FMO DATABASE

FMODB ID: 6YY7Z

Calculation Name: 4QYW-A-Xray372

Preferred Name:

Target Type:

Ligand Name: 2-amino-3-phosphonomethylsulfanyl-propionic acid

ligand 3-letter code: CYQ

PDB ID: 4QYW

Chain ID: A

ChEMBL ID:

UniProt ID: Q56312

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	118
LigandCharge	CYQ=-2
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-988584.808169
FMO2-HF: Nuclear repulsion	941154.538763
FMO2-HF: Total energy	-47430.269407
FMO2-MP2: Total energy	-47561.596237

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:2:GLY)

Summations of interaction energy for fragment #1(A:2:GLY)

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.
-6.012	-1.84	3.871	-4.38	-3.662	-0.035

Interaction energy analysis for fragmet #1(A:2:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.018 / q_NPA : -0.009

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	4	ARG	1	0.869	0.948	3.784	0.685	2.858	-0.024	-1.118	-1.030	-0.001
4	A	5	VAL	0	-0.019	-0.018	5.954	-0.278	-0.278	0.000	0.000	0.000	0.000
5	A	6	LEU	0	-0.010	0.009	8.813	0.233	0.233	0.000	0.000	0.000	0.000
6	A	7	ILE	0	-0.009	-0.003	11.829	-0.008	-0.008	0.000	0.000	0.000	0.000
7	A	8	VAL	0	-0.016	-0.015	14.926	0.055	0.055	0.000	0.000	0.000	0.000
8	A	9	ASP	-1	-0.753	-0.895	17.883	-0.237	-0.237	0.000	0.000	0.000	0.000
9	A	10	ASH	0	-0.062	-0.070	21.282	0.011	0.011	0.000	0.000	0.000	0.000
10	A	11	ALA	0	0.017	0.019	24.474	0.018	0.018	0.000	0.000	0.000	0.000
11	A	12	ALA	0	0.012	-0.008	23.717	-0.014	-0.014	0.000	0.000	0.000	0.000
12	A	13	PHE	0	0.019	0.003	23.651	-0.007	-0.007	0.000	0.000	0.000	0.000
13	A	14	MET	0	0.018	0.016	22.400	0.000	0.000	0.000	0.000	0.000	0.000
14	A	15	ARG	1	0.882	0.932	18.880	0.215	0.215	0.000	0.000	0.000	0.000
15	A	16	MET	0	-0.016	0.000	18.979	-0.015	-0.015	0.000	0.000	0.000	0.000
16	A	17	MET	0	-0.007	-0.009	20.219	0.007	0.007	0.000	0.000	0.000	0.000
17	A	18	LEU	0	-0.011	0.005	15.863	0.002	0.002	0.000	0.000	0.000	0.000
18	A	19	LYS	1	0.936	0.949	15.354	0.204	0.204	0.000	0.000	0.000	0.000
19	A	20	ASP	-1	-0.843	-0.880	15.684	-0.091	-0.091	0.000	0.000	0.000	0.000
20	A	21	ILE	0	-0.002	-0.006	15.724	0.026	0.026	0.000	0.000	0.000	0.000
21	A	22	ILE	0	0.004	0.000	10.657	0.015	0.015	0.000	0.000	0.000	0.000
22	A	23	THR	0	-0.031	-0.031	12.100	0.026	0.026	0.000	0.000	0.000	0.000
23	A	24	LYS	1	0.802	0.887	13.551	0.140	0.140	0.000	0.000	0.000	0.000
24	A	25	ALA	0	-0.054	-0.012	12.489	0.056	0.056	0.000	0.000	0.000	0.000
25	A	26	GLY	0	-0.027	-0.012	11.014	0.052	0.052	0.000	0.000	0.000	0.000
26	A	27	TYR	0	-0.091	-0.055	5.783	0.499	0.499	0.000	0.000	0.000	0.000
27	A	28	GLU	-1	-0.883	-0.947	7.130	-0.112	-0.112	0.000	0.000	0.000	0.000
28	A	29	VAL	0	-0.041	-0.028	8.709	-0.274	-0.274	0.000	0.000	0.000	0.000
29	A	30	ALA	0	0.012	0.008	8.903	0.105	0.105	0.000	0.000	0.000	0.000
30	A	31	GLY	0	0.019	0.004	10.908	0.101	0.101	0.000	0.000	0.000	0.000
31	A	32	GLU	-1	-0.856	-0.906	14.152	-0.297	-0.297	0.000	0.000	0.000	0.000
32	A	33	ALA	0	-0.014	0.002	16.929	0.024	0.024	0.000	0.000	0.000	0.000
33	A	34	THR	0	-0.043	-0.040	19.177	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	35	ASN	0	0.034	-0.006	22.079	0.005	0.005	0.000	0.000	0.000	0.000
35	A	36	GLY	0	0.086	0.030	21.310	-0.023	-0.023	0.000	0.000	0.000	0.000
36	A	37	ARG	1	0.872	0.897	21.144	0.153	0.153	0.000	0.000	0.000	0.000
37	A	38	GLU	-1	-0.816	-0.901	19.961	-0.237	-0.237	0.000	0.000	0.000	0.000
38	A	39	ALA	0	-0.004	-0.003	17.429	-0.024	-0.024	0.000	0.000	0.000	0.000
39	A	40	VAL	0	0.020	0.012	16.568	-0.049	-0.049	0.000	0.000	0.000	0.000
40	A	41	GLU	-1	-0.859	-0.913	17.555	-0.247	-0.247	0.000	0.000	0.000	0.000
41	A	42	LYS	1	0.875	0.928	15.302	0.266	0.266	0.000	0.000	0.000	0.000
42	A	43	TYR	0	-0.050	-0.045	10.548	-0.081	-0.081	0.000	0.000	0.000	0.000
43	A	44	LYS	1	0.808	0.880	12.874	0.206	0.206	0.000	0.000	0.000	0.000
44	A	45	GLU	-1	-0.973	-0.971	14.876	-0.249	-0.249	0.000	0.000	0.000	0.000
45	A	46	LEU	0	-0.030	-0.014	11.009	0.008	0.008	0.000	0.000	0.000	0.000
46	A	47	LYS	1	0.937	0.974	8.431	0.660	0.660	0.000	0.000	0.000	0.000
47	A	48	PRO	0	-0.053	-0.011	7.191	-0.090	-0.090	0.000	0.000	0.000	0.000
48	A	49	ASP	-1	-0.815	-0.904	2.482	-8.033	-6.139	3.897	-3.245	-2.546	-0.034
49	A	50	ILE	0	-0.048	-0.031	4.928	0.399	0.440	-0.001	-0.010	-0.030	0.000
50	A	51	VAL	0	0.017	0.015	7.921	0.167	0.167	0.000	0.000	0.000	0.000
51	A	52	THR	0	-0.003	0.000	11.547	0.024	0.024	0.000	0.000	0.000	0.000
52	A	53	MET	0	0.004	0.000	14.399	0.043	0.043	0.000	0.000	0.000	0.000
53	A	54	CYQ	-2	-1.652	-1.700	17.642	-0.363	-0.363	0.000	0.000	0.000	0.000
54	A	55	ILE	0	0.013	0.002	21.158	0.001	0.001	0.000	0.000	0.000	0.000
55	A	56	THR	0	-0.036	-0.058	23.792	0.007	0.007	0.000	0.000	0.000	0.000
56	A	57	MET	0	-0.026	0.010	21.012	-0.006	-0.006	0.000	0.000	0.000	0.000
57	A	58	PRO	0	0.048	0.026	26.413	0.006	0.006	0.000	0.000	0.000	0.000
58	A	59	GLU	-1	-0.808	-0.857	27.109	-0.171	-0.171	0.000	0.000	0.000	0.000
59	A	60	MET	0	-0.076	-0.044	23.795	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	61	ASN	0	0.009	0.005	25.073	-0.023	-0.023	0.000	0.000	0.000	0.000
61	A	62	GLY	0	0.071	0.016	21.883	-0.012	-0.012	0.000	0.000	0.000	0.000
62	A	63	ILE	0	-0.027	-0.017	21.389	-0.029	-0.029	0.000	0.000	0.000	0.000
63	A	64	ASP	-1	-0.847	-0.923	22.876	-0.202	-0.202	0.000	0.000	0.000	0.000
64	A	65	ALA	0	0.015	0.010	19.926	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	66	ILE	0	-0.042	-0.018	17.727	-0.031	-0.031	0.000	0.000	0.000	0.000
66	A	67	LYS	1	0.871	0.935	18.820	0.187	0.187	0.000	0.000	0.000	0.000
67	A	68	GLU	-1	-0.915	-0.955	20.871	-0.232	-0.232	0.000	0.000	0.000	0.000
68	A	69	ILE	0	-0.020	-0.015	14.115	-0.009	-0.009	0.000	0.000	0.000	0.000
69	A	70	MET	0	-0.046	-0.006	15.904	-0.051	-0.051	0.000	0.000	0.000	0.000
70	A	71	LYS	1	0.924	0.963	17.424	0.231	0.231	0.000	0.000	0.000	0.000
71	A	72	ILE	0	-0.051	-0.021	15.599	0.015	0.015	0.000	0.000	0.000	0.000
72	A	73	ASP	-1	-0.831	-0.911	11.212	-0.698	-0.698	0.000	0.000	0.000	0.000
73	A	74	PRO	0	0.014	0.015	14.419	-0.049	-0.049	0.000	0.000	0.000	0.000
74	A	75	ASN	0	-0.098	-0.051	11.085	0.050	0.050	0.000	0.000	0.000	0.000
75	A	76	ALA	0	0.022	0.031	10.459	-0.176	-0.176	0.000	0.000	0.000	0.000
76	A	77	LYS	1	0.847	0.913	5.722	1.772	1.772	0.000	0.000	0.000	0.000
77	A	78	ILE	0	0.033	0.017	10.466	-0.095	-0.095	0.000	0.000	0.000	0.000
78	A	79	ILE	0	-0.017	-0.003	11.160	0.073	0.073	0.000	0.000	0.000	0.000
79	A	80	VAL	0	-0.010	-0.006	14.773	0.012	0.012	0.000	0.000	0.000	0.000
80	A	81	ALA	0	0.013	-0.003	18.343	0.008	0.008	0.000	0.000	0.000	0.000
81	A	82	SER	0	0.011	-0.013	20.221	0.008	0.008	0.000	0.000	0.000	0.000
82	A	83	ALA	0	0.060	0.056	24.008	0.002	0.002	0.000	0.000	0.000	0.000
83	A	84	MET	0	0.002	-0.007	27.199	0.000	0.000	0.000	0.000	0.000	0.000
84	A	85	GLY	0	0.014	0.005	29.080	0.005	0.005	0.000	0.000	0.000	0.000
85	A	86	GLN	0	0.008	-0.001	27.275	-0.003	-0.003	0.000	0.000	0.000	0.000
86	A	87	GLN	0	0.076	0.028	27.172	-0.015	-0.015	0.000	0.000	0.000	0.000
87	A	88	ALA	0	0.011	0.007	27.414	-0.009	-0.009	0.000	0.000	0.000	0.000
88	A	89	MET	0	0.036	0.019	27.115	-0.003	-0.003	0.000	0.000	0.000	0.000
89	A	90	VAL	0	0.034	0.019	22.165	-0.015	-0.015	0.000	0.000	0.000	0.000
90	A	91	ILE	0	-0.027	-0.019	23.297	-0.018	-0.018	0.000	0.000	0.000	0.000
91	A	92	GLU	-1	-0.871	-0.935	24.825	-0.189	-0.189	0.000	0.000	0.000	0.000
92	A	93	ALA	0	0.037	0.010	21.140	-0.008	-0.008	0.000	0.000	0.000	0.000
93	A	94	ILE	0	-0.022	-0.015	19.635	-0.022	-0.022	0.000	0.000	0.000	0.000
94	A	95	LYS	1	0.883	0.949	20.832	0.161	0.161	0.000	0.000	0.000	0.000
95	A	96	ALA	0	-0.025	0.004	22.017	0.006	0.006	0.000	0.000	0.000	0.000
96	A	97	GLY	0	0.023	0.006	18.389	-0.012	-0.012	0.000	0.000	0.000	0.000
97	A	98	ALA	0	-0.045	-0.011	16.230	-0.058	-0.058	0.000	0.000	0.000	0.000
98	A	99	LYS	1	0.861	0.923	11.959	0.645	0.645	0.000	0.000	0.000	0.000
99	A	100	ASP	-1	-0.839	-0.916	14.498	-0.319	-0.319	0.000	0.000	0.000	0.000
100	A	101	PHE	0	-0.057	-0.029	16.372	-0.010	-0.010	0.000	0.000	0.000	0.000
101	A	102	ILE	0	-0.016	0.009	16.307	0.019	0.019	0.000	0.000	0.000	0.000
102	A	103	VAL	0	-0.012	-0.011	19.433	0.001	0.001	0.000	0.000	0.000	0.000
103	A	104	LYS	1	0.731	0.838	22.357	0.226	0.226	0.000	0.000	0.000	0.000
104	A	105	PRO	0	0.003	-0.028	24.793	0.008	0.008	0.000	0.000	0.000	0.000
105	A	106	PHE	0	0.046	0.008	20.255	0.001	0.001	0.000	0.000	0.000	0.000
106	A	107	GLN	0	0.033	0.019	21.627	0.020	0.020	0.000	0.000	0.000	0.000
107	A	108	PRO	0	0.043	0.005	18.889	-0.019	-0.019	0.000	0.000	0.000	0.000
108	A	109	SER	0	0.014	0.006	17.564	-0.024	-0.024	0.000	0.000	0.000	0.000
109	A	110	ARG	1	0.917	0.944	17.383	0.113	0.113	0.000	0.000	0.000	0.000
110	A	111	VAL	0	0.015	0.010	14.493	-0.034	-0.034	0.000	0.000	0.000	0.000
111	A	112	VAL	0	0.015	0.002	12.965	-0.076	-0.076	0.000	0.000	0.000	0.000
112	A	113	GLU	-1	-0.888	-0.921	12.272	-0.182	-0.182	0.000	0.000	0.000	0.000
113	A	114	ALA	0	0.028	0.013	12.903	-0.023	-0.023	0.000	0.000	0.000	0.000
114	A	115	LEU	0	-0.007	0.004	9.090	-0.102	-0.102	0.000	0.000	0.000	0.000
115	A	116	ASN	0	-0.002	-0.001	8.105	-0.195	-0.195	0.000	0.000	0.000	0.000
116	A	117	LYS	1	0.880	0.945	8.727	0.322	0.322	0.000	0.000	0.000	0.000
117	A	118	VAL	0	-0.019	0.002	8.073	0.010	0.010	0.000	0.000	0.000	0.000
118	A	119	SER	0	-0.007	0.001	4.454	-0.470	-0.406	-0.001	-0.007	-0.056	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:GLY)