FMO DATABASE

FMODB ID: LVMQ9

Calculation Name: 1GQA-A-Xray547

Preferred Name:

Target Type:

Ligand Name: heme c

Ligand 3-letter code: HEC

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1GQA

Chain ID: A

ChEMBL ID:

UniProt ID: P00148

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	130
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-942194.263549
FMO2-HF: Nuclear repulsion	894689.16941
FMO2-HF: Total energy	-47505.094139
FMO2-MP2: Total energy	-47642.14719

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:1:ALA)

Summations of interaction energy for fragment #1(A:1: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.
-73.274	-69.945	1.141	-1.884	-2.589	-0.013

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.845 / q_NPA : 0.920

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	3	ALA	0	0.068	0.007	3.043	-7.280	-5.384	0.176	-1.094	-0.979	-0.006
5	A	5	HIS	0	0.029	-0.016	2.561	2.544	3.119	0.604	-0.406	-0.773	-0.003
6	A	6	VAL	0	-0.035	-0.006	2.485	0.240	1.046	0.362	-0.375	-0.794	-0.004
7	A	7	VAL	0	-0.019	-0.008	4.684	6.277	6.329	-0.001	-0.009	-0.043	0.000
4	A	4	GLU	-1	-0.961	-0.960	5.726	-24.118	-24.118	0.000	0.000	0.000	0.000
8	A	8	GLU	-1	-0.965	-0.983	7.438	-24.874	-24.874	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.010	0.008	6.544	3.088	3.088	0.000	0.000	0.000	0.000
10	A	10	ARG	1	0.794	0.865	8.281	31.664	31.664	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.839	0.912	10.290	24.301	24.301	0.000	0.000	0.000	0.000
12	A	12	GLY	0	0.031	0.031	11.565	1.822	1.822	0.000	0.000	0.000	0.000
13	A	13	TYR	0	-0.008	-0.013	12.259	1.483	1.483	0.000	0.000	0.000	0.000
14	A	14	PHE	0	0.002	-0.014	14.030	1.450	1.450	0.000	0.000	0.000	0.000
15	A	15	SER	0	-0.058	-0.034	15.940	1.352	1.352	0.000	0.000	0.000	0.000
16	A	16	LEU	0	-0.002	0.005	15.538	0.993	0.993	0.000	0.000	0.000	0.000
17	A	17	VAL	0	0.018	0.014	18.296	0.911	0.911	0.000	0.000	0.000	0.000
18	A	18	ALA	0	-0.039	-0.024	20.278	0.812	0.812	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.058	-0.016	21.512	0.747	0.747	0.000	0.000	0.000	0.000
20	A	20	GLU	-1	-0.763	-0.873	22.516	-11.570	-11.570	0.000	0.000	0.000	0.000
21	A	21	PHE	0	-0.008	-0.009	24.381	0.618	0.618	0.000	0.000	0.000	0.000
22	A	22	GLY	0	0.017	0.016	26.016	0.481	0.481	0.000	0.000	0.000	0.000
23	A	23	PRO	0	-0.004	-0.015	27.743	0.466	0.466	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.026	0.029	28.658	0.437	0.437	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.016	0.002	29.982	0.361	0.361	0.000	0.000	0.000	0.000
26	A	26	ALA	0	0.005	0.001	31.853	0.316	0.316	0.000	0.000	0.000	0.000
27	A	27	MET	0	-0.039	-0.002	34.060	0.321	0.321	0.000	0.000	0.000	0.000
28	A	28	ALA	0	-0.031	-0.006	34.708	0.302	0.302	0.000	0.000	0.000	0.000
29	A	29	LYS	1	0.779	0.882	32.796	9.453	9.453	0.000	0.000	0.000	0.000
30	A	30	GLY	0	-0.008	0.008	37.946	0.232	0.232	0.000	0.000	0.000	0.000
31	A	31	GLU	-1	-0.860	-0.918	34.606	-8.833	-8.833	0.000	0.000	0.000	0.000
32	A	32	MET	0	-0.038	-0.011	33.907	-0.066	-0.066	0.000	0.000	0.000	0.000
33	A	33	PRO	0	0.003	-0.010	37.587	0.051	0.051	0.000	0.000	0.000	0.000
34	A	34	TYR	0	-0.039	-0.058	37.577	-0.078	-0.078	0.000	0.000	0.000	0.000
35	A	35	ASP	-1	-0.816	-0.913	37.175	-8.163	-8.163	0.000	0.000	0.000	0.000
36	A	36	ALA	0	0.038	0.008	36.742	-0.246	-0.246	0.000	0.000	0.000	0.000
37	A	37	ALA	0	-0.030	-0.010	36.466	-0.163	-0.163	0.000	0.000	0.000	0.000
38	A	38	ALA	0	0.020	0.004	33.293	-0.298	-0.298	0.000	0.000	0.000	0.000
39	A	39	ALA	0	-0.012	-0.012	32.019	-0.370	-0.370	0.000	0.000	0.000	0.000
40	A	40	LYS	1	0.947	0.988	31.768	8.032	8.032	0.000	0.000	0.000	0.000
41	A	41	ALA	0	0.006	0.018	30.137	-0.269	-0.269	0.000	0.000	0.000	0.000
42	A	42	HIS	1	0.877	0.906	26.796	10.675	10.675	0.000	0.000	0.000	0.000
43	A	43	ALA	0	-0.009	0.010	26.827	-0.414	-0.414	0.000	0.000	0.000	0.000
44	A	44	SER	0	0.000	0.008	27.265	-0.338	-0.338	0.000	0.000	0.000	0.000
45	A	45	ASP	-1	-0.886	-0.931	23.714	-13.215	-13.215	0.000	0.000	0.000	0.000
46	A	46	LEU	0	-0.032	-0.022	22.268	-0.720	-0.720	0.000	0.000	0.000	0.000
47	A	47	VAL	0	0.033	0.005	22.792	-0.575	-0.575	0.000	0.000	0.000	0.000
48	A	48	THR	0	-0.049	-0.024	20.293	-0.430	-0.430	0.000	0.000	0.000	0.000
49	A	49	LEU	0	-0.025	-0.018	17.509	-0.885	-0.885	0.000	0.000	0.000	0.000
50	A	50	THR	0	-0.079	-0.040	18.299	-0.733	-0.733	0.000	0.000	0.000	0.000
51	A	51	LYS	1	0.913	0.961	20.501	12.651	12.651	0.000	0.000	0.000	0.000
52	A	52	TYR	0	-0.039	0.001	9.967	-0.161	-0.161	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.795	-0.874	13.299	-22.268	-22.268	0.000	0.000	0.000	0.000
54	A	54	PRO	0	-0.007	-0.013	12.246	-1.849	-1.849	0.000	0.000	0.000	0.000
55	A	55	SER	0	-0.012	-0.030	10.740	-1.519	-1.519	0.000	0.000	0.000	0.000
56	A	56	ASP	-1	-0.914	-0.955	5.699	-42.869	-42.869	0.000	0.000	0.000	0.000
57	A	57	LEU	0	-0.087	-0.042	5.895	-5.559	-5.559	0.000	0.000	0.000	0.000
58	A	58	TYR	0	-0.009	-0.015	8.346	1.637	1.637	0.000	0.000	0.000	0.000
59	A	59	ALA	0	0.071	0.056	4.904	1.541	1.541	0.000	0.000	0.000	0.000
60	A	60	PRO	0	0.011	0.010	6.891	2.163	2.163	0.000	0.000	0.000	0.000
61	A	61	GLY	0	0.023	0.016	8.078	-3.355	-3.355	0.000	0.000	0.000	0.000
62	A	62	THR	0	-0.030	-0.020	6.238	-0.593	-0.593	0.000	0.000	0.000	0.000
63	A	63	SER	0	-0.013	-0.021	9.606	1.470	1.470	0.000	0.000	0.000	0.000
64	A	64	ALA	0	-0.050	-0.049	13.318	-0.267	-0.267	0.000	0.000	0.000	0.000
65	A	65	ASP	-1	-0.933	-0.961	15.906	-15.734	-15.734	0.000	0.000	0.000	0.000
66	A	66	ASP	-1	-0.882	-0.895	12.449	-23.085	-23.085	0.000	0.000	0.000	0.000
67	A	67	VAL	0	-0.009	-0.004	9.893	-0.270	-0.270	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.957	0.962	13.078	17.574	17.574	0.000	0.000	0.000	0.000
69	A	69	GLY	0	0.033	0.023	12.835	-1.207	-1.207	0.000	0.000	0.000	0.000
70	A	70	THR	0	0.025	0.027	11.865	-0.181	-0.181	0.000	0.000	0.000	0.000
71	A	71	ALA	0	0.006	-0.007	13.864	1.072	1.072	0.000	0.000	0.000	0.000
72	A	72	ALA	0	0.018	0.022	13.654	1.069	1.069	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.869	0.926	15.698	13.029	13.029	0.000	0.000	0.000	0.000
74	A	74	ALA	0	0.092	0.041	16.035	-0.618	-0.618	0.000	0.000	0.000	0.000
75	A	75	ALA	0	-0.009	-0.013	17.113	-0.156	-0.156	0.000	0.000	0.000	0.000
76	A	76	ILE	0	-0.024	-0.001	14.697	0.433	0.433	0.000	0.000	0.000	0.000
77	A	77	TRP	0	-0.049	-0.039	10.270	0.676	0.676	0.000	0.000	0.000	0.000
78	A	78	GLN	0	-0.059	-0.022	16.007	0.564	0.564	0.000	0.000	0.000	0.000
79	A	79	ASP	-1	-0.853	-0.927	19.751	-12.789	-12.789	0.000	0.000	0.000	0.000
80	A	80	ALA	0	0.033	0.016	17.672	-0.135	-0.135	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.890	-0.941	19.087	-13.851	-13.851	0.000	0.000	0.000	0.000
82	A	82	GLY	0	-0.001	0.000	22.409	0.301	0.301	0.000	0.000	0.000	0.000
83	A	83	PHE	0	-0.051	-0.036	15.591	0.174	0.174	0.000	0.000	0.000	0.000
84	A	84	GLN	0	0.049	0.015	18.759	-0.391	-0.391	0.000	0.000	0.000	0.000
85	A	85	ALA	0	-0.013	0.007	20.973	0.363	0.363	0.000	0.000	0.000	0.000
86	A	86	LYS	1	0.747	0.859	22.168	12.471	12.471	0.000	0.000	0.000	0.000
87	A	87	GLY	0	0.021	0.009	20.644	0.195	0.195	0.000	0.000	0.000	0.000
88	A	88	MET	0	-0.027	-0.005	21.549	0.026	0.026	0.000	0.000	0.000	0.000
89	A	89	ALA	0	0.037	0.017	24.341	0.363	0.363	0.000	0.000	0.000	0.000
90	A	90	PHE	0	-0.018	-0.020	20.371	0.383	0.383	0.000	0.000	0.000	0.000
91	A	91	PHE	0	0.011	0.010	22.466	0.343	0.343	0.000	0.000	0.000	0.000
92	A	92	GLU	-1	-0.917	-0.969	24.754	-10.466	-10.466	0.000	0.000	0.000	0.000
93	A	93	ALA	0	-0.060	-0.029	28.047	0.417	0.417	0.000	0.000	0.000	0.000
94	A	94	VAL	0	-0.008	-0.010	24.502	0.387	0.387	0.000	0.000	0.000	0.000
95	A	95	ALA	0	-0.005	0.004	27.582	0.242	0.242	0.000	0.000	0.000	0.000
96	A	96	ALA	0	-0.044	-0.018	29.355	0.356	0.356	0.000	0.000	0.000	0.000
97	A	97	LEU	0	-0.042	-0.020	28.582	0.368	0.368	0.000	0.000	0.000	0.000
98	A	98	GLU	-1	-0.859	-0.945	29.750	-10.387	-10.387	0.000	0.000	0.000	0.000
99	A	99	PRO	0	-0.042	-0.016	32.505	0.265	0.265	0.000	0.000	0.000	0.000
100	A	100	ALA	0	0.036	0.016	35.244	0.226	0.226	0.000	0.000	0.000	0.000
101	A	101	ALA	0	0.002	-0.002	33.402	0.221	0.221	0.000	0.000	0.000	0.000
102	A	102	GLY	0	-0.049	-0.043	35.565	0.121	0.121	0.000	0.000	0.000	0.000
103	A	103	ALA	0	0.004	0.027	38.528	0.198	0.198	0.000	0.000	0.000	0.000
104	A	104	GLY	0	0.043	0.016	40.228	0.242	0.242	0.000	0.000	0.000	0.000
105	A	105	GLN	0	-0.066	-0.035	39.531	0.050	0.050	0.000	0.000	0.000	0.000
106	A	106	LYS	1	0.941	0.968	39.690	7.005	7.005	0.000	0.000	0.000	0.000
107	A	107	GLU	-1	-0.882	-0.940	39.736	-7.661	-7.661	0.000	0.000	0.000	0.000
108	A	108	LEU	0	0.003	0.013	33.557	-0.214	-0.214	0.000	0.000	0.000	0.000
109	A	109	ALA	0	0.023	-0.006	35.306	-0.270	-0.270	0.000	0.000	0.000	0.000
110	A	110	ALA	0	-0.031	-0.005	36.125	-0.166	-0.166	0.000	0.000	0.000	0.000
111	A	111	ALA	0	0.021	0.009	33.440	-0.159	-0.159	0.000	0.000	0.000	0.000
112	A	112	VAL	0	0.013	0.006	31.209	-0.322	-0.322	0.000	0.000	0.000	0.000
113	A	113	GLY	0	-0.001	0.002	31.451	-0.268	-0.268	0.000	0.000	0.000	0.000
114	A	114	LYS	1	0.897	0.951	32.426	8.654	8.654	0.000	0.000	0.000	0.000
115	A	115	VAL	0	0.087	0.056	26.496	-0.243	-0.243	0.000	0.000	0.000	0.000
116	A	116	GLY	0	0.038	0.030	27.526	-0.444	-0.444	0.000	0.000	0.000	0.000
117	A	117	GLY	0	-0.014	-0.006	28.500	-0.189	-0.189	0.000	0.000	0.000	0.000
118	A	118	THR	0	-0.038	-0.036	26.184	-0.237	-0.237	0.000	0.000	0.000	0.000
119	A	119	CYS	0	-0.033	-0.017	23.970	-0.543	-0.543	0.000	0.000	0.000	0.000
120	A	120	LYS	1	0.820	0.895	24.414	10.260	10.260	0.000	0.000	0.000	0.000
121	A	121	SER	0	0.027	0.011	26.398	-0.253	-0.253	0.000	0.000	0.000	0.000
122	A	122	CYS	0	0.030	0.033	20.323	-0.275	-0.275	0.000	0.000	0.000	0.000
123	A	123	HIS	0	-0.011	-0.022	20.998	-0.043	-0.043	0.000	0.000	0.000	0.000
124	A	124	ASP	-1	-0.829	-0.898	23.181	-11.044	-11.044	0.000	0.000	0.000	0.000
125	A	125	ASP	-1	-0.826	-0.907	24.337	-11.774	-11.774	0.000	0.000	0.000	0.000
126	A	126	PHE	0	0.032	0.017	19.159	-0.276	-0.276	0.000	0.000	0.000	0.000
127	A	127	ARG	1	0.897	0.971	18.586	13.138	13.138	0.000	0.000	0.000	0.000
128	A	128	VAL	0	-0.036	-0.015	19.358	0.790	0.790	0.000	0.000	0.000	0.000
129	A	129	LYS	1	0.870	0.922	21.654	11.540	11.540	0.000	0.000	0.000	0.000
130	A	130	ARG	0	0.075	0.056	24.056	0.048	0.048	0.000	0.000	0.000	0.000

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