	-0.022	-0.004	6.298	-0.312	-0.312	0.000	0.000	0.000	0.000
89	A	92	GLU	-1	-0.978	-1.005	3.955	0.394	0.617	0.000	-0.019	-0.203	0.000
90	A	93	GLY	0	0.011	0.034	6.023	0.074	0.074	0.000	0.000	0.000	0.000
91	A	94	DGL	-1	-0.969	-1.003	9.689	-0.433	-0.433	0.000	0.000	0.000	0.000
92	A	95	GLU	-1	-0.968	-0.981	12.352	-0.198	-0.198	0.000	0.000	0.000	0.000
93	A	97	VAL	0	0.045	0.033	14.594	0.039	0.039	0.000	0.000	0.000	0.000
94	A	98	PRO	0	-0.034	-0.017	17.233	-0.006	-0.006	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:SER)