FMO DATABASE

FMODB ID: QKQZY

Calculation Name: 2D2M-A-Xray547

Preferred Name:

Target Type:

Ligand Name: protoporphyrin ix containing fe | oxygen molecule

Ligand 3-letter code: HEM | OXY

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2D2M

Chain ID: A

ChEMBL ID:

UniProt ID: Q7M419

Base Structure: X-ray

Registration Date: 2025-10-03

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	139
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1218054.785846
FMO2-HF: Nuclear repulsion	1163742.389459
FMO2-HF: Total energy	-54312.396387
FMO2-MP2: Total energy	-54467.729633

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.
-134.467	-128.185	9.536	-5.67	-10.15	-0.058

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 : 0.824 / q_NPA : 0.914

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	ASN	0	0.063	0.047	3.848	8.190	9.107	-0.001	-0.203	-0.713	0.001
4	A	4	ARG	1	0.967	0.959	5.279	30.252	30.338	-0.001	-0.008	-0.077	0.000
129	A	129	GLU	-1	-0.882	-0.950	2.273	-82.805	-79.796	6.989	-4.304	-5.695	-0.052
130	A	131	TYR	0	-0.016	0.005	5.251	1.343	1.418	-0.001	-0.006	-0.068	0.000
131	A	132	GLU	-1	-0.834	-0.897	2.207	-40.467	-40.249	1.878	-0.560	-1.536	-0.004
132	A	133	ARG	1	0.783	0.874	2.484	39.395	41.083	0.658	-0.537	-1.809	-0.003
133	A	134	ILE	0	-0.028	-0.021	3.716	3.757	3.943	0.015	-0.038	-0.164	0.000
135	A	136	SER	0	0.032	0.012	4.343	1.202	1.305	-0.001	-0.014	-0.088	0.000
5	A	5	LEU	0	0.009	0.007	8.861	3.067	3.067	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-0.811	-0.915	5.306	-49.758	-49.758	0.000	0.000	0.000	0.000
7	A	7	GLN	0	0.008	-0.023	6.045	6.709	6.709	0.000	0.000	0.000	0.000
8	A	8	ILE	0	-0.031	0.003	9.737	2.204	2.204	0.000	0.000	0.000	0.000
9	A	9	LEU	0	-0.007	0.016	11.093	1.421	1.421	0.000	0.000	0.000	0.000
10	A	10	VAL	0	0.040	0.030	8.505	1.381	1.381	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.816	0.900	11.773	23.070	23.070	0.000	0.000	0.000	0.000
12	A	12	THR	0	-0.065	-0.045	14.046	1.412	1.412	0.000	0.000	0.000	0.000
13	A	13	GLN	0	0.104	0.046	14.334	0.008	0.008	0.000	0.000	0.000	0.000
14	A	14	TRP	0	-0.007	0.006	14.500	0.439	0.439	0.000	0.000	0.000	0.000
15	A	15	ALA	0	-0.046	-0.022	16.479	0.916	0.916	0.000	0.000	0.000	0.000
16	A	16	GLN	0	0.009	-0.008	19.387	-0.028	-0.028	0.000	0.000	0.000	0.000
17	A	17	SER	0	-0.001	0.004	17.906	0.326	0.326	0.000	0.000	0.000	0.000
18	A	18	TYR	0	-0.036	-0.032	19.173	0.776	0.776	0.000	0.000	0.000	0.000
19	A	19	GLY	0	-0.096	-0.054	20.997	0.466	0.466	0.000	0.000	0.000	0.000
20	A	20	GLU	-1	-0.898	-0.954	22.923	-11.982	-11.982	0.000	0.000	0.000	0.000
21	A	21	ALA	0	-0.035	-0.002	24.278	0.488	0.488	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.953	-0.963	25.952	-9.350	-9.350	0.000	0.000	0.000	0.000
23	A	23	ASN	0	0.021	-0.001	29.104	-0.112	-0.112	0.000	0.000	0.000	0.000
24	A	24	ARG	1	0.966	0.982	23.478	12.619	12.619	0.000	0.000	0.000	0.000
25	A	25	ALA	0	-0.025	-0.001	25.402	-0.307	-0.307	0.000	0.000	0.000	0.000
26	A	26	ALA	0	-0.013	0.015	27.851	0.109	0.109	0.000	0.000	0.000	0.000
27	A	27	PHE	0	0.112	0.060	18.894	-0.250	-0.250	0.000	0.000	0.000	0.000
28	A	28	SER	0	-0.021	-0.038	21.903	-0.661	-0.661	0.000	0.000	0.000	0.000
29	A	29	ARG	1	0.860	0.918	22.736	9.881	9.881	0.000	0.000	0.000	0.000
30	A	30	ASP	-1	-0.868	-0.938	23.940	-11.214	-11.214	0.000	0.000	0.000	0.000
31	A	31	LEU	0	-0.007	0.005	16.657	-0.183	-0.183	0.000	0.000	0.000	0.000
32	A	32	PHE	0	-0.010	-0.028	19.814	-0.353	-0.353	0.000	0.000	0.000	0.000
33	A	33	SER	0	-0.014	-0.006	22.151	0.287	0.287	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.857	-0.922	20.238	-12.043	-12.043	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.025	-0.016	17.284	-0.133	-0.133	0.000	0.000	0.000	0.000
36	A	36	PHE	0	-0.061	-0.046	20.136	0.171	0.171	0.000	0.000	0.000	0.000
37	A	37	ASN	0	-0.032	-0.018	23.664	0.537	0.537	0.000	0.000	0.000	0.000
38	A	38	ILE	0	-0.039	-0.007	17.477	0.176	0.176	0.000	0.000	0.000	0.000
39	A	39	GLN	0	0.005	0.005	18.147	-0.230	-0.230	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.067	0.056	21.786	0.032	0.032	0.000	0.000	0.000	0.000
41	A	41	SER	0	-0.044	-0.031	22.804	0.209	0.209	0.000	0.000	0.000	0.000
42	A	42	SER	0	-0.001	-0.011	20.785	0.120	0.120	0.000	0.000	0.000	0.000
43	A	43	ARG	1	0.896	0.936	22.793	10.029	10.029	0.000	0.000	0.000	0.000
44	A	44	ALA	0	0.024	-0.003	25.802	0.158	0.158	0.000	0.000	0.000	0.000
45	A	45	LEU	0	-0.010	0.007	20.804	0.281	0.281	0.000	0.000	0.000	0.000
46	A	46	PHE	0	0.002	-0.004	19.686	-0.186	-0.186	0.000	0.000	0.000	0.000
47	A	47	SER	0	0.014	0.000	25.758	0.268	0.268	0.000	0.000	0.000	0.000
48	A	48	GLY	0	-0.022	-0.002	28.901	0.272	0.272	0.000	0.000	0.000	0.000
49	A	49	VAL	0	-0.078	-0.042	25.943	0.199	0.199	0.000	0.000	0.000	0.000
50	A	50	GLY	0	0.045	0.018	29.288	0.009	0.009	0.000	0.000	0.000	0.000
51	A	51	VAL	0	-0.008	0.000	26.855	0.099	0.099	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.950	-0.964	29.781	-8.898	-8.898	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.826	-0.915	33.203	-8.578	-8.578	0.000	0.000	0.000	0.000
54	A	54	MET	0	-0.002	0.015	28.086	-0.206	-0.206	0.000	0.000	0.000	0.000
55	A	55	ASN	0	-0.027	-0.029	30.163	-0.366	-0.366	0.000	0.000	0.000	0.000
56	A	56	SER	0	0.019	0.025	32.520	0.038	0.038	0.000	0.000	0.000	0.000
57	A	57	ALA	0	0.016	0.005	31.999	-0.297	-0.297	0.000	0.000	0.000	0.000
58	A	58	ALA	0	-0.021	-0.005	31.536	-0.253	-0.253	0.000	0.000	0.000	0.000
59	A	59	PHE	0	0.052	0.037	24.618	-0.367	-0.367	0.000	0.000	0.000	0.000
60	A	60	THR	0	0.044	0.016	27.147	-0.473	-0.473	0.000	0.000	0.000	0.000
61	A	61	ALA	0	-0.007	-0.009	27.153	-0.365	-0.365	0.000	0.000	0.000	0.000
62	A	62	HIS	0	-0.022	-0.017	21.937	-0.072	-0.072	0.000	0.000	0.000	0.000
63	A	63	CYS	0	-0.021	-0.001	22.823	-0.579	-0.579	0.000	0.000	0.000	0.000
64	A	64	LEU	0	-0.001	-0.003	22.191	-0.553	-0.553	0.000	0.000	0.000	0.000
65	A	65	ARG	1	0.901	0.969	22.572	10.913	10.913	0.000	0.000	0.000	0.000
66	A	66	VAL	0	0.010	0.020	17.401	-0.587	-0.587	0.000	0.000	0.000	0.000
67	A	67	THR	0	0.039	0.007	17.698	-0.895	-0.895	0.000	0.000	0.000	0.000
68	A	68	GLY	0	0.029	0.017	18.335	-0.546	-0.546	0.000	0.000	0.000	0.000
69	A	69	ALA	0	-0.045	-0.027	16.458	-0.383	-0.383	0.000	0.000	0.000	0.000
70	A	70	LEU	0	0.064	0.024	12.876	-0.951	-0.951	0.000	0.000	0.000	0.000
71	A	71	ASN	0	0.025	0.033	13.885	-1.073	-1.073	0.000	0.000	0.000	0.000
72	A	72	ARG	1	0.765	0.855	15.863	16.083	16.083	0.000	0.000	0.000	0.000
73	A	73	LEU	0	0.013	0.018	11.038	-0.382	-0.382	0.000	0.000	0.000	0.000
74	A	74	ILE	0	0.046	0.020	10.849	-1.586	-1.586	0.000	0.000	0.000	0.000
75	A	75	SER	0	-0.082	-0.073	12.059	-0.651	-0.651	0.000	0.000	0.000	0.000
76	A	76	GLN	0	0.003	-0.011	12.759	0.740	0.740	0.000	0.000	0.000	0.000
77	A	77	LEU	0	0.031	0.016	6.560	-0.913	-0.913	0.000	0.000	0.000	0.000
78	A	78	ASP	-1	-0.870	-0.913	8.370	-26.002	-26.002	0.000	0.000	0.000	0.000
79	A	79	GLN	0	-0.023	-0.001	10.626	-0.861	-0.861	0.000	0.000	0.000	0.000
80	A	80	GLN	0	-0.035	-0.026	6.747	-3.136	-3.136	0.000	0.000	0.000	0.000
81	A	81	ALA	0	0.017	0.009	10.111	-0.072	-0.072	0.000	0.000	0.000	0.000
82	A	82	THR	0	0.016	0.004	13.305	0.452	0.452	0.000	0.000	0.000	0.000
83	A	83	ILE	0	0.025	0.014	8.652	0.697	0.697	0.000	0.000	0.000	0.000
84	A	84	ASN	0	0.028	0.023	8.676	-2.183	-2.183	0.000	0.000	0.000	0.000
85	A	85	ALA	0	0.010	0.016	11.121	0.693	0.693	0.000	0.000	0.000	0.000
86	A	86	ASP	-1	-0.776	-0.862	14.397	-16.804	-16.804	0.000	0.000	0.000	0.000
87	A	87	LEU	0	-0.050	-0.004	8.274	0.491	0.491	0.000	0.000	0.000	0.000
88	A	88	ALA	0	0.063	0.036	12.390	0.697	0.697	0.000	0.000	0.000	0.000
89	A	89	HIS	0	-0.042	-0.015	14.153	1.036	1.036	0.000	0.000	0.000	0.000
90	A	90	LEU	0	-0.021	-0.019	14.243	0.926	0.926	0.000	0.000	0.000	0.000
91	A	91	ALA	0	0.057	0.043	12.951	0.790	0.790	0.000	0.000	0.000	0.000
92	A	92	GLY	0	0.000	0.003	14.896	0.808	0.808	0.000	0.000	0.000	0.000
93	A	93	GLN	0	-0.086	-0.049	18.456	0.448	0.448	0.000	0.000	0.000	0.000
94	A	94	HIS	0	-0.073	-0.054	16.399	0.745	0.745	0.000	0.000	0.000	0.000
95	A	95	ALA	0	0.021	0.025	18.558	0.403	0.403	0.000	0.000	0.000	0.000
96	A	96	SER	0	-0.042	-0.017	19.512	0.216	0.216	0.000	0.000	0.000	0.000
97	A	97	ARG	1	0.868	0.943	20.813	12.955	12.955	0.000	0.000	0.000	0.000
98	A	98	ASN	0	0.014	-0.001	20.698	-0.553	-0.553	0.000	0.000	0.000	0.000
99	A	99	LEU	0	-0.007	0.005	16.815	0.201	0.201	0.000	0.000	0.000	0.000
100	A	100	ASP	-1	-0.777	-0.846	17.332	-15.213	-15.213	0.000	0.000	0.000	0.000
101	A	101	ALA	0	0.054	0.004	12.491	-0.459	-0.459	0.000	0.000	0.000	0.000
102	A	102	SER	0	-0.063	-0.058	13.019	-0.778	-0.778	0.000	0.000	0.000	0.000
103	A	103	ASN	0	0.003	-0.016	15.473	-0.113	-0.113	0.000	0.000	0.000	0.000
104	A	104	PHE	0	0.013	0.022	10.694	-0.076	-0.076	0.000	0.000	0.000	0.000
105	A	105	ALA	0	0.039	0.019	11.137	-0.951	-0.951	0.000	0.000	0.000	0.000
106	A	106	ALA	0	-0.017	0.010	12.134	0.075	0.075	0.000	0.000	0.000	0.000
107	A	107	MET	0	0.020	0.006	13.339	0.297	0.297	0.000	0.000	0.000	0.000
108	A	108	GLY	0	0.025	-0.001	10.717	-0.112	-0.112	0.000	0.000	0.000	0.000
109	A	109	GLN	0	-0.040	-0.029	11.526	0.675	0.675	0.000	0.000	0.000	0.000
110	A	110	ALA	0	0.018	0.041	14.380	0.629	0.629	0.000	0.000	0.000	0.000
111	A	111	VAL	0	-0.005	-0.016	12.545	0.457	0.457	0.000	0.000	0.000	0.000
112	A	112	MET	0	-0.095	-0.043	9.716	-0.398	-0.398	0.000	0.000	0.000	0.000
113	A	113	SER	0	-0.011	-0.017	14.161	0.553	0.553	0.000	0.000	0.000	0.000
114	A	114	VAL	0	0.019	0.007	17.960	0.606	0.606	0.000	0.000	0.000	0.000
115	A	115	VAL	0	-0.026	-0.008	14.745	0.400	0.400	0.000	0.000	0.000	0.000
116	A	116	PRO	0	-0.027	-0.015	15.875	0.427	0.427	0.000	0.000	0.000	0.000
117	A	117	THR	0	-0.029	-0.015	18.306	0.548	0.548	0.000	0.000	0.000	0.000
118	A	118	HIS	0	-0.060	-0.034	20.912	0.944	0.944	0.000	0.000	0.000	0.000
119	A	119	LEU	0	-0.024	-0.005	17.310	-0.169	-0.169	0.000	0.000	0.000	0.000
120	A	120	ASP	-1	-0.882	-0.921	21.548	-11.823	-11.823	0.000	0.000	0.000	0.000
121	A	121	CYS	0	-0.110	-0.069	19.079	-0.020	-0.020	0.000	0.000	0.000	0.000
122	A	122	PHE	0	0.072	0.030	13.096	-0.414	-0.414	0.000	0.000	0.000	0.000
123	A	123	ASN	0	-0.031	-0.009	11.829	0.695	0.695	0.000	0.000	0.000	0.000
124	A	124	GLN	0	0.053	0.021	10.863	-2.525	-2.525	0.000	0.000	0.000	0.000
125	A	125	HIS	0	-0.009	0.003	5.716	3.189	3.189	0.000	0.000	0.000	0.000
126	A	126	ALA	0	0.028	0.012	6.710	-2.915	-2.915	0.000	0.000	0.000	0.000
127	A	127	TRP	0	0.026	-0.007	6.605	-3.368	-3.368	0.000	0.000	0.000	0.000
128	A	128	GLY	0	0.040	0.023	6.693	-0.808	-0.808	0.000	0.000	0.000	0.000
134	A	135	ALA	0	0.000	-0.001	6.776	2.599	2.599	0.000	0.000	0.000	0.000
136	A	137	GLY	0	-0.034	-0.011	6.485	2.386	2.386	0.000	0.000	0.000	0.000
137	A	138	ILE	0	-0.070	-0.048	8.210	2.472	2.472	0.000	0.000	0.000	0.000
138	A	139	SER	0	-0.081	-0.072	9.984	1.770	1.770	0.000	0.000	0.000	0.000
139	A	140	GLY	-1	-0.923	-0.945	8.184	-26.010	-26.010	0.000	0.000	0.000	0.000

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