FMO DATABASE

FMODB ID: 2466R

Calculation Name: 2DN3-B-Xray547

Preferred Name: Hemoglobin alpha subunit

Target Type: SINGLE PROTEIN

Ligand Name: protoporphyrin ix containing fe | carbon monoxide

Ligand 3-letter code: HEM | CMO

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2DN3

Chain ID: B

ChEMBL ID: CHEMBL2887

UniProt ID: P69905

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	146
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1291917.179074
FMO2-HF: Nuclear repulsion	1236987.890688
FMO2-HF: Total energy	-54929.288386
FMO2-MP2: Total energy	-55092.046169

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:VAL)

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

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.
5.806	14.915	4.084	-4.26	-8.93	-0.04

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.828 / q_NPA : 0.912

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	LEU	0	-0.003	0.022	2.564	5.414	8.074	0.481	-1.011	-2.129	-0.005
4	A	4	THR	0	0.041	-0.006	5.177	0.762	0.797	-0.001	-0.003	-0.030	0.000
78	A	78	LEU	0	0.039	0.021	3.780	-3.802	-3.448	0.008	-0.057	-0.306	0.000
79	A	79	ASP	-1	-0.877	-0.940	3.129	-58.212	-57.041	0.091	-0.643	-0.618	-0.006
80	A	80	ASN	0	-0.037	-0.023	5.355	-1.029	-0.968	-0.001	-0.001	-0.059	0.000
81	A	81	LEU	0	0.024	0.039	2.880	3.500	4.035	0.421	-0.160	-0.795	-0.001
132	A	132	LYS	1	0.809	0.885	2.399	33.630	34.317	0.683	-0.246	-1.124	-0.001
133	A	133	VAL	0	-0.003	0.004	2.482	-13.181	-10.836	1.528	-1.658	-2.215	-0.024
134	A	134	VAL	0	-0.025	-0.004	4.329	-2.312	-2.167	-0.001	-0.014	-0.130	0.000
135	A	135	ALA	0	0.019	0.019	3.696	1.176	1.318	0.001	-0.029	-0.114	0.000
136	A	136	GLY	0	-0.030	-0.021	2.458	-3.312	-2.240	0.830	-0.776	-1.126	-0.002
137	A	137	VAL	0	-0.015	-0.007	3.397	2.489	2.391	0.044	0.338	-0.284	-0.001
5	A	5	PRO	0	0.035	-0.003	8.847	-0.441	-0.441	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-0.899	-0.939	11.202	-18.476	-18.476	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.777	-0.848	7.661	-31.762	-31.762	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.858	0.925	5.786	38.512	38.512	0.000	0.000	0.000	0.000
9	A	9	SER	0	0.000	0.025	9.046	1.291	1.291	0.000	0.000	0.000	0.000
10	A	10	ALA	0	0.014	0.003	12.247	0.784	0.784	0.000	0.000	0.000	0.000
11	A	11	VAL	0	-0.006	-0.004	8.063	0.752	0.752	0.000	0.000	0.000	0.000
12	A	12	THR	0	-0.019	-0.026	10.694	1.537	1.537	0.000	0.000	0.000	0.000
13	A	13	ALA	0	0.006	0.006	12.999	1.072	1.072	0.000	0.000	0.000	0.000
14	A	14	LEU	0	-0.024	-0.006	14.635	0.885	0.885	0.000	0.000	0.000	0.000
15	A	15	TRP	0	0.031	-0.012	12.636	0.301	0.301	0.000	0.000	0.000	0.000
16	A	16	GLY	0	-0.021	-0.007	15.160	0.569	0.569	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.807	0.901	18.292	14.469	14.469	0.000	0.000	0.000	0.000
18	A	18	VAL	0	-0.038	-0.010	15.724	0.540	0.540	0.000	0.000	0.000	0.000
19	A	19	ASN	0	0.021	0.012	19.029	-0.082	-0.082	0.000	0.000	0.000	0.000
20	A	20	VAL	0	0.041	-0.003	17.785	-0.122	-0.122	0.000	0.000	0.000	0.000
21	A	21	ASP	-1	-0.872	-0.912	20.186	-11.912	-11.912	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.945	-0.980	22.335	-10.647	-10.647	0.000	0.000	0.000	0.000
23	A	23	VAL	0	-0.009	-0.006	16.985	-0.008	-0.008	0.000	0.000	0.000	0.000
24	A	24	GLY	0	0.041	0.018	17.887	-0.413	-0.413	0.000	0.000	0.000	0.000
25	A	25	GLY	0	-0.022	0.001	18.853	-0.035	-0.035	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.817	-0.891	21.074	-11.685	-11.685	0.000	0.000	0.000	0.000
27	A	27	ALA	0	0.002	-0.010	16.998	0.090	0.090	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.032	-0.012	19.115	-0.095	-0.095	0.000	0.000	0.000	0.000
29	A	29	GLY	0	0.062	0.007	20.669	0.264	0.264	0.000	0.000	0.000	0.000
30	A	30	ARG	1	0.867	0.895	20.984	12.451	12.451	0.000	0.000	0.000	0.000
31	A	31	LEU	0	-0.035	-0.009	17.632	0.056	0.056	0.000	0.000	0.000	0.000
32	A	32	LEU	0	0.001	0.007	20.892	0.258	0.258	0.000	0.000	0.000	0.000
33	A	33	VAL	0	0.000	0.010	24.427	0.459	0.459	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.039	-0.020	21.527	0.265	0.265	0.000	0.000	0.000	0.000
35	A	35	TYR	0	0.004	0.005	18.175	-0.069	-0.069	0.000	0.000	0.000	0.000
36	A	36	PRO	0	0.051	0.036	23.088	-0.184	-0.184	0.000	0.000	0.000	0.000
37	A	37	TRP	0	0.011	-0.003	20.848	0.443	0.443	0.000	0.000	0.000	0.000
38	A	38	THR	0	-0.038	-0.038	20.540	0.038	0.038	0.000	0.000	0.000	0.000
39	A	39	GLN	0	0.000	-0.023	23.674	0.120	0.120	0.000	0.000	0.000	0.000
40	A	40	ARG	1	0.897	0.964	26.227	11.377	11.377	0.000	0.000	0.000	0.000
41	A	41	PHE	0	-0.036	-0.011	23.112	0.065	0.065	0.000	0.000	0.000	0.000
42	A	42	PHE	0	-0.005	-0.005	21.403	-0.339	-0.339	0.000	0.000	0.000	0.000
43	A	43	GLU	-1	-0.808	-0.900	27.489	-9.943	-9.943	0.000	0.000	0.000	0.000
44	A	44	SER	0	-0.035	-0.010	29.683	0.255	0.255	0.000	0.000	0.000	0.000
45	A	45	PHE	0	-0.045	-0.053	25.170	0.088	0.088	0.000	0.000	0.000	0.000
46	A	46	GLY	0	-0.014	0.007	30.764	0.151	0.151	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.829	-0.894	33.631	-8.569	-8.569	0.000	0.000	0.000	0.000
48	A	48	LEU	0	0.007	-0.009	28.358	-0.314	-0.314	0.000	0.000	0.000	0.000
49	A	49	SER	0	-0.051	-0.045	31.585	-0.102	-0.102	0.000	0.000	0.000	0.000
50	A	50	THR	0	0.026	0.012	33.503	0.073	0.073	0.000	0.000	0.000	0.000
51	A	51	PRO	0	0.029	-0.002	29.755	-0.186	-0.186	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.873	-0.931	30.430	-8.999	-8.999	0.000	0.000	0.000	0.000
53	A	53	ALA	0	-0.026	0.005	32.465	-0.078	-0.078	0.000	0.000	0.000	0.000
54	A	54	VAL	0	-0.041	-0.010	26.785	-0.186	-0.186	0.000	0.000	0.000	0.000
55	A	55	MET	0	-0.067	-0.028	24.289	-0.410	-0.410	0.000	0.000	0.000	0.000
56	A	56	GLY	0	0.001	0.017	28.354	-0.110	-0.110	0.000	0.000	0.000	0.000
57	A	57	ASN	0	-0.028	-0.016	29.323	0.050	0.050	0.000	0.000	0.000	0.000
58	A	58	PRO	0	0.022	0.001	28.754	-0.398	-0.398	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.862	0.939	28.223	9.051	9.051	0.000	0.000	0.000	0.000
60	A	60	VAL	0	0.039	0.035	24.253	-0.494	-0.494	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.983	0.988	23.846	10.064	10.064	0.000	0.000	0.000	0.000
62	A	62	ALA	0	-0.016	-0.011	23.768	-0.472	-0.472	0.000	0.000	0.000	0.000
63	A	63	HIS	0	-0.005	-0.014	21.149	-0.031	-0.031	0.000	0.000	0.000	0.000
64	A	64	GLY	0	0.083	0.030	19.851	-0.676	-0.676	0.000	0.000	0.000	0.000
65	A	65	LYS	1	0.856	0.927	18.775	11.249	11.249	0.000	0.000	0.000	0.000
66	A	66	LYS	1	0.901	0.961	18.910	11.748	11.748	0.000	0.000	0.000	0.000
67	A	67	VAL	0	0.012	0.015	14.917	-0.857	-0.857	0.000	0.000	0.000	0.000
68	A	68	LEU	0	0.025	0.013	14.344	-1.295	-1.295	0.000	0.000	0.000	0.000
69	A	69	GLY	0	0.022	0.023	14.542	-0.731	-0.731	0.000	0.000	0.000	0.000
70	A	70	ALA	0	0.025	0.012	13.087	-0.750	-0.750	0.000	0.000	0.000	0.000
71	A	71	PHE	0	0.011	-0.007	8.744	-1.906	-1.906	0.000	0.000	0.000	0.000
72	A	72	SER	0	-0.030	-0.019	10.012	-1.450	-1.450	0.000	0.000	0.000	0.000
73	A	73	ASP	-1	-0.851	-0.933	11.899	-22.056	-22.056	0.000	0.000	0.000	0.000
74	A	74	GLY	0	-0.002	-0.011	8.108	-1.423	-1.423	0.000	0.000	0.000	0.000
75	A	75	LEU	0	-0.045	-0.028	7.187	-3.589	-3.589	0.000	0.000	0.000	0.000
76	A	76	ALA	0	-0.021	0.000	8.613	-0.705	-0.705	0.000	0.000	0.000	0.000
77	A	77	HIS	1	0.825	0.918	8.296	25.104	25.104	0.000	0.000	0.000	0.000
82	A	82	LYS	1	0.975	0.988	6.387	29.951	29.951	0.000	0.000	0.000	0.000
83	A	83	GLY	0	-0.013	-0.007	8.614	2.982	2.982	0.000	0.000	0.000	0.000
84	A	84	THR	0	-0.036	-0.023	9.078	2.268	2.268	0.000	0.000	0.000	0.000
85	A	85	PHE	0	0.019	-0.006	8.275	1.625	1.625	0.000	0.000	0.000	0.000
86	A	86	ALA	0	0.014	0.026	11.847	1.123	1.123	0.000	0.000	0.000	0.000
87	A	87	THR	0	0.049	0.010	14.241	0.400	0.400	0.000	0.000	0.000	0.000
88	A	88	LEU	0	0.009	0.010	13.600	0.966	0.966	0.000	0.000	0.000	0.000
89	A	89	SER	0	0.019	0.011	13.395	0.799	0.799	0.000	0.000	0.000	0.000
90	A	90	GLU	-1	-0.862	-0.924	15.354	-15.199	-15.199	0.000	0.000	0.000	0.000
91	A	91	LEU	0	-0.065	-0.028	18.958	0.862	0.862	0.000	0.000	0.000	0.000
92	A	92	HIS	0	-0.017	-0.038	16.735	1.108	1.108	0.000	0.000	0.000	0.000
93	A	93	CYS	0	-0.032	0.013	16.289	0.284	0.284	0.000	0.000	0.000	0.000
94	A	94	ASP	-1	-0.807	-0.903	19.084	-14.598	-14.598	0.000	0.000	0.000	0.000
95	A	95	LYS	1	0.817	0.911	22.025	12.999	12.999	0.000	0.000	0.000	0.000
96	A	96	LEU	0	-0.004	-0.007	21.056	0.523	0.523	0.000	0.000	0.000	0.000
97	A	97	HIS	1	0.840	0.936	21.655	13.331	13.331	0.000	0.000	0.000	0.000
98	A	98	VAL	0	0.011	0.011	18.434	0.364	0.364	0.000	0.000	0.000	0.000
99	A	99	ASP	-1	-0.828	-0.902	18.125	-16.629	-16.629	0.000	0.000	0.000	0.000
100	A	100	PRO	0	0.070	0.027	13.425	-0.169	-0.169	0.000	0.000	0.000	0.000
101	A	101	GLU	-1	-0.762	-0.837	13.541	-19.654	-19.654	0.000	0.000	0.000	0.000
102	A	102	ASN	0	-0.042	-0.043	14.690	0.262	0.262	0.000	0.000	0.000	0.000
103	A	103	PHE	0	0.018	0.012	11.845	0.166	0.166	0.000	0.000	0.000	0.000
104	A	104	ARG	1	0.825	0.888	9.956	18.215	18.215	0.000	0.000	0.000	0.000
105	A	105	LEU	0	-0.044	-0.010	11.493	-0.051	-0.051	0.000	0.000	0.000	0.000
106	A	106	LEU	0	0.026	0.011	14.214	0.306	0.306	0.000	0.000	0.000	0.000
107	A	107	GLY	0	0.023	0.005	10.362	0.097	0.097	0.000	0.000	0.000	0.000
108	A	108	ASN	0	0.038	0.001	11.115	-1.117	-1.117	0.000	0.000	0.000	0.000
109	A	109	VAL	0	0.000	0.019	12.951	0.835	0.835	0.000	0.000	0.000	0.000
110	A	110	LEU	0	0.008	0.008	11.142	0.730	0.730	0.000	0.000	0.000	0.000
111	A	111	VAL	0	-0.021	-0.011	10.736	0.489	0.489	0.000	0.000	0.000	0.000
112	A	112	CYS	0	-0.041	-0.022	13.686	0.909	0.909	0.000	0.000	0.000	0.000
113	A	113	VAL	0	-0.011	0.000	17.227	0.828	0.828	0.000	0.000	0.000	0.000
114	A	114	LEU	0	-0.027	-0.005	12.767	0.611	0.611	0.000	0.000	0.000	0.000
115	A	115	ALA	0	0.010	-0.002	17.000	0.624	0.624	0.000	0.000	0.000	0.000
116	A	116	HIS	0	-0.015	-0.007	18.556	0.345	0.345	0.000	0.000	0.000	0.000
117	A	117	HIS	1	0.855	0.919	20.278	13.236	13.236	0.000	0.000	0.000	0.000
118	A	118	PHE	0	0.046	0.031	17.647	0.241	0.241	0.000	0.000	0.000	0.000
119	A	119	GLY	0	0.038	0.030	21.188	0.289	0.289	0.000	0.000	0.000	0.000
120	A	120	LYS	1	0.920	0.951	21.039	11.236	11.236	0.000	0.000	0.000	0.000
121	A	121	GLU	-1	-0.795	-0.893	19.666	-13.710	-13.710	0.000	0.000	0.000	0.000
122	A	122	PHE	0	-0.015	0.006	12.922	-0.970	-0.970	0.000	0.000	0.000	0.000
123	A	123	THR	0	-0.013	-0.012	17.098	-0.147	-0.147	0.000	0.000	0.000	0.000
124	A	124	PRO	0	0.065	0.019	15.298	-0.888	-0.888	0.000	0.000	0.000	0.000
125	A	125	PRO	0	0.020	0.005	12.636	-1.104	-1.104	0.000	0.000	0.000	0.000
126	A	126	VAL	0	0.026	0.027	11.307	-1.854	-1.854	0.000	0.000	0.000	0.000
127	A	127	GLN	0	-0.013	0.001	11.268	-0.800	-0.800	0.000	0.000	0.000	0.000
128	A	128	ALA	0	-0.009	-0.008	9.317	-1.658	-1.658	0.000	0.000	0.000	0.000
129	A	129	ALA	0	0.018	0.012	6.970	-3.288	-3.288	0.000	0.000	0.000	0.000
130	A	130	TYR	0	0.046	-0.003	6.435	-4.078	-4.078	0.000	0.000	0.000	0.000
131	A	131	GLN	0	-0.033	-0.020	7.165	0.057	0.057	0.000	0.000	0.000	0.000
138	A	138	ALA	0	-0.001	0.004	6.354	2.233	2.233	0.000	0.000	0.000	0.000
139	A	139	ASN	0	0.006	-0.002	5.148	5.944	5.944	0.000	0.000	0.000	0.000
140	A	140	ALA	0	-0.036	-0.010	6.532	1.714	1.714	0.000	0.000	0.000	0.000
141	A	141	LEU	0	-0.015	-0.010	8.070	2.697	2.697	0.000	0.000	0.000	0.000
142	A	142	ALA	0	0.013	0.014	10.414	2.441	2.441	0.000	0.000	0.000	0.000
143	A	143	HIS	0	0.029	0.019	10.386	-0.783	-0.783	0.000	0.000	0.000	0.000
144	A	144	LYS	1	0.788	0.862	11.968	17.172	17.172	0.000	0.000	0.000	0.000
145	A	145	TYR	0	-0.074	-0.061	14.880	1.635	1.635	0.000	0.000	0.000	0.000
146	A	146	HIS	-1	-0.958	-0.956	9.717	-17.948	-17.948	0.000	0.000	0.000	0.000

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