FMO DATABASE

FMODB ID: 6Z99Z

Calculation Name: 2DN3-A-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: A

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	141
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1206697.097542
FMO2-HF: Nuclear repulsion	1154231.453144
FMO2-HF: Total energy	-52465.644399
FMO2-MP2: Total energy	-52620.837265

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.
34.37	36.933	0.321	-1.071	-1.813	-0.006

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 : 0.872 / q_NPA : 0.924

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	SER	0	0.018	-0.014	2.962	3.144	5.372	0.324	-0.992	-1.560	-0.006
4	A	4	PRO	0	0.056	0.000	4.595	1.180	1.232	-0.001	-0.005	-0.046	0.000
127	A	127	LYS	1	0.930	0.966	4.505	38.035	38.165	-0.001	-0.021	-0.108	0.000
131	A	131	SER	0	-0.059	-0.029	4.044	-5.726	-5.573	-0.001	-0.053	-0.099	0.000
5	A	5	ALA	0	0.045	0.045	7.814	2.062	2.062	0.000	0.000	0.000	0.000
6	A	6	ASP	-1	-0.760	-0.843	6.145	-41.746	-41.746	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.815	0.885	5.239	37.889	37.889	0.000	0.000	0.000	0.000
8	A	8	THR	0	-0.022	-0.014	9.214	2.548	2.548	0.000	0.000	0.000	0.000
9	A	9	ASN	0	-0.011	-0.022	11.796	2.786	2.786	0.000	0.000	0.000	0.000
10	A	10	VAL	0	-0.004	0.003	9.698	1.600	1.600	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.884	0.949	11.731	24.697	24.697	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.016	0.000	15.372	1.286	1.286	0.000	0.000	0.000	0.000
13	A	13	ALA	0	0.022	0.008	16.219	1.063	1.063	0.000	0.000	0.000	0.000
14	A	14	TRP	0	0.023	0.002	16.309	0.801	0.801	0.000	0.000	0.000	0.000
15	A	15	GLY	0	-0.007	-0.003	18.288	0.829	0.829	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.821	0.896	20.848	14.270	14.270	0.000	0.000	0.000	0.000
17	A	17	VAL	0	-0.018	0.018	20.029	0.607	0.607	0.000	0.000	0.000	0.000
18	A	18	GLY	0	0.029	0.015	23.095	0.661	0.661	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.008	-0.013	25.235	-0.185	-0.185	0.000	0.000	0.000	0.000
20	A	20	HIS	1	0.827	0.909	25.684	11.357	11.357	0.000	0.000	0.000	0.000
21	A	21	ALA	0	0.035	0.025	22.642	-0.193	-0.193	0.000	0.000	0.000	0.000
22	A	22	GLY	0	0.029	-0.008	23.346	-0.294	-0.294	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.861	-0.904	25.686	-10.907	-10.907	0.000	0.000	0.000	0.000
24	A	24	TYR	0	0.045	-0.001	22.033	-0.073	-0.073	0.000	0.000	0.000	0.000
25	A	25	GLY	0	0.025	0.025	21.512	-0.417	-0.417	0.000	0.000	0.000	0.000
26	A	26	ALA	0	-0.015	-0.012	22.503	-0.037	-0.037	0.000	0.000	0.000	0.000
27	A	27	GLU	-1	-0.764	-0.839	25.011	-11.892	-11.892	0.000	0.000	0.000	0.000
28	A	28	ALA	0	-0.001	0.001	20.303	0.043	0.043	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.017	-0.010	22.431	-0.116	-0.116	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.842	-0.900	24.107	-10.067	-10.067	0.000	0.000	0.000	0.000
31	A	31	ARG	1	0.874	0.908	23.571	12.462	12.462	0.000	0.000	0.000	0.000
32	A	32	MET	0	0.019	0.018	21.604	-0.242	-0.242	0.000	0.000	0.000	0.000
33	A	33	PHE	0	-0.019	-0.026	23.759	0.194	0.194	0.000	0.000	0.000	0.000
34	A	34	LEU	0	-0.025	-0.014	27.190	0.399	0.399	0.000	0.000	0.000	0.000
35	A	35	SER	0	-0.030	-0.023	24.575	0.306	0.306	0.000	0.000	0.000	0.000
36	A	36	PHE	0	-0.012	-0.009	21.202	-0.130	-0.130	0.000	0.000	0.000	0.000
37	A	37	PRO	0	0.006	0.020	25.523	-0.110	-0.110	0.000	0.000	0.000	0.000
38	A	38	THR	0	0.056	0.014	25.342	0.257	0.257	0.000	0.000	0.000	0.000
39	A	39	THR	0	0.012	-0.005	22.722	0.179	0.179	0.000	0.000	0.000	0.000
40	A	40	LYS	1	0.952	0.982	25.466	9.891	9.891	0.000	0.000	0.000	0.000
41	A	41	THR	0	-0.052	-0.029	28.112	0.186	0.186	0.000	0.000	0.000	0.000
42	A	42	TYR	0	0.014	0.020	23.417	0.122	0.122	0.000	0.000	0.000	0.000
43	A	43	PHE	0	-0.064	-0.038	24.107	-0.158	-0.158	0.000	0.000	0.000	0.000
44	A	44	PRO	0	0.037	0.026	29.836	0.225	0.225	0.000	0.000	0.000	0.000
45	A	45	HIS	0	-0.013	0.002	29.470	0.465	0.465	0.000	0.000	0.000	0.000
46	A	46	PHE	0	-0.077	-0.054	28.169	-0.018	-0.018	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.748	-0.834	33.548	-8.650	-8.650	0.000	0.000	0.000	0.000
48	A	48	LEU	0	-0.063	-0.036	29.662	-0.280	-0.280	0.000	0.000	0.000	0.000
49	A	49	SER	0	-0.048	-0.034	32.517	-0.115	-0.115	0.000	0.000	0.000	0.000
50	A	50	HIS	0	0.000	-0.027	32.306	0.046	0.046	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.001	0.002	33.307	0.255	0.255	0.000	0.000	0.000	0.000
52	A	52	SER	0	0.009	-0.003	32.900	0.123	0.123	0.000	0.000	0.000	0.000
53	A	53	ALA	0	0.023	-0.007	32.821	-0.287	-0.287	0.000	0.000	0.000	0.000
54	A	54	GLN	0	-0.003	0.010	32.121	-0.120	-0.120	0.000	0.000	0.000	0.000
55	A	55	VAL	0	0.042	0.030	27.718	-0.405	-0.405	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.894	0.944	27.883	8.770	8.770	0.000	0.000	0.000	0.000
57	A	57	GLY	0	0.000	0.004	28.343	-0.314	-0.314	0.000	0.000	0.000	0.000
58	A	58	HIS	0	-0.012	-0.022	23.560	0.063	0.063	0.000	0.000	0.000	0.000
59	A	59	GLY	0	0.069	0.030	24.044	-0.586	-0.586	0.000	0.000	0.000	0.000
60	A	60	LYS	1	0.825	0.882	23.411	11.707	11.707	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.945	0.986	23.558	10.897	10.897	0.000	0.000	0.000	0.000
62	A	62	VAL	0	0.011	0.012	18.729	-0.660	-0.660	0.000	0.000	0.000	0.000
63	A	63	ALA	0	0.008	0.003	18.821	-0.973	-0.973	0.000	0.000	0.000	0.000
64	A	64	ASP	-1	-0.800	-0.875	19.434	-13.657	-13.657	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.002	0.008	17.417	-0.555	-0.555	0.000	0.000	0.000	0.000
66	A	66	LEU	0	0.019	0.009	14.002	-1.332	-1.332	0.000	0.000	0.000	0.000
67	A	67	THR	0	-0.045	-0.038	15.104	-0.892	-0.892	0.000	0.000	0.000	0.000
68	A	68	ASN	0	0.036	0.015	16.354	-0.609	-0.609	0.000	0.000	0.000	0.000
69	A	69	ALA	0	0.022	0.014	11.460	-0.751	-0.751	0.000	0.000	0.000	0.000
70	A	70	VAL	0	-0.007	-0.012	11.263	-2.080	-2.080	0.000	0.000	0.000	0.000
71	A	71	ALA	0	-0.054	-0.025	12.949	-0.670	-0.670	0.000	0.000	0.000	0.000
72	A	72	HIS	0	-0.011	-0.014	12.835	0.296	0.296	0.000	0.000	0.000	0.000
73	A	73	VAL	0	-0.022	-0.010	7.062	-1.379	-1.379	0.000	0.000	0.000	0.000
74	A	74	ASP	-1	-0.837	-0.917	6.603	-36.910	-36.910	0.000	0.000	0.000	0.000
75	A	75	ASP	-1	-0.849	-0.908	8.174	-21.888	-21.888	0.000	0.000	0.000	0.000
76	A	76	MET	0	-0.036	0.004	7.484	1.180	1.180	0.000	0.000	0.000	0.000
77	A	77	PRO	0	0.010	-0.021	8.333	1.581	1.581	0.000	0.000	0.000	0.000
78	A	78	ASN	0	-0.037	-0.015	11.263	2.317	2.317	0.000	0.000	0.000	0.000
79	A	79	ALA	0	0.019	0.013	13.278	1.194	1.194	0.000	0.000	0.000	0.000
80	A	80	LEU	0	-0.004	0.001	12.065	1.239	1.239	0.000	0.000	0.000	0.000
81	A	81	SER	0	0.035	0.046	15.279	0.589	0.589	0.000	0.000	0.000	0.000
82	A	82	ALA	0	0.072	0.021	16.693	0.289	0.289	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.011	-0.002	16.978	0.639	0.639	0.000	0.000	0.000	0.000
84	A	84	SER	0	0.028	-0.004	15.299	-0.259	-0.259	0.000	0.000	0.000	0.000
85	A	85	ASP	-1	-0.816	-0.894	17.336	-15.259	-15.259	0.000	0.000	0.000	0.000
86	A	86	LEU	0	-0.046	-0.017	20.703	0.658	0.658	0.000	0.000	0.000	0.000
87	A	87	HIS	0	-0.025	-0.041	18.593	0.756	0.756	0.000	0.000	0.000	0.000
88	A	88	ALA	0	0.042	0.034	18.716	0.468	0.468	0.000	0.000	0.000	0.000
89	A	89	HIS	0	-0.085	-0.059	20.735	1.149	1.149	0.000	0.000	0.000	0.000
90	A	90	LYS	1	0.912	0.963	24.125	11.442	11.442	0.000	0.000	0.000	0.000
91	A	91	LEU	0	-0.060	-0.042	22.983	0.471	0.471	0.000	0.000	0.000	0.000
92	A	92	ARG	1	0.908	0.973	23.349	12.443	12.443	0.000	0.000	0.000	0.000
93	A	93	VAL	0	0.010	0.017	19.741	0.114	0.114	0.000	0.000	0.000	0.000
94	A	94	ASP	-1	-0.818	-0.896	20.016	-15.513	-15.513	0.000	0.000	0.000	0.000
95	A	95	PRO	0	0.052	0.009	15.751	-0.343	-0.343	0.000	0.000	0.000	0.000
96	A	96	VAL	0	-0.030	-0.013	15.758	-1.306	-1.306	0.000	0.000	0.000	0.000
97	A	97	ASN	0	-0.013	-0.022	17.275	-0.065	-0.065	0.000	0.000	0.000	0.000
98	A	98	PHE	0	0.015	0.018	13.875	0.056	0.056	0.000	0.000	0.000	0.000
99	A	99	LYS	1	0.993	1.010	12.273	21.357	21.357	0.000	0.000	0.000	0.000
100	A	100	LEU	0	-0.008	0.015	14.761	0.023	0.023	0.000	0.000	0.000	0.000
101	A	101	LEU	0	0.051	0.017	17.159	0.419	0.419	0.000	0.000	0.000	0.000
102	A	102	SER	0	-0.013	-0.022	12.788	-0.342	-0.342	0.000	0.000	0.000	0.000
103	A	103	HIS	0	0.026	0.011	14.794	-0.621	-0.621	0.000	0.000	0.000	0.000
104	A	104	CYS	0	-0.039	0.000	16.902	0.722	0.722	0.000	0.000	0.000	0.000
105	A	105	LEU	0	0.001	0.009	15.627	0.674	0.674	0.000	0.000	0.000	0.000
106	A	106	LEU	0	-0.011	-0.002	12.957	0.402	0.402	0.000	0.000	0.000	0.000
107	A	107	VAL	0	0.005	0.004	16.936	0.622	0.622	0.000	0.000	0.000	0.000
108	A	108	THR	0	-0.056	-0.032	20.503	0.858	0.858	0.000	0.000	0.000	0.000
109	A	109	LEU	0	-0.029	-0.026	16.314	0.461	0.461	0.000	0.000	0.000	0.000
110	A	110	ALA	0	-0.001	-0.001	20.056	0.500	0.500	0.000	0.000	0.000	0.000
111	A	111	ALA	0	-0.039	-0.015	21.471	0.530	0.530	0.000	0.000	0.000	0.000
112	A	112	HIS	1	0.788	0.881	23.757	12.499	12.499	0.000	0.000	0.000	0.000
113	A	113	LEU	0	-0.037	-0.007	20.814	0.325	0.325	0.000	0.000	0.000	0.000
114	A	114	PRO	0	0.043	0.014	22.108	-0.675	-0.675	0.000	0.000	0.000	0.000
115	A	115	ALA	0	-0.016	0.002	23.733	-0.081	-0.081	0.000	0.000	0.000	0.000
116	A	116	GLU	-1	-0.800	-0.893	19.469	-14.035	-14.035	0.000	0.000	0.000	0.000
117	A	117	PHE	0	-0.013	0.005	16.390	-1.138	-1.138	0.000	0.000	0.000	0.000
118	A	118	THR	0	0.034	0.008	18.165	-0.110	-0.110	0.000	0.000	0.000	0.000
119	A	119	PRO	0	0.036	-0.005	17.091	-1.062	-1.062	0.000	0.000	0.000	0.000
120	A	120	ALA	0	-0.001	0.010	13.819	-1.302	-1.302	0.000	0.000	0.000	0.000
121	A	121	VAL	0	0.017	0.010	12.774	-2.241	-2.241	0.000	0.000	0.000	0.000
122	A	122	HIS	0	0.013	0.017	13.220	-2.024	-2.024	0.000	0.000	0.000	0.000
123	A	123	ALA	0	0.054	0.019	10.703	-1.650	-1.650	0.000	0.000	0.000	0.000
124	A	124	SER	0	-0.068	-0.045	8.731	-2.968	-2.968	0.000	0.000	0.000	0.000
125	A	125	LEU	0	-0.012	-0.010	8.613	-3.087	-3.087	0.000	0.000	0.000	0.000
126	A	126	ASP	-1	-0.912	-0.945	9.583	-30.164	-30.164	0.000	0.000	0.000	0.000
128	A	128	PHE	0	-0.033	0.000	5.214	-6.488	-6.488	0.000	0.000	0.000	0.000
129	A	129	LEU	0	0.033	0.014	7.386	0.173	0.173	0.000	0.000	0.000	0.000
130	A	130	ALA	0	0.043	0.036	6.431	1.490	1.490	0.000	0.000	0.000	0.000
132	A	132	VAL	0	0.045	0.004	6.057	2.733	2.733	0.000	0.000	0.000	0.000
133	A	133	SER	0	-0.046	-0.033	9.795	2.718	2.718	0.000	0.000	0.000	0.000
134	A	134	THR	0	-0.045	-0.016	6.958	1.372	1.372	0.000	0.000	0.000	0.000
135	A	135	VAL	0	-0.020	0.002	8.621	1.524	1.524	0.000	0.000	0.000	0.000
136	A	136	LEU	0	-0.035	-0.006	10.922	2.048	2.048	0.000	0.000	0.000	0.000
137	A	137	THR	0	-0.045	-0.039	12.128	1.190	1.190	0.000	0.000	0.000	0.000
138	A	138	SER	0	-0.082	-0.050	12.037	1.092	1.092	0.000	0.000	0.000	0.000
139	A	139	LYS	1	0.829	0.908	13.888	18.192	18.192	0.000	0.000	0.000	0.000
140	A	140	TYR	0	-0.043	-0.052	16.447	0.722	0.722	0.000	0.000	0.000	0.000
141	A	141	ARG	0	0.031	0.044	19.708	-0.405	-0.405	0.000	0.000	0.000	0.000

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