FMO DATABASE

FMODB ID: JKR29

Calculation Name: 2FPW-B-Xray547

Preferred Name:

Target Type:

Ligand Name: aspartyl phosphate | calcium ion | zinc ion

Ligand 3-letter code: PHD | CA | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2FPW

Chain ID: B

ChEMBL ID:

UniProt ID: Q9S5G5

Base Structure: X-ray

Registration Date: 2025-10-06

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	163
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1712092.392676
FMO2-HF: Nuclear repulsion	1645701.179018
FMO2-HF: Total energy	-66391.213658
FMO2-MP2: Total energy	-66581.250781

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(B:4:GLN)

Summations of interaction energy for fragment #1(B:4:GLN)

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.
-195.598	-187.908	19.847	-10.713	-16.825	-0.1

Interaction energy analysis for fragmet #1(B:4:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.808 / q_NPA : 0.901

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	B	6	TYR	0	0.042	0.005	1.835	-25.341	-24.918	13.583	-5.813	-8.193	-0.069
4	B	7	LEU	0	-0.001	0.008	4.459	4.328	4.477	-0.001	-0.041	-0.107	0.000
45	B	48	GLY	0	-0.004	-0.003	4.330	-1.474	-1.323	-0.001	-0.057	-0.093	0.000
46	B	49	TYR	0	-0.084	-0.066	2.120	-19.331	-18.498	3.008	-1.691	-2.151	-0.026
47	B	50	LYS	1	0.821	0.915	2.320	39.963	42.046	3.112	-1.388	-3.807	0.006
48	B	51	LEU	0	0.017	0.010	3.933	-1.293	-1.191	0.002	-0.013	-0.092	0.000
117	B	120	ALA	0	-0.042	0.005	4.628	-8.277	-8.155	-0.001	-0.009	-0.111	0.000
118	B	121	MET	0	-0.050	-0.026	2.831	-13.586	-11.849	0.085	-0.833	-0.988	-0.007
119	B	122	ASP	-1	-0.860	-0.914	2.973	-44.588	-42.537	0.061	-0.849	-1.264	-0.004
120	B	123	ARG	1	0.890	0.945	4.519	32.135	32.174	-0.001	-0.019	-0.019	0.000
5	B	8	PHE	0	0.010	-0.002	6.802	0.311	0.311	0.000	0.000	0.000	0.000
6	B	9	ILE	0	-0.034	-0.020	10.153	1.500	1.500	0.000	0.000	0.000	0.000
7	B	10	ASP	-1	-0.742	-0.866	13.049	-14.907	-14.907	0.000	0.000	0.000	0.000
8	B	11	ARG	1	0.815	0.862	16.801	12.696	12.696	0.000	0.000	0.000	0.000
9	B	12	ASP	-1	-0.743	-0.846	19.195	-12.385	-12.385	0.000	0.000	0.000	0.000
10	B	13	GLY	0	0.018	0.017	22.724	0.008	0.008	0.000	0.000	0.000	0.000
11	B	14	THR	0	-0.056	-0.034	16.862	-0.050	-0.050	0.000	0.000	0.000	0.000
12	B	15	LEU	0	-0.047	-0.025	14.754	-0.377	-0.377	0.000	0.000	0.000	0.000
13	B	16	ILE	0	-0.024	-0.018	18.924	0.329	0.329	0.000	0.000	0.000	0.000
14	B	17	SER	0	0.006	0.009	22.636	-0.051	-0.051	0.000	0.000	0.000	0.000
15	B	18	GLU	-1	-0.818	-0.905	25.660	-11.021	-11.021	0.000	0.000	0.000	0.000
16	B	19	PRO	0	-0.015	-0.007	27.076	0.323	0.323	0.000	0.000	0.000	0.000
17	B	20	PRO	0	-0.019	-0.012	30.682	0.022	0.022	0.000	0.000	0.000	0.000
18	B	21	SER	0	-0.081	-0.038	32.898	0.157	0.157	0.000	0.000	0.000	0.000
19	B	22	ASP	-1	-0.798	-0.902	32.608	-9.054	-9.054	0.000	0.000	0.000	0.000
20	B	23	PHE	0	-0.036	-0.011	28.627	-0.093	-0.093	0.000	0.000	0.000	0.000
21	B	24	GLN	0	-0.015	0.003	27.959	-0.538	-0.538	0.000	0.000	0.000	0.000
22	B	25	VAL	0	-0.034	-0.032	25.944	0.355	0.355	0.000	0.000	0.000	0.000
23	B	26	ASP	-1	-0.818	-0.880	28.160	-9.421	-9.421	0.000	0.000	0.000	0.000
24	B	27	ARG	1	0.878	0.899	31.055	8.754	8.754	0.000	0.000	0.000	0.000
25	B	28	PHE	0	0.000	-0.009	29.026	-0.190	-0.190	0.000	0.000	0.000	0.000
26	B	29	ASP	-1	-0.865	-0.902	31.453	-8.604	-8.604	0.000	0.000	0.000	0.000
27	B	30	LYS	1	0.750	0.867	30.952	9.363	9.363	0.000	0.000	0.000	0.000
28	B	31	LEU	0	-0.007	0.010	24.591	-0.345	-0.345	0.000	0.000	0.000	0.000
29	B	32	ALA	0	-0.004	-0.002	26.936	0.220	0.220	0.000	0.000	0.000	0.000
30	B	33	PHE	0	0.007	-0.001	19.720	-0.294	-0.294	0.000	0.000	0.000	0.000
31	B	34	GLU	-1	-0.712	-0.791	20.539	-11.630	-11.630	0.000	0.000	0.000	0.000
32	B	35	PRO	0	-0.004	-0.017	21.721	-0.216	-0.216	0.000	0.000	0.000	0.000
33	B	36	GLY	0	-0.008	-0.010	20.951	-0.398	-0.398	0.000	0.000	0.000	0.000
34	B	37	VAL	0	0.018	0.014	16.404	-0.601	-0.601	0.000	0.000	0.000	0.000
35	B	38	ILE	0	0.038	0.026	15.983	-0.939	-0.939	0.000	0.000	0.000	0.000
36	B	39	PRO	0	0.003	-0.004	15.699	-0.820	-0.820	0.000	0.000	0.000	0.000
37	B	40	GLN	0	0.024	0.009	15.116	-1.244	-1.244	0.000	0.000	0.000	0.000
38	B	41	LEU	0	0.044	0.027	11.077	-1.475	-1.475	0.000	0.000	0.000	0.000
39	B	42	LEU	0	-0.042	-0.013	10.804	-1.748	-1.748	0.000	0.000	0.000	0.000
40	B	43	LYS	1	0.822	0.909	11.345	16.420	16.420	0.000	0.000	0.000	0.000
41	B	44	LEU	0	0.030	0.013	8.545	-0.991	-0.991	0.000	0.000	0.000	0.000
42	B	45	GLN	0	0.015	0.007	6.640	-3.363	-3.363	0.000	0.000	0.000	0.000
43	B	46	LYS	1	0.907	0.950	6.813	15.934	15.934	0.000	0.000	0.000	0.000
44	B	47	ALA	0	-0.013	0.016	7.993	0.545	0.545	0.000	0.000	0.000	0.000
49	B	52	VAL	0	0.006	0.009	7.015	0.289	0.289	0.000	0.000	0.000	0.000
50	B	53	MET	0	-0.030	0.009	9.562	0.906	0.906	0.000	0.000	0.000	0.000
51	B	54	ILE	0	-0.003	-0.005	13.303	0.067	0.067	0.000	0.000	0.000	0.000
52	B	55	THR	0	0.002	0.017	15.179	0.588	0.588	0.000	0.000	0.000	0.000
53	B	56	ASN	0	0.009	0.009	18.972	-0.429	-0.429	0.000	0.000	0.000	0.000
54	B	57	GLN	0	-0.013	-0.039	22.245	0.516	0.516	0.000	0.000	0.000	0.000
55	B	58	ASP	-1	-0.753	-0.863	25.096	-11.189	-11.189	0.000	0.000	0.000	0.000
56	B	59	GLY	0	0.049	0.030	28.200	0.306	0.306	0.000	0.000	0.000	0.000
57	B	60	LEU	0	-0.012	0.022	24.833	0.280	0.280	0.000	0.000	0.000	0.000
58	B	61	GLY	0	-0.024	-0.005	28.784	-0.097	-0.097	0.000	0.000	0.000	0.000
59	B	62	THR	0	-0.092	-0.059	30.587	0.459	0.459	0.000	0.000	0.000	0.000
60	B	63	GLN	0	-0.021	-0.037	33.863	0.033	0.033	0.000	0.000	0.000	0.000
61	B	64	SER	0	-0.045	-0.014	34.145	0.043	0.043	0.000	0.000	0.000	0.000
62	B	65	PHE	0	0.069	0.035	27.175	-0.043	-0.043	0.000	0.000	0.000	0.000
63	B	66	PRO	0	0.014	0.015	31.343	-0.275	-0.275	0.000	0.000	0.000	0.000
64	B	67	GLN	0	-0.026	-0.032	25.816	-0.137	-0.137	0.000	0.000	0.000	0.000
65	B	68	ALA	0	0.003	0.003	29.311	-0.244	-0.244	0.000	0.000	0.000	0.000
66	B	69	ASP	-1	-0.878	-0.947	31.038	-8.941	-8.941	0.000	0.000	0.000	0.000
67	B	70	PHE	0	0.021	0.016	22.190	-0.227	-0.227	0.000	0.000	0.000	0.000
68	B	71	ASP	-1	-0.868	-0.937	26.318	-11.204	-11.204	0.000	0.000	0.000	0.000
69	B	72	GLY	0	-0.035	-0.011	26.809	-0.231	-0.231	0.000	0.000	0.000	0.000
70	B	73	PRO	0	0.016	-0.007	27.095	-0.216	-0.216	0.000	0.000	0.000	0.000
71	B	74	HIS	0	0.055	0.046	19.370	-0.153	-0.153	0.000	0.000	0.000	0.000
72	B	75	ASN	0	0.001	-0.012	22.365	-0.975	-0.975	0.000	0.000	0.000	0.000
73	B	76	LEU	0	-0.020	0.007	23.441	-0.212	-0.212	0.000	0.000	0.000	0.000
74	B	77	MET	0	0.004	0.013	18.739	-0.306	-0.306	0.000	0.000	0.000	0.000
75	B	78	MET	0	0.020	0.005	15.567	-0.652	-0.652	0.000	0.000	0.000	0.000
76	B	79	GLN	0	-0.007	0.016	19.140	-0.496	-0.496	0.000	0.000	0.000	0.000
77	B	80	ILE	0	0.003	0.010	21.137	-0.101	-0.101	0.000	0.000	0.000	0.000
78	B	81	PHE	0	0.017	-0.015	15.954	-0.282	-0.282	0.000	0.000	0.000	0.000
79	B	82	THR	0	-0.012	-0.014	16.651	-0.553	-0.553	0.000	0.000	0.000	0.000
80	B	83	SER	0	-0.091	-0.049	17.698	0.037	0.037	0.000	0.000	0.000	0.000
81	B	84	GLN	0	-0.058	-0.027	18.484	0.455	0.455	0.000	0.000	0.000	0.000
82	B	85	GLY	0	0.014	0.020	15.515	-0.245	-0.245	0.000	0.000	0.000	0.000
83	B	86	VAL	0	-0.065	-0.028	12.356	-1.330	-1.330	0.000	0.000	0.000	0.000
84	B	87	GLN	0	-0.009	-0.020	10.527	1.532	1.532	0.000	0.000	0.000	0.000
85	B	88	PHE	0	0.022	-0.002	9.948	-1.669	-1.669	0.000	0.000	0.000	0.000
86	B	89	ASP	-1	-0.847	-0.914	5.241	-34.507	-34.507	0.000	0.000	0.000	0.000
87	B	90	GLU	-1	-0.863	-0.914	8.842	-22.952	-22.952	0.000	0.000	0.000	0.000
88	B	91	VAL	0	-0.004	-0.015	11.430	-0.509	-0.509	0.000	0.000	0.000	0.000
89	B	92	LEU	0	-0.057	-0.013	11.976	0.916	0.916	0.000	0.000	0.000	0.000
90	B	93	ILE	0	0.044	0.004	16.024	0.029	0.029	0.000	0.000	0.000	0.000
91	B	94	CYS	0	-0.065	0.019	19.665	0.365	0.365	0.000	0.000	0.000	0.000
92	B	95	PRO	0	0.014	0.007	22.190	0.107	0.107	0.000	0.000	0.000	0.000
93	B	96	HIS	0	-0.013	-0.018	24.927	0.616	0.616	0.000	0.000	0.000	0.000
94	B	97	LEU	0	0.024	0.009	27.477	-0.185	-0.185	0.000	0.000	0.000	0.000
95	B	98	PRO	0	-0.054	-0.045	29.381	-0.144	-0.144	0.000	0.000	0.000	0.000
96	B	99	ALA	0	-0.020	-0.011	30.405	-0.055	-0.055	0.000	0.000	0.000	0.000
97	B	100	ASP	-1	-0.811	-0.896	29.696	-9.883	-9.883	0.000	0.000	0.000	0.000
98	B	101	GLU	-1	-1.002	-0.997	29.655	-9.705	-9.705	0.000	0.000	0.000	0.000
99	B	102	CYS	0	-0.022	0.016	25.756	-0.459	-0.459	0.000	0.000	0.000	0.000
100	B	103	ASP	-1	-0.844	-0.946	22.872	-12.686	-12.686	0.000	0.000	0.000	0.000
101	B	104	CYS	0	-0.062	-0.038	20.440	-0.446	-0.446	0.000	0.000	0.000	0.000
102	B	105	ARG	1	0.846	0.893	20.345	11.196	11.196	0.000	0.000	0.000	0.000
103	B	106	LYS	1	0.814	0.898	17.132	16.289	16.289	0.000	0.000	0.000	0.000
104	B	107	PRO	0	-0.003	-0.013	19.706	0.722	0.722	0.000	0.000	0.000	0.000
105	B	108	LYS	1	0.842	0.922	19.646	11.763	11.763	0.000	0.000	0.000	0.000
106	B	109	VAL	0	0.058	0.016	15.530	-0.271	-0.271	0.000	0.000	0.000	0.000
107	B	110	LYS	1	0.815	0.904	15.874	14.842	14.842	0.000	0.000	0.000	0.000
108	B	111	LEU	0	0.001	-0.006	15.608	-0.374	-0.374	0.000	0.000	0.000	0.000
109	B	112	VAL	0	0.026	0.003	11.413	-0.840	-0.840	0.000	0.000	0.000	0.000
110	B	113	GLU	-1	-0.799	-0.875	11.529	-19.362	-19.362	0.000	0.000	0.000	0.000
111	B	114	ARG	1	0.936	0.957	10.048	20.295	20.295	0.000	0.000	0.000	0.000
112	B	115	TYR	0	-0.046	-0.063	5.776	-2.889	-2.889	0.000	0.000	0.000	0.000
113	B	116	LEU	0	-0.029	-0.002	8.237	-2.284	-2.284	0.000	0.000	0.000	0.000
114	B	117	ALA	0	0.030	0.023	9.835	1.501	1.501	0.000	0.000	0.000	0.000
115	B	118	GLU	-1	-0.947	-0.975	8.799	-25.867	-25.867	0.000	0.000	0.000	0.000
116	B	119	GLN	0	-0.034	-0.027	6.091	-2.187	-2.187	0.000	0.000	0.000	0.000
121	B	124	ALA	0	0.010	0.025	7.885	3.226	3.226	0.000	0.000	0.000	0.000
122	B	125	ASN	0	-0.071	-0.051	6.617	6.263	6.263	0.000	0.000	0.000	0.000
123	B	126	SER	0	0.015	-0.015	5.896	-4.893	-4.893	0.000	0.000	0.000	0.000
124	B	127	TYR	0	0.018	0.002	7.769	3.328	3.328	0.000	0.000	0.000	0.000
125	B	128	VAL	0	-0.006	0.020	9.959	-1.338	-1.338	0.000	0.000	0.000	0.000
126	B	129	ILE	0	-0.039	-0.022	11.182	0.752	0.752	0.000	0.000	0.000	0.000
127	B	130	GLY	0	0.052	0.021	14.364	-0.052	-0.052	0.000	0.000	0.000	0.000
128	B	131	ASP	-1	-0.766	-0.865	17.923	-12.956	-12.956	0.000	0.000	0.000	0.000
129	B	132	ARG	1	0.779	0.882	21.534	12.838	12.838	0.000	0.000	0.000	0.000
130	B	133	ALA	0	0.037	0.008	21.698	-0.609	-0.609	0.000	0.000	0.000	0.000
131	B	134	THR	0	0.021	0.007	21.728	-0.169	-0.169	0.000	0.000	0.000	0.000
132	B	135	ASP	-1	-0.797	-0.895	17.360	-16.536	-16.536	0.000	0.000	0.000	0.000
133	B	136	ILE	0	-0.013	-0.012	17.116	-1.118	-1.118	0.000	0.000	0.000	0.000
134	B	137	GLN	0	-0.031	-0.027	18.745	-0.086	-0.086	0.000	0.000	0.000	0.000
135	B	138	LEU	0	-0.004	-0.004	14.503	-0.267	-0.267	0.000	0.000	0.000	0.000
136	B	139	ALA	0	-0.006	-0.010	14.320	-0.947	-0.947	0.000	0.000	0.000	0.000
137	B	140	GLU	-1	-0.891	-0.925	15.210	-16.054	-16.054	0.000	0.000	0.000	0.000
138	B	141	ASN	0	-0.038	-0.032	17.268	-0.110	-0.110	0.000	0.000	0.000	0.000
139	B	142	MET	0	-0.047	-0.016	10.288	0.062	0.062	0.000	0.000	0.000	0.000
140	B	143	GLY	0	-0.016	0.007	12.472	-1.952	-1.952	0.000	0.000	0.000	0.000
141	B	144	ILE	0	-0.081	-0.050	9.469	-2.590	-2.590	0.000	0.000	0.000	0.000
142	B	145	ASN	0	-0.020	-0.009	11.231	4.103	4.103	0.000	0.000	0.000	0.000
143	B	146	GLY	0	0.031	0.006	13.396	-0.869	-0.869	0.000	0.000	0.000	0.000
144	B	147	LEU	0	-0.050	-0.026	13.372	0.749	0.749	0.000	0.000	0.000	0.000
145	B	148	ARG	1	0.874	0.940	16.300	12.654	12.654	0.000	0.000	0.000	0.000
146	B	149	TYR	0	-0.041	-0.048	18.067	0.266	0.266	0.000	0.000	0.000	0.000
147	B	150	ASP	-1	-0.815	-0.920	19.717	-11.128	-11.128	0.000	0.000	0.000	0.000
148	B	151	ARG	1	0.801	0.862	22.984	11.052	11.052	0.000	0.000	0.000	0.000
149	B	152	GLU	-1	-0.976	-0.974	24.467	-9.941	-9.941	0.000	0.000	0.000	0.000
150	B	153	THR	0	-0.036	-0.042	25.075	-0.334	-0.334	0.000	0.000	0.000	0.000
151	B	154	LEU	0	-0.031	-0.017	17.955	-0.350	-0.350	0.000	0.000	0.000	0.000
152	B	155	ASN	0	0.050	0.032	19.860	-0.939	-0.939	0.000	0.000	0.000	0.000
153	B	156	TRP	0	0.083	0.010	12.922	-1.035	-1.035	0.000	0.000	0.000	0.000
154	B	157	PRO	0	-0.051	-0.030	16.893	-0.820	-0.820	0.000	0.000	0.000	0.000
155	B	158	MET	0	-0.003	0.026	18.308	-0.521	-0.521	0.000	0.000	0.000	0.000
156	B	159	ILE	0	0.011	0.012	13.250	-0.683	-0.683	0.000	0.000	0.000	0.000
157	B	160	GLY	0	0.048	0.018	13.581	-1.304	-1.304	0.000	0.000	0.000	0.000
158	B	161	GLU	-1	-1.015	-0.985	14.413	-14.714	-14.714	0.000	0.000	0.000	0.000
159	B	162	GLN	0	0.005	0.000	15.489	-1.269	-1.269	0.000	0.000	0.000	0.000
160	B	163	LEU	0	0.005	0.010	9.967	-0.536	-0.536	0.000	0.000	0.000	0.000
161	B	164	THR	0	-0.091	-0.060	10.589	-1.903	-1.903	0.000	0.000	0.000	0.000
162	B	165	ARG	1	0.950	0.990	12.411	16.618	16.618	0.000	0.000	0.000	0.000
163	B	166	ARG	0	0.026	0.022	13.037	1.456	1.456	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:4:GLN)