FMO DATABASE

FMODB ID: 2NNRR

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

Total energy (hartree)

FMO2-HF: Electronic energy	-987062.560433
FMO2-HF: Nuclear repulsion	939633.149961
FMO2-HF: Total energy	-47429.410472
FMO2-MP2: Total energy	-47560.72724

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.
-5.983	-1.575	3.037	-4.141	-3.304	-0.032

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 : -0.007 / q_NPA : -0.006

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	0.902	0.959	3.784	0.725	2.812	-0.025	-1.065	-0.997	-0.001
4	A	5	VAL	0	-0.022	-0.013	5.950	-0.295	-0.295	0.000	0.000	0.000	0.000
5	A	6	LEU	0	-0.007	0.005	8.809	0.244	0.244	0.000	0.000	0.000	0.000
6	A	7	ILE	0	-0.007	-0.004	11.825	-0.019	-0.019	0.000	0.000	0.000	0.000
7	A	8	VAL	0	-0.007	-0.008	14.923	0.060	0.060	0.000	0.000	0.000	0.000
8	A	9	ASP	-1	-0.754	-0.911	17.880	-0.261	-0.261	0.000	0.000	0.000	0.000
9	A	10	ASH	0	-0.159	-0.174	21.279	0.016	0.016	0.000	0.000	0.000	0.000
10	A	11	ALA	0	0.034	0.026	24.544	0.019	0.019	0.000	0.000	0.000	0.000
11	A	12	ALA	0	0.007	-0.014	23.714	-0.016	-0.016	0.000	0.000	0.000	0.000
12	A	13	PHE	0	0.011	0.001	23.647	-0.008	-0.008	0.000	0.000	0.000	0.000
13	A	14	MET	0	0.011	0.010	22.390	-0.004	-0.004	0.000	0.000	0.000	0.000
14	A	15	ARG	1	0.877	0.936	19.240	0.218	0.218	0.000	0.000	0.000	0.000
15	A	16	MET	0	-0.001	0.007	18.979	-0.017	-0.017	0.000	0.000	0.000	0.000
16	A	17	MET	0	-0.006	-0.011	20.219	0.004	0.004	0.000	0.000	0.000	0.000
17	A	18	LEU	0	-0.010	0.006	15.740	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	19	LYS	1	1.011	0.995	15.221	0.193	0.193	0.000	0.000	0.000	0.000
19	A	20	ASP	-1	-0.835	-0.892	15.684	-0.122	-0.122	0.000	0.000	0.000	0.000
20	A	21	ILE	0	-0.016	-0.011	15.641	0.024	0.024	0.000	0.000	0.000	0.000
21	A	22	ILE	0	0.005	-0.002	10.668	0.011	0.011	0.000	0.000	0.000	0.000
22	A	23	THR	0	-0.037	-0.022	12.100	0.018	0.018	0.000	0.000	0.000	0.000
23	A	24	LYS	1	0.825	0.900	13.551	0.161	0.161	0.000	0.000	0.000	0.000
24	A	25	ALA	0	-0.056	-0.011	12.452	0.058	0.058	0.000	0.000	0.000	0.000
25	A	26	GLY	0	-0.031	-0.013	11.012	0.029	0.029	0.000	0.000	0.000	0.000
26	A	27	TYR	0	-0.083	-0.056	5.838	0.107	0.107	0.000	0.000	0.000	0.000
27	A	28	GLU	-1	-0.916	-0.960	7.177	0.140	0.140	0.000	0.000	0.000	0.000
28	A	29	VAL	0	-0.044	-0.027	8.711	-0.285	-0.285	0.000	0.000	0.000	0.000
29	A	30	ALA	0	-0.006	-0.003	8.949	0.111	0.111	0.000	0.000	0.000	0.000
30	A	31	GLY	0	0.013	0.004	10.911	0.105	0.105	0.000	0.000	0.000	0.000
31	A	32	GLU	-1	-0.928	-0.956	14.148	-0.315	-0.315	0.000	0.000	0.000	0.000
32	A	33	ALA	0	-0.003	0.001	16.926	0.027	0.027	0.000	0.000	0.000	0.000
33	A	34	THR	0	-0.038	-0.025	19.174	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	35	ASN	0	0.047	0.009	22.055	0.007	0.007	0.000	0.000	0.000	0.000
35	A	36	GLY	0	0.084	0.027	21.304	-0.023	-0.023	0.000	0.000	0.000	0.000
36	A	37	ARG	1	0.943	0.972	21.141	0.154	0.154	0.000	0.000	0.000	0.000
37	A	38	GLU	-1	-0.871	-0.953	20.117	-0.235	-0.235	0.000	0.000	0.000	0.000
38	A	39	ALA	0	-0.008	-0.006	17.409	-0.024	-0.024	0.000	0.000	0.000	0.000
39	A	40	VAL	0	0.011	0.009	16.565	-0.050	-0.050	0.000	0.000	0.000	0.000
40	A	41	GLU	-1	-0.940	-0.971	17.552	-0.237	-0.237	0.000	0.000	0.000	0.000
41	A	42	LYS	1	0.929	0.966	15.383	0.267	0.267	0.000	0.000	0.000	0.000
42	A	43	TYR	0	-0.077	-0.070	10.611	-0.076	-0.076	0.000	0.000	0.000	0.000
43	A	44	LYS	1	0.918	0.949	12.871	0.208	0.208	0.000	0.000	0.000	0.000
44	A	45	GLU	-1	-0.987	-0.974	14.873	-0.221	-0.221	0.000	0.000	0.000	0.000
45	A	46	LEU	0	-0.029	-0.012	10.990	0.013	0.013	0.000	0.000	0.000	0.000
46	A	47	LYS	1	0.978	0.993	8.201	0.483	0.483	0.000	0.000	0.000	0.000
47	A	48	PRO	0	-0.056	-0.012	7.201	-0.071	-0.071	0.000	0.000	0.000	0.000
48	A	49	ASP	-1	-0.833	-0.922	2.530	-7.408	-5.188	3.064	-3.058	-2.226	-0.031
49	A	50	ILE	0	-0.042	-0.026	4.926	0.383	0.425	-0.001	-0.011	-0.030	0.000
50	A	51	VAL	0	0.024	0.017	7.919	0.184	0.184	0.000	0.000	0.000	0.000
51	A	52	THR	0	-0.033	-0.012	11.544	0.016	0.016	0.000	0.000	0.000	0.000
52	A	53	MET	0	0.027	0.013	14.397	0.049	0.049	0.000	0.000	0.000	0.000
53	A	54	CYQ	-2	-1.649	-1.695	17.640	-0.397	-0.397	0.000	0.000	0.000	0.000
54	A	55	ILE	0	-0.015	-0.012	21.156	0.001	0.001	0.000	0.000	0.000	0.000
55	A	56	THR	0	-0.011	-0.007	23.790	0.007	0.007	0.000	0.000	0.000	0.000
56	A	57	MET	0	0.041	0.037	21.085	-0.007	-0.007	0.000	0.000	0.000	0.000
57	A	58	PRO	0	0.043	0.024	26.410	0.006	0.006	0.000	0.000	0.000	0.000
58	A	59	GLU	-1	-0.885	-0.939	27.106	-0.174	-0.174	0.000	0.000	0.000	0.000
59	A	60	MET	0	-0.077	-0.043	23.379	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	61	ASN	0	0.068	0.041	25.071	-0.019	-0.019	0.000	0.000	0.000	0.000
61	A	62	GLY	0	0.067	0.015	21.882	-0.012	-0.012	0.000	0.000	0.000	0.000
62	A	63	ILE	0	-0.022	-0.020	21.388	-0.029	-0.029	0.000	0.000	0.000	0.000
63	A	64	ASP	-1	-0.879	-0.939	22.875	-0.214	-0.214	0.000	0.000	0.000	0.000
64	A	65	ALA	0	0.016	0.006	19.863	-0.006	-0.006	0.000	0.000	0.000	0.000
65	A	66	ILE	0	-0.045	-0.018	17.868	-0.030	-0.030	0.000	0.000	0.000	0.000
66	A	67	LYS	1	0.937	0.967	18.819	0.214	0.214	0.000	0.000	0.000	0.000
67	A	68	GLU	-1	-0.917	-0.954	20.806	-0.237	-0.237	0.000	0.000	0.000	0.000
68	A	69	ILE	0	-0.018	-0.014	14.149	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	70	MET	0	-0.036	-0.002	15.473	-0.044	-0.044	0.000	0.000	0.000	0.000
70	A	71	LYS	1	0.921	0.957	17.424	0.233	0.233	0.000	0.000	0.000	0.000
71	A	72	ILE	0	-0.072	-0.026	15.581	0.021	0.021	0.000	0.000	0.000	0.000
72	A	73	ASP	-1	-0.833	-0.896	11.016	-0.737	-0.737	0.000	0.000	0.000	0.000
73	A	74	PRO	0	-0.008	0.003	14.419	-0.052	-0.052	0.000	0.000	0.000	0.000
74	A	75	ASN	0	-0.097	-0.045	11.069	0.036	0.036	0.000	0.000	0.000	0.000
75	A	76	ALA	0	0.036	0.035	10.460	-0.186	-0.186	0.000	0.000	0.000	0.000
76	A	77	LYS	1	0.848	0.934	6.089	1.788	1.788	0.000	0.000	0.000	0.000
77	A	78	ILE	0	0.039	0.022	10.466	-0.100	-0.100	0.000	0.000	0.000	0.000
78	A	79	ILE	0	-0.030	-0.010	11.187	0.070	0.070	0.000	0.000	0.000	0.000
79	A	80	VAL	0	0.010	0.007	14.772	0.016	0.016	0.000	0.000	0.000	0.000
80	A	81	ALA	0	0.008	-0.008	18.342	0.006	0.006	0.000	0.000	0.000	0.000
81	A	82	SER	0	0.007	-0.006	20.219	0.013	0.013	0.000	0.000	0.000	0.000
82	A	83	ALA	0	0.066	0.058	24.007	0.000	0.000	0.000	0.000	0.000	0.000
83	A	84	MET	0	-0.003	-0.011	27.198	0.000	0.000	0.000	0.000	0.000	0.000
84	A	85	GLY	0	0.007	0.001	29.038	0.007	0.007	0.000	0.000	0.000	0.000
85	A	86	GLN	0	0.004	-0.013	27.179	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	87	GLN	0	0.068	0.025	27.169	-0.014	-0.014	0.000	0.000	0.000	0.000
87	A	88	ALA	0	0.017	0.008	27.417	-0.010	-0.010	0.000	0.000	0.000	0.000
88	A	89	MET	0	0.050	0.028	27.097	-0.003	-0.003	0.000	0.000	0.000	0.000
89	A	90	VAL	0	0.030	0.012	22.125	-0.016	-0.016	0.000	0.000	0.000	0.000
90	A	91	ILE	0	-0.032	-0.015	23.315	-0.020	-0.020	0.000	0.000	0.000	0.000
91	A	92	GLU	-1	-0.957	-0.972	24.860	-0.196	-0.196	0.000	0.000	0.000	0.000
92	A	93	ALA	0	0.023	-0.001	21.045	-0.008	-0.008	0.000	0.000	0.000	0.000
93	A	94	ILE	0	-0.021	-0.010	19.833	-0.023	-0.023	0.000	0.000	0.000	0.000
94	A	95	LYS	1	0.888	0.946	20.884	0.183	0.183	0.000	0.000	0.000	0.000
95	A	96	ALA	0	-0.049	-0.013	21.954	0.010	0.010	0.000	0.000	0.000	0.000
96	A	97	GLY	0	0.023	0.007	18.387	-0.008	-0.008	0.000	0.000	0.000	0.000
97	A	98	ALA	0	-0.036	0.000	16.233	-0.058	-0.058	0.000	0.000	0.000	0.000
98	A	99	LYS	1	0.890	0.932	11.655	0.695	0.695	0.000	0.000	0.000	0.000
99	A	100	ASP	-1	-0.875	-0.923	14.614	-0.399	-0.399	0.000	0.000	0.000	0.000
100	A	101	PHE	0	-0.073	-0.055	16.367	-0.005	-0.005	0.000	0.000	0.000	0.000
101	A	102	ILE	0	-0.015	0.009	16.125	0.017	0.017	0.000	0.000	0.000	0.000
102	A	103	VAL	0	-0.006	-0.011	19.383	0.004	0.004	0.000	0.000	0.000	0.000
103	A	104	LYS	1	0.746	0.879	22.548	0.248	0.248	0.000	0.000	0.000	0.000
104	A	105	PRO	0	0.005	-0.025	24.729	0.009	0.009	0.000	0.000	0.000	0.000
105	A	106	PHE	0	0.047	0.015	20.138	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	107	GLN	0	0.033	0.013	21.531	0.020	0.020	0.000	0.000	0.000	0.000
107	A	108	PRO	0	0.040	0.008	18.768	-0.024	-0.024	0.000	0.000	0.000	0.000
108	A	109	SER	0	0.037	-0.010	17.452	-0.025	-0.025	0.000	0.000	0.000	0.000
109	A	110	ARG	1	0.955	1.007	17.277	0.152	0.152	0.000	0.000	0.000	0.000
110	A	111	VAL	0	0.030	0.021	14.382	-0.036	-0.036	0.000	0.000	0.000	0.000
111	A	112	VAL	0	0.011	0.001	12.763	-0.089	-0.089	0.000	0.000	0.000	0.000
112	A	113	GLU	-1	-0.970	-0.981	12.168	-0.278	-0.278	0.000	0.000	0.000	0.000
113	A	114	ALA	0	0.052	0.026	12.828	-0.037	-0.037	0.000	0.000	0.000	0.000
114	A	115	LEU	0	-0.022	-0.004	8.963	-0.109	-0.109	0.000	0.000	0.000	0.000
115	A	116	ASN	0	0.018	0.008	8.036	-0.329	-0.329	0.000	0.000	0.000	0.000
116	A	117	LYS	1	0.962	0.983	8.666	0.360	0.360	0.000	0.000	0.000	0.000
117	A	118	VAL	0	-0.054	-0.012	7.863	0.031	0.031	0.000	0.000	0.000	0.000
118	A	119	SER	0	-0.047	-0.027	4.457	-0.526	-0.467	-0.001	-0.007	-0.051	0.000

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