FMO DATABASE

FMODB ID: GR551

Calculation Name: 3HM2-A-Xray547

Preferred Name:

Target Type:

Ligand Name: acetic acid | calcium ion

Ligand 3-letter code: ACY | CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3HM2

Chain ID: A

ChEMBL ID:

UniProt ID: Q6NHA4

Base Structure: X-ray

Registration Date: 2025-10-04

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	172
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1623252.281138
FMO2-HF: Nuclear repulsion	1559170.589939
FMO2-HF: Total energy	-64081.691199
FMO2-MP2: Total energy	-64271.619025

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:3:GLY)

Summations of interaction energy for fragment #1(A:3: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.
54.944	63.129	4.193	-5.308	-7.07	-0.069

Interaction energy analysis for fragmet #1(A:3:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.877 / 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	5	LEU	0	0.021	0.032	2.322	4.568	7.217	1.185	-1.248	-2.586	-0.013
4	A	6	THR	0	0.110	0.044	2.349	-4.400	-2.036	1.312	-1.697	-1.979	-0.023
5	A	7	LYS	1	0.944	0.979	4.034	56.829	57.106	-0.001	-0.073	-0.203	0.000
149	A	151	HIS	0	-0.056	-0.048	2.439	-31.292	-28.453	1.698	-2.287	-2.250	-0.033
162	A	164	ALA	0	-0.056	-0.031	4.624	-3.117	-3.061	-0.001	-0.003	-0.052	0.000
6	A	8	GLN	0	0.008	0.024	6.119	4.499	4.499	0.000	0.000	0.000	0.000
7	A	9	HIS	0	0.042	0.005	6.632	4.468	4.468	0.000	0.000	0.000	0.000
8	A	10	VAL	0	0.019	0.006	7.584	2.933	2.933	0.000	0.000	0.000	0.000
9	A	11	ARG	1	0.925	0.979	9.810	30.590	30.590	0.000	0.000	0.000	0.000
10	A	12	ALA	0	0.004	0.000	11.654	1.999	1.999	0.000	0.000	0.000	0.000
11	A	13	LEU	0	-0.002	0.004	11.150	1.420	1.420	0.000	0.000	0.000	0.000
12	A	14	ALA	0	0.038	0.030	13.891	1.526	1.526	0.000	0.000	0.000	0.000
13	A	15	ILE	0	-0.004	-0.008	15.767	1.157	1.157	0.000	0.000	0.000	0.000
14	A	16	SER	0	-0.075	-0.042	17.335	1.143	1.143	0.000	0.000	0.000	0.000
15	A	17	ALA	0	0.006	0.001	18.454	0.953	0.953	0.000	0.000	0.000	0.000
16	A	18	LEU	0	-0.039	-0.024	18.885	0.714	0.714	0.000	0.000	0.000	0.000
17	A	19	ALA	0	-0.021	-0.002	21.908	0.733	0.733	0.000	0.000	0.000	0.000
18	A	20	PRO	0	0.009	0.009	22.389	0.589	0.589	0.000	0.000	0.000	0.000
19	A	21	LYS	1	0.859	0.925	25.299	10.797	10.797	0.000	0.000	0.000	0.000
20	A	22	PRO	0	0.021	-0.004	28.982	-0.072	-0.072	0.000	0.000	0.000	0.000
21	A	23	HIS	0	-0.038	-0.033	31.591	0.334	0.334	0.000	0.000	0.000	0.000
22	A	24	GLU	-1	-0.775	-0.823	28.332	-11.116	-11.116	0.000	0.000	0.000	0.000
23	A	25	THR	0	-0.003	-0.013	28.623	-0.326	-0.326	0.000	0.000	0.000	0.000
24	A	26	LEU	0	-0.030	-0.006	20.822	-0.070	-0.070	0.000	0.000	0.000	0.000
25	A	27	TRP	0	0.025	0.003	25.072	0.058	0.058	0.000	0.000	0.000	0.000
26	A	28	ASP	-1	-0.809	-0.917	18.753	-17.786	-17.786	0.000	0.000	0.000	0.000
27	A	29	ILE	0	0.033	0.003	20.617	0.245	0.245	0.000	0.000	0.000	0.000
28	A	30	GLY	0	0.030	0.012	19.318	-0.593	-0.593	0.000	0.000	0.000	0.000
29	A	31	GLY	0	-0.029	-0.031	15.471	-0.282	-0.282	0.000	0.000	0.000	0.000
30	A	32	GLY	0	-0.022	-0.017	13.866	-1.009	-1.009	0.000	0.000	0.000	0.000
31	A	33	SER	0	-0.004	0.026	14.846	-0.215	-0.215	0.000	0.000	0.000	0.000
32	A	34	GLY	0	0.083	0.014	18.145	0.087	0.087	0.000	0.000	0.000	0.000
33	A	35	SER	0	-0.114	-0.068	13.135	-0.771	-0.771	0.000	0.000	0.000	0.000
34	A	36	ILE	0	-0.043	-0.015	14.086	-0.827	-0.827	0.000	0.000	0.000	0.000
35	A	37	ALA	0	0.037	0.012	16.963	0.505	0.505	0.000	0.000	0.000	0.000
36	A	38	ILE	0	0.033	0.013	18.576	0.515	0.515	0.000	0.000	0.000	0.000
37	A	39	GLU	-1	-0.838	-0.892	16.041	-18.446	-18.446	0.000	0.000	0.000	0.000
38	A	40	TRP	0	0.018	0.006	18.659	0.288	0.288	0.000	0.000	0.000	0.000
39	A	41	LEU	0	-0.045	-0.007	21.303	0.537	0.537	0.000	0.000	0.000	0.000
40	A	42	ARG	1	0.801	0.873	17.214	17.546	17.546	0.000	0.000	0.000	0.000
41	A	43	SER	0	-0.066	-0.031	20.117	-0.014	-0.014	0.000	0.000	0.000	0.000
42	A	44	THR	0	-0.018	-0.001	22.144	0.496	0.496	0.000	0.000	0.000	0.000
43	A	45	PRO	0	0.019	0.008	25.555	0.033	0.033	0.000	0.000	0.000	0.000
44	A	46	GLN	0	-0.010	-0.018	28.837	0.056	0.056	0.000	0.000	0.000	0.000
45	A	47	THR	0	0.044	0.046	26.278	0.134	0.134	0.000	0.000	0.000	0.000
46	A	48	THR	0	0.036	0.018	28.440	-0.048	-0.048	0.000	0.000	0.000	0.000
47	A	49	ALA	0	0.011	0.001	23.859	-0.355	-0.355	0.000	0.000	0.000	0.000
48	A	50	VAL	0	0.012	0.018	25.672	0.195	0.195	0.000	0.000	0.000	0.000
49	A	51	CYS	0	-0.024	0.003	21.363	-0.511	-0.511	0.000	0.000	0.000	0.000
50	A	52	PHE	0	0.002	-0.005	22.715	0.537	0.537	0.000	0.000	0.000	0.000
51	A	53	GLU	-1	-0.837	-0.916	19.740	-16.364	-16.364	0.000	0.000	0.000	0.000
52	A	54	ILE	0	0.003	-0.003	22.276	0.721	0.721	0.000	0.000	0.000	0.000
53	A	55	SER	0	-0.048	-0.024	21.873	0.407	0.407	0.000	0.000	0.000	0.000
54	A	56	GLU	-1	-0.878	-0.942	24.007	-10.953	-10.953	0.000	0.000	0.000	0.000
55	A	57	GLU	-1	-0.818	-0.923	22.333	-12.473	-12.473	0.000	0.000	0.000	0.000
56	A	58	ARG	1	0.832	0.924	14.811	17.974	17.974	0.000	0.000	0.000	0.000
57	A	59	ARG	1	0.880	0.931	21.220	11.460	11.460	0.000	0.000	0.000	0.000
58	A	60	GLU	-1	-0.883	-0.930	24.009	-11.669	-11.669	0.000	0.000	0.000	0.000
59	A	61	ARG	1	0.868	0.928	17.038	16.991	16.991	0.000	0.000	0.000	0.000
60	A	62	ILE	0	-0.034	-0.016	19.213	-0.457	-0.457	0.000	0.000	0.000	0.000
61	A	63	LEU	0	0.058	0.025	20.941	-0.117	-0.117	0.000	0.000	0.000	0.000
62	A	64	SER	0	-0.014	0.006	22.491	0.010	0.010	0.000	0.000	0.000	0.000
63	A	65	ASN	0	-0.010	-0.026	16.557	0.333	0.333	0.000	0.000	0.000	0.000
64	A	66	ALA	0	0.022	0.019	20.710	-0.154	-0.154	0.000	0.000	0.000	0.000
65	A	67	ILE	0	0.023	0.010	23.083	0.302	0.302	0.000	0.000	0.000	0.000
66	A	68	ASN	0	-0.062	-0.031	21.551	0.698	0.698	0.000	0.000	0.000	0.000
67	A	69	LEU	0	-0.052	-0.025	18.316	-0.508	-0.508	0.000	0.000	0.000	0.000
68	A	70	GLY	0	-0.013	0.005	22.980	0.099	0.099	0.000	0.000	0.000	0.000
69	A	71	VAL	0	-0.009	-0.020	23.028	0.193	0.193	0.000	0.000	0.000	0.000
70	A	72	SER	0	-0.032	-0.015	26.224	-0.125	-0.125	0.000	0.000	0.000	0.000
71	A	73	ASP	-1	-0.916	-0.954	27.799	-10.516	-10.516	0.000	0.000	0.000	0.000
72	A	74	ARG	1	0.802	0.899	26.477	12.142	12.142	0.000	0.000	0.000	0.000
73	A	75	ILE	0	-0.018	-0.012	22.803	-0.340	-0.340	0.000	0.000	0.000	0.000
74	A	76	ALA	0	0.032	0.025	27.312	0.359	0.359	0.000	0.000	0.000	0.000
75	A	77	VAL	0	-0.050	-0.032	23.916	-0.457	-0.457	0.000	0.000	0.000	0.000
76	A	78	GLN	0	0.077	0.048	26.427	0.353	0.353	0.000	0.000	0.000	0.000
77	A	79	GLN	0	0.001	-0.006	26.228	-0.601	-0.601	0.000	0.000	0.000	0.000
78	A	80	GLY	0	0.010	0.002	25.405	-0.223	-0.223	0.000	0.000	0.000	0.000
79	A	81	ALA	0	0.013	0.026	25.530	0.502	0.502	0.000	0.000	0.000	0.000
80	A	82	PRO	0	-0.025	-0.039	26.853	-0.222	-0.222	0.000	0.000	0.000	0.000
81	A	83	ARG	1	0.983	0.986	29.477	9.846	9.846	0.000	0.000	0.000	0.000
82	A	84	ALA	0	0.025	0.023	28.813	0.271	0.271	0.000	0.000	0.000	0.000
83	A	85	PHE	0	0.002	-0.015	26.371	-0.019	-0.019	0.000	0.000	0.000	0.000
84	A	86	ASP	-1	-0.932	-0.975	31.535	-9.021	-9.021	0.000	0.000	0.000	0.000
85	A	87	ASP	-1	-0.928	-0.952	34.079	-8.665	-8.665	0.000	0.000	0.000	0.000
86	A	88	VAL	0	-0.054	-0.011	30.387	-0.132	-0.132	0.000	0.000	0.000	0.000
87	A	89	PRO	0	0.021	0.011	33.812	0.024	0.024	0.000	0.000	0.000	0.000
88	A	90	ASP	-1	-0.884	-0.927	34.433	-8.749	-8.749	0.000	0.000	0.000	0.000
89	A	91	ASN	0	-0.016	-0.011	33.403	-0.303	-0.303	0.000	0.000	0.000	0.000
90	A	92	PRO	0	-0.041	0.000	28.464	0.001	0.001	0.000	0.000	0.000	0.000
91	A	93	ASP	-1	-0.780	-0.893	29.643	-9.932	-9.932	0.000	0.000	0.000	0.000
92	A	94	VAL	0	-0.053	-0.033	24.034	-0.084	-0.084	0.000	0.000	0.000	0.000
93	A	95	ILE	0	0.009	0.007	23.448	-0.093	-0.093	0.000	0.000	0.000	0.000
94	A	96	PHE	0	0.023	0.003	14.861	-0.615	-0.615	0.000	0.000	0.000	0.000
95	A	97	ILE	0	-0.007	0.001	19.355	0.291	0.291	0.000	0.000	0.000	0.000
96	A	98	GLY	0	0.070	0.039	15.382	-0.701	-0.701	0.000	0.000	0.000	0.000
97	A	99	GLY	0	-0.024	-0.013	15.084	0.238	0.238	0.000	0.000	0.000	0.000
98	A	100	GLY	0	-0.015	-0.037	15.702	0.493	0.493	0.000	0.000	0.000	0.000
99	A	101	LEU	0	-0.005	0.021	19.054	0.759	0.759	0.000	0.000	0.000	0.000
100	A	102	THR	0	-0.028	-0.017	20.421	0.801	0.801	0.000	0.000	0.000	0.000
101	A	103	ALA	0	0.041	0.030	22.435	0.036	0.036	0.000	0.000	0.000	0.000
102	A	104	PRO	0	0.006	-0.017	24.397	0.287	0.287	0.000	0.000	0.000	0.000
103	A	105	GLY	0	0.031	0.021	28.285	0.078	0.078	0.000	0.000	0.000	0.000
104	A	106	VAL	0	-0.018	-0.001	23.896	0.201	0.201	0.000	0.000	0.000	0.000
105	A	107	PHE	0	0.090	0.038	25.104	0.079	0.079	0.000	0.000	0.000	0.000
106	A	108	ALA	0	0.024	0.008	26.903	0.201	0.201	0.000	0.000	0.000	0.000
107	A	109	ALA	0	-0.024	-0.013	30.082	0.301	0.301	0.000	0.000	0.000	0.000
108	A	110	ALA	0	0.059	0.020	26.939	0.198	0.198	0.000	0.000	0.000	0.000
109	A	111	TRP	0	0.017	-0.002	28.363	0.117	0.117	0.000	0.000	0.000	0.000
110	A	112	LYS	1	0.836	0.926	30.588	9.598	9.598	0.000	0.000	0.000	0.000
111	A	113	ARG	1	0.768	0.876	31.321	9.643	9.643	0.000	0.000	0.000	0.000
112	A	114	LEU	0	-0.014	0.019	28.439	0.097	0.097	0.000	0.000	0.000	0.000
113	A	115	PRO	0	0.019	0.017	31.915	0.265	0.265	0.000	0.000	0.000	0.000
114	A	116	VAL	0	0.020	0.003	33.592	-0.233	-0.233	0.000	0.000	0.000	0.000
115	A	117	GLY	0	-0.015	-0.008	33.771	0.097	0.097	0.000	0.000	0.000	0.000
116	A	118	GLY	0	-0.001	0.015	31.139	-0.174	-0.174	0.000	0.000	0.000	0.000
117	A	119	ARG	1	0.797	0.875	25.703	11.546	11.546	0.000	0.000	0.000	0.000
118	A	120	LEU	0	-0.024	-0.009	22.945	-0.079	-0.079	0.000	0.000	0.000	0.000
119	A	121	VAL	0	-0.013	-0.003	18.570	-0.100	-0.100	0.000	0.000	0.000	0.000
120	A	122	ALA	0	0.000	-0.002	18.913	-0.146	-0.146	0.000	0.000	0.000	0.000
121	A	123	ASN	0	0.008	0.005	12.403	0.476	0.476	0.000	0.000	0.000	0.000
122	A	124	ALA	0	-0.006	0.006	15.405	0.750	0.750	0.000	0.000	0.000	0.000
123	A	125	VAL	0	-0.031	-0.018	10.172	-1.151	-1.151	0.000	0.000	0.000	0.000
124	A	126	THR	0	-0.010	-0.001	13.394	-0.657	-0.657	0.000	0.000	0.000	0.000
125	A	127	VAL	0	0.087	0.046	16.372	0.206	0.206	0.000	0.000	0.000	0.000
126	A	128	GLU	-1	-0.809	-0.906	19.544	-15.082	-15.082	0.000	0.000	0.000	0.000
127	A	129	SER	0	-0.044	-0.033	17.745	0.565	0.565	0.000	0.000	0.000	0.000
128	A	130	GLU	-1	-0.868	-0.938	18.290	-15.547	-15.547	0.000	0.000	0.000	0.000
129	A	131	GLN	0	0.010	-0.007	19.951	0.585	0.585	0.000	0.000	0.000	0.000
130	A	132	MET	0	-0.001	0.016	22.562	0.779	0.779	0.000	0.000	0.000	0.000
131	A	133	LEU	0	-0.004	-0.004	18.386	0.497	0.497	0.000	0.000	0.000	0.000
132	A	134	TRP	0	-0.037	-0.032	22.037	0.911	0.911	0.000	0.000	0.000	0.000
133	A	135	ALA	0	-0.004	-0.007	25.295	0.530	0.530	0.000	0.000	0.000	0.000
134	A	136	LEU	0	-0.005	-0.002	24.605	0.466	0.466	0.000	0.000	0.000	0.000
135	A	137	ARG	1	0.880	0.941	25.386	11.851	11.851	0.000	0.000	0.000	0.000
136	A	138	LYS	1	0.833	0.915	27.863	11.103	11.103	0.000	0.000	0.000	0.000
137	A	139	GLN	0	-0.039	0.002	31.028	0.533	0.533	0.000	0.000	0.000	0.000
138	A	140	PHE	0	0.023	-0.006	29.275	0.222	0.222	0.000	0.000	0.000	0.000
139	A	141	GLY	0	0.054	0.055	30.540	0.003	0.003	0.000	0.000	0.000	0.000
140	A	142	GLY	0	0.068	0.027	27.130	-0.410	-0.410	0.000	0.000	0.000	0.000
141	A	143	THR	0	-0.041	-0.030	23.131	0.377	0.377	0.000	0.000	0.000	0.000
142	A	144	ILE	0	-0.002	0.009	19.778	-0.340	-0.340	0.000	0.000	0.000	0.000
143	A	145	SER	0	-0.004	0.014	17.320	0.614	0.614	0.000	0.000	0.000	0.000
144	A	146	SER	0	-0.014	-0.009	15.480	-0.461	-0.461	0.000	0.000	0.000	0.000
145	A	147	PHE	0	0.021	0.004	11.366	-0.013	-0.013	0.000	0.000	0.000	0.000
146	A	148	ALA	0	0.031	0.017	10.614	-1.982	-1.982	0.000	0.000	0.000	0.000
147	A	149	ILE	0	-0.003	-0.001	5.901	-0.308	-0.308	0.000	0.000	0.000	0.000
148	A	150	SER	0	0.031	0.011	7.120	-2.353	-2.353	0.000	0.000	0.000	0.000
150	A	152	GLU	-1	-0.844	-0.913	6.611	-24.918	-24.918	0.000	0.000	0.000	0.000
151	A	153	HIS	0	-0.031	-0.026	7.384	-7.538	-7.538	0.000	0.000	0.000	0.000
152	A	154	THR	0	0.048	0.022	9.144	1.859	1.859	0.000	0.000	0.000	0.000
153	A	155	VAL	0	-0.030	-0.001	12.336	-0.136	-0.136	0.000	0.000	0.000	0.000
154	A	156	GLY	0	0.021	0.018	14.390	1.314	1.314	0.000	0.000	0.000	0.000
155	A	157	SER	0	-0.010	-0.014	17.260	-0.386	-0.386	0.000	0.000	0.000	0.000
156	A	158	PHE	0	0.009	0.005	17.569	0.493	0.493	0.000	0.000	0.000	0.000
157	A	159	ILE	0	0.007	0.007	12.338	-1.049	-1.049	0.000	0.000	0.000	0.000
158	A	160	THR	0	-0.034	-0.016	11.664	0.501	0.501	0.000	0.000	0.000	0.000
159	A	161	MET	0	0.029	0.008	10.019	-2.353	-2.353	0.000	0.000	0.000	0.000
160	A	162	LYS	1	0.932	0.972	6.963	37.728	37.728	0.000	0.000	0.000	0.000
161	A	163	PRO	0	0.018	0.013	7.058	-5.215	-5.215	0.000	0.000	0.000	0.000
163	A	165	LEU	0	0.018	-0.003	6.646	4.369	4.369	0.000	0.000	0.000	0.000
164	A	166	PRO	0	-0.011	-0.011	8.611	-2.385	-2.385	0.000	0.000	0.000	0.000
165	A	167	VAL	0	-0.036	-0.005	9.092	0.062	0.062	0.000	0.000	0.000	0.000
166	A	168	HIS	0	0.005	-0.002	11.857	0.590	0.590	0.000	0.000	0.000	0.000
167	A	169	GLN	0	-0.029	-0.040	14.688	-0.003	-0.003	0.000	0.000	0.000	0.000
168	A	170	TRP	0	-0.031	-0.011	17.183	0.488	0.488	0.000	0.000	0.000	0.000
169	A	171	THR	0	0.008	0.000	20.822	-0.154	-0.154	0.000	0.000	0.000	0.000
170	A	172	VAL	0	-0.021	-0.012	22.883	0.395	0.395	0.000	0.000	0.000	0.000
171	A	173	VAL	0	-0.003	-0.006	26.596	-0.206	-0.206	0.000	0.000	0.000	0.000
172	A	174	LYS	0	-0.018	0.013	29.702	0.303	0.303	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:GLY)