FMO DATABASE

FMODB ID: 74VQK

Calculation Name: 1H4X-A-Xray549

Preferred Name:

Target Type:

Ligand Name: phosphoserine | 2-amino-2-hydroxymethyl-propane-1,3-diol

Ligand 3-letter code: SEP | TRS

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1H4X

Chain ID: A

ChEMBL ID:

UniProt ID: O32723

Base Structure: X-ray

Registration Date: 2025-10-11

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	111
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-913915.839457
FMO2-HF: Nuclear repulsion	869422.322436
FMO2-HF: Total energy	-44493.517021
FMO2-MP2: Total energy	-44621.28349

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:2:ALA)

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

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.
-145.888	-143.095	18.313	-11.687	-9.418	-0.126

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.780 / q_NPA : 0.884

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	GLN	0	0.029	0.027	3.846	3.183	5.127	-0.022	-1.025	-0.897	-0.003
17	A	18	PHE	0	-0.002	-0.008	2.454	7.791	9.204	0.445	-0.646	-1.211	-0.003
18	A	19	GLY	0	-0.008	0.004	1.750	-44.001	-45.972	10.720	-5.395	-3.354	-0.068
19	A	20	GLU	-1	-0.870	-0.932	3.904	-39.466	-39.070	0.004	-0.166	-0.234	-0.001
20	A	21	LEU	0	-0.056	-0.042	2.075	-42.449	-41.698	7.166	-4.381	-3.536	-0.050
21	A	22	ASP	-1	-0.755	-0.882	3.780	-31.262	-31.066	0.001	-0.066	-0.131	-0.001
24	A	25	ALA	0	-0.001	-0.003	4.418	0.861	0.925	-0.001	-0.008	-0.055	0.000
4	A	5	LEU	0	-0.002	-0.007	6.704	0.486	0.486	0.000	0.000	0.000	0.000
5	A	6	GLU	-1	-0.838	-0.893	10.277	-20.554	-20.554	0.000	0.000	0.000	0.000
6	A	7	MET	0	-0.024	0.000	12.644	0.193	0.193	0.000	0.000	0.000	0.000
7	A	8	VAL	0	0.025	0.016	16.001	0.938	0.938	0.000	0.000	0.000	0.000
8	A	9	THR	0	0.000	-0.002	17.547	1.060	1.060	0.000	0.000	0.000	0.000
9	A	10	ARG	1	0.884	0.925	20.443	10.823	10.823	0.000	0.000	0.000	0.000
10	A	11	GLU	-1	-0.849	-0.906	21.394	-12.000	-12.000	0.000	0.000	0.000	0.000
11	A	12	THR	0	0.006	0.007	19.068	-0.090	-0.090	0.000	0.000	0.000	0.000
12	A	13	VAL	0	-0.013	-0.014	13.372	-0.349	-0.349	0.000	0.000	0.000	0.000
13	A	14	VAL	0	0.005	0.008	11.912	0.036	0.036	0.000	0.000	0.000	0.000
14	A	15	ILE	0	-0.028	-0.018	9.095	-1.820	-1.820	0.000	0.000	0.000	0.000
15	A	16	ARG	1	0.765	0.836	8.146	25.545	25.545	0.000	0.000	0.000	0.000
16	A	17	LEU	0	-0.009	-0.010	5.248	-7.137	-7.137	0.000	0.000	0.000	0.000
22	A	23	HIS	0	0.063	0.010	6.749	-1.504	-1.504	0.000	0.000	0.000	0.000
23	A	24	HIS	0	-0.016	0.006	8.465	2.652	2.652	0.000	0.000	0.000	0.000
25	A	26	VAL	0	-0.005	-0.003	6.376	1.546	1.546	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-0.764	-0.848	8.740	-18.220	-18.220	0.000	0.000	0.000	0.000
27	A	28	GLN	0	-0.038	-0.025	6.620	-1.729	-1.729	0.000	0.000	0.000	0.000
28	A	29	ILE	0	-0.018	-0.004	6.286	2.293	2.293	0.000	0.000	0.000	0.000
29	A	30	ARG	1	0.825	0.876	10.007	20.986	20.986	0.000	0.000	0.000	0.000
30	A	31	ALA	0	-0.004	-0.003	13.275	1.549	1.549	0.000	0.000	0.000	0.000
31	A	32	LYS	1	0.903	0.966	11.761	23.992	23.992	0.000	0.000	0.000	0.000
32	A	33	ILE	0	0.027	-0.002	12.534	1.177	1.177	0.000	0.000	0.000	0.000
33	A	34	SER	0	-0.037	-0.025	15.277	1.160	1.160	0.000	0.000	0.000	0.000
34	A	35	THR	0	-0.040	-0.034	17.845	1.151	1.151	0.000	0.000	0.000	0.000
35	A	36	ALA	0	0.004	-0.001	17.428	0.751	0.751	0.000	0.000	0.000	0.000
36	A	37	ILE	0	-0.003	0.007	18.458	0.602	0.602	0.000	0.000	0.000	0.000
37	A	38	PHE	0	-0.041	-0.022	21.281	0.737	0.737	0.000	0.000	0.000	0.000
38	A	39	GLN	0	-0.061	-0.030	21.657	0.258	0.258	0.000	0.000	0.000	0.000
39	A	40	GLY	0	0.009	0.017	23.991	0.402	0.402	0.000	0.000	0.000	0.000
40	A	41	ALA	0	-0.027	-0.011	20.766	0.081	0.081	0.000	0.000	0.000	0.000
41	A	42	VAL	0	-0.063	-0.041	17.021	-0.631	-0.631	0.000	0.000	0.000	0.000
42	A	43	THR	0	0.028	0.017	20.444	0.129	0.129	0.000	0.000	0.000	0.000
43	A	44	THR	0	-0.003	-0.005	20.279	0.577	0.577	0.000	0.000	0.000	0.000
44	A	45	ILE	0	0.001	0.005	14.852	-0.693	-0.693	0.000	0.000	0.000	0.000
45	A	46	ILE	0	0.013	0.016	15.213	0.622	0.622	0.000	0.000	0.000	0.000
46	A	47	TRP	0	0.031	0.004	10.460	-2.330	-2.330	0.000	0.000	0.000	0.000
47	A	48	ASN	0	-0.005	-0.015	11.233	1.105	1.105	0.000	0.000	0.000	0.000
48	A	49	PHE	0	0.002	-0.028	9.601	-3.926	-3.926	0.000	0.000	0.000	0.000
49	A	50	GLU	-1	-0.806	-0.887	10.072	-24.248	-24.248	0.000	0.000	0.000	0.000
50	A	51	ARG	1	0.824	0.908	7.686	26.985	26.985	0.000	0.000	0.000	0.000
51	A	52	LEU	0	-0.020	0.010	5.086	-5.910	-5.910	0.000	0.000	0.000	0.000
52	A	53	SER	0	-0.042	-0.021	6.096	3.232	3.232	0.000	0.000	0.000	0.000
53	A	54	PHE	0	-0.047	-0.033	7.042	4.534	4.534	0.000	0.000	0.000	0.000
54	A	55	MET	0	-0.015	0.014	6.408	-7.201	-7.201	0.000	0.000	0.000	0.000
55	A	56	ASP	-1	-0.751	-0.852	7.786	-21.074	-21.074	0.000	0.000	0.000	0.000
56	A	57	SER	0	-0.050	-0.015	10.014	0.805	0.805	0.000	0.000	0.000	0.000
57	A	58	SER	0	-0.034	-0.049	11.865	0.455	0.455	0.000	0.000	0.000	0.000
58	A	59	GLY	0	0.040	-0.005	10.386	0.555	0.555	0.000	0.000	0.000	0.000
59	A	60	VAL	0	-0.007	-0.017	11.200	0.432	0.432	0.000	0.000	0.000	0.000
60	A	61	GLY	0	0.015	0.009	14.611	0.912	0.912	0.000	0.000	0.000	0.000
61	A	62	LEU	0	-0.066	-0.015	9.695	1.002	1.002	0.000	0.000	0.000	0.000
62	A	63	VAL	0	0.047	0.033	12.538	0.804	0.804	0.000	0.000	0.000	0.000
63	A	64	LEU	0	0.038	0.015	14.921	1.029	1.029	0.000	0.000	0.000	0.000
64	A	65	GLY	0	-0.024	-0.011	17.660	0.924	0.924	0.000	0.000	0.000	0.000
65	A	66	ARG	1	0.786	0.849	14.911	19.153	19.153	0.000	0.000	0.000	0.000
66	A	67	MET	0	-0.001	0.013	18.122	0.433	0.433	0.000	0.000	0.000	0.000
67	A	68	ARG	1	0.904	0.953	20.508	13.028	13.028	0.000	0.000	0.000	0.000
68	A	69	GLU	-1	-0.749	-0.823	19.009	-16.175	-16.175	0.000	0.000	0.000	0.000
69	A	70	LEU	0	0.009	0.002	19.504	0.478	0.478	0.000	0.000	0.000	0.000
70	A	71	GLU	-1	-0.949	-0.963	23.164	-11.289	-11.289	0.000	0.000	0.000	0.000
71	A	72	ALA	0	-0.067	-0.029	26.108	0.532	0.532	0.000	0.000	0.000	0.000
72	A	73	VAL	0	-0.041	-0.021	24.875	0.393	0.393	0.000	0.000	0.000	0.000
73	A	74	ALA	0	-0.040	-0.013	27.887	0.126	0.126	0.000	0.000	0.000	0.000
74	A	75	GLY	0	0.024	0.018	24.217	0.029	0.029	0.000	0.000	0.000	0.000
75	A	76	ARG	1	0.829	0.903	23.367	12.756	12.756	0.000	0.000	0.000	0.000
76	A	77	THR	0	0.017	-0.003	17.872	-0.917	-0.917	0.000	0.000	0.000	0.000
77	A	78	ILE	0	0.010	0.006	17.961	0.712	0.712	0.000	0.000	0.000	0.000
78	A	79	LEU	0	-0.049	-0.029	15.621	-1.482	-1.482	0.000	0.000	0.000	0.000
79	A	80	LEU	0	0.032	0.017	15.029	0.808	0.808	0.000	0.000	0.000	0.000
80	A	81	ASN	0	0.013	0.009	14.118	-0.912	-0.912	0.000	0.000	0.000	0.000
81	A	82	PRO	0	-0.025	-0.002	13.874	-1.610	-1.610	0.000	0.000	0.000	0.000
82	A	83	SER	0	0.086	0.038	12.034	1.989	1.989	0.000	0.000	0.000	0.000
83	A	84	PRO	0	0.034	-0.001	14.613	0.397	0.397	0.000	0.000	0.000	0.000
84	A	85	THR	0	0.003	-0.004	14.223	1.172	1.172	0.000	0.000	0.000	0.000
85	A	86	MET	0	0.004	0.018	11.793	0.235	0.235	0.000	0.000	0.000	0.000
86	A	87	ARG	1	0.842	0.873	14.883	17.463	17.463	0.000	0.000	0.000	0.000
87	A	88	LYS	1	0.937	0.973	18.309	14.864	14.864	0.000	0.000	0.000	0.000
88	A	89	VAL	0	-0.003	-0.004	15.633	0.894	0.894	0.000	0.000	0.000	0.000
89	A	90	PHE	0	0.054	0.010	13.586	0.591	0.591	0.000	0.000	0.000	0.000
90	A	91	GLN	0	-0.012	-0.012	19.356	0.561	0.561	0.000	0.000	0.000	0.000
91	A	92	PHE	0	-0.069	-0.021	22.114	0.675	0.675	0.000	0.000	0.000	0.000
92	A	93	SER	0	-0.026	-0.013	21.206	0.399	0.399	0.000	0.000	0.000	0.000
93	A	94	GLY	0	0.020	0.016	23.156	0.142	0.142	0.000	0.000	0.000	0.000
94	A	95	LEU	0	-0.018	-0.026	19.129	0.227	0.227	0.000	0.000	0.000	0.000
95	A	96	GLY	0	0.019	0.010	22.362	-0.388	-0.388	0.000	0.000	0.000	0.000
96	A	97	PRO	0	-0.026	-0.025	24.198	-0.172	-0.172	0.000	0.000	0.000	0.000
97	A	98	TRP	0	0.012	0.021	20.983	0.142	0.142	0.000	0.000	0.000	0.000
98	A	99	MET	0	-0.093	-0.024	18.602	-1.217	-1.217	0.000	0.000	0.000	0.000
99	A	100	MET	0	-0.009	0.005	19.472	0.835	0.835	0.000	0.000	0.000	0.000
100	A	101	ASP	-1	-0.801	-0.868	18.846	-17.552	-17.552	0.000	0.000	0.000	0.000
101	A	102	ALA	0	-0.010	0.002	19.048	0.908	0.908	0.000	0.000	0.000	0.000
102	A	103	THR	0	0.005	-0.022	18.465	-1.076	-1.076	0.000	0.000	0.000	0.000
103	A	104	GLU	-1	-0.753	-0.860	12.737	-23.921	-23.921	0.000	0.000	0.000	0.000
104	A	105	GLU	-1	-0.869	-0.943	17.131	-16.538	-16.538	0.000	0.000	0.000	0.000
105	A	106	GLU	-1	-0.826	-0.882	20.111	-13.175	-13.175	0.000	0.000	0.000	0.000
106	A	107	ALA	0	-0.011	-0.011	18.717	0.491	0.491	0.000	0.000	0.000	0.000
107	A	108	ILE	0	-0.033	-0.031	16.565	0.265	0.265	0.000	0.000	0.000	0.000
108	A	109	ASP	-1	-0.832	-0.906	20.723	-12.807	-12.807	0.000	0.000	0.000	0.000
109	A	110	ARG	1	0.857	0.936	23.991	12.397	12.397	0.000	0.000	0.000	0.000
110	A	111	VAL	0	-0.084	-0.044	21.430	0.443	0.443	0.000	0.000	0.000	0.000
111	A	112	ARG	0	-0.070	-0.015	21.592	2.044	2.044	0.000	0.000	0.000	0.000

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