FMO DATABASE

FMODB ID: GV731

Calculation Name: 3AXY-A-Xray547

Preferred Name:

Target Type:

Ligand Name: phosphoserine

Ligand 3-letter code: SEP

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3AXY

Chain ID: A

ChEMBL ID:

UniProt ID: Q6ZKC0

Base Structure: X-ray

Registration Date: 2025-10-05

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	166
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1717966.319003
FMO2-HF: Nuclear repulsion	1652475.016246
FMO2-HF: Total energy	-65491.302757
FMO2-MP2: Total energy	-65681.802887

3D Structure Molmil

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:5:MET)

Summations of interaction energy for fragment #1(A:5: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.
-59.625	-46.042	16.442	-9.313	-20.707	-0.092

Interaction energy analysis for fragmet #1(A:5:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.816 / q_NPA : 0.932

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	7	ASP	-1	-0.813	-0.909	3.027	-41.454	-39.101	0.159	-1.147	-1.364	-0.005
5	A	9	ASP	-1	-0.795	-0.845	2.535	-57.076	-53.409	1.742	-1.936	-3.473	-0.020
6	A	10	PRO	0	0.056	0.006	4.418	1.694	1.879	-0.001	-0.018	-0.165	0.000
7	A	11	LEU	0	0.013	0.020	2.267	1.766	1.975	1.685	-0.324	-1.571	0.000
8	A	12	VAL	0	0.049	0.042	3.349	0.967	1.694	0.115	-0.184	-0.657	0.000
9	A	13	VAL	0	-0.057	-0.020	6.078	2.860	2.861	-0.001	-0.003	0.004	0.000
13	A	17	VAL	0	-0.069	-0.035	2.730	-1.643	-1.350	2.411	-0.727	-1.977	-0.004
14	A	18	GLY	0	-0.001	-0.011	6.039	-0.044	-0.042	-0.001	-0.004	0.003	0.000
19	A	23	ALA	0	-0.047	-0.051	2.744	-4.608	-3.825	2.257	-1.195	-1.845	0.001
20	A	24	PHE	0	0.033	0.015	2.377	-4.077	-3.715	5.600	-0.627	-5.334	-0.024
21	A	25	VAL	0	-0.035	-0.030	2.411	-26.247	-22.478	2.180	-2.841	-3.107	-0.038
22	A	26	ARG	1	0.794	0.864	3.034	49.990	51.181	0.297	-0.305	-1.183	-0.002
157	A	161	ALA	0	0.034	0.015	4.702	0.900	0.941	-0.001	-0.002	-0.038	0.000
4	A	8	ARG	1	0.894	0.929	5.456	31.930	31.930	0.000	0.000	0.000	0.000
10	A	14	GLY	0	0.024	0.011	8.798	1.825	1.825	0.000	0.000	0.000	0.000
11	A	15	ARG	1	0.872	0.925	8.873	25.352	25.352	0.000	0.000	0.000	0.000
12	A	16	VAL	0	0.057	0.043	6.469	0.567	0.567	0.000	0.000	0.000	0.000
15	A	19	ASP	-1	-0.811	-0.889	9.333	-17.851	-17.851	0.000	0.000	0.000	0.000
16	A	20	VAL	0	-0.014	0.003	8.946	1.086	1.086	0.000	0.000	0.000	0.000
17	A	21	LEU	0	-0.033	-0.009	4.849	-0.046	-0.046	0.000	0.000	0.000	0.000
18	A	22	ASP	-1	-0.800	-0.898	7.025	-26.927	-26.927	0.000	0.000	0.000	0.000
23	A	27	SER	0	0.019	0.008	5.802	1.436	1.436	0.000	0.000	0.000	0.000
24	A	28	THR	0	-0.021	-0.004	9.281	2.759	2.759	0.000	0.000	0.000	0.000
25	A	29	ASN	0	-0.015	-0.002	10.169	-2.398	-2.398	0.000	0.000	0.000	0.000
26	A	30	LEU	0	0.054	0.022	9.513	0.694	0.694	0.000	0.000	0.000	0.000
27	A	31	LYS	1	0.824	0.919	12.223	13.246	13.246	0.000	0.000	0.000	0.000
28	A	32	VAL	0	0.042	0.037	13.366	0.847	0.847	0.000	0.000	0.000	0.000
29	A	33	THR	0	-0.017	-0.011	15.946	-0.146	-0.146	0.000	0.000	0.000	0.000
30	A	34	TYR	0	0.067	0.028	17.627	0.126	0.126	0.000	0.000	0.000	0.000
31	A	35	GLY	0	0.007	0.002	21.915	0.159	0.159	0.000	0.000	0.000	0.000
32	A	36	SER	0	-0.032	-0.021	24.638	-0.096	-0.096	0.000	0.000	0.000	0.000
33	A	37	LYS	1	0.926	0.962	21.414	10.907	10.907	0.000	0.000	0.000	0.000
34	A	38	THR	0	0.006	-0.005	15.758	0.085	0.085	0.000	0.000	0.000	0.000
35	A	39	VAL	0	-0.008	0.003	12.861	0.093	0.093	0.000	0.000	0.000	0.000
36	A	40	SER	0	0.000	-0.002	12.322	-1.182	-1.182	0.000	0.000	0.000	0.000
37	A	41	ASN	0	0.030	-0.007	6.806	1.067	1.067	0.000	0.000	0.000	0.000
38	A	42	GLY	0	0.006	0.017	10.681	-0.115	-0.115	0.000	0.000	0.000	0.000
39	A	43	LEU	0	-0.031	-0.009	13.343	0.973	0.973	0.000	0.000	0.000	0.000
40	A	44	GLU	-1	-0.878	-0.923	16.314	-12.468	-12.468	0.000	0.000	0.000	0.000
41	A	45	LEU	0	-0.041	-0.018	18.165	0.403	0.403	0.000	0.000	0.000	0.000
42	A	46	LYS	1	0.991	1.000	20.977	9.991	9.991	0.000	0.000	0.000	0.000
43	A	47	PRO	0	0.051	0.017	23.884	-0.093	-0.093	0.000	0.000	0.000	0.000
44	A	48	SER	0	-0.058	-0.049	24.911	-0.085	-0.085	0.000	0.000	0.000	0.000
45	A	49	MET	0	-0.092	-0.030	23.165	0.161	0.161	0.000	0.000	0.000	0.000
46	A	50	VAL	0	-0.012	-0.003	20.272	-0.200	-0.200	0.000	0.000	0.000	0.000
47	A	51	THR	0	0.013	0.004	23.204	-0.176	-0.176	0.000	0.000	0.000	0.000
48	A	52	HIS	0	0.019	0.018	25.357	0.003	0.003	0.000	0.000	0.000	0.000
49	A	53	GLN	0	0.017	0.011	21.986	-0.393	-0.393	0.000	0.000	0.000	0.000
50	A	54	PRO	0	-0.044	-0.003	18.135	0.291	0.291	0.000	0.000	0.000	0.000
51	A	55	ARG	1	0.964	0.979	20.815	10.693	10.693	0.000	0.000	0.000	0.000
52	A	56	VAL	0	0.010	-0.005	15.207	-0.462	-0.462	0.000	0.000	0.000	0.000
53	A	57	GLU	-1	-0.857	-0.910	17.644	-13.295	-13.295	0.000	0.000	0.000	0.000
54	A	58	VAL	0	0.005	-0.009	15.263	-1.177	-1.177	0.000	0.000	0.000	0.000
55	A	59	GLY	0	-0.011	0.001	14.763	0.590	0.590	0.000	0.000	0.000	0.000
56	A	60	GLY	0	0.046	0.029	15.677	0.369	0.369	0.000	0.000	0.000	0.000
57	A	61	ASN	0	-0.035	-0.034	16.960	0.607	0.607	0.000	0.000	0.000	0.000
58	A	62	ASP	-1	-0.807	-0.885	20.335	-11.769	-11.769	0.000	0.000	0.000	0.000
59	A	63	MET	0	0.037	0.025	21.216	-0.328	-0.328	0.000	0.000	0.000	0.000
60	A	64	ARG	1	0.847	0.900	23.661	11.693	11.693	0.000	0.000	0.000	0.000
61	A	65	THR	0	-0.061	-0.019	17.452	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	66	PHE	0	-0.034	-0.007	19.887	0.289	0.289	0.000	0.000	0.000	0.000
63	A	67	TYR	0	0.012	0.002	13.626	-0.511	-0.511	0.000	0.000	0.000	0.000
64	A	68	THR	0	0.006	-0.002	15.330	1.014	1.014	0.000	0.000	0.000	0.000
65	A	69	LEU	0	-0.062	-0.023	12.915	-1.311	-1.311	0.000	0.000	0.000	0.000
66	A	70	VAL	0	0.046	0.024	12.569	0.993	0.993	0.000	0.000	0.000	0.000
67	A	71	MET	0	-0.050	-0.016	13.111	-0.607	-0.607	0.000	0.000	0.000	0.000
68	A	72	VAL	0	0.024	0.007	12.419	0.889	0.889	0.000	0.000	0.000	0.000
69	A	73	ASP	-1	-0.817	-0.890	14.226	-14.127	-14.127	0.000	0.000	0.000	0.000
70	A	74	PRO	0	-0.022	-0.007	12.305	0.460	0.460	0.000	0.000	0.000	0.000
71	A	75	ASP	-1	-0.725	-0.830	15.261	-15.969	-15.969	0.000	0.000	0.000	0.000
72	A	76	ALA	0	-0.016	0.021	18.072	0.678	0.678	0.000	0.000	0.000	0.000
73	A	77	PRO	0	0.010	0.003	20.893	-0.158	-0.158	0.000	0.000	0.000	0.000
74	A	78	SER	0	0.002	-0.028	23.043	0.120	0.120	0.000	0.000	0.000	0.000
75	A	79	PRO	0	-0.015	-0.005	18.882	-0.190	-0.190	0.000	0.000	0.000	0.000
76	A	80	SER	0	-0.049	-0.034	20.188	-0.375	-0.375	0.000	0.000	0.000	0.000
77	A	81	ASP	-1	-0.901	-0.950	23.060	-10.882	-10.882	0.000	0.000	0.000	0.000
78	A	82	PRO	0	-0.019	0.017	18.910	0.242	0.242	0.000	0.000	0.000	0.000
79	A	83	ASN	0	0.033	-0.001	20.709	-0.346	-0.346	0.000	0.000	0.000	0.000
80	A	84	LEU	0	-0.037	-0.020	22.440	0.247	0.247	0.000	0.000	0.000	0.000
81	A	85	ARG	1	0.811	0.917	14.848	16.434	16.434	0.000	0.000	0.000	0.000
82	A	86	GLU	-1	-0.777	-0.874	13.458	-17.774	-17.774	0.000	0.000	0.000	0.000
83	A	87	TYR	0	-0.053	-0.064	17.119	0.498	0.498	0.000	0.000	0.000	0.000
84	A	88	LEU	0	-0.008	-0.002	17.318	-0.435	-0.435	0.000	0.000	0.000	0.000
85	A	89	HIS	1	0.846	0.914	18.160	12.961	12.961	0.000	0.000	0.000	0.000
86	A	90	TRP	0	-0.026	-0.023	18.039	0.253	0.253	0.000	0.000	0.000	0.000
87	A	91	LEU	0	0.009	0.012	17.236	-0.749	-0.749	0.000	0.000	0.000	0.000
88	A	92	VAL	0	0.004	0.013	18.247	0.646	0.646	0.000	0.000	0.000	0.000
89	A	93	THR	0	0.005	-0.004	18.286	-0.697	-0.697	0.000	0.000	0.000	0.000
90	A	94	ASP	-1	-0.809	-0.917	20.349	-11.473	-11.473	0.000	0.000	0.000	0.000
91	A	95	ILE	0	-0.037	-0.007	17.269	0.383	0.383	0.000	0.000	0.000	0.000
92	A	96	PRO	0	-0.006	0.000	19.686	-0.596	-0.596	0.000	0.000	0.000	0.000
93	A	97	GLY	0	0.059	0.018	18.556	-0.348	-0.348	0.000	0.000	0.000	0.000
94	A	98	THR	0	-0.094	-0.060	19.003	0.595	0.595	0.000	0.000	0.000	0.000
95	A	99	THR	0	0.013	0.028	20.166	0.748	0.748	0.000	0.000	0.000	0.000
96	A	100	ALA	0	-0.013	-0.011	19.828	-0.589	-0.589	0.000	0.000	0.000	0.000
97	A	101	ALA	0	0.042	-0.003	18.247	0.296	0.296	0.000	0.000	0.000	0.000
98	A	102	SER	0	-0.027	-0.016	20.193	0.133	0.133	0.000	0.000	0.000	0.000
99	A	103	PHE	0	-0.037	-0.019	23.250	0.488	0.488	0.000	0.000	0.000	0.000
100	A	104	GLY	0	0.018	0.024	22.371	0.087	0.087	0.000	0.000	0.000	0.000
101	A	105	GLN	0	0.022	0.012	23.430	0.358	0.358	0.000	0.000	0.000	0.000
102	A	106	GLU	-1	-0.914	-0.975	23.026	-10.956	-10.956	0.000	0.000	0.000	0.000
103	A	107	VAL	0	-0.026	-0.003	22.091	0.328	0.328	0.000	0.000	0.000	0.000
104	A	108	MET	0	-0.007	-0.002	21.689	0.384	0.384	0.000	0.000	0.000	0.000
105	A	109	SER	0	0.058	0.036	22.469	-0.473	-0.473	0.000	0.000	0.000	0.000
106	A	110	TYR	0	-0.042	-0.021	19.611	-0.434	-0.434	0.000	0.000	0.000	0.000
107	A	111	GLU	-1	-0.836	-0.887	22.779	-10.397	-10.397	0.000	0.000	0.000	0.000
108	A	112	SER	0	-0.035	-0.015	22.737	-0.279	-0.279	0.000	0.000	0.000	0.000
109	A	113	PRO	0	0.005	0.006	20.305	0.232	0.232	0.000	0.000	0.000	0.000
110	A	114	ARG	1	0.939	0.970	22.727	9.852	9.852	0.000	0.000	0.000	0.000
111	A	115	PRO	0	0.013	0.031	21.481	0.147	0.147	0.000	0.000	0.000	0.000
112	A	116	THR	0	0.008	-0.012	23.556	0.353	0.353	0.000	0.000	0.000	0.000
113	A	117	MET	0	0.016	0.008	24.529	-0.244	-0.244	0.000	0.000	0.000	0.000
114	A	118	GLY	0	0.077	0.055	23.222	-0.203	-0.203	0.000	0.000	0.000	0.000
115	A	119	ILE	0	-0.020	-0.009	18.315	0.142	0.142	0.000	0.000	0.000	0.000
116	A	120	HIS	1	0.781	0.869	18.058	12.398	12.398	0.000	0.000	0.000	0.000
117	A	121	ARG	1	0.704	0.804	11.406	18.427	18.427	0.000	0.000	0.000	0.000
118	A	122	LEU	0	-0.029	-0.019	14.520	0.475	0.475	0.000	0.000	0.000	0.000
119	A	123	VAL	0	-0.010	-0.016	8.687	-0.678	-0.678	0.000	0.000	0.000	0.000
120	A	124	PHE	0	0.013	-0.001	10.612	1.053	1.053	0.000	0.000	0.000	0.000
121	A	125	VAL	0	-0.001	-0.014	7.475	-2.198	-2.198	0.000	0.000	0.000	0.000
122	A	126	LEU	0	-0.002	0.010	9.075	1.598	1.598	0.000	0.000	0.000	0.000
123	A	127	PHE	0	0.061	0.015	9.635	-2.314	-2.314	0.000	0.000	0.000	0.000
124	A	128	GLN	0	0.010	0.001	11.927	0.727	0.727	0.000	0.000	0.000	0.000
125	A	129	GLN	0	0.001	-0.001	14.178	-0.437	-0.437	0.000	0.000	0.000	0.000
126	A	130	LEU	0	0.015	0.007	17.454	-0.060	-0.060	0.000	0.000	0.000	0.000
127	A	131	GLY	0	-0.006	-0.006	19.535	0.468	0.468	0.000	0.000	0.000	0.000
128	A	132	ARG	1	0.940	0.973	21.930	10.316	10.316	0.000	0.000	0.000	0.000
129	A	133	GLN	0	-0.030	-0.032	20.179	-0.178	-0.178	0.000	0.000	0.000	0.000
130	A	134	THR	0	-0.002	0.004	24.324	-0.069	-0.069	0.000	0.000	0.000	0.000
131	A	135	VAL	0	-0.002	0.014	20.465	-0.095	-0.095	0.000	0.000	0.000	0.000
132	A	136	TYR	0	-0.011	-0.009	23.575	0.461	0.461	0.000	0.000	0.000	0.000
133	A	137	ALA	0	0.018	-0.002	23.797	-0.437	-0.437	0.000	0.000	0.000	0.000
134	A	138	PRO	0	-0.018	-0.012	21.267	0.260	0.260	0.000	0.000	0.000	0.000
135	A	139	GLY	0	0.006	0.008	24.521	0.158	0.158	0.000	0.000	0.000	0.000
136	A	140	TRP	0	-0.055	-0.025	24.098	0.579	0.579	0.000	0.000	0.000	0.000
137	A	141	ARG	1	0.838	0.911	22.493	10.730	10.730	0.000	0.000	0.000	0.000
138	A	142	GLN	0	0.050	0.018	21.266	-0.607	-0.607	0.000	0.000	0.000	0.000
139	A	143	ASN	0	-0.085	-0.046	20.538	0.594	0.594	0.000	0.000	0.000	0.000
140	A	144	PHE	0	0.008	0.016	14.982	0.116	0.116	0.000	0.000	0.000	0.000
141	A	145	ASN	0	0.026	0.016	14.931	-1.186	-1.186	0.000	0.000	0.000	0.000
142	A	146	THR	0	-0.022	-0.065	10.427	0.139	0.139	0.000	0.000	0.000	0.000
143	A	147	LYS	1	0.844	0.932	10.284	22.270	22.270	0.000	0.000	0.000	0.000
144	A	148	ASP	-1	-0.850	-0.931	13.214	-15.321	-15.321	0.000	0.000	0.000	0.000
145	A	149	PHE	0	-0.019	-0.017	14.978	0.626	0.626	0.000	0.000	0.000	0.000
146	A	150	ALA	0	-0.017	-0.017	12.766	0.419	0.419	0.000	0.000	0.000	0.000
147	A	151	GLU	-1	-0.931	-0.959	14.784	-16.132	-16.132	0.000	0.000	0.000	0.000
148	A	152	LEU	0	-0.035	-0.005	17.202	0.547	0.547	0.000	0.000	0.000	0.000
149	A	153	TYR	0	-0.004	-0.001	18.311	0.931	0.931	0.000	0.000	0.000	0.000
150	A	154	ASN	0	-0.026	-0.011	17.757	-0.031	-0.031	0.000	0.000	0.000	0.000
151	A	155	LEU	0	-0.014	-0.004	13.916	-0.291	-0.291	0.000	0.000	0.000	0.000
152	A	156	GLY	0	0.007	0.019	12.702	-1.097	-1.097	0.000	0.000	0.000	0.000
153	A	157	SER	0	-0.002	-0.014	7.001	-0.702	-0.702	0.000	0.000	0.000	0.000
154	A	158	PRO	0	-0.021	-0.008	5.710	1.025	1.025	0.000	0.000	0.000	0.000
155	A	159	VAL	0	0.011	0.013	6.428	-3.055	-3.055	0.000	0.000	0.000	0.000
156	A	160	ALA	0	-0.028	-0.027	6.435	-1.701	-1.701	0.000	0.000	0.000	0.000
158	A	162	VAL	0	-0.075	-0.025	6.337	-1.814	-1.814	0.000	0.000	0.000	0.000
159	A	163	TYR	0	0.019	0.017	8.348	1.310	1.310	0.000	0.000	0.000	0.000
160	A	164	PHE	0	0.025	0.017	10.928	-0.172	-0.172	0.000	0.000	0.000	0.000
161	A	165	ASN	0	0.012	-0.006	14.489	-0.390	-0.390	0.000	0.000	0.000	0.000
162	A	166	SER	0	0.000	-0.023	16.687	0.592	0.592	0.000	0.000	0.000	0.000
163	A	167	GLN	0	-0.029	-0.031	20.189	0.023	0.023	0.000	0.000	0.000	0.000
164	A	168	ARG	1	0.926	0.965	23.367	9.419	9.419	0.000	0.000	0.000	0.000
165	A	169	GLU	-1	-0.833	-0.904	26.999	-9.789	-9.789	0.000	0.000	0.000	0.000
166	A	170	ALA	-1	-0.912	-0.947	29.102	-8.431	-8.431	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:MET)