FMO DATABASE

FMODB ID: ZVVLN

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	OptAll
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	-992655.95159
FMO2-HF: Nuclear repulsion	945225.573343
FMO2-HF: Total energy	-47430.378247
FMO2-MP2: Total energy	-47561.699174

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.
-3.308	-0.348	5.13	-4.405	-3.684	-0.034

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 : 0.005 / q_NPA : -0.003

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	4	ARG	1	0.804	0.905	3.578	0.568	2.286	-0.011	-0.931	-0.775	0.001
4	A	5	VAL	0	-0.021	-0.018	5.594	-0.298	-0.298	0.000	0.000	0.000	0.000
5	A	6	LEU	0	-0.009	0.008	8.885	0.197	0.197	0.000	0.000	0.000	0.000
6	A	7	ILE	0	-0.027	-0.014	12.124	-0.022	-0.022	0.000	0.000	0.000	0.000
7	A	8	VAL	0	0.004	-0.009	15.284	0.046	0.046	0.000	0.000	0.000	0.000
8	A	9	ASP	-1	-0.757	-0.887	18.219	-0.197	-0.197	0.000	0.000	0.000	0.000
9	A	10	ASH	0	-0.034	-0.053	21.499	0.015	0.015	0.000	0.000	0.000	0.000
10	A	11	ALA	0	0.023	0.021	24.893	0.015	0.015	0.000	0.000	0.000	0.000
11	A	12	ALA	0	0.014	-0.004	23.721	-0.010	-0.010	0.000	0.000	0.000	0.000
12	A	13	PHE	0	0.017	0.005	23.603	-0.003	-0.003	0.000	0.000	0.000	0.000
13	A	14	MET	0	0.017	0.017	22.610	-0.002	-0.002	0.000	0.000	0.000	0.000
14	A	15	ARG	1	0.856	0.906	18.817	0.144	0.144	0.000	0.000	0.000	0.000
15	A	16	MET	0	-0.008	0.003	19.085	-0.008	-0.008	0.000	0.000	0.000	0.000
16	A	17	MET	0	-0.010	-0.010	20.345	0.006	0.006	0.000	0.000	0.000	0.000
17	A	18	LEU	0	0.007	0.007	15.952	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	19	LYS	1	0.918	0.946	15.563	0.079	0.079	0.000	0.000	0.000	0.000
19	A	20	ASP	-1	-0.829	-0.882	15.872	-0.050	-0.050	0.000	0.000	0.000	0.000
20	A	21	ILE	0	-0.004	-0.006	15.865	0.015	0.015	0.000	0.000	0.000	0.000
21	A	22	ILE	0	-0.005	-0.007	10.749	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	23	THR	0	-0.032	-0.030	12.149	0.019	0.019	0.000	0.000	0.000	0.000
23	A	24	LYS	1	0.799	0.884	13.746	0.109	0.109	0.000	0.000	0.000	0.000
24	A	25	ALA	0	-0.053	-0.012	12.214	0.037	0.037	0.000	0.000	0.000	0.000
25	A	26	GLY	0	-0.028	-0.006	10.878	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	27	TYR	0	-0.078	-0.048	5.963	0.443	0.443	0.000	0.000	0.000	0.000
27	A	28	GLU	-1	-0.831	-0.910	7.133	0.241	0.241	0.000	0.000	0.000	0.000
28	A	29	VAL	0	-0.027	-0.027	8.698	-0.243	-0.243	0.000	0.000	0.000	0.000
29	A	30	ALA	0	0.009	0.012	8.555	0.096	0.096	0.000	0.000	0.000	0.000
30	A	31	GLY	0	0.019	0.013	10.650	0.066	0.066	0.000	0.000	0.000	0.000
31	A	32	GLU	-1	-0.842	-0.894	14.035	-0.185	-0.185	0.000	0.000	0.000	0.000
32	A	33	ALA	0	-0.011	0.004	16.967	0.018	0.018	0.000	0.000	0.000	0.000
33	A	34	THR	0	-0.044	-0.045	19.463	-0.006	-0.006	0.000	0.000	0.000	0.000
34	A	35	ASN	0	0.012	-0.025	22.551	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	36	GLY	0	0.083	0.030	21.314	-0.015	-0.015	0.000	0.000	0.000	0.000
36	A	37	ARG	1	0.884	0.900	21.333	0.100	0.100	0.000	0.000	0.000	0.000
37	A	38	GLU	-1	-0.822	-0.892	20.692	-0.147	-0.147	0.000	0.000	0.000	0.000
38	A	39	ALA	0	0.011	0.001	17.505	-0.008	-0.008	0.000	0.000	0.000	0.000
39	A	40	VAL	0	0.001	0.005	17.106	-0.028	-0.028	0.000	0.000	0.000	0.000
40	A	41	GLU	-1	-0.833	-0.899	18.323	-0.148	-0.148	0.000	0.000	0.000	0.000
41	A	42	LYS	1	0.866	0.920	15.653	0.153	0.153	0.000	0.000	0.000	0.000
42	A	43	TYR	0	-0.039	-0.051	10.479	-0.052	-0.052	0.000	0.000	0.000	0.000
43	A	44	LYS	1	0.759	0.863	13.315	0.144	0.144	0.000	0.000	0.000	0.000
44	A	45	GLU	-1	-0.955	-0.971	15.340	-0.111	-0.111	0.000	0.000	0.000	0.000
45	A	46	LEU	0	-0.020	-0.005	11.287	0.023	0.023	0.000	0.000	0.000	0.000
46	A	47	LYS	1	0.925	0.962	8.602	0.421	0.421	0.000	0.000	0.000	0.000
47	A	48	PRO	0	-0.047	-0.006	7.203	0.010	0.010	0.000	0.000	0.000	0.000
48	A	49	ASP	-1	-0.821	-0.908	2.578	-5.062	-3.925	5.143	-3.457	-2.823	-0.035
49	A	50	ILE	0	-0.050	-0.031	5.025	0.231	0.271	-0.001	-0.008	-0.031	0.000
50	A	51	VAL	0	0.010	0.006	7.814	0.185	0.185	0.000	0.000	0.000	0.000
51	A	52	THR	0	-0.023	-0.003	11.599	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	53	MET	0	0.004	0.014	14.400	0.055	0.055	0.000	0.000	0.000	0.000
53	A	54	CYQ	-2	-1.642	-1.698	17.550	-0.300	-0.300	0.000	0.000	0.000	0.000
54	A	55	ILE	0	0.008	-0.002	21.090	0.004	0.004	0.000	0.000	0.000	0.000
55	A	56	THR	0	-0.042	-0.059	23.752	0.007	0.007	0.000	0.000	0.000	0.000
56	A	57	MET	0	-0.026	0.017	21.300	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	58	PRO	0	0.024	0.016	26.669	0.005	0.005	0.000	0.000	0.000	0.000
58	A	59	GLU	-1	-0.802	-0.860	27.676	-0.114	-0.114	0.000	0.000	0.000	0.000
59	A	60	MET	0	-0.051	-0.027	23.644	0.002	0.002	0.000	0.000	0.000	0.000
60	A	61	ASN	0	0.016	0.003	25.147	-0.020	-0.020	0.000	0.000	0.000	0.000
61	A	62	GLY	0	0.071	0.008	21.544	-0.007	-0.007	0.000	0.000	0.000	0.000
62	A	63	ILE	0	-0.020	-0.012	20.967	-0.025	-0.025	0.000	0.000	0.000	0.000
63	A	64	ASP	-1	-0.794	-0.895	22.465	-0.164	-0.164	0.000	0.000	0.000	0.000
64	A	65	ALA	0	0.003	0.009	20.009	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	66	ILE	0	-0.050	-0.022	17.351	-0.023	-0.023	0.000	0.000	0.000	0.000
66	A	67	LYS	1	0.807	0.902	18.649	0.156	0.156	0.000	0.000	0.000	0.000
67	A	68	GLU	-1	-0.902	-0.951	20.782	-0.168	-0.168	0.000	0.000	0.000	0.000
68	A	69	ILE	0	-0.019	-0.011	14.163	-0.004	-0.004	0.000	0.000	0.000	0.000
69	A	70	MET	0	-0.052	-0.010	15.524	-0.037	-0.037	0.000	0.000	0.000	0.000
70	A	71	LYS	1	0.910	0.945	17.186	0.182	0.182	0.000	0.000	0.000	0.000
71	A	72	ILE	0	-0.061	-0.012	16.158	0.023	0.023	0.000	0.000	0.000	0.000
72	A	73	ASP	-1	-0.807	-0.882	11.299	-0.464	-0.464	0.000	0.000	0.000	0.000
73	A	74	PRO	0	0.022	0.014	13.875	-0.054	-0.054	0.000	0.000	0.000	0.000
74	A	75	ASN	0	-0.076	-0.049	10.238	0.000	0.000	0.000	0.000	0.000	0.000
75	A	76	ALA	0	0.017	0.025	10.180	-0.131	-0.131	0.000	0.000	0.000	0.000
76	A	77	LYS	1	0.863	0.917	5.113	1.653	1.653	0.000	0.000	0.000	0.000
77	A	78	ILE	0	0.015	0.013	9.778	-0.078	-0.078	0.000	0.000	0.000	0.000
78	A	79	ILE	0	-0.011	0.006	11.275	0.045	0.045	0.000	0.000	0.000	0.000
79	A	80	VAL	0	-0.002	-0.003	14.396	0.023	0.023	0.000	0.000	0.000	0.000
80	A	81	ALA	0	0.006	-0.010	18.092	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	82	SER	0	0.012	-0.012	20.231	0.009	0.009	0.000	0.000	0.000	0.000
82	A	83	ALA	0	0.072	0.046	24.074	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	84	MET	0	-0.018	-0.009	27.233	-0.004	-0.004	0.000	0.000	0.000	0.000
84	A	85	GLY	0	0.016	0.007	28.939	0.008	0.008	0.000	0.000	0.000	0.000
85	A	86	GLN	0	0.015	0.002	27.210	0.000	0.000	0.000	0.000	0.000	0.000
86	A	87	GLN	0	0.068	0.025	26.777	-0.010	-0.010	0.000	0.000	0.000	0.000
87	A	88	ALA	0	0.020	0.011	27.039	-0.009	-0.009	0.000	0.000	0.000	0.000
88	A	89	MET	0	0.028	0.018	26.799	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	90	VAL	0	0.027	0.015	21.852	-0.013	-0.013	0.000	0.000	0.000	0.000
90	A	91	ILE	0	-0.018	-0.009	22.802	-0.017	-0.017	0.000	0.000	0.000	0.000
91	A	92	GLU	-1	-0.880	-0.938	24.474	-0.164	-0.164	0.000	0.000	0.000	0.000
92	A	93	ALA	0	0.033	0.011	20.719	-0.008	-0.008	0.000	0.000	0.000	0.000
93	A	94	ILE	0	-0.012	-0.011	19.129	-0.020	-0.020	0.000	0.000	0.000	0.000
94	A	95	LYS	1	0.882	0.944	20.181	0.158	0.158	0.000	0.000	0.000	0.000
95	A	96	ALA	0	-0.013	0.009	21.462	0.006	0.006	0.000	0.000	0.000	0.000
96	A	97	GLY	0	0.022	0.008	17.807	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	98	ALA	0	-0.029	-0.004	15.506	-0.055	-0.055	0.000	0.000	0.000	0.000
98	A	99	LYS	1	0.851	0.909	11.787	0.566	0.566	0.000	0.000	0.000	0.000
99	A	100	ASP	-1	-0.820	-0.911	13.961	-0.452	-0.452	0.000	0.000	0.000	0.000
100	A	101	PHE	0	-0.058	-0.024	16.022	0.010	0.010	0.000	0.000	0.000	0.000
101	A	102	ILE	0	-0.013	0.010	16.388	0.003	0.003	0.000	0.000	0.000	0.000
102	A	103	VAL	0	-0.015	-0.012	19.508	0.009	0.009	0.000	0.000	0.000	0.000
103	A	104	LYS	1	0.744	0.839	22.428	0.183	0.183	0.000	0.000	0.000	0.000
104	A	105	PRO	0	-0.004	-0.025	25.000	0.008	0.008	0.000	0.000	0.000	0.000
105	A	106	PHE	0	0.046	0.006	20.257	-0.002	-0.002	0.000	0.000	0.000	0.000
106	A	107	GLN	0	0.029	0.015	22.216	0.011	0.011	0.000	0.000	0.000	0.000
107	A	108	PRO	0	0.046	0.010	19.054	-0.025	-0.025	0.000	0.000	0.000	0.000
108	A	109	SER	0	0.016	0.007	17.684	-0.030	-0.030	0.000	0.000	0.000	0.000
109	A	110	ARG	1	0.895	0.930	17.408	0.154	0.154	0.000	0.000	0.000	0.000
110	A	111	VAL	0	0.024	0.024	14.206	-0.043	-0.043	0.000	0.000	0.000	0.000
111	A	112	VAL	0	0.013	0.004	13.151	-0.086	-0.086	0.000	0.000	0.000	0.000
112	A	113	GLU	-1	-0.873	-0.909	12.516	-0.294	-0.294	0.000	0.000	0.000	0.000
113	A	114	ALA	0	0.033	0.015	13.160	-0.055	-0.055	0.000	0.000	0.000	0.000
114	A	115	LEU	0	0.004	0.010	9.336	-0.096	-0.096	0.000	0.000	0.000	0.000
115	A	116	ASN	0	-0.033	-0.020	8.282	-0.329	-0.329	0.000	0.000	0.000	0.000
116	A	117	LYS	1	0.845	0.924	8.877	0.322	0.322	0.000	0.000	0.000	0.000
117	A	118	VAL	0	0.009	0.014	8.249	0.019	0.019	0.000	0.000	0.000	0.000
118	A	119	SER	0	-0.024	-0.009	4.777	-0.389	-0.324	-0.001	-0.009	-0.055	0.000

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