FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

tag_button

FMODB ID: 9MQ62

Calculation Name: 1J1V-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1J1V

Chain ID: A

ChEMBL ID:

UniProt ID: P03004

Base Structure: X-ray

Registration Date: 2025-07-08

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 183
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -709483.18167
FMO2-HF: Nuclear repulsion 671855.243502
FMO2-HF: Total energy -37627.938168
FMO2-MP2: Total energy -37737.338799


3D Structure Molmil
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
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/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:374:VAL)


Summations of interaction energy for fragment #1(A:374: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.
-3.215-0.8520.134-0.769-1.730.008
Interaction energy analysis for fragmet #1(A:374:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.126 / q_NPA : 0.001
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   
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].
4A375THR0-0.0190.0653.843-0.3700.0410.007-0.186-0.2320.001
5A376ILE00.150-0.0753.809-2.069-0.677-0.015-0.873-0.5040.006
6A376ILE0-0.0240.1237.1850.0250.0250.0000.0000.0000.000
7A377ASP00.070-0.0906.789-0.077-0.0770.0000.0000.0000.000
8A377ASP-1-0.959-0.8398.1830.1720.1720.0000.0000.0000.000
9A378ASN00.111-0.0904.864-0.0320.013-0.002-0.004-0.0390.000
10A378ASN0-0.1090.0794.131-0.207-0.115-0.001-0.019-0.0730.000
11A379ILE00.144-0.0955.8970.3320.3320.0000.0000.0000.000
12A379ILE0-0.1180.1153.9850.0290.1240.000-0.031-0.0650.000
13A380GLN00.064-0.1196.8610.2300.2300.0000.0000.0000.000
14A380GLN0-0.1530.0689.9800.1540.1540.0000.0000.0000.000
15A381LYS00.069-0.1029.7700.0330.0330.0000.0000.0000.000
16A381LYS10.8321.0599.853-0.269-0.2690.0000.0000.0000.000
17A382THR00.056-0.0699.2990.1490.1490.0000.0000.0000.000
18A382THR0-0.0200.0797.8820.0520.0520.0000.0000.0000.000
19A383VAL00.063-0.08210.4050.1040.1040.0000.0000.0000.000
20A383VAL0-0.0710.0859.760-0.011-0.0110.0000.0000.0000.000
21A384ALA00.099-0.10412.1070.0470.0470.0000.0000.0000.000
22A384ALA0-0.1160.09014.4600.0120.0120.0000.0000.0000.000
23A385GLU00.101-0.13314.1520.0270.0270.0000.0000.0000.000
24A385GLU-1-1.030-0.83014.194-0.067-0.0670.0000.0000.0000.000
25A386TYR00.087-0.11814.3700.0810.0810.0000.0000.0000.000
26A386TYR0-0.1190.07913.696-0.028-0.0280.0000.0000.0000.000
27A387TYR0-0.033-0.09315.6860.0390.0390.0000.0000.0000.000
28A387TYR0-0.1320.03814.566-0.049-0.0490.0000.0000.0000.000
29A388LYS00.046-0.11218.1530.0190.0190.0000.0000.0000.000
30A388LYS10.8511.07218.6560.1880.1880.0000.0000.0000.000
31A389ILE00.036-0.07918.5880.0380.0380.0000.0000.0000.000
32A389ILE0-0.1160.04917.221-0.005-0.0050.0000.0000.0000.000
33A390LYS00.145-0.08418.4950.0050.0050.0000.0000.0000.000
34A390LYS10.8471.05420.0510.1280.1280.0000.0000.0000.000
35A391VAL00.155-0.07815.570-0.054-0.0540.0000.0000.0000.000
36A391VAL0-0.0040.14213.7420.0110.0110.0000.0000.0000.000
37A392ALA00.091-0.09416.334-0.056-0.0560.0000.0000.0000.000
38A392ALA0-0.0580.10720.5380.0090.0090.0000.0000.0000.000
39A393ASP00.008-0.15719.470-0.001-0.0010.0000.0000.0000.000
40A393ASP-1-0.912-0.80519.398-0.244-0.2440.0000.0000.0000.000
41A394LEU00.041-0.14015.5740.0150.0150.0000.0000.0000.000
42A394LEU0-0.0280.16813.061-0.012-0.0120.0000.0000.0000.000
43A395LEU00.059-0.12717.026-0.067-0.0670.0000.0000.0000.000
44A395LEU0-0.0480.15215.3700.0100.0100.0000.0000.0000.000
45A396SER00.086-0.05318.4400.0140.0140.0000.0000.0000.000
46A396SER0-0.0270.07821.9560.0020.0020.0000.0000.0000.000
47A397LYS00.068-0.08721.462-0.046-0.0460.0000.0000.0000.000
48A397LYS10.9361.10524.4750.2040.2040.0000.0000.0000.000
49A398ARG00.118-0.09723.9700.0000.0000.0000.0000.0000.000
50A398ARG10.8571.10124.0590.2230.2230.0000.0000.0000.000
51A399ARG00.061-0.12023.378-0.036-0.0360.0000.0000.0000.000
52A399ARG10.9301.11424.7660.2690.2690.0000.0000.0000.000
53A400SER00.094-0.07025.078-0.017-0.0170.0000.0000.0000.000
54A400SER0-0.0140.08825.7980.0070.0070.0000.0000.0000.000
55A401ARG00.101-0.05823.784-0.023-0.0230.0000.0000.0000.000
56A401ARG10.9131.08723.9270.3110.3110.0000.0000.0000.000
57A402SER00.078-0.07022.471-0.039-0.0390.0000.0000.0000.000
58A402SER0-0.0070.08424.3540.0090.0090.0000.0000.0000.000
59A403VAL00.044-0.10120.365-0.011-0.0110.0000.0000.0000.000
60A403VAL0-0.0690.09820.6800.0110.0110.0000.0000.0000.000
61A404ALA00.173-0.08219.123-0.055-0.0550.0000.0000.0000.000
62A404ALA0-0.0920.09721.6490.0070.0070.0000.0000.0000.000
63A405ARG0-0.041-0.12118.920-0.057-0.0570.0000.0000.0000.000
64A405ARG10.9271.07019.6880.4470.4470.0000.0000.0000.000
65A406PRO00.046-0.03916.243-0.071-0.0710.0000.0000.0000.000
66A407ARG00.1460.02714.595-0.138-0.1380.0000.0000.0000.000
67A407ARG10.6570.96216.1850.4690.4690.0000.0000.0000.000
68A408GLN00.081-0.09214.339-0.131-0.1310.0000.0000.0000.000
69A408GLN0-0.1170.06417.2040.0300.0300.0000.0000.0000.000
70A409MET00.153-0.06713.744-0.101-0.1010.0000.0000.0000.000
71A409MET0-0.0970.11212.346-0.032-0.0320.0000.0000.0000.000
72A410ALA00.117-0.10410.345-0.258-0.2580.0000.0000.0000.000
73A410ALA0-0.0780.09610.8790.0410.0410.0000.0000.0000.000
74A411MET00.038-0.0909.641-0.450-0.4500.0000.0000.0000.000
75A411MET0-0.1450.04913.2180.1020.1020.0000.0000.0000.000
76A412ALA00.172-0.08211.230-0.130-0.1300.0000.0000.0000.000
77A412ALA0-0.0760.10412.6710.0420.0420.0000.0000.0000.000
78A413LEU00.058-0.1218.1670.0150.0150.0000.0000.0000.000
79A413LEU0-0.0720.1127.118-0.032-0.0320.0000.0000.0000.000
80A414ALA00.124-0.0816.388-1.092-1.0920.0000.0000.0000.000
81A414ALA0-0.0990.0838.3610.1420.1420.0000.0000.0000.000
82A415LYS00.019-0.0787.095-0.597-0.5970.0000.0000.0000.000
83A415LYS10.8971.06111.0911.2721.2720.0000.0000.0000.000
84A416GLU00.083-0.1048.8030.0990.0990.0000.0000.0000.000
85A416GLU-1-1.030-0.8788.744-1.422-1.4220.0000.0000.0000.000
86A417LEU00.024-0.1094.2430.9160.9870.0000.009-0.0800.000
87A417LEU0-0.1120.0943.167-0.127-0.3070.1480.230-0.1970.001
88A418THR00.012-0.0924.115-2.298-2.1730.005-0.067-0.0630.000
89A418THR0-0.0810.0073.3930.8350.746-0.0020.215-0.1240.000
90A419ASN00.093-0.0455.2190.4060.498-0.002-0.004-0.0860.000
91A419ASN0-0.1070.0646.0060.0260.0260.0000.0000.0000.000
92A420HIS00.092-0.0717.7550.4900.4900.0000.0000.0000.000
93A420HIS0-0.1120.0676.681-0.066-0.0660.0000.0000.0000.000
94A421SER00.005-0.0949.553-0.147-0.1470.0000.0000.0000.000
95A421SER0-0.0080.07413.9570.0410.0410.0000.0000.0000.000
96A422LEU00.063-0.09713.058-0.121-0.1210.0000.0000.0000.000
97A422LEU0-0.0940.08114.3590.0110.0110.0000.0000.0000.000
98A423PRO00.012-0.10515.254-0.022-0.0220.0000.0000.0000.000
99A424GLU00.1520.03713.0570.0530.0530.0000.0000.0000.000
100A424GLU-1-0.894-0.80311.966-0.590-0.5900.0000.0000.0000.000
101A425ILE00.093-0.09411.7670.0380.0380.0000.0000.0000.000
102A425ILE0-0.1100.09610.0630.0080.0080.0000.0000.0000.000
103A426GLY0-0.003-0.11212.5330.0240.0240.0000.0000.0000.000
104A427ASP00.110-0.02916.0920.0120.0120.0000.0000.0000.000
105A427ASP-1-0.965-0.81915.939-0.355-0.3550.0000.0000.0000.000
106A428ALA00.063-0.09812.5200.1280.1280.0000.0000.0000.000
107A428ALA0-0.0680.11411.927-0.046-0.0460.0000.0000.0000.000
108A429PHE0-0.035-0.11013.9900.0150.0150.0000.0000.0000.000
109A429PHE0-0.1350.07610.3650.0150.0150.0000.0000.0000.000
110A430GLY00.047-0.10115.5440.0260.0260.0000.0000.0000.000
111A431GLY0-0.0190.00818.3280.0390.0390.0000.0000.0000.000
112A432ARG00.045-0.00618.6130.0470.0470.0000.0000.0000.000
113A432ARG10.6450.91317.8630.4400.4400.0000.0000.0000.000
114A433ASP00.197-0.04719.403-0.022-0.0220.0000.0000.0000.000
115A433ASP-1-0.902-0.80522.507-0.349-0.3490.0000.0000.0000.000
116A434HIS00.477-0.40318.182-0.047-0.0470.0000.0000.0000.000
117A434HIS0-0.2330.42218.251-0.011-0.0110.0000.0000.0000.000
118A435THR0-0.171-0.11118.775-0.084-0.0840.0000.0000.0000.000
119A435THR0-0.0520.06322.9770.0070.0070.0000.0000.0000.000
120A436THR00.038-0.09020.422-0.009-0.0090.0000.0000.0000.000
121A436THR0-0.0420.06819.2070.0190.0190.0000.0000.0000.000
122A437VAL00.032-0.10915.8230.0070.0070.0000.0000.0000.000
123A437VAL0-0.0400.12513.859-0.006-0.0060.0000.0000.0000.000
124A438LEU00.111-0.09416.529-0.094-0.0940.0000.0000.0000.000
125A438LEU0-0.0890.11318.2950.0100.0100.0000.0000.0000.000
126A439HIS00.070-0.08518.295-0.017-0.0170.0000.0000.0000.000
127A439HIS0-0.1280.05820.9810.0090.0090.0000.0000.0000.000
128A440ALA00.043-0.10716.6920.0510.0510.0000.0000.0000.000
129A440ALA0-0.0810.09315.977-0.009-0.0090.0000.0000.0000.000
130A441CYS00.070-0.11415.209-0.001-0.0010.0000.0000.0000.000
131A441CYS0-0.1160.10714.220-0.056-0.0560.0000.0000.0000.000
132A442ARG00.197-0.01416.030-0.019-0.0190.0000.0000.0000.000
133A442ARG10.8611.05719.6120.5040.5040.0000.0000.0000.000
134A443LYS00.123-0.07419.5610.0350.0350.0000.0000.0000.000
135A443LYS10.7281.00519.8220.4260.4260.0000.0000.0000.000
136A444ILE00.015-0.12416.2240.0900.0900.0000.0000.0000.000
137A444ILE0-0.0400.10714.4880.0000.0000.0000.0000.0000.000
138A445GLU00.034-0.14217.732-0.006-0.0060.0000.0000.0000.000
139A445GLU-1-0.960-0.84417.029-0.683-0.6830.0000.0000.0000.000
140A446GLN00.199-0.03818.5670.0220.0220.0000.0000.0000.000
141A446GLN0-0.1600.05622.435-0.003-0.0030.0000.0000.0000.000
142A447LEU00.056-0.09121.0060.0420.0420.0000.0000.0000.000
143A447LEU0-0.1330.04119.9600.0060.0060.0000.0000.0000.000
144A448ARG00.073-0.09118.6330.0480.0480.0000.0000.0000.000
145A448ARG10.8331.07115.4240.7530.7530.0000.0000.0000.000
146A449GLU00.019-0.18319.8220.0090.0090.0000.0000.0000.000
147A449GLU-1-0.974-0.82022.137-0.407-0.4070.0000.0000.0000.000
148A450GLU00.039-0.10523.1430.0310.0310.0000.0000.0000.000
149A450GLU-1-0.978-0.82025.117-0.348-0.3480.0000.0000.0000.000
150A451SER00.001-0.07723.2940.0370.0370.0000.0000.0000.000
151A451SER0-0.0560.05522.967-0.008-0.0080.0000.0000.0000.000
152A452HIS00.122-0.08421.980-0.051-0.0510.0000.0000.0000.000
153A452HIS0-0.0420.10824.197-0.013-0.0130.0000.0000.0000.000
154A453ASP00.235-0.06821.432-0.028-0.0280.0000.0000.0000.000
155A453ASP-1-1.013-0.84122.041-0.312-0.3120.0000.0000.0000.000
156A454ILE00.070-0.09818.703-0.030-0.0300.0000.0000.0000.000
157A454ILE0-0.1270.06917.850-0.003-0.0030.0000.0000.0000.000
158A455LYS00.082-0.10717.211-0.107-0.1070.0000.0000.0000.000
159A455LYS10.8321.06718.8810.4380.4380.0000.0000.0000.000
160A456GLU00.021-0.17317.083-0.084-0.0840.0000.0000.0000.000
161A456GLU-1-1.022-0.81019.142-0.337-0.3370.0000.0000.0000.000
162A457ASP00.133-0.10315.914-0.030-0.0300.0000.0000.0000.000
163A457ASP-1-0.881-0.78215.581-0.526-0.5260.0000.0000.0000.000
164A458PHE00.065-0.09912.863-0.114-0.1140.0000.0000.0000.000
165A458PHE0-0.1010.07811.7480.0060.0060.0000.0000.0000.000
166A459SER00.046-0.05211.824-0.230-0.2300.0000.0000.0000.000
167A459SER0-0.0430.05815.2750.0020.0020.0000.0000.0000.000
168A460ASN00.084-0.09212.481-0.076-0.0760.0000.0000.0000.000
169A460ASN0-0.1010.07214.7080.0270.0270.0000.0000.0000.000
170A461LEU00.065-0.08710.6130.1280.1280.0000.0000.0000.000
171A461LEU0-0.0620.0949.648-0.046-0.0460.0000.0000.0000.000
172A462ILE00.129-0.0977.689-0.216-0.2160.0000.0000.0000.000
173A462ILE0-0.0940.1177.918-0.032-0.0320.0000.0000.0000.000
174A463ARG00.090-0.1108.118-0.132-0.1320.0000.0000.0000.000
175A463ARG10.8531.07812.2690.3260.3260.0000.0000.0000.000
176A464THR00.001-0.0889.7920.1710.1710.0000.0000.0000.000
177A464THR0-0.0370.0519.1010.0620.0620.0000.0000.0000.000
178A465LEU0-0.012-0.1075.3260.8250.858-0.002-0.002-0.0290.000
179A465LEU0-0.0710.1014.238-0.340-0.2730.000-0.018-0.0490.000
180A466SER0-0.041-0.1004.6230.0440.253-0.002-0.019-0.1890.000
181A466SER0-0.0490.0716.3890.0690.0690.0000.0000.0000.000
182A467SER0-0.118-0.1646.3670.3810.3810.0000.0000.0000.000
183A467SER00.0390.0538.9020.0190.0190.0000.0000.0000.000