FMO DATABASE

FMODB ID: QK4JY

Calculation Name: 1I3D-A-Xray547

Preferred Name:

Target Type:

Ligand Name: protoporphyrin ix containing fe | carbon monoxide

Ligand 3-letter code: HEM | CMO

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1I3D

Chain ID: A

ChEMBL ID:

UniProt ID: P69891

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1312533.077546
FMO2-HF: Nuclear repulsion	1256959.242174
FMO2-HF: Total energy	-55573.835372
FMO2-MP2: Total energy	-55738.084205

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:GLY)

Summations of interaction energy for fragment #1(A:1: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.
-30.795	-29.456	-0.015	-0.607	-0.717	-0.003

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.852 / q_NPA : 0.910

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	PHE	0	0.010	0.014	3.845	3.304	4.643	-0.015	-0.607	-0.717	-0.003
4	A	4	THR	0	0.010	-0.008	6.811	1.790	1.790	0.000	0.000	0.000	0.000
5	A	5	GLU	-1	-0.793	-0.905	10.094	-24.425	-24.425	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-0.833	-0.924	13.337	-21.266	-21.266	0.000	0.000	0.000	0.000
7	A	7	ASP	-1	-0.770	-0.819	8.710	-30.989	-30.989	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.792	0.891	9.659	30.556	30.556	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.021	0.024	12.671	1.261	1.261	0.000	0.000	0.000	0.000
10	A	10	THR	0	-0.005	0.008	14.046	1.508	1.508	0.000	0.000	0.000	0.000
11	A	11	ILE	0	-0.040	-0.023	9.972	0.799	0.799	0.000	0.000	0.000	0.000
12	A	12	THR	0	-0.015	-0.027	14.544	1.077	1.077	0.000	0.000	0.000	0.000
13	A	13	SER	0	-0.066	-0.055	17.140	1.115	1.115	0.000	0.000	0.000	0.000
14	A	14	LEU	0	-0.011	0.004	18.082	0.726	0.726	0.000	0.000	0.000	0.000
15	A	15	TRP	0	0.035	0.004	17.562	0.483	0.483	0.000	0.000	0.000	0.000
16	A	16	GLY	0	-0.022	-0.007	19.607	0.568	0.568	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.800	0.890	22.646	13.158	13.158	0.000	0.000	0.000	0.000
18	A	18	VAL	0	-0.030	-0.008	20.682	0.383	0.383	0.000	0.000	0.000	0.000
19	A	19	ASN	0	0.013	0.004	23.974	-0.085	-0.085	0.000	0.000	0.000	0.000
20	A	20	VAL	0	0.017	0.000	22.848	0.001	0.001	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.848	-0.908	25.463	-11.050	-11.050	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.906	-0.930	28.504	-9.765	-9.765	0.000	0.000	0.000	0.000
23	A	23	ALA	0	0.093	0.042	23.684	-0.053	-0.053	0.000	0.000	0.000	0.000
24	A	24	GLY	0	0.012	0.017	23.937	-0.451	-0.451	0.000	0.000	0.000	0.000
25	A	25	GLY	0	-0.018	-0.013	24.998	-0.134	-0.134	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.933	-0.963	26.366	-11.018	-11.018	0.000	0.000	0.000	0.000
27	A	27	THR	0	-0.023	-0.029	20.452	-0.155	-0.155	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.026	-0.010	23.787	-0.147	-0.147	0.000	0.000	0.000	0.000
29	A	29	GLY	0	0.042	-0.006	25.107	0.156	0.156	0.000	0.000	0.000	0.000
30	A	30	ARG	1	0.963	0.977	24.282	11.743	11.743	0.000	0.000	0.000	0.000
31	A	31	LEU	0	0.000	0.007	21.323	-0.031	-0.031	0.000	0.000	0.000	0.000
32	A	32	LEU	0	-0.013	0.006	24.724	0.223	0.223	0.000	0.000	0.000	0.000
33	A	33	VAL	0	-0.021	-0.009	28.096	0.396	0.396	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.037	-0.015	25.554	0.237	0.237	0.000	0.000	0.000	0.000
35	A	35	TYR	0	0.019	0.011	22.117	-0.029	-0.029	0.000	0.000	0.000	0.000
36	A	36	PRO	0	0.045	0.041	26.388	-0.209	-0.209	0.000	0.000	0.000	0.000
37	A	37	TRP	0	0.035	0.010	23.602	0.459	0.459	0.000	0.000	0.000	0.000
38	A	38	THR	0	-0.037	-0.042	23.579	0.029	0.029	0.000	0.000	0.000	0.000
39	A	39	GLN	0	-0.021	-0.035	26.444	0.119	0.119	0.000	0.000	0.000	0.000
40	A	40	ARG	1	0.965	1.005	25.558	11.824	11.824	0.000	0.000	0.000	0.000
41	A	41	PHE	0	-0.044	-0.005	24.037	-0.038	-0.038	0.000	0.000	0.000	0.000
42	A	42	PHE	0	-0.040	-0.030	24.505	-0.131	-0.131	0.000	0.000	0.000	0.000
43	A	43	ASP	-1	-0.794	-0.884	30.487	-9.314	-9.314	0.000	0.000	0.000	0.000
44	A	44	SER	0	-0.037	-0.019	32.780	0.254	0.254	0.000	0.000	0.000	0.000
45	A	45	PHE	0	-0.041	-0.050	28.879	0.155	0.155	0.000	0.000	0.000	0.000
46	A	46	GLY	0	-0.007	0.014	34.365	0.174	0.174	0.000	0.000	0.000	0.000
47	A	47	ASN	0	0.018	0.017	37.123	-0.161	-0.161	0.000	0.000	0.000	0.000
48	A	48	LEU	0	0.058	0.020	31.695	-0.160	-0.160	0.000	0.000	0.000	0.000
49	A	49	SER	0	-0.020	-0.021	35.264	-0.058	-0.058	0.000	0.000	0.000	0.000
50	A	50	SER	0	0.040	0.017	37.148	0.069	0.069	0.000	0.000	0.000	0.000
51	A	51	ALA	0	0.077	0.032	34.178	-0.146	-0.146	0.000	0.000	0.000	0.000
52	A	52	SER	0	-0.003	-0.003	35.009	-0.147	-0.147	0.000	0.000	0.000	0.000
53	A	53	ALA	0	-0.025	0.000	37.521	0.018	0.018	0.000	0.000	0.000	0.000
54	A	54	ILE	0	-0.023	-0.008	30.778	-0.078	-0.078	0.000	0.000	0.000	0.000
55	A	55	MET	0	-0.039	-0.011	29.236	-0.245	-0.245	0.000	0.000	0.000	0.000
56	A	56	GLY	0	0.014	0.026	33.372	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	57	ASN	0	-0.040	-0.022	33.562	0.040	0.040	0.000	0.000	0.000	0.000
58	A	58	PRO	0	0.027	0.008	33.505	-0.303	-0.303	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.875	0.942	32.605	8.616	8.616	0.000	0.000	0.000	0.000
60	A	60	VAL	0	0.028	0.026	28.704	-0.393	-0.393	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.942	0.959	28.650	9.486	9.486	0.000	0.000	0.000	0.000
62	A	62	ALA	0	-0.011	-0.004	28.957	-0.328	-0.328	0.000	0.000	0.000	0.000
63	A	63	HIS	0	0.006	-0.015	24.504	0.048	0.048	0.000	0.000	0.000	0.000
64	A	64	GLY	0	0.068	0.024	24.619	-0.557	-0.557	0.000	0.000	0.000	0.000
65	A	65	LYS	1	0.881	0.931	23.899	10.354	10.354	0.000	0.000	0.000	0.000
66	A	66	LYS	1	0.902	0.971	24.290	10.806	10.806	0.000	0.000	0.000	0.000
67	A	67	VAL	0	0.003	0.010	19.384	-0.540	-0.540	0.000	0.000	0.000	0.000
68	A	68	LEU	0	0.040	0.018	19.526	-0.882	-0.882	0.000	0.000	0.000	0.000
69	A	69	THR	0	-0.039	-0.035	20.133	-0.260	-0.260	0.000	0.000	0.000	0.000
70	A	70	SER	0	-0.038	-0.012	18.364	-0.598	-0.598	0.000	0.000	0.000	0.000
71	A	71	LEU	0	0.016	0.007	13.603	-0.891	-0.891	0.000	0.000	0.000	0.000
72	A	72	GLY	0	0.045	0.010	15.949	-0.910	-0.910	0.000	0.000	0.000	0.000
73	A	73	ASP	-1	-0.863	-0.933	17.992	-16.679	-16.679	0.000	0.000	0.000	0.000
74	A	74	ALA	0	0.025	0.024	12.756	-0.662	-0.662	0.000	0.000	0.000	0.000
75	A	75	ILE	0	0.006	0.000	12.768	-1.799	-1.799	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.816	0.912	14.235	15.154	15.154	0.000	0.000	0.000	0.000
77	A	77	HIS	1	0.834	0.905	12.368	20.606	20.606	0.000	0.000	0.000	0.000
78	A	78	LEU	0	0.028	0.021	9.020	-2.044	-2.044	0.000	0.000	0.000	0.000
79	A	79	ASP	-1	-0.845	-0.926	7.144	-38.682	-38.682	0.000	0.000	0.000	0.000
80	A	80	ASP	-1	-0.901	-0.953	7.578	-30.209	-30.209	0.000	0.000	0.000	0.000
81	A	81	LEU	0	0.003	0.014	6.976	2.845	2.845	0.000	0.000	0.000	0.000
82	A	82	LYS	1	0.945	0.971	7.426	32.744	32.744	0.000	0.000	0.000	0.000
83	A	83	GLY	0	0.023	0.016	9.257	2.256	2.256	0.000	0.000	0.000	0.000
84	A	84	THR	0	-0.054	-0.039	12.036	2.281	2.281	0.000	0.000	0.000	0.000
85	A	85	PHE	0	0.009	-0.011	10.922	1.691	1.691	0.000	0.000	0.000	0.000
86	A	86	ALA	0	0.023	0.033	13.832	1.033	1.033	0.000	0.000	0.000	0.000
87	A	87	GLN	0	0.043	0.011	15.081	0.786	0.786	0.000	0.000	0.000	0.000
88	A	88	LEU	0	-0.013	-0.015	16.775	0.899	0.899	0.000	0.000	0.000	0.000
89	A	89	SER	0	0.001	0.006	14.454	0.438	0.438	0.000	0.000	0.000	0.000
90	A	90	GLU	-1	-0.889	-0.947	16.539	-15.008	-15.008	0.000	0.000	0.000	0.000
91	A	91	LEU	0	-0.113	-0.052	19.790	0.899	0.899	0.000	0.000	0.000	0.000
92	A	92	HIS	0	-0.051	-0.061	18.678	1.042	1.042	0.000	0.000	0.000	0.000
93	A	93	CYS	0	-0.043	0.001	17.342	0.067	0.067	0.000	0.000	0.000	0.000
94	A	94	ASP	-1	-0.767	-0.850	20.111	-14.619	-14.619	0.000	0.000	0.000	0.000
95	A	95	LYS	1	0.884	0.952	22.782	12.663	12.663	0.000	0.000	0.000	0.000
96	A	96	LEU	0	-0.042	-0.025	23.585	0.575	0.575	0.000	0.000	0.000	0.000
97	A	97	HIS	0	0.024	0.029	22.777	0.001	0.001	0.000	0.000	0.000	0.000
98	A	98	VAL	0	-0.048	-0.022	19.773	0.260	0.260	0.000	0.000	0.000	0.000
99	A	99	ASP	-1	-0.864	-0.920	19.573	-16.128	-16.128	0.000	0.000	0.000	0.000
100	A	100	PRO	0	0.066	0.011	14.504	-0.141	-0.141	0.000	0.000	0.000	0.000
101	A	101	GLU	-1	-0.801	-0.864	15.635	-19.541	-19.541	0.000	0.000	0.000	0.000
102	A	102	ASN	0	-0.046	-0.047	17.321	0.343	0.343	0.000	0.000	0.000	0.000
103	A	103	PHE	0	0.013	0.018	14.487	0.229	0.229	0.000	0.000	0.000	0.000
104	A	104	LYS	1	0.900	0.932	13.327	19.088	19.088	0.000	0.000	0.000	0.000
105	A	105	LEU	0	-0.054	-0.002	14.462	0.194	0.194	0.000	0.000	0.000	0.000
106	A	106	LEU	0	0.021	0.001	17.920	0.461	0.461	0.000	0.000	0.000	0.000
107	A	107	GLY	0	0.037	0.013	14.467	0.305	0.305	0.000	0.000	0.000	0.000
108	A	108	ASN	0	-0.003	-0.020	14.347	0.085	0.085	0.000	0.000	0.000	0.000
109	A	109	VAL	0	-0.022	0.003	17.114	0.810	0.810	0.000	0.000	0.000	0.000
110	A	110	LEU	0	0.018	0.008	15.994	0.603	0.603	0.000	0.000	0.000	0.000
111	A	111	VAL	0	0.006	0.002	14.891	0.402	0.402	0.000	0.000	0.000	0.000
112	A	112	THR	0	-0.044	-0.026	17.940	0.747	0.747	0.000	0.000	0.000	0.000
113	A	113	VAL	0	-0.029	-0.018	21.558	0.599	0.599	0.000	0.000	0.000	0.000
114	A	114	LEU	0	-0.010	0.001	17.097	0.473	0.473	0.000	0.000	0.000	0.000
115	A	115	ALA	0	0.015	0.005	21.194	0.431	0.431	0.000	0.000	0.000	0.000
116	A	116	ILE	0	-0.076	-0.043	22.585	0.580	0.580	0.000	0.000	0.000	0.000
117	A	117	HIS	0	-0.041	-0.012	24.404	0.687	0.687	0.000	0.000	0.000	0.000
118	A	118	PHE	0	0.014	0.009	21.822	0.244	0.244	0.000	0.000	0.000	0.000
119	A	119	GLY	0	0.037	0.029	25.013	0.228	0.228	0.000	0.000	0.000	0.000
120	A	120	LYS	1	0.910	0.942	24.493	10.014	10.014	0.000	0.000	0.000	0.000
121	A	121	GLU	-1	-0.820	-0.890	23.042	-12.796	-12.796	0.000	0.000	0.000	0.000
122	A	122	PHE	0	0.012	0.005	16.764	-0.788	-0.788	0.000	0.000	0.000	0.000
123	A	123	THR	0	0.029	0.012	19.794	-0.208	-0.208	0.000	0.000	0.000	0.000
124	A	124	PRO	0	0.037	0.000	18.398	-0.642	-0.642	0.000	0.000	0.000	0.000
125	A	125	GLU	-1	-0.941	-0.958	15.532	-17.203	-17.203	0.000	0.000	0.000	0.000
126	A	126	VAL	0	0.012	0.008	14.564	-1.418	-1.418	0.000	0.000	0.000	0.000
127	A	127	GLN	0	-0.023	-0.010	14.885	-0.376	-0.376	0.000	0.000	0.000	0.000
128	A	128	ALA	0	0.000	-0.001	11.946	-1.334	-1.334	0.000	0.000	0.000	0.000
129	A	129	SER	0	0.015	-0.015	9.988	-1.815	-1.815	0.000	0.000	0.000	0.000
130	A	130	TRP	0	0.012	-0.002	9.922	-2.569	-2.569	0.000	0.000	0.000	0.000
131	A	131	GLN	0	-0.029	-0.011	11.104	0.340	0.340	0.000	0.000	0.000	0.000
132	A	132	LYS	1	0.803	0.896	4.962	37.575	37.575	0.000	0.000	0.000	0.000
133	A	133	MET	0	0.002	0.014	6.685	-4.588	-4.588	0.000	0.000	0.000	0.000
134	A	134	VAL	0	-0.021	0.004	8.779	-0.663	-0.663	0.000	0.000	0.000	0.000
135	A	135	THR	0	-0.050	-0.030	6.328	0.904	0.904	0.000	0.000	0.000	0.000
136	A	136	ALA	0	-0.021	-0.010	4.995	-1.870	-1.870	0.000	0.000	0.000	0.000
137	A	137	VAL	0	0.008	-0.001	6.429	0.925	0.925	0.000	0.000	0.000	0.000
138	A	138	ALA	0	0.010	0.008	10.233	1.357	1.357	0.000	0.000	0.000	0.000
139	A	139	SER	0	-0.049	-0.001	6.629	-0.520	-0.520	0.000	0.000	0.000	0.000
140	A	140	ALA	0	0.005	-0.001	8.361	1.407	1.407	0.000	0.000	0.000	0.000
141	A	141	LEU	0	-0.006	-0.009	9.723	2.159	2.159	0.000	0.000	0.000	0.000
142	A	142	SER	0	-0.023	-0.017	11.548	1.467	1.467	0.000	0.000	0.000	0.000
143	A	143	SER	0	-0.005	-0.015	10.750	-0.093	-0.093	0.000	0.000	0.000	0.000
144	A	144	ARG	1	0.814	0.872	12.214	16.600	16.600	0.000	0.000	0.000	0.000
145	A	145	TYR	0	-0.077	-0.057	15.079	1.478	1.478	0.000	0.000	0.000	0.000
146	A	146	HIS	-1	-0.970	-0.962	10.899	-21.361	-21.361	0.000	0.000	0.000	0.000

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